Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 78 of 143
Found at i:25052368 original size:20 final size:21
Alignment explanation
Indices: 25052343--25052384 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
25052333 TTTAAAAATA
25052343 AAAAAT-TAAAAAAATCATTT
1 AAAAATATAAAAAAATCATTT
*
25052363 AAAAATATAAAAAAATTATTT
1 AAAAATATAAAAAAATCATTT
25052384 A
1 A
25052385 CTCCTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATATAAAAAAATCATTT
Found at i:25053086 original size:24 final size:24
Alignment explanation
Indices: 25053038--25053086 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
25053028 TACACATGAA
* **
25053038 ATTTGAATTGTGGTTCGTATGTAT
1 ATTTGAATAGTGGTTCAAATGTAT
*
25053062 ATTTGAATAGTGGTTCAAATTTAT
1 ATTTGAATAGTGGTTCAAATGTAT
25053086 A
1 A
25053087 AATGGATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (24 bp):
ATTTGAATAGTGGTTCAAATGTAT
Found at i:25055954 original size:44 final size:44
Alignment explanation
Indices: 25055904--25055993 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
25055894 GATATATGAT
25055904 TTGGATGCTAAAATCCCACTCCTATCAAAGCTAATCCTACGAGA
1 TTGGATGCTAAAATCCCACTCCTATCAAAGCTAATCCTACGAGA
25055948 TTGGATGCTAAAATCCCACTCCTATCAAAGCTAATCCTACGAGA
1 TTGGATGCTAAAATCCCACTCCTATCAAAGCTAATCCTACGAGA
25055992 TT
1 TT
25055994 TGTTTTGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (44 bp):
TTGGATGCTAAAATCCCACTCCTATCAAAGCTAATCCTACGAGA
Found at i:25059348 original size:13 final size:13
Alignment explanation
Indices: 25059330--25059401 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
25059320 TACTTTAGCC
*
25059330 ATTTTTTATTTTT
1 ATTTTTTATTTTA
*
25059343 ATTTTTTACTATTTGC
1 ATTTTTTA-T-TTT-A
*
25059359 A-TTTTTAATTTA
1 ATTTTTTATTTTA
25059371 ATTTTTATATTTTA
1 ATTTTT-TATTTTA
* *
25059385 ATTTTTTCTTTTT
1 ATTTTTTATTTTA
25059398 ATTT
1 ATTT
25059402 GCTTCTGGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 24 0.50
14 13 0.27
15 9 0.19
16 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (13 bp):
ATTTTTTATTTTA
Found at i:25059398 original size:14 final size:14
Alignment explanation
Indices: 25059332--25059390 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
25059322 CTTTAGCCAT
*
25059332 TTTTTAT-TTTTAT
1 TTTTTATATTTTAA
**
25059345 TTTTTACTATTTGCA
1 TTTTTA-TATTTTAA
25059360 TTTTTA-A-TTTAA
1 TTTTTATATTTTAA
25059372 TTTTTATATTTTAA
1 TTTTTATATTTTAA
25059386 TTTTT
1 TTTTT
25059391 TCTTTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 9 0.24
13 8 0.22
14 11 0.30
15 9 0.24
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:25062226 original size:26 final size:25
Alignment explanation
Indices: 25062197--25062246 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
25062187 GTATAAAATA
*
25062197 TTAACAATTTAAAATAAATTAAAAAG
1 TTAACAAATT-AAATAAATTAAAAAG
*
25062223 TTAATAAATTAAATAAATTAAAAA
1 TTAACAAATTAAATAAATTAAAAA
25062247 ATAAGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
TTAACAAATTAAATAAATTAAAAAG
Found at i:25062239 original size:9 final size:9
Alignment explanation
Indices: 25062208--25062248 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
25062198 TAACAATTTA
25062208 AAATAAATT
1 AAATAAATT
*
25062217 AAA-AAGTT
1 AAATAAATT
25062225 -AATAAATT
1 AAATAAATT
25062233 AAATAAATT
1 AAATAAATT
25062242 AAA-AAAT
1 AAATAAAT
25062249 AAGAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 2 0.07
8 12 0.43
9 14 0.50
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAATAAATT
Found at i:25062991 original size:15 final size:14
Alignment explanation
Indices: 25062969--25063004 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
25062959 AAATTTTGAA
25062969 AAATAAAAATAAAT
1 AAATAAAAATAAAT
25062983 AACATAAAAATAAAT
1 AA-ATAAAAATAAAT
25062998 AAATAAA
1 AAATAAA
25063005 TGAAAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:25063010 original size:19 final size:21
Alignment explanation
Indices: 25062965--25063010 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
25062955 TATCAAATTT
25062965 TGAAAAATAAAAATAAATAACA
1 TGAAAAAT-AAAATAAATAACA
25062987 T-AAAAAT-AAATAAATAA-A
1 TGAAAAATAAAATAAATAACA
25063005 TGAAAA
1 TGAAAA
25063011 CTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
21 6 0.26
22 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
TGAAAAATAAAATAAATAACA
Found at i:25083152 original size:6 final size:6
Alignment explanation
Indices: 25083141--25083282 Score: 53
Period size: 6 Copynumber: 22.8 Consensus size: 6
25083131 TTCCCATTTC
*
25083141 TTTATT TTTA-T TTTA-T TTTATT ATTTATC TTTA-T TTTATT ATTTA-T
1 TTTATT TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT -TTTATT
* * * * *
25083187 TTTA-T TTAATT ATTTATT TAATT-TCA TTTATG TTGATT TTATTTT TATTACTT
1 TTTATT TTTATT -TTTATT T--TTAT-T TTTATT TTTATT TT-TATT T-TTA-TT
* * * *
25083240 TTTAGTAT TTTGTT ATTATT ATTATT ATTATT TTTATT TTTAT
1 TTTA-T-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
25083283 ATACTTCTGT
Statistics
Matches: 106, Mismatches: 16, Indels: 28
0.71 0.11 0.19
Matches are distributed among these distances:
5 22 0.21
6 48 0.45
7 25 0.24
8 11 0.10
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:25083167 original size:17 final size:17
Alignment explanation
Indices: 25083141--25083279 Score: 124
Period size: 18 Copynumber: 7.9 Consensus size: 17
25083131 TTCCCATTTC
25083141 TTTATT-TTTATTTTAT
1 TTTATTATTTATTTTAT
25083157 TTTATTATTTATCTTTAT
1 TTTATTATTTAT-TTTAT
25083175 TTTATTATTTATTTTAT
1 TTTATTATTTATTTTAT
* *
25083192 TTAATTATTTATTTAAT
1 TTTATTATTTATTTTAT
*
25083209 TTCATTTATGTTGATTTTATT
1 TTTA-TTAT-TT-ATTTTA-T
*
25083230 TTTATTACTTT-TTAGTAT
1 TTTATTA-TTTATT-TTAT
*
25083248 TTTGTTA-TTATTATTAT
1 TTTATTATTTATT-TTAT
25083265 TATTATT-TTTATTTT
1 T-TTATTATTTATTTT
25083280 TATATACTTC
Statistics
Matches: 103, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.08
17 37 0.36
18 39 0.38
19 4 0.04
20 10 0.10
21 5 0.05
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTATTATTTATTTTAT
Found at i:25083191 original size:23 final size:23
Alignment explanation
Indices: 25083141--25083188 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25083131 TTCCCATTTC
* *
25083141 TTTATTTTTATTTTATTTTATTA
1 TTTATCTTTATTTTATTATATTA
25083164 TTTATCTTTATTTTATTAT-TTA
1 TTTATCTTTATTTTATTATATTA
25083186 TTT
1 TTT
25083189 TATTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATCTTTATTTTATTATATTA
Found at i:25093422 original size:24 final size:24
Alignment explanation
Indices: 25093384--25093430 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
25093374 TTGGTTGATG
* *
25093384 GATAAAAAGAGGAAGAGGCACAAA
1 GATAAAAAGAAGAAGAAGCACAAA
*
25093408 GATAAAAGGAAGAAGAAGCACAA
1 GATAAAAAGAAGAAGAAGCACAA
25093431 GGAAGAGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.28, T:0.04
Consensus pattern (24 bp):
GATAAAAAGAAGAAGAAGCACAAA
Found at i:25094172 original size:12 final size:13
Alignment explanation
Indices: 25094154--25094222 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 13
25094144 TCAGTCACTT
25094154 GAAAAAG-GAAAA
1 GAAAAAGAGAAAA
*
25094166 TAAAAAGA-AAGAA
1 GAAAAAGAGAA-AA
*
25094179 AAAAAAGAGAAAA
1 GAAAAAGAGAAAA
25094192 GAGAAAAGAGAAAA
1 GA-AAAAGAGAAAA
*
25094206 G-AAAAGA-AGAA
1 GAAAAAGAGAAAA
25094217 GAAAAA
1 GAAAAA
25094223 TATTGCTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
11 4 0.08
12 18 0.38
13 12 0.25
14 14 0.29
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (13 bp):
GAAAAAGAGAAAA
Found at i:25094193 original size:7 final size:7
Alignment explanation
Indices: 25094181--25094221 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
25094171 AGAAAGAAAA
25094181 AAAAGAG
1 AAAAGAG
25094188 AAAAGAG
1 AAAAGAG
25094195 AAAAGAG
1 AAAAGAG
*
25094202 AAAAGAA
1 AAAAGAG
25094209 AAGAAGAAG
1 AA-AAG-AG
25094218 AAAA
1 AAAA
25094222 ATATTGCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 22 0.73
8 5 0.17
9 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:25094198 original size:14 final size:14
Alignment explanation
Indices: 25094155--25094221 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
25094145 CAGTCACTTG
*
25094155 AAAAAG-GAAAA-T
1 AAAAAGAGAAAAGA
25094167 AAAAAGA-AAGAA-A
1 AAAAAGAGAA-AAGA
25094180 AAAAAGAGAAAAGA
1 AAAAAGAGAAAAGA
*
25094194 GAAAAGAGAAAAGA
1 AAAAAGAGAAAAGA
25094208 AAAGAAGAAGAAAA
1 AAA-AAG-AGAAAA
25094222 ATATTGCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 8 0.17
13 11 0.24
14 18 0.39
15 3 0.07
16 6 0.13
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (14 bp):
AAAAAGAGAAAAGA
Found at i:25097146 original size:16 final size:18
Alignment explanation
Indices: 25097123--25097170 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
25097113 CTCCATTAGA
*
25097123 GTGAATTTTTGTT-ATTT
1 GTGAATTTTTATTGATTT
25097140 G-GAATTTTTATTGATTT
1 GTGAATTTTTATTGATTT
25097157 GTGAATCTTTTATT
1 GTGAAT-TTTTATT
25097171 TATTGGGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 6 0.22
18 4 0.15
19 7 0.26
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (18 bp):
GTGAATTTTTATTGATTT
Found at i:25097722 original size:18 final size:18
Alignment explanation
Indices: 25097701--25097747 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
25097691 AAGAAAAGTC
**
25097701 AAAAAGAAAAATTGCAAA
1 AAAAAGAAAAATTAAAAA
25097719 AAAAAGACAAAATTAAAAA
1 AAAAAGA-AAAATTAAAAA
25097738 AAAAAGAAAA
1 AAAAAGAAAA
25097748 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAAATTAAAAA
Found at i:25098894 original size:20 final size:20
Alignment explanation
Indices: 25098869--25098912 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
25098859 ATATTGATTA
25098869 TAAATAG-GATTAATTAAGGT
1 TAAATAGAGATTAATTAA-GT
25098889 TAAATAGATGATTAATTAAGT
1 TAAATAGA-GATTAATTAAGT
25098910 TAA
1 TAA
25098913 TCATGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 5 0.23
22 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
TAAATAGAGATTAATTAAGT
Found at i:25115071 original size:32 final size:36
Alignment explanation
Indices: 25115022--25115100 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 36
25115012 GCGTGATCAG
25115022 TAAAGATT-TTAAAATTATTA-A-T-TTTTT-AAATA
1 TAAA-ATTATTAAAATTATTATATTATTTTTGAAATA
25115054 TAAAATTATTAAAATTATTATATTATTTTTGAAATA
1 TAAAATTATTAAAATTATTATATTATTTTTGAAATA
25115090 TAAAATTATTA
1 TAAAATTATTA
25115101 TATTATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
31 3 0.07
32 16 0.38
33 1 0.02
34 1 0.02
35 5 0.12
36 16 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (36 bp):
TAAAATTATTAAAATTATTATATTATTTTTGAAATA
Found at i:25122666 original size:13 final size:13
Alignment explanation
Indices: 25122650--25122674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25122640 ATTTATAAAT
25122650 TTATTTTATTTTA
1 TTATTTTATTTTA
25122663 TTATTTTATTTT
1 TTATTTTATTTT
25122675 GGGATTTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:25133262 original size:2 final size:2
Alignment explanation
Indices: 25133255--25133292 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25133245 CATATGCAAC
25133255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25133293 TGCGTCTAAA
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):
AT
Found at i:25146080 original size:2 final size:2
Alignment explanation
Indices: 25146073--25146109 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25146063 AATGAAATTA
25146073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25146110 AAATAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25153534 original size:15 final size:16
Alignment explanation
Indices: 25153510--25153542 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25153500 TATAAGCTCC
25153510 CATAAACATTT-CAAG
1 CATAAACATTTACAAG
*
25153525 CATAATCATTTACAAG
1 CATAAACATTTACAAG
25153541 CA
1 CA
25153543 CATTTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (16 bp):
CATAAACATTTACAAG
Found at i:25153696 original size:50 final size:50
Alignment explanation
Indices: 25153630--25153839 Score: 204
Period size: 50 Copynumber: 4.2 Consensus size: 50
25153620 ATGTATTTCT
* * * * * *
25153630 GCTCACCAGCTTGCACATGTTCACGCTCTTCAACTTATTTATGCGTTTAC
1 GCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTAATTATGCGTTTAC
* * * * * *
25153680 GCTCGTCAACTTGCACACTTTTACCCTCGTCAGCTTAATTACGCGTTTAT
1 GCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTAATTATGCGTTTAC
* * * * ** *
25153730 GCTAGCCAGCTTGCATACGTTTACACTCGTCTGCTTATTTATGCGTTTAC
1 GCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTAATTATGCGTTTAC
* * * * *
25153780 TCTTGCCAGCTTGCACACATTTACGCTTGTCAACTTAATTATGCGTTTAC
1 GCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTAATTATGCGTTTAC
25153830 GCTCGCCAAC
1 GCTCGCCAAC
25153840 GTAATTATGC
Statistics
Matches: 126, Mismatches: 34, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 126 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (50 bp):
GCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTAATTATGCGTTTAC
Found at i:25153828 original size:26 final size:26
Alignment explanation
Indices: 25153799--25153854 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
25153789 CTTGCACACA
* * *
25153799 TTTACGCTTGTCAACTTAATTATGCG
1 TTTACGCTCGCCAACGTAATTATGCG
25153825 TTTACGCTCGCCAACGTAATTATGCG
1 TTTACGCTCGCCAACGTAATTATGCG
25153851 TTTA
1 TTTA
25153855 TTCAAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (26 bp):
TTTACGCTCGCCAACGTAATTATGCG
Found at i:25160536 original size:26 final size:26
Alignment explanation
Indices: 25160507--25160566 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
25160497 CTTAAGATAC
*
25160507 ACAAAACTTAGGTAAAACCAAATTAT
1 ACAAAACATAGGTAAAACCAAATTAT
25160533 ACAAAACATAGGTAAAACCAAATTAT
1 ACAAAACATAGGTAAAACCAAATTAT
25160559 ACAAAACA
1 ACAAAACA
25160567 AGACCACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.58, C:0.17, G:0.07, T:0.18
Consensus pattern (26 bp):
ACAAAACATAGGTAAAACCAAATTAT
Found at i:25160822 original size:94 final size:94
Alignment explanation
Indices: 25160656--25160845 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
25160646 TCTGACAGTC
*
25160656 CAACCGGAAAGGAGTTCAAAAGATTAAAATCTACAACACAAAAAAGTTTAGGTAAGAAATACAAA
1 CAACCGGAAAAGAGTTCAAAAGATTAAAATCTACAACACAAAAAAGTTTAGGTAAGAAATACAAA
25160721 CATGAAACACACCTCCAATGAATTACTTG
66 CATGAAACACACCTCCAATGAATTACTTG
*
25160750 CAACTGGAAAAGAGTTCAAAAGATTAAAATCTACAACACAAAAAAGTTTAGGTAAGAAATACAAA
1 CAACCGGAAAAGAGTTCAAAAGATTAAAATCTACAACACAAAAAAGTTTAGGTAAGAAATACAAA
25160815 CATGAAACACACCTCCAATGAATTACTTG
66 CATGAAACACACCTCCAATGAATTACTTG
25160844 CA
1 CA
25160846 TCTCATTTAT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (94 bp):
CAACCGGAAAAGAGTTCAAAAGATTAAAATCTACAACACAAAAAAGTTTAGGTAAGAAATACAAA
CATGAAACACACCTCCAATGAATTACTTG
Found at i:25161016 original size:24 final size:24
Alignment explanation
Indices: 25160989--25161118 Score: 107
Period size: 24 Copynumber: 5.2 Consensus size: 24
25160979 TTACGCTTAC
*
25160989 CAGCTTGCACACATTTACGCTCGT
1 CAGCTTGCACACGTTTACGCTCGT
** ** *
25161013 CAGCTTATTTATGCGTTTACGCTCGC
1 CAGC-T-TGCACACGTTTACGCTCGT
*
25161039 CAGCTAGCACACGTTTACGCTCGT
1 CAGCTTGCACACGTTTACGCTCGT
** ** * *
25161063 CAGCTTATTTATGCGTTTACACTCGC
1 CAGC-T-TGCACACGTTTACGCTCGT
25161089 CAGCTTGCACACGTTTACGCTCGT
1 CAGCTTGCACACGTTTACGCTCGT
25161113 CAGCTT
1 CAGCTT
25161119 AATTATGCTT
Statistics
Matches: 77, Mismatches: 25, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
24 40 0.52
25 4 0.05
26 33 0.43
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.32
Consensus pattern (24 bp):
CAGCTTGCACACGTTTACGCTCGT
Found at i:25161033 original size:26 final size:26
Alignment explanation
Indices: 25161002--25161131 Score: 115
Period size: 26 Copynumber: 5.2 Consensus size: 26
25160992 CTTGCACACA
25161002 TTTACGCTCGTCAGCTTATTTATGCG
1 TTTACGCTCGTCAGCTTATTTATGCG
* ** **
25161028 TTTACGCTCGCCAGC-TA-GCACACG
1 TTTACGCTCGTCAGCTTATTTATGCG
25161052 TTTACGCTCGTCAGCTTATTTATGCG
1 TTTACGCTCGTCAGCTTATTTATGCG
* * ** **
25161078 TTTACACTCGCCAGC-T-TGCACACG
1 TTTACGCTCGTCAGCTTATTTATGCG
* *
25161102 TTTACGCTCGTCAGCTTAATTATGCT
1 TTTACGCTCGTCAGCTTATTTATGCG
25161128 TTTA
1 TTTA
25161132 TTCAAGATTT
Statistics
Matches: 76, Mismatches: 24, Indels: 8
0.70 0.22 0.07
Matches are distributed among these distances:
24 34 0.45
25 6 0.08
26 36 0.47
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (26 bp):
TTTACGCTCGTCAGCTTATTTATGCG
Found at i:25161049 original size:50 final size:50
Alignment explanation
Indices: 25160973--25161131 Score: 255
Period size: 50 Copynumber: 3.2 Consensus size: 50
25160963 ATTCATAATA
** *
25160973 ATGCGTTTACGCTTACCAGCTTGCACACATTTACGCTCGTCAGCTTATTT
1 ATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTT
*
25161023 ATGCGTTTACGCTCGCCAGCTAGCACACGTTTACGCTCGTCAGCTTATTT
1 ATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTT
* *
25161073 ATGCGTTTACACTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAATT
1 ATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTT
*
25161123 ATGCTTTTA
1 ATGCGTTTA
25161132 TTCAAGATTT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 101 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (50 bp):
ATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTT
Found at i:25164547 original size:101 final size:101
Alignment explanation
Indices: 25164354--25166121 Score: 1542
Period size: 101 Copynumber: 17.6 Consensus size: 101
25164344 CATAAGATTT
* * ** * * * * *
25164354 TGAAGCTACCACACCAAATCCTATATCTTTCAAGTTGCAGTGGATTGGATTAAAACTATAGTAGT
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * * *
25164419 AAATCTCAATCTCCCTGAAGTTACAATGTAATAGAG
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * * * * *
25164455 TAAAGTTACAACACCTAATTCTATATCCCTAAAGTTGTAATGGATTGGATTAAAACTATAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * * *
25164520 ATATCTCTATCTCCCT-AGAGTTTCAATGGAATGAAA
66 AGATCTCAATCTCCCTGA-AGTTTCAGTGGAATGGAG
* * *
25164556 TGAAGTTACAACAACAAATCCTATATCCATGAAGTTGTAGTGGATCGGGTTAAAACTACAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * * *
25164621 AGATCTCAATCTCTCTGAAGTTACAGTAGACTAGAG
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
** * * * * *
25164657 TGAAGTTACAACATGAAATCCAATATCGCTAAAGTTGCAGTGGATTGGATTAAAACTACAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* *
25164722 -GAATCTCAATCTCCCTAAAGTTACAGTGGAATGGAG
66 AG-ATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * * * * * * * *
25164758 TGAAGCTAGAACACCAAATCCTATAACCCTAAAGTTGTACTTGATCGAATTAAAACAACAGCAAC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
*
25164823 TGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * * * *
25164859 AGAAGCT-CGAACACCAAATCCTTTATACCTAAAGTTGTAGTGGATCGGATTAAAACTACAGTAA
1 TGAAGTTAC-AACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAG
* * * *
25164923 CAGATCTCAATCTCCCTAAAGTTGCAATTGAATGGAG
65 CAGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * ** * * * * * * ** *
25164960 TGAAGCTATAACGCCAAATAATATATCCTTGAAGTTGTAATAGAAT-GGAGTGAAATTACAACAC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGT-GGATCGGATTAAAACTACAGTAG
* * * * * * *
25165024 CA-AACCCTATATCCCTGAAGTTGCAGTGG-ATCAGAT
65 CAGATCTCAATCTCCCTGAAGTTTCAGTGGAAT-GGAG
* ** ** * * * * * * *
25165060 TAAAACTACAGTAGCAAATCTCAATCTCCCTAAAGTTGTAGTGAATCAGATTAAAACTATAGTAG
1 TGAAGTTACAACACCAAATC-CTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAG
* * * *
25165125 CAGATCTAAATCTTCTTGAAGTTGT-AGCGGAATGGAG
65 CAGATCTCAATCTCCCTGAAGTT-TCAGTGGAATGGAG
* * * * * *
25165162 TGAAGTTATAACACTAAATCCTATATCCTTGAAGTTGTAGTGGATCGAATTAAAACTACAATAAC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
** *
25165227 AGATCTCAATCTCCCTGAAGTTAAAGTGGAACGGAG
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * * * *
25165263 TGAAATTACAACACCAAATCCTATATCCCTAAAGTTATAGTGGATTGGATTAAAACCACAGTAAC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * **
25165328 ATATCTCAATCTCCTTGAAGTTGT-AATGGAATAAAG
66 AGATCTCAATCTCCCTGAAGTT-TCAGTGGAATGGAG
* * ** * **
25165364 TGAAGTTACAACACCAAGTCCTATATCCCTTAAGTTACAATGGATCATATTAAAACTACAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* ** * *
25165429 A-ATCTCAATTTGTCTGAAGTTAT-AGAGGAGTGGAG
66 AGATCTCAATCTCCCTGAAGTT-TCAGTGGAATGGAG
* * * *
25165464 TGAAGTTATAACACCAAATCCTATATCCTTGAAGTTGCAGTGGATTGGATTAAAACTACAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* **
25165529 ATATCTCAATCTCTTTGAAGTTGT-AGTGGAATGGAG
66 AGATCTCAATCTCCCTGAAGTT-TCAGTGGAATGGAG
* * * *
25165565 TGAAGTTACAACACTAAATCCTATATCCCTGAAGTTGCAATGGATCGAATTAAAACTACAGTAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* *
25165630 GGATCTCAATCACCCTGAAGTTGT-AGTGGAATGGAG
66 AGATCTCAATCTCCCTGAAGTT-TCAGTGGAATGGAG
* * * *
25165666 TGAAGTTACAATACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGGATTAAAACTACAATAAC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * *
25165731 AGATCTTAATCTCCTTGAAG--T---TGCAATGGAA
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * * * ** * * *
25165762 TGAAGTTACAACACCAAATCCTATAACTCTAAAATTATAAAGGATCAGATTAAGACTACAATAGC
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * *
25165827 -GAATCTCAATCTCCCTAAAGTTGCAGTGGAATAGAG
66 AG-ATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * ** *
25165863 TGAAGCTACAACACCAAATCCTATTTCTCC-GAAGTTACAGTGGATTGGATTAAAACTACAGTAG
1 TGAAGTTACAACACCAAATCCTATATC-CCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAG
* * *
25165927 CAAATCTCAATCTCCTTGAAGTTGCAGTGGAATGGAG
65 CAGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * ** * *** * *
25165964 TAAAGTTACCACACCAAATCCTATATGACTGAAGTTGCAGTGGATTTTATTAAAACTACAATAGT
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
* * * *
25166029 AGATCTTAATCTTCCTGAAGTTGCAGTGTAATGGAG
66 AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
* * * *
25166065 TGAAGCTACAACACCAAATCCTATATCCTTGAAGTTGCAG-GGATCAGATTAAAACTA
1 TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTA
25166122 AAAGTTGTAA
Statistics
Matches: 1339, Mismatches: 303, Indels: 51
0.79 0.18 0.03
Matches are distributed among these distances:
95 1 0.00
96 76 0.06
98 1 0.00
99 2 0.00
100 136 0.10
101 1084 0.81
102 37 0.03
103 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (101 bp):
TGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTAAAACTACAGTAGC
AGATCTCAATCTCCCTGAAGTTTCAGTGGAATGGAG
Found at i:25165027 original size:50 final size:50
Alignment explanation
Indices: 25164935--25165048 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
25164925 GATCTCAATC
* * * * * *
25164935 TCCCTAAAGTTGCAATTGAATGGAGTGAAGCTATAACGCCAAATAATATA
1 TCCCTGAAGTTGCAATAGAATGGAGTGAAACTACAACACCAAACAATATA
* * * **
25164985 TCCTTGAAGTTGTAATAGAATGGAGTGAAATTACAACACCAAACCCTATA
1 TCCCTGAAGTTGCAATAGAATGGAGTGAAACTACAACACCAAACAATATA
25165035 TCCCTGAAGTTGCA
1 TCCCTGAAGTTGCA
25165049 GTGGATCAGA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (50 bp):
TCCCTGAAGTTGCAATAGAATGGAGTGAAACTACAACACCAAACAATATA
Found at i:25165255 original size:51 final size:51
Alignment explanation
Indices: 25165035--25165752 Score: 222
Period size: 51 Copynumber: 14.2 Consensus size: 51
25165025 AAACCCTATA
** * * *
25165035 TCCCTGAAGTTGCAGTGGATCAGATTAAAACTACAGTAGCAAATCTCAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * * * * * * *
25165086 TCCCTAAAGTTGTAGTGAATCAGATTAAAACTATAGTAGCAGATCTAAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * * * * ** * * * *
25165137 TTCTTGAAGTTGTAGCGGAAT-GGAGTGAAGTTATAA-CACTAAATC-CTATA
1 TCCCTGAAGTTATAGTGG-ATCGGATTAAAACTACAATAAC-AAATCTCAATC
* * * *
25165187 TCCTTGAAGTTGTAGTGGATCGAATTAAAACTACAATAACAGATCTCAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * * * * * * *
25165238 TCCCTGAAGTTAAAGTGGAACGGAGTGAAATTACAACACCAAATC-CTATA
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * * *
25165288 TCCCTAAAGTTATAGTGGATTGGATTAAAACCACAGTAACATATCTCAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * ** * * ** * * * * *
25165339 TCCTTGAAGTTGTAATGGAAT-AAAGTGAAGTTACAACACCAAGTC-CTATA
1 TCCCTGAAGTTATAGTGG-ATCGGATTAAAACTACAATAACAAATCTCAATC
* * * ** * * *
25165389 TCCCTTAAGTTACAATGGATCATATTAAAACTACAGTAGC-AATCTCAATT
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
** * * * ** * * * * *
25165439 TGTCTGAAGTTATAGAGGAGT-GGAGTGAAGTTATAACACCAAATC-CTATA
1 TCCCTGAAGTTATAGTGGA-TCGGATTAAAACTACAATAACAAATCTCAATC
* ** * * * *
25165489 TCCTTGAAGTTGCAGTGGATTGGATTAAAACTACAGTAGCATATCTCAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
** * * * ** * * *
25165540 TCTTTGAAGTTGTAGTGGAAT-GGAGTGAAGTTACAA-CACTAAATC-CTATA
1 TCCCTGAAGTTATAGTGG-ATCGGATTAAAACTACAATAAC-AAATCTCAATC
** * * * * **
25165590 TCCCTGAAGTTGCAATGGATCGAATTAAAACTACAGTAGCGGATCTCAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
* * * * ** * * *
25165641 ACCCTGAAGTTGTAGTGGAAT-GGAGTGAAGTTACAATACCAAATC-CTATA
1 TCCCTGAAGTTATAGTGG-ATCGGATTAAAACTACAATAACAAATCTCAATC
** * *
25165691 TCCCTGAAGTTGCAGTGGATCGGATTAAAACTACAATAACAGATCTTAATC
1 TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
*
25165742 TCCTTGAAGTT
1 TCCCTGAAGTT
25165753 GCAATGGAAT
Statistics
Matches: 462, Mismatches: 184, Indels: 42
0.67 0.27 0.06
Matches are distributed among these distances:
49 12 0.03
50 219 0.47
51 223 0.48
52 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (51 bp):
TCCCTGAAGTTATAGTGGATCGGATTAAAACTACAATAACAAATCTCAATC
Found at i:25166783 original size:10 final size:10
Alignment explanation
Indices: 25166768--25166798 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25166758 AAAAAGGCAG
*
25166768 AGAAAAAGAA
1 AGAAAAAAAA
25166778 AGAAAAAAAA
1 AGAAAAAAAA
25166788 AGAAAAAAAA
1 AGAAAAAAAA
25166798 A
1 A
25166799 TATTGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:25167840 original size:30 final size:26
Alignment explanation
Indices: 25167791--25167888 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 26
25167781 TTAATCCCTG
25167791 TATTTTTTTATTTTAATTTAGCTCCTT
1 TATTTTTTTATTTTAATTTAG-TCCTT
*
25167818 TATTTTTTTAGTTTTGTAATTTA-TACTT
1 TATTTTTTTA--TTT-TAATTTAGTCCTT
*
25167846 TATATTTATTTAAGTTTCAATTTAGTCCTTT
1 TAT-TTT-TTT-A-TTTTAATTTAGTCC-TT
*
25167877 TCTTTTTTTATT
1 TATTTTTTTATT
25167889 ATTTATTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
27 12 0.21
28 8 0.14
29 15 0.26
30 18 0.31
31 5 0.09
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.66
Consensus pattern (26 bp):
TATTTTTTTATTTTAATTTAGTCCTT
Found at i:25167846 original size:28 final size:28
Alignment explanation
Indices: 25167791--25167862 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 28
25167781 TTAATCCCTG
*
25167791 TATTTTTTTA--TTTTAATTTAGCTCCTT
1 TATTTTTTTAGTTTTTAATTTA-CTACTT
25167818 TATTTTTTTAGTTTTGTAATTTA-TACTT
1 TATTTTTTTAGTTTT-TAATTTACTACTT
25167846 TATATTTATTTAAGTTT
1 TAT-TTT-TTT-AGTTT
25167863 CAATTTAGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 10 0.26
28 7 0.18
29 6 0.16
30 10 0.26
31 5 0.13
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (28 bp):
TATTTTTTTAGTTTTTAATTTACTACTT
Found at i:25168006 original size:15 final size:15
Alignment explanation
Indices: 25167973--25168022 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
25167963 CCTTTGCATA
25167973 TTTATTTATTTATTTTT
1 TTTATTT-TTTA-TTTT
25167990 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
* *
25168005 TTTGTTATTTATTTT
1 TTTATTTTTTATTTT
25168020 TTT
1 TTT
25168023 TAATTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 20 0.65
16 4 0.13
17 7 0.23
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:25168012 original size:11 final size:11
Alignment explanation
Indices: 25167971--25168021 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
25167961 AGCCTTTGCA
25167971 TATTTATTTATT
1 TATTT-TTTATT
25167983 TA-TTTTT-TT
1 TATTTTTTATT
25167992 TATTTTTTATT
1 TATTTTTTATT
25168003 T-TTTTGTTATT
1 TATTTT-TTATT
25168014 TATTTTTT
1 TATTTTTT
25168022 TTAATTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.11
10 12 0.34
11 13 0.37
12 6 0.17
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:25168235 original size:11 final size:11
Alignment explanation
Indices: 25168214--25168272 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
25168204 CCATTACTAC
25168214 TATTCTTATTAT
1 TATT-TTATTAT
25168226 TATTTTATTAT
1 TATTTTATTAT
* *
25168237 TATTTGATTGT
1 TATTTTATTAT
*
25168248 TATATTATTATT
1 TATTTTATTA-T
25168260 TCATTTTATTAT
1 T-ATTTTATTAT
25168272 T
1 T
25168273 CATGTATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 23 0.59
12 8 0.21
13 8 0.21
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:25168255 original size:19 final size:19
Alignment explanation
Indices: 25168230--25168286 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
25168220 TATTATTATT
25168230 TTATTATTATTTGATTGTTA
1 TTATTATTATTT-ATTGTTA
25168250 -TATTATTATTTCATT-TTA
1 TTATTATTATTT-ATTGTTA
25168268 TTATTCATGTATTTATTGT
1 TTATT-AT-TATTTATTGT
25168287 ATTTTTGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.09
19 18 0.56
20 5 0.16
21 6 0.19
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.65
Consensus pattern (19 bp):
TTATTATTATTTATTGTTA
Found at i:25170877 original size:41 final size:41
Alignment explanation
Indices: 25170820--25170912 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
25170810 TTTTATTTTA
*
25170820 ACAAGAATTATAGTCACCCAATTCTAACAATCTCCACCTCT-
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCT-TG
25170861 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
25170902 ACAAGAATTCT
1 ACAAGAATTCT
25170913 CTACGAACAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 1 0.02
41 49 0.98
ACGTcount: A:0.37, C:0.30, G:0.06, T:0.27
Consensus pattern (41 bp):
ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
Found at i:25170924 original size:17 final size:17
Alignment explanation
Indices: 25170902--25170940 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
25170892 CTCCACCTTG
* *
25170902 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
25170919 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
25170936 ACAAG
1 ACAAG
25170941 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:25177839 original size:59 final size:59
Alignment explanation
Indices: 25177748--25178077 Score: 426
Period size: 59 Copynumber: 5.7 Consensus size: 59
25177738 ACCCGAGGGT
* * * * * *
25177748 AAAATGGTAATTTTGG-ACGTGCGGGGGCAAAATGGTAATTTTTGGTGAAACCGGGGTTA
1 AAAATGG-AATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
* *
25177807 AAAATGGAATTTTGAAAAGTTCGAGGATAAAATGGTAATTTTTGATGAAATCGGGGTT-
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
* **
25177865 AAAATGGAATTTTGGAAAGTTC-AGGGGTAAAATGGTAATTTTTGATGACATCTAGGTTA
1 AAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
* *
25177924 AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
*
25177983 AAAATGGAATTTTGGAAAGTTC--GGG----ATGGTAATTTTTGATGAAATCGGGGCTA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
* * *
25178036 AAAACGGAATTTTGGAAAGTTCGGGGGTAAAATGGCAATTTT
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT
25178078 CGGACAGTCC
Statistics
Matches: 239, Mismatches: 22, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
53 47 0.20
55 3 0.01
57 4 0.02
58 58 0.24
59 127 0.53
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTA
Found at i:25177955 original size:117 final size:115
Alignment explanation
Indices: 25177747--25178077 Score: 447
Period size: 117 Copynumber: 2.9 Consensus size: 115
25177737 TACCCGAGGG
* * * *
25177747 TAAAATGGTAATTTTGG-ACGTGCGGGGGCAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAA
1 TAAAATGG-AATTTTGGAAAGTTC-GGGG-AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAA
* * *
25177811 TGGAATTTTGAAAAGTTCGAGGATAAAATGGTAATTTTTGATGAAATCGGGGT
63 TGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGT
* **
25177864 TAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGACATCTAGGTTAAAAAT
1 TAAAATGGAATTTTGGAAAGTTC-GGGG-AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAAT
*
25177929 GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATTGGGGT
64 GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGT
* *
25177981 TAAAAATGGAATTTTGGAAAGTTC-GGG---ATGGTAATTTTTGATGAAATCGGGGCTAAAAACG
1 T-AAAATGGAATTTTGGAAAGTTCGGGGAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATG
*
25178042 GAATTTTGGAAAGTTCGGGGGTAAAATGGCAATTTT
65 GAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
25178078 CGGACAGTCC
Statistics
Matches: 193, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
112 64 0.33
116 11 0.06
117 96 0.50
118 22 0.11
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (115 bp):
TAAAATGGAATTTTGGAAAGTTCGGGGAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGG
AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGT
Found at i:25178075 original size:29 final size:29
Alignment explanation
Indices: 25177744--25178077 Score: 186
Period size: 29 Copynumber: 11.6 Consensus size: 29
25177734 AGATACCCGA
* *
25177744 GGGTAAAATGGTAATTTTGG-ACGTGCGG
1 GGGTAAAATGGTAATTTTGGAAAGTTCGG
* *
25177772 GGGCAAAATGGTAATTTTTGGTGAAA--CCGG
1 GGGTAAAATGGTAA-TTTT-G-GAAAGTTCGG
* * *
25177802 GGTTAAAAATGG-AATTTTGAAAAGTTCGA
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGG
*
25177831 GGATAAAATGGTAATTTTTGATGAAA--TCGG
1 GGGTAAAATGGTAA-TTTTG--GAAAGTTCGG
* *
25177861 GGTTAAAATGG-AATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTGGAAAGTTCGG
* * ** **
25177889 GGGTAAAATGGTAATTTTTGATGACATCTA
1 GGGTAAAATGGTAATTTTGGA-AAGTTCGG
*
25177919 GGTTAAAAATGG-AATTTTGGAAAGTTCGG
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGG
25177948 GGGTAAAATGGTAATTTTTGATGAAA-TT-GG
1 GGGTAAAATGGTAA-TTTTG--GAAAGTTCGG
*
25177978 GGTTAAAAATGG-AATTTTGGAAAGTTC--
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGG
25178005 GGG----ATGGTAATTTTTGATGAAA--TCGG
1 GGGTAAAATGGTAA-TTTTG--GAAAGTTCGG
* *
25178031 GGCTAAAAACGG-AATTTTGGAAAGTTCGG
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGG
*
25178060 GGGTAAAATGGCAATTTT
1 GGGTAAAATGGTAATTTT
25178078 CGGACAGTCC
Statistics
Matches: 235, Mismatches: 34, Indels: 73
0.69 0.10 0.21
Matches are distributed among these distances:
22 4 0.02
23 2 0.01
24 7 0.03
26 10 0.04
27 13 0.06
28 54 0.23
29 56 0.24
30 54 0.23
31 27 0.11
32 8 0.03
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.32
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCGG
Found at i:25178331 original size:161 final size:161
Alignment explanation
Indices: 25178153--25178482 Score: 520
Period size: 162 Copynumber: 2.0 Consensus size: 161
25178143 CATCCAAAAG
25178153 TCAAAGGACTAATTT-AAAATCTCAAAAAATTCCTAGGTCAATTTTGTAATTAAGCAAAAGTTGA
1 TCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTAGGTCAATTTTGTAATTAAGCAAAAGTTGA
* ** *
25178217 TTTGAGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTTAATGCACAAATAAG-CCAAAAAG
66 TTTGAAGATTAAATTAAAACAAATTAAAAATAACAGGGACTAAATGCA-AAATAAGCCCAAAAA-
*
25178281 TGACACGTGGCGGCCTCTGGTGCAGTCAAACAA
129 TGACACGTGGCAGCCTCTGGTGCAGTCAAACAA
* *
25178314 TCAAAGGACTAATTTAAAAATCTCAAAAGATTCCTGGGTCAATTTTGTAATTAAGCAAAAGTTGA
1 TCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTAGGTCAATTTTGTAATTAAGCAAAAGTTGA
* * *
25178379 TTTGAAGATTAAATTAAAATAAATTAAAAATAACATGGACTAAATGCAAAATGAGCCCAAAAATG
66 TTTGAAGATTAAATTAAAACAAATTAAAAATAACAGGGACTAAATGCAAAATAAGCCCAAAAATG
*
25178444 ACACGTGGCAGCCTCTGGTGCAGTCAAACAG
131 ACACGTGGCAGCCTCTGGTGCAGTCAAACAA
*
25178475 TCGAAGGA
1 TCAAAGGA
25178483 TTAAATTGAA
Statistics
Matches: 155, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
161 59 0.38
162 96 0.62
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (161 bp):
TCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTAGGTCAATTTTGTAATTAAGCAAAAGTTGA
TTTGAAGATTAAATTAAAACAAATTAAAAATAACAGGGACTAAATGCAAAATAAGCCCAAAAATG
ACACGTGGCAGCCTCTGGTGCAGTCAAACAA
Found at i:25180037 original size:17 final size:17
Alignment explanation
Indices: 25180000--25180043 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
25179990 AATATTATTT
* **
25180000 TAAACTTAAATTTAAGG
1 TAAATTTAAATTTAAAA
25180017 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
25180034 TAAATTTAAA
1 TAAATTTAAA
25180044 ACCCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:25186589 original size:56 final size:56
Alignment explanation
Indices: 25186498--25186729 Score: 308
Period size: 56 Copynumber: 4.2 Consensus size: 56
25186488 AAAATCTAAA
* * *
25186498 AAAAAATAATGAGAGAAAATGGATATTTGG--AAAGAGAAAGTTTGAAAAAATATG
1 AAAAAATAATGAGAGAAAATGGATGTTTGGAAAAAGAGAAAGTTTGAGAAAATCTG
* *
25186552 AAAAAATAATGAGAGAAAATGAATGTTTGGAAAAAGAGAAAGTTTGAGAAAGTCTG
1 AAAAAATAATGAGAGAAAATGGATGTTTGGAAAAAGAGAAAGTTTGAGAAAATCTG
* * *
25186608 GAAAAATAACGAGAGAAAATGGATGTTTGGAAAAAGCGAAAGTTTGAGAAAATCTG
1 AAAAAATAATGAGAGAAAATGGATGTTTGGAAAAAGAGAAAGTTTGAGAAAATCTG
* * * * *
25186664 AAAAAATAATAAGAGAAAATGGGTGTTT-GAAAAGAGAGAACGTCTGAGAAAATTTG
1 AAAAAATAATGAGAGAAAATGGATGTTTGGAAAA-AGAGAAAGTTTGAGAAAATCTG
*
25186720 AGAAAATAAT
1 AAAAAATAAT
25186730 TAGAAGGGAA
Statistics
Matches: 156, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
54 28 0.18
55 5 0.03
56 123 0.79
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (56 bp):
AAAAAATAATGAGAGAAAATGGATGTTTGGAAAAAGAGAAAGTTTGAGAAAATCTG
Found at i:25194931 original size:46 final size:46
Alignment explanation
Indices: 25194879--25194966 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
25194869 ACTACTAATT
* ** *
25194879 TGTAATACTAGTTACGCACTTGGATGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTACGCACTTGAAAAATATTGTAGTTATCATGTGG
*
25194925 TGTAATACTAGTTATGCACTTGAAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTACGCACTTGAAAAATATTGTAGTTATCAT
25194967 CAATTCGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (46 bp):
TGTAATACTAGTTACGCACTTGAAAAATATTGTAGTTATCATGTGG
Found at i:25196057 original size:16 final size:16
Alignment explanation
Indices: 25196036--25196080 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25196026 ATAAGTCACT
25196036 CTTTTCATTCACAATG
1 CTTTTCATTCACAATG
*
25196052 CTTTTCACTCATTCAATG
1 CTTTTCATTCA--CAATG
25196070 CTTTT-ATTCAC
1 CTTTTCATTCAC
25196081 TCTCTATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 10 0.40
17 4 0.16
18 10 0.40
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (16 bp):
CTTTTCATTCACAATG
Found at i:25196081 original size:21 final size:19
Alignment explanation
Indices: 25196047--25196118 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 19
25196037 TTTTCATTCA
*
25196047 CAATGCTTTTCACTCA-T-T
1 CAATGCTTTT-ATTCACTCT
25196065 CAATGCTTTTATTCACTCT
1 CAATGCTTTTATTCACTCT
* * *
25196084 CTATGCTTTTA-TCCCTCA
1 CAATGCTTTTATTCACTCT
**
25196102 CCTTGCTTTTATTCACT
1 CAATGCTTTTATTCACT
25196119 TAATTTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.09
18 25 0.57
19 15 0.34
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (19 bp):
CAATGCTTTTATTCACTCT
Found at i:25196091 original size:19 final size:20
Alignment explanation
Indices: 25196067--25196118 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
25196057 CACTCATTCA
*
25196067 ATGCTTTTATTCACTC-TCT
1 ATGCTTTTATTCACTCACCT
*
25196086 ATGCTTTTA-TCCCTCACCT
1 ATGCTTTTATTCACTCACCT
25196105 -TGCTTTTATTCACT
1 ATGCTTTTATTCACT
25196119 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.15, C:0.29, G:0.06, T:0.50
Consensus pattern (20 bp):
ATGCTTTTATTCACTCACCT
Found at i:25198718 original size:28 final size:28
Alignment explanation
Indices: 25198687--25198749 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
25198677 GAAAAAGGAC
*
25198687 TTTTGGA-TACCCGAGGGTAAAATGGTAA
1 TTTTGGACT-CCCGAGGGCAAAATGGTAA
** *
25198715 TTTTGGACTTTCGAGGGCAAAATTGTAA
1 TTTTGGACTCCCGAGGGCAAAATGGTAA
25198743 TTTTGGA
1 TTTTGGA
25198750 GAAATTGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:25199114 original size:30 final size:30
Alignment explanation
Indices: 25198763--25199104 Score: 372
Period size: 30 Copynumber: 11.4 Consensus size: 30
25198753 ATTGAGGCTA
* * *
25198763 AAAATGTAACTTTGG-AAAGTTTGGGGGGT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* *
25198792 AAAATGGTAAATTTTGGTAAAA---TCGGGGTCA
1 AAAAT-GT-AATTTTGG-AAAAGTTTTGGGGT-T
* * *
25198823 AAAATGAAATTTTGG--AAGGTTCGCGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTG-GGGTT
*
25198852 AAAATGTAATATTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* * *
25198882 AAAATGTAATATTGGAAAAGTTTTTGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* * *
25198912 AAAATATAATATTGGAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
25198942 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
*
25198972 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* * *
25199002 AAAATGTATTTTTGAAAAAGTTTTGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* * *
25199032 AAAATGTAATTTTAGAAAAGTTTCGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
**
25199062 AAAATGTAATTTTCAAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
*
25199092 AAAATATAATTTT
1 AAAATGTAATTTT
25199105 TGGATAGTTT
Statistics
Matches: 270, Mismatches: 32, Indels: 21
0.84 0.10 0.07
Matches are distributed among these distances:
26 2 0.01
29 29 0.11
30 218 0.81
31 18 0.07
33 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTT
Found at i:25200220 original size:3 final size:3
Alignment explanation
Indices: 25200212--25200245 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
25200202 TATTTAAACC
25200212 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25200246 ATGGCTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25200318 original size:36 final size:37
Alignment explanation
Indices: 25200251--25200322 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
25200241 TATTAATGGC
* *
25200251 TATTGATTGCTGTTATTAATATCATATTTATTATTAT
1 TATTGATTGCTGTTATTAATATCAGAATTATTATTAT
** *
25200288 TATTGA-TGCTGTTATTGTTATTAGAATTATTATTA
1 TATTGATTGCTGTTATTAATATCAGAATTATTATTA
25200323 ATACTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (37 bp):
TATTGATTGCTGTTATTAATATCAGAATTATTATTAT
Found at i:25200983 original size:6 final size:6
Alignment explanation
Indices: 25200972--25201034 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
25200962 TTATTATAAT
** *
25200972 TTTAAA TTTAAA -TTAAA TCCAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
25201018 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
25201035 ACAAATTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 14 0.32
6 30 0.68
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:25200987 original size:11 final size:11
Alignment explanation
Indices: 25200973--25201027 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
25200963 TATTATAATT
25200973 TTAAATTTAAA
1 TTAAATTTAAA
**
25200984 TTAAATCCAAA
1 TTAAATTTAAA
25200995 TTTAAA-TTAAA
1 -TTAAATTTAAA
25201006 TTCAAATTTAAA
1 TT-AAATTTAAA
*
25201018 ATAAATTTAA
1 TTAAATTTAA
25201028 TTTTAAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 2 0.06
11 23 0.64
12 11 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:25201024 original size:17 final size:17
Alignment explanation
Indices: 25200975--25201045 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
25200965 TTATAATTTT
* *
25200975 AAATTTAAATTAAATCC
1 AAATTTAAAATAAATTC
*
25200992 AAATTTAAATTAAATTC
1 AAATTTAAAATAAATTC
*
25201009 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATTC
* *
25201026 AATTTTAAAACAAATTC
1 AAATTTAAAATAAATTC
25201043 AAA
1 AAA
25201046 ATGGTTTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATAAATTC
Found at i:25201461 original size:92 final size:92
Alignment explanation
Indices: 25201308--25202035 Score: 1237
Period size: 92 Copynumber: 7.9 Consensus size: 92
25201298 CGAGGTTTCG
* * ** * *
25201308 TCTTGCTCTTACTTCAATTTCAGAGAGGA--ATGATTTGATATCCAGCTCTACTTCAATTTCAAG
1 TCTTACTCTTACTTCAATTTCAGAG-GGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAG
* * * *
25201371 AGGATAGAAAAATGATGTTTGTGCTTCA
65 AGGATAGGAAAATGATGTTGGTCCTTCT
* *
25201399 TCTTACTCTCACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGTTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
25201464 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCT
*
25201491 TCTAACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
25201556 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCT
*
25201583 TCTTACTCTTACTTCAATTTCAGAGGGATGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
25201648 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCT
*
25201675 TCTTACTCTTACTT-AGATTTCAGAGGGACGAAGGCTTGTTATCTAGCTTTACTTCAATTTCAAG
1 TCTTACTCTTACTTCA-ATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAG
25201739 AGGATAGGAAAATGATGTTGGTCCTTCT
65 AGGATAGGAAAATGATGTTGGTCCTTCT
25201767 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
25201832 GGATAGGAAAATAATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCT
*
25201859 TCTTACTCTTACTTCAATTTCAGAGGGATGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
* *
25201924 GGATAGGAAAATGATGTTGGTGCTTCA
66 GGATAGGAAAATGATGTTGGTCCTTCT
25201951 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
25202016 GGATAGGAAAATTATGTTGG
66 GGATAGGAAAATGATGTTGG
25202036 ATTGATGTGA
Statistics
Matches: 606, Mismatches: 27, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
90 3 0.00
91 24 0.04
92 578 0.95
93 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (92 bp):
TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
GGATAGGAAAATGATGTTGGTCCTTCT
Found at i:25214073 original size:28 final size:28
Alignment explanation
Indices: 25214042--25214104 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
25214032 AAAACGGGAC
*
25214042 TTTTGGA-TACTCGGGGATAAAATGGTAA
1 TTTTGGACT-CTCGGGGACAAAATGGTAA
* * * *
25214070 TTTTAGACTTTCGGGGGCAAAATTGTAA
1 TTTTGGACTCTCGGGGACAAAATGGTAA
25214098 TTTTGGA
1 TTTTGGA
25214105 GAAATCGGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (28 bp):
TTTTGGACTCTCGGGGACAAAATGGTAA
Found at i:25214243 original size:30 final size:30
Alignment explanation
Indices: 25214172--25214369 Score: 247
Period size: 30 Copynumber: 6.6 Consensus size: 30
25214162 GGTAAAATCG
* * *
25214172 GGGTCTAAAATGAAATTTTAG--AAGGTTCA
1 GGGT-TAAAATGTAATTTTAGAAAAGTTTTA
25214201 GAGGTTAAAATGTAATTTTAGAAAAGTTTTA
1 G-GGTTAAAATGTAATTTTAGAAAAGTTTTA
* * *
25214232 GGGTCAAAATGTAATATTGGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTTA
*
25214262 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTTA
* * * *
25214292 AGGTCAAAATGTAATTTTGGAAAAATTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTTA
25214322 GGGTTAAAATGTAATTTTAGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTTA
* *
25214352 AGGTTAAAATATAATTTT
1 GGGTTAAAATGTAATTTT
25214370 TGGACAGTTT
Statistics
Matches: 149, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.11
30 126 0.85
31 7 0.05
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTTA
Found at i:25215486 original size:3 final size:3
Alignment explanation
Indices: 25215478--25215502 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25215468 TATTTAAACC
25215478 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
25215503 ATGGCTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:25216024 original size:16 final size:17
Alignment explanation
Indices: 25216003--25216034 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25215993 CAGGGCATGG
25216003 TGGAGCTGGTG-GCAGA
1 TGGAGCTGGTGAGCAGA
25216019 TGGAGCTGGTGAGCAG
1 TGGAGCTGGTGAGCAG
25216035 CAAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.12, G:0.50, T:0.19
Consensus pattern (17 bp):
TGGAGCTGGTGAGCAGA
Found at i:25216240 original size:6 final size:6
Alignment explanation
Indices: 25216229--25216291 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
25216219 TTATAAAAAT
** *
25216229 TTTAAA TTTAAA -TTAAA TCCAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
25216275 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
25216292 ACAAATTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 14 0.32
6 30 0.68
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:25216244 original size:11 final size:11
Alignment explanation
Indices: 25216230--25216284 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
25216220 TATAAAAATT
25216230 TTAAATTTAAA
1 TTAAATTTAAA
**
25216241 TTAAATCCAAA
1 TTAAATTTAAA
25216252 TTTAAA-TTAAA
1 -TTAAATTTAAA
25216263 TTCAAATTTAAA
1 TT-AAATTTAAA
*
25216275 ATAAATTTAA
1 TTAAATTTAA
25216285 TTTTAAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 2 0.06
11 23 0.64
12 11 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:25216281 original size:17 final size:17
Alignment explanation
Indices: 25216232--25216302 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
25216222 TAAAAATTTT
* *
25216232 AAATTTAAATTAAATCC
1 AAATTTAAAATAAATTC
*
25216249 AAATTTAAATTAAATTC
1 AAATTTAAAATAAATTC
*
25216266 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATTC
* *
25216283 AATTTTAAAACAAATTC
1 AAATTTAAAATAAATTC
25216300 AAA
1 AAA
25216303 ATGGTTTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATAAATTC
Found at i:25219666 original size:58 final size:58
Alignment explanation
Indices: 25219599--25219712 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
25219589 CCAAACTATT
*
25219599 ATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATATTCATGTGACTAATGTG
1 ATTAAATGTGATTAATATGTGATGTGATAAATGCTT-AAATACTCATGTGACTAATGTG
* * * *
25219657 ATTAAATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTCATGTGATTAATG
1 ATTAAATGTGATTAATATGTGATGTGATAAATGCTTAAATACTCATGTGACTAATG
25219713 CGACTAATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 48 0.96
59 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.41
Consensus pattern (58 bp):
ATTAAATGTGATTAATATGTGATGTGATAAATGCTTAAATACTCATGTGACTAATGTG
Found at i:25220483 original size:95 final size:96
Alignment explanation
Indices: 25220312--25220508 Score: 297
Period size: 95 Copynumber: 2.1 Consensus size: 96
25220302 AGCACTCTTG
*
25220312 ATTTTTATTCCAAACTTGAAATATTTTTAAAAAAAAAAAAGATGTTCGATTATTTCGGTTTAAAG
1 ATTTTTATTCCAAACTTGAAATATTTTT-AAAAAAAAAAAGATATTCGATTATTTCGGTTTAAAG
25220377 AGAAAAACCGCACCTAGTAAGTTAAGGCCTCA
65 AGAAAAACCGCACCTAGTAAGTTAAGGCCTCA
* *** * * *
25220409 ATTTTTATTCCAAACTTTAAATATTTTT-TTTAAAAAAGGATATTCGGTTATTTCGGTTTGAAGA
1 ATTTTTATTCCAAACTTGAAATATTTTTAAAAAAAAAAAGATATTCGATTATTTCGGTTTAAAGA
*
25220473 GAAAAACCGCATCTAGTAAGTTAAGGCCTCA
66 GAAAAACCGCACCTAGTAAGTTAAGGCCTCA
25220504 ATTTT
1 ATTTT
25220509 GAGATAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 64 0.70
97 27 0.30
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (96 bp):
ATTTTTATTCCAAACTTGAAATATTTTTAAAAAAAAAAAGATATTCGATTATTTCGGTTTAAAGA
GAAAAACCGCACCTAGTAAGTTAAGGCCTCA
Found at i:25232505 original size:26 final size:25
Alignment explanation
Indices: 25232476--25232559 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
25232466 GATTATAGAA
*
25232476 AAAATTTCAATAAATAAAAAATATAT
1 AAAATTTTAATAAATAAAAAATA-AT
* *
25232502 AAAATTATTAATTATTAAAATAA-AAT
1 AAAATT-TTAATAAATAAAA-AATAAT
* *
25232528 AAATATTTTAAAAAATAAAAAATTAAA
1 AAA-ATTTTAATAAATAAAAAA-TAAT
25232555 AAAAT
1 AAAAT
25232560 AATATGGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.04
26 23 0.50
27 19 0.41
28 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAATTTTAATAAATAAAAAATAAT
Found at i:25232544 original size:16 final size:16
Alignment explanation
Indices: 25232523--25232561 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25232513 TTATTAAAAT
* * *
25232523 AAAATAAATATTTTAA
1 AAAATAAAAAATTAAA
25232539 AAAATAAAAAATTAAA
1 AAAATAAAAAATTAAA
25232555 AAAATAA
1 AAAATAA
25232562 TATGGATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAAAATTAAA
Found at i:25238827 original size:27 final size:26
Alignment explanation
Indices: 25238789--25238845 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
25238779 GGCGAATCGT
*
25238789 AACTCGCCAAACATACTAG-CAAACACC
1 AACTCGCCAAACACACT-GTCAAAC-CC
*
25238816 AACTCTCCAAACACACTGTCAAACCC
1 AACTCGCCAAACACACTGTCAAACCC
25238842 AACT
1 AACT
25238846 GGCAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.42, C:0.39, G:0.05, T:0.14
Consensus pattern (26 bp):
AACTCGCCAAACACACTGTCAAACCC
Found at i:25240611 original size:31 final size:30
Alignment explanation
Indices: 25240576--25240665 Score: 119
Period size: 31 Copynumber: 3.0 Consensus size: 30
25240566 AATAGTATTT
*
25240576 TATTAATTTAATATTAAAATGATTATCTTAA
1 TATTAAATTAA-ATTAAAATGATTATCTTAA
*
25240607 TATTAAATTAAATTTAATATGATTATCTTAA
1 TATTAAATTAAA-TTAAAATGATTATCTTAA
* *
25240638 TATTAAATTAAATT-TAATGTTTATCTTA
1 TATTAAATTAAATTAAAATGATTATCTTA
25240666 TAGATAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
29 11 0.21
30 3 0.06
31 39 0.74
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
TATTAAATTAAATTAAAATGATTATCTTAA
Found at i:25240723 original size:62 final size:59
Alignment explanation
Indices: 25240634--25240750 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
25240624 TATGATTATC
* * *
25240634 TTAATATTAAATTAAATTTAATGTTTATCTTATAGATAAATATTCTATTAATTTAATAAAAT
1 TTAATATTAAATTAAATCTAATATTTATC-T-TA-ATAAATATTATATTAATTTAATAAAAT
* *
25240696 TTAATATTAAATTTAATCTAATATTTATCTTAATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTAAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
25240751 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
60 2 0.04
61 1 0.02
62 26 0.52
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTAAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAAAT
Found at i:25244559 original size:47 final size:46
Alignment explanation
Indices: 25244490--25244586 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 46
25244480 ATAATCATGA
* * *
25244490 CAGTTACATTTAGAGGTGTTTGGTTCGCCAAATGTAACATTACGGTC
1 CAGTTACATTTAGAGGCGTTTGGTTCACCAAATATAACATTACGG-C
* *
25244537 CAGTTACATTTAGGGGCGTTTGGTTCACCAAATATGACATTACGGC
1 CAGTTACATTTAGAGGCGTTTGGTTCACCAAATATAACATTACGGC
25244583 CAGT
1 CAGT
25244587 AATGTTACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 5 0.11
47 40 0.89
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (46 bp):
CAGTTACATTTAGAGGCGTTTGGTTCACCAAATATAACATTACGGC
Found at i:25252108 original size:48 final size:48
Alignment explanation
Indices: 25252037--25252131 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
25252027 ATCAAATGCT
* *
25252037 CATTTTGATTCTTTTACGAGATTACGTACTCATTTAGATTATCTACTA
1 CATTTGGATTCTTTTACGAGATTACGGACTCATTTAGATTATCTACTA
25252085 CATTTGGATTCTTTTACGAGATTACGGACTCATTTAGATTATCTACT
1 CATTTGGATTCTTTTACGAGATTACGGACTCATTTAGATTATCTACT
25252132 GAAGTAAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (48 bp):
CATTTGGATTCTTTTACGAGATTACGGACTCATTTAGATTATCTACTA
Found at i:25254424 original size:41 final size:41
Alignment explanation
Indices: 25254378--25254472 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
25254368 GAATTTTATT
* **
25254378 TTAACAAGAATTCTAGTCACCCAATTTTAACAATCTTTACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
25254419 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
25254460 TTGACAAGAATTC
1 TTAACAAGAATTC
25254473 CCTACGAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:25257576 original size:41 final size:41
Alignment explanation
Indices: 25257519--25257596 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
25257509 GAATTTTATT
*
25257519 TTAACAAGAATTCTAGTCGCCCAATTCTAACAATCTCTACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCTACC
*
25257560 TTAACAAGAGTTCTAGTCACCCAATTCTAACAATCTC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTC
25257597 CAACTCTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCTACC
Found at i:25262760 original size:15 final size:15
Alignment explanation
Indices: 25262740--25262768 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25262730 AAAGATCCAG
25262740 AACCTACACTTTTGC
1 AACCTACACTTTTGC
25262755 AACCTACACTTTTG
1 AACCTACACTTTTG
25262769 TACTATTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (15 bp):
AACCTACACTTTTGC
Found at i:25267206 original size:23 final size:22
Alignment explanation
Indices: 25267112--25267206 Score: 65
Period size: 23 Copynumber: 4.3 Consensus size: 22
25267102 TAAATATTAC
*
25267112 TTAATTATCATTAAATTAAATGT
1 TTAATTATCATTAAATTTAAT-T
*
25267135 TTATTTATC-TTAATATTTAATT
1 TTAATTATCATTAA-ATTTAATT
*
25267157 TT--TTATCATTATACTTT--TT
1 TTAATTATCATTA-AATTTAATT
*
25267176 TAAAAATTATCATTATAATTTAATT
1 T--TAATTATCATTA-AATTTAATT
25267201 TTAATT
1 TTAATT
25267207 TTGTTTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
19 3 0.05
20 5 0.09
21 6 0.11
22 8 0.14
23 32 0.56
25 3 0.05
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (22 bp):
TTAATTATCATTAAATTTAATT
Found at i:25274770 original size:1 final size:1
Alignment explanation
Indices: 25274766--25274800 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
25274756 ATCATCAAAC
* *
25274766 AAAAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25274801 GAAAGGGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:25274785 original size:11 final size:11
Alignment explanation
Indices: 25274769--25274804 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
25274759 ATCAAACAAA
25274769 AAAAAAAAAAG
1 AAAAAAAAAAG
25274780 AAAAAAAAAAG
1 AAAAAAAAAAG
25274791 AAAAAAAAAAG
1 AAAAAAAAAAG
25274802 AAA
1 AAA
25274805 GGGCTTTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:25285769 original size:126 final size:126
Alignment explanation
Indices: 25285621--25285872 Score: 468
Period size: 126 Copynumber: 2.0 Consensus size: 126
25285611 CCCGATATCG
*
25285621 AGGAATGATGTTTGTTTGATGTTTACTTTTGTAATTGCAATTAATTTTACTTACTTAACTTTTAA
1 AGGAATGATGTTTGTTTGATGTTTACTTTTGTAATTGCAAATAATTTTACTTACTTAACTTTTAA
*
25285686 TCTTTACTAAACTATTGTTATTTTTCTAATTGTTTTCTTTTTCAGATTTTTAATTATTGTA
66 TCTTTACTAAACTATTGTTATTTTTCTAATTATTTTCTTTTTCAGATTTTTAATTATTGTA
*
25285747 AGGAATGATGTTTGTTTGATGTTTACTTTTGTAGTTGCAAATAATTTTACTTACTTAACTTTTAA
1 AGGAATGATGTTTGTTTGATGTTTACTTTTGTAATTGCAAATAATTTTACTTACTTAACTTTTAA
*
25285812 TCTTTACTAAACTATTGTTATTTTTCTAATTATTTTCTTTTTCAGATTTTTAATTGTTGTA
66 TCTTTACTAAACTATTGTTATTTTTCTAATTATTTTCTTTTTCAGATTTTTAATTATTGTA
25285873 TGTCCACATG
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (126 bp):
AGGAATGATGTTTGTTTGATGTTTACTTTTGTAATTGCAAATAATTTTACTTACTTAACTTTTAA
TCTTTACTAAACTATTGTTATTTTTCTAATTATTTTCTTTTTCAGATTTTTAATTATTGTA
Found at i:25294464 original size:52 final size:52
Alignment explanation
Indices: 25294381--25294515 Score: 243
Period size: 52 Copynumber: 2.6 Consensus size: 52
25294371 TAAATATAAA
25294381 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* *
25294433 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
*
25294485 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
25294516 CAAATGCGAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:25300673 original size:51 final size:50
Alignment explanation
Indices: 25300596--25300783 Score: 259
Period size: 51 Copynumber: 3.6 Consensus size: 50
25300586 GTTGTAAACG
25300596 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
1 AAAGG-TCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGACT
25300648 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGACT
1 AAAGGTCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGACT
* * * * * *
25300699 AAAGGTTCGATGACTCAATGTTATCGTGAGTATATGAATTCCTATATGGAAT
1 AAAGGTCCGATGACT-AATGTCATCGTGAGTAAATGAA-TCCTTTACGGACT
25300751 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-ATGTCATCGTGAGTA
25300784 TTAAATGAAA
Statistics
Matches: 124, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
51 78 0.63
52 20 0.16
53 26 0.21
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (50 bp):
AAAGGTCCGATGACTAATGTCATCGTGAGTAAATGAATCCTTTACGGACT
Found at i:25300822 original size:59 final size:61
Alignment explanation
Indices: 25300732--25300849 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 61
25300722 TCGTGAGTAT
* * *
25300732 ATGAATTCCTATATGGAATAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAATTCCTATATGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATGAA
* *
25300793 ATGAATTCC-A-ATGCGAACAAG-GGTCCGATGACTTTGTGTCATCGTGAGAAATAAATG
1 ATGAATTCCTATATG-GAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATG
25300850 CAAGTGAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 35 0.69
60 7 0.14
61 9 0.18
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (61 bp):
ATGAATTCCTATATGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATGAA
Found at i:25305568 original size:30 final size:30
Alignment explanation
Indices: 25305532--25305610 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
25305522 GATTAAAGAT
25305532 TAAATTGGAAATTTAGTGAAATTTAGGG-A
1 TAAATTGGAAATTTAGTGAAATTTAGGGTA
* * *
25305561 CTAAATTGTAAGTTTAGTGAATTTTAGGGTA
1 -TAAATTGGAAATTTAGTGAAATTTAGGGTA
* *
25305592 TAAATTAGAATTTTAGTGA
1 TAAATTGGAAATTTAGTGA
25305611 CATTCGAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 41 0.98
31 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.39
Consensus pattern (30 bp):
TAAATTGGAAATTTAGTGAAATTTAGGGTA
Found at i:25308684 original size:34 final size:34
Alignment explanation
Indices: 25308586--25308686 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
25308576 GTGTCATTTT
* *
25308586 TACATACTAA-TTCTTCAGTTTGAAAACTTAAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
*
25308619 TGCATACTAATTTCTTGAGTTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
* * *
25308653 TACATATTGATTTCTTGAGCTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
25308687 AATGAGTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
33 9 0.15
34 51 0.85
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (34 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTACAA
Found at i:25310077 original size:14 final size:14
Alignment explanation
Indices: 25310058--25310112 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
25310048 TGACCCGAAT
25310058 CATTGACTTTGACC
1 CATTGACTTTGACC
25310072 CATTGACTTTGACC
1 CATTGACTTTGACC
*
25310086 CGA-TGAC-TCGACC
1 C-ATTGACTTTGACC
* *
25310099 CGTTAACTTTGACC
1 CATTGACTTTGACC
25310113 GTTGACTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.26
14 24 0.71
15 1 0.03
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (14 bp):
CATTGACTTTGACC
Found at i:25310077 original size:27 final size:27
Alignment explanation
Indices: 25310012--25310078 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
25310002 ACCATTAACA
* *
25310012 TTGACCCATTAACCCGACTAGTTGACT
1 TTGACCCATTGACCCGAATAGTTGACT
***
25310039 TTGACTTGTTGACCCGAATCA-TTGACT
1 TTGACCCATTGACCCGAAT-AGTTGACT
25310066 TTGACCCATTGAC
1 TTGACCCATTGAC
25310079 TTTGACCCGA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (27 bp):
TTGACCCATTGACCCGAATAGTTGACT
Found at i:25313686 original size:20 final size:20
Alignment explanation
Indices: 25313649--25313686 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25313639 GTAGCTTGAA
*
25313649 TGATATTGTGATATTATGGT
1 TGATATTGTAATATTATGGT
25313669 TGATA-TGTAATATATATG
1 TGATATTGTAATAT-TATG
25313687 TCATAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (20 bp):
TGATATTGTAATATTATGGT
Found at i:25323443 original size:3 final size:3
Alignment explanation
Indices: 25323435--25323490 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
25323425 TAAGTAGTGA
25323435 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25323483 AAT AAT AA
1 AAT AAT AA
25323491 AACTTGTGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25324193 original size:14 final size:14
Alignment explanation
Indices: 25324174--25324202 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25324164 AATTATAAAA
25324174 TTATAGAGATGATT
1 TTATAGAGATGATT
25324188 TTATAGAGATGATT
1 TTATAGAGATGATT
25324202 T
1 T
25324203 CATGAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTATAGAGATGATT
Found at i:25327812 original size:11 final size:11
Alignment explanation
Indices: 25327793--25327881 Score: 81
Period size: 11 Copynumber: 8.0 Consensus size: 11
25327783 TTTTGATTTT
*
25327793 TTAAGTTTAAA
1 TTAAATTTAAA
*
25327804 TTAATTTTAAA
1 TTAAATTTAAA
**
25327815 TTTTATTTAAA
1 TTAAATTTAAA
**
25327826 TTTAAATTTATC
1 -TTAAATTTAAA
25327838 TTAAATTTAAA
1 TTAAATTTAAA
* *
25327849 TTTATTTTAAA
1 TTAAATTTAAA
25327860 TTTAAATTT-AA
1 -TTAAATTTAAA
25327871 TTAAATTTAAA
1 TTAAATTTAAA
25327882 ATGATATTAA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
10 8 0.13
11 40 0.66
12 13 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:25327813 original size:6 final size:6
Alignment explanation
Indices: 25327792--25327881 Score: 86
Period size: 6 Copynumber: 16.0 Consensus size: 6
25327782 CTTTTGATTT
* * *
25327792 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
25327836 TCTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25327882 ATGATATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.06
5 18 0.26
6 45 0.65
7 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:25327829 original size:28 final size:28
Alignment explanation
Indices: 25327792--25327845 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
25327782 CTTTTGATTT
* *
25327792 TTTAAGTTTAAATTAATTTTAAATTTTA
1 TTTAAATTTAAATTAATCTTAAATTTTA
*
25327820 TTTAAATTTAAATTTATCTTAAATTT
1 TTTAAATTTAAATTAATCTTAAATTT
25327846 AAATTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTAAATTTAAATTAATCTTAAATTTTA
Found at i:25327883 original size:23 final size:24
Alignment explanation
Indices: 25327793--25327881 Score: 61
Period size: 23 Copynumber: 4.0 Consensus size: 24
25327783 TTTTGATTTT
* *
25327793 TTAAGTTTAAATTAAT-TTTAAAT
1 TTAAATTTAATTTAATATTTAAAT
*
25327816 TT-TATTTAAATTTAA-ATTT--AT
1 TTAAATTT-AATTTAATATTTAAAT
25327837 CTTAAATTTAAATTT-AT-TTTAAAT
1 -TTAAATTT-AATTTAATATTTAAAT
25327861 TTAAATTTAA-TTAA-ATTTAAA
1 TTAAATTTAATTTAATATTTAAA
25327882 ATGATATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
21 4 0.08
22 18 0.34
23 29 0.55
24 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TTAAATTTAATTTAATATTTAAAT
Found at i:25327890 original size:17 final size:17
Alignment explanation
Indices: 25327792--25327897 Score: 117
Period size: 17 Copynumber: 6.3 Consensus size: 17
25327782 CTTTTGATTT
* * *
25327792 TTTAAGTTTAAATTAAT
1 TTTAAATTTATATTAAA
25327809 TTTAAATTT-TATTTAAA
1 TTTAAATTTATA-TTAAA
*
25327826 TTTAAATTTATCTTAAA
1 TTTAAATTTATATTAAA
*
25327843 TTTAAATTTATTTTAAA
1 TTTAAATTTATATTAAA
25327860 TTTAAATTTA-ATTAAA
1 TTTAAATTTATATTAAA
* *
25327876 TTTAAAATGATATTAAA
1 TTTAAATTTATATTAAA
*
25327893 ATTAA
1 TTTAA
25327898 TAAATAGAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
16 14 0.18
17 62 0.81
18 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:25328665 original size:21 final size:21
Alignment explanation
Indices: 25328641--25328719 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
25328631 AACGTTCCAG
* *
25328641 TAATAATAATAAGTGCTTT-AA
1 TAATAATAATAAAT-ATTTAAA
*
25328662 TAATATTAATAAATATTTAAA
1 TAATAATAATAAATATTTAAA
* * *
25328683 TAATAATAATGTTAAGATTTTAA
1 TAATAATAA--TAAATATTTAAA
25328706 TAATAAATAATAAA
1 TAAT-AATAATAAA
25328720 AAAGGGAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 3 0.07
21 22 0.48
22 3 0.07
23 13 0.28
24 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (21 bp):
TAATAATAATAAATATTTAAA
Found at i:25329846 original size:29 final size:28
Alignment explanation
Indices: 25329814--25329898 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
25329804 AACAATCCAG
*
25329814 AAATTGCATTTTGACCCCAAAATTTTAGA
1 AAATTACATTTTGACCCCAAAATTTTA-A
* * *
25329843 AAATTACATTTTGACCTCGAAACTTTCAA
1 AAATTACATTTTGACC-CCAAAATTTTAA
* *
25329872 AAATTACCATTTTTACCTCAAAATTTT
1 AAATTA-CATTTTGACCCCAAAATTTT
25329899 CCAAAATCCC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
29 28 0.62
30 17 0.38
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (28 bp):
AAATTACATTTTGACCCCAAAATTTTAA
Found at i:25329890 original size:30 final size:29
Alignment explanation
Indices: 25329842--25329973 Score: 87
Period size: 30 Copynumber: 4.5 Consensus size: 29
25329832 AAAATTTTAG
*
25329842 AAAATTA-CATTTTGACCTCGAAACTTTCA
1 AAAATTACCATTTTTACCTCG-AACTTTCA
* * *
25329871 AAAATTACCATTTTTACCTCAAAATTTTCC
1 AAAATTACCATTTTTACCTC-GAACTTTCA
*
25329901 AAAA-TCCCATTTTTAACC-CTG-A-TTTCA
1 AAAATTACCATTTTT-ACCTC-GAACTTTCA
* *
25329928 CCAAAATTACCATTTTTACCCCCGAACTTTCC
1 --AAAATTACCATTTTTA-CCTCGAACTTTCA
*
25329960 AAAATT-TCATTTTT
1 AAAATTACCATTTTT
25329974 GACCCCAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
27 4 0.05
28 1 0.01
29 29 0.35
30 42 0.51
31 2 0.02
32 4 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTTACCTCGAACTTTCA
Found at i:25329934 original size:59 final size:60
Alignment explanation
Indices: 25329871--25330008 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 60
25329861 GAAACTTTCA
* * **
25329871 AAAATTACCATTTTTACCTCAAAATTTTCCAAAATCCCATTTTTAACCCTGATTTCAC-C
1 AAAATTACCATTTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACTC
** ** * *
25329930 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTTCATTTTTGACCCCAATTTCACTG
1 AAAATTACCATTTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACTC
*
25329990 AAATTTACCA-TTTTACCCC
1 AAAATTACCATTTTTACCCC
25330009 TGAGGATCCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 58 0.87
60 9 0.13
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (60 bp):
AAAATTACCATTTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACTC
Found at i:25329948 original size:29 final size:29
Alignment explanation
Indices: 25329820--25329948 Score: 79
Period size: 29 Copynumber: 4.4 Consensus size: 29
25329810 CCAGAAATTG
* *
25329820 CATTTTGACCCCAAAATTTTA-GAAAATTA-
1 CATTTTTA-CCCAAAA-TTTACCAAAATTAC
* * *
25329849 CATTTTGACCTCGAAACTTT-CAAAAATTAC
1 CATTTTTACC-C-AAAATTTACCAAAATTAC
* *
25329879 CATTTTTACCTCAAAATTTTCCAAAA-TCC
1 CATTTTTACC-CAAAATTTACCAAAATTAC
**
25329908 CATTTTTAACCC-TGATTTCACCAAAATTAC
1 CATTTTT-ACCCAAAATTT-ACCAAAATTAC
25329938 CATTTTTACCC
1 CATTTTTACCC
25329949 CCGAACTTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
28 6 0.07
29 45 0.55
30 31 0.38
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
CATTTTTACCCAAAATTTACCAAAATTAC
Found at i:25330031 original size:28 final size:28
Alignment explanation
Indices: 25329994--25330049 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
25329984 TCACTGAAAT
25329994 TTACCATTTTACCCCTGAGGATCCAAAA
1 TTACCATTTTACCCCTGAGGATCCAAAA
* *
25330022 TTACCATTTTGCCCCTGAGTATCCAAAA
1 TTACCATTTTACCCCTGAGGATCCAAAA
25330050 GTCCCGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (28 bp):
TTACCATTTTACCCCTGAGGATCCAAAA
Found at i:25331959 original size:30 final size:29
Alignment explanation
Indices: 25331876--25331959 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 29
25331866 TTTGATCTAA
*
25331876 TAAAATACAAACTTTAATATAATATT-TT
1 TAAAATACAAAATTTAATATAATATTATT
* *
25331904 TAATTAAT-TAAAA--T-ATATAGGTATTATT
1 TAA--AATACAAAATTTAATATA-ATATTATT
25331932 TAAAATACAAAATTTAATATATATATTA
1 TAAAATACAAAATTTAATATA-ATATTA
25331960 AATTTTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
26 8 0.19
27 9 0.21
28 8 0.19
29 4 0.10
30 13 0.31
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
TAAAATACAAAATTTAATATAATATTATT
Found at i:25332654 original size:4 final size:4
Alignment explanation
Indices: 25332645--25332694 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
25332635 ATGAAACCAC
* * *
25332645 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATAT GTAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
25332693 AT
1 AT
25332695 GAATCCATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:25332656 original size:6 final size:6
Alignment explanation
Indices: 25332645--25332694 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
25332635 ATGAAACCAC
* * *
25332645 ATATAT ATATAT ATATAT ATATAT ATATAT ATATGT ATATGT ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
25332693 AT
1 AT
25332695 GAATCCATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:25332660 original size:10 final size:10
Alignment explanation
Indices: 25332645--25332694 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
25332635 ATGAAACCAC
25332645 ATATATATAT
1 ATATATATAT
25332655 ATATATATAT
1 ATATATATAT
25332665 ATATATATAT
1 ATATATATAT
*
25332675 ATATGTATAT
1 ATATATATAT
* *
25332685 GTATACATAT
1 ATATATATAT
25332695 GAATCCATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:25333259 original size:16 final size:16
Alignment explanation
Indices: 25333235--25333268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25333225 TTTATAAATA
*
25333235 ATATATGTAATATATT
1 ATATATGTAAGATATT
*
25333251 ATATCTGTAAGATATT
1 ATATATGTAAGATATT
25333267 AT
1 AT
25333269 GTACTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (16 bp):
ATATATGTAAGATATT
Found at i:25335771 original size:95 final size:96
Alignment explanation
Indices: 25335574--25335778 Score: 243
Period size: 95 Copynumber: 2.1 Consensus size: 96
25335564 AATCAAATAT
* *
25335574 ATATTTATTTAAATAATTTAACAATTGAAATTATTTCTTCACTCATGAAGGTTAATACAGTGGGG
1 ATATTTATTTAAATAATTTAACAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGCGGGG
** ** ** ** * *
25335639 GAGTTCTAATTACTTATTAAATTTCAAATAT
66 GAGGGCTAAGGACTTACCAAATTAAAAAAAA
*
25335670 ACATTTATTTAAATAATTTAA-AATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGCGGGG
1 ATATTTATTTAAATAATTTAACAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGCGGGG
* *
25335734 GAGGGCTAGGGACTTCCCCAAA-TAAAAAAAA
66 GAGGGCTAAGGACTT-ACCAAATTAAAAAAAA
*
25335765 ATATTTATATAAAT
1 ATATTTATTTAAAT
25335779 GTAATTAGAA
Statistics
Matches: 91, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
95 68 0.75
96 23 0.25
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (96 bp):
ATATTTATTTAAATAATTTAACAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGCGGGG
GAGGGCTAAGGACTTACCAAATTAAAAAAAA
Found at i:25335884 original size:22 final size:22
Alignment explanation
Indices: 25335859--25335900 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25335849 AAAATAAAAA
*
25335859 TTAATATATGATAATTTTAATT
1 TTAATATATGATAAATTTAATT
*
25335881 TTAATATTTGATAAATTTAA
1 TTAATATATGATAAATTTAA
25335901 AACTCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAATATATGATAAATTTAATT
Found at i:25336420 original size:30 final size:30
Alignment explanation
Indices: 25336384--25336448 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
25336374 CAACTTAACA
* * *
25336384 AACAAATGTCTCTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAAAAATAACAAAATT
25336414 AACAAATGCCTCTAAAAAAATAACAAAATT
1 AACAAATGCCTCTAAAAAAATAACAAAATT
25336444 AACAA
1 AACAA
25336449 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAAATGCCTCTAAAAAAATAACAAAATT
Found at i:25337149 original size:10 final size:9
Alignment explanation
Indices: 25337133--25337160 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25337123 GCCCACTCAT
25337133 ATTTTTTTA
1 ATTTTTTTA
25337142 ATTTTTTTA
1 ATTTTTTTA
25337151 ATTTTTTTA
1 ATTTTTTTA
25337160 A
1 A
25337161 AAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:25339184 original size:26 final size:25
Alignment explanation
Indices: 25339146--25339218 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
25339136 AAAATATAGA
25339146 AAAATATTAATAAATTAATAAATTAAC
1 AAAATATT-ATAAATTAATAAATT-AC
**
25339173 AAAATATTATAAAAAAATAAATTAC
1 AAAATATTATAAATTAATAAATTAC
* *
25339198 AAATATATGAAAAATT-ATAAA
1 AAA-ATATTATAAATTAATAAA
25339219 ATAAAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 10 0.26
26 21 0.54
27 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (25 bp):
AAAATATTATAAATTAATAAATTAC
Found at i:25356781 original size:24 final size:24
Alignment explanation
Indices: 25356749--25356810 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
25356739 AAATTAAATG
25356749 TTACAAATAATTAATATTAATTAC
1 TTACAAATAATTAATATTAATTAC
* *
25356773 TTATAAATAATTAATATTAATTAT
1 TTACAAATAATTAATATTAATTAC
*
25356797 TTACAAATATTTAA
1 TTACAAATAATTAA
25356811 AATCTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
TTACAAATAATTAATATTAATTAC
Found at i:25357045 original size:26 final size:26
Alignment explanation
Indices: 25357016--25357085 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
25357006 TAAACAACAA
* *
25357016 TTTTCAAAATAATTTTTCATAAGCACT
1 TTTTCAAAAAAATTTTT-AAAAGCACT
** *
25357043 TTTTCCTAACAATTTTTAAAAGCAC-
1 TTTTCAAAAAAATTTTTAAAAGCACT
*
25357068 TTTCCAAAAGAAATTTTT
1 TTTTCAAAA-AAATTTTT
25357086 TTTGTTACAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 6 0.18
26 14 0.41
27 14 0.41
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (26 bp):
TTTTCAAAAAAATTTTTAAAAGCACT
Found at i:25357970 original size:16 final size:16
Alignment explanation
Indices: 25357949--25357979 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
25357939 ATGAGGCCAT
25357949 AGTAAGAGTGTAAGAA
1 AGTAAGAGTGTAAGAA
25357965 AGTAAGAGTGTAAGA
1 AGTAAGAGTGTAAGA
25357980 CAATTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (16 bp):
AGTAAGAGTGTAAGAA
Found at i:25359000 original size:20 final size:20
Alignment explanation
Indices: 25358987--25359023 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
25358977 AAAGTTTGAT
25358987 CATGTGCAAAAAAGATTAGG
1 CATGTGCAAAAAAGATTAGG
25359007 CATGTGC-AAAAAGATTA
1 CATGTGCAAAAAAGATTA
25359024 TCGTCTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (20 bp):
CATGTGCAAAAAAGATTAGG
Found at i:25360971 original size:60 final size:60
Alignment explanation
Indices: 25360862--25360982 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
25360852 AGAGCACTTA
* * ** ** *
25360862 GTGTTCGTGAGAACATATTTCTAGCTCCAGAGTATTGGGTGTCTGTGAGCGTATATCGAT
1 GTGTTCGTGAGAACATATTTCTAGCTCCAAAGCATTGGGAATCCATGAGCGTACATCGAT
* *
25360922 GTGTTCGTTAGAACATATTGT-TAGCTCCAAAGCATTGGGAATCCATGAGCGTGCATCGAT
1 GTGTTCGTGAGAACATATT-TCTAGCTCCAAAGCATTGGGAATCCATGAGCGTACATCGAT
25360982 G
1 G
25360983 AATTAGTTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (60 bp):
GTGTTCGTGAGAACATATTTCTAGCTCCAAAGCATTGGGAATCCATGAGCGTACATCGAT
Done.