Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 173 of 195
Found at i:28923329 original size:2 final size:2
Alignment explanation
Indices: 28923322--28923359 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28923312 TAAAACACAT
28923322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28923360 ACAAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28923431 original size:17 final size:18
Alignment explanation
Indices: 28923406--28923442 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28923396 ACACAGTCAA
28923406 TAAAACACTT-AACAATT
1 TAAAACACTTAAACAATT
*
28923423 TAAATCACTTAAACAATT
1 TAAAACACTTAAACAATT
28923441 TA
1 TA
28923443 CTTGGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAACACTTAAACAATT
Found at i:28928153 original size:15 final size:15
Alignment explanation
Indices: 28928133--28928199 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 15
28928123 CTCAATAATT
28928133 AATAAAAAT-CAGTAA
1 AATAAAAATACA-TAA
28928148 AAT-AAAATACATAA
1 AATAAAAATACATAA
28928162 AATAAAAA-ATCAATAA
1 AATAAAAATA-C-ATAA
*
28928178 AAT-AAAATGCATAA
1 AATAAAAATACATAA
28928192 AATAAAAA
1 AATAAAAA
28928200 ATTGAAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
14 19 0.42
15 19 0.42
16 7 0.16
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (15 bp):
AATAAAAATACATAA
Found at i:28928162 original size:14 final size:14
Alignment explanation
Indices: 28928145--28928198 Score: 72
Period size: 14 Copynumber: 3.7 Consensus size: 14
28928135 TAAAAATCAG
28928145 TAAAATAAAATACA
1 TAAAATAAAATACA
*
28928159 TAAAATAAAAAATCAA
1 TAAAATAAAATA-C-A
*
28928175 TAAAATAAAATGCA
1 TAAAATAAAATACA
28928189 TAAAATAAAA
1 TAAAATAAAA
28928199 AATTGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 22 0.63
15 2 0.06
16 11 0.31
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAAATAAAATACA
Found at i:28928172 original size:30 final size:30
Alignment explanation
Indices: 28928136--28928213 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
28928126 AATAATTAAT
28928136 AAAAATCAGTAAAATAAAATACATAAAATA
1 AAAAATCAGTAAAATAAAATACATAAAATA
* *
28928166 AAAAATCAATAAAATAAAATGCATAAAATA
1 AAAAATCAGTAAAATAAAATACATAAAATA
*
28928196 AAAAAT-TG-AAAATAAAAT
1 AAAAATCAGTAAAATAAAAT
28928214 CAAAATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 10 0.23
30 34 0.77
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.21
Consensus pattern (30 bp):
AAAAATCAGTAAAATAAAATACATAAAATA
Found at i:28928218 original size:6 final size:5
Alignment explanation
Indices: 28928145--28928251 Score: 71
Period size: 5 Copynumber: 21.0 Consensus size: 5
28928135 TAAAAATCAG
* **
28928145 TAAAA TAAAA T-ACA TAAAA TAAAA -AATCAA TAAAA TAAAA T-GCA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA--AA TAAAA TAAAA TAAAA TAAAA
* *
28928194 T-AAA -AAAT TGAAAA TAAAA TCAAAA TCAAAA TAAAAA TAAAA GAAAA
1 TAAAA TAAAA T-AAAA TAAAA T-AAAA T-AAAA T-AAAA TAAAA TAAAA
28928241 TAAAA CTAAAA
1 TAAAA -TAAAA
28928252 CAGGAAAACC
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
4 12 0.15
5 40 0.49
6 27 0.33
7 2 0.02
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:28928251 original size:11 final size:11
Alignment explanation
Indices: 28928204--28928251 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
28928194 TAAAAAATTG
*
28928204 AAAATAAAATC
1 AAAATAAAATA
28928215 AAAATCAAAATA
1 AAAAT-AAAATA
*
28928227 AAAATAAAA-G
1 AAAATAAAATA
28928237 AAAATAAAACTA
1 AAAATAAAA-TA
28928249 AAA
1 AAA
28928252 CAGGAAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.29
11 9 0.29
12 13 0.42
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:28929086 original size:3 final size:3
Alignment explanation
Indices: 28929078--28929302 Score: 70
Period size: 3 Copynumber: 81.7 Consensus size: 3
28929068 AAAGAAAATA
*
28929078 AAT AAT AAT AAT AAT -AT AACT -AT AAT AAT AAT AAT AGT AA- AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
28929121 -AT AAT -AT AAT -AC AAT ACCAT -AT ACT -AT ACT -AC AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
28929161 ACT -AT ACT AAT -AT ATT AAT -AT ACT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
28929205 AAT -AT AAT -AT AAT -AT ACT -AT AAT AA- AAT -AT AAT -AC AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
28929245 AAT -AT AAT -AT ACT ACACT -AT AGT AAT -AT AAT ACT AGT AAC AAT
1 AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
28929288 AAT AAT AAAT AAT AA
1 AAT AAT -AAT AAT AA
28929303 AAACGACACC
Statistics
Matches: 159, Mismatches: 31, Indels: 64
0.63 0.12 0.25
Matches are distributed among these distances:
2 42 0.26
3 110 0.69
4 4 0.03
5 3 0.02
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:28929104 original size:20 final size:20
Alignment explanation
Indices: 28929079--28929301 Score: 117
Period size: 20 Copynumber: 10.8 Consensus size: 20
28929069 AAGAAAATAA
28929079 ATAATAATAATAATATAACT
1 ATAATAATAATAATATAACT
*
28929099 ATAATAATAATAATAGTAAAAT
1 ATAATAATAATAATA-T-AACT
*
28929121 ATAAT-ATAATACA-ATACCAT
1 ATAATAATAATA-ATATAAC-T
*
28929141 ATACTATACTACAATAATAT-ACT
1 ATA--ATA--ATAATAATATAACT
*
28929164 ATACTAATATATTAATAT-ACT
1 ATAATAATA-A-TAATATAACT
28929185 ATAATAATAATAATAATAA-T
1 ATAATAATAATAAT-ATAACT
28929205 A-ATATAAT-ATAATAT-ACT
1 ATA-ATAATAATAATATAACT
* *
28929223 ATAATAAAATATAATACAA-T
1 ATAATAATA-ATAATATAACT
28929243 ATAAT-ATAAT-ATACTACACT
1 ATAATAATAATAATA-TA-ACT
* * *
28929263 ATAGTAATATAATACTAGTAACA
1 ATAAT-A-ATAATAATA-TAACT
28929286 ATAATAATAAATAATA
1 ATAATAAT-AATAATA
28929302 AAAACGACAC
Statistics
Matches: 157, Mismatches: 18, Indels: 54
0.69 0.08 0.24
Matches are distributed among these distances:
17 4 0.03
18 11 0.07
19 17 0.11
20 48 0.31
21 31 0.20
22 18 0.11
23 15 0.10
24 6 0.04
25 7 0.04
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (20 bp):
ATAATAATAATAATATAACT
Found at i:28929275 original size:5 final size:5
Alignment explanation
Indices: 28929082--28929255 Score: 122
Period size: 5 Copynumber: 33.6 Consensus size: 5
28929072 AAAATAAATA
* *
28929082 ATAAT AATAAT ATAACT ATAAT AATAAT AATAGT AAAAT ATAAT ATAAT
1 ATAAT -ATAAT ATAA-T ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT
* ** * * *
28929131 ACAAT ACCAT ATACT ATACT A-CA- ATAAT ATACTAT ACTAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT A-TAAT ATAAT
* *
28929176 -TAAT ATACT ATAAT AATAAT AATAAT AATAAT ATAAT ATAAT ATACT
1 ATAAT ATAAT ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT
* *
28929223 ATAAT AAAAT ATAAT ACAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
28929256 CTACACTATA
Statistics
Matches: 138, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
3 2 0.01
4 5 0.04
5 86 0.62
6 40 0.29
7 3 0.02
8 2 0.01
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:28929520 original size:55 final size:55
Alignment explanation
Indices: 28929454--28929696 Score: 181
Period size: 55 Copynumber: 4.4 Consensus size: 55
28929444 AATGATCGAT
* * *
28929454 ATTAAGCCACAAGTCTGAAAAATTATCTAAACT-AAGCTGAAATCGAACGACCAAG
1 ATTAAACCACAAGTCTAAAAAATGATCTAAACTGAA-CTGAAATCGAACGACCAAG
* * * * * *
28929509 ATTAAATCACAAGTCTAGAAAATGATCTGAACTGAACTGATATCGAATGACCAGG
1 ATTAAACCACAAGTCTAAAAAATGATCTAAACTGAACTGAAATCGAACGACCAAG
* * * * * *
28929564 ATTAAACCATAAGTC-AGGAAAATGATTTAGATTG---TGGCAAGATCGAACGACCGAG
1 ATTAAACCACAAGTCTA-AAAAATGATCTAAACTGAACT-G-AA-ATCGAACGACCAAG
* * * * * * * * * *
28929619 ATTGAATCACAAGTCAAAAAAATAATCTGAATTGTACCGAGATCGAACAACCAAG
1 ATTAAACCACAAGTCTAAAAAATGATCTAAACTGAACTGAAATCGAACGACCAAG
28929674 ATTAAACCACAAGTCTAAAAAAT
1 ATTAAACCACAAGTCTAAAAAAT
28929697 TATTTGAATT
Statistics
Matches: 145, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
52 1 0.01
53 1 0.01
54 2 0.01
55 136 0.94
56 4 0.03
57 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.21
Consensus pattern (55 bp):
ATTAAACCACAAGTCTAAAAAATGATCTAAACTGAACTGAAATCGAACGACCAAG
Found at i:28929621 original size:110 final size:110
Alignment explanation
Indices: 28929454--28929763 Score: 286
Period size: 110 Copynumber: 2.8 Consensus size: 110
28929444 AATGATCGAT
* * * * * * * *
28929454 ATTAAGCCACAAGTCTGAAAAATTATCTAAACTAAGCTGAA-ATCGAACGACCAAGATTAAATCA
1 ATTAAACCACAAGTCTAAAAAATGATTTGAATTGAGCT-AAGATCGAACGACCGAGATTAAATCA
* * ** *
28929518 CAAGTCTAGAAAATGATCTGAACTGAACTGATATCGAATGACCAGG
65 CAAGTCTAGAAAATGATCTGAACTGAACCGAGATCGAACAACCAAG
* * * *
28929564 ATTAAACCATAAGTC-AGGAAAATGATTT-AGATTGTGGC-AAGATCGAACGACCGAGATTGAAT
1 ATTAAACCACAAGTCTA-AAAAATGATTTGA-ATTG-AGCTAAGATCGAACGACCGAGATTAAAT
* * * * *
28929626 CACAAGTCAAAAAAATAATCTGAATTGTACCGAGATCGAACAACCAAG
63 CACAAGTCTAGAAAATGATCTGAACTGAACCGAGATCGAACAACCAAG
* * * * * *
28929674 ATTAAACCACAAGTCTAAAAAATTATTTGAATTGAGCTAAGGTCAAATGATCGAGATTAAATCAT
1 ATTAAACCACAAGTCTAAAAAATGATTTGAATTGAGCTAAGATCGAACGACCGAGATTAAATCAC
* *
28929739 AAGTCTTGAAAATGATCTGGACTGA
66 AAGTCTAGAAAATGATCTGAACTGA
28929764 GTCAAGATTG
Statistics
Matches: 155, Mismatches: 38, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
109 5 0.03
110 146 0.94
111 4 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (110 bp):
ATTAAACCACAAGTCTAAAAAATGATTTGAATTGAGCTAAGATCGAACGACCGAGATTAAATCAC
AAGTCTAGAAAATGATCTGAACTGAACCGAGATCGAACAACCAAG
Found at i:28929705 original size:55 final size:55
Alignment explanation
Indices: 28929495--28929707 Score: 196
Period size: 55 Copynumber: 3.9 Consensus size: 55
28929485 CTAAGCTGAA
* * * * * *
28929495 ATCGAACGACCAAGATTAAATCACAAGTCTAGAAAATGATCTGAACTGAACTGAT
1 ATCGAACGACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAATTGTACCGAG
* * * * * ** *
28929550 ATCGAATGACCAGGATTAAACCATAAGTC-AGGAAAATGAT-TTAGATTGTGGCAAG
1 ATCGAACGACCAAGATTAAACCACAAGTCTA-AAAAATGATCTGA-ATTGTACCGAG
* * * * *
28929605 ATCGAACGACCGAGATTGAATCACAAGTCAAAAAAATAATCTGAATTGTACCGAG
1 ATCGAACGACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAATTGTACCGAG
* * *
28929660 ATCGAACAACCAAGATTAAACCACAAGTCTAAAAAATTATTTGAATTG
1 ATCGAACGACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAATTG
28929708 AGCTAAGGTC
Statistics
Matches: 123, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
54 3 0.02
55 117 0.95
56 3 0.02
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (55 bp):
ATCGAACGACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAATTGTACCGAG
Found at i:28929814 original size:165 final size:165
Alignment explanation
Indices: 28929495--28929797 Score: 356
Period size: 165 Copynumber: 1.8 Consensus size: 165
28929485 CTAAGCTGAA
* * * * * *
28929495 ATCGAACGACCAAGATTAAATCACAAGTCTAGAAAATGATCTGAACTGAACTGATATCGAATGAC
1 ATCGAACAACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAACTGAACTAAGATCAAATGAC
* * * *
28929560 CAGGATTAAACCATAAGTCAGGAAAATGATTTAGATTGTGGCAAGATCGAACGACCGAGATTGAA
66 CAGGATTAAACCATAAGTCAGGAAAATGATCTAGACTGAGGCAAGATCGAACGACCGAGATTAAA
*
28929625 TCACAAGTCAAAAAAATAATCTGAATTGTACCGAG
131 CCACAAGTCAAAAAAATAATCTGAATTGTACCGAG
* * * * * *
28929660 ATCGAACAACCAAGATTAAACCACAAGTCTAAAAAATTATTTGAATTGAGCTAAGGTCAAATGAT
1 ATCGAACAACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAACTGAACTAAGATCAAATGAC
* ** * * * ** *
28929725 C-GAGATTAAATCATAAGTCTTGAAAATGATCTGGACTGAGTCAAGATTGAACGATTGGGATTAA
66 CAG-GATTAAACCATAAGTCAGGAAAATGATCTAGACTGAGGCAAGATCGAACGACCGAGATTAA
28929789 ACCACAAGT
130 ACCACAAGT
28929798 TAGGAAAATG
Statistics
Matches: 111, Mismatches: 26, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
164 1 0.01
165 110 0.99
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (165 bp):
ATCGAACAACCAAGATTAAACCACAAGTCTAAAAAATGATCTGAACTGAACTAAGATCAAATGAC
CAGGATTAAACCATAAGTCAGGAAAATGATCTAGACTGAGGCAAGATCGAACGACCGAGATTAAA
CCACAAGTCAAAAAAATAATCTGAATTGTACCGAG
Found at i:28929886 original size:55 final size:55
Alignment explanation
Indices: 28929723--28929886 Score: 202
Period size: 55 Copynumber: 3.0 Consensus size: 55
28929713 AGGTCAAATG
* * * ** **
28929723 ATCGAGATTAAATCATAAGTCTTGAAAATGATCTGGACTGAGTCAAGATTGAACG
1 ATCGGGATTAAACCACAAGTCAGGAAAATGATCTGGACTGAGTCAAGATTGAATA
* * *
28929778 ATTGGGATTAAACCACAAGTTAGGAAAATGATCTGAACTGAGTCAAGATTGAATA
1 ATCGGGATTAAACCACAAGTCAGGAAAATGATCTGGACTGAGTCAAGATTGAATA
* * * *
28929833 ATCGGGATTGAACCACAAGTCAGGAAAATAATCTGGATTGAGACAAGATTGAAT
1 ATCGGGATTAAACCACAAGTCAGGAAAATGATCTGGACTGAGTCAAGATTGAAT
28929887 GACCATGACC
Statistics
Matches: 92, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (55 bp):
ATCGGGATTAAACCACAAGTCAGGAAAATGATCTGGACTGAGTCAAGATTGAATA
Found at i:28929990 original size:16 final size:15
Alignment explanation
Indices: 28929965--28929996 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
28929955 TTAATTTAAA
28929965 TCTTTCTTTTTTTTT
1 TCTTTCTTTTTTTTT
28929980 TCTTGTCTTTTTTTTT
1 TCTT-TCTTTTTTTTT
28929996 T
1 T
28929997 ATATTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (15 bp):
TCTTTCTTTTTTTTT
Found at i:28930549 original size:21 final size:21
Alignment explanation
Indices: 28930504--28930558 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
28930494 GTTTTGATAG
**
28930504 AAGGGATCGATCCCCTAAGGG
1 AAGGGATCGATCCCCTAAGAA
28930525 AAGGGATCGATCCCCT-AGCAA
1 AAGGGATCGATCCCCTAAG-AA
*
28930546 AAGGGATCAATCC
1 AAGGGATCGATCC
28930559 TATTTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (21 bp):
AAGGGATCGATCCCCTAAGAA
Found at i:28935988 original size:14 final size:15
Alignment explanation
Indices: 28935970--28936008 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28935960 TTATTTGAAA
28935970 ATATTTTTTCTTATT
1 ATATTTTTTCTTATT
*
28935985 -TATTTATTTTTTATT
1 ATATTT-TTTCTTATT
28936000 ATATTTTTT
1 ATATTTTTT
28936009 TATTTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.24
15 11 0.52
16 5 0.24
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATATTTTTTCTTATT
Found at i:28935994 original size:18 final size:20
Alignment explanation
Indices: 28935971--28936015 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28935961 TATTTGAAAA
28935971 TATTTTTT-CT-TATTTATT
1 TATTTTTTACTATATTTATT
* *
28935989 TATTTTTTATTATATTTTTT
1 TATTTTTTACTATATTTATT
28936009 TATTTTT
1 TATTTTT
28936016 CAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (20 bp):
TATTTTTTACTATATTTATT
Found at i:28936057 original size:19 final size:20
Alignment explanation
Indices: 28936035--28936077 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28936025 AAAAATTTTG
*
28936035 TAAAATGT-TTAATAATTAA
1 TAAAATGTCTTAATAAATAA
*
28936054 T-AAATTTCTTAATAAATAA
1 TAAAATGTCTTAATAAATAA
28936073 TAAAA
1 TAAAA
28936078 ATCAGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 12 0.60
20 3 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATGTCTTAATAAATAA
Found at i:28936115 original size:16 final size:15
Alignment explanation
Indices: 28936071--28936138 Score: 77
Period size: 14 Copynumber: 4.6 Consensus size: 15
28936061 CTTAATAAAT
*
28936071 AATAAAAATCAGTAA
1 AATAAAAAACAGTAA
*
28936086 AATAAAATAC-GTAA
1 AATAAAAAACAGTAA
28936100 AATAAAAAACTAGTAA
1 AATAAAAAAC-AGTAA
**
28936116 AATAAAATGCA-TAA
1 AATAAAAAACAGTAA
28936130 AATAAAAAA
1 AATAAAAAA
28936139 ATTGAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 23 0.52
15 9 0.20
16 12 0.27
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAAAACAGTAA
Found at i:28936115 original size:30 final size:29
Alignment explanation
Indices: 28936071--28936138 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
28936061 CTTAATAAAT
* *
28936071 AATAAAAATCAGTAAAATAAAATACGTAA
1 AATAAAAAACAGTAAAATAAAATACATAA
*
28936100 AATAAAAAACTAGTAAAATAAAATGCATAA
1 AATAAAAAAC-AGTAAAATAAAATACATAA
28936130 AATAAAAAA
1 AATAAAAAA
28936139 ATTGAAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (29 bp):
AATAAAAAACAGTAAAATAAAATACATAA
Found at i:28936178 original size:26 final size:26
Alignment explanation
Indices: 28936084--28936192 Score: 85
Period size: 30 Copynumber: 3.9 Consensus size: 26
28936074 AAAAATCAGT
* *
28936084 AAAATAAAATACGTAAAATAAAAAACTAG
1 AAAATAAAAT-C--AAAATAAAAAAATTG
28936113 TAAAATAAAATGCATAAAATAAAAAAATTG
1 -AAAATAAAAT-C--AAAATAAAAAAATTG
* *
28936143 AAAATCAAATCAAAATCAAAAAATT-
1 AAAATAAAATCAAAATAAAAAAATTG
*
28936168 AAAATTAAAATTAAAATAGAAAAAA
1 AAAA-TAAAATCAAAATA-AAAAAA
28936193 AACCTGCGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.06
26 23 0.34
27 6 0.09
28 1 0.01
29 9 0.13
30 25 0.37
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.20
Consensus pattern (26 bp):
AAAATAAAATCAAAATAAAAAAATTG
Found at i:28936941 original size:11 final size:11
Alignment explanation
Indices: 28936927--28936979 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
28936917 GAAAGGAAAA
28936927 AAAATAATAAT
1 AAAATAATAAT
28936938 AAAATAATAAT
1 AAAATAATAAT
28936949 --AAT-ATAACT
1 AAAATAATAA-T
* *
28936958 ATAATAATAGT
1 AAAATAATAAT
28936969 AAAAT-ATAAT
1 AAAATAATAAT
28936979 A
1 A
28936980 TACTACAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
10 5 0.14
11 19 0.54
12 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:28936941 original size:14 final size:14
Alignment explanation
Indices: 28936924--28936979 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
28936914 AAAGAAAGGA
28936924 AAAAAAATAATAAT
1 AAAAAAATAATAAT
*
28936938 AAAATAATAATAAT
1 AAAAAAATAATAAT
* **
28936952 ATAACTATAATAAT
1 AAAAAAATAATAAT
**
28936966 AGTAAAAT-ATAAT
1 AAAAAAATAATAAT
28936979 A
1 A
28936980 TACTACAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
13 6 0.18
14 28 0.82
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAAAAATAATAAT
Found at i:28937074 original size:3 final size:3
Alignment explanation
Indices: 28937053--28937225 Score: 115
Period size: 3 Copynumber: 62.3 Consensus size: 3
28937043 ATATACTATG
* *
28937053 ATA ATG ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
28937101 ATA ATA ATA AT- ATA ACA AT- ATA AT- ATA AT- ACA AT- GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
28937144 AT- ATA AT- ATA CT- ATT ATG A-A AT- ATA AT- ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
28937184 AT- ATA GTA AT- ATA ATA CTA GTA ACA CTA ATA ATAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA A
28937226 AAATGATACC
Statistics
Matches: 131, Mismatches: 23, Indels: 32
0.70 0.12 0.17
Matches are distributed among these distances:
2 26 0.20
3 102 0.78
4 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28937142 original size:46 final size:46
Alignment explanation
Indices: 28937054--28937153 Score: 51
Period size: 49 Copynumber: 2.0 Consensus size: 46
28937044 TATACTATGA
* * * *
28937054 TAATGATAATAGTAATAATAATAATAATAATAATAATAATAATAATAATAA
1 TAATAATAATAATAATAATAAT-ATAACAAT-ATAAT-ATAAT-ACAAT-A
* * *
28937105 TAATAAT-ATAACAAT-ATAATATAATACAATGTAATAATAATATAATA
1 TAATAATAATAATAATAATAATAT-A-ACAATATAAT-ATAATACAATA
28937152 TA
1 TA
28937154 CTATTATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
47 3 0.07
48 7 0.17
49 16 0.38
50 10 0.24
51 6 0.14
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (46 bp):
TAATAATAATAATAATAATAATATAACAATATAATATAATACAATA
Found at i:28939024 original size:21 final size:21
Alignment explanation
Indices: 28938977--28939025 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
28938967 TAGCAAGAGA
28938977 AGAAAAAATGCATTAAATGTC
1 AGAAAAAATGCATTAAATGTC
* *
28938998 ATAAAAAATGCATTCAATG-C
1 AGAAAAAATGCATTAAATGTC
28939018 TAGAAAAA
1 -AGAAAAA
28939026 GCTATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (21 bp):
AGAAAAAATGCATTAAATGTC
Found at i:28941251 original size:30 final size:30
Alignment explanation
Indices: 28941200--28941258 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28941190 CCTTAAATTC
**
28941200 ATCTCCAATTCGATTTGATTTTAAAAAAAA
1 ATCTCCAATTCGATTCAATTTTAAAAAAAA
*
28941230 ATCT-CAATTCGATTACAATTTTTAAAAAA
1 ATCTCCAATTCGATT-CAATTTTAAAAAAA
28941259 TGCATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (30 bp):
ATCTCCAATTCGATTCAATTTTAAAAAAAA
Found at i:28941582 original size:5 final size:5
Alignment explanation
Indices: 28941572--28941596 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28941562 AAGTTAAAAA
28941572 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
28941597 AAGAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:28941640 original size:15 final size:14
Alignment explanation
Indices: 28941622--28941668 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
28941612 AAAAGGCTTA
28941622 AAAAACTAATAAAAT
1 AAAAAC-AATAAAAT
*
28941637 AAAAA-AATAAAGT
1 AAAAACAATAAAAT
28941650 AAAAACAAATAAAAT
1 AAAAAC-AATAAAAT
28941665 AAAA
1 AAAA
28941669 GAAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
15 16 0.57
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAACAATAAAAT
Found at i:28945463 original size:21 final size:21
Alignment explanation
Indices: 28945437--28945477 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28945427 ATACTCATTC
*
28945437 AAATTTTAATGATTAAATAAA
1 AAATTTTAATAATTAAATAAA
28945458 AAATTTTAATAATTAAATAA
1 AAATTTTAATAATTAAATAA
28945478 TTCTTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTTAATAATTAAATAAA
Found at i:28954322 original size:203 final size:199
Alignment explanation
Indices: 28954076--28954442 Score: 472
Period size: 204 Copynumber: 1.8 Consensus size: 199
28954066 ATTAATTAAT
* * *
28954076 ATAATAAAAAATAAGAAAAAAAAATTTTTATCCGACGATGAGATTC-ATAGGTA-CTCAGAGTAG
1 ATAATAAAAAATAAGAAAAAAAAATTTTTATCCAACGATGAGATTCTAAAAGTATCTC-GAGTAG
* * * * *
28954139 TGATACCTAT-GAAATCTCTAGGTGAGAAAATTTTTTTTAATACTACCAGTGTATTAGAGTATTT
65 TGAT-CCTATAAAAATCCCTAAGTGAGAAAATTTTTTTAAATACTACCAGTGTATTAGAATATTT
28954203 ATAAAAAAAAATTTAATACAATAAAAGATTTTTTTCTTATAAAATAGCAAAAAAGTAATTAATAT
129 AT-AAAAAAAATTTAATACAATAAAA-ATTTTTTTCTTATAAAATAGCAAAAAAGTAATTAATAT
28954268 ATTAAAAA
192 ATTAAAAA
* * *
28954276 ATAATAATATAAATAAGGAAAAAGAAGA-TTTTATCCAATGATGAGATTCTAAAAGTATTTCGAG
1 ATAATAA-A-AAATAA-GAAAAA-AAAATTTTTATCCAACGATGAGATTCTAAAAGTATCTCGAG
* * * * *
28954340 TAGTGATGCTTTAAAAATCCCTAAGTGAGAATATTTTTTTAAATATTACTAGTGTATTAGAATAT
62 TAGTGATCCTATAAAAATCCCTAAGTGAGAAAATTTTTTTAAATACTACCAGTGTATTAGAATAT
* *
28954405 TTATAGAAAAATTTTAATACAATAAAAATTTTTTTCTT
127 TTATAAAAAAAATTTAATACAATAAAAATTTTTTTCTT
28954443 CAAAATTAAA
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
200 7 0.05
201 1 0.01
202 17 0.12
203 49 0.35
204 66 0.46
205 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (199 bp):
ATAATAAAAAATAAGAAAAAAAAATTTTTATCCAACGATGAGATTCTAAAAGTATCTCGAGTAGT
GATCCTATAAAAATCCCTAAGTGAGAAAATTTTTTTAAATACTACCAGTGTATTAGAATATTTAT
AAAAAAAATTTAATACAATAAAAATTTTTTTCTTATAAAATAGCAAAAAAGTAATTAATATATTA
AAAA
Found at i:28956179 original size:11 final size:11
Alignment explanation
Indices: 28956165--28956190 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28956155 AAACATTTCC
28956165 TAAACAAAAAA
1 TAAACAAAAAA
28956176 TAAACAAAAAA
1 TAAACAAAAAA
28956187 TAAA
1 TAAA
28956191 TAAATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (11 bp):
TAAACAAAAAA
Found at i:28958170 original size:29 final size:31
Alignment explanation
Indices: 28958120--28958181 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
28958110 CCTTAAATTC
***
28958120 ATCTCCAATTCGATTTTGA-TTTTTAAAAAA
1 ATCTCCAATTCGATTACAATTTTTTAAAAAA
28958150 ATCT-CAATTCGATTACAATTTTTTTAAAAAA
1 ATCTCCAATTCGATTACAA-TTTTTTAAAAAA
28958181 A
1 A
28958182 ATGAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.41
30 4 0.15
31 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (31 bp):
ATCTCCAATTCGATTACAATTTTTTAAAAAA
Found at i:28967401 original size:10 final size:10
Alignment explanation
Indices: 28967388--28967422 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28967378 TATCATAAAT
28967388 TATAATCAAG
1 TATAATCAAG
28967398 TATAATCAAG
1 TATAATCAAG
*
28967408 TAAAATCAAG
1 TATAATCAAG
28967418 T-TAAT
1 TATAAT
28967423 ACAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.13
10 20 0.87
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (10 bp):
TATAATCAAG
Found at i:28972526 original size:21 final size:21
Alignment explanation
Indices: 28972493--28972557 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
28972483 AAAACAAAAC
*
28972493 AAAACA-AACAAAAAAATCTT
1 AAAACATAAAAAAAAAATCTT
*
28972513 AAAACATAAAAAAAAAA-CACT
1 AAAACATAAAAAAAAAATC-TT
* **
28972534 AAAAAATAAAAAAAATTTCTT
1 AAAACATAAAAAAAAAATCTT
28972555 AAA
1 AAA
28972558 CCACATCCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 7 0.19
21 28 0.78
22 1 0.03
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAACATAAAAAAAAAATCTT
Found at i:28972531 original size:13 final size:15
Alignment explanation
Indices: 28972512--28972544 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28972502 AAAAAAATCT
28972512 TAAAACA-TAAAAAA
1 TAAAACACTAAAAAA
28972526 -AAAACACTAAAAAA
1 TAAAACACTAAAAAA
28972540 TAAAA
1 TAAAA
28972545 AAAATTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
TAAAACACTAAAAAA
Found at i:28972660 original size:16 final size:16
Alignment explanation
Indices: 28972637--28972669 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28972627 TTTTGTATCG
28972637 AGATAT-TTTCTTT-A
1 AGATATATTTCTTTCA
28972651 AGATATATTTCTTTCA
1 AGATATATTTCTTTCA
28972667 AGA
1 AGA
28972670 AGTTTGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (16 bp):
AGATATATTTCTTTCA
Found at i:28982921 original size:48 final size:49
Alignment explanation
Indices: 28982809--28983822 Score: 904
Period size: 50 Copynumber: 20.9 Consensus size: 49
28982799 TGAAGAACAT
* * ** *
28982809 ATGAGATTTTTAAAGTTATTGAGCCTTTATTGATATGGA-CC-TTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGA-GGAGCCTTTTTCAAG
* * **
28982858 ATGA-TTTTTAAAGTTGTTGAACCTCTATTGAGAGGAG-CTTTTTCCAA-
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTT-CAAG
* * *
28982905 ATGAGATTTTAAAGTTGTTGAGCCTCTTCCT-AGAAGAGCCCTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTC-TGCTGAGAGGAGCCTTTTTCAAG
*** *
28982954 ATGAGATGTTTAAAGTT-TTGAG-C-CT-CT----GGTTTC-TCTTCAAG
1 ATGAGAT-TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * * * *
28982995 ATGAAATTTTTAAAGTTGTTGAGCATCTGCTAAAAGGAGCCCTTTTCAAA
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* *
28983045 ATGAGATTTTTAAAGTTATTGAGCCTCTGCTAAGAGGAGCCTTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * * * *
28983095 ATGA-TTTTTAAAGTTGTTGAACCTTTGTTGAGATGAG-CTTTTTAAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * *
28983142 -TGAGATTTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCCCTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
** *
28983191 ATGAGATTTTTAAAGTCATTGAGCCTCTACTGAGAGGAGCCTTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * * *
28983241 ATGAAATTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCCCTTTTCAAA
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * *
28983291 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTAAGAGAAACTTTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * *
28983340 AT--GATTTTTAAGATTGTTGAGCCTCTGTTGAGATGAG-C-TTTTCAAG
1 ATGAGATTTTAAAG-TTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * * *
28983386 ATGAGAATTTTAAAGTCGTTAAGCCTCTACTGAAAAGAGCCTTTTTCAAG
1 ATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * * *
28983436 ATAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA--ATTTTATC-AT
1 AT-GAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-TCAAG
* * *
28983485 ATGAGAATTTTAAAGTTGTTGAGCCTCTGTTAAGAGGAG-CTTTTCCAA-
1 ATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * *
28983533 ATGAGATTTTAAAGTTATTGAGCCTTTGCTGAGAGGAGCCCTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* ** *
28983582 ATGAGATTTTAAAGTTGTTGAGTCTCCACTAAGAGGAGCCTTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* *
28983631 ATGA-TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG-CTATTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCT-TTTTCAAG
* * * * *
28983679 ATAAGATTTCAAAAATTGTTAAGCCTCTGCTGAGAGAAG-CTTTTTC-AG
1 ATGAGATTT-TAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
* * *
28983727 ATGAAATTTTTAAAGTCGTTGAGCCTCTGCTGAGAGGGGCCCTTTTT-AAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CCTTTTTCAAG
* *
28983777 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGTCTTTTT
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTT
28983823 TAGATTTTAA
Statistics
Matches: 789, Mismatches: 133, Indels: 86
0.78 0.13 0.09
Matches are distributed among these distances:
41 21 0.03
42 8 0.01
44 2 0.00
45 4 0.01
46 18 0.02
47 82 0.10
48 234 0.30
49 156 0.20
50 237 0.30
51 27 0.03
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (49 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTCAAG
Found at i:28982958 original size:49 final size:48
Alignment explanation
Indices: 28982809--28983804 Score: 644
Period size: 48 Copynumber: 20.6 Consensus size: 48
28982799 TGAAGAACAT
* * * *
28982809 ATGAGATTTTTAAAGTTATTGAGCCTTTATTGATATG-GACCTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAG-CCTTTTCAAG
* * * *
28982858 ATGA-TTTTTAAAGTTGTTGAACCTCTATTGAGAGGAGCTTTTTCCAA-
1 ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTTT-CAAG
28982905 ATGAGATTTTAAAGTTGTTGAGCCTCT-TCCT-AGAAGAGCCCTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTAT--TGAGAAGAG-CCTTTTCAAG
*** *
28982954 ATGAGATGTTTAAAGTT-TTGAGCCTC---T--G--GTTTCTCTTCAAG
1 ATGAGAT-TTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTTTCAAG
* * ** * *
28982995 ATGAAATTTTTAAAGTTGTTGAGCATCTGCT-AAAAGGAGCCCTTTTCAAA
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAA-GAG-CCTTTTCAAG
* ** * *
28983045 ATGAGATTTTTAAAGTTATTGAGCCTCTGCTAAGAGGAGCCTTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCC-TTTTCAAG
* * * * * * *
28983095 ATGA-TTTTTAAAGTTGTTGAACCTTTGTTGAGATGAGCTTTTTAAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTTTCAAG
* ** *
28983142 -TGAGATTTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCCCTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAG-CCTTTTCAAG
** * *
28983191 ATGAGATTTTTAAAGTCATTGAGCCTCTACTGAGAGGAGCCTTTTTCAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCC-TTTTCAAG
* * * *
28983241 ATGAAATTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCCCTTTTCAAA
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAG-CCTTTTCAAG
* * *
28983291 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTAAGAGAA-A-CTTTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCT-AT-TGAGAAGAGC-CTTTTCAAG
* * *
28983340 AT--GATTTTTAAGATTGTTGAGCCTCTGTTGAGATGAG-CTTTTCAAG
1 ATGAGATTTTAAAG-TTGTTGAGCCTCTATTGAGAAGAGCCTTTTCAAG
* * * *
28983386 ATGAGAATTTTAAAGTCGTTAAGCCTCTACTGAAAAGAGCCTTTTTCAAG
1 ATGAG-ATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCC-TTTTCAAG
* * ** * ** *
28983436 ATAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA-ATTTTATC-AT
1 AT-GAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTT-TCAAG
* * *
28983485 ATGAGAATTTTAAAGTTGTTGAGCCTCTGTTAAGAGGAG-CTTTTCCAA-
1 ATGAG-ATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTTT-CAAG
* * ** *
28983533 ATGAGATTTTAAAGTTATTGAGCCTTTGCTGAGAGGAGCCCTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAG-CCTTTTCAAG
* * * * *
28983582 ATGAGATTTTAAAGTTGTTGAGTCTCCACTAAGAGGAGCCTTTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCC-TTTTCAAG
* * * *
28983631 ATGA-TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTATTTTCAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGC-CTTTTCAAG
* * * * ** *
28983679 ATAAGATTTCAAAAATTGTTAAGCCTCTGCTGAG-AGAAGCTTTTTC-AG
1 ATGAGATTT-TAAAGTTGTTGAGCCTCTATTGAGAAG-AGCCTTTTCAAG
* * ** * * *
28983727 ATGAAATTTTTAAAGTCGTTGAGCCTCTGCTGAGAGGGGCCCTTTTTAAG
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAG-CCTTTTCAAG
28983777 ATGAGATTTTTAAAGTTGTTGAGCCTCT
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCT
28983805 GCTGAGATGA
Statistics
Matches: 765, Mismatches: 126, Indels: 111
0.76 0.13 0.11
Matches are distributed among these distances:
41 22 0.03
42 10 0.01
44 1 0.00
45 2 0.00
46 17 0.02
47 83 0.11
48 231 0.30
49 153 0.20
50 211 0.28
51 35 0.05
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (48 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCCTTTTCAAG
Found at i:28983067 original size:50 final size:50
Alignment explanation
Indices: 28982989--28983811 Score: 853
Period size: 48 Copynumber: 16.8 Consensus size: 50
28982979 CTGGTTTCTC
* * * *
28982989 TTCAAGATGAAATTTTTAAAGTTGTTGAGCATCTGCTAAAAGGAGCCCTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * * *
28983039 TTCAAAATGAGATTTTTAAAGTTATTGAGCCTCTGCTAAGAGGAGCCTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * * * *
28983089 TTCAAGAT--GATTTTTAAAGTTGTTGAACCTTTGTTGAGATGAG-CTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * *
28983136 TTAAAG-TGAGATTTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCCCTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
** * *
28983185 TTCAAGATGAGATTTTTAAAGTCATTGAGCCTCTACTGAGAGGAGCCTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * *
28983235 TTCAAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCCCTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * * * **
28983285 TTCAAAATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTAAGAGAAACTTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* *
28983334 TTCAAGAT--GATTTTT-AAGATTGTTGAGCCTCTGTTGAGATGAG--CTT
1 TTCAAGATGAGATTTTTAAAG-TTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * * * * * *
28983380 TTCAAGATGAGAATTTTAAAGTCGTTAAGCCTCTACTGAAAAGAGCCTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * **
28983430 TTCAAGATAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA--ATTT
1 TTCAAGAT-GAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * * *
28983479 TATC-ATATGAGAATTTTAAAGTTGTTGAGCCTCTGTTAAGAGGAG--CTT
1 T-TCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* *
28983527 TTCCAA-ATGAGA-TTTTAAAGTTATTGAGCCTTTGCTGAGAGGAGCCCTT
1 TT-CAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* ** * *
28983576 TTCAAGATGAGA-TTTTAAAGTTGTTGAGTCTCCACTAAGAGGAGCCTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* **
28983625 TTCAAGAT--GATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTATT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* ** * * * *
28983673 TTCAAGATAAGATTTCAAAAATTGTTAAGCCTCTGCTGAGAGAAG-CTTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
* * *
28983722 TTC-AGATGAAATTTTTAAAGTCGTTGAGCCTCTGCTGAGAGGGGCCCTT
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
*
28983771 TTTAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA
1 TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA
28983812 TGAGTCTTTT
Statistics
Matches: 639, Mismatches: 110, Indels: 48
0.80 0.14 0.06
Matches are distributed among these distances:
46 11 0.02
47 45 0.07
48 221 0.35
49 115 0.18
50 219 0.34
51 28 0.04
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (50 bp):
TTCAAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTT
Found at i:28988667 original size:26 final size:27
Alignment explanation
Indices: 28988608--28988668 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
28988598 TTGAATAATA
*
28988608 AATTTTTTAAAATAAAACCAAACAAAC
1 AATTTTTTAAAATAAAACCAAAAAAAC
* * *
28988635 AAATTTTTAAAA-AAAATCAAAAAAAT
1 AATTTTTTAAAATAAAACCAAAAAAAC
*
28988661 TATTTTTT
1 AATTTTTT
28988669 CAAACACCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.34
Consensus pattern (27 bp):
AATTTTTTAAAATAAAACCAAAAAAAC
Found at i:28989612 original size:31 final size:31
Alignment explanation
Indices: 28989577--28989635 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
28989567 TGTATAATAC
28989577 AAAACA-AAACAAAACAAACA-AAAAAAATCTT
1 AAAACATAAA-AAAA-AAACACAAAAAAATCTT
*
28989608 AAAACATAAAAAAAAAACACTAAAAAAT
1 AAAACATAAAAAAAAAACACAAAAAAAT
28989636 AAAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 5 0.20
31 17 0.68
32 3 0.12
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (31 bp):
AAAACATAAAAAAAAAACACAAAAAAATCTT
Found at i:28989626 original size:13 final size:15
Alignment explanation
Indices: 28989607--28989639 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28989597 AAAAAAATCT
28989607 TAAAACA-TAAAAAA
1 TAAAACACTAAAAAA
28989621 -AAAACACTAAAAAA
1 TAAAACACTAAAAAA
28989635 TAAAA
1 TAAAA
28989640 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
TAAAACACTAAAAAA
Found at i:28991154 original size:19 final size:18
Alignment explanation
Indices: 28991130--28991167 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
28991120 GCTTGTCAAG
28991130 AAAAAATAAAAAGATGAAA
1 AAAAAATAAAAAGA-GAAA
28991149 AAAAAATAAAAAGAGAAA
1 AAAAAATAAAAAGAGAAA
28991167 A
1 A
28991168 TTTGAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAAAATAAAAAGAGAAA
Found at i:28999691 original size:50 final size:49
Alignment explanation
Indices: 28999452--29000459 Score: 805
Period size: 48 Copynumber: 20.7 Consensus size: 49
28999442 TAAAGAACAT
* *
28999452 ATGAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGATGA-ACTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * ** *
28999501 AT--GATTATTAAAGTTGTTGAACCTCTATTGAGAGGAG-CTTTTCCAA-
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * *
28999547 ATGAGA-TTTTAAAGTTGTTGAGTCTCTACTAAGAGGAGCCCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * *
28999596 ATGAGATTTTTAAAGTT-TTGAGCTTCTGCTGAGAGAAACCATTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAG-AGCCTTTTTCAAG
* * * * * *
28999645 ATAAAATTTTTAAAGTTGTTGAGCATCTACTGAGAGAAACTTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAG-AGCCTTTTTCAAG
* * * * *
28999695 ATGAAATTTTTAAAGCTT-TTGAGCATCTGCTGAAATGAGCCCTTTTCAAA
1 ATGAGATTTTTAAAG-TTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * *
28999745 ATGAGA-TTTTAAAGTTATTGAGCCTCTACTAAGAGGACCCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * *
28999794 AT--GATTTTTAAAGTTGTTGAGCCTTTGTTGAAATGAG-CTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * *
28999841 -TGAGATTTTTAAAATTGTTGAGCCTCTACTGAGATGAACCCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* ** *
28999890 ATGAGATTTTTAAAGTCGTTGAGCCTCTATTGAGAAGAACCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAG-AGAGCCTTTTTCAAG
* * ** * *
28999940 ATGAAATTTTTAAAGTTGTTGAGCCTTTATTGAGATGAGCCCTTTTCAAA
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * ** * *
28999990 ATGAGA-TTTTAAAGTTGTTAAACCTCTGCAAAAAAGAGCTTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGC-TGAGAGAGCCTTTTTCAAG
* * *
29000039 AT--GATTTTTAAGGTTGTTGAGCCTCTGTTGAGA-AGAACTTTTT-AAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGAG-CCTTTTTCAAG
* * * * *
29000085 ATGAGATTTTTAAAGTCGTTAAACCTCTACTGAGATGAGCTTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * *
29000135 ATGAGAATTTTTAAAGTTGTTAAGCCTCTGTTGAGAGGAG-TTTTTTC-AT
1 ATGAG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * *
29000184 ATGAGATTTTTAAAGTTGTTGAGCTTCTGCTAAGAGGAG-CTTTTCCAA-
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * * *
29000232 ATAAGA-TTTTAAAG-TATTGAGCCTTTGCTTAGAGGAGCCCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * * * *
29000280 ATAAGA-TTTTAAAATTATTGAGTCTCTGCTAAGATGAGCCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * *
29000329 AT--GATTTTTAAAGTTGTTGAACCTCTGTTGAGAGGAGCTTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAGCCTTTTTCAAG
* * ** * * * *
29000377 ATAAAATTTCAAAAATTGTTAAGCATCTGCTAAGAGAAG-CTTTTTC-AG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAG-AGCCTTTTTCAAG
* *
29000425 ATGAAATTTTTAAAGTCGTTGAGCCTCTGCTGAGA
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA
29000460 AGAGTTTTTT
Statistics
Matches: 777, Mismatches: 147, Indels: 71
0.78 0.15 0.07
Matches are distributed among these distances:
46 29 0.04
47 101 0.13
48 228 0.29
49 172 0.22
50 214 0.28
51 33 0.04
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (49 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGAGCCTTTTTCAAG
Found at i:28999888 original size:245 final size:245
Alignment explanation
Indices: 28999452--29000457 Score: 926
Period size: 245 Copynumber: 4.1 Consensus size: 245
28999442 TAAAGAACAT
* * * * * *
28999452 ATGAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGATGA-ACTTTTTCAAGAT--GATTATTAAAG
1 ATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAAATGAGCCCTTTTCAAAATGAGATT-TTAAAG
* * ** * * * * * **
28999514 TTGTTGAACCTCTATTGAGAGGA-GCTTTTCCAA-ATGAGATTTTAAAGTTGTTGAGTCTCTACT
65 TTATTGAGCCTCTGCTAAGAGGACCCTTTTTCAAGATGA-TTTTTAAAGTTGTTGAGCCTCTGTT
* * * * * *
28999577 -AAGAGGAGCCCTTTTCAAGATGAGATTTTTAAAGTT-TTGAGCTTCTGCTGAGA-GAAACCATT
129 GAA-ATGAG-CTTTTTCAAGATGAGATTTTTAAAGTTGTTGAACCTCTACTGAGATG-AACCTTT
*
28999639 TTCAAGATAAAATTTTTAAAGTTGTTGAGCATCTACTGAGAGAAACTTTTTTCAAG
191 TTCAAGATAAAATTTTTAAAGTTGTTAAGCATCTACTGAGAGAAACTTTTTTC-AG
*
28999695 ATGAAATTTTTAAAGCTT-TTGAGCATCTGCTGAAATGAGCCCTTTTCAAAATGAGATTTTAAAG
1 ATGAAATTTTTAAAG-TTGTTGAGCCTCTGCTGAAATGAGCCCTTTTCAAAATGAGATTTTAAAG
* *
28999759 TTATTGAGCCTCTACTAAGAGGACCCTTTTTCAAGATGATTTTTAAAGTTGTTGAGCCTTTGTTG
65 TTATTGAGCCTCTGCTAAGAGGACCCTTTTTCAAGATGATTTTTAAAGTTGTTGAGCCTCTGTTG
* * *
28999824 AAATGAGCTTTTTCAAG-TGAGATTTTTAAAATTGTTGAGCCTCTACTGAGATGAACCCTTTTCA
130 AAATGAGCTTTTTCAAGATGAGATTTTTAAAGTTGTTGAACCTCTACTGAGATGAACCTTTTTCA
* * * * * * *
28999888 AGATGAGATTTTTAAAGTCGTTGAGCCTCTATTGAGA-AGAACCTTTTTCAAG
195 AGATAAAATTTTTAAAGTTGTTAAGCATCTACTGAGAGA-AACTTTTTTC-AG
* ** *
28999940 ATGAAATTTTTAAAGTTGTTGAGCCTTTATTGAGATGAGCCCTTTTCAAAATGAGATTTTAAAGT
1 ATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAAATGAGCCCTTTTCAAAATGAGATTTTAAAGT
* * * * * * * * *
29000005 TGTTAAACCTCTGCAAAAAAGAGCTTTTTTCAAGATGATTTTTAAGGTTGTTGAGCCTCTGTTGA
66 TATTGAGCCTCTGCTAAGAGGACCCTTTTTCAAGATGATTTTTAAAGTTGTTGAGCCTCTGTTGA
* * * * *
29000070 GAA-GAACTTTTT-AAGATGAGATTTTTAAAGTCGTTAAACCTCTACTGAGATGAGCTTTTTTCA
131 -AATGAGCTTTTTCAAGATGAGATTTTTAAAGTTGTTGAACCTCTACTGAGATGAACCTTTTTCA
* * ** * * *
29000133 AGATGAGAATTTTTAAAGTTGTTAAGCCTCTGTTGAGAG-GAGTTTTTTCAT
195 AGAT-AAAATTTTTAAAGTTGTTAAGCATCTACTGAGAGAAACTTTTTTCAG
* * * * *
29000184 ATGAGATTTTTAAAGTTGTTGAGCTTCTGCT-AAGAGGAG--CTTTTCCAAATAAGATTTTAAAG
1 ATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAA-ATGAGCCCTTTTCAAAATGAGATTTTAAAG
* * * * *
29000246 -TATTGAGCCTTTGCTTAGAGGAGCCC-TTTTCAAGATAAGA-TTTTAAAATTATTGAGTCTCTG
65 TTATTGAGCCTCTGCTAAGAGGA-CCCTTTTTCAAGAT--GATTTTTAAAGTTGTTGAGCCTCTG
* ** * * *
29000308 CT-AAGATGAGCCTTTTTCAAGAT--GATTTTTAAAGTTGTTGAACCTCTGTTGAGAGGAGCTTT
127 TTGAA-ATGAG-CTTTTTCAAGATGAGATTTTTAAAGTTGTTGAACCTCTACTGAGATGAACCTT
** * * * *
29000370 TTTCAAGATAAAATTTCAAAAATTGTTAAGCATCTGCTAAGAGAAGC-TTTTTCAG
190 TTTCAAGATAAAATTTTTAAAGTTGTTAAGCATCTACTGAGAGAAACTTTTTTCAG
*
29000425 ATGAAATTTTTAAAGTCGTTGAGCCTCTGCTGA
1 ATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGA
29000458 GAAGAGTTTT
Statistics
Matches: 630, Mismatches: 108, Indels: 51
0.80 0.14 0.06
Matches are distributed among these distances:
240 1 0.00
241 88 0.14
242 87 0.14
243 40 0.06
244 69 0.11
245 273 0.43
246 66 0.10
247 6 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (245 bp):
ATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAAATGAGCCCTTTTCAAAATGAGATTTTAAAGT
TATTGAGCCTCTGCTAAGAGGACCCTTTTTCAAGATGATTTTTAAAGTTGTTGAGCCTCTGTTGA
AATGAGCTTTTTCAAGATGAGATTTTTAAAGTTGTTGAACCTCTACTGAGATGAACCTTTTTCAA
GATAAAATTTTTAAAGTTGTTAAGCATCTACTGAGAGAAACTTTTTTCAG
Found at i:29002492 original size:26 final size:27
Alignment explanation
Indices: 29002434--29002493 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
29002424 TGAATAATAA
*
29002434 ATTTTTTAAAATAAAACCAAACAAACC
1 ATTTTTTAAAATAAAACCAAAAAAACC
* * **
29002461 AATTTTTAAAA-AAAATCAAAAAAATT
1 ATTTTTTAAAATAAAACCAAAAAAACC
29002487 ATTTTTT
1 ATTTTTT
29002494 CAAACACCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTTTTTAAAATAAAACCAAAAAAACC
Found at i:29009206 original size:124 final size:124
Alignment explanation
Indices: 29009051--29009524 Score: 453
Period size: 121 Copynumber: 3.8 Consensus size: 124
29009041 AATAAAAATT
*
29009051 TTTGTAACAA-TTT-TTTAGTCATTATATAAAATATTAAAAAAATAACTTAAGTAATGACTTCGA
1 TTTGTAACAACTTTATTT-GTCATTATATAAAATATT-AAAAAATAACTTAAGCAATGACTTCGA
* * * *
29009114 AAAATCATTGTAAATAAAACAAGTTTACACAATAAGCTTTTTTTTGTCGTTA-AAAATATGA
64 AAAATCATTGTAAATAAAACAAATTTACACAACAA-CTTTATGTTGTCGTTACAAAATATGA
* * * * * *
29009175 TCTGTAATAA-TTTTTTTGTCGTTATATAAAATATTAAATAAATAACTTAAGTAAAGACATT-GA
1 TTTGTAACAACTTTATTTGTCATTATATAAAATATTAAA-AAATAACTTAAGCAATGAC-TTCGA
** * * * * *
29009238 AAAATGGTTGTAAATAAAATAAGTTTTCATAACAACTTTATGTTGTCATTACAAATATTATGAAA
64 AAAATCATTGTAAATAAAACAAATTTACACAACAACTTTATGTTGTCGTTACAAA-A-TATG---
29009303 A
124 A
* * * *
29009304 TTTTCGTAACAACTTTATTTGTCATTATATAAAATATTAAAAAATATCTTAAACAATGATTTCAA
1 -TTT-GTAACAACTTTATTTGTCATTATATAAAATATTAAAAAATAACTTAAGCAATGACTTCGA
** * * *
29009369 AAAATCATTACAAATAAAACAAATTTTCACAACAACTTTATGTTGTTGTTATAAAAT-T--
64 AAAATCATTGTAAATAAAACAAATTTACACAACAACTTTATGTTGTCGTTACAAAATATGA
* * ** * * *
29009427 TTTATAACAACTTTATTTGTCATTGTATAAAATATTAAAAAATATTTTAAGCAACGATTTTGAAA
1 TTTGTAACAACTTTATTTGTCATTATATAAAATATTAAAAAATAACTTAAGCAATGACTTCGAAA
*
29009492 AAGT-ATTGTAAATAAAACAAATTTACGCAACAA
66 AA-TCATTGTAAATAAAACAAATTTACACAACAA
29009525 ATTTTTTTAT
Statistics
Matches: 292, Mismatches: 44, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
121 82 0.28
122 4 0.01
123 16 0.05
124 80 0.27
125 6 0.02
126 4 0.01
128 1 0.00
129 2 0.01
130 5 0.02
131 66 0.23
132 26 0.09
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (124 bp):
TTTGTAACAACTTTATTTGTCATTATATAAAATATTAAAAAATAACTTAAGCAATGACTTCGAAA
AATCATTGTAAATAAAACAAATTTACACAACAACTTTATGTTGTCGTTACAAAATATGA
Found at i:29012451 original size:30 final size:30
Alignment explanation
Indices: 29012401--29012460 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29012391 TCCATAACTG
*
29012401 TTTTTTAAAGTCTCAATTTTCATTTGTGAC
1 TTTTTTAAAGTCTCAATTTTCATCTGTGAC
* * *
29012431 TTTTTTTAAGTTTCATTTTTCATCTGTGAC
1 TTTTTTAAAGTCTCAATTTTCATCTGTGAC
29012461 CTAAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (30 bp):
TTTTTTAAAGTCTCAATTTTCATCTGTGAC
Found at i:29013538 original size:4 final size:4
Alignment explanation
Indices: 29013511--29013544 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
29013501 TATATAAATA
*
29013511 TATT TATT TATT TATT TATA TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TA
29013545 AAATTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:29016501 original size:19 final size:19
Alignment explanation
Indices: 29016456--29016501 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
29016446 GTCAAATTTC
29016456 AATTAAAATCAGATTTATT
1 AATTAAAATCAGATTTATT
*
29016475 AATAAAAATCTA-ATTTATT
1 AATTAAAATC-AGATTTATT
*
29016494 CATTAAAA
1 AATTAAAA
29016502 CATAATCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTAAAATCAGATTTATT
Found at i:29017048 original size:1 final size:1
Alignment explanation
Indices: 29017042--29017066 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29017032 TAGAAGAGTG
29017042 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
29017067 GAGGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29017415 original size:20 final size:20
Alignment explanation
Indices: 29017390--29017429 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29017380 GAAGTCATAC
29017390 AATTAGGCTATATTTGAATT
1 AATTAGGCTATATTTGAATT
29017410 AATTAGGCTATATTTGAATT
1 AATTAGGCTATATTTGAATT
29017430 CCACCGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
AATTAGGCTATATTTGAATT
Found at i:29019984 original size:71 final size:71
Alignment explanation
Indices: 29019868--29020010 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
29019858 TTGCTTATCA
29019868 GGTACACTTCAAATCCTTTATAATTTAATGGGTTAAAATTGTTTTTAAGTTTTTTTTTTCTACTT
1 GGTACACTTCAAATCCTTTATAATTTAATGGGTTAAAATTGTTTTTAAGTTTTTTTTTTCTACTT
29019933 ATTTGG
66 ATTTGG
29019939 GGTACACTTCAAATCCTTTATAATTTAATGGGTTAAAATTGTTTTTAAGTTTTTTTTTTCTACTT
1 GGTACACTTCAAATCCTTTATAATTTAATGGGTTAAAATTGTTTTTAAGTTTTTTTTTTCTACTT
29020004 ATTTGG
66 ATTTGG
29020010 G
1 G
29020011 ATTTTGTCGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (71 bp):
GGTACACTTCAAATCCTTTATAATTTAATGGGTTAAAATTGTTTTTAAGTTTTTTTTTTCTACTT
ATTTGG
Found at i:29023773 original size:4 final size:4
Alignment explanation
Indices: 29023764--29023800 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
29023754 AACTTTTAAC
* *
29023764 ACAT ACAT ACAT ACAT ACAT AAAT ACAT ACAG ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
29023801 TATATATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:29023843 original size:14 final size:15
Alignment explanation
Indices: 29023819--29023848 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29023809 ACACCATTTT
*
29023819 CATTCAAAAAATAAA
1 CATTAAAAAAATAAA
29023834 CATTAAAAAAATAAA
1 CATTAAAAAAATAAA
29023849 TTTGAGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (15 bp):
CATTAAAAAAATAAA
Found at i:29026537 original size:16 final size:17
Alignment explanation
Indices: 29026511--29026551 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
29026501 TATTCAATTT
*
29026511 AAATA-ATTTATTAA-A
1 AAATATATTTATAAATA
29026526 AAATATATTTATAAATA
1 AAATATATTTATAAATA
29026543 AAATGATAT
1 AAAT-ATAT
29026552 AAGTATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATATATTTATAAATA
Found at i:29034123 original size:47 final size:47
Alignment explanation
Indices: 29034063--29034156 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
29034053 AATATCTAAT
* * *
29034063 GAGTTATATTAATCAATCACGATTATGTTCATGGTTATAAAATTAAC
1 GAGTTATATTAATCAACCACGATTATGTTCACGATTATAAAATTAAC
*
29034110 GAGTTATATTAATCAACCATGATTATGTTCACGATTATAAAATTAAC
1 GAGTTATATTAATCAACCACGATTATGTTCACGATTATAAAATTAAC
29034157 CAATTTATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (47 bp):
GAGTTATATTAATCAACCACGATTATGTTCACGATTATAAAATTAAC
Found at i:29039632 original size:87 final size:86
Alignment explanation
Indices: 29039508--29039684 Score: 257
Period size: 87 Copynumber: 2.0 Consensus size: 86
29039498 TCTTTCTAAA
* * *
29039508 TTTTAACGACATATTGAAAAAAATTTTAAAAAATTTCAATATCAAAATTCTAGCAAAATTTTTCA
1 TTTTAACAACATATTG-AAAAAATTTAAAAAAATTTCAATATCAAAATTCTAGCAAAATCTTTCA
*
29039573 CTTGTCATGAATAAAGAAGTTT
65 CTTGTCATGAATAAAAAAGTTT
* * *
29039595 TTTTAACAACATATTG-AAGAATTTAAAAAAGATTTTCAATATCAAGATTCTTGCAAAATCTTTC
1 TTTTAACAACATATTGAAAAAATTTAAAAAA-A-TTTCAATATCAAAATTCTAGCAAAATCTTTC
29039659 ACTTGTCATGAATAAAAAAGTTT
64 ACTTGTCATGAATAAAAAAGTTT
29039682 TTT
1 TTT
29039685 ATAAAATATT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
85 12 0.15
86 1 0.01
87 68 0.84
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (86 bp):
TTTTAACAACATATTGAAAAAATTTAAAAAAATTTCAATATCAAAATTCTAGCAAAATCTTTCAC
TTGTCATGAATAAAAAAGTTT
Found at i:29040668 original size:16 final size:17
Alignment explanation
Indices: 29040641--29040672 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29040631 TGGCATTTTT
29040641 ATTTTTTATAAAAATAA
1 ATTTTTTATAAAAATAA
29040658 ATTTTTT-TAAAAATA
1 ATTTTTTATAAAAATA
29040673 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTTATAAAAATAA
Found at i:29042872 original size:59 final size:59
Alignment explanation
Indices: 29042756--29043151 Score: 548
Period size: 59 Copynumber: 6.7 Consensus size: 59
29042746 TTTTGTGCAG
* * * *
29042756 GAAAAATCGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTGAAAATTT-ATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGGAAACTTTGATTTTCAA
*
29042816 GAAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTGGAAACTTTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTGGAAACTTTGATTTTCAA
* *
29042875 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAA
*
29042934 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGGAACTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAA
* * * *
29042993 GGAAAATTGATACTTTTAACTTTT-CTCCAAAAATATTTTTTTGGCAACTTTGATATTCAA
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAAATA-TTTTTTGGAAACTTTGATTTTCAA
* * * * * *
29043053 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATCTTTTTTTGAAAATTT-ATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAA
*
29043111 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
29043152 TATTTTTATT
Statistics
Matches: 305, Mismatches: 25, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
58 60 0.20
59 161 0.53
60 82 0.27
61 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAA
Found at i:29043207 original size:16 final size:16
Alignment explanation
Indices: 29043167--29043263 Score: 90
Period size: 16 Copynumber: 5.9 Consensus size: 16
29043157 TTATTTAAAG
*
29043167 AAAATAGAATAATAAAAC
1 AAAATA-AA-AATAAAAT
*
29043185 AAAATAAAAGTGAAAAT
1 AAAATAAAAAT-AAAAT
29043202 -AAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
* *
29043217 AAAATAAAGA-AAAGT
1 AAAATAAAAATAAAAT
*
29043232 AAAACAAAAATAAAAAT
1 AAAATAAAAAT-AAAAT
*
29043249 AAAATAAAGATAAAA
1 AAAATAAAAATAAAA
29043264 AGAATATTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
15 17 0.26
16 23 0.35
17 19 0.29
18 6 0.09
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:29043213 original size:6 final size:6
Alignment explanation
Indices: 29043185--29043264 Score: 53
Period size: 6 Copynumber: 13.7 Consensus size: 6
29043175 ATAATAAAAC
* * *
29043185 AAAATA AAAGTG AAAAT- -AAATA AAAAT- AAAAT- AAAATA AAGAAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA
* *
29043230 GTAAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 --AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
29043265 GAATATTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
4 4 0.07
5 15 0.25
6 32 0.54
7 3 0.05
8 3 0.05
9 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:29043217 original size:5 final size:5
Alignment explanation
Indices: 29043177--29043263 Score: 70
Period size: 5 Copynumber: 16.4 Consensus size: 5
29043167 AAAATAGAAT
*
29043177 AATAA AACAA AATAA AAGTGAA AAT-A AATAAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AA-T-AA AATAA AAT-AA AATAA AATAA AATAA
* *
29043224 AGA-AA AGTAA AACAAA AATAAA AATAA AATAA AGATAA AA
1 A-ATAA AATAA AA-TAA AAT-AA AATAA AATAA A-ATAA AA
29043264 AGAATATTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
4 4 0.06
5 38 0.57
6 21 0.31
7 4 0.06
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:29043218 original size:11 final size:11
Alignment explanation
Indices: 29043167--29043264 Score: 71
Period size: 11 Copynumber: 8.9 Consensus size: 11
29043157 TTATTTAAAG
29043167 AAAATAGAATAAT
1 AAAATA-AA-AAT
*
29043180 AAAA-CAAAAT
1 AAAATAAAAAT
*
29043190 AAAAGTGAAAAT
1 AAAA-TAAAAAT
29043202 -AAATAAAAAT
1 AAAATAAAAAT
29043212 AAAAT-AAAAT
1 AAAATAAAAAT
* *
29043222 -AAAGAAAAGT
1 AAAATAAAAAT
*
29043232 AAAACAAAAAT
1 AAAATAAAAAT
29043243 AAAA-ATAAAAT
1 AAAATA-AAAAT
29043254 AAAGATAAAAA
1 AAA-ATAAAAA
29043265 GAATATTAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
9 3 0.04
10 23 0.33
11 29 0.41
12 10 0.14
13 5 0.07
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:29044298 original size:5 final size:5
Alignment explanation
Indices: 29044274--29044341 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
29044264 ATAATTAGAT
* * *
29044274 AAATAA AAATA CATATA AAATA AAA-A AGA-A AAATA AAAGAA AAATA
1 AAAT-A AAATA -AAATA AAATA AAATA AAATA AAATA AAA-TA AAATA
*
29044320 AAAGAA AAATA AAATA AAATA A
1 AAA-TA AAATA AAATA AAATA A
29044342 TATATATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
4 6 0.12
5 28 0.56
6 16 0.32
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:29044311 original size:11 final size:11
Alignment explanation
Indices: 29044297--29044338 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
29044287 TATAAAATAA
29044297 AAAAGAAAAAT
1 AAAAGAAAAAT
29044308 AAAAGAAAAAT
1 AAAAGAAAAAT
29044319 AAAAGAAAAAT
1 AAAAGAAAAAT
*
29044330 AAAATAAAA
1 AAAAGAAAA
29044339 TAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAGAAAAAT
Found at i:29044316 original size:16 final size:16
Alignment explanation
Indices: 29044303--29044341 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29044293 ATAAAAAAGA
29044303 AAAATAAAAGAAAAAT
1 AAAATAAAAGAAAAAT
*
29044319 AAAAGAAAA-ATAAAAT
1 AAAATAAAAGA-AAAAT
29044335 AAAATAA
1 AAAATAA
29044342 TATATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAATAAAAGAAAAAT
Found at i:29044358 original size:17 final size:17
Alignment explanation
Indices: 29044331--29044378 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
29044321 AAGAAAAATA
29044331 AAATAAAATAAT-ATATAT
1 AAAT-AAATAATAATA-AT
*
29044349 TAATAAATAATAATAAT
1 AAATAAATAATAATAAT
29044366 AAATAAATAATAA
1 AAATAAATAATAA
29044379 ATACATAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAATAATAATAAT
Found at i:29044376 original size:11 final size:11
Alignment explanation
Indices: 29044226--29044381 Score: 58
Period size: 11 Copynumber: 13.6 Consensus size: 11
29044216 ATTTTATAAG
29044226 ATAAATAAA-A
1 ATAAATAAATA
29044236 A-AAAT-AATA
1 ATAAATAAATA
29044245 ATAACAGATAAATA
1 AT-A-A-ATAAATA
* *
29044259 AGTATATAATTA
1 A-TAAATAAATA
29044271 GATAAATAAA-A
1 -ATAAATAAATA
29044282 ATACATATAAAATA
1 ATA-A-AT-AAATA
* *
29044296 AAAAAGAAA-A
1 ATAAATAAATA
*
29044306 ATAAA-AGAAAA
1 ATAAATA-AATA
*
29044317 ATAAA-AGAAAA
1 ATAAATA-AATA
29044328 ATAAAATAAAATA
1 AT-AAAT-AAATA
* *
29044341 ATATAT-ATTA
1 ATAAATAAATA
29044351 ATAAATAATAATA
1 ATAAAT-A-AATA
29044364 ATAAATAAATA
1 ATAAATAAATA
29044375 ATAAATA
1 ATAAATA
29044382 CATAGGATAT
Statistics
Matches: 114, Mismatches: 12, Indels: 39
0.69 0.07 0.24
Matches are distributed among these distances:
8 2 0.02
9 7 0.06
10 19 0.17
11 31 0.27
12 23 0.20
13 21 0.18
14 10 0.09
15 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:29044422 original size:20 final size:20
Alignment explanation
Indices: 29044272--29044434 Score: 66
Period size: 20 Copynumber: 8.6 Consensus size: 20
29044262 ATATAATTAG
*
29044272 ATAAAT-AAAAAT-ACATAT
1 ATAAATAAAAAATAAAATAT
*
29044290 A-AAATAAAAAAGAAAA-AT
1 ATAAATAAAAAATAAAATAT
* *
29044308 A-AAA-GAAAAATAAAAGA-
1 ATAAATAAAAAATAAAATAT
29044325 A-AAAT--AAAATAAAATAAT
1 ATAAATAAAAAATAAAAT-AT
* *
29044343 ATATATTAATAAATAATAATA-
1 ATA-AATAAAAAATAA-AATAT
* *
29044364 ATAAATAAATAAT-AAATAC
1 ATAAATAAAAAATAAAATAT
* * **
29044383 ATAGGATATAAAGGAAAATAT
1 ATA-AATAAAAAATAAAATAT
*
29044404 ATACATAAAAAATAAAATA-
1 ATAAATAAAAAATAAAATAT
29044423 A-AAATAACAAAA
1 ATAAATAA-AAAA
29044435 ATATAAAATA
Statistics
Matches: 109, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.08
17 18 0.17
18 23 0.21
19 12 0.11
20 26 0.24
21 11 0.10
22 7 0.06
23 3 0.03
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
ATAAATAAAAAATAAAATAT
Found at i:29047779 original size:19 final size:18
Alignment explanation
Indices: 29047737--29047779 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
29047727 ATTAGATATC
*
29047737 TTTAAAATTTAAGTATAA
1 TTTAAAATTTAACTATAA
*
29047755 TATTAAACATTTTACTATAA
1 T-TTAAA-ATTTAACTATAA
29047775 TTTAA
1 TTTAA
29047780 GAATAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTAAAATTTAACTATAA
Found at i:29052586 original size:3 final size:3
Alignment explanation
Indices: 29052578--29052615 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29052568 TGTCGTGGTT
29052578 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29052616 TCCTTTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29053747 original size:1 final size:1
Alignment explanation
Indices: 29053741--29053771 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
29053731 AGGTGTTAGG
29053741 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29053772 AAATTCCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29057627 original size:19 final size:20
Alignment explanation
Indices: 29057590--29057627 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29057580 CAAAGTCATA
*
29057590 ATTTTTTTCTTATTATTTCT
1 ATTTTTTTCTTAATATTTCT
*
29057610 ATTTTTTTTTTAAT-TTTC
1 ATTTTTTTCTTAATATTTC
29057628 CAATAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTTTCTTAATATTTCT
Found at i:29058753 original size:59 final size:57
Alignment explanation
Indices: 29058627--29059017 Score: 513
Period size: 59 Copynumber: 6.7 Consensus size: 57
29058617 TTGTGCAGGA
*
29058627 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTAGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTT-G-AAA-TTTTATTTTCAAGG
*
29058687 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAATTTT-ATTTTCAAGG
*
29058746 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTGAAATTTTATTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAATTTTATTTTCAAGG
** *
29058804 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTATTTTCAAGG
* *
29058860 AAAATTGATACTTTCAACTTTT-GTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTT-GAAA-TTTTATTTTCAAGG
* * *
29058919 AAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTTGAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA---TATTTTTTGAAATTTTATTTTCAAGG
29058979 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTT
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
29059018 TTATTTTTAT
Statistics
Matches: 300, Mismatches: 17, Indels: 31
0.86 0.05 0.09
Matches are distributed among these distances:
55 1 0.00
56 46 0.15
57 21 0.07
58 42 0.14
59 91 0.30
60 80 0.27
61 12 0.04
62 7 0.02
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTATTTTCAAGG
Found at i:29058925 original size:173 final size:179
Alignment explanation
Indices: 29058627--29059017 Score: 602
Period size: 173 Copynumber: 2.2 Consensus size: 179
29058617 TTGTGCAGGA
*
29058627 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTAGAAAACTTTGATTTTCAAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAACATTTTTTAGAAAACTTTGATTTTCAAGGAAAA
*
29058691 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTGATTTTCAAGAAAAATTGATA
65 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATA
29058756 CTTTCAACTTTTCCTCAAAAA-CC-TTTTTTTGAAATTTTATTTTAAAGG
130 CTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAATTTTATTTTAAAGG
* *
29058804 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTT-G-AAA-TTT-ATTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTAGAAAACTTTGATTTTCAAGGAAAAT
* * *
29058865 TGATACTTTCAACTTTT-GTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATA
66 TGATACTTTCAACTTTTCCT-CAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATA
* *
29058929 CTTTCAACTTTTTCTCAAAAACCCTTTTTTTTGAAATTTTATTTTTAAGG
130 CTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAATTTTATTTTAAAGG
*
29058979 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTT
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAACATTTTTT
29059018 TTATTTTTAT
Statistics
Matches: 198, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
172 1 0.01
173 92 0.46
174 5 0.03
175 57 0.29
176 7 0.04
177 34 0.17
178 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (179 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTAGAAAACTTTGATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATAC
TTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAATTTTATTTTAAAGG
Found at i:29059067 original size:6 final size:6
Alignment explanation
Indices: 29059052--29059132 Score: 71
Period size: 6 Copynumber: 13.7 Consensus size: 6
29059042 ATAATAAAAC
* *
29059052 AAAATA AAAATG AAAAT- -AAATA AAAATA AAAATAA AATAATGA AAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A AA-AAT-A AAAATA
* *
29059100 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
29059133 GAATATTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.07
5 8 0.13
6 38 0.62
7 5 0.08
8 6 0.10
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:29059082 original size:32 final size:33
Alignment explanation
Indices: 29059030--29059133 Score: 90
Period size: 32 Copynumber: 3.1 Consensus size: 33
29059020 ATTTTTATTT
29059030 AAAG-AAAATAGAATAATAAAACAAAATAAAAATGA
1 AAAGTAAAATA-AA-AATAAAA-AAAATAAAAATGA
* *
29059065 AAA-T-AAATAAAAATAAAAATAA-AATAATGA
1 AAAGTAAAATAAAAATAAAAAAAATAAAAATGA
* * *
29059095 AAAGTAAAACAAAAATAAAAATAAAATAAAGATAA
1 AAAGTAAAATAAAAAT-AAAA-AAAATAAAAATGA
29059130 AAAG
1 AAAG
29059134 AATATTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
30 10 0.18
31 4 0.07
32 16 0.29
33 6 0.11
34 8 0.14
35 12 0.21
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (33 bp):
AAAGTAAAATAAAAATAAAAAAAATAAAAATGA
Found at i:29059090 original size:11 final size:11
Alignment explanation
Indices: 29059047--29059131 Score: 77
Period size: 11 Copynumber: 7.8 Consensus size: 11
29059037 ATAGAATAAT
*
29059047 AAAACAAAATA
1 AAAATAAAATA
29059058 AAAATGAAAATA
1 AAAAT-AAAATA
*
29059070 AATA-AAAATA
1 AAAATAAAATA
29059080 AAAATAAAATA
1 AAAATAAAATA
** *
29059091 ATGA-AAAGTA
1 AAAATAAAATA
29059101 AAACA-AAAATA
1 AAA-ATAAAATA
29059112 AAAATAAAATA
1 AAAATAAAATA
*
29059123 AAGATAAAA
1 AAAATAAAA
29059132 AGAATATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
10 16 0.27
11 35 0.58
12 9 0.15
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:29060026 original size:10 final size:9
Alignment explanation
Indices: 29060007--29060061 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 9
29059997 CTAGCCAGAT
29060007 AAATAAAAA
1 AAATAAAAA
29060016 AAATAAAAA
1 AAATAAAAA
29060025 AAATCAAACAA
1 AAAT-AAA-AA
29060036 AAATAAATCAGA
1 AAATAAA--A-A
29060048 TAAATAAAAA
1 -AAATAAAAA
29060058 AAAT
1 AAAT
29060062 TAACAGATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 17 0.41
10 7 0.17
11 9 0.22
12 1 0.02
13 7 0.17
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (9 bp):
AAATAAAAA
Found at i:29060095 original size:21 final size:21
Alignment explanation
Indices: 29060002--29060111 Score: 73
Period size: 22 Copynumber: 5.1 Consensus size: 21
29059992 AATTTCTAGC
*
29060002 CAGATAAATAAAAAAAA-TAA
1 CAGATAATTAAAAAAAATTAA
* * * *
29060022 -AAAAAATCAAACAAAAATAAA
1 CAGATAATTAAA-AAAAATTAA
*
29060043 TCAGATAAATAAAAAAAATTAA
1 -CAGATAATTAAAAAAAATTAA
*
29060065 CAGATAAATTAAAATTAAA-TAA
1 CAGAT-AATTAAAA-AAAATTAA
* *
29060087 CAGATAATTACATAAATATTAA
1 CAGATAATTA-AAAAAAATTAA
29060109 CAG
1 CAG
29060112 GAAAAAAAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
19 7 0.10
20 5 0.07
21 14 0.21
22 31 0.46
23 10 0.15
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
CAGATAATTAAAAAAAATTAA
Found at i:29060256 original size:33 final size:32
Alignment explanation
Indices: 29060183--29060286 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 32
29060173 AATACCTAAG
29060183 ATAAAAAATAATAATAAAAGAAA-AAAATATATACA
1 ATAAAAAATAATAATAAAA-AAATAAAA-ATA-A-A
*
29060218 TATAAAAAATAATAATAATAATAATAAAAATAAA
1 -ATAAAAAATAATAATAA-AAAAATAAAAATAAA
*
29060252 ATAAAAATGTAA-AATACAAAAAATAAAAATAAA
1 ATAAAAA-ATAATAATA-AAAAAATAAAAATAAA
29060285 AT
1 AT
29060287 GAAGAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
33 27 0.44
34 5 0.08
35 1 0.02
36 22 0.36
37 6 0.10
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (32 bp):
ATAAAAAATAATAATAAAAAAATAAAAATAAA
Found at i:29060266 original size:13 final size:11
Alignment explanation
Indices: 29060219--29060300 Score: 62
Period size: 12 Copynumber: 7.3 Consensus size: 11
29060209 ATATATACAT
*
29060219 ATAAAAA-ATA
1 ATAAAAATAAA
*
29060229 ATAATAATAATA
1 ATAAAAATAA-A
29060241 ATAAAAATAAA
1 ATAAAAATAAA
29060252 ATAAAAATGTAAA
1 ATAAAAA--TAAA
*
29060265 AT-ACAA-AAA
1 ATAAAAATAAA
29060274 ATAAAAATAAA
1 ATAAAAATAAA
*
29060285 ATGAAGAAAAAAA
1 AT-AA-AAATAAA
29060298 ATA
1 ATA
29060301 TAGACTTACC
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
9 5 0.09
10 9 0.16
11 14 0.24
12 16 0.28
13 14 0.24
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.20
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:29060272 original size:7 final size:6
Alignment explanation
Indices: 29060186--29060285 Score: 51
Period size: 6 Copynumber: 15.7 Consensus size: 6
29060176 ACCTAAGATA
* * * * *
29060186 AAAAAT AATAAT AAAAGAA AAAAAT ATATACAT ATAAAA- AATAAT AATAAT
1 AAAAAT AAAAAT AAAA-AT AAAAAT A-A-AAAT A-AAAAT AAAAAT AAAAAT
* *
29060237 AATAAT AAAAAT -AAAAT AAAAATGT AAAATACA AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAA--T AAAA-A-T AAAAAT AAAAAT AAAA
29060286 TGAAGAAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
5 8 0.11
6 42 0.56
7 9 0.12
8 15 0.20
9 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:29060469 original size:18 final size:18
Alignment explanation
Indices: 29060448--29060486 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29060438 ACCTTTTCAC
*
29060448 TTTTTGTTTTTTTTTATT
1 TTTTTATTTTTTTTTATT
*
29060466 TTTTTATTTTTTTTTGTT
1 TTTTTATTTTTTTTTATT
29060484 TTT
1 TTT
29060487 GATCAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.00, G:0.05, T:0.90
Consensus pattern (18 bp):
TTTTTATTTTTTTTTATT
Found at i:29060635 original size:42 final size:42
Alignment explanation
Indices: 29060571--29061135 Score: 831
Period size: 42 Copynumber: 13.4 Consensus size: 42
29060561 ACTTTAAAAA
*
29060571 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
* *
29060613 AAAAGTAAATTGCTCTTCTAAACAGAGGCACCACAACTTTGG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29060655 -AAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTT-G
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29060695 AGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-T
1 A-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
* * *
29060737 AGAAAGTAAATTGCTCCTCTAAATAGAGGTACCACGACTTTTGAA
1 A-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTG-G
* *
29060782 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGATTTTGA
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29060824 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACATT-G
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29060865 AAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTT-G
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
* *
29060906 AGAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGACTTT-T
1 A-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
29060948 AGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGG
1 A-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGG
* *
29060992 AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGA
1 -AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29061035 AAAAGTAAATTGCTCCTCTATACAGAGGCACCACGACTTTGG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
*
29061077 -AAAGTAAATTACTCCTCTAAACAGAGGCACCACGACTTT-G
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
29061117 AGAAAGTAAATTGCTCCTC
1 A-AAAGTAAATTGCTCCTC
29061136 GACAATCATG
Statistics
Matches: 480, Mismatches: 32, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.00
41 113 0.24
42 281 0.59
43 14 0.03
44 68 0.14
45 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (42 bp):
AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
Found at i:29060689 original size:83 final size:82
Alignment explanation
Indices: 29060576--29061135 Score: 859
Period size: 83 Copynumber: 6.7 Consensus size: 82
29060566 AAAAAAAAAA
*
29060576 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCTTCTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGG
*
29060641 CACCACAACTTTGGAAAG
65 CACCACGACTTTGGAAAG
*
29060659 TAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGG
*
29060724 CACCACGACTTTTAGAAAG
65 CACCACGAC-TTTGGAAAG
* *
29060743 TAAATTGCTCCTCTAAATAGAGGTACCACGACTTTTGAAAAAAGTAAATTGCTCCTCTAAACAGA
1 TAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTG--AAAAGTAAATTGCTCCTCTAAACAGA
* *
29060808 GGCACCACGATTTTGAAAAAG
63 GGCACCACGACTTTG-GAAAG
* *
29060829 TAAATTGCTCCTCTAAACAGAGGCACCACGACATTGAAAAGTAAATTGCTCCTCTAAATAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
29060894 ACCACGACTTTGAGAAAG
66 ACCACGACTTTG-GAAAG
* *
29060912 TAAATTGCTCCTTTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGG
29060977 CACCACGACTTTTGGAAAAAG
65 CACCACGAC-TTTGG--AAAG
* *
29060998 TAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTATACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGG
29061063 CACCACGACTTTGGAAAG
65 CACCACGACTTTGGAAAG
*
29061081 TAAATTACTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTC
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTC
29061136 GACAATCATG
Statistics
Matches: 439, Mismatches: 26, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
82 3 0.01
83 201 0.46
84 73 0.17
85 19 0.04
86 141 0.32
87 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (82 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
ACCACGACTTTGGAAAG
Found at i:29060940 original size:211 final size:211
Alignment explanation
Indices: 29060569--29061135 Score: 990
Period size: 211 Copynumber: 2.7 Consensus size: 211
29060559 CAACTTTAAA
* * *
29060569 AAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCTTCTAA
1 AAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAA
* *
29060634 ACAGAGGCACCACAACTTTGGAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAGAA
66 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAA
*
29060699 AGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAATAGA
131 AGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAACAGA
*
29060764 GGTACCACGACTTTTG
196 GGCACCACGACTTTTG
*
29060780 AAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGATTTTGAAAAAGTAAATTGCTCCTCTAA
1 AAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAA
* * *
29060845 ACAGAGGCACCACGACATTGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTTGAGAA
66 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAA
*
29060910 AGTAAATTGCTCCTTTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAACAGA
131 AGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAACAGA
29060975 GGCACCACGACTTTTG
196 GGCACCACGACTTTTG
* * *
29060991 GAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTAT
1 AAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAA
*
29061056 ACAGAGGCACCACGACTTTGGAAAGTAAATTACTCCTCTAAACAGAGGCACCACGACTTTGAGAA
66 ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAA
29061121 AGTAAATTGCTCCTC
131 AGTAAATTGCTCCTC
29061136 GACAATCATG
Statistics
Matches: 335, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
211 335 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (211 bp):
AAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAA
ACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAA
AGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTAGAAAGTAAATTGCTCCTCTAAACAGA
GGCACCACGACTTTTG
Found at i:29066454 original size:56 final size:56
Alignment explanation
Indices: 29066333--29066525 Score: 243
Period size: 56 Copynumber: 3.4 Consensus size: 56
29066323 TTGTGCAGAA
*
29066333 AAAATTGATACTGTTTCAACTTTCCTCAAAAACCTTTTTTTTGGAAAATTTT-TTTTAAAGG
1 AAAATTGATAC--TTTCAACTTTTCTCAAAAA-C-TTTTTTT-G-AAATTTTATTTTAAAGG
29066394 AAAATTGATACTTTCAACTTTTCTCAAAAA-TTTTTTTGAAATTTTGATTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCTCAAAAACTTTTTTTGAAATTTT-ATTTTAAAGG
29066450 AAAATTGA-ACTTT-AACTTTTCTCAAAAACCTTTTTTTTGAAA-TTTATTTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCTCAAAAA-C-TTTTTTTGAAATTTTA-TTTTAAAGG
*
29066506 AAAATTGATACTTTTAACTT
1 AAAATTGATACTTTCAACTT
29066526 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 1, Indels: 19
0.86 0.01 0.13
Matches are distributed among these distances:
54 22 0.18
55 7 0.06
56 44 0.36
57 16 0.13
58 5 0.04
59 18 0.15
61 11 0.09
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAACTTTTTTTGAAATTTTATTTTAAAGG
Found at i:29067628 original size:30 final size:30
Alignment explanation
Indices: 29067556--29067628 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
29067546 CTTTCTTGAA
*
29067556 AAAAAATTGAAATATTTATAAACTTAGGTTTG
1 AAAAAATT-AAA-AGTTATAAACTTAGGTTTG
* *
29067588 AAAAAA-TAAAAGTTATAAATTTTGGTTTG
1 AAAAAATTAAAAGTTATAAACTTAGGTTTG
29067617 AAAAAATTAAAA
1 AAAAAATTAAAA
29067629 ATTAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 22 0.59
30 8 0.22
31 1 0.03
32 6 0.16
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.34
Consensus pattern (30 bp):
AAAAAATTAAAAGTTATAAACTTAGGTTTG
Found at i:29071655 original size:18 final size:18
Alignment explanation
Indices: 29071618--29071654 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29071608 AATGATAAAT
29071618 AATAAAAAAAACAAGAAA
1 AATAAAAAAAACAAGAAA
*
29071636 AATAAAAATAA-AAGAAA
1 AATAAAAAAAACAAGAAA
29071653 AA
1 AA
29071655 AAATTAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (18 bp):
AATAAAAAAAACAAGAAA
Found at i:29071656 original size:20 final size:19
Alignment explanation
Indices: 29071618--29071696 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 19
29071608 AATGATAAAT
* *
29071618 AATAAAAA-AAACAAGAAA
1 AATAAAAATAAAAAAAAAA
29071636 AATAAAAATAAAAGAAAAAA
1 AATAAAAATAAAA-AAAAAA
* *
29071656 AATTAGATAATAAAAAATAAA
1 AA-TA-AAAATAAAAAAAAAA
*
29071677 ATTAAAAAATAAAAAAAAAA
1 AAT-AAAAATAAAAAAAAAA
29071697 CGAAAATCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 8 0.16
19 3 0.06
20 21 0.43
21 9 0.18
22 8 0.16
ACGTcount: A:0.81, C:0.01, G:0.04, T:0.14
Consensus pattern (19 bp):
AATAAAAATAAAAAAAAAA
Found at i:29072842 original size:12 final size:12
Alignment explanation
Indices: 29072827--29072892 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
29072817 GATTAAACCA
*
29072827 AAAATTAAAATT
1 AAAATTAAAATC
* *
29072839 AAAATCACAATC
1 AAAATTAAAATC
*
29072851 CAAATTAAAAATC
1 AAAATT-AAAATC
* *
29072864 AGAATTAAAACC
1 AAAATTAAAATC
29072876 AAAATTAAAATC
1 AAAATTAAAATC
*
29072888 CAAAT
1 AAAAT
29072893 CAACACATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
12 32 0.78
13 9 0.22
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.23
Consensus pattern (12 bp):
AAAATTAAAATC
Found at i:29073576 original size:27 final size:27
Alignment explanation
Indices: 29073539--29073604 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
29073529 TTACAAGTAG
29073539 GATT-AATCATCCTTTTAGTATAAGAT
1 GATTCAATCATCCTTTTAGTATAAGAT
29073565 GATTCAATCATCCTTTTAGTATAAGAT
1 GATTCAATCATCCTTTTAGTATAAGAT
29073592 GATTCAATCATCC
1 GATTCAATCATCC
29073605 CAAAGTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 4 0.10
27 35 0.90
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (27 bp):
GATTCAATCATCCTTTTAGTATAAGAT
Found at i:29080660 original size:21 final size:22
Alignment explanation
Indices: 29080621--29080664 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
29080611 TTGAGCTATT
29080621 ATAAGTTATTTTTAGTACAATAAA
1 ATAAGTTATTTTTA-TAC-ATAAA
29080645 ATAAGTT-TTTTT-TACATAAA
1 ATAAGTTATTTTTATACATAAA
29080665 GTTAGATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
23 5 0.25
24 7 0.35
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
ATAAGTTATTTTTATACATAAA
Found at i:29086574 original size:19 final size:20
Alignment explanation
Indices: 29086545--29086585 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
29086535 TTAAGCTAGT
29086545 GGAGAGATTGGATGGGGTGG
1 GGAGAGATTGGATGGGGTGG
* *
29086565 GGAG-GATTGGGTGTGGTGG
1 GGAGAGATTGGATGGGGTGG
29086584 GG
1 GG
29086586 CGTTGGCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.00, G:0.63, T:0.22
Consensus pattern (20 bp):
GGAGAGATTGGATGGGGTGG
Found at i:29086615 original size:38 final size:40
Alignment explanation
Indices: 29086560--29086651 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 40
29086550 GATTGGATGG
*
29086560 GGTGGGGA-GGATTGGGTGTGGTGGGGCGTT-GGCGG-AA
1 GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGCGGAAA
* *
29086597 GGTGGGGAGGGATTGGGTGTGGTGGGATGTTGGGGGGAAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGCGGAAA
*
29086637 GGTGGAGAGGGATTG
1 GGTGGGGAGGGATTG
29086652 ATGGGGGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
37 8 0.17
38 20 0.42
39 4 0.08
40 16 0.33
ACGTcount: A:0.14, C:0.02, G:0.62, T:0.22
Consensus pattern (40 bp):
GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGCGGAAA
Found at i:29086924 original size:20 final size:20
Alignment explanation
Indices: 29086886--29086923 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29086876 GATTGTGTTA
*
29086886 TATATTAATTTATAATTTTG
1 TATATGAATTTATAATTTTG
29086906 TATATGAATTT-TAATTTT
1 TATATGAATTTATAATTTT
29086924 TTTTGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATGAATTTATAATTTTG
Found at i:29087177 original size:26 final size:26
Alignment explanation
Indices: 29087149--29087197 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
29087139 TAAAAAATAA
*
29087149 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
29087174 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
29087198 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:29090599 original size:6 final size:6
Alignment explanation
Indices: 29090590--29090638 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
29090580 AGAGTGATAA
* * ** *
29090590 TGATGG TGATAG AGATGG TGATGG ACATGA TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
29090638 T
1 T
29090639 ACAAATTTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.43, T:0.31
Consensus pattern (6 bp):
TGATGG
Found at i:29090613 original size:18 final size:18
Alignment explanation
Indices: 29090590--29090636 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
29090580 AGAGTGATAA
29090590 TGATGGTGATAGA-GATGG
1 TGATGGTGAT-GATGATGG
**
29090608 TGATGGACATGATGATGG
1 TGATGGTGATGATGATGG
29090626 TGATGGTGATG
1 TGATGGTGATG
29090637 GTACAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.26, C:0.02, G:0.43, T:0.30
Consensus pattern (18 bp):
TGATGGTGATGATGATGG
Found at i:29091006 original size:18 final size:18
Alignment explanation
Indices: 29090983--29091107 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
29090973 ATGGTTATTA
29090983 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
29091001 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
*
29091022 TCCACCTCAAATGTATCGG
1 TCCACCTCAAATGTATC-C
* * * *
29091041 T-TACCACAAATATACCC
1 TCCACCTCAAATGTATCC
* *
29091058 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
29091076 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
29091091 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
29091108 AAGAACAAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 52 0.63
19 1 0.01
21 17 0.20
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:29091013 original size:21 final size:21
Alignment explanation
Indices: 29090987--29091029 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29090977 TTATTATCCA
*
29090987 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
29091008 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
29091029 C
1 C
29091030 AAATGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.44, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:29091093 original size:33 final size:33
Alignment explanation
Indices: 29091007--29091108 Score: 141
Period size: 33 Copynumber: 3.0 Consensus size: 33
29090997 ATCCTCCACC
*
29091007 TCCTCAAATATATCCTCCACCTCAAATGTATCGGT
1 TCCTCAAATATATCCTCCACCTCAAATGTATC--A
* * *
29091042 TACCACAAATATACCCTCCACCACAAATGTATCA
1 T-CCTCAAATATATCCTCCACCTCAAATGTATCA
29091076 TCCTCAAATATATCCTCCACCTCAAATGTATCA
1 TCCTCAAATATATCCTCCACCTCAAATGTATCA
29091109 AGAACAAAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 29 0.49
34 1 0.02
35 1 0.02
36 28 0.47
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.27
Consensus pattern (33 bp):
TCCTCAAATATATCCTCCACCTCAAATGTATCA
Found at i:29091499 original size:6 final size:6
Alignment explanation
Indices: 29091488--29091515 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29091478 ATAAGAGTTT
29091488 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
29091516 TACATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:29092979 original size:54 final size:54
Alignment explanation
Indices: 29092897--29093004 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
29092887 GGAGAAACAT
** *
29092897 AGACTTTATATGAGAAGACATAAAGAGAGAGTTGGAGGTGGCGTTGGGGAGTTA
1 AGACTTTATATGAGAAGACATAAAGAGAGAGTCAGAGGTGGCGTCGGGGAGTTA
* *
29092951 AGACTTTATATGAGCAGATATAAAGAGAGAGTCAGAGGTGGCGTCGGGGAGTTA
1 AGACTTTATATGAGAAGACATAAAGAGAGAGTCAGAGGTGGCGTCGGGGAGTTA
29093005 GCCACTTGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.33, C:0.07, G:0.36, T:0.23
Consensus pattern (54 bp):
AGACTTTATATGAGAAGACATAAAGAGAGAGTCAGAGGTGGCGTCGGGGAGTTA
Found at i:29093798 original size:18 final size:15
Alignment explanation
Indices: 29093763--29093792 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29093753 TATTATTTAA
29093763 TAAATATATTAAATT
1 TAAATATATTAAATT
29093778 TAAATTATATTAAAT
1 TAAA-TATATTAAAT
29093793 ATTTAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATATTAAATT
Found at i:29093864 original size:16 final size:16
Alignment explanation
Indices: 29093845--29093875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29093835 ATAAATGATT
*
29093845 AAATGATTAAATTCAA
1 AAATAATTAAATTCAA
29093861 AAATAATTAAATTCA
1 AAATAATTAAATTCA
29093876 TTCAATTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAATTAAATTCAA
Found at i:29095515 original size:8 final size:8
Alignment explanation
Indices: 29095502--29095540 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
29095492 TTTTTGGATA
29095502 ATTCCTAG
1 ATTCCTAG
29095510 ATTCCTAG
1 ATTCCTAG
29095518 ATTCCTAG
1 ATTCCTAG
* *
29095526 ATTACTTG
1 ATTCCTAG
29095534 ATTCCTA
1 ATTCCTA
29095541 AATGATTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (8 bp):
ATTCCTAG
Found at i:29102698 original size:27 final size:27
Alignment explanation
Indices: 29102658--29102709 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
29102648 AGGCTGCAAA
**
29102658 GCTCTGATGTCATTTCTATACACAGTG
1 GCTCTGATACCATTTCTATACACAGTG
*
29102685 GCTCTGATACCATTTTTATACACAG
1 GCTCTGATACCATTTCTATACACAG
29102710 CGACAGGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (27 bp):
GCTCTGATACCATTTCTATACACAGTG
Found at i:29109861 original size:615 final size:614
Alignment explanation
Indices: 29108686--29110563 Score: 2898
Period size: 644 Copynumber: 3.0 Consensus size: 614
29108676 ACAAGGCTCT
* * *
29108686 GATCACAGTGTTGACTGACTTGGCCCAACTTATGTTCAATTCTGTGTAGGTATGAATTCTGCTGG
1 GATCAAAGTGTTGACTGACTTGGCCCAACTTATGTTCAATTCTGTGCAGGTATGAATTCTACTGG
* * *
29108751 AGAAAATTTTTAGTTTGTCAGTTTAAAACTGCTTCAGCACGAGAAATAATTTTTTGGTTCCCATA
66 AGAGAATTTTTAGTTTGCCAGTTTAAAACTGCTTCAGCATGAGAAATAATTTTTTGGTTCCCATA
*
29108816 TTCATCTCTGTCAATAGGAGTGGGGATTTTTGGAATGTGTTTGTACTGGTCTTTATGAAACTCTT
131 TTCATCTCTGTCAGTAGGAGTGGGGATTTTTGGAATGTGTTTGTACTGGTCTTTATGAAACTCTT
* * *
29108881 AAAAAAGAGGAAATCTGAGCTTAGGAAGGTTGGTTGCATCATTGAAATTTATGGTAAAGGTTGGG
196 AAAAAAGAGGAAATCTGAGCTTAGGAAGGTTAGTTGCATCTTTGAAATTTGTGGTAAAGGTTGGG
* * * **
29108946 TGAAATTTTGAGTGGAATATGGTTTTTGTGTGGGTTGATTTGAATAGGTTTGAGAGAGTCATTTT
261 TGGAATTTTGAGTGGAATCTGGTTTTTGTGTGGGTTGATTTGAATAGGTTTAAGAGAGTGGTTTT
* *
29109011 CCTTTT-TTAGGATAGATGACATAGTAGTCAAACTTTTTTGAGGGTTTATTAAGGAGATCAACTT
326 -CTTTTCTTAGGATAGATGACATAGTAGTCAAACTTTCTTGAGGGTTTACTAAGGAGATCAACTT
* * * * *
29109075 CAGGGTCTCCATTCTCATATCTTTCTTTGAGTTTTTGCTGGGAAAATTTTTTCTTCTTTTACTTT
390 CAGGGTCTCCATTCTCATATCTTTCTTTGAGCTTTTGCTGGGAAGACTTTTTCTTCTTTTGCTTC
* * * *
29109140 TTTGAAACATCATCATCATCATCCAGGAAGCTTTTATTTGCATCTAACTGGCATTCTTTGCATTA
455 TTTGAAACATCATCATCATCATCCAAGAAGCTTTTATTTGCGTCTAACTAGCATTCTTTGCATTG
* * * *
29109205 ATAATTTATGTCCCAATAACAATGTCATTGTGGATATCTATATGCATACACAGGATTTTCATTAG
520 ACAATTTATGTCCCAATAACAATGTCCTTGTGGAGATCTATATGCATACACGGGATTTTCATTAG
*
29109270 ACTAAAAGTGTATGACTAGAACATCAAGGA
585 ACTGAAAGTGTATGACTAGAACATCAAGGA
* *
29109300 GATCAAAGTGTTGACTGACTTGGCCCAACTTATGTTCAATTCTGTGCAAGTATGAATTCTACTAG
1 GATCAAAGTGTTGACTGACTTGGCCCAACTTATGTTCAATTCTGTGCAGGTATGAATTCTACTGG
29109365 AGAGAATTTTTAGTTTGCCAGTTTAAAACTGCTTCAGCATGAGAAATAATTTTTTGGTTCCCATA
66 AGAGAATTTTTAGTTTGCCAGTTTAAAACTGCTTCAGCATGAGAAATAATTTTTTGGTTCCCATA
*
29109430 TTCATCTCTGTCAGTAAGAGTGGGGATTTTTGGAATGTGTTTGTACTGGTCTTTATGAAACTCTT
131 TTCATCTCTGTCAGTAGGAGTGGGGATTTTTGGAATGTGTTTGTACTGGTCTTTATGAAACTCTT
* *
29109495 AAAAAAGAGAGAAATCTGAGCTT-GAGAAGGTTAGTTGCATCTTTGAAAATTGTGATAAAGGTTG
196 AAAAAAGAG-GAAATCTGAGCTTAG-GAAGGTTAGTTGCATCTTTGAAATTTGTGGTAAAGGTTG
* *
29109559 AGTGGAATTTTGAATGGAATCTGGTTTTTGTGTGGGTTGATTTGAATAGGTTTAAGAGAGTGGTT
259 GGTGGAATTTTGAGTGGAATCTGGTTTTTGTGTGGGTTGATTTGAATAGGTTTAAGAGAGTGGTT
* *
29109624 TTATTTTCTTAGGATAGATGACATAGTAGTCAAACTTTCTTGAGGGTTTACTAAAGAGATCAACT
324 TTCTTTTCTTAGGATAGATGACATAGTAGTCAAACTTTCTTGAGGGTTTACTAAGGAGATCAACT
*
29109689 TCAAGGTCTCCATTCTCATATCTTTCTTTGAGCTTTTGCTGGGAAGACTTTTTCTTCTTTTGCTT
389 TCAGGGTCTCCATTCTCATATCTTTCTTTGAGCTTTTGCTGGGAAGACTTTTTCTTCTTTTGCTT
*
29109754 CTTTAAAACATCATCATCATCATCCAAGAAGCTTTTATTTGCGTCTAACTAGCATTCTTTGCATT
454 CTTTGAAACATCATCATCATCATCCAAGAAGCTTTTATTTGCGTCTAACTAGCATTCTTTGCATT
*
29109819 GACAATTTATGTCCCAATAACAATGTCCTTGTGGAGATCTATATGCATACATGGGATTTTCATTA
519 GACAATTTATGTCCCAATAACAATGTCCTTGTGGAGATCTATATGCATACACGGGATTTTCATTA
*
29109884 GACTGAAAGTGTATGACTAAAACATCAAGGA
584 GACTGAAAGTGTATGACTAGAACATCAAGGA
29109915 GATCAAAGTGTATGACTAAAACATCAAGGAGATCAAAGTGTTGATTGACTTGCCCCAACTTATGT
1 GATCAAAGTGT-TG------AC-T------GA-C----------TTG----G-CCCAACTTATGT
* * *
29109980 TCAATTTTGTGCAGGTATAAATTCTACTGGAGAGAATTTTTAGTTTGCTAGTTTAAAACTGCTTC
36 TCAATTCTGTGCAGGTATGAATTCTACTGGAGAGAATTTTTAGTTTGCCAGTTTAAAACTGCTTC
*
29110045 AGCATGAGAAACAATTTTTTGGTTCCCATATTCATCTCTGTCAGTAGGAGTGGGGATTTTTGGAA
101 AGCATGAGAAATAATTTTTTGGTTCCCATATTCATCTCTGTCAGTAGGAGTGGGGATTTTTGGAA
29110110 TGTGTTTGTACTGGTCTTTATGAAACTCTT-AAAAAGAGGGAAATCTGAGCTTAGGAAGGTTAGT
166 TGTGTTTGTACTGGTCTTTATGAAACTCTTAAAAAAGA-GGAAATCTGAGCTTAGGAAGGTTAGT
** *
29110174 TGCATCTTTGAAATTTGTGGTAAAGGTTGGGTGGAATTTTGAGTGGAATCTAATTTTTGTGTAGG
230 TGCATCTTTGAAATTTGTGGTAAAGGTTGGGTGGAATTTTGAGTGGAATCTGGTTTTTGTGTGGG
*
29110239 TTGATTTGAATAGGTTTAAGAGAGTGGTTTTCTTTTCTTAGGATAGATGACATAATAGTCAAACT
295 TTGATTTGAATAGGTTTAAGAGAGTGGTTTTCTTTTCTTAGGATAGATGACATAGTAGTCAAACT
* * *
29110304 TTCTTGAGGGTTTACTAAGGAGATCAACTTCAGGGTTTTCATTCTCATATCTTTCTTTAAGCTTT
360 TTCTTGAGGGTTTACTAAGGAGATCAACTTCAGGGTCTCCATTCTCATATCTTTCTTTGAGCTTT
*
29110369 TACTGGGAAGACTTTTTCTTCTTTTGCTTCTTTGAAACATCATCATCATCATCCAAGAAGCTTTT
425 TGCTGGGAAGACTTTTTCTTCTTTTGCTTCTTTGAAACATCATCATCATCATCCAAGAAGCTTTT
*
29110434 ATTTGCGTCTAACTAGCTTTCTTTGCATTGACAATTTATGTCCCAATAACAATGTCCTTGTGGAG
490 ATTTGCGTCTAACTAGCATTCTTTGCATTGACAATTTATGTCCCAATAACAATGTCCTTGTGGAG
* *
29110499 ATCTATATGCATACACGGGATTTTCATTAGACTGAAAGTATATGACTAGAACATCAAAGA
555 ATCTATATGCATACACGGGATTTTCATTAGACTGAAAGTGTATGACTAGAACATCAAGGA
29110559 GATCA
1 GATCA
29110564 GCATTATTTT
Statistics
Matches: 1157, Mismatches: 72, Indels: 40
0.91 0.06 0.03
Matches are distributed among these distances:
614 199 0.17
615 380 0.33
616 2 0.00
622 2 0.00
623 1 0.00
629 2 0.00
630 1 0.00
640 3 0.00
644 400 0.35
645 167 0.14
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (614 bp):
GATCAAAGTGTTGACTGACTTGGCCCAACTTATGTTCAATTCTGTGCAGGTATGAATTCTACTGG
AGAGAATTTTTAGTTTGCCAGTTTAAAACTGCTTCAGCATGAGAAATAATTTTTTGGTTCCCATA
TTCATCTCTGTCAGTAGGAGTGGGGATTTTTGGAATGTGTTTGTACTGGTCTTTATGAAACTCTT
AAAAAAGAGGAAATCTGAGCTTAGGAAGGTTAGTTGCATCTTTGAAATTTGTGGTAAAGGTTGGG
TGGAATTTTGAGTGGAATCTGGTTTTTGTGTGGGTTGATTTGAATAGGTTTAAGAGAGTGGTTTT
CTTTTCTTAGGATAGATGACATAGTAGTCAAACTTTCTTGAGGGTTTACTAAGGAGATCAACTTC
AGGGTCTCCATTCTCATATCTTTCTTTGAGCTTTTGCTGGGAAGACTTTTTCTTCTTTTGCTTCT
TTGAAACATCATCATCATCATCCAAGAAGCTTTTATTTGCGTCTAACTAGCATTCTTTGCATTGA
CAATTTATGTCCCAATAACAATGTCCTTGTGGAGATCTATATGCATACACGGGATTTTCATTAGA
CTGAAAGTGTATGACTAGAACATCAAGGA
Found at i:29109925 original size:30 final size:30
Alignment explanation
Indices: 29109889--29109955 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
29109879 CATTAGACTG
29109889 AAAGTGTATGACTAAAACATCAAGGAGATC
1 AAAGTGTATGACTAAAACATCAAGGAGATC
29109919 AAAGTGTATGACTAAAACATCAAGGAGATC
1 AAAGTGTATGACTAAAACATCAAGGAGATC
29109949 AAAGTGT
1 AAAGTGT
29109956 TGATTGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (30 bp):
AAAGTGTATGACTAAAACATCAAGGAGATC
Found at i:29112516 original size:8 final size:8
Alignment explanation
Indices: 29112503--29112556 Score: 72
Period size: 8 Copynumber: 6.8 Consensus size: 8
29112493 CTTAGATTTA
*
29112503 TAGATTAC
1 TAGATTCC
*
29112511 TTGATTCC
1 TAGATTCC
29112519 TAGATTCC
1 TAGATTCC
*
29112527 TAGATTAC
1 TAGATTCC
*
29112535 TTGATTCC
1 TAGATTCC
29112543 TAGATTCC
1 TAGATTCC
29112551 TAGATT
1 TAGATT
29112557 ATTTGATTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (8 bp):
TAGATTCC
Found at i:29112522 original size:16 final size:16
Alignment explanation
Indices: 29112503--29112571 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 16
29112493 CTTAGATTTA
*
29112503 TAGATTACTTGATTCC
1 TAGATTACTAGATTCC
* *
29112519 TAGATTCCTAGATTAC
1 TAGATTACTAGATTCC
* *
29112535 TTGATTCCTAGATTCC
1 TAGATTACTAGATTCC
* *
29112551 TAGATTATTTGATTCC
1 TAGATTACTAGATTCC
*
29112567 CAGAT
1 TAGAT
29112572 GATTTTTTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TAGATTACTAGATTCC
Found at i:29112522 original size:24 final size:24
Alignment explanation
Indices: 29112503--29112571 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
29112493 CTTAGATTTA
29112503 TAGATTACTTGATTCCTAGATTCC
1 TAGATTACTTGATTCCTAGATTCC
29112527 TAGATTACTTGATTCCTAGATTCC
1 TAGATTACTTGATTCCTAGATTCC
* *
29112551 TAGATTATTTGATTCCCAGAT
1 TAGATTACTTGATTCCTAGAT
29112572 GATTTTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (24 bp):
TAGATTACTTGATTCCTAGATTCC
Found at i:29118826 original size:13 final size:13
Alignment explanation
Indices: 29118808--29118833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29118798 CTATGGTACA
29118808 ATGACTCATCACT
1 ATGACTCATCACT
29118821 ATGACTCATCACT
1 ATGACTCATCACT
29118834 TTTTTGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
ATGACTCATCACT
Found at i:29122385 original size:2 final size:2
Alignment explanation
Indices: 29122380--29122421 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
29122370 TGTGTGTCAC
29122380 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29122422 GGATACCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.