Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000293.1 Hibiscus syriacus cultivar Beakdansim tig00000538_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 557133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:404588 original size:20 final size:21
Alignment explanation
Indices: 404564--404619 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
404554 TTGACCCCCC
404564 CTTTTTCTTCTTTTTTTCTTT
1 CTTTTTCTTCTTTTTTTCTTT
*
404585 -TTTTTCTTTTTTTTTTCTTT
1 CTTTTTCTTCTTTTTTTCTTT
404605 CTTTTT-TTCTTTTTT
1 CTTTTTCTTCTTTTTT
404620 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
CTTTTTCTTCTTTTTTTCTTT
Found at i:415265 original size:13 final size:12
Alignment explanation
Indices: 415247--415286 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
415237 TTAATTCTTG
415247 AATAAAATAAATA
1 AATAAAAT-AATA
415260 AATAAAATAATA
1 AATAAAATAATA
415272 AATAATAATAATA
1 AATAA-AATAATA
415285 AA
1 AA
415287 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:415273 original size:16 final size:17
Alignment explanation
Indices: 415247--415293 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
415237 TTAATTCTTG
415247 AATAA-AATAAATAAAT
1 AATAATAATAAATAAAT
415263 AA-AATAATAAAT-AAT
1 AATAATAATAAATAAAT
*
415278 AATAATAAAAAATAAA
1 AATAATAATAAATAAA
415294 AAATTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.26
16 18 0.67
17 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAATAATAAATAAAT
Found at i:416975 original size:19 final size:17
Alignment explanation
Indices: 416940--416978 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
416930 ATTTGATTTC
416940 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
416957 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
416976 TCT
1 TCT
416979 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:417195 original size:16 final size:16
Alignment explanation
Indices: 417170--417209 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
417160 GGACGTGGCA
417170 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
*
417185 GCGGCTGGAGGCAGAT
1 GCGGCTGGAGGCAGAG
417201 GCGGCTGGA
1 GCGGCTGGA
417210 TTAGAGGCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.17, C:0.17, G:0.55, T:0.10
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:417331 original size:19 final size:22
Alignment explanation
Indices: 417290--417333 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 22
417280 TTTGGGCTGG
*
417290 ATATTTGAATTGTAATTTTATA
1 ATATTTGAATTGTAATTTAATA
417312 ATATTT-AA-TGT-ATTTAATA
1 ATATTTGAATTGTAATTTAATA
417331 ATA
1 ATA
417334 ATAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 2 0.10
22 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTGAATTGTAATTTAATA
Found at i:417334 original size:3 final size:3
Alignment explanation
Indices: 417326--417416 Score: 94
Period size: 3 Copynumber: 30.7 Consensus size: 3
417316 TTAATGTATT
* * * * *
417326 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAT TTA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
417374 TTA TAA TAA TTA TAA TTA TAA TTA TAA TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
417417 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:417370 original size:18 final size:17
Alignment explanation
Indices: 417302--417389 Score: 71
Period size: 18 Copynumber: 5.2 Consensus size: 17
417292 ATTTGAATTG
417302 TAAT-TTTATAATATT-
1 TAATATTTATAATATTA
417317 TAATGTATTTAATAATA--A
1 TAA--TATTT-ATAATATTA
*
417335 TAATAATTATAATA--A
1 TAATATTTATAATATTA
417350 TAATATTTATAATATTTA
1 TAATATTTATAATA-TTA
*
417368 TAATAATTATAATAATTA
1 TAATATTTATAAT-ATTA
417386 TAAT
1 TAAT
417390 TATAATTATA
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
15 23 0.38
16 4 0.07
17 1 0.02
18 26 0.43
19 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (17 bp):
TAATATTTATAATATTA
Found at i:423279 original size:2 final size:2
Alignment explanation
Indices: 423268--423297 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
423258 CACCACATCG
423268 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
423298 TATGAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:423960 original size:16 final size:15
Alignment explanation
Indices: 423939--423978 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
423929 TTAAGGTATA
423939 TTTTATTATATTTTAT
1 TTTTATTAT-TTTTAT
423955 TTTTATT-TTTTTAT
1 TTTTATTATTTTTAT
423969 TTTT-TTATTT
1 TTTTATTATTT
423979 AAGTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 1 0.04
16 7 0.30
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:423963 original size:21 final size:22
Alignment explanation
Indices: 423937--423978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
423927 GTTTAAGGTA
423937 TATTTTATTA-TATTTTATTTT
1 TATTTTATTATTATTTTATTTT
* *
423958 TATTTTTTTATTTTTTTATTT
1 TATTTTATTATTATTTTATTT
423979 AAGTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (22 bp):
TATTTTATTATTATTTTATTTT
Found at i:423967 original size:8 final size:8
Alignment explanation
Indices: 423954--423978 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
423944 TTATATTTTA
423954 TTTTTATT
1 TTTTTATT
423962 TTTTTATT
1 TTTTTATT
423970 TTTTTATT
1 TTTTTATT
423978 T
1 T
423979 AAGTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:423985 original size:16 final size:15
Alignment explanation
Indices: 423966--424020 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
423956 TTTATTTTTT
423966 TATTTTTTTATTTAA
1 TATTTTTTTATTTAA
*
423981 GTATTTAATTT-TTTAA
1 -TATTT-TTTTATTTAA
*
423997 TATTTTATTTAATTAA
1 TATTTT-TTTATTTAA
424013 T-TTTTTTT
1 TATTTTTTT
424021 GTAGATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.09
15 12 0.36
16 15 0.45
17 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TATTTTTTTATTTAA
Found at i:425034 original size:13 final size:13
Alignment explanation
Indices: 425008--425040 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
424998 ATAATTATTT
425008 TTTCTTTTCTTCC
1 TTTCTTTTCTTCC
425021 TTTCATTTTC-TCC
1 TTTC-TTTTCTTCC
425034 TTTCTTT
1 TTTCTTT
425041 ATTTATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 11 0.58
14 5 0.26
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTTTCTTCC
Found at i:425037 original size:21 final size:20
Alignment explanation
Indices: 425002--425060 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
424992 TCATCTATAA
* * *
425002 TTATTTTTTCTTTTCTTCCT
1 TTATTTTCTCCTTTCTTCAT
*
425022 TTCATTTTCTCCTTTCTTTAT
1 TT-ATTTTCTCCTTTCTTCAT
425043 TTATTCTTCTCC-TTCTTC
1 TTATT-TTCTCCTTTCTTC
425061 TCTCCTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.31
21 22 0.69
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTCTCCTTTCTTCAT
Found at i:426639 original size:37 final size:36
Alignment explanation
Indices: 426564--426639 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
426554 TTTTTATATT
*
426564 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
426600 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
426637 TTT
1 TTT
426640 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:426823 original size:20 final size:20
Alignment explanation
Indices: 426787--426824 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
426777 ATCCTATTCC
**
426787 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
426807 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
426825 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:437192 original size:27 final size:27
Alignment explanation
Indices: 437162--437265 Score: 172
Period size: 27 Copynumber: 3.9 Consensus size: 27
437152 CGATTTTTTT
* *
437162 ACCGGATTAAAAATCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGGTTTTTTTCAA
437189 ACCGGATAAAAAACCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGGTTTTTTTCAA
437216 ACCGGATAAAAAACCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGGTTTTTTTCAA
* *
437243 ACCGGATAAAAAACTGATTTTTT
1 ACCGGATAAAAAACCGGTTTTTT
437266 ATTCGAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (27 bp):
ACCGGATAAAAAACCGGTTTTTTTCAA
Found at i:437228 original size:54 final size:54
Alignment explanation
Indices: 437150--437265 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
437140 AAATTGAACG
* *
437150 ACCGATTTTTTT---ACCGGATTAAAAATCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGATTTTTTTCAAACCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAA
*
437201 ACCGGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGATTTTTTTCAAACCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAA
*
437255 ACTGATTTTTT
1 ACCGATTTTTT
437266 ATTCGAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 11 0.19
54 46 0.81
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (54 bp):
ACCGATTTTTTTCAAACCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAA
Found at i:437335 original size:18 final size:18
Alignment explanation
Indices: 437271--437345 Score: 62
Period size: 18 Copynumber: 4.0 Consensus size: 18
437261 TTTTTATTCG
*
437271 AAAAAAAATCCGGGTTTTT
1 AAAAAAAATCC-GATTTTT
* *
437290 AAAAAAACT-GGATTTTT
1 AAAAAAAATCCGATTTTT
*
437307 ATCCGAAAAAATCCGATTTTT
1 A---AAAAAAATCCGATTTTT
*
437328 AAAAAAAAACCGATTTTT
1 AAAAAAAATCCGATTTTT
437346 TTGCAAACCG
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 7 0.16
18 15 0.34
19 8 0.18
20 6 0.14
21 8 0.18
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAAAAAATCCGATTTTT
Found at i:437335 original size:39 final size:40
Alignment explanation
Indices: 437250--437334 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
437240 CAAACCGGAT
* *
437250 AAAAAACTGATTTTTTATTCGAAAAAAAATCCGGGTTTTTA
1 AAAAAACTGATTTTTTATCCG-AAAAAAATCCGGATTTTTA
437291 AAAAAACTGGA-TTTTTATCCG-AAAAAATCC-GATTTTTA
1 AAAAAACT-GATTTTTTATCCGAAAAAAATCCGGATTTTTA
437329 AAAAAA
1 AAAAAA
437335 AACCGATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
38 13 0.32
39 9 0.22
41 17 0.41
42 2 0.05
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (40 bp):
AAAAAACTGATTTTTTATCCGAAAAAAATCCGGATTTTTA
Found at i:437343 original size:39 final size:39
Alignment explanation
Indices: 437250--437345 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
437240 CAAACCGGAT
* * *
437250 AAAAAACTGATTTTTTATTCGAAAAAAAATCCGGGTTTTTA
1 AAAAAACCGA-TTTTTATCCG-AAAAAAATCCGGATTTTTA
*
437291 AAAAAACTGGATTTTTATCCG-AAAAAATCC-GATTTTTAAA
1 AAAAAAC-CGATTTTTATCCGAAAAAAATCCGGATTTTT--A
437331 AAAAAACCGATTTTT
1 AAAAAACCGATTTTT
437346 TTGCAAACCG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
38 6 0.12
39 16 0.33
40 8 0.17
41 16 0.33
42 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (39 bp):
AAAAAACCGATTTTTATCCGAAAAAAATCCGGATTTTTA
Found at i:438250 original size:30 final size:30
Alignment explanation
Indices: 438215--438280 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
438205 TATTAATGTA
438215 ATTATTTCTAAATACATGAGAAATAATTAT
1 ATTATTTCTAAATACATGAGAAATAATTAT
438245 ATTATTTCTAAATACATGAGAAATAATTAT
1 ATTATTTCTAAATACATGAGAAATAATTAT
438275 ATTATT
1 ATTATT
438281 CTCTCAGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (30 bp):
ATTATTTCTAAATACATGAGAAATAATTAT
Found at i:444524 original size:20 final size:20
Alignment explanation
Indices: 444492--444538 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
444482 CTATATACCA
444492 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
444512 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
444532 GGTAAAA
1 GGTAAAA
444539 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:444634 original size:181 final size:182
Alignment explanation
Indices: 444280--444752 Score: 644
Period size: 181 Copynumber: 2.6 Consensus size: 182
444270 GATCCAAATT
* * * *
444280 AAAAATGTGTCGATCCAAAACAATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
444344 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
444409 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* *
444462 AAAAATGTATCGATCCAAAACTATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
444527 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAATGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
444591 GTGAATTTTAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * * * * *
444643 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGATATCAAAATGATA
1 AAAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
444708 AAACCGGTAAAATGATATCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
444753 CGTAAGTACG
Statistics
Matches: 258, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
181 162 0.63
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:447402 original size:18 final size:18
Alignment explanation
Indices: 447371--447407 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
447361 TCTATCAGCC
447371 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
447389 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
447407 T
1 T
447408 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:447708 original size:39 final size:39
Alignment explanation
Indices: 447665--447751 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
447655 TCCGATGCTC
* *
447665 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
* *
447704 ATCAAAATTCAAATCTCATATGATGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
447743 ATCAAAATC
1 ATCAAAATC
447752 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
Found at i:448202 original size:23 final size:23
Alignment explanation
Indices: 448176--448240 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
448166 AAATATGATA
448176 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
* *
448199 TAATAGGTATCGTTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
* *
448222 TAATAGGTAGTGGTTATAT
1 TAATAGGTAGCGCTTATAT
448241 TGTAAAGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.40
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATG
Found at i:448629 original size:23 final size:23
Alignment explanation
Indices: 448598--448670 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
448588 ATAGGTAAAA
*
448598 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
448621 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
448644 ATATAATGTAGTAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
448667 ATAT
1 ATAT
448671 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:449057 original size:23 final size:23
Alignment explanation
Indices: 449026--449098 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
449016 ATAGGTAAAA
*
449026 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
449049 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
449072 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
449095 ATAT
1 ATAT
449099 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:449132 original size:428 final size:429
Alignment explanation
Indices: 447967--449395 Score: 2709
Period size: 428 Copynumber: 3.3 Consensus size: 429
447957 GTTAATGTTG
447967 TTAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
448031 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
448096 ATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTAAATATAATA
131 ATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTAAATATAATA
*
448161 GGTAAAAATATGATATAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
196 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
*
448226 AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTG
261 AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
448291 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
326 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
448356 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
448395 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
*
448460 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAATATA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATA
* *
448525 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTAAATATAAT
* *
448590 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAG
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
* *
448655 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAATTTTTTCACCGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
448720 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
448785 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
448825 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAA-TTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
*
448889 TAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
*
448954 ATTACATAACTTTAAAAGAAGTATCGATTATTTTTATAAAAAGTATGGACACTTTAAATATAATA
131 ATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTAAATATAATA
449019 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
196 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
*
449084 AGGTAGTGGTTATATTGTAAAGTGTATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
261 AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
*
449149 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCG
326 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
449214 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
449253 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
449318 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
449383 ATTACATAACTTT
131 ATTACATAACTTT
449396 GCAATACTAT
Statistics
Matches: 976, Mismatches: 22, Indels: 5
0.97 0.02 0.00
Matches are distributed among these distances:
428 382 0.39
429 234 0.24
430 360 0.37
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (429 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTAAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:458938 original size:17 final size:17
Alignment explanation
Indices: 458916--458950 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
458906 TAAGCTGAGG
*
458916 GGAAATAAGAAGGGTCA
1 GGAAATAAGAAAGGTCA
*
458933 GGAAATGAGAAAGGTCA
1 GGAAATAAGAAAGGTCA
458950 G
1 G
458951 ATTGCCTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.37, T:0.11
Consensus pattern (17 bp):
GGAAATAAGAAAGGTCA
Found at i:459452 original size:8 final size:8
Alignment explanation
Indices: 459439--459466 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
459429 AGATCCTCCC
459439 ATATGTAT
1 ATATGTAT
459447 ATATGTAT
1 ATATGTAT
459455 ATATGTAT
1 ATATGTAT
459463 ATAT
1 ATAT
459467 ATCTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:462994 original size:12 final size:12
Alignment explanation
Indices: 462975--463010 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
462965 AAAGAAAAAG
462975 AAAA-AATGAAA
1 AAAATAATGAAA
462986 AAAATAATGAAA
1 AAAATAATGAAA
462998 AAAATAAT-AAA
1 AAAATAATGAAA
463009 AA
1 AA
463011 TGAGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAATAATGAAA
Found at i:463040 original size:30 final size:29
Alignment explanation
Indices: 462953--463046 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 29
462943 TTTCGCTTGA
462953 AGAAGAAATAAAAAAG-AAAAAGAAAAAATG
1 AGAAGAAA-AAAAAAGAAAAAAG-AAAAATG
*
462983 A-AA-AAAATAATGAAA-AAAATAATAAAAATG
1 AGAAGAAAA-AA--AAAGAAAA-AAGAAAAATG
463013 AGAAGAAAAAAAAAGAAGAAAAGAAAAATG
1 AGAAGAAAAAAAAAGAA-AAAAGAAAAATG
463043 AGAA
1 AGAA
463047 AAATGAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
27 1 0.02
28 5 0.09
29 5 0.09
30 30 0.57
31 8 0.15
32 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (29 bp):
AGAAGAAAAAAAAAGAAAAAAGAAAAATG
Found at i:463085 original size:19 final size:18
Alignment explanation
Indices: 462991--463128 Score: 72
Period size: 18 Copynumber: 8.2 Consensus size: 18
462981 TGAAAAAAAT
*
462991 AATGAAAAAAATAAT-AAA
1 AATGAAGAAAA-AATGAAA
463009 AATG-AGAAGAAAA--AAA
1 AATGAAGAA-AAAATGAAA
463025 AA-GAAG--AAAA-GAAA
1 AATGAAGAAAAAATGAAA
463039 AATG-AG-AAAAATGAAA
1 AATGAAGAAAAAATGAAA
* * *
463055 AATGATGGAAAAATGGAA
1 AATGAAGAAAAAATGAAA
463073 AATGGAAGAAAAAATGAAA
1 AAT-GAAGAAAAAATGAAA
*
463092 GA-GAA-AACAAAA-GAGAA
1 AATGAAGAA-AAAATGA-AA
463109 AATGAA-AAATAAA-GAAA
1 AATGAAGAAA-AAATGAAA
463126 AAT
1 AAT
463129 AAAAGGGGGT
Statistics
Matches: 99, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
13 4 0.04
14 7 0.07
15 6 0.06
16 19 0.19
17 22 0.22
18 28 0.28
19 13 0.13
ACGTcount: A:0.71, C:0.01, G:0.18, T:0.10
Consensus pattern (18 bp):
AATGAAGAAAAAATGAAA
Found at i:463548 original size:157 final size:158
Alignment explanation
Indices: 463320--463634 Score: 623
Period size: 157 Copynumber: 2.0 Consensus size: 158
463310 TTGGTAATCA
463320 GGATTGAGACTAAAGATTAATGAGTCTTGATTGAAACAACCAAGAGAGAAATTGAATGCACATGA
1 GGATTGAGACTAAAGATTAATGAGTCTTGATTGAAACAACCAAGAGAGAAATTGAATGCACATGA
463385 GATTCAATACTGGTTTAGGGCATCCAATGATGGAGATTTGGGAGTTTAGACGTAGCTTCATACTC
66 GATTCAATACTGGTTTAGGGCATCCAATGATGGAGATTTGGGAGTTTAGACGTAGCTTCATACTC
463450 TTAAGCATCAC-ATTTTGGAGATCCTTT
131 TTAAGCATCACAATTTTGGAGATCCTTT
463477 GGATTGAGACTAAAGATTAATGAGTCTTGATTGAAACAACCAAGAGAGAAATTGAATGCACATGA
1 GGATTGAGACTAAAGATTAATGAGTCTTGATTGAAACAACCAAGAGAGAAATTGAATGCACATGA
463542 GATTCAATACTGGTTTAGGGCATCCAATGATGGAGATTTGGGAGTTTAGACGTAGCTTCATACTC
66 GATTCAATACTGGTTTAGGGCATCCAATGATGGAGATTTGGGAGTTTAGACGTAGCTTCATACTC
463607 TTAAGCATCACAATTTTGGAGATCCTTT
131 TTAAGCATCACAATTTTGGAGATCCTTT
463635 TGACAGAGGC
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 141 0.90
158 16 0.10
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (158 bp):
GGATTGAGACTAAAGATTAATGAGTCTTGATTGAAACAACCAAGAGAGAAATTGAATGCACATGA
GATTCAATACTGGTTTAGGGCATCCAATGATGGAGATTTGGGAGTTTAGACGTAGCTTCATACTC
TTAAGCATCACAATTTTGGAGATCCTTT
Found at i:464623 original size:37 final size:36
Alignment explanation
Indices: 464566--464637 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
464556 AAACAGGTCA
464566 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
* *
464602 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACAGAAGAGTAGTGAAGCAAAC
464638 TCATTTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
Found at i:464872 original size:111 final size:110
Alignment explanation
Indices: 464711--465022 Score: 396
Period size: 111 Copynumber: 2.8 Consensus size: 110
464701 GATTGAGTCA
* * *
464711 TATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGT-TCTATACTCTC
1 TATACTCTCTGAAAGAATAGAGAGCGGACC-GTTTAATGAAGATTGTTCGAGTCT-TATACTCTC
*
464775 TGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTTT
64 TGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTTC
* * **
464822 TATACTCTCTGAATGAATAGAGAGCAGACACGTTTGCTGAAGATTGTTCGAGTCTTATACTCTCT
1 TATACTCTCTGAAAGAATAGAGAGCGGAC-CGTTTAATGAAGATTGTTCGAGTCTTATACTCTCT
* * *
464887 GAAGGAATAGAGAGC-GAACCCATTTTTATGAAGATTGTTCGAGTTC
65 GAAGGAATAGAGAGCAG-ACCCGTTTTAATGAAGATTGTTCAAGTTC
* *
464933 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTCTTATACTC-CT
1 TATACTCTCTGAAAGAATAGAGAGCGGA-CCGTTTAATGAAGATTGTTCGAGTCTTATACTCTC-
* * * *
464997 TGAATGAAAAGGGAGCAGACACGTTT
64 TGAAGGAATAGAGAGCAGACCCGTTT
465023 GCTGAAGATT
Statistics
Matches: 176, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
110 2 0.01
111 170 0.97
112 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (110 bp):
TATACTCTCTGAAAGAATAGAGAGCGGACCGTTTAATGAAGATTGTTCGAGTCTTATACTCTCTG
AAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTTC
Found at i:465015 original size:166 final size:166
Alignment explanation
Indices: 464703--465062 Score: 539
Period size: 166 Copynumber: 2.2 Consensus size: 166
464693 TTGTTAAAGA
* * * * *
464703 TTGAGTCATATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTA
1 TTGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCTGTTTATTGAAGATTGTTCGAGTTCTA
*
464768 TACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTTTTATACTCTCTG
66 TACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCTCTG
*
464833 AATGAATAGAGAGCAGACACGTTTGCTGAAGATT-G
131 AATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
*
464868 TTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCCATTTTTA-TGAAGATTGTTCGAGTT
1 TT-GAGTCTTATACTCTCTGAAGGAATAGAGAGCGAA-CC-TGTTTATTGAAGATTGTTCGAGTT
* *
464932 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-ATGAAGATTGTTCGAGTCTTATACTC-
63 CTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCT
*
464995 CTTGAATGAAAAGGGAGCAGACACGTTTGCTGAAGATTGG
128 C-TGAATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
* *
465035 TTGAGTCTTATACTCCCTGAAGGGATAG
1 TTGAGTCTTATACTCTCTGAAGGAATAG
465063 GGAGAAGACC
Statistics
Matches: 177, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
165 3 0.02
166 112 0.63
167 57 0.32
168 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (166 bp):
TTGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCTGTTTATTGAAGATTGTTCGAGTTCTA
TACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCTCTG
AATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
Found at i:465065 original size:55 final size:55
Alignment explanation
Indices: 464652--465071 Score: 403
Period size: 55 Copynumber: 7.7 Consensus size: 55
464642 TTTATGAAGA
* * * * * *
464652 TCGAGTCATATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTAAAGA---T
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * * * *
464704 T-GAGTCATATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTT-ATTGAAGATTTT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTTTGA-TGAAGATTGT
* *
464758 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACG-TTTGATGAAGATTGT
* * * *
464814 TCAAGTTTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTGCTGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * *
464869 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGC-GAACCCATTTTTATGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAG-ACAC-GTTTGATGAAGATTGT
* * *
464925 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * * *
464980 TCGAGTCTTATACTC-CTTGAATGAAAAGGGAGCAGACACGTTTGCTGAAGATTGGT
1 TCGAGTCTTATACTCTC-TGAAGGAATAGAGAGCAGACACGTTTGATGAAGATT-GT
* * * *
465036 T-GAGTCTTATACTCCCTGAAGGGATAGGGAGAAGAC
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC
465072 CCGTCATTCG
Statistics
Matches: 316, Mismatches: 33, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
50 1 0.00
51 42 0.13
52 1 0.00
54 4 0.01
55 164 0.52
56 101 0.32
57 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (55 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
Found at i:474800 original size:3 final size:3
Alignment explanation
Indices: 474794--474867 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
474784 ATAATAATAA
* * *
474794 TAT TAT TAT TAT TAT TAT TAT TAT AAT TA- TAT T-T AAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
474840 AAAC TAA TAT TAT TAT TAAT TAT TAT TA
1 -TAT TAT TAT TAT TAT T-AT TAT TAT TA
474868 CAACGGGCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
2 3 0.05
3 49 0.88
4 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:474866 original size:16 final size:16
Alignment explanation
Indices: 474795--474867 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
474785 TAATAATAAT
474795 ATTATTATTATTATT-
1 ATTATTATTATTATTA
*
474810 ATTATTATAATTA-TA
1 ATTATTATTATTATTA
* * *
474825 TTTAATTATAATTATAA
1 ATT-ATTATTATTATTA
* *
474842 ACTAATATTATTATTA
1 ATTATTATTATTATTA
474858 ATTATTATTA
1 ATTATTATTA
474868 CAACGGGCCA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
14 1 0.02
15 14 0.31
16 28 0.62
17 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:478353 original size:8 final size:7
Alignment explanation
Indices: 478329--478370 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
478319 TTTTCATACA
478329 TGCA-TT
1 TGCATTT
478335 TGCATTT
1 TGCATTT
478342 TGCATCTT
1 TGCAT-TT
478350 TGCATTT
1 TGCATTT
* *
478357 TTCATTG
1 TGCATTT
478364 TGCATTT
1 TGCATTT
478371 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:478353 original size:15 final size:14
Alignment explanation
Indices: 478329--478370 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
478319 TTTTCATACA
478329 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
478342 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
478357 TTCATTGTGCATTT
1 TGCATTTTGCATTT
478371 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:478459 original size:26 final size:26
Alignment explanation
Indices: 478430--478488 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
478420 CATTCACATA
*
478430 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
478456 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
478482 TTTACAT
1 TTTACAT
478489 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:480123 original size:2 final size:2
Alignment explanation
Indices: 480116--480155 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
480106 TTATCCTTTA
480116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480156 CCTTTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:483079 original size:83 final size:83
Alignment explanation
Indices: 482604--483077 Score: 743
Period size: 83 Copynumber: 5.7 Consensus size: 83
482594 CATTAACTAA
*
482604 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
*
482669 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* *
482687 AAGATGAATTTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
*
482752 ACCAATCATTGAATTAGG
66 ACCAATCATTGAATTTGG
* *
482770 AAGATGAATTTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
*
482835 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* * * *
482853 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-CAG
*
482917 AATCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
* * *
482936 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
*
483001 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
* * * *
483019 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATTTGATCTGGTTT
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTT
483078 GGTAGGAACT
Statistics
Matches: 370, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
82 3 0.01
83 363 0.98
84 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
ACCAATCATTGAATTTGG
Found at i:484343 original size:74 final size:74
Alignment explanation
Indices: 484192--484352 Score: 193
Period size: 74 Copynumber: 2.2 Consensus size: 74
484182 AAGCAAATAT
* * *
484192 TGGGGCATGCTG-AAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
484256 GCAAAATGC
66 GCAAAATGC
* * ** *
484265 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
484330 TAGC-CAATG-
64 CAGCAAAATGC
484339 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
484353 GGCCTATATC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
73 12 0.16
74 51 0.68
75 6 0.08
76 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Found at i:485666 original size:22 final size:22
Alignment explanation
Indices: 485640--485694 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
485630 ATCTACACTC
*
485640 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
485662 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
485684 TTCAAAGATGA
1 TTCAAAGATGA
485695 AAACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:486654 original size:113 final size:113
Alignment explanation
Indices: 486163--487418 Score: 1625
Period size: 113 Copynumber: 11.2 Consensus size: 113
486153 CATTTGAAGA
* *** * * * *
486163 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGATAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCA-TTTCCAGAGAAAG
*
486227 TTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATG
65 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * * * *** *
486275 AGAAGAATTTGTTCAACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
486340 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
486387 AGAAGAACTTGTTTAACCTTTTGCTCAAATCCATCATTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
486452 TCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *
486499 AGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
486564 TCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
486612 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAG-AAAG
*
486676 TTCATAATGAGAAGAACTCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATG
65 TTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
486728 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATAGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
* *
486793 TCATAATGAGAATAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ** * * *
486840 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
486905 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * * *
486953 AGAAGAATTTGTTCAATCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
487018 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
487066 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
*
487131 TCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
487179 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
487244 TCATAATGAGAAG-A---A---G--G-A--AA-AAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
487279 AGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAG-AAAG
* *
487343 TTCATAATGAGAAGAACTCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATA
65 TTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
487395 AGAAGAACTTGTTCAACTTTTTGC
1 AGAAGAACTTGTTCAACCTTTTGC
487419 ATAATTCTAT
Statistics
Matches: 1011, Mismatches: 108, Indels: 46
0.87 0.09 0.04
Matches are distributed among these distances:
99 1 0.00
100 84 0.08
101 3 0.00
103 1 0.00
104 1 0.00
106 1 0.00
107 1 0.00
109 1 0.00
110 1 0.00
111 2 0.00
112 373 0.37
113 400 0.40
114 1 0.00
115 3 0.00
116 138 0.14
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCATTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:486801 original size:341 final size:339
Alignment explanation
Indices: 486163--487418 Score: 1769
Period size: 341 Copynumber: 3.7 Consensus size: 339
486153 CATTTGAAGA
* ** * * * *
486163 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGATAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCA-TTTCCAGAGAAAG
486227 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
65 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * * * * *** * *
486292 CTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGA-AGTTCATAATGAGAAGAAC
130 CTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGTAGAGTTCATAATGAGAAGAAC
* *
486356 TT-ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCAAATCC
195 TTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCC
* *
486419 ATCATTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
260 ATCATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
486484 AAGAAGTTCATAATG
325 AAGAAGTTCATAATG
* *
486499 AGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
* * *
486564 TCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * *
486629 TTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAAC
130 CTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGTAGAGTTCATAATGAGAAGAA-
* *
486693 TCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAAT
194 -CTTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAAT
* * * * *
486758 TCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAATAACTTATCTGAAGAGGA
258 CCATCATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
486823 AGAAGAAGTTCATAATG
323 AGAAGAAGTTCATAATG
* ** * *
486840 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
*
486905 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAT
66 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * * *
486970 CTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAG-AAAGTTCATAATGAGAAGAAC
130 CTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGTAGAGTTCATAATGAGAAGAAC
* * *
487034 -TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
195 TTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCC
* * *
487098 ATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
260 ATCATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAA
487163 GAAGAAGTTCATAATG
324 GAAGAAGTTCATAATG
* * *
487179 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
*
487244 TCATAATGAGAAG-A---A---G--GA--AA-AAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
*
487297 TTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACT
131 TTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGTAGAGTTCATAATGAGAAGAA--
* *
487361 CTTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
194 CTTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
487419 ATAATTCTAT
Statistics
Matches: 824, Mismatches: 83, Indels: 33
0.88 0.09 0.04
Matches are distributed among these distances:
325 1 0.00
326 86 0.10
327 2 0.00
328 1 0.00
329 52 0.06
330 1 0.00
332 1 0.00
335 3 0.00
336 81 0.10
337 82 0.10
338 112 0.14
339 94 0.11
340 8 0.01
341 299 0.36
342 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (339 bp):
AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
TTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGTAGAGTTCATAATGAGAAGAACT
TCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCA
TCATTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
AGAAGTTCATAATG
Found at i:487326 original size:100 final size:100
Alignment explanation
Indices: 487153--487358 Score: 315
Period size: 100 Copynumber: 2.1 Consensus size: 100
487143 GAACTCATCT
* *
487153 GAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTT
1 GAAGAAAGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
* * *
487218 GATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGA
66 GATGGATCAACATTGCCAG-GTAAAGTTCATAATGA
* * *
487253 GAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTT
1 GAAGAAAGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
*
487318 GATGGATCAACATTGCCAGGTAGAGTTCATAATGA
66 GATGGATCAACATTGCCAGGTAAAGTTCATAATGA
487353 GAAGAA
1 GAAGAA
487359 CTCTTCATCT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.01
100 95 0.99
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (100 bp):
GAAGAAAGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
GATGGATCAACATTGCCAGGTAAAGTTCATAATGA
Found at i:487817 original size:3 final size:3
Alignment explanation
Indices: 487809--487929 Score: 154
Period size: 3 Copynumber: 39.7 Consensus size: 3
487799 TTCATTTAAA
487809 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
487857 TAT AAT TAT TAT TAT TAT AAT TAT AAT TACT AAT T-T TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT
* *
487903 TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT T-AT TAT TAT TA
487930 CAAACGGGCC
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.02
3 93 0.90
4 8 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:488334 original size:7 final size:7
Alignment explanation
Indices: 488318--488354 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
488308 GAACGACAAC
488318 AAAA-AA
1 AAAAGAA
488324 AAAAGAA
1 AAAAGAA
488331 AAAAGAA
1 AAAAGAA
*
488338 AAGA-AA
1 AAAAGAA
488344 AAAAGAA
1 AAAAGAA
488351 AAAA
1 AAAA
488355 ATAATAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 9 0.33
7 18 0.67
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:488339 original size:12 final size:13
Alignment explanation
Indices: 488318--488352 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
488308 GAACGACAAC
488318 AAAAAA-AAAAG-
1 AAAAAAGAAAAGA
488329 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
488342 AAAAAAGAAAA
1 AAAAAAGAAAA
488353 AAATAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 11 0.50
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:488339 original size:13 final size:14
Alignment explanation
Indices: 488318--488353 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
488308 GAACGACAAC
488318 AAAAA-AAAAAG-A
1 AAAAAGAAAAAGAA
488330 AAAAAG-AAAAGAA
1 AAAAAGAAAAAGAA
488343 AAAAAGAAAAA
1 AAAAAGAAAAA
488354 AATAATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 7 0.33
14 4 0.19
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:499229 original size:3 final size:3
Alignment explanation
Indices: 499221--499247 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
499211 TTAGCATGGC
499221 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
499248 GAGAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:499426 original size:21 final size:21
Alignment explanation
Indices: 499400--499467 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
499390 GATTCGTAAC
499400 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
499421 GCGAACTTCGACTATCACAAT
1 GCGAACTTCGACTATCGCAAT
*
499442 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
499463 GCGAA
1 GCGAA
499468 TATGTAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:499506 original size:21 final size:21
Alignment explanation
Indices: 499476--499528 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
499466 AATATGTAAA
* *
499476 TCGCAATGCGATATTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
499497 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
499518 TCGCGTTGCGA
1 TCGCATTGCGA
499529 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:502161 original size:34 final size:34
Alignment explanation
Indices: 502106--502196 Score: 130
Period size: 34 Copynumber: 2.6 Consensus size: 34
502096 GATGTGTTAA
*
502106 AAAATTAATATAATAAT-AATAATATTTGGGTGACC
1 AAAA-TAAAATAA-AATCAATAATATTTGGGTGACC
502141 AAAATAAAATAAAATCAATAATATTTGGGTGACC
1 AAAATAAAATAAAATCAATAATATTTGGGTGACC
* *
502175 AAAATATAATAAAAGCAATAAT
1 AAAATAAAATAAAATCAATAAT
502197 TAGGATTCTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.06
34 45 0.87
35 4 0.08
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (34 bp):
AAAATAAAATAAAATCAATAATATTTGGGTGACC
Found at i:503403 original size:35 final size:35
Alignment explanation
Indices: 503316--503452 Score: 131
Period size: 35 Copynumber: 4.0 Consensus size: 35
503306 GAGAAAAATT
*
503316 TCTCACTTACCCTTCATGTGAC--GCGCGCGAAA-
1 TCTCATTTACCCTTCATGTGACGTGCGCGCGAAAC
* *
503348 TTTCGTATTTACCCTTCATGTGACGTGCACGCGAAAC
1 TCTC--ATTTACCCTTCATGTGACGTGCGCGCGAAAC
* * *
503385 TCTCATGTACCCTTCATGTGACGTG-GCGAGTAATC
1 TCTCATTTACCCTTCATGTGACGTGCGCGCG-AAAC
* * *
503420 TCTCATTTACCATTCATGTTACGTG-GCGGGAAA
1 TCTCATTTACCCTTCATGTGACGTGCGCGCGAAA
503453 TCCATGACTT
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
32 3 0.03
34 22 0.26
35 49 0.57
36 9 0.10
37 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (35 bp):
TCTCATTTACCCTTCATGTGACGTGCGCGCGAAAC
Found at i:505383 original size:117 final size:121
Alignment explanation
Indices: 505190--505428 Score: 409
Period size: 117 Copynumber: 2.0 Consensus size: 121
505180 GTAATTATTA
505190 TCTAATTTTTCTATTATTATTATATATTTTCCCTCTCTCTCATATTTAGCTATTATATATATGGA
1 TCTAATTTTTCTATTATTATTATATATTTTCCCTCTCTCTCATATTTAGCTATTATATATATGGA
505255 ATTAATATTATTATATGTTTTTATTAATTTTACCTTATACGCTA-T-TTTTACATT
66 ATTAATATTATTATATGTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
*
505309 TCTAA-TTTTCTATTATTA-TATATATTTT-TC-CTCTCTCATATTTAGCTATTATGTATATATG
1 TCTAATTTTTCTATTATTATTATATATTTTCCCTCTCTCTCATATTTAGCTATTA--TATATATG
505370 GAATTAATATTATTATATGTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
64 GAATTAATATTATTATATGTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
505428 T
1 T
505429 TTATATACAT
Statistics
Matches: 115, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
115 21 0.18
116 1 0.01
117 64 0.56
118 14 0.12
119 15 0.13
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (121 bp):
TCTAATTTTTCTATTATTATTATATATTTTCCCTCTCTCTCATATTTAGCTATTATATATATGGA
ATTAATATTATTATATGTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
Found at i:506631 original size:26 final size:26
Alignment explanation
Indices: 506602--506652 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
506592 TTTTTCCTAA
*
506602 CCATTTGTTT-TTCTTATGTTTTATTG
1 CCATTTATTTCTTCTTAT-TTTTATTG
*
506628 CCATTTATTTCTTGTTATTTTTATT
1 CCATTTATTTCTTCTTATTTTTATT
506653 TATTTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.14, C:0.12, G:0.08, T:0.67
Consensus pattern (26 bp):
CCATTTATTTCTTCTTATTTTTATTG
Found at i:517077 original size:105 final size:105
Alignment explanation
Indices: 516895--517627 Score: 1266
Period size: 105 Copynumber: 7.0 Consensus size: 105
516885 AGGTTTTACC
*
516895 CAGAGCCAATTTCAACTTCCCAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
516960 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
517000 CAGAGCCAATTTCAACTTCCCAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
517065 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
517105 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
517170 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
517210 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
517275 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
517316 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
517381 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
517421 CAAGAGCCAA--T----TT--CAACGAAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
517478 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAATT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
517519 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * *
517584 GCGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
517625 CAG
1 CAG
517628 CTCCACAACG
Statistics
Matches: 603, Mismatches: 14, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
97 8 0.01
98 82 0.14
99 1 0.00
100 2 0.00
103 2 0.00
104 1 0.00
105 382 0.63
106 125 0.21
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:517316 original size:211 final size:210
Alignment explanation
Indices: 516895--517626 Score: 1273
Period size: 211 Copynumber: 3.5 Consensus size: 210
516885 AGGTTTTACC
* *
516895 CAGAGCCAATTTCAACTTCCCAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
516960 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC-AGAGCCAATTTCAACTTCCCAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAATTTCAACTT-CCAAC
517024 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
517089 AAACATTTCTCAATTT
195 AAACATTTCTCAATTT
*
517105 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
517170 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAATTTCAACTTC-CAAC
517235 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
517300 AAACATTTCTCAATTT
195 AAACATTTCTCAATTT
*
517316 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
517381 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAA--T----TT-CAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAATTTCAACTTCCAACG
* *
517439 AAGGATATTGGACTCCGGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* *
517504 AACATTTCCCAAATT
196 AACATTTCTCAATTT
*
517519 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
517584 GCGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCA
517627 GCTCCACAAC
Statistics
Matches: 505, Mismatches: 14, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
203 170 0.34
204 13 0.03
205 2 0.00
209 1 0.00
210 104 0.21
211 215 0.43
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAAGAGCCAATTTCAACTTCCAACG
AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAATTT
Found at i:517714 original size:20 final size:20
Alignment explanation
Indices: 517685--517726 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
517675 CCAGAACTCT
517685 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
517705 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
517725 GA
1 GA
517727 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:517967 original size:22 final size:23
Alignment explanation
Indices: 517939--517986 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
517929 AATTTCGTCC
517939 TTATATTATATAA-TATA-TATAT
1 TTATATTATA-AATTATATTATAT
517961 TTATATTATAAATTATATTATAT
1 TTATATTATAAATTATATTATAT
517984 TTA
1 TTA
517987 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATTATAAATTATATTATAT
Found at i:519283 original size:59 final size:58
Alignment explanation
Indices: 519220--519417 Score: 141
Period size: 59 Copynumber: 3.3 Consensus size: 58
519210 ATTTTTCTAT
*
519220 TATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATATGTATATGGAATTAA
1 TATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTAT-TATATATGGAATTAA
* *** * * * * * * ** **
519279 TATTATTATATGTTTTTTATTAAT-TTTACCT-TATACGCTATTATTTTACATTTCTAATTTTTC
1 TATTATTATATATTTTTCCCT-CTCTCT-CATATTTA-GCTATTA--TTATATATGGAA--TTAA
519342 TATTATTAT-TATATTTTCCCTCTCTCTCATATTTAGCTATTATGTATATATGGAATTAA
1 TATTATTATATAT-TTTTCCCTCTCTCTCATATTTAGCTATTAT-TATATATGGAATTAA
*
519401 TATTATTATATGTTTTT
1 TATTATTATATATTTTT
519418 TATTAATTTT
Statistics
Matches: 97, Mismatches: 30, Indels: 24
0.64 0.20 0.16
Matches are distributed among these distances:
59 37 0.38
60 13 0.13
61 13 0.13
62 13 0.13
63 21 0.22
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (58 bp):
TATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATTATATATGGAATTAA
Found at i:519370 original size:122 final size:125
Alignment explanation
Indices: 519206--519453 Score: 457
Period size: 122 Copynumber: 2.0 Consensus size: 125
519196 GTAATTATTA
*
519206 TCTAATTTTTCTATTATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATATGTATAT
1 TCTAATTTTTCTATTATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATATATATAT
519271 GGAATTAATATTATTATATGTTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
66 GGAATTAATATTATTATATGTTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
*
519331 TCTAATTTTTCTATTATTA-T-TATA-TTTTCCCTCTCTCTCATATTTAGCTATTATGTATATAT
1 TCTAATTTTTCTATTATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATATATATAT
519393 GGAATTAATATTATTATATGTTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
66 GGAATTAATATTATTATATGTTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
519453 T
1 T
519454 TTTATATACA
Statistics
Matches: 121, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
122 97 0.80
123 4 0.03
124 1 0.01
125 19 0.16
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (125 bp):
TCTAATTTTTCTATTATTATTATATATTTTTCCCTCTCTCTCATATTTAGCTATTATATATATAT
GGAATTAATATTATTATATGTTTTTTATTAATTTTACCTTATACGCTATTATTTTACATT
Found at i:520397 original size:111 final size:111
Alignment explanation
Indices: 520266--520471 Score: 387
Period size: 111 Copynumber: 1.9 Consensus size: 111
520256 TTTGCCCTTT
520266 GAGAGAGAGAGAGAGGGGGGCATGAGGCCAGGCTTCACCAGAGTTCTCTCTTCTCTGGTTTTGAC
1 GAGAGAGAGAGAGAGGGGGGCATGAGGCCAGGCTTCACCAGAGTTCTCTCTTCTCTGGTTTTGAC
520331 ATAGATTGTCCTGGCTGGCTATAGTAATTGGTCGGCATGAGGCCAC
66 ATAGATTGTCCTGGCTGGCTATAGTAATTGGTCGGCATGAGGCCAC
*
520377 GAGAGAGAGAGAG-GAGGGGGCATGAGGCCAGGCTTCACCAGAGTTCTCTCTTTTCTGGTTTTGA
1 GAGAGAGAGAGAGAG-GGGGGCATGAGGCCAGGCTTCACCAGAGTTCTCTCTTCTCTGGTTTTGA
520441 CATAGATTGTCCTGGCTGGCTATAGTAATTG
65 CATAGATTGTCCTGGCTGGCTATAGTAATTG
520472 ATCACAATGT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
110 1 0.01
111 92 0.99
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (111 bp):
GAGAGAGAGAGAGAGGGGGGCATGAGGCCAGGCTTCACCAGAGTTCTCTCTTCTCTGGTTTTGAC
ATAGATTGTCCTGGCTGGCTATAGTAATTGGTCGGCATGAGGCCAC
Found at i:529951 original size:21 final size:21
Alignment explanation
Indices: 529925--529964 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
529915 CAGAACCCCA
*
529925 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
529946 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
529965 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:529997 original size:21 final size:21
Alignment explanation
Indices: 529946--530008 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
529936 ATTCCCCTGT
529946 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
529969 AGGAGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
529990 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
530009 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.57
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:537855 original size:19 final size:20
Alignment explanation
Indices: 537833--537876 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
537823 TTGAAAAGTT
537833 GGGAAATTGAG-AATTTAGA
1 GGGAAATTGAGAAATTTAGA
*
537852 GGGAAATTGGGAAATTTAGA
1 GGGAAATTGAGAAATTTAGA
537872 GGGAA
1 GGGAA
537877 TAGAGAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (20 bp):
GGGAAATTGAGAAATTTAGA
Found at i:538235 original size:18 final size:19
Alignment explanation
Indices: 538195--538237 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
538185 ATGGATAATA
* *
538195 CATACATGCATATATTTAT
1 CATACATGCATACATTGAT
538214 -ATACATGCAT-CATTGAT
1 CATACATGCATACATTGAT
538231 CATACAT
1 CATACAT
538238 AATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (19 bp):
CATACATGCATACATTGAT
Found at i:538279 original size:18 final size:19
Alignment explanation
Indices: 538240--538307 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
538230 TCATACATAA
* *
538240 TTATATA-TATATATATAGT
1 TTATATATTTTATAT-TATT
538259 TTATATATTTTATATT-TT
1 TTATATATTTTATATTATT
* *
538277 TTATGTATATATTATATTATA
1 TTA--TATATTTTATATTATT
538298 TTAT-TATTTT
1 TTATATATTTT
538308 GTTTCTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 9 0.22
19 9 0.22
20 18 0.45
21 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATATATTTTATATTATT
Found at i:545225 original size:19 final size:19
Alignment explanation
Indices: 545201--545263 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
545191 TGCATATAAA
545201 ATTAAGAGATAAATGATTC
1 ATTAAGAGATAAATGATTC
* * *
545220 ATTAAGA-CTATAT-ATTTT
1 ATTAAGAGATAAATGA-TTC
545238 ATTAAGAGATAAATGATTC
1 ATTAAGAGATAAATGATTC
545257 ATTAAGA
1 ATTAAGA
545264 CTATATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
ATTAAGAGATAAATGATTC
Found at i:545242 original size:37 final size:37
Alignment explanation
Indices: 545201--545276 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
545191 TGCATATAAA
545201 ATTAAGAGATAAATGATTCATTAAGACTATATATTTT
1 ATTAAGAGATAAATGATTCATTAAGACTATATATTTT
545238 ATTAAGAGATAAATGATTCATTAAGACTATATATTTT
1 ATTAAGAGATAAATGATTCATTAAGACTATATATTTT
545275 AT
1 AT
545277 CTCTAGGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (37 bp):
ATTAAGAGATAAATGATTCATTAAGACTATATATTTT
Found at i:545243 original size:18 final size:18
Alignment explanation
Indices: 545220--545276 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
545210 TAAATGATTC
545220 ATTAAGACTATATATTTT
1 ATTAAGACTATATATTTT
* * *
545238 ATTAAGA-GATAAATGATTC
1 ATTAAGACTATATAT--TTT
545257 ATTAAGACTATATATTTT
1 ATTAAGACTATATATTTT
545275 AT
1 AT
545277 CTCTAGGTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 5 0.17
18 11 0.37
19 9 0.30
20 5 0.17
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTAAGACTATATATTTT
Found at i:549811 original size:19 final size:17
Alignment explanation
Indices: 549775--549808 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
549765 TAACTTCAAA
549775 ATATTTTAAAATAAAAT
1 ATATTTTAAAATAAAAT
549792 ATATATTTAAAATAAAA
1 ATAT-TTTAAAATAAAA
549809 ATAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTTTAAAATAAAAT
Found at i:550995 original size:20 final size:20
Alignment explanation
Indices: 550967--551108 Score: 148
Period size: 20 Copynumber: 7.1 Consensus size: 20
550957 CCTAATTCGT
550967 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
550987 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
*
551008 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
551028 AATGTGAATACGT-AATCGC
1 AATGCGAATACGTAAATCGC
* *
551047 AATGCGATTAC--AACTATTGC
1 AATGCGAATACGTAA--ATCGC
551067 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
551087 AATGCGAAT-CTGTAAATCGC
1 AATGCGAATAC-GTAAATCGC
551107 AA
1 AA
551109 CGAGATTCTG
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
18 1 0.01
19 16 0.16
20 65 0.66
21 15 0.15
22 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:551055 original size:39 final size:40
Alignment explanation
Indices: 550967--551108 Score: 148
Period size: 39 Copynumber: 3.5 Consensus size: 40
550957 CCTAATTCGT
* * ** *
550967 AATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGC
1 AATGCGATTACGTAAATCGCAATGCGAA-TACGTAAATCGC
*
551008 AATGCGATTACGTAAATCGCAATGTGAATACGT-AATCGC
1 AATGCGATTACGTAAATCGCAATGCGAATACGTAAATCGC
*
551047 AATGCGATTAC--AACTATTGCAATGCGAATACGTAAATCGC
1 AATGCGATTACGTAA--ATCGCAATGCGAATACGTAAATCGC
*
551087 AATGCGAAT-CTGTAAATCGCAA
1 AATGCGATTAC-GTAAATCGCAA
551109 CGAGATTCTG
Statistics
Matches: 85, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
37 2 0.02
39 34 0.40
40 22 0.26
41 25 0.29
42 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (40 bp):
AATGCGATTACGTAAATCGCAATGCGAATACGTAAATCGC
Found at i:551118 original size:20 final size:20
Alignment explanation
Indices: 551078--551118 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
551068 ATGCGAATAC
* *
551078 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
551098 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
551118 G
1 G
551119 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:552011 original size:24 final size:24
Alignment explanation
Indices: 551960--552013 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
551950 GTATTCGAAA
* * *
551960 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCATGGTCAATACACAGAC
* *
551984 TTTGATCATGGTCAATACACATAT
1 TTTGATCATGGTCAATACACAGAC
552008 TTTGAT
1 TTTGAT
552014 GATTTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (24 bp):
TTTGATCATGGTCAATACACAGAC
Found at i:554469 original size:20 final size:19
Alignment explanation
Indices: 554432--554520 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 19
554422 TAACGCGGAA
554432 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
* *
554452 ATCTCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
554472 ATCGCAATGCGAAATTGACT
1 ATCGCAACGCGAAA-TGACT
554492 ATCGCAACGCAGAAATGACT
1 ATCGCAACGC-GAAATGACT
554512 ATCGCAACG
1 ATCGCAACG
554521 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.07
20 49 0.82
21 7 0.12
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:554580 original size:34 final size:33
Alignment explanation
Indices: 554492--554587 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
554482 GAAATTGACT
* **
554492 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
554526 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
554559 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
554588 CGAAAGTCTG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:554583 original size:20 final size:19
Alignment explanation
Indices: 554525--554592 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
554515 GCAACGAGAG
554525 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
554544 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
554558 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
554578 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
554593 GTCTGTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:554712 original size:14 final size:14
Alignment explanation
Indices: 554693--554729 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
554683 CATCAATTAA
554693 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
554707 ACAAATCATCTTTT
1 ACAAATCAACATTT
554721 ACAAATCAA
1 ACAAATCAA
554730 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:556144 original size:21 final size:21
Alignment explanation
Indices: 556068--556149 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
556058 GTTGGGAGGA
* *
556068 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGACAGGGG
* **
556089 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
556110 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
556131 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
556150 TGAGTCGAGC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:556698 original size:34 final size:33
Alignment explanation
Indices: 556615--556699 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
556605 TCTGAAACTT
** * *
556615 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
* * *
556649 AGAATTGCAATGCGAAATGAAAATCGCAAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGC-AACAAC
556683 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
556700 ATGACTATCG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
33 11 0.28
34 29 0.73
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:556711 original size:20 final size:20
Alignment explanation
Indices: 556686--556751 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
556676 AAACAACAAA
556686 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
556706 ATCGC-ACGCGAAAA-G-CT
1 ATCGCAACGCGAAAATGACT
* **
556723 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
556743 ATCGCAACG
1 ATCGCAACG
556752 AGAGAATCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.18
18 7 0.18
19 10 0.26
20 15 0.38
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:556843 original size:54 final size:54
Alignment explanation
Indices: 556774--556878 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
556764 TACAATTTTA
* *
556774 TTTCTCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
**
556828 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGT
556879 AAACTATTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (54 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
Found at i:556874 original size:20 final size:20
Alignment explanation
Indices: 556795--556878 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
556785 GATTCTTTCG
**
556795 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
556815 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
556835 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
556849 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
556869 TTGCGATAGT
1 TTGCGATAGT
556879 AAACTATTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
16 6 0.11
18 6 0.11
20 35 0.65
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Done.