Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 114 of 135
Found at i:38572881 original size:76 final size:76
Alignment explanation
Indices: 38572780--38573281 Score: 723
Period size: 76 Copynumber: 6.8 Consensus size: 76
38572770 AAGTCTTTAT
* * * *
38572780 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
*
38572845 TATTTCCTATC
66 CATTTCCTATC
*
38572856 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
*
38572921 TATTTCCTATC
66 CATTTCCTATC
*
38572932 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
38572997 CATTTCCTATC
66 CATTTCCTATC
*
38573008 CTCTTGAAATT---G---A-----ATATCCAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
38573062 CATTTCCTATC
66 CATTTCCTATC
*
38573073 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
38573138 CATTTCCTATC
66 CATTTCCTATC
* * * *
38573149 CTCTTGAAATTAAAGTAAAGCTGGATATCAAGTCCTTATCTCTGAAATTGAAATAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
38573214 CA-TTCCTATC
66 CATTTCCTATC
* *
38573224 CTCTTGAAATTGAAGT-----TGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGCAAGAGCA
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC-C-GAAATTGAAGTAAGAGCA
38573282 GGATGAAGCC
Statistics
Matches: 392, Mismatches: 21, Indels: 30
0.88 0.05 0.07
Matches are distributed among these distances:
65 61 0.16
68 1 0.00
70 20 0.05
71 1 0.00
72 16 0.04
73 1 0.00
75 23 0.06
76 269 0.69
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (76 bp):
CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATC
Found at i:38572988 original size:267 final size:267
Alignment explanation
Indices: 38572513--38573021 Score: 912
Period size: 267 Copynumber: 1.9 Consensus size: 267
38572503 ATTTCCTATC
* *
38572513 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
38572578 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTCATCTCTGAAATTGAAGT
66 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTCATCTCTGAAATTGAAGT
* *
38572643 AAGAGCAAGATCATTTCCTATCCTTTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCCCT
131 AAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCCCT
*
38572708 GAAATTGAAGTAAGAGCAAGATTATTTCCTATCATCTTGAAATTGAAGTAAAGCTGGATATCAAG
196 GAAATTGAAGTAAGAGCAAGATCATTTCCTATCATCTTGAAATTGAAGTAAAGCTGGATATCAAG
38572773 TCTTTAT
261 TCTTTAT
38572780 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
* * *
38572845 TATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
66 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTCATCTCTGAAATTGAAGT
*
38572910 AAGAGCAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCC
131 AAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATC-CC
*
38572975 -GAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAA
195 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCATCTTGAAATTGAA
38573022 TATCCAGTCT
Statistics
Matches: 231, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
267 229 0.99
268 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (267 bp):
CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTCATCTCTGAAATTGAAGT
AAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCCCT
GAAATTGAAGTAAGAGCAAGATCATTTCCTATCATCTTGAAATTGAAGTAAAGCTGGATATCAAG
TCTTTAT
Found at i:38573080 original size:32 final size:32
Alignment explanation
Indices: 38572979--38573080 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
38572969 ATCTCCGAAA
38572979 TTGAAGTAAGAGCAAGATCATTTCCTATCCTC
1 TTGAAGTAAGAGCAAGATCATTTCCTATCCTC
* * * * * * **
38573011 TTGAAATTGAATATCCAG-TC-TTT-ATCTCCGAAA
1 TTG-AAGT-AAGAGCAAGATCATTTCCTATCC--TC
38573044 TTGAAGTAAGAGCAAGATCATTTCCTATCCTC
1 TTGAAGTAAGAGCAAGATCATTTCCTATCCTC
38573076 TTGAA
1 TTGAA
38573081 ATTGAAGTAA
Statistics
Matches: 47, Mismatches: 16, Indels: 14
0.61 0.21 0.18
Matches are distributed among these distances:
31 10 0.21
32 16 0.34
33 11 0.23
34 10 0.21
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (32 bp):
TTGAAGTAAGAGCAAGATCATTTCCTATCCTC
Found at i:38573134 original size:141 final size:144
Alignment explanation
Indices: 38572780--38573281 Score: 653
Period size: 141 Copynumber: 3.4 Consensus size: 144
38572770 AAGTCTTTAT
* * * *
38572780 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAACAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
*
38572845 TATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
66 CATTTCCTATCCTCTTGAAATT--AG--AA----GATATCAAGTCTTTATCTCTGAAATTGAAGT
*
38572910 AAGAGCAAGATTATTTCCTATC
123 AAGAGCAAGATCATTTCCTATC
*
38572932 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
* *
38572997 CATTTCCTATCCTCTTGAAATT-G-A-ATATCCAGTCTTTATCTCCGAAATTGAAGTAAGAGCAA
66 CATTTCCTATCCTCTTGAAATTAGAAGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
38573059 GATCATTTCCTATC
131 GATCATTTCCTATC
*
38573073 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
* *
38573138 CATTTCCTATCCTCTTGAAATTAAAGTAAAGCTGGATATCAAGTCCTTATCTCTGAAATTGAAAT
66 CATTTCCTATCCTCTTGAAATT--AG--AA----GATATCAAGTCTTTATCTCTGAAATTGAAGT
38573203 AAGAGCAAGATCA-TTCCTATC
123 AAGAGCAAGATCATTTCCTATC
* *
38573224 CTCTTGAAATTGAAGT-----TGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGCAAGAGCA
1 CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTA--TCTCTGAAATTGAAGTAAGAGCA
38573282 GGATGAAGCC
Statistics
Matches: 322, Mismatches: 15, Indels: 30
0.88 0.04 0.08
Matches are distributed among these distances:
141 134 0.42
144 1 0.00
146 17 0.05
147 1 0.00
148 22 0.07
149 1 0.00
151 24 0.07
152 122 0.38
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (144 bp):
CTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATCCTCTTGAAATTAGAAGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
GATCATTTCCTATC
Found at i:38573190 original size:217 final size:216
Alignment explanation
Indices: 38572810--38573237 Score: 775
Period size: 217 Copynumber: 2.0 Consensus size: 216
38572800 TTGGATAACA
*
38572810 AGTCTTTATCTCCGAAATTGAAGTAACAGCAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAA
1 AGTCTTTATCTCCGAAATTGAAGTAACAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
*
38572875 GCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATTATTTCCTATCCTCTTGAA
66 GCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAA
* * *
38572940 ATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCT
131 ATTAAAGTAAAGCTGGATAACAAGTCCTTATCTCCGAAATTGAAATAAGAGCAAGATCA-TTCCT
38573005 ATCCTCTTGAAATTGAATATCC
195 ATCCTCTTGAAATTGAATATCC
*
38573027 AGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
1 AGTCTTTATCTCCGAAATTGAAGTAACAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
38573092 GCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAA
66 GCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAA
* *
38573157 ATTAAAGTAAAGCTGGATATCAAGTCCTTATCTCTGAAATTGAAATAAGAGCAAGATCATTCCTA
131 ATTAAAGTAAAGCTGGATAACAAGTCCTTATCTCCGAAATTGAAATAAGAGCAAGATCATTCCTA
38573222 TCCTCTTGAAATTGAA
196 TCCTCTTGAAATTGAA
38573238 GTTGGATAGC
Statistics
Matches: 203, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
216 22 0.11
217 181 0.89
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (216 bp):
AGTCTTTATCTCCGAAATTGAAGTAACAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
GCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAA
ATTAAAGTAAAGCTGGATAACAAGTCCTTATCTCCGAAATTGAAATAAGAGCAAGATCATTCCTA
TCCTCTTGAAATTGAATATCC
Found at i:38574128 original size:3 final size:3
Alignment explanation
Indices: 38574120--38574156 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
38574110 TATAGCATTC
* *
38574120 ATA ATA ATA ATG TTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38574157 ATATTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:38575125 original size:160 final size:161
Alignment explanation
Indices: 38574930--38575303 Score: 434
Period size: 162 Copynumber: 2.3 Consensus size: 161
38574920 TTTTAATTGG
* * **
38574930 TTTTAATTTAATCCTTCGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCTTTTTTTGGGCTTA
1 TTTTAAATTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTT-GGCTTA
* * *
38574995 TTT-TGCATTTAGTCCCTGT-TGTGTAATTTATTTTAATTTAATCCTCAAATCAACTTTTGCTTA
65 TTTATGCATTTAATCCCTATATGTGTAATTTATTTTAATTTAATCCTCAAATCAACTTTTACTTA
* * *
38575058 ATTACAAAATTGACCCAGGAATCTTTT-GAGAT
130 ATTACAAAATTGACCCAAGAAT-TTTTCAAGAA
* * * *
38575090 TTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAAGCTACCACGTGTCACTTTTTGGTTTAT
1 TTTTAAATTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTAT
* * * * * * *
38575155 TTATGTATTTAATCCCTATCATTTTTAATTTGTTTTAATTTAATCTTTAAATCAACTTTTATTTA
66 TTATGCATTTAATCCCTAT-ATGTGTAATTTATTTTAATTTAATCCTCAAATCAACTTTTACTTA
*
38575220 ATTACAAAATTGGCCCAAGAATTTTTCAAGAA
130 ATTACAAAATTGACCCAAGAATTTTTCAAGAA
** * * *
38575252 TTACAAATTAATCCTTTGACT-TTTGAATGC-CTATGGGGCTGCCACGTGTCAC
1 TTTTAAATTAATCCTTTGACTGTTTGACTGCACCA-GAGGCTGCCACGTGTCAC
38575304 CCAATCTTTG
Statistics
Matches: 179, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
159 8 0.04
160 66 0.37
161 27 0.15
162 78 0.44
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.43
Consensus pattern (161 bp):
TTTTAAATTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTAT
TTATGCATTTAATCCCTATATGTGTAATTTATTTTAATTTAATCCTCAAATCAACTTTTACTTAA
TTACAAAATTGACCCAAGAATTTTTCAAGAA
Found at i:38575405 original size:29 final size:28
Alignment explanation
Indices: 38575373--38575999 Score: 309
Period size: 29 Copynumber: 21.5 Consensus size: 28
38575363 CACGAACTTT
*
38575373 CCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
*
38575402 CCAAAAATTACCATTTT-ACCCCTAAACTTT--
1 CC-AAAATT-CCATTTTAACCCC--GA-TTTCA
*
38575432 -CTAAATTCCATTTTCAACCCCGATTTCA
1 CCAAAATTCCATTTT-AACCCCGATTTCA
* *
38575460 CCAAAAATTACCATTTTACCCCCGAACTTC-
1 CC-AAAATT-CCATTTTAACCCCG-ATTTCA
38575490 CCAAAATTCCATTTTAACCCC-AGTTTCA
1 CCAAAATTCCATTTTAACCCCGA-TTTCA
* *
38575518 CCAAAAATTACCATTTTACCCCCGAACTTC-
1 CC-AAAATT-CCATTTTAACCCCG-ATTTCA
*
38575548 CCAAAATTCCATTTTAA-CCCTAGTTTCA
1 CCAAAATTCCATTTTAACCCCGA-TTTCA
*
38575576 CCAAAAATTACCATTTT-ACCCTCGAACTTC-
1 CC-AAAATT-CCATTTTAACCC-CG-ATTTCA
*
38575606 CCAAAATTCCATTTTAACCTCGATTTCA
1 CCAAAATTCCATTTTAACCCCGATTTCA
*
38575634 CCAAAAATTACCATTTT-ACCCCGAACTTC-
1 CC-AAAATT-CCATTTTAACCCCG-ATTTCA
* *
38575663 CCAAAATTCCATTTTTAA-CTCAATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
*
38575691 CCAAAAATTACCATTTT-ACCCCTAAACTTT--
1 CC-AAAATT-CCATTTTAACCCC--GA-TTTCA
*
38575721 CCAAAATTCCATTTTAACCCC-ATATTTA
1 CCAAAATTCCATTTTAACCCCGAT-TTCA
* *
38575749 CCAAAAATCACCATTTT-ACCCCTAAACTTT--
1 CC-AAAAT-TCCATTTTAACCCC--GA-TTTCA
* *
38575779 CCAAAATTTCATTTTTAACCCCGATTTAA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
* * *
38575808 CCAAAAATTTCTATTTT-ACCCTCAAATTT-T
1 CC-AAAA-TTCCATTTTAACCC-C-GATTTCA
*
38575838 CCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
* *
38575867 CCCAAAATTACCATCTT-ACCCCTAAACTTT--
1 -CCAAAATT-CCATTTTAACCCC--GA-TTTCA
** *
38575897 CCAAAATTCCATTTTCAACCTTGAGTTCA
1 CCAAAATTCCATTTT-AACCCCGATTTCA
* *
38575926 CCAAAAATTACTATTTT-ACCCTCGAATTT-T
1 CC-AAAATT-CCATTTTAACCC-CG-ATTTCA
* *
38575956 CTAAAATTCCATTTTAACCCTGATTTCA
1 CCAAAATTCCATTTTAACCCCGATTTCA
*
38575984 CCGAAATTACCATTTT
1 CCAAAATT-CCATTTT
38576000 GCCCCCTGCG
Statistics
Matches: 466, Mismatches: 55, Indels: 154
0.69 0.08 0.23
Matches are distributed among these distances:
25 1 0.00
26 8 0.02
27 37 0.08
28 95 0.20
29 153 0.33
30 114 0.24
31 43 0.09
32 14 0.03
33 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
CCAAAATTCCATTTTAACCCCGATTTCA
Found at i:38575415 original size:59 final size:58
Alignment explanation
Indices: 38575343--38576004 Score: 806
Period size: 58 Copynumber: 11.4 Consensus size: 58
38575333 CCTGGATGTT
*
38575343 CCAAAAATTACCATTTTACCCACGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
38575402 CCAAAAATTACCATTTTACCCCTAAACTTT-CTAAATTCCATTTTCAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
38575460 CCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCA-TTTTAACCCC-AGTTTCA
1 CCAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
* *
38575518 CCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCA-TTTTAA-CCCTAGTTTCA
1 CCAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
* *
38575576 CCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
38575634 CCAAAAATTACCATTTTACCCCGAACTTCCCAAAATTCCATTTTTAA-CTCAATTTCA
1 CCAAAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
38575691 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCC-ATATTTA
1 CCAAAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGAT-TTCA
* * * *
38575749 CCAAAAATCACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCCCGATTTAA
1 CCAAAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
38575808 CCAAAAATTTCTATTTTACCCTCAAATTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * ** *
38575867 CCCAAAATTACCATCTTACCCCTAAACTTTCCAAAATTCCATTTTCAACCTTGAGTTCA
1 CCAAAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
38575926 CCAAAAATTACTATTTTACCCTCGAATTTTCTAAAATTCCA-TTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
38575984 CC-GAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
38576005 CTGCGAGTCC
Statistics
Matches: 542, Mismatches: 45, Indels: 35
0.87 0.07 0.06
Matches are distributed among these distances:
56 1 0.00
57 80 0.15
58 269 0.50
59 188 0.35
60 4 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:38576136 original size:15 final size:16
Alignment explanation
Indices: 38576109--38576154 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
38576099 ATTTATTTGC
*
38576109 ATCTGCATTTTATATT
1 ATCTGCATATTATATT
*
38576125 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
38576139 ATCTGCCTATTATATT
1 ATCTGCATATTATATT
38576155 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:38577611 original size:3 final size:3
Alignment explanation
Indices: 38577603--38577632 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38577593 CCCCTAAATC
38577603 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38577633 CAAGGACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38578267 original size:19 final size:19
Alignment explanation
Indices: 38578245--38578289 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
38578235 CAAATAATTT
*
38578245 AAAAATTATAAAA-TATTCA
1 AAAAATTAAAAAAGTATT-A
38578264 AAAAATTAAAAAAGTATTA
1 AAAAATTAAAAAAGTATTA
38578283 AAAAATT
1 AAAAATT
38578290 CTTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATTAAAAAAGTATTA
Found at i:38581517 original size:26 final size:26
Alignment explanation
Indices: 38581488--38581557 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
38581478 TGCCCAAACA
* * *
38581488 TAAACATAAGCATAAATATAACTAAT
1 TAAACACAAACATAAACATAACTAAT
* *
38581514 TAAATACAAACATAAACATAATTAAT
1 TAAACACAAACATAAACATAACTAAT
*
38581540 TAAATACAAACATAAACA
1 TAAACACAAACATAAACA
38581558 AAAACATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.24
Consensus pattern (26 bp):
TAAACACAAACATAAACATAACTAAT
Found at i:38583800 original size:12 final size:12
Alignment explanation
Indices: 38583781--38583823 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
38583771 TGTTTTGATA
*
38583781 GTTGTTTTCG-T
1 GTTGTTTTTGCT
38583792 GTTGTTTTTGCT
1 GTTGTTTTTGCT
* *
38583804 GTTATTTTTGTT
1 GTTGTTTTTGCT
38583816 GTTGTTTT
1 GTTGTTTT
38583824 GGTTATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.02, C:0.05, G:0.23, T:0.70
Consensus pattern (12 bp):
GTTGTTTTTGCT
Found at i:38583817 original size:32 final size:31
Alignment explanation
Indices: 38583743--38583818 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
38583733 TTGCTTGTTG
*
38583743 TTTTTTGTTGTTTTGGTGCTTTTTTTACTGT
1 TTTTTTGTTGTTTTCGTGCTTTTTTTACTGT
* * *
38583774 TTTGATAGTTGTTTTCGTG-TTGTTTTTGCTGT
1 TTT-TTTGTTGTTTTCGTGCTT-TTTTTACTGT
38583806 TATTTTTGTTGTT
1 T-TTTTTGTTGTT
38583819 GTTTTGGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
31 5 0.14
32 29 0.81
33 2 0.06
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.68
Consensus pattern (31 bp):
TTTTTTGTTGTTTTCGTGCTTTTTTTACTGT
Found at i:38583832 original size:24 final size:24
Alignment explanation
Indices: 38583791--38583842 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38583781 GTTGTTTTCG
* *
38583791 TGTTGTTTTTGCTGTTATTTTTGT
1 TGTTGTTTTGGCTATTATTTTTGT
*
38583815 TGTTGTTTTGGTTATTATTTTTGT
1 TGTTGTTTTGGCTATTATTTTTGT
38583839 TGTT
1 TGTT
38583843 TGGATGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.02, G:0.21, T:0.71
Consensus pattern (24 bp):
TGTTGTTTTGGCTATTATTTTTGT
Found at i:38583857 original size:21 final size:22
Alignment explanation
Indices: 38583728--38583857 Score: 81
Period size: 20 Copynumber: 6.0 Consensus size: 22
38583718 AAGTATATTA
** *
38583728 TTGTTTTGCTTGTTGTTTTTTG
1 TTGTTTTGGATGTTATTTTTTG
* *
38583750 TTGTTTTGG-TGCT-TTTTTTA
1 TTGTTTTGGATGTTATTTTTTG
* * *
38583770 CTGTTTT-GATAGTTGTTTTCGTG
1 TTGTTTTGGAT-GTTATTTT-TTG
* *
38583793 TTGTTTTTGCTGTTATTTTTGTTG
1 TTGTTTTGGATGTTA-TTTT-TTG
* *
38583817 TTGTTTTGGTTATTA-TTTTTG
1 TTGTTTTGGATGTTATTTTTTG
38583838 TTG-TTTGGATGTTATTTTTT
1 TTGTTTTGGATGTTATTTTTT
38583858 ATGCGTTTTA
Statistics
Matches: 84, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 22 0.26
21 16 0.19
22 15 0.18
23 10 0.12
24 20 0.24
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (22 bp):
TTGTTTTGGATGTTATTTTTTG
Found at i:38584020 original size:23 final size:22
Alignment explanation
Indices: 38583970--38584030 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
38583960 TAATATAAAA
*
38583970 TTTTTTTAATGTATTTTAAATT
1 TTTTTTTAATGTATTTTAAATG
* *
38583992 TATTTTTTAATGTTTGTTTTAATG
1 T-TTTTTTAATGTAT-TTTAAATG
*
38584016 -TTTTTAAATGTATTT
1 TTTTTTTAATGTATTT
38584031 GATATATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.06
22 12 0.38
23 12 0.38
24 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTTTTTAATGTATTTTAAATG
Found at i:38584335 original size:30 final size:29
Alignment explanation
Indices: 38584265--38584319 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
38584255 AGATACAAGG
38584265 CTCCAAAAATGATAATATTATACTTTAGC
1 CTCCAAAAATGATAATATTATACTTTAGC
38584294 CTCCAAAAATGA-AATATATATA-TTTA
1 CTCCAAAAATGATAATAT-TATACTTTA
38584320 ATCCTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (29 bp):
CTCCAAAAATGATAATATTATACTTTAGC
Found at i:38594140 original size:41 final size:42
Alignment explanation
Indices: 38594060--38594145 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
38594050 AGAGTTGGCG
**
38594060 ATTCACAATCGATTATGGACCTAATAAGACTTGAGCAAATTC
1 ATTCACAATCGATTATAAACCTAATAAGACTTGAGCAAATTC
* * *
38594102 ATTCACCATCGATTATAAACCT-GTAAGACTTGGGCAAATTC
1 ATTCACAATCGATTATAAACCTAATAAGACTTGAGCAAATTC
38594143 ATT
1 ATT
38594146 TTAACCCAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (42 bp):
ATTCACAATCGATTATAAACCTAATAAGACTTGAGCAAATTC
Found at i:38597895 original size:16 final size:16
Alignment explanation
Indices: 38597874--38597910 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
38597864 AAACATCATC
38597874 TTATTAAGGGTAAACT
1 TTATTAAGGGTAAACT
*
38597890 TTATTAAGGTTAAACT
1 TTATTAAGGGTAAACT
38597906 TTATT
1 TTATT
38597911 GATGGTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (16 bp):
TTATTAAGGGTAAACT
Found at i:38598903 original size:21 final size:21
Alignment explanation
Indices: 38598878--38598917 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38598868 ACTTGAACTT
38598878 TCAAAATACATCAAAAAAACC
1 TCAAAATACATCAAAAAAACC
* * *
38598899 TCAAACTTCTTCAAAAAAA
1 TCAAAATACATCAAAAAAA
38598918 AGCAATTAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAAATACATCAAAAAAACC
Found at i:38599351 original size:12 final size:12
Alignment explanation
Indices: 38599334--38599358 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38599324 AAAAAATAAT
38599334 AAAAATTATAGA
1 AAAAATTATAGA
38599346 AAAAATTATAGA
1 AAAAATTATAGA
38599358 A
1 A
38599359 TACTTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAATTATAGA
Found at i:38599438 original size:47 final size:44
Alignment explanation
Indices: 38599375--38599494 Score: 118
Period size: 47 Copynumber: 2.6 Consensus size: 44
38599365 TTTTGGTACG
* *
38599375 ATAATTTTTATA--ATTTTACAAAATTTATATTTCTTTACATTTTAT
1 ATAATTTTT-TACGATTTTATAAAATTTATATTTCTATACA-TTT-T
* * *
38599420 ATAATTTTCTTAGGATTTTATAATATATTTTGTATTTCTATATATTTT
1 ATAATTTT-TTACGATTTTATAA-A-A-TTTATATTTCTATACATTTT
38599468 ATAATTTTTTACGATTTTATAAAATTT
1 ATAATTTTTTACGATTTTATAAAATTT
38599495 TACAATTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
44 3 0.05
45 11 0.17
46 2 0.03
47 21 0.33
48 10 0.16
49 4 0.06
50 13 0.20
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (44 bp):
ATAATTTTTTACGATTTTATAAAATTTATATTTCTATACATTTT
Found at i:38599484 original size:18 final size:18
Alignment explanation
Indices: 38599463--38599513 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
38599453 ATTTCTATAT
*
38599463 ATTTTATAATTTTTTACG
1 ATTTTATAATTTTTTACA
**
38599481 ATTTTATAAAATTTTACA
1 ATTTTATAATTTTTTACA
*
38599499 ATTTTACAATTTTTT
1 ATTTTATAATTTTTT
38599514 TTCTAATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTATAATTTTTTACA
Found at i:38599555 original size:19 final size:18
Alignment explanation
Indices: 38599509--38599560 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
38599499 ATTTTACAAT
*
38599509 TTTTTTTCTAAT-TTTTAA
1 TTTTTTT-TAATATTTGAA
*
38599527 TATTTTTTAATATTTGAA
1 TTTTTTTTAATATTTGAA
*
38599545 TTTTTTATTAAAATTT
1 TTTTTT-TTAATATTT
38599561 ATAGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.14
18 16 0.57
19 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTTTTAATATTTGAA
Found at i:38599823 original size:88 final size:89
Alignment explanation
Indices: 38599610--38599824 Score: 256
Period size: 88 Copynumber: 2.4 Consensus size: 89
38599600 AAGCAATGGT
* *
38599610 TTAATTGCTTTTTTTGAAAAAAGTTTCAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCA
1 TTAATTGCTTTTTTT-AAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCCA
* * * *
38599675 ATTGAGTGCAAAAAAATGTAGGGGC
65 AATGAGTGCAAAAAAAAGTACGAGC
* * * * * *
38599700 TTAATTGC-TTTTTTGAAAAGGTTTGAGGGTATTTTTAATGCATTTTGAAAGTTTAAGTACTCAA
1 TTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCCAA
38599764 ATGAGTGCAAAAAAAAAG-ACGAGC
66 ATGAGTGC-AAAAAAAAGTACGAGC
* * *
38599788 TTAATTACTTTTTTTTAAAAAGTTTGAGTG-CTTTTTA
1 TTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTA
38599825 CAGCCTTAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
88 66 0.62
89 32 0.30
90 8 0.08
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (89 bp):
TTAATTGCTTTTTTTAAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCCAA
ATGAGTGCAAAAAAAAGTACGAGC
Found at i:38600038 original size:8 final size:8
Alignment explanation
Indices: 38600027--38600051 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38600017 TAACTTAATA
38600027 TAAATTTT
1 TAAATTTT
38600035 TAAATTTT
1 TAAATTTT
38600043 TAAATTTT
1 TAAATTTT
38600051 T
1 T
38600052 TTATCCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAAATTTT
Found at i:38602715 original size:21 final size:21
Alignment explanation
Indices: 38602691--38602730 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38602681 GAAAGAATCA
38602691 ATATCCATA-TCACATATCATG
1 ATATCCATATTC-CATATCATG
*
38602712 ATATCTATATTCCATATCA
1 ATATCCATATTCCATATCA
38602731 AACTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.38
Consensus pattern (21 bp):
ATATCCATATTCCATATCATG
Found at i:38604101 original size:71 final size:71
Alignment explanation
Indices: 38603983--38604401 Score: 568
Period size: 71 Copynumber: 5.9 Consensus size: 71
38603973 TGTCACATAT
*
38603983 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAACCATCGGACCAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
38604048 CTTTAC
66 CTTTAC
* * *
38604054 AATGACTCACGATGCTGTAGAGAATCCGTAACAAATGCAAGGTCTCAACCATCGGACCAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
38604119 CTTTAC
66 CTTTAC
* * * * * * * *
38604125 AGTGACTCACGATGCGGTATAGAATTCGTAAAAAATGCAAGATCTCAGCCATCGAACTAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
*
38604190 CTTTAT
66 CTTTAC
* * *
38604196 AGTGACTCACGATGCTGTAGAGAATCCCCAATAAATGCAAGATCTCAGCCATCGGACCAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
38604261 CTTTAC
66 CTTTAC
* * * * * * * *
38604267 AGTGAGTCACGATGATATAAAGAATCTGCAACACATGCAAGATCTCAACCATCAGACCAGTTTTA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
*
38604332 TTTTAC
66 CTTTAC
* * * * *
38604338 AATGACTCACGATGTTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACCATTTTC
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTC
38604402 TATCTTTGGC
Statistics
Matches: 303, Mismatches: 45, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 303 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (71 bp):
AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGGACCAGTTTCA
CTTTAC
Found at i:38604886 original size:16 final size:16
Alignment explanation
Indices: 38604862--38604893 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38604852 TCCTTACAAA
*
38604862 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
38604878 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
38604894 AAAAATTACT
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:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:38606508 original size:55 final size:55
Alignment explanation
Indices: 38606436--38606699 Score: 262
Period size: 55 Copynumber: 4.8 Consensus size: 55
38606426 TAATTCATCT
* * *
38606436 ATAGTTCGGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATC
1 ATAGCTCGAGTAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGCGTAAAACTATC
* *
38606491 ATAGCTCGAGTAGAGCTTTGGTTTGCTTACTTCTCGATTAGAGCATAAAACTATC
1 ATAGCTCGAGTAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGCGTAAAACTATC
* * *
38606546 ATAGCTC-AGGTAGAGCTTTGGTTTGCTTACGTCTCGATTAAAGCGTAAAGCTATT
1 ATAGCTCGA-GTAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGCGTAAAACTATC
* * **** * * * * * * *
38606601 ATAACTCGGGTAGAGCTTTAAACTCCTTACGTTTCAATTAGAGTGTAAAGCTGTG
1 ATAGCTCGAGTAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGCGTAAAACTATC
* * * * *
38606656 ATAGCTCG-GTTAGATCTTCGGTCTGCTTACATCTCGTTTAGAGC
1 ATAGCTCGAG-TAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGC
38606700 TTAAGGCTAT
Statistics
Matches: 171, Mismatches: 35, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
54 2 0.01
55 169 0.99
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (55 bp):
ATAGCTCGAGTAGAGCTTTGGTTTGCTTACGTCTCGATTAGAGCGTAAAACTATC
Found at i:38608504 original size:30 final size:29
Alignment explanation
Indices: 38608426--38608559 Score: 101
Period size: 30 Copynumber: 4.4 Consensus size: 29
38608416 TTTTTAATTA
* *
38608426 AGGACTAAATTGGAAATTTT-GTAAAAATTTA
1 AGGACTAAATTGG-AATTTTAG--AGAATTTG
** * *
38608457 AGGTTTAATTTGTAATTTTAGAGAAGTTTG
1 AGGACTAAATTGGAATTTTAGAGAA-TTTG
* *
38608487 AGGACAAAATTGGAATTTTAGTGACATTT-
1 AGGACTAAATTGGAATTTTAGAGA-ATTTG
* *
38608516 AGGGACTAAATTGTAATTTTAGTGGAATTTG
1 A-GGACTAAATTGGAATTTTAG-AGAATTTG
38608547 AGGACTAAATTGG
1 AGGACTAAATTGG
38608560 GTTTTAATTA
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
29 4 0.05
30 63 0.78
31 14 0.17
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (29 bp):
AGGACTAAATTGGAATTTTAGAGAATTTG
Found at i:38609847 original size:30 final size:30
Alignment explanation
Indices: 38609812--38609871 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
38609802 GCCGCTTGAG
38609812 GTGTGTCTCTGTCC-GTGCTACATATTTGTT
1 GTGTGTCTCT-TCCTGTGCTACATATTTGTT
* * *
38609842 GTGTGTTTCTTCCTGTGCTATATGTTTGTT
1 GTGTGTCTCTTCCTGTGCTACATATTTGTT
38609872 TTGTAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.08, C:0.17, G:0.23, T:0.52
Consensus pattern (30 bp):
GTGTGTCTCTTCCTGTGCTACATATTTGTT
Found at i:38615612 original size:19 final size:19
Alignment explanation
Indices: 38615585--38615621 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38615575 TCCAAATTTT
*
38615585 ATTTTAAAAAATTATAAAA
1 ATTTAAAAAAATTATAAAA
*
38615604 ATTTAAAAAAATTCTAAA
1 ATTTAAAAAAATTATAAA
38615622 GAACATATAA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTTAAAAAAATTATAAAA
Found at i:38616873 original size:29 final size:27
Alignment explanation
Indices: 38616834--38616891 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
38616824 CTTTCTTATT
38616834 TTATTTCAATAAATCATTATACTTTTA
1 TTATTTCAATAAATCATTATACTTTTA
* **
38616861 TTATATTCAAATAACTTGTTATACTTTTA
1 TTAT-TTC-AATAAATCATTATACTTTTA
38616890 TT
1 TT
38616892 GCATTGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.12
29 19 0.73
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (27 bp):
TTATTTCAATAAATCATTATACTTTTA
Found at i:38622840 original size:7 final size:7
Alignment explanation
Indices: 38622828--38622868 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
38622818 GTATTTTTAA
38622828 AATATTT
1 AATATTT
38622835 AATATTT
1 AATATTT
38622842 AATATTT
1 AATATTT
38622849 AATATTT
1 AATATTT
*
38622856 GATATTT
1 AATATTT
38622863 AATATT
1 AATATT
38622869 ATTAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:38628053 original size:30 final size:30
Alignment explanation
Indices: 38627991--38628084 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
38627981 GAAACACCGT
* * * * *
38627991 CACACAACAAA-ACATAACACAGGCAAAAA
1 CACACAACAAATATATAGCACAGACAGAGA
* *
38628020 CACACAGCAAATATGTAGCACAGACAGAGA
1 CACACAACAAATATATAGCACAGACAGAGA
*
38628050 CACACAACAAATATATAGCACGGACAGAGA
1 CACACAACAAATATATAGCACAGACAGAGA
38628080 CACAC
1 CACAC
38628085 CTCAAACGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 10 0.19
30 44 0.81
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.07
Consensus pattern (30 bp):
CACACAACAAATATATAGCACAGACAGAGA
Found at i:38632694 original size:22 final size:22
Alignment explanation
Indices: 38632653--38632694 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38632643 TTTTAGAAGA
*
38632653 ATAAAAAAAACTTGATTTTTAT
1 ATAAAAAAAACTTGAGTTTTAT
*
38632675 ATAAAAAAAACTTGGGTTTT
1 ATAAAAAAAACTTGAGTTTT
38632695 TACCGGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (22 bp):
ATAAAAAAAACTTGAGTTTTAT
Found at i:38635478 original size:28 final size:30
Alignment explanation
Indices: 38635367--38635489 Score: 102
Period size: 29 Copynumber: 4.3 Consensus size: 30
38635357 AATATTTAAC
* *
38635367 ACTTGAATTTGATAT-TTTTTTAATTTGGT
1 ACTTAAATTTGATATATTTTTAAATTTGGT
* **
38635396 ACTTAAATTT--T-T-TTGTCT-AATTAAGT
1 ACTTAAATTTGATATATT-TTTAAATTTGGT
* *
38635422 ACTCAAACTTGATATATTTTTAAATTTGGT
1 ACTTAAATTTGATATATTTTTAAATTTGGT
38635452 A-TCTAAATTTGATAT-TTTTTAAA-TTGGT
1 ACT-TAAATTTGATATATTTTTAAATTTGGT
38635480 ACTTAAATTT
1 ACTTAAATTT
38635490 TTTGGAGTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
26 17 0.23
27 3 0.04
28 14 0.19
29 22 0.29
30 19 0.25
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
ACTTAAATTTGATATATTTTTAAATTTGGT
Found at i:38635946 original size:31 final size:31
Alignment explanation
Indices: 38635910--38635968 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
38635900 TAGTGACTTA
* * *
38635910 AATGAAAATTTTTGAATAATTTAATGATTTT
1 AATGAAAACTTTCGAATAATTCAATGATTTT
38635941 AATGAAAACTTTCGAATAATTCAATGAT
1 AATGAAAACTTTCGAATAATTCAATGAT
38635969 CATTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (31 bp):
AATGAAAACTTTCGAATAATTCAATGATTTT
Found at i:38636503 original size:11 final size:12
Alignment explanation
Indices: 38636483--38636520 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
38636473 TTACTCTAAT
*
38636483 ATAAACATTAAA
1 ATAATCATTAAA
38636495 ATAAT-ATTAAA
1 ATAATCATTAAA
38636506 ATAATCATATAAA
1 ATAATCAT-TAAA
38636519 AT
1 AT
38636521 TTTTCAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 11 0.48
12 6 0.26
13 6 0.26
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATCATTAAA
Found at i:38636779 original size:20 final size:20
Alignment explanation
Indices: 38636754--38636795 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
38636744 GTCTTACCTG
38636754 ACCCATGACCACATATAGTC
1 ACCCATGACCACATATAGTC
38636774 ACCCATGACCACATATAGTC
1 ACCCATGACCACATATAGTC
38636794 AC
1 AC
38636796 GAGTAAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.19
Consensus pattern (20 bp):
ACCCATGACCACATATAGTC
Found at i:38642516 original size:3 final size:3
Alignment explanation
Indices: 38642508--38642544 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38642498 TTCAAATAGA
38642508 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
38642545 GATAAGATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:38647351 original size:11 final size:11
Alignment explanation
Indices: 38647319--38647380 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
38647309 TGTTATGTTT
38647319 TGTTGGCTTTA
1 TGTTGGCTTTA
* **
38647330 TGATGATTTTA
1 TGTTGGCTTTA
38647341 TGTCT-GCTTTA
1 TGT-TGGCTTTA
38647352 TGTTGGCTTTAA
1 TGTTGGCTTT-A
38647364 TGTTGGCTTTA
1 TGTTGGCTTTA
*
38647375 TATTGG
1 TGTTGG
38647381 ATGCTGTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 1 0.02
11 28 0.68
12 12 0.29
ACGTcount: A:0.15, C:0.08, G:0.24, T:0.53
Consensus pattern (11 bp):
TGTTGGCTTTA
Found at i:38647368 original size:12 final size:12
Alignment explanation
Indices: 38647346--38647374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38647336 TTTTATGTCT
38647346 GCTTT-ATGTTG
1 GCTTTAATGTTG
38647357 GCTTTAATGTTG
1 GCTTTAATGTTG
38647369 GCTTTA
1 GCTTTA
38647375 TATTGGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (12 bp):
GCTTTAATGTTG
Found at i:38647372 original size:23 final size:23
Alignment explanation
Indices: 38647319--38647382 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
38647309 TGTTATGTTT
* *
38647319 TGTTGGCTTTATGAT-GATTTTA
1 TGTTGGCTTTATGTTGGATTTAA
*
38647341 TGTCT-GCTTTATGTTGGCTTTAA
1 TGT-TGGCTTTATGTTGGATTTAA
*
38647364 TGTTGGCTTTATATTGGAT
1 TGTTGGCTTTATGTTGGAT
38647383 GCTGTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.23, T:0.53
Consensus pattern (23 bp):
TGTTGGCTTTATGTTGGATTTAA
Found at i:38648114 original size:24 final size:21
Alignment explanation
Indices: 38648059--38648108 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
38648049 GTGAGGACCC
38648059 CAACTCAGCAAGTGAGCAGCA
1 CAACTCAGCAAGTGAGCAGCA
*
38648080 CATCTCAGCAAGTGAGCAGCA
1 CAACTCAGCAAGTGAGCAGCA
38648101 CAACTCAG
1 CAACTCAG
38648109 TTGCAAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.22, T:0.12
Consensus pattern (21 bp):
CAACTCAGCAAGTGAGCAGCA
Found at i:38648841 original size:19 final size:19
Alignment explanation
Indices: 38648817--38648858 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
38648807 AACATCTGGT
*
38648817 ATAATCACACAAGAGTTCC
1 ATAATCACACAAGAGTTAC
38648836 ATAATCACACAAGAGTTAC
1 ATAATCACACAAGAGTTAC
38648855 ATAA
1 ATAA
38648859 GGTAACCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (19 bp):
ATAATCACACAAGAGTTAC
Found at i:38648930 original size:16 final size:16
Alignment explanation
Indices: 38648909--38648941 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38648899 AAACCAGCAG
*
38648909 CCATGAGAAGTAACAA
1 CCATGAGAAGCAACAA
38648925 CCATGAGAAGCAACAA
1 CCATGAGAAGCAACAA
38648941 C
1 C
38648942 TAACAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (16 bp):
CCATGAGAAGCAACAA
Found at i:38649282 original size:3 final size:3
Alignment explanation
Indices: 38649274--38649316 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
38649264 AATCTCTATT
* *
38649274 TTC TTC TTC GTC TTC TTC TTC TTC TTC TTA TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
38649317 TTTTTCTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:38649321 original size:8 final size:8
Alignment explanation
Indices: 38649286--38649324 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
38649276 CTTCTTCGTC
38649286 TTCTTCTT
1 TTCTTCTT
38649294 CTTCTTCTT
1 -TTCTTCTT
38649303 ATTCTTCTT
1 -TTCTTCTT
*
38649312 TTCTTTTT
1 TTCTTCTT
38649320 TTCTT
1 TTCTT
38649325 AAACCCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCTTCTT
Found at i:38649565 original size:3 final size:3
Alignment explanation
Indices: 38649557--38649589 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
38649547 TAATTTACCC
38649557 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38649590 GGTTAATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38653026 original size:8 final size:8
Alignment explanation
Indices: 38653013--38653039 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38653003 TATGTCGTAC
38653013 ATACATAT
1 ATACATAT
38653021 ATACATAT
1 ATACATAT
38653029 ATACATAT
1 ATACATAT
38653037 ATA
1 ATA
38653040 TGTATCTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:38654997 original size:20 final size:20
Alignment explanation
Indices: 38654962--38655004 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
38654952 AAATGTCCTT
*
38654962 AAATTATTGTTCAAATTTTA
1 AAATTATTGTTCAAATTTCA
38654982 AAATTATT-TTCAAAATTTCA
1 AAATTATTGTTC-AAATTTCA
38655002 AAA
1 AAA
38655005 CATTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATTATTGTTCAAATTTCA
Found at i:38659888 original size:17 final size:17
Alignment explanation
Indices: 38659866--38659904 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
38659856 AGGTGTAGAA
* *
38659866 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
38659883 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
38659900 CTTGT
1 CTTGT
38659905 CAAGATGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:38660751 original size:21 final size:21
Alignment explanation
Indices: 38660725--38660765 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
38660715 AATGGAAATA
38660725 TGAAAATGTAAGTGATTGGTG
1 TGAAAATGTAAGTGATTGGTG
38660746 TGAAAATGTAAGTGATTGGT
1 TGAAAATGTAAGTGATTGGT
38660766 ATTGAGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (21 bp):
TGAAAATGTAAGTGATTGGTG
Found at i:38667630 original size:23 final size:23
Alignment explanation
Indices: 38667604--38667787 Score: 86
Period size: 23 Copynumber: 8.4 Consensus size: 23
38667594 AAAACGCATA
*
38667604 AAAAATAACATCCAAACAACAAC
1 AAAAATAACATCAAAACAACAAC
*
38667627 AAAAAT-A-ATCAAAATAACATA-
1 AAAAATAACATCAAAACAACA-AC
38667648 AAAAATAACAGT-AAAACAACAAC
1 AAAAATAACA-TCAAAACAACAAC
* * *
38667671 AAAAACAA-A--AAAA-ACCAGC
1 AAAAATAACATCAAAACAACAAC
** *
38667690 AAAAATAACAAAAAAAAAACAAC
1 AAAAATAACATCAAAACAACAAC
** * * ** *
38667713 AAAAGCAGCACCAAAACAGTAAA
1 AAAAATAACATCAAAACAACAAC
**
38667736 AAAAATAGTATCAAAACAAC-A-
1 AAAAATAACATCAAAACAACAAC
* * *
38667757 AAAAATAGCACCAAAATAACAA-
1 AAAAATAACATCAAAACAACAAC
38667779 AAAAA-AACA
1 AAAAATAACA
38667788 CCATAAATAG
Statistics
Matches: 123, Mismatches: 28, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
19 11 0.09
20 5 0.04
21 36 0.29
22 16 0.13
23 54 0.44
24 1 0.01
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (23 bp):
AAAAATAACATCAAAACAACAAC
Found at i:38667651 original size:21 final size:21
Alignment explanation
Indices: 38667600--38667655 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
38667590 AGTAAAAACG
*
38667600 CATAAAAAATAACATCCAAACAA
1 CATAAAAAAT-A-ATCAAAACAA
*
38667623 CA-ACAAAAATAATCAAAATAA
1 CATA-AAAAATAATCAAAACAA
38667644 CATAAAAAATAA
1 CATAAAAAATAA
38667656 CAGTAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 18 0.62
22 3 0.10
23 8 0.28
ACGTcount: A:0.70, C:0.16, G:0.00, T:0.14
Consensus pattern (21 bp):
CATAAAAAATAATCAAAACAA
Found at i:38667761 original size:21 final size:21
Alignment explanation
Indices: 38667705--38667782 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
38667695 TAACAAAAAA
**
38667705 AAAACAAC-AAAAGCAGCACC
1 AAAACAACAAAAAATAGCACC
* * *
38667725 AAAACAGTAAAAAAAATAGTATC
1 AAAACA--ACAAAAAATAGCACC
38667748 AAAACAACAAAAAATAGCACC
1 AAAACAACAAAAAATAGCACC
*
38667769 AAAATAACAAAAAA
1 AAAACAACAAAAAA
38667783 AAACACCATA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.13
21 25 0.54
22 1 0.02
23 14 0.30
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAACAACAAAAAATAGCACC
Found at i:38667795 original size:22 final size:21
Alignment explanation
Indices: 38667747--38667796 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38667737 AAAATAGTAT
* * *
38667747 CAAAACAACAAAAAATAGCAC
1 CAAAATAACAAAAAAAAACAC
38667768 CAAAATAACAAAAAAAAACAC
1 CAAAATAACAAAAAAAAACAC
38667789 CATAAATA
1 CA-AAATA
38667797 GTAAACAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.08
Consensus pattern (21 bp):
CAAAATAACAAAAAAAAACAC
Found at i:38667930 original size:31 final size:32
Alignment explanation
Indices: 38667895--38667959 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
38667885 ATTTAGAAAA
*
38667895 CGGGTCT-TATTTTTTGTCCAAGCC-CATTTTT
1 CGGGTCTATA-TTTTTGTCCAAACCTCATTTTT
*
38667926 CGGGTCTATATTTTTGTTCAAACCTCATTTTT
1 CGGGTCTATATTTTTGTCCAAACCTCATTTTT
38667958 CG
1 CG
38667960 AGCGAGTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (32 bp):
CGGGTCTATATTTTTGTCCAAACCTCATTTTT
Found at i:38670120 original size:28 final size:28
Alignment explanation
Indices: 38670088--38670304 Score: 222
Period size: 28 Copynumber: 7.6 Consensus size: 28
38670078 ATTGATTTCT
38670088 ATATCCGTAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
*
38670116 ATATCCGTAAGGATATCATTGAAAAGGTT
1 ATATCCGTAAGGATATCATTGAAAAGG-G
* *
38670145 ATATCAGTAAGGATAT-ATTTTGAAAAGAG
1 ATATCCGTAAGGATATCA--TTGAAAAGGG
* *
38670174 ATACCCGCAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
*** * *
38670202 ATATCTACAATGATATCATTGAAAAAGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
*
38670230 ATATCCGCAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
* *
38670258 TATATCCATAAGGA-ATACATTTGAAAAGGA
1 -ATATCCGTAAGGATAT-CA-TTGAAAAGGG
* * *
38670288 ATGTTCGTAAGGGTATC
1 ATATCCGTAAGGATATC
38670305 GTCGAAAGAG
Statistics
Matches: 157, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
28 86 0.55
29 51 0.32
30 20 0.13
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (28 bp):
ATATCCGTAAGGATATCATTGAAAAGGG
Found at i:38670282 original size:86 final size:85
Alignment explanation
Indices: 38670087--38670286 Score: 228
Period size: 86 Copynumber: 2.3 Consensus size: 85
38670077 TATTGATTTC
**
38670087 TATATCCGTAAGGATATCATTGAAAAGGGATATCCGTAAGGATATCATTGAAAAGGTTATATCAG
1 TATATCCGTAAGGATATCATTGAAAAGGGATATCCACAAGGATATCATTGAAAAGG-TATATCAG
*
38670152 TAAGGATATATTTTGAAAAGAG
65 CAAGGATATA-TTTGAAAAGAG
* * * * *
38670174 -ATACCCGCAAGGATATCATTGAAAAGGGATATCTACAATGATATCATTGAAAAAGG-ATATCCG
1 TATATCCGTAAGGATATCATTGAAAAGGGATATCCACAAGGATATCATTG-AAAAGGTATATCAG
*
38670237 CAAGGATATCA-TTGAAAAGGG
65 CAAGGATAT-ATTTGAAAAGAG
*
38670258 TATATCCATAAGGA-ATACATTTGAAAAGG
1 TATATCCGTAAGGATAT-CA-TTGAAAAGG
38670287 AATGTTCGTA
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
84 11 0.11
85 26 0.27
86 53 0.55
87 6 0.06
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (85 bp):
TATATCCGTAAGGATATCATTGAAAAGGGATATCCACAAGGATATCATTGAAAAGGTATATCAGC
AAGGATATATTTGAAAAGAG
Found at i:38679873 original size:10 final size:9
Alignment explanation
Indices: 38679842--38679867 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38679832 CTTTTTTTTT
38679842 TTTTGTCTA
1 TTTTGTCTA
38679851 TTTTGTCTA
1 TTTTGTCTA
38679860 TTTTGTCT
1 TTTTGTCT
38679868 TCTTTTGGCT
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:0.12, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTGTCTA
Found at i:38683988 original size:27 final size:27
Alignment explanation
Indices: 38683958--38684131 Score: 188
Period size: 27 Copynumber: 6.5 Consensus size: 27
38683948 TCGTGTACAA
* * *
38683958 AGTATCGTTCATTCGAGCCAGAAATAG
1 AGTATCGCTCTTTCGAGCCAAAAATAG
* *
38683985 AGTATCGTTCATTCGAGCCAAAAATAG
1 AGTATCGCTCTTTCGAGCCAAAAATAG
* * * * *
38684012 AGTACCGCTCTTTTGA-CCTAGAACAG
1 AGTATCGCTCTTTCGAGCCAAAAATAG
* *
38684038 AGTATCGCTCTTTCGAGCCGAAAACAG
1 AGTATCGCTCTTTCGAGCCAAAAATAG
* *
38684065 AGTATTGCTCTTTTGAGCCAAAAATAG
1 AGTATCGCTCTTTCGAGCCAAAAATAG
* *
38684092 AGTATCGCTCTTTCGAGCAAAAAATAA
1 AGTATCGCTCTTTCGAGCCAAAAATAG
*
38684119 AGTATCGCCCTTT
1 AGTATCGCTCTTT
38684132 GCTCAGAATT
Statistics
Matches: 125, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 21 0.17
27 104 0.83
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (27 bp):
AGTATCGCTCTTTCGAGCCAAAAATAG
Found at i:38684067 original size:53 final size:54
Alignment explanation
Indices: 38683972--38684115 Score: 173
Period size: 53 Copynumber: 2.7 Consensus size: 54
38683962 TCGTTCATTC
* * * * *
38683972 GAGCCAGAAATAGAGTATCGTTCATTCGAGCCAAAAATAGAGTACCGCTCTTTT
1 GAGCCAAAAACAGAGTATCGCTCTTTCGAGCCAAAAACAGAGTACCGCTCTTTT
* * * **
38684026 GA-CCTAGAACAGAGTATCGCTCTTTCGAGCCGAAAACAGAGTATTGCTCTTTT
1 GAGCCAAAAACAGAGTATCGCTCTTTCGAGCCAAAAACAGAGTACCGCTCTTTT
* *
38684079 GAGCCAAAAATAGAGTATCGCTCTTTCGAGCAAAAAA
1 GAGCCAAAAACAGAGTATCGCTCTTTCGAGCCAAAAA
38684116 TAAAGTATCG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
53 43 0.58
54 31 0.42
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (54 bp):
GAGCCAAAAACAGAGTATCGCTCTTTCGAGCCAAAAACAGAGTACCGCTCTTTT
Found at i:38686305 original size:25 final size:25
Alignment explanation
Indices: 38686276--38686323 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38686266 CTCGATAAAT
38686276 GGGGAAAC-TAATCTTAAAAGATTGA
1 GGGGAAACAT-ATCTTAAAAGATTGA
* *
38686301 GGGGAATCATATCTTATAAGATT
1 GGGGAAACATATCTTAAAAGATT
38686324 AGATTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (25 bp):
GGGGAAACATATCTTAAAAGATTGA
Found at i:38686680 original size:395 final size:395
Alignment explanation
Indices: 38685950--38686731 Score: 1555
Period size: 395 Copynumber: 2.0 Consensus size: 395
38685940 AAGTCGAGCG
38685950 AGGGTTTCGAAACAAGGGATGAATCGATAATAAGACTAGTTGGGAAGGAGCCAAGTCGACGAGAC
1 AGGGTTTCGAAACAAGGGATGAATCGATAATAAGACTAGTTGGGAAGGAGCCAAGTCGACGAGAC
38686015 GAGTTCGAGGTGAATCATGTCAATGTCATTCTGCAGACGCAATGAGAGCGTTGCGAGAATGGGTG
66 GAGTTCGAGGTGAATCATGTCAATGTCATTCTGCAGACGCAATGAGAGCGTTGCGAGAATGGGTG
38686080 GGGGAGAATGTCACGGCCAAGGTGCAAGGCCCGTGACCATGGCACAAAATGTACCCCATGGAGGT
131 GGGGAGAATGTCACGGCCAAGGTGCAAGGCCCGTGACCATGGCACAAAATGTACCCCATGGAGGT
38686145 CTATCAATTAAATGAGGATTATTTAGCCCACTAAAACTGGCCCAATTCAACAAATTGATGGAGAA
196 CTATCAATTAAATGAGGATTATTTAGCCCACTAAAACTGGCCCAATTCAACAAATTGATGGAGAA
38686210 GTCTATCAGATTAAAGCCTAGGTGGCCCAATGATGCAGATTTGGAAAGATACTTATCTCGATAAA
261 GTCTATCAGATTAAAGCCTAGGTGGCCCAATGATGCAGATTTGGAAAGATACTTATCTCGATAAA
*
38686275 TGGGGAAACTAATCTTAAAAGATTGAGGGGAATCATATCTTATAAGATTAGATTTGATTTTAATA
326 TGGGGAAACTAATCTTAAAAGATTGAGGGGAATCATATCTTAAAAGATTAGATTTGATTTTAATA
38686340 AGACT
391 AGACT
38686345 AGGGTTTCGAAACAAGGGATGAATCGATAATAAGACTAGTTGGGAAGGAGCCAAGTCGACGAGAC
1 AGGGTTTCGAAACAAGGGATGAATCGATAATAAGACTAGTTGGGAAGGAGCCAAGTCGACGAGAC
38686410 GAGTTCGAGGTGAATCATGTCAATGTCATTCTGCAGACGCAATGAGAGCGTTGCGAGAATGGGTG
66 GAGTTCGAGGTGAATCATGTCAATGTCATTCTGCAGACGCAATGAGAGCGTTGCGAGAATGGGTG
38686475 GGGGAGAATGTCACGGCCAAGGTGCAAGGCCCGTGACCATGGCACAAAATGTACCCCATGGAGGT
131 GGGGAGAATGTCACGGCCAAGGTGCAAGGCCCGTGACCATGGCACAAAATGTACCCCATGGAGGT
38686540 CTATCAATTAAATGAGGATTATTTAGCCCACTAAAACTGGCCCAATTCAACAAATTGATGGAGAA
196 CTATCAATTAAATGAGGATTATTTAGCCCACTAAAACTGGCCCAATTCAACAAATTGATGGAGAA
38686605 GTCTATCAGATTAAAGCCTAGGTGGCCCAATGATGCAGATTTGGAAAGATACTTATCTCGATAAA
261 GTCTATCAGATTAAAGCCTAGGTGGCCCAATGATGCAGATTTGGAAAGATACTTATCTCGATAAA
38686670 TGGGGAAACTAATCTTAAAAGATTGAGGGGAATCATATCTTAAAAGATTAGATTTGATTTTA
326 TGGGGAAACTAATCTTAAAAGATTGAGGGGAATCATATCTTAAAAGATTAGATTTGATTTTA
38686732 TTATTTAAAT
Statistics
Matches: 386, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
395 386 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (395 bp):
AGGGTTTCGAAACAAGGGATGAATCGATAATAAGACTAGTTGGGAAGGAGCCAAGTCGACGAGAC
GAGTTCGAGGTGAATCATGTCAATGTCATTCTGCAGACGCAATGAGAGCGTTGCGAGAATGGGTG
GGGGAGAATGTCACGGCCAAGGTGCAAGGCCCGTGACCATGGCACAAAATGTACCCCATGGAGGT
CTATCAATTAAATGAGGATTATTTAGCCCACTAAAACTGGCCCAATTCAACAAATTGATGGAGAA
GTCTATCAGATTAAAGCCTAGGTGGCCCAATGATGCAGATTTGGAAAGATACTTATCTCGATAAA
TGGGGAAACTAATCTTAAAAGATTGAGGGGAATCATATCTTAAAAGATTAGATTTGATTTTAATA
AGACT
Found at i:38686700 original size:25 final size:25
Alignment explanation
Indices: 38686671--38686718 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
38686661 CTCGATAAAT
38686671 GGGGAAAC-TAATCTTAAAAGATTGA
1 GGGGAAACAT-ATCTTAAAAGATTGA
*
38686696 GGGGAATCATATCTTAAAAGATT
1 GGGGAAACATATCTTAAAAGATT
38686719 AGATTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (25 bp):
GGGGAAACATATCTTAAAAGATTGA
Found at i:38687507 original size:16 final size:17
Alignment explanation
Indices: 38687482--38687515 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38687472 ACTTTCTGTA
38687482 TTTTTATTTTTA-ATTT
1 TTTTTATTTTTAGATTT
*
38687498 TTTTTTTTTTTAGATTT
1 TTTTTATTTTTAGATTT
38687515 T
1 T
38687516 AAAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTAGATTT
Found at i:38688015 original size:7 final size:7
Alignment explanation
Indices: 38688003--38688027 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38687993 TTAACATGCA
38688003 TATAATT
1 TATAATT
38688010 TATAATT
1 TATAATT
38688017 TATAATT
1 TATAATT
38688024 TATA
1 TATA
38688028 TGTATGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATAATT
Found at i:38689516 original size:23 final size:24
Alignment explanation
Indices: 38689489--38689541 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
38689479 AAGCAACCTG
38689489 CAAAACAG-AGAAGAGCAAA-GCAA
1 CAAAACAGAAGAAGA-CAAATGCAA
38689512 CAAAA-AGCAAGAAGACAAATGCAA
1 CAAAACAG-AAGAAGACAAATGCAA
38689536 -AAAACA
1 CAAAACA
38689542 AAATACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.08
23 13 0.50
24 11 0.42
ACGTcount: A:0.64, C:0.17, G:0.17, T:0.02
Consensus pattern (24 bp):
CAAAACAGAAGAAGACAAATGCAA
Found at i:38690631 original size:25 final size:25
Alignment explanation
Indices: 38690603--38690651 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
38690593 TTATTTATTT
*
38690603 TAAAATTTAACCCTTTCATTTTTAA
1 TAAAAATTAACCCTTTCATTTTTAA
*
38690628 TAAAAATTAATCCTTTCATTTTTA
1 TAAAAATTAACCCTTTCATTTTTA
38690652 TTTCTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAAAATTAACCCTTTCATTTTTAA
Found at i:38690725 original size:24 final size:24
Alignment explanation
Indices: 38690692--38690737 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
38690682 TTTTATATTT
*
38690692 AAATCCTTTTGTATCTTTTTAATC
1 AAATCCTTTTGTATCATTTTAATC
* *
38690716 AAATCTTTTTTTATCATTTTAA
1 AAATCCTTTTGTATCATTTTAA
38690738 AATTAATCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATCCTTTTGTATCATTTTAATC
Found at i:38694345 original size:59 final size:59
Alignment explanation
Indices: 38694271--38694399 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
38694261 TGTTATCTTA
* * *
38694271 AAAAAAGAGAGAGGGTCGAGATGGAAACCCACAAAG-GGCATTTTAAAACCTAAATAAAAG
1 AAAAAAGAGAAAGGGTCGAGATGAAAACCCACAAAGAGG-ATCTTAAAACCTAAA-AAAAG
* * *
38694331 AAAAAAGA-AAAGGGTCGAGATGAAAATCCGCAAAGAGGATCTTGAAACCTAAAAAAAG
1 AAAAAAGAGAAAGGGTCGAGATGAAAACCCACAAAGAGGATCTTAAAACCTAAAAAAAG
*
38694389 AAAAAAAAGAA
1 AAAAAAGAGAA
38694400 GAAGAAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 12 0.20
59 38 0.63
60 10 0.17
ACGTcount: A:0.55, C:0.12, G:0.22, T:0.12
Consensus pattern (59 bp):
AAAAAAGAGAAAGGGTCGAGATGAAAACCCACAAAGAGGATCTTAAAACCTAAAAAAAG
Found at i:38696262 original size:98 final size:98
Alignment explanation
Indices: 38696017--38696650 Score: 539
Period size: 98 Copynumber: 6.5 Consensus size: 98
38696007 GCCAGAATGG
* * ** * * * * *
38696017 TGAATCTTATACCTTAGAGATGTAAAGGG-AGGGATTAAAGCCGCAATGGCGAATCTTGTACCCT
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGG-TTGAAGCCGCAACGACGAACCTTGTACCCT
* * *
38696081 AGAGATATGGAGGGAAAGGTTGAAGCCACAA-TGA
65 AGAGATAT-GAGGGAAAGATTGAAGCCGCAACAGA
* * * * * *
38696115 CGTACCTTATA-CCTAGAGATGTGAAGGGAAAGGTTGAAGCCGTAACGACGAGCCTTGTACCTTA
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTA
38696179 GAGATATGATGGGAAAGATTGAAGCCGCAACAG-
66 GAGATATGA-GGGAAAGATTGAAGCCGCAACAGA
* * * * *
38696212 TGAATCTTTTACCCTAGAGATGTGGAGAGAAAGCTTGAAGCCGCAACGACGAATCTTGTACCCTA
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTA
* * * *
38696277 GAGATATGGAGGGAAAGGTTGAAGTCGTAA-TGA
66 GAGATAT-GAGGGAAAGATTGAAGCCGCAACAGA
* * * * ** *
38696310 CGAACCTTATACCCTAGAAATGTGGAGGGAAAGGTTAAAGCCACAACGGTGAACCTTGTACCTTA
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTA
* * * * *
38696375 GAGATATAATGAGAAATATTGAAACCGCAA-TGA
66 GAGATATGA-GGGAAAGATTGAAGCCGCAACAGA
* * * * * * *
38696408 CGAATCTTTTACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCACAACAATGAACCTTGTACCTTA
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTA
**
38696473 GAGATATGATGGGAAAGATTGAAGCAACAAC-GA
66 GAGATATGA-GGGAAAGATTGAAGCCGCAACAGA
* * * * * * * *
38696506 TGAATCTTGTACCTTAAAGATAT-GATGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCT
1 TGAACCTTATACCCTAGAGATGTGGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCT
* * * *
38696570 AAAGATAGGGAGGGAAAGATTAAAGCCGTAACA-A
65 AGAGATA-TGAGGGAAAGATTGAAGCCGCAACAGA
* * * * * *
38696604 TAAACCTTATACCTTAGAAATGTGAAGGGAAAGATTGAAGTCGCAAC
1 TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAAC
38696651 AATGAATCTT
Statistics
Matches: 436, Mismatches: 88, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
96 2 0.00
97 75 0.17
98 354 0.81
99 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (98 bp):
TGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTA
GAGATATGAGGGAAAGATTGAAGCCGCAACAGA
Found at i:38696351 original size:147 final size:147
Alignment explanation
Indices: 38696022--38696665 Score: 641
Period size: 147 Copynumber: 4.4 Consensus size: 147
38696012 AATGGTGAAT
* * * * ** * ** *
38696022 CTTATACCTTAGAGATGTAAAGGGAGGGATTAAAGCCGCAATGGCGAATCTTGTACCCTAGAGAT
1 CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCCGCAACAGTGAATCTTGTACCCTAGAGAT
* * * * * * * *
38696087 ATGGA-GGGAAAGGTTGAAGCCACAATGACGTACCTTATA-CCTAGAGATGTGAAGGGAAAGGTT
66 AT-GATGAGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATATGGAGGGAAAGGTT
* *
38696150 GAAGCCGTAACGACGAGC
130 GAAGCCGTAACAACGAAC
* * *
38696168 CTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACAGTGAATCTTTTACCCTAGAGAT
1 CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCCGCAACAGTGAATCTTGTACCCTAGAGAT
* * *
38696233 GTGGA-GAGAAAGCTTGAAGCCGCAACGACGAATCTTGTACCCTAGAGATATGGAGGGAAAGGTT
66 AT-GATGAGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATATGGAGGGAAAGGTT
* **
38696297 GAAGTCGTAATGACGAAC
130 GAAGCCGTAACAACGAAC
* * * * * * * *
38696315 CTTATACCCTAGAAATGTGGA-GGGAAAGGTTAAAGCCACAACGGTGAACCTTGTACCTTAGAGA
1 CTTATACCTTAGAAATAT-GATGGGAAAGATTGAAGCCGCAACAGTGAATCTTGTACCCTAGAGA
* * * * * *
38696379 TATAATGAGAAATATTGAAACCGCAATGACGAATCTTTTACCCTAGAGATGTGGAGGGAAAGGTT
65 TATGATGAGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATATGGAGGGAAAGGTT
** *
38696444 GAAGCCACAACAATGAAC
130 GAAGCCGTAACAACGAAC
* * ** * *
38696462 CTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCAACAAC-GATGAATCTTGTACCTTAAAGA
1 CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCCGCAACAG-TGAATCTTGTACCCTAGAGA
* * * *
38696526 TATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAAAGATAGGGAGGGAAAGATT
65 TATGATGAGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATATGGAGGGAAAGGTT
* **
38696591 AAAGCCGTAACAATAAAC
130 GAAGCCGTAACAACGAAC
* * * * *
38696609 CTTATACCTTAGAAATGTGAAGGGAAAGATTGAAGTCGCAACAATGAATCTTATACC
1 CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCCGCAACAGTGAATCTTGTACC
38696666 GTGAAGATGA
Statistics
Matches: 411, Mismatches: 81, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
146 89 0.22
147 320 0.78
148 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (147 bp):
CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCCGCAACAGTGAATCTTGTACCCTAGAGAT
ATGATGAGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATATGGAGGGAAAGGTTG
AAGCCGTAACAACGAAC
Found at i:38696573 original size:49 final size:48
Alignment explanation
Indices: 38696018--38696665 Score: 472
Period size: 49 Copynumber: 13.2 Consensus size: 48
38696008 CCAGAATGGT
* * * ** * * *
38696018 GAATCTTATACCTTAGAGATGTAAAGGGAGGGATTAAAGCCGCAATGGC
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * *
38696067 GAATCTTGTACCCTAGAGATATGGAGGGAAAGGTTGAAGCCACAATGAC
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * * *
38696116 GTACCTTATA-CCTAGAGATGTGAAGGGAAAGGTTGAAGCCGTAACGAC
1 GAATCTTATACCCTAGAGATATG-AGGGAAAGATTGAAGCCGCAACGAC
** * * *
38696164 GAGCCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAAC-AGT
1 GAATCTTATACCCTAGAGATATGA-GGGAAAGATTGAAGCCGCAACGA-C
* * * *
38696213 GAATCTTTTACCCTAGAGATGTGGAGAGAAAGCTTGAAGCCGCAACGAC
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * * *
38696262 GAATCTTGTACCCTAGAGATATGGAGGGAAAGGTTGAAGTCGTAATGAC
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * * * * **
38696311 GAACCTTATACCCTAGAAATGTGGAGGGAAAGGTTAAAGCCACAACGGT
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * * * * * *
38696360 GAACCTTGTACCTTAGAGATATAATGAGAAATATTGAAACCGCAATGAC
1 GAATCTTATACCCTAGAGATATGA-GGGAAAGATTGAAGCCGCAACGAC
* * * * * *
38696409 GAATCTTTTACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCACAACAAT
1 GAATCTTATACCCTAGAGATAT-GAGGGAAAGATTGAAGCCGCAACGAC
* * * ** *
38696458 GAACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCAACAACGAT
1 GAATCTTATACCCTAGAGATATGA-GGGAAAGATTGAAGCCGCAACGAC
* * *
38696507 GAATCTTGTACCTTAAAGATATGATGGGAAAGATTGAAGCCGCAACGAC
1 GAATCTTATACCCTAGAGATATGA-GGGAAAGATTGAAGCCGCAACGAC
* * * * * *
38696556 GAATCTTATACCCTAAAGATAGGGAGGGAAAGATTAAAGCCGTAACAAT
1 GAATCTTATACCCTAGAGATA-TGAGGGAAAGATTGAAGCCGCAACGAC
* * * * * * * *
38696605 AAACCTTATACCTTAGAAATGTGAAGGGAAAGATTGAAGTCGCAACAAT
1 GAATCTTATACCCTAGAGATATG-AGGGAAAGATTGAAGCCGCAACGAC
38696654 GAATCTTATACC
1 GAATCTTATACC
38696666 GTGAAGATGA
Statistics
Matches: 478, Mismatches: 110, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
47 1 0.00
48 45 0.09
49 426 0.89
50 6 0.01
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (48 bp):
GAATCTTATACCCTAGAGATATGAGGGAAAGATTGAAGCCGCAACGAC
Found at i:38696690 original size:98 final size:98
Alignment explanation
Indices: 38696515--38696698 Score: 230
Period size: 98 Copynumber: 1.9 Consensus size: 98
38696505 ATGAATCTTG
* *
38696515 TACCTTAAAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAAAGATAGGG
1 TACCTTAAAGATATGAAGGGAAAGATTGAAGCCGCAACAACGAATCTTATACCCTAAAGATAGGG
** *
38696580 AGGGAAAGATTAAAGCCGTAACAATAAACCTTA
66 AGAAAAAAATTAAAGCCGTAACAATAAACCTTA
* * * * *
38696613 TACCTTAGAA-ATGTGAAGGGAAAGATTGAAGTCGCAACAATGAATCTTATACCGTGAAGAT-GA
1 TACCTTA-AAGATATGAAGGGAAAGATTGAAGCCGCAACAACGAATCTTATACCCTAAAGATAG-
38696676 GGA-AAAATAAATTAAAGCCGTAA
64 GGAGAAAA-AAATTAAAGCCGTAA
38696699 AGGCGAATCT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 3 0.04
98 68 0.93
99 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (98 bp):
TACCTTAAAGATATGAAGGGAAAGATTGAAGCCGCAACAACGAATCTTATACCCTAAAGATAGGG
AGAAAAAAATTAAAGCCGTAACAATAAACCTTA
Found at i:38697440 original size:24 final size:24
Alignment explanation
Indices: 38697406--38697455 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
38697396 AGCAACCTGC
38697406 AAAATAGAGAAGAGCAAA-GCAACAA
1 AAAATAGAGAAGA-CAAATGCAA-AA
38697431 AAAATA-AGAAGACAAATGCAAAA
1 AAAATAGAGAAGACAAATGCAAAA
38697454 AA
1 AA
38697456 CAAAATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.68, C:0.10, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAATAGAGAAGACAAATGCAAAA
Found at i:38698588 original size:232 final size:231
Alignment explanation
Indices: 38698166--38698619 Score: 692
Period size: 232 Copynumber: 2.0 Consensus size: 231
38698156 TTTTTGGACC
* * *
38698166 AATGGGTTATTTACGCCCTTGGTCCTTCCGGTTTTACATGCTATTGCAATTTGATCCTAATATGC
1 AATGGGCTATTTACGCCCTTGGTCCTTCCGCTTTTACATGCTATTGCAATTTGATCATAATATGC
* *
38698231 CCTTTCTTTCAATTTGTAATTTGGCCCAAAAGTTTTATTCTGTCTTCACATTGGTCCTTTGACCA
66 CCTTTCATTCAATTTGTAATGTGGCCCAAAAGTTTTATTCTGTCTTCACATTGGTCCTTTGACCA
*
38698296 ATAATCTTTGGGCAGACACGTGTATAGGCTTGGGCCAATTGCCCATTCAGTCCCTGTGCATCCCG
131 ATAATCTTTGGGCAGACACGTGTATAGGCTTGGGCCAATTACCCATTCAGTCCCTGTGCATCCCG
* *
38698361 AAATTTTGATTTTGACCCCAAACTTTTTATTTAGCCT
196 AAATTCTGATTTT-AACCCAAACTTTTTATTTAGCCT
* * *
38698398 AATGGGCTATTTATGCCCTTGGTCCTTTCGCTTTTACATGCTATTGCAATTTGATCATAATCTGC
1 AATGGGCTATTTACGCCCTTGGTCCTTCCGCTTTTACATGCTATTGCAATTTGATCATAATATGC
* * * * * *
38698463 CGTTTCATTCAATTTTTAATGTGGCCTAGAAGTTTTATTTTGTCTTCAGATTGGTCCTTTGACCA
66 CCTTTCATTCAATTTGTAATGTGGCCCAAAAGTTTTATTCTGTCTTCACATTGGTCCTTTGACCA
* * * * * *
38698528 TTAATTTTTGGGCAGACATGTGTATAGGCTTGGGCTAATTACCCATTCAGTCCTTGTGCATCTCG
131 ATAATCTTTGGGCAGACACGTGTATAGGCTTGGGCCAATTACCCATTCAGTCCCTGTGCATCCCG
38698593 AAATTCTGATTTTAACCCAAACTTTTT
196 AAATTCTGATTTTAACCCAAACTTTTT
38698620 GTTTTCCTTT
Statistics
Matches: 199, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
231 13 0.07
232 186 0.93
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (231 bp):
AATGGGCTATTTACGCCCTTGGTCCTTCCGCTTTTACATGCTATTGCAATTTGATCATAATATGC
CCTTTCATTCAATTTGTAATGTGGCCCAAAAGTTTTATTCTGTCTTCACATTGGTCCTTTGACCA
ATAATCTTTGGGCAGACACGTGTATAGGCTTGGGCCAATTACCCATTCAGTCCCTGTGCATCCCG
AAATTCTGATTTTAACCCAAACTTTTTATTTAGCCT
Found at i:38698764 original size:25 final size:25
Alignment explanation
Indices: 38698744--38698792 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
38698734 TTATTTTTGT
*
38698744 TAAAATTTAACCCTTTCATTTTTAA
1 TAAAAATTAACCCTTTCATTTTTAA
* *
38698769 TAAAAATTAATCCTTTGATTTTTA
1 TAAAAATTAACCCTTTCATTTTTA
38698793 TTTCTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (25 bp):
TAAAAATTAACCCTTTCATTTTTAA
Found at i:38698863 original size:24 final size:25
Alignment explanation
Indices: 38698834--38698880 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
38698824 TTTTATATTT
38698834 AAATCCTTTTTTAT-ATTTTTAATC
1 AAATCCTTTTTTATCATTTTTAATC
*
38698858 AAATCCTTTTTTATCCTTTTTAA
1 AAATCCTTTTTTATCATTTTTAA
38698881 ATTAATCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATCCTTTTTTATCATTTTTAATC
Found at i:38701196 original size:4 final size:4
Alignment explanation
Indices: 38701189--38701250 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
38701179 TTACTAATAA
* * * * *
38701189 ATAC ATAC GTAC GTAC ATAC ATAC ATAC ATGC ATAC GTAC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
38701237 ATAC ATGC ATAC AT
1 ATAC ATAC ATAC AT
38701251 GATATAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:38701247 original size:16 final size:16
Alignment explanation
Indices: 38701189--38701251 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
38701179 TTACTAATAA
* * *
38701189 ATACATACGTACGTAC
1 ATACATACATACATGC
38701205 ATACATACATACATGC
1 ATACATACATACATGC
*
38701221 ATACGTACATACATGC
1 ATACATACATACATGC
*
38701237 ATACATGCATACATG
1 ATACATACATACATG
38701252 ATATAATATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (16 bp):
ATACATACATACATGC
Found at i:38701849 original size:2 final size:2
Alignment explanation
Indices: 38701842--38701899 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
38701832 GTTTATCCTC
38701842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38701884 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
38701900 TCATTTAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38702717 original size:39 final size:39
Alignment explanation
Indices: 38702663--38702944 Score: 287
Period size: 39 Copynumber: 7.2 Consensus size: 39
38702653 GCAATGTTGT
* *
38702663 AGTGTCACTGCCAGTTCAGTATAGTATTACGGTGTTTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
* * * *
38702702 AGTGTCACCGTCAGTTTAGTACAATATTACGATGTTTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
* * *** *
38702741 AGTGTCACCGTCAGTTCAGTGTTGTATTGTAGTGTCTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
* * * * *
38702780 AATGTCACTG-CTAGTTCAGTATGGTATTACAGTGTTTAT
1 AGTGTCACCGTC-AGTTCAGTATAGTATTACGGTGTTTAC
* *
38702819 AGTGTCACCGTCAGTTCAGTACAGTATTACGGTATTTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
* * * * * *
38702858 AGTGTCATCGTCAGTTCAATTTTGTATTGCAGTGTTTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
* * **
38702897 AGTGTCACTGCCAGTTCAGTACGGTATTACGGTGTTTAC
1 AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
38702936 AGTGTCACC
1 AGTGTCACC
38702945 TTTAGTCAGT
Statistics
Matches: 192, Mismatches: 49, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
38 1 0.01
39 190 0.99
40 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (39 bp):
AGTGTCACCGTCAGTTCAGTATAGTATTACGGTGTTTAC
Found at i:38702815 original size:117 final size:117
Alignment explanation
Indices: 38702665--38702944 Score: 425
Period size: 117 Copynumber: 2.4 Consensus size: 117
38702655 AATGTTGTAG
* *
38702665 TGTCACTGCCAGTTCAGTATAGTATTACGGTGTTTACAGTGTCACCGTCAGTTTAGTACAATATT
1 TGTCACTGCCAGTTCAGTATGGTATTACGGTGTTTACAGTGTCACCGTCAGTTCAGTACAATATT
* * *
38702730 ACGATGTTTACAGTGTCACCGTCAGTTCAGTGTTGTATTGTAGTGTCTACAA
66 ACGATATTTACAGTGTCACCGTCAGTTCAATGTTGTATTGCAGTGTCTACAA
* * * *
38702782 TGTCACTGCTAGTTCAGTATGGTATTACAGTGTTTATAGTGTCACCGTCAGTTCAGTACAGTATT
1 TGTCACTGCCAGTTCAGTATGGTATTACGGTGTTTACAGTGTCACCGTCAGTTCAGTACAATATT
* * * * *
38702847 ACGGTATTTACAGTGTCATCGTCAGTTCAATTTTGTATTGCAGTGTTTACAG
66 ACGATATTTACAGTGTCACCGTCAGTTCAATGTTGTATTGCAGTGTCTACAA
*
38702899 TGTCACTGCCAGTTCAGTACGGTATTACGGTGTTTACAGTGTCACC
1 TGTCACTGCCAGTTCAGTATGGTATTACGGTGTTTACAGTGTCACC
38702945 TTTAGTCAGT
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 145 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (117 bp):
TGTCACTGCCAGTTCAGTATGGTATTACGGTGTTTACAGTGTCACCGTCAGTTCAGTACAATATT
ACGATATTTACAGTGTCACCGTCAGTTCAATGTTGTATTGCAGTGTCTACAA
Found at i:38706041 original size:19 final size:19
Alignment explanation
Indices: 38706017--38706054 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
38706007 TAATTTTTTC
38706017 TCATAAAATAATTAA-AAAA
1 TCATAAAA-AATTAATAAAA
38706036 TCATAAAAAATTAATAAAA
1 TCATAAAAAATTAATAAAA
38706055 AGTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TCATAAAAAATTAATAAAA
Found at i:38706053 original size:21 final size:22
Alignment explanation
Indices: 38706021--38706070 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
38706011 TTTTTCTCAT
38706021 AAAA-TAATTAAAAAATCA-TAA
1 AAAATTAATTAAAAAAT-ATTAA
*
38706042 AAAATTAA-TAAAAAGTATTAA
1 AAAATTAATTAAAAAATATTAA
38706063 AAAATTAA
1 AAAATTAA
38706071 AATTGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAATTAATTAAAAAATATTAA
Found at i:38706302 original size:11 final size:10
Alignment explanation
Indices: 38706282--38706450 Score: 92
Period size: 10 Copynumber: 17.4 Consensus size: 10
38706272 ATAAACTTAT
38706282 AAAATTATAA
1 AAAATTATAA
38706292 AAAATTTATAA
1 AAAA-TTATAA
*
38706303 AAACTTAT-A
1 AAAATTATAA
38706312 AAAATTATAA
1 AAAATTATAA
*
38706322 AAAA-AATATA
1 AAAATTATA-A
* *
38706332 AAAA-TCTAG
1 AAAATTATAA
*
38706341 TAAATTATAA
1 AAAATTATAA
38706351 AAAATTAT--
1 AAAATTATAA
38706359 -AAATTAATAA
1 AAAATT-ATAA
38706369 AATATATT-TAA
1 AA-A-ATTATAA
**
38706380 AATTTTATAA
1 AAAATTATAA
38706390 AAACA-TATAA
1 AAA-ATTATAA
* *
38706400 AAACTTGTAA
1 AAAATTATAA
*
38706410 ATAA-TAT--
1 AAAATTATAA
*
38706417 AAAATTTTAA
1 AAAATTATAA
38706427 ATAAATTATAA
1 A-AAATTATAA
38706438 AAAA-TATAA
1 AAAATTATAA
38706447 AAAA
1 AAAA
38706451 AAGTCATACA
Statistics
Matches: 120, Mismatches: 22, Indels: 35
0.68 0.12 0.20
Matches are distributed among these distances:
7 8 0.07
8 4 0.03
9 27 0.22
10 53 0.44
11 24 0.20
12 1 0.01
13 3 0.03
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:38706312 original size:29 final size:29
Alignment explanation
Indices: 38706274--38706401 Score: 115
Period size: 29 Copynumber: 4.4 Consensus size: 29
38706264 ACTTTAATAT
38706274 AAACTTATAAAATTATAAAAAATTTATAA
1 AAACTTATAAAATTATAAAAAATTTATAA
**
38706303 AAACTTATAAAAATTATAAAAAAAATATAA
1 AAACTTAT-AAAATTATAAAAAATTTATAA
38706333 AAA-TCTAGT-AAATTATAAAAAA-TTAT--
1 AAACT-TA-TAAAATTATAAAAAATTTATAA
* *
38706359 AAA-TTAATAAAATATATTTAAAATTTTATAA
1 AAACTT-ATAAAAT-TA-TAAAAAATTTATAA
*
38706390 AAACATATAAAA
1 AAACTTATAAAA
38706402 ACTTGTAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
25 2 0.02
26 9 0.11
27 2 0.02
28 8 0.10
29 26 0.32
30 24 0.29
31 10 0.12
32 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
AAACTTATAAAATTATAAAAAATTTATAA
Found at i:38706388 original size:39 final size:37
Alignment explanation
Indices: 38706345--38706438 Score: 93
Period size: 39 Copynumber: 2.5 Consensus size: 37
38706335 ATCTAGTAAA
*
38706345 TTATAAAAAATTATAAA-TTAATAAAATATATTTAAAATT
1 TTATAAAAAATTATAAACTT-AT-AAATA-ATATAAAATT
* *
38706384 TTATAAAAACATATAAAAACTTGTAAATAATATAAAATT
1 TTATAAAAA-AT-TATAAACTTATAAATAATATAAAATT
*
38706423 TTA-AATAAATTATAAA
1 TTATAAAAAATTATAAA
38706439 AAATATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
36 5 0.11
37 2 0.04
38 4 0.09
39 21 0.45
40 7 0.15
41 6 0.13
42 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (37 bp):
TTATAAAAAATTATAAACTTATAAATAATATAAAATT
Found at i:38706623 original size:3 final size:3
Alignment explanation
Indices: 38706615--38706674 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
38706605 TTATTTACGA
* *
38706615 ATT ATT ATT AGT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38706663 ATT ATT ATT ATT
1 ATT ATT ATT ATT
38706675 TAAGTACAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:38707110 original size:28 final size:28
Alignment explanation
Indices: 38707079--38707150 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
38707069 TTTAAGATTT
38707079 TTTTATAATTTTTAT-ATATTTATATCAA
1 TTTTATAATTTTTATAATATTT-TATCAA
* *
38707107 TTTTAGT-ATTTTTATAATATTTTATGAT
1 TTTTA-TAATTTTTATAATATTTTATCAA
38707135 TTCTTATAAGTTTTTA
1 TT-TTATAA-TTTTTA
38707151 AGAATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 20 0.54
29 11 0.30
30 6 0.16
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTATAATTTTTATAATATTTTATCAA
Found at i:38707120 original size:20 final size:19
Alignment explanation
Indices: 38707075--38707122 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
38707065 AGATTTTAAG
*
38707075 ATTTTTTTATAATTTTTAT
1 ATTTTTATATAATTTTTAT
*
38707094 ATATTTATATCAA-TTTTAGT
1 ATTTTTATAT-AATTTTTA-T
38707114 ATTTTTATA
1 ATTTTTATA
38707123 ATATTTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTTATATAATTTTTAT
Found at i:38707149 original size:20 final size:20
Alignment explanation
Indices: 38707078--38707171 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
38707068 TTTTAAGATT
38707078 TTTTTATAA-TTTTTAT-ATA
1 TTTTTATAAGTTTTTATGA-A
* *
38707097 TTTATATCAA--TTTTA-GTA
1 TTTTTAT-AAGTTTTTATGAA
38707115 TTTTTATAA-TATTTTATG-A
1 TTTTTATAAGT-TTTTATGAA
*
38707134 TTTCTTATAAGTTTTTAAGAA
1 TTT-TTATAAGTTTTTATGAA
*
38707155 TTTTTATACGTTTTTAT
1 TTTTTATAAGTTTTTAT
38707172 AAACTTAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
17 2 0.03
18 7 0.11
19 20 0.33
20 27 0.44
21 5 0.08
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTATAAGTTTTTATGAA
Found at i:38711967 original size:107 final size:107
Alignment explanation
Indices: 38711781--38711992 Score: 388
Period size: 107 Copynumber: 2.0 Consensus size: 107
38711771 CTGACATTAC
38711781 TAGCTTTTACAGAAAATTATGGGGATTACAATTGCCTGAAAAAGTTAAAATCATGGTATGGAAAG
1 TAGCTTTTACAGAAAATTATGGGGATTACAATTGCCTGAAAAAGTTAAAATCATGGTATGGAAAG
* *
38711846 TTACATGGTCCTATCTTCCTACTTTAATGATGCTGCAGTTAA
66 CTACATGGTCCTATCTTCCTACTTTAATGATGCTACAGTTAA
*
38711888 TAGCTTTTACAGAAAATTATGGGGATTACAATTGCTTGAAAAAGTTAAAATCATGGTATGGAAAG
1 TAGCTTTTACAGAAAATTATGGGGATTACAATTGCCTGAAAAAGTTAAAATCATGGTATGGAAAG
*
38711953 CTACATGGTCCTATCTTCCTACTTTAGTGATGCTACAGTT
66 CTACATGGTCCTATCTTCCTACTTTAATGATGCTACAGTT
38711993 TAGGCGAGGT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (107 bp):
TAGCTTTTACAGAAAATTATGGGGATTACAATTGCCTGAAAAAGTTAAAATCATGGTATGGAAAG
CTACATGGTCCTATCTTCCTACTTTAATGATGCTACAGTTAA
Found at i:38715058 original size:21 final size:18
Alignment explanation
Indices: 38715013--38715066 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 18
38715003 CCTCATCAAA
38715013 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
38715031 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
38715049 GTAATCTTCATCCTTATC
1 G---TCTTCATCCTTATC
38715067 TTTTCCTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 19 0.58
21 14 0.42
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (18 bp):
GTCTTCATCCTTATCCAT
Found at i:38718993 original size:15 final size:15
Alignment explanation
Indices: 38718973--38719004 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38718963 GGTTTTGAAC
*
38718973 AAGATTCAGTTTCTG
1 AAGATTCAGATTCTG
38718988 AAGATTCAGATTCTG
1 AAGATTCAGATTCTG
38719003 AA
1 AA
38719005 TGTTGATCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (15 bp):
AAGATTCAGATTCTG
Found at i:38719259 original size:15 final size:15
Alignment explanation
Indices: 38719239--38719275 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
38719229 TCTTTGCTCA
38719239 GCTTCTTTCTTTTTT
1 GCTTCTTTCTTTTTT
38719254 GCTTCTTTCTTTTTT
1 GCTTCTTTCTTTTTT
38719269 GCTTCTT
1 GCTTCTT
38719276 CTTGCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.70
Consensus pattern (15 bp):
GCTTCTTTCTTTTTT
Found at i:38720244 original size:9 final size:9
Alignment explanation
Indices: 38720226--38720271 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
38720216 GTTAATTTGT
38720226 TAAT-TTTA
1 TAATATTTA
38720234 TAATATTTA
1 TAATATTTA
38720243 TAATATTTA
1 TAATATTTA
* *
38720252 TTATTTTTTA
1 -TAATATTTA
38720262 TAA-ATTTA
1 TAATATTTA
38720270 TA
1 TA
38720272 TCAGTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 10 0.31
9 15 0.47
10 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAATATTTA
Found at i:38720250 original size:27 final size:27
Alignment explanation
Indices: 38720220--38720330 Score: 72
Period size: 27 Copynumber: 4.0 Consensus size: 27
38720210 GAATTTGTTA
*
38720220 ATTTGTTA-ATTTTATAATATTTATAAT
1 ATTTATTATATTTTATAA-ATTTATAAT
*
38720247 ATTTATTATTTTTTATAAATTTAT-AT
1 ATTTATTATATTTTATAAATTTATAAT
*
38720273 CAGTTTTAATATATACTTTTA-ATATTTAATAAT
1 -A--TTT-AT-TATA-TTTTATAAATTT-ATAAT
*
38720306 -TTTTTTAT-TTTTATAAATTT-TAAT
1 ATTTATTATATTTTATAAATTTATAAT
38720330 A
1 A
38720331 ATGTTTTATG
Statistics
Matches: 67, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
24 4 0.06
25 5 0.07
26 7 0.10
27 17 0.25
28 9 0.13
29 6 0.09
30 2 0.03
31 8 0.12
32 7 0.10
33 2 0.03
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTATTATATTTTATAAATTTATAAT
Found at i:38720251 original size:18 final size:18
Alignment explanation
Indices: 38720226--38720271 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
38720216 GTTAATTTGT
38720226 TAAT-TTTATAATATTTA
1 TAATATTTATAATATTTA
* *
38720243 TAATATTTATTATTTTTTA
1 TAATATTTA-TAATATTTA
38720262 TAA-ATTTATA
1 TAATATTTATA
38720272 TCAGTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATATTTATAATATTTA
Found at i:38726070 original size:39 final size:39
Alignment explanation
Indices: 38726001--38726191 Score: 240
Period size: 39 Copynumber: 4.9 Consensus size: 39
38725991 CAATATAATG
* * *
38726001 TTGCAGTG-TTACAGTGTCACCGCCAGTTCAGTATAACA
1 TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATATCA
*
38726039 TTGCAGTGTTTATAGTGTCACTGCCAATTCAGTATATCA
1 TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATATCA
* * * * *
38726078 TTGTACTGTTTATAGTGTCACTACCAGTTCAATATAGCA
1 TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATATCA
* * ** *
38726117 TTGCAGTGTTTACAATGTCACAACCAGTTCAATATATCA
1 TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATATCA
*
38726156 TTGCAGTGTTTATAGTGTCAATGCCAGTTCAGTATA
1 TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATA
38726192 CTTCTGATGT
Statistics
Matches: 130, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 8 0.06
39 122 0.94
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (39 bp):
TTGCAGTGTTTATAGTGTCACTGCCAGTTCAGTATATCA
Found at i:38732575 original size:39 final size:39
Alignment explanation
Indices: 38732532--38732733 Score: 233
Period size: 39 Copynumber: 5.2 Consensus size: 39
38732522 TAATAGTCTA
** *
38732532 CAGTATAATGTTGCAGTGTTTATAGTGTCACCGCCAGTT
1 CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
* *
38732571 CAGTATAGCATTGCAGTGCTTATAGTGTCACTGCCAGTT
1 CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
* * *
38732610 CATTATATCATTGCAGTGTTTCTAGTGTCACTGCCAGTT
1 CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
* * * *
38732649 CAGTATAGCATTGTAGTGTTTACAGTGTCACTGCTAGTT
1 CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
* * ** * * *
38732688 AAGTATATCATTGCCCTATTTACAGTGTCACTGCCAGCT
1 CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
38732727 CAGTATA
1 CAGTATA
38732734 CTTTCGATAT
Statistics
Matches: 139, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 139 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (39 bp):
CAGTATAACATTGCAGTGTTTATAGTGTCACTGCCAGTT
Found at i:38732676 original size:78 final size:78
Alignment explanation
Indices: 38732542--38732733 Score: 260
Period size: 78 Copynumber: 2.5 Consensus size: 78
38732532 CAGTATAATG
* * *
38732542 TTGCAGTGTTTATAGTGTCACCGCCAGTTCAGTATAGCATTGCAGTGCTTATAGTGTCACTGCCA
1 TTGCAGTGTTTCTAGTGTCACTGCCAGTTCAGTATAGCATTGCAGTGCTTACAGTGTCACTGCCA
* *
38732607 GTTCATTATATCA
66 GTTAAGTATATCA
* * *
38732620 TTGCAGTGTTTCTAGTGTCACTGCCAGTTCAGTATAGCATTGTAGTGTTTACAGTGTCACTGCTA
1 TTGCAGTGTTTCTAGTGTCACTGCCAGTTCAGTATAGCATTGCAGTGCTTACAGTGTCACTGCCA
38732685 GTTAAGTATATCA
66 GTTAAGTATATCA
** * *
38732698 TTGCCCTATTTAC-AGTGTCACTGCCAGCTCAGTATA
1 TTGCAGTGTTT-CTAGTGTCACTGCCAGTTCAGTATA
38732734 CTTTCGATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 100 0.99
79 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (78 bp):
TTGCAGTGTTTCTAGTGTCACTGCCAGTTCAGTATAGCATTGCAGTGCTTACAGTGTCACTGCCA
GTTAAGTATATCA
Found at i:38740605 original size:60 final size:60
Alignment explanation
Indices: 38740509--38740622 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
38740499 ACTTTGAACA
*
38740509 TTAAAAAACATATTTCTTTCTTTATTTTTTTCCCATATCATATATTTTAACTTTTTAACT
1 TTAAAAAACATATTTATTTCTTTATTTTTTTCCCATATCATATATTTTAACTTTTTAACT
* *
38740569 TTAAATAA-ATATTTATTT-TTTATTTCTTTTTTCCATATCATATATTTTAACTTT
1 TTAAAAAACATATTTATTTCTTTA-TT-TTTTTCCCATATCATATATTTTAACTTT
38740623 AAATATTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 4 0.08
59 11 0.22
60 34 0.69
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (60 bp):
TTAAAAAACATATTTATTTCTTTATTTTTTTCCCATATCATATATTTTAACTTTTTAACT
Found at i:38740659 original size:60 final size:59
Alignment explanation
Indices: 38740529--38740659 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 59
38740519 TATTTCTTTC
* * *
38740529 TTTA-TTTTTTTCCCATATCATATATTTTAACTTTTTAACTTTAAATAAATATTTATTT
1 TTTATTTTTTTTCCCATATCATATATTTTAACTTTTAAAATTTAAATAAATATTTATAT
* *
38740587 TTTATTTCTTTTTTCCATATCATATATTTTAAC-TTTAAATATTTATATAATATATTTCA-AT
1 TTTATTT-TTTTTCCCATATCATATATTTTAACTTTTAAA-ATTTAAATAA-ATATTT-ATAT
*
38740648 TTTCTTTTTTTT
1 TTTATTTTTTTT
38740660 AGATGATAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
58 4 0.06
59 7 0.11
60 37 0.60
61 13 0.21
62 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (59 bp):
TTTATTTTTTTTCCCATATCATATATTTTAACTTTTAAAATTTAAATAAATATTTATAT
Found at i:38740907 original size:16 final size:17
Alignment explanation
Indices: 38740872--38740910 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38740862 TGTTTTAAAG
38740872 TTTATAGTTTATTTTAT
1 TTTATAGTTTATTTTAT
*
38740889 TTTATAG-TTATTATTTT
1 TTTATAGTTTATT-TTAT
38740906 TTTAT
1 TTTAT
38740911 CTTTTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTATAGTTTATTTTAT
Found at i:38743073 original size:38 final size:38
Alignment explanation
Indices: 38743022--38743159 Score: 141
Period size: 38 Copynumber: 3.6 Consensus size: 38
38743012 CGGTGTTGTA
* *
38743022 GGGCTTAGTGCCTAGCAGGCTTCGTGCAGGTTTTTATT
1 GGGCTTAGTGCCTAGCAGGCTTCGTGCAGGTGTTTATC
* * *
38743060 GGGCTTAGTGCCTAGCAGACTTCATGCCGGTGTTTATC
1 GGGCTTAGTGCCTAGCAGGCTTCGTGCAGGTGTTTATC
* * * * * **
38743098 GGGCTGAATACTTAGCAGGCTTTGTGTTGGTGTTTATC
1 GGGCTTAGTGCCTAGCAGGCTTCGTGCAGGTGTTTATC
* * *
38743136 GGGCTTTGTGCTTAGTAGGCTTCG
1 GGGCTTAGTGCCTAGCAGGCTTCG
38743160 GGTCAGTGTA
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (38 bp):
GGGCTTAGTGCCTAGCAGGCTTCGTGCAGGTGTTTATC
Found at i:38745672 original size:200 final size:190
Alignment explanation
Indices: 38745314--38745673 Score: 443
Period size: 200 Copynumber: 1.8 Consensus size: 190
38745304 TACTATAAAT
* * * * *
38745314 TGTTCCTTAACGATGCTGCTCACACGAGCTGTCGAGAGTATGTAATAAGCATAATCCCAGCAATC
1 TGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAACAATC
* * * *
38745379 GTAGGGCCTGTAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCTGCTTACACAAGC
66 GTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCGACTCACAATGCTGCTCACACAAGC
* *
38745444 TGTCGAGGACTCGCAACATATGCGGTACCTTACCATTGATACGGTATTTATGCATATAAC
131 TGTCGAGGACTCACAACATATACGGTACCTTACCATTGATACGGTATTTATGCATATAAC
* * * *
38745504 TGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAACCA
1 TGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCA-ATAAGCAT-AATCCCAACAA
* *
38745569 TCGTAGGGCCTATAATCCATTTAGGATCTATATTTATTTTCTCATTTCCTGACTCACAATGCTGC
64 TCGTAGGGCCTATAATCCATTTAGGATC--CA--TA---TCTC-TTTCCCGACTCACAATGCTGC
* *
38745634 TCGCACGAA-CTGTCGAGGGCTCACAACATATACGGTACCT
121 TCACAC-AAGCTGTCGAGGACTCACAACATATACGGTACCT
38745674 CAGCCATCAC
Statistics
Matches: 140, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
190 40 0.29
191 6 0.04
192 35 0.25
194 1 0.01
196 2 0.01
199 4 0.03
200 50 0.36
201 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (190 bp):
TGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAACAATC
GTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCGACTCACAATGCTGCTCACACAAGC
TGTCGAGGACTCACAACATATACGGTACCTTACCATTGATACGGTATTTATGCATATAAC
Found at i:38749720 original size:15 final size:15
Alignment explanation
Indices: 38749702--38749751 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
38749692 TAACTTATTT
38749702 TTATTTATTAAATTA
1 TTATTTATTAAATTA
*
38749717 TTATTTAATT-AATTT
1 TTATTT-ATTAAATTA
38749732 TTATTT-TTAAAATTA
1 TTATTTATT-AAATTA
38749747 TTATT
1 TTATT
38749752 ATTGTTCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 2 0.07
15 25 0.83
16 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTATTAAATTA
Found at i:38749748 original size:30 final size:31
Alignment explanation
Indices: 38749676--38749751 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
38749666 TTCAAATAAA
*
38749676 TTTTAAAATT-TCATTCTAACTTATTTTTAT
1 TTTTAAAATTATTATTCTAACTTATTTTTAT
38749706 TTATT-AAATTATTATT-TAA-TTAATTTTTAT
1 TT-TTAAAATTATTATTCTAACTT-ATTTTTAT
38749736 TTTTAAAATTATTATT
1 TTTTAAAATTATTATT
38749752 ATTGTTCATC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
29 4 0.10
30 31 0.76
31 6 0.15
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTAAAATTATTATTCTAACTTATTTTTAT
Found at i:38749925 original size:15 final size:17
Alignment explanation
Indices: 38749905--38749945 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
38749895 TCGATGGTGA
38749905 ATATAAGATT-TTGG-C
1 ATATAAGATTATTGGAC
38749920 ATATAAAGATTATTGGAC
1 ATAT-AAGATTATTGGAC
38749938 ATA-AAGAT
1 ATATAAGAT
38749946 GACTTGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 4 0.17
18 4 0.17
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (17 bp):
ATATAAGATTATTGGAC
Found at i:38750494 original size:28 final size:28
Alignment explanation
Indices: 38750386--38750494 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 28
38750376 ATTGTTTTTC
38750386 AATTTTTAAAGGGCCCTAAAAA-TTTTT-A
1 AATTTTT-AAGGGCCC-AAAAATTTTTTAA
* * * *
38750414 ACTTTTTAAAGG-CCAAATATTTTTTACC
1 AATTTTTAAGGGCCCAAAAATTTTTTA-A
* *
38750442 AATTTGTAAGGGGCCTC-AAATTTTTTTAA
1 AATTTTTAA-GGGCC-CAAAAATTTTTTAA
38750471 AATTTTTAAGGGCCCAAAAATTTT
1 AATTTTTAAGGGCCCAAAAATTTT
38750495 GTTTTTTTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
25 4 0.06
26 7 0.11
27 5 0.08
28 25 0.40
29 10 0.16
30 10 0.16
31 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (28 bp):
AATTTTTAAGGGCCCAAAAATTTTTTAA
Found at i:38750907 original size:17 final size:17
Alignment explanation
Indices: 38750885--38750918 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38750875 TCTTAATGTG
*
38750885 TTAGGATTAGGGGAGTA
1 TTAGGATTAAGGGAGTA
38750902 TTAGGATTAAGGGAGTA
1 TTAGGATTAAGGGAGTA
38750919 AAGTGGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (17 bp):
TTAGGATTAAGGGAGTA
Found at i:38751576 original size:27 final size:25
Alignment explanation
Indices: 38751515--38751576 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
38751505 TTTTAATAGG
*
38751515 ATTATTT-TTAAATATAATTTAATA
1 ATTATTTATTAAATATAATTAAATA
*
38751539 ATAATTATATTAAAATATAATTAAATTA
1 ATTATT-TATT-AAATATAATTAAA-TA
*
38751567 TTTATTTATT
1 ATTATTTATT
38751577 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
24 5 0.17
25 1 0.03
26 2 0.07
27 16 0.53
28 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTTATTAAATATAATTAAATA
Found at i:38751584 original size:33 final size:33
Alignment explanation
Indices: 38751546--38751635 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
38751536 ATAATAATTA
*
38751546 TATTAAAATATA-ATTAAATTATTTATTTATTTT
1 TATTAAAAT-TACATTAAAATATTTATTTATTTT
38751579 TATT-AAATTACATTAAAATATTT-TTTATTTT
1 TATTAAAATTACATTAAAATATTTATTTATTTT
*
38751610 TATATAAAATTATATTAAAATATTTA
1 TAT-TAAAATTACATTAAAATATTTA
38751636 AAATATTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
31 13 0.25
32 16 0.31
33 22 0.43
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TATTAAAATTACATTAAAATATTTATTTATTTT
Done.