Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:433348 original size:19 final size:19
Alignment explanation
Indices: 433302--433350 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
433292 TTATATTCAC
*
433302 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
433321 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
433340 ATACAAAATTA
1 ATACAAAATTA
433351 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:435198 original size:32 final size:33
Alignment explanation
Indices: 435139--435203 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
435129 CATCTTAATA
*
435139 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
**
435172 TCACCCCTCAACA-CCTTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
435204 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:435261 original size:21 final size:21
Alignment explanation
Indices: 435236--435300 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
435226 CCCCTTATGC
* *
435236 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
435257 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
435278 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
435299 CT
1 CT
435301 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:435403 original size:15 final size:15
Alignment explanation
Indices: 435383--435414 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
435373 ACTCTGTTTT
*
435383 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
435398 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
435413 CC
1 CC
435415 AATACAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.62, G:0.09, T:0.19
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:437712 original size:20 final size:20
Alignment explanation
Indices: 437685--437731 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
437675 ATCGGTAACG
437685 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
437704 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
437725 TTTTACC
1 TTTTACC
437732 TGGTATATCG
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:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:437825 original size:177 final size:179
Alignment explanation
Indices: 437477--437942 Score: 638
Period size: 181 Copynumber: 2.6 Consensus size: 179
437467 CGTACTTACG
* * * *
437477 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGTTTTTATCATTTTGATACCGGTAT
1 AAAGTATCGACACTTT-AA-ATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
437542 TATCATATTTTTACCTGTTATATCG-TGTGGATCGATATATTTTTTAAAGTATCGACACATTATA
64 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
* *
437606 GGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
129 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
437656 -AAGTATCGACACTTTTAATAT-CGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTTTA
1 AAAGTATCGACACTTTAAATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTA
* *
437719 TCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTATAG
66 TCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTATAG
** *
437784 GATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * *
437834 AAAGT-CCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAA--TATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
437897 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
63 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
437943 AATTTGGATC
Statistics
Matches: 254, Mismatches: 25, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
175 59 0.23
176 22 0.09
177 63 0.25
178 27 0.11
179 4 0.02
180 3 0.01
181 75 0.30
182 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (179 bp):
AAAGTATCGACACTTTAAATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTA
TCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAGG
AGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:443981 original size:14 final size:14
Alignment explanation
Indices: 443962--443990 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
443952 TTTGTGCTTC
443962 AATCATGTAGAGAT
1 AATCATGTAGAGAT
443976 AATCATGTAGAGAT
1 AATCATGTAGAGAT
443990 A
1 A
443991 TTTTTCATTG
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:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
AATCATGTAGAGAT
Found at i:446752 original size:17 final size:17
Alignment explanation
Indices: 446730--446762 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
446720 TCCTCTTGGT
446730 GAGCTAGTA-GTTTTTTC
1 GAGCTA-TATGTTTTTTC
446747 GAGCTATATGTTTTTT
1 GAGCTATATGTTTTTT
446763 TTTTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.52
Consensus pattern (17 bp):
GAGCTATATGTTTTTTC
Found at i:449997 original size:24 final size:24
Alignment explanation
Indices: 449970--450021 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
449960 AGTTTATGTG
*
449970 TTTTCTTTTTAAAAATATATATAA
1 TTTTATTTTTAAAAATATATATAA
* *
449994 TTTTATTTTTAAAATTTTATATAA
1 TTTTATTTTTAAAAATATATATAA
450018 TTTT
1 TTTT
450022 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATTTTTAAAAATATATATAA
Found at i:452870 original size:20 final size:21
Alignment explanation
Indices: 452832--452871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
452822 CCAAACCCAA
*
452832 AATATCGATATTGGGATGAAC
1 AATATCGATACTGGGATGAAC
452853 AATATCGATACT-GGATGAA
1 AATATCGATACTGGGATGAA
452872 TTGGGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
AATATCGATACTGGGATGAAC
Found at i:452982 original size:20 final size:20
Alignment explanation
Indices: 452957--453018 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
452947 TCAAGATCGC
* **
452957 CTGGTCTCTATACCGAAGGA
1 CTGGTCTCAATACCGAAAAA
*
452977 CTGGTCTCAATACTGAAAAA
1 CTGGTCTCAATACCGAAAAA
* *
452997 CTGCTCTCCATACCGAATAAA
1 CTGGTCTCAATACCGAA-AAA
453018 C
1 C
453019 GGATATCCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (20 bp):
CTGGTCTCAATACCGAAAAA
Found at i:456449 original size:29 final size:29
Alignment explanation
Indices: 456403--456491 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 29
456393 ATAAATTACT
* *
456403 AAAGAATGGAGCCATAATTGTAATGATTA
1 AAAGAATGGAGCCATAATTATAAAGATTA
*
456432 AAAGAGTGAGAGCC-TAATTATAAAGATTA
1 AAAGAATG-GAGCCATAATTATAAAGATTA
* * * * *
456461 AAAGTATAGAGCCCTAAGTATAAATATTA
1 AAAGAATGGAGCCATAATTATAAAGATTA
456490 AA
1 AA
456492 GGAACGGGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.10
29 40 0.80
30 5 0.10
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (29 bp):
AAAGAATGGAGCCATAATTATAAAGATTA
Found at i:458320 original size:44 final size:44
Alignment explanation
Indices: 458267--458355 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
458257 TGCATAAATA
458267 AATAAAATCCCATAATTTGAAGAAAACCAGGAATCAAAAATCAT
1 AATAAAATCCCATAATTTGAAGAAAACCAGGAATCAAAAATCAT
458311 AATAAAATCCCATAATTTGAAGAAAACCAGGAATCAAAAATCAT
1 AATAAAATCCCATAATTTGAAGAAAACCAGGAATCAAAAATCAT
458355 A
1 A
458356 CTTTTGTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (44 bp):
AATAAAATCCCATAATTTGAAGAAAACCAGGAATCAAAAATCAT
Found at i:459411 original size:20 final size:20
Alignment explanation
Indices: 459365--459403 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
459355 TATAAATATT
*
459365 AAATTTAAAAAATATATTCA
1 AAATTTTAAAAATATATTCA
459385 AAATTTTAAAAA-ATATTCA
1 AAATTTTAAAAATATATTCA
459404 CTAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTAAAAATATATTCA
Found at i:460195 original size:2 final size:2
Alignment explanation
Indices: 460188--460223 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
460178 TTCAACTTCC
* *
460188 CT CT CT CT GT CT CT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
460224 GTATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:460207 original size:14 final size:14
Alignment explanation
Indices: 460188--460225 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
460178 TTCAACTTCC
460188 CTCTCTCTGTCTCT
1 CTCTCTCTGTCTCT
*
460202 CTCTCTCTTTCTCT
1 CTCTCTCTGTCTCT
460216 CTCTCTCTGT
1 CTCTCTCTGT
460226 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.05, T:0.53
Consensus pattern (14 bp):
CTCTCTCTGTCTCT
Found at i:471315 original size:37 final size:37
Alignment explanation
Indices: 471242--471316 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
471232 GTTGGAAAAT
* *
471242 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
471279 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
471316 A
1 A
471317 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:475126 original size:22 final size:22
Alignment explanation
Indices: 475101--475149 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
475091 ACTTTTTGGG
475101 TGAAATGAATTAACTA-TTTTCA
1 TGAAAT-AATTAACTATTTTTCA
*
475123 TGAAAATACTTAACTATTTTTCA
1 TG-AAATAATTAACTATTTTTCA
475146 TGAA
1 TGAA
475150 TAGAGATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (22 bp):
TGAAATAATTAACTATTTTTCA
Found at i:475129 original size:23 final size:23
Alignment explanation
Indices: 475103--475149 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
475093 TTTTTGGGTG
475103 AAATGAATTAACTA-TTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
475126 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
475149 A
1 A
475150 TAGAGATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:479217 original size:325 final size:324
Alignment explanation
Indices: 478382--479341 Score: 1593
Period size: 324 Copynumber: 3.0 Consensus size: 324
478372 AGCCTGATCG
* * * *
478382 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAGTGTACTGAAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
* * ** *
478447 ATGTTGATAGCAAGATGCAGGCATTGTTGGAAGAGTTAAGTGTTACTAAAGAAATGCTTGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
* * *
478512 TCCGAGAAAGAAAATGCTAGTCTGAAGCTTGA-GAAGAAGCAGTTTTATGAGAAAATTCAAAATT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACG-AGAAGCAGTTTTATGAGAAAATTCAAGATT
478576 TGCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGA
195 TGCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGA
* * * *
478641 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTTGAAATTTGAGTGCAGGAGGCTTAA
260 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
478706 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGC-AC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
478770 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
*
478835 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGATAAAATTCAAGATTT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
*
478900 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTTGCTGAGAAA
196 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGC-TTGCTGAGAGA
*
478965 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAGATTGGAGAGCAGAAGGCTTAA
260 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
*
479030 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCGGCGTACTGGAGAAAGAAAAGCAAC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
*
479095 ATGTTGACAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
479160 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
* * * *
479225 GCAGTGTCAGCTCGATACGGTTCAAAGAGAAATTGCGGAGTTGAAACTGGAGCTTGTTGAGAGCA
196 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAA
* * * * * *
479290 GCAGTTGTAT-TAAAGTCTTAAATGAAGACCTTGAGACTTCAAAATCGGAGAG
261 GCAGCTGCATGGAAA-TCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAG
479342 AAACGTGCTT
Statistics
Matches: 598, Mismatches: 34, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
323 177 0.30
324 240 0.40
325 181 0.30
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (324 bp):
AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAA
GCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
Found at i:479897 original size:17 final size:17
Alignment explanation
Indices: 479875--479909 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
479865 GATCTGATGC
*
479875 ATAATGCAAGTATTCTT
1 ATAATGCAAGTAATCTT
479892 ATAATGCAAGTAATCTT
1 ATAATGCAAGTAATCTT
479909 A
1 A
479910 CCATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
ATAATGCAAGTAATCTT
Found at i:485590 original size:11 final size:11
Alignment explanation
Indices: 485557--485599 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
485547 ATTCGTATTA
485557 AAAAATATTATAT
1 AAAAATATT-T-T
*
485570 AATAATATTTT
1 AAAAATATTTT
*
485581 AAATATATTTT
1 AAAAATATTTT
485592 AAAAATAT
1 AAAAATAT
485600 ATATGTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 1 0.04
13 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:485627 original size:124 final size:125
Alignment explanation
Indices: 485498--485730 Score: 321
Period size: 124 Copynumber: 1.9 Consensus size: 125
485488 AACATATTAA
*
485498 AATAATAAAATTTTAAGTCAATATATTTTAAAAATATATATCCTATTATATTCGTATTAAAAA-A
1 AATAATAAAATTTTAAGTCAATATATTTTAAAAATATAT-TCCTA-TATATTCATATTAAAAATA
485562 TATTATATAATAATATTTT-A-AATATATTTTAAAA-ATATATATGTTCGATTATATTCGTAT
64 TATTATATAATAAT-TTTTAATAATATATTTTAAAATATATATATGTTCGATTATATTCGTAT
** * *
485622 AATAATAATTTTTTAAGTTAATATATTTTAAAAATATATTCTTATATATTCATATTAAAAATATA
1 AATAATAAAATTTTAAGTCAATATATTTTAAAAATATATTCCTATATATTCATATTAAAAATATA
* * *
485687 TTTTATATTTATTTTTAAGTTAATATATTTTAAAATATATATAT
66 TTATATAATAATTTTTAA--TAATATATTTTAAAATATATATAT
485731 ATTTGTATTT
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
122 20 0.21
123 17 0.18
124 36 0.38
126 14 0.15
127 8 0.08
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (125 bp):
AATAATAAAATTTTAAGTCAATATATTTTAAAAATATATTCCTATATATTCATATTAAAAATATA
TTATATAATAATTTTTAATAATATATTTTAAAATATATATATGTTCGATTATATTCGTAT
Found at i:485704 original size:25 final size:26
Alignment explanation
Indices: 485646--485701 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
485636 AAGTTAATAT
485646 ATTTTAAAAATATATTCTTATATATTC
1 ATTTTAAAAATATATT-TTATATATTC
*
485673 ATATTAAAAATATATTTTATAT-TT-
1 ATTTTAAAAATATATTTTATATATTC
485697 ATTTT
1 ATTTT
485702 TAAGTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 2 0.07
26 6 0.22
27 15 0.56
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTAAAAATATATTTTATATATTC
Found at i:491770 original size:15 final size:15
Alignment explanation
Indices: 491726--491772 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
491716 GCTGTCATCA
*
491726 TCATCGTCATCGTCA
1 TCATCGTCATCGTCG
* *
491741 CCATTGTCATCGTCG
1 TCATCGTCATCGTCG
491756 TCATCGTCATCGTCG
1 TCATCGTCATCGTCG
491771 TC
1 TC
491773 GTCCTGAGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
TCATCGTCATCGTCG
Found at i:493793 original size:111 final size:111
Alignment explanation
Indices: 493661--493882 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
493651 ATTACAAAAA
* *
493661 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
493726 AATTAAAACGTTAAAATGTTACCGTATCAATAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
493772 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
493837 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
493883 ATGATTTCTA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:494010 original size:10 final size:10
Alignment explanation
Indices: 493997--494038 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
493987 ACATTAAAAA
493997 GAGAGAATTT
1 GAGAGAATTT
494007 GAGAGAAATTT
1 GAGAG-AATTT
494018 -AGAGAATTT
1 GAGAGAATTT
494027 GAGAGAATTT
1 GAGAGAATTT
494037 GA
1 GA
494039 TGTGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.17
10 20 0.67
11 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:503525 original size:27 final size:27
Alignment explanation
Indices: 503487--503542 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
503477 GATCGGCGTT
503487 GAGGGTAAAGCTGAAGACGAGGGGGAA
1 GAGGGTAAAGCTGAAGACGAGGGGGAA
503514 GAGGGTAAAGCTGAAGACGAGGGGGAA
1 GAGGGTAAAGCTGAAGACGAGGGGGAA
503541 GA
1 GA
503543 AGAAGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.48, T:0.07
Consensus pattern (27 bp):
GAGGGTAAAGCTGAAGACGAGGGGGAA
Found at i:509346 original size:20 final size:20
Alignment explanation
Indices: 509279--509346 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
509269 TTACCTTTGG
*
509279 TATCGATATTGCAAGAACAA
1 TATCGATATTGTAAGAACAA
* * * **
509299 TATCAATATTGTTCA-TACGG
1 TATCGATATTG-TAAGAACAA
*
509319 TATTGATATTGTAAGAACAA
1 TATCGATATTGTAAGAACAA
509339 TATCGATA
1 TATCGATA
509347 CTACTTACCT
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.91
21 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (20 bp):
TATCGATATTGTAAGAACAA
Found at i:510008 original size:24 final size:24
Alignment explanation
Indices: 509976--510044 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
509966 GTTAAAATGA
*
509976 TAAACGAACATAAACAAACGAACG
1 TAAACGAACACAAACAAACGAACG
* *
510000 TAAATGAACACAAACGAACGAACG
1 TAAACGAACACAAACAAACGAACG
* * *
510024 TAAACAAATACAAACGAACGA
1 TAAACGAACACAAACAAACGA
510045 TTACAAACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.58, C:0.20, G:0.13, T:0.09
Consensus pattern (24 bp):
TAAACGAACACAAACAAACGAACG
Found at i:510169 original size:16 final size:17
Alignment explanation
Indices: 510145--510187 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
510135 ATTTTTTTAT
*
510145 TTGGGTTTAAA-ATTAA
1 TTGGATTTAAATATTAA
510161 TTGGATTTAAAATATTAA
1 TTGGATTT-AAATATTAA
510179 -TGGATTTAA
1 TTGGATTTAA
510188 GGTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (17 bp):
TTGGATTTAAATATTAA
Found at i:512298 original size:16 final size:16
Alignment explanation
Indices: 512279--512316 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
512269 AATTGATCAT
512279 GTTAATAATTCACGTG
1 GTTAATAATTCACGTG
*
512295 GTTAA-CATTCACGTG
1 GTTAATAATTCACGTG
512310 GTCTAAT
1 GT-TAAT
512317 TATGTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (16 bp):
GTTAATAATTCACGTG
Found at i:516066 original size:2 final size:2
Alignment explanation
Indices: 516059--516093 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
516049 GTTACTTTAT
516059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
516094 TTCAAAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:518038 original size:44 final size:44
Alignment explanation
Indices: 517927--518024 Score: 187
Period size: 44 Copynumber: 2.2 Consensus size: 44
517917 ATGAAAACAA
517927 AACTATCAATTAAATACACGTTTCATATTAAAAAAAAAACCCTT
1 AACTATCAATTAAATACACGTTTCATATTAAAAAAAAAACCCTT
*
517971 AACTATCAATTAAATACACGTTTCATATTAAAAAAAAACCCCTT
1 AACTATCAATTAAATACACGTTTCATATTAAAAAAAAAACCCTT
518015 AACTATCAAT
1 AACTATCAAT
518025 AATCTCTTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (44 bp):
AACTATCAATTAAATACACGTTTCATATTAAAAAAAAAACCCTT
Found at i:520248 original size:10 final size:10
Alignment explanation
Indices: 520235--520259 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
520225 TTTATTTCTT
520235 AATTAAAATA
1 AATTAAAATA
520245 AATTAAAATA
1 AATTAAAATA
520255 AATTA
1 AATTA
520260 TTTATCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAAAATA
Found at i:527207 original size:29 final size:30
Alignment explanation
Indices: 527172--527234 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
527162 AAGCCTTAGA
* * * *
527172 AAAAATTA-GGGACTATTCTATAATTTTTG
1 AAAAATTAGGGGACCAATCAATAATTTTGG
527201 AAAAATTAGGGGACCAATCAATAATTTTGG
1 AAAAATTAGGGGACCAATCAATAATTTTGG
527231 AAAA
1 AAAA
527235 GTTTTGGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (30 bp):
AAAAATTAGGGGACCAATCAATAATTTTGG
Found at i:529663 original size:18 final size:18
Alignment explanation
Indices: 529633--529734 Score: 95
Period size: 17 Copynumber: 5.8 Consensus size: 18
529623 ATTCTAAATG
*
529633 TTTACAATTATCAGATGA
1 TTTACAGTTATCAGATGA
**
529651 TTTTTAGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
*
529668 TTTACAGATATCAGATGA
1 TTTACAGTTATCAGATGA
*
529686 -TTACAGTTATCAAAT-A
1 TTTACAGTTATCAGATGA
** *
529702 TTTACAGACATAAGAT-A
1 TTTACAGTTATCAGATGA
529719 TTTTACAGTTATCAGA
1 -TTTACAGTTATCAGA
529735 CACATATTAA
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
16 1 0.02
17 39 0.59
18 26 0.39
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:529680 original size:35 final size:35
Alignment explanation
Indices: 529633--529734 Score: 120
Period size: 34 Copynumber: 2.9 Consensus size: 35
529623 ATTCTAAATG
*
529633 TTTACA-ATTATCAGATGATTTTTAGTTATCAGATA
1 TTTACAGA-TATCAGATGATTTTCAGTTATCAGATA
* *
529668 TTTACAGATATCAGATGA-TTACAGTTATCAAATA
1 TTTACAGATATCAGATGATTTTCAGTTATCAGATA
* *
529702 TTTACAGACATAAGAT-ATTTTACAGTTATCAGA
1 TTTACAGATATCAGATGATTTT-CAGTTATCAGA
529735 CACATATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.51
35 26 0.46
36 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (35 bp):
TTTACAGATATCAGATGATTTTCAGTTATCAGATA
Found at i:535053 original size:20 final size:20
Alignment explanation
Indices: 535009--535081 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
534999 GACCAACAAA
*
535009 ATCGCAATGCGATCTCT-A-A
1 ATCGCAATGCGAT-TCTGACT
535028 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
* *
535048 ATCGCAACGCGATTATGACT
1 ATCGCAATGCGATTCTGACT
*
535068 ATCGCATTGCGATT
1 ATCGCAATGCGATT
535082 TTCCAAATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
18 3 0.06
19 14 0.30
20 30 0.64
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:535114 original size:21 final size:21
Alignment explanation
Indices: 535068--535123 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
535058 GATTATGACT
*
535068 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
535089 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
535110 ATCGCAATGCGATT
1 ATCGCATTGCGATT
535124 ATGACTATCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:535135 original size:20 final size:20
Alignment explanation
Indices: 535028--535142 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
535018 CGATCTCTAA
*
535028 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTATGACT
*
535048 ATCGCAACGCGATTATGACT
1 ATCGCAATGCGATTATGACT
* ** *
535068 ATCGCATTGCGATT-TTCCAA
1 ATCGCAATGCGATTATGAC-T
** * **
535088 ATTCGCGTTGCGATTTTAGAAA
1 A-TCGCAATGCGATTAT-GACT
535110 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTATGACT
*
535130 ATCGCAACGCGAT
1 ATCGCAATGCGAT
535143 AATACATAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.61
21 24 0.32
22 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
ATCGCAATGCGATTATGACT
Found at i:535349 original size:17 final size:17
Alignment explanation
Indices: 535327--535364 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
535317 CGACATCCGT
535327 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
*
535344 TCCTATATCCAATGACA
1 TCCTATATCCAACGACA
535361 TCCT
1 TCCT
535365 TTCCCATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:536057 original size:24 final size:25
Alignment explanation
Indices: 536012--536059 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
536002 AGTCAGTATT
536012 CGAAATTTGATCTTTGGTCAATACC
1 CGAAATTTGATCTTTGGTCAATACC
*
536037 CGAACTTTGATC-TTGGTCAATAC
1 CGAAATTTGATCTTTGGTCAATAC
536060 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (25 bp):
CGAAATTTGATCTTTGGTCAATACC
Found at i:536071 original size:24 final size:25
Alignment explanation
Indices: 536017--536064 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
536007 GTATTCGAAA
*
536017 TTTGATCTTTGGTCAATACCCGAAC
1 TTTGATCTTTGGTCAATACCAGAAC
536042 TTTGATC-TTGGTCAATACTCAGA
1 TTTGATCTTTGGTCAATAC-CAGA
536065 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTGATCTTTGGTCAATACCAGAAC
Found at i:538718 original size:140 final size:140
Alignment explanation
Indices: 538425--538971 Score: 1028
Period size: 140 Copynumber: 3.9 Consensus size: 140
538415 AAACGTTGTA
*
538425 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
538490 TGATCTGTTCA---GTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
538552 TATGTGTATT
131 TATGTGTATT
*
538562 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
538627 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
538692 TATGTGTATT
131 TATGTGTATT
*
538702 TTATGTGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
538767 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
538832 TATGTGTATT
131 TATGTGTATT
538842 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
538907 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCTAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
538972 CGCAACGCAA
Statistics
Matches: 400, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
137 74 0.19
140 326 0.81
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTCAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:538972 original size:20 final size:20
Alignment explanation
Indices: 538949--539120 Score: 122
Period size: 20 Copynumber: 9.2 Consensus size: 20
538939 TTCATTTCAA
538949 TATCGCAACGCTAATTTGAC
1 TATCGCAACGCTAATTTGAC
538969 TATCGCAACGC-AA----A-
1 TATCGCAACGCTAATTTGAC
* * * * *
538983 AAACGCAACACGAATATGAC
1 TATCGCAACGCTAATTTGAC
539003 TATCGCAACG-TGAATTTGAC
1 TATCGCAACGCT-AATTTGAC
539023 TATCGCAACGC-AA----A-
1 TATCGCAACGCTAATTTGAC
* * *
539037 AATCACAACGCGAATTTGAC
1 TATCGCAACGCTAATTTGAC
*
539057 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCTAATTTGAC
*
539077 TATCGCAACG-TGAATTTGAT
1 TATCGCAACGCT-AATTTGAC
539097 TATCGCAACG-TGAATTTGAC
1 TATCGCAACGCT-AATTTGAC
539117 TATC
1 TATC
539121 TCAATGAGAA
Statistics
Matches: 122, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.14
15 6 0.05
19 6 0.05
20 93 0.76
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
TATCGCAACGCTAATTTGAC
Found at i:539031 original size:54 final size:54
Alignment explanation
Indices: 538949--539086 Score: 215
Period size: 54 Copynumber: 2.6 Consensus size: 54
538939 TTCATTTCAA
*
538949 TATCGCAACGCT-AATTTGACTATCGCAACGCAAAAAACGCAACACGAATATGAC
1 TATCGCAACG-TGAATTTGACTATCGCAACGCAAAAAACACAACACGAATATGAC
* * *
539003 TATCGCAACGTGAATTTGACTATCGCAACGCAAAAATCACAACGCGAATTTGAC
1 TATCGCAACGTGAATTTGACTATCGCAACGCAAAAAACACAACACGAATATGAC
*
539057 TATCGCAACGCGAATTTGACTATCGCAACG
1 TATCGCAACGTGAATTTGACTATCGCAACG
539087 TGAATTTGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.01
54 77 0.99
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (54 bp):
TATCGCAACGTGAATTTGACTATCGCAACGCAAAAAACACAACACGAATATGAC
Found at i:539101 original size:40 final size:40
Alignment explanation
Indices: 538986--539120 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
538976 ACGCAAAAAA
* *
538986 CGCAACACGAATATGACTATCGCAACGTGAATTTGACTAT
1 CGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTAT
* * *
539026 CGCAACGC-AA----A-AATCACAACGCGAATTTGACTAT
1 CGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTAT
*
539060 CGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTAT
1 CGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTAT
*
539100 CGCAACGTGAATTTGACTATC
1 CGCAACGCGAATTTGACTATC
539121 TCAATGAGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
34 28 0.35
35 3 0.04
39 3 0.04
40 46 0.57
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (40 bp):
CGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTAT
Found at i:539115 original size:94 final size:93
Alignment explanation
Indices: 538994--539175 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 93
538984 AACGCAACAC
* *
538994 GAATATGACTATCGCAACGTGAATTTGACTATCGCAACGCA-AAAATCA-CAACGCGAATTTGAC
1 GAATATGACTATCGCAACGTGAATTTGACTATCGCAACG-AGAAAAT-ATCAAAGCGAATTAGAC
539057 TATCGCAACGCGAATTTGACTATCGCAACGT
64 TATCGCAACGCGAA-TTGACTATCGCAACGT
* * * * *
539088 GAATTTGATTATCGCAACGTGAATTTGACTATCTCAATGAGAAAATATCAAAGCGTATTAGACTA
1 GAATATGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAATATCAAAGCGAATTAGACTA
* *
539153 TCGCAATGCGAATTGACTTTCGC
66 TCGCAACGCGAATTGACTATCGC
539176 GTTGCGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
93 12 0.16
94 65 0.84
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (93 bp):
GAATATGACTATCGCAACGTGAATTTGACTATCGCAACGAGAAAATATCAAAGCGAATTAGACTA
TCGCAACGCGAATTGACTATCGCAACGT
Found at i:539373 original size:13 final size:13
Alignment explanation
Indices: 539355--539380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
539345 TTATTTACAC
539355 ATCAATTAAACAA
1 ATCAATTAAACAA
539368 ATCAATTAAACAA
1 ATCAATTAAACAA
539381 GCAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:540794 original size:42 final size:42
Alignment explanation
Indices: 540735--540857 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
540725 ATGAATCGGG
* *
540735 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
** *
540777 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
* * *
540819 CTCTTGAACGATAGGAGAGG-CCTCTTGAACAATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGG
540858 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 62 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:540795 original size:21 final size:21
Alignment explanation
Indices: 540735--540848 Score: 95
Period size: 21 Copynumber: 5.4 Consensus size: 21
540725 ATGAATCGGG
* *
540735 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
540756 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
540777 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
540798 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
540819 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
540840 CTCTTGAAC
1 CTCTTGAAC
540849 AATGACAGGT
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:541403 original size:33 final size:34
Alignment explanation
Indices: 541338--541415 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
541328 CAAGAAACTT
* *
541338 AAAATCGCAACGCGAAAATGACTATCGCAACAAG
1 AAAATCGCAACGCGAAAATAACAATCGCAACAAG
* *
541372 ATAATCGCAATGCG-AAATAACAATCGCAACAAG
1 AAAATCGCAACGCGAAAATAACAATCGCAACAAG
541405 AAAATCGCAAC
1 AAAATCGCAAC
541416 ATGAAACTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (34 bp):
AAAATCGCAACGCGAAAATAACAATCGCAACAAG
Found at i:541412 original size:14 final size:14
Alignment explanation
Indices: 541361--541421 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
541351 GAAAATGACT
*
541361 ATCGCAACAAGATA
1 ATCGCAACAAGAAA
*
541375 ATCGCAATGCGAAATAACA
1 ATCGCAA--C--AAGAA-A
541394 ATCGCAACAAGAAA
1 ATCGCAACAAGAAA
*
541408 ATCGCAACATGAAA
1 ATCGCAACAAGAAA
541422 CTAAATTCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 21 0.55
15 4 0.11
16 1 0.03
17 1 0.03
18 3 0.08
19 8 0.21
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (14 bp):
ATCGCAACAAGAAA
Found at i:541456 original size:20 final size:20
Alignment explanation
Indices: 541427--541464 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
541417 TGAAACTAAA
*
541427 TTCGCGTTGCAATTTTCATT
1 TTCGCATTGCAATTTTCATT
*
541447 TTCGCATTGCGATTTTCA
1 TTCGCATTGCAATTTTCA
541465 CGTTGCGATT
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:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCAATTTTCATT
Found at i:541488 original size:33 final size:33
Alignment explanation
Indices: 541431--541506 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
541421 ACTAAATTCG
* *
541431 CGTTGCAATTTTCATTTTCGCATTGCGATTTTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATC
* *
541464 ACGTTGCGATTTTTA-TTTCGCATTGTGATTATC
1 -CGTTGCGATTTTCATTTTCGCATTGCGATTATC
541497 CTGTTGCGAT
1 C-GTTGCGAT
541507 AGTCAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.03
33 24 0.65
34 12 0.32
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATC
Found at i:541577 original size:19 final size:19
Alignment explanation
Indices: 541499--541659 Score: 145
Period size: 20 Copynumber: 8.4 Consensus size: 19
541489 TGATTATCCT
*
541499 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTC-ATTTCGC
*
541519 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTT-CGC
541539 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCA-TTTCGC
* *
541559 GTTGCGATTGTTATTTCGC
1 GTTGCGATAGTCATTTCGC
*
541578 ATTGCGAT--T-ATCTT---
1 GTTGCGATAGTCAT-TTCGC
* *
541592 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTC-ATTTCGC
*
541612 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTT-CGC
541632 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCA-TTTCGC
541652 GTTGCGAT
1 GTTGCGAT
541660 TTTAAGTTTC
Statistics
Matches: 117, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.06
16 3 0.03
17 5 0.04
18 1 0.01
19 19 0.16
20 76 0.65
21 6 0.05
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGC
Found at i:541578 original size:93 final size:93
Alignment explanation
Indices: 541458--541660 Score: 361
Period size: 93 Copynumber: 2.2 Consensus size: 93
541448 TCGCATTGCG
* * * *
541458 ATTTTCACGTTGCGATTTTTATTTCGCATTGTGATTATCCTGTTGCGATAGTCAAATTCGCGTTG
1 ATTTTCGCGTTGCGATTGTTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTG
541523 CGATAGTCATTTCCGTGTTGCGATAGTC
66 CGATAGTCATTTCCGTGTTGCGATAGTC
*
541551 ATTTTCGCGTTGCGATTGTTATTTCGCATTGCGATTATCTTGTTGCGATAGTCAAATTCACGTTG
1 ATTTTCGCGTTGCGATTGTTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTG
541616 CGATAGTCATTTCCGTGTTGCGATAGTC
66 CGATAGTCATTTCCGTGTTGCGATAGTC
541644 ATTTTCGCGTTGCGATT
1 ATTTTCGCGTTGCGATT
541661 TTAAGTTTCG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 105 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (93 bp):
ATTTTCGCGTTGCGATTGTTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTG
CGATAGTCATTTCCGTGTTGCGATAGTC
Found at i:542238 original size:18 final size:19
Alignment explanation
Indices: 542205--542240 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
542195 TGGTCGATCA
542205 GGTGATGGTAATGGCTCTG
1 GGTGATGGTAATGGCTCTG
*
542224 GGTGA-GGTGATGGCTCT
1 GGTGATGGTAATGGCTCT
542241 CGAAGTGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.14, C:0.11, G:0.44, T:0.31
Consensus pattern (19 bp):
GGTGATGGTAATGGCTCTG
Found at i:543611 original size:20 final size:20
Alignment explanation
Indices: 543553--543603 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
543543 TCTGAAACTT
543553 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
543573 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
543593 ACTATCGCAAC
1 AAAATCGCAAC
543604 GAGAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:544037 original size:22 final size:22
Alignment explanation
Indices: 544007--544057 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
543997 GATGGAGATA
544007 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
544029 GAGGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
544051 GACGGAT
1 GACGGAT
544058 GTCGGCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:544267 original size:20 final size:20
Alignment explanation
Indices: 544202--544354 Score: 136
Period size: 20 Copynumber: 7.7 Consensus size: 20
544192 GCGCTTTGAA
544202 AATCGCATTGCGATTATGT-AT
1 AATCGCATTGCGA-TA-GTCAT
*
544223 TATCGCATTGCGATAG--AT
1 AATCGCATTGCGATAGTCAT
* *
544241 TATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAT
544261 AATCGCATTGCGATTATGT-AT
1 AATCGCATTGCGA-TA-GTCAT
* * *
544282 TATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAT
*
544302 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAT
* *
544322 ATTCGCATTGCGATAGTCAA
1 AATCGCATTGCGATAGTCAT
*
544342 AATCGCGTTGCGA
1 AATCGCATTGCGA
544355 ATCTGGAAAC
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
18 18 0.17
19 4 0.04
20 58 0.53
21 27 0.25
22 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:544293 original size:41 final size:40
Alignment explanation
Indices: 544224--544354 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 40
544214 ATTATGTATT
544224 ATCGCATTGCGA-TA-GATTATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATTATGATTATCGCATTGCGATAGTCAGA
*
544262 ATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTATG-ATTATCGCATTGCGATAGTCAGA
* *
544303 ATCGCATTGCGATT-T-ACATATTCGCATTGCGATAGTCAAA
1 ATCGCATTGCGATTATGA-TTA-TCGCATTGCGATAGTCAGA
*
544343 ATCGCGTTGCGA
1 ATCGCATTGCGA
544355 ATCTGGAAAC
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
38 13 0.16
39 4 0.05
40 30 0.36
41 36 0.43
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
ATCGCATTGCGATTATGATTATCGCATTGCGATAGTCAGA
Found at i:544294 original size:59 final size:60
Alignment explanation
Indices: 544202--544315 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 60
544192 GCGCTTTGAA
**
544202 AATCGCATTGCGATTATGTATTATCGCATTGCGATAG-ATTATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCATTGCGATAGCAGAATCGCATTGCGATAGTCAG
*
544261 AATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCATTGCGAT
1 AATCGCATTGCGATTATGTATTATCGCATTGCGATAG-CAGAATCGCATTGCGAT
544316 TTACATATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 36 0.72
61 14 0.28
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (60 bp):
AATCGCATTGCGATTATGTATTATCGCATTGCGATAGCAGAATCGCATTGCGATAGTCAG
Found at i:544392 original size:20 final size:19
Alignment explanation
Indices: 544369--544414 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
544359 GGAAACTGAT
* *
544369 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
544389 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
544408 TTGCGAT
1 TTGCGAT
544415 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:544404 original size:19 final size:19
Alignment explanation
Indices: 544380--544416 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
544370 TGCGATACTG
*
544380 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
544399 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
544417 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:546141 original size:6 final size:6
Alignment explanation
Indices: 546132--546250 Score: 76
Period size: 6 Copynumber: 19.8 Consensus size: 6
546122 CTGGCGGTGG
* ** * ** ** *
546132 CTGTTC CTGTTC CTGTTC TTGTTC CTGTGG CTATGG CTGTGG CTGTTG
1 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC
* * * * * *
546180 CTGTTC TTGTTC CTGATC CTGATC CTGATC CTGTTC CTGTTC TTGTTG
1 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC
* * *
546228 TTGTTG CTGTTC CTGTTG CTGTT
1 CTGTTC CTGTTC CTGTTC CTGTT
546251 GTTTCAAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 96 1.00
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.49
Consensus pattern (6 bp):
CTGTTC
Found at i:546250 original size:36 final size:36
Alignment explanation
Indices: 546132--546250 Score: 112
Period size: 36 Copynumber: 3.3 Consensus size: 36
546122 CTGGCGGTGG
* * **
546132 CTGTTCCTGTTCCTGTTCTTGTTCCTGTGGCTATGG
1 CTGTTCCTGTTCCTGTTCTTGTTCCTGTTGCTGTTC
** * * * *
546168 CTGTGGCTGTTGCTGTTCTTGTTCCTGATCCTGATC
1 CTGTTCCTGTTCCTGTTCTTGTTCCTGTTGCTGTTC
* **
546204 CTGATCCTGTTCCTGTTCTTGTTGTTGTTGCTGTTC
1 CTGTTCCTGTTCCTGTTCTTGTTCCTGTTGCTGTTC
*
546240 CTGTTGCTGTT
1 CTGTTCCTGTT
546251 GTTTCAAAAG
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.49
Consensus pattern (36 bp):
CTGTTCCTGTTCCTGTTCTTGTTCCTGTTGCTGTTC
Found at i:549740 original size:21 final size:22
Alignment explanation
Indices: 549716--549764 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
549706 AACTAAAAAT
549716 ATTAATATAT-AATATGCATAA
1 ATTAATATATCAATATGCATAA
* *
549737 ATT-ATATATCTATATGCGTAA
1 ATTAATATATCAATATGCATAA
549758 ATTAATA
1 ATTAATA
549765 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
ATTAATATATCAATATGCATAA
Found at i:549846 original size:17 final size:17
Alignment explanation
Indices: 549795--549849 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
549785 ATATAAGTGT
549795 TACGCATGTTATATATA
1 TACGCATGTTATATATA
*** *
549812 TAAAAATAATTATAATATA
1 TACGCAT-GTTAT-ATATA
549831 TACGCATGTTATATATA
1 TACGCATGTTATATATA
549848 TA
1 TA
549850 TTACATAATG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
17 11 0.39
18 8 0.29
19 9 0.32
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (17 bp):
TACGCATGTTATATATA
Found at i:549933 original size:22 final size:22
Alignment explanation
Indices: 549884--549950 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
549874 TACATTCTAC
549884 ATAC-TAT-ATAATATATATAAT
1 ATACTTATAATAATATATAT-AT
*
549905 ACACTTA-AATAATATAATATAT
1 ATACTTATAATAATAT-ATATAT
* *
549927 ATGCTTATAA-AATATGTTATAT
1 ATACTTATAATAATAT-ATATAT
549949 AT
1 AT
549951 CGTATGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.08
22 28 0.76
23 6 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (22 bp):
ATACTTATAATAATATATATAT
Found at i:551798 original size:113 final size:112
Alignment explanation
Indices: 551581--552235 Score: 994
Period size: 113 Copynumber: 5.8 Consensus size: 112
551571 TTCAGGGAAT
* *
551581 ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGGAGAT
1 ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGA-GAGAC
* * * * *
551646 ATGTTCTGCTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCC
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* * *
551694 ATTGAATCTAGGTAGACTTGTTCCACTTACTCTGAATGGAATACCAAATCTTGGAAAAAAGAGAC
1 ATTGAATC-AGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
551759 ATGTTCCGCTTACTCTGAAGGGAATATCATATCTGGGGGAATTGATCC
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
551807 ATTGAATCATGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGATAT
1 ATTGAATCA-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
551872 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCT-GGGGAATTGATCA
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
551919 ATTGAATCAGGGTAGACTTGCTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGAC
1 ATTGAATCA-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* * *
551984 CTGTTCCGCTTACTCTGAAGGGAATATCAGATATGGGGGAGTTGATTC
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
*
552032 ATTAAATCGAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-G-AAAGAGAGAC
1 ATTGAATC-AGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
552095 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGAGGAGTTGATCC
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
552143 ATTGAATCGAGGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG-AAAGAGAGAC
1 ATTGAATC-AGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
552207 ATGTTCCGCTTACTCTGAAGGGAATATCA
65 ATGTTCCGCTTACTCTGAAGGGAATATCA
552236 TATTCTGAAG
Statistics
Matches: 503, Mismatches: 34, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
111 104 0.21
112 145 0.29
113 204 0.41
114 50 0.10
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (112 bp):
ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACA
TGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
Found at i:551991 original size:225 final size:223
Alignment explanation
Indices: 551581--552238 Score: 1009
Period size: 225 Copynumber: 2.9 Consensus size: 223
551571 TTCAGGGAAT
*
551581 ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGGAGAT
1 ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGA-GAGAT
* * * *
551646 ATGTTCTGCTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCCATTGAATCTA-GGTAGA
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGA-TCTGGGGAGTTGATCCATTGAATC-AGGGTAGA
* * *
551710 CTTGTTCCACTTACTCTGAATGGAATACCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTCT
128 CTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGG-AAAGAGAGACATGTTCCGCTTACTCT
*
551775 GAAGGGAATATCATATCTGGGGGAATTGATCC
192 GAAGGGAATATCATATATGGGGGAATTGATCC
*
551807 ATTGAATCATGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGATAT
1 ATTGAATCA-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAT
* *
551872 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAATTGATCAATTGAATCAGGGTAGACT
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAGTTGATCCATTGAATCAGGGTAGACT
* *
551937 TGCTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTCCGCTTACTCTGA
130 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA-AAGAGAGACATGTTCCGCTTACTCTGA
* * *
552002 AGGGAATATCAGATATGGGGGAGTTGATTC
194 AGGGAATATCATATATGGGGGAATTGATCC
* *
552032 ATTAAATCGAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-G-AAAGAGAGAC
1 ATTGAATC-AGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAT
* *
552095 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATC-GAGGAAGA
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGG-GGAGTTGATCCATTGAATCAG-GGTAGA
*
552159 CTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAAAGAGAGACATGTTCCGCTTACTCTG
128 CTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAGAGACATGTTCCGCTTACTCTG
552224 AAGGGAATATCATAT
193 AAGGGAATATCATAT
552239 TCTGAAGGGA
Statistics
Matches: 398, Mismatches: 28, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
223 83 0.21
224 62 0.16
225 161 0.40
226 43 0.11
227 49 0.12
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (223 bp):
ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGATA
TGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAGTTGATCCATTGAATCAGGGTAGACTT
GTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAGAGACATGTTCCGCTTACTCTGAAG
GGAATATCATATATGGGGGAATTGATCC
Found at i:557010 original size:4 final size:4
Alignment explanation
Indices: 556977--557025 Score: 55
Period size: 4 Copynumber: 11.5 Consensus size: 4
556967 TCCCATATCA
556977 AAAT AGAAT GAAAT -AAT AATAT ATAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT A-AAT -AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
557024 AA
1 AA
557026 GGAGAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.08
4 23 0.57
5 12 0.30
6 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:557022 original size:16 final size:17
Alignment explanation
Indices: 556977--557025 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
556967 TCCCATATCA
556977 AAATAGAATGAAAT-AAT
1 AAATAGAAT-AAATAAAT
*
556994 AATATATAATAAATAAAT
1 AA-ATAGAATAAATAAAT
557012 AAATA-AATAAATAA
1 AAATAGAATAAATAA
557026 GGAGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.31
17 9 0.31
18 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (17 bp):
AAATAGAATAAATAAAT
Found at i:564961 original size:21 final size:22
Alignment explanation
Indices: 564937--564985 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
564927 AACTAAAAAT
564937 ATTAATATAT-AATATGCATAA
1 ATTAATATATCAATATGCATAA
* **
564958 ATT-ATATATCTATATGTGTAA
1 ATTAATATATCAATATGCATAA
564979 ATTAATA
1 ATTAATA
564986 AAAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
ATTAATATATCAATATGCATAA
Found at i:567021 original size:15 final size:16
Alignment explanation
Indices: 566988--567022 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
566978 CCATATTTCA
566988 TGTTTGATATGTATTT
1 TGTTTGATATGTATTT
*
567004 TGTTTGATA-GTGTTT
1 TGTTTGATATGTATTT
567019 TGTT
1 TGTT
567023 AACAGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (16 bp):
TGTTTGATATGTATTT
Found at i:567210 original size:33 final size:33
Alignment explanation
Indices: 567173--567238 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
567163 ACAAATGCAC
*
567173 GTTAGAATATGCACATCTGTTCTTTATTACAGT
1 GTTAGAATATGCACATATGTTCTTTATTACAGT
567206 GTTAGAATATGCACATATGTTCTTTATTACAGT
1 GTTAGAATATGCACATATGTTCTTTATTACAGT
567239 ATTTGGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
GTTAGAATATGCACATATGTTCTTTATTACAGT
Found at i:567606 original size:21 final size:21
Alignment explanation
Indices: 567582--567623 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
567572 AGTTTATTAT
567582 TGAGAAGATGCTATAGCAGGG
1 TGAGAAGATGCTATAGCAGGG
* * *
567603 TGAGAAGTTGTTGTAGCAGGG
1 TGAGAAGATGCTATAGCAGGG
567624 GCTTGAGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.40, T:0.24
Consensus pattern (21 bp):
TGAGAAGATGCTATAGCAGGG
Found at i:569009 original size:21 final size:21
Alignment explanation
Indices: 568984--569041 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
568974 TATCCAAATT
*
568984 ATCCTTTAGTA-CTGATATTGA
1 ATCCTTCAGTATC-GATATTGA
569005 ATCC-TCAGTATCGATATTGA
1 ATCCTTCAGTATCGATATTGA
* *
569025 ACCCTT-GGTATCGATAT
1 ATCCTTCAGTATCGATAT
569042 CAACATGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (21 bp):
ATCCTTCAGTATCGATATTGA
Found at i:569020 original size:20 final size:20
Alignment explanation
Indices: 568997--569041 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
568987 CTTTAGTACT
*
568997 GATATTGAATCCTCAGTATC
1 GATATTGAACCCTCAGTATC
**
569017 GATATTGAACCCTTGGTATC
1 GATATTGAACCCTCAGTATC
569037 GATAT
1 GATAT
569042 CAACATGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GATATTGAACCCTCAGTATC
Found at i:569052 original size:20 final size:20
Alignment explanation
Indices: 569029--569100 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
569019 TATTGAACCC
*
569029 TTGGTATCGATATCAACATG
1 TTGGTATCGATATCCACATG
569049 TTGGTATCGATATCCACATG
1 TTGGTATCGATATCCACATG
*
569069 TTGGTATCGATACCCACATG
1 TTGGTATCGATATCCACATG
569089 TTGGTATCGATA
1 TTGGTATCGATA
569101 CCTTCTAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGGTATCGATATCCACATG
Found at i:569056 original size:40 final size:40
Alignment explanation
Indices: 569012--569100 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
569002 TGAATCCTCA
* *
569012 GTATCGATATTGAAC-CCTTGGTATCGATATCAACATGTTG
1 GTATCGATA-TCAACACCTTGGTATCGATACCAACATGTTG
* ** *
569052 GTATCGATATCCACATGTTGGTATCGATACCCACATGTTG
1 GTATCGATATCAACACCTTGGTATCGATACCAACATGTTG
569092 GTATCGATA
1 GTATCGATA
569101 CCTTCTAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.07
40 39 0.93
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (40 bp):
GTATCGATATCAACACCTTGGTATCGATACCAACATGTTG
Found at i:575020 original size:2 final size:2
Alignment explanation
Indices: 575008--575056 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
574998 TTTAAACATT
575008 TA TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
575048 TA TA TA TA T
1 TA TA TA TA T
575057 TCATGAGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:576511 original size:11 final size:11
Alignment explanation
Indices: 576491--576549 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
576481 AACAAATAGG
576491 TTAA-ATGTTA
1 TTAACATGTTA
576501 TTAACATGTTA
1 TTAACATGTTA
* *
576512 TTAAGGAATATT-
1 TTAA--CATGTTA
* *
576524 TTAATATATTA
1 TTAACATGTTA
576535 TTAACATGTTA
1 TTAACATGTTA
576546 TTAA
1 TTAA
576550 AGTGTATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.22
11 23 0.57
12 4 0.10
13 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (11 bp):
TTAACATGTTA
Found at i:576590 original size:38 final size:38
Alignment explanation
Indices: 576546--576623 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
576536 TAACATGTTA
* * *
576546 TTAAAGTGTATTATTTTATTAGTTTTCTACTTTATTAG
1 TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
*
576584 TTAAAGTGTATTACTTTATTAATTTACTATTTTATTAG
1 TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
576622 TT
1 TT
576624 TAGAAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (38 bp):
TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
Found at i:576619 original size:16 final size:16
Alignment explanation
Indices: 576595--576723 Score: 116
Period size: 16 Copynumber: 8.1 Consensus size: 16
576585 TAAAGTGTAT
*
576595 TACTTTATTAATTTAC
1 TACTTTATTAGTTTAC
* *
576611 TATTTTATTAGTTTAG
1 TACTTTATTAGTTTAC
* * * * *
576627 AAATTGATTAATTTAT
1 TACTTTATTAGTTTAC
**
576643 TACTCAATTAGTTTTA-
1 TACTTTATTAG-TTTAC
576659 TACTTTATTAGTTTAC
1 TACTTTATTAGTTTAC
* *
576675 TACTTAATTAGTTTAA
1 TACTTTATTAGTTTAC
576691 TACTTTATTAGTTTAC
1 TACTTTATTAGTTTAC
* *
576707 TATTTTATTAATTTAC
1 TACTTTATTAGTTTAC
576723 T
1 T
576724 GTTTTTCATG
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
15 4 0.04
16 82 0.91
17 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (16 bp):
TACTTTATTAGTTTAC
Found at i:576723 original size:48 final size:48
Alignment explanation
Indices: 576595--576723 Score: 143
Period size: 48 Copynumber: 2.7 Consensus size: 48
576585 TAAAGTGTAT
* ** * *
576595 TACTTTATTAATTTACTATTTTATTAGTTTAGAAATTGATTAATTTAT
1 TACTTTATTAGTTTACTATTTTATTAGTTTACTAATTAATTAATTTAA
** * * *
576643 TACTCAATTAGTTTTA-TACTTTATTAGTTTACTACTTAATTAGTTTAA
1 TACTTTATTAG-TTTACTATTTTATTAGTTTACTAATTAATTAATTTAA
*
576691 TACTTTATTAGTTTACTATTTTATTAATTTACT
1 TACTTTATTAGTTTACTATTTTATTAGTTTACT
576724 GTTTTTCATG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
47 4 0.06
48 57 0.88
49 4 0.06
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (48 bp):
TACTTTATTAGTTTACTATTTTATTAGTTTACTAATTAATTAATTTAA
Found at i:576991 original size:40 final size:40
Alignment explanation
Indices: 576931--577017 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
576921 TGTCCATAGA
* * *
576931 AACACAATGTACGCAGAACATTTTTGTCCACAAAATCATC
1 AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
*
576971 AACACAATGTACACAAAACATTTATGTTCACAAAATCATC
1 AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
577011 AACACAA
1 AACACAA
577018 ATATCTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (40 bp):
AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
Found at i:577660 original size:19 final size:19
Alignment explanation
Indices: 577619--577661 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
577609 GGAAGAGAAT
* *
577619 AAACTCTTTTAGACAATCA
1 AAACCCTTTTAGACAACCA
* *
577638 AAACCCTTTTTGACAACCG
1 AAACCCTTTTAGACAACCA
577657 AAACC
1 AAACC
577662 TTACTCTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (19 bp):
AAACCCTTTTAGACAACCA
Found at i:580664 original size:23 final size:24
Alignment explanation
Indices: 580638--580682 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
580628 ATTTAATTTT
*
580638 TTTTTCATATT-TAACTTGATTGG
1 TTTTACATATTCTAACTTGATTGG
* *
580661 TTTTACTTATTCTAATTTGATT
1 TTTTACATATTCTAACTTGATT
580683 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTTACATATTCTAACTTGATTGG
Found at i:581474 original size:34 final size:34
Alignment explanation
Indices: 581401--581474 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
581391 TTCCATTCTC
*
581401 CTGAAAACATGGTACTCTGAATGTTTCTTATGAA
1 CTGAAAACATGGTACTCTGAATGTTTCCTATGAA
* *
581435 TTGAAAACATGGTACTCTGAATGTTTCCTATTAA
1 CTGAAAACATGGTACTCTGAATGTTTCCTATGAA
581469 CTGAAA
1 CTGAAA
581475 TCTTCATTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (34 bp):
CTGAAAACATGGTACTCTGAATGTTTCCTATGAA
Found at i:582772 original size:18 final size:18
Alignment explanation
Indices: 582751--582785 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
582741 ATGACCATTG
582751 CCAGCATTAGACCCACTA
1 CCAGCATTAGACCCACTA
* *
582769 CCAGTATTTGACCCACT
1 CCAGCATTAGACCCACT
582786 GGTAGCATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.37, G:0.11, T:0.23
Consensus pattern (18 bp):
CCAGCATTAGACCCACTA
Found at i:582846 original size:11 final size:11
Alignment explanation
Indices: 582828--582889 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
582818 TAAATAGATT
582828 AAATGTTATTA
1 AAATGTTATTA
*
582839 ACATGTTATTA
1 AAATGTTATTA
*
582850 AGGAATATT-TTA
1 A--AATGTTATTA
* *
582862 ATATATTATTA
1 AAATGTTATTA
*
582873 ACATGTTATTA
1 AAATGTTATTA
582884 AAATGT
1 AAATGT
582890 ATCATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.12
11 28 0.68
12 4 0.10
13 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (11 bp):
AAATGTTATTA
Found at i:582953 original size:30 final size:30
Alignment explanation
Indices: 582897--582953 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
582887 TGTATCATTT
*
582897 TATTACTTTACTACTTTATTAGTTAAAGTG
1 TATTACTTTACTAATTTATTAGTTAAAGTG
* * *
582927 TATTACTTTATTAATTTTTTATTTAAA
1 TATTACTTTACTAATTTATTAGTTAAA
582954 TATAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (30 bp):
TATTACTTTACTAATTTATTAGTTAAAGTG
Found at i:588714 original size:28 final size:30
Alignment explanation
Indices: 588681--588746 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
588671 ATTAAAAAAG
*
588681 ATAAATATATATATTAAAT-TAT-T-TGTAT
1 ATAAAT-TATATATTAAATATATATATATAT
588709 ATAAATT-T-TATTAAATATATATATATAT
1 ATAAATTATATATTAAATATATATATATAT
588737 ATAAATTATA
1 ATAAATTATA
588747 AATAATAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 8 0.25
26 4 0.12
27 2 0.06
28 17 0.53
29 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
ATAAATTATATATTAAATATATATATATAT
Found at i:589724 original size:21 final size:21
Alignment explanation
Indices: 589684--589724 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
589674 TTAGATTTGA
**
589684 TACTAATAATTTAATAATAAT
1 TACTAATAATAAAATAATAAT
*
589705 TACTAATAATAAAATTATAA
1 TACTAATAATAAAATAATAA
589725 GATTTGATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
TACTAATAATAAAATAATAAT
Found at i:590040 original size:15 final size:15
Alignment explanation
Indices: 590020--590048 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
590010 TTTATTATTA
590020 ATATTTAATGATTTG
1 ATATTTAATGATTTG
590035 ATATTTAATGATTT
1 ATATTTAATGATTT
590049 AGTAATGATA
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:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:590063 original size:16 final size:16
Alignment explanation
Indices: 590042--590073 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
590032 TTGATATTTA
590042 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
590058 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
590074 TATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:590084 original size:24 final size:23
Alignment explanation
Indices: 590040--590196 Score: 95
Period size: 24 Copynumber: 6.4 Consensus size: 23
590030 ATTTGATATT
*
590040 TAATGATTTAGTAATGATATGATTTA
1 TAATGA-TTAATAAT-A-ATGATTTA
* *
590066 GTAATGATTATTAATTATGATTTA
1 -TAATGATTAATAATAATGATTTA
*
590090 T--T-ATTAATATTTAATGAATTTATA
1 TAATGATTAATA-ATAATG-A-TT-TA
* *
590114 GTAATTATTAATAATAATGAAATTA
1 -TAATGATTAATAATAATG-ATTTA
* *
590139 TAATAATTACTAATAATGATTTAA
1 TAATGATTAATAATAATGATTT-A
* *
590163 TAATGATTACTAATAATTATTTAA
1 TAATGATTAATAATAATGATTT-A
590187 TAATGATTAA
1 TAATGATTAA
590197 ATATTTAAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.06
21 5 0.05
22 1 0.01
23 6 0.06
24 58 0.54
25 3 0.03
26 8 0.07
27 14 0.13
28 7 0.06
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (23 bp):
TAATGATTAATAATAATGATTTA
Found at i:590139 original size:27 final size:27
Alignment explanation
Indices: 590089--590155 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
590079 ATTATGATTT
* * *
590089 ATTATTAATATTTAATGAATTTATAGTA
1 ATTATTAATA-ATAATGAAATTATAATA
590117 ATTATTAATAATAATGAAATTATAATA
1 ATTATTAATAATAATGAAATTATAATA
*
590144 ATTACTAATAAT
1 ATTATTAATAAT
590156 GATTTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTATTAATAATAATGAAATTATAATA
Found at i:590165 original size:11 final size:11
Alignment explanation
Indices: 590149--590199 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
590139 TAATAATTAC
590149 TAATAATGATT
1 TAATAATGATT
590160 TAATAATGATT
1 TAATAATGATT
*
590171 ACTAATAATTATT
1 --TAATAATGATT
590184 TAATAATGATT
1 TAATAATGATT
*
590195 AAATA
1 TAATA
590200 TTTAAATAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 25 0.71
13 10 0.29
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (11 bp):
TAATAATGATT
Found at i:590255 original size:22 final size:22
Alignment explanation
Indices: 590230--590273 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
590220 TTTAAATCGA
590230 ATTTATAAATAGTCAAATTTAT
1 ATTTATAAATAGTCAAATTTAT
*
590252 ATTTATAAATAGTCGAATTTAT
1 ATTTATAAATAGTCAAATTTAT
590274 TCTTTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
ATTTATAAATAGTCAAATTTAT
Found at i:590336 original size:17 final size:15
Alignment explanation
Indices: 590302--590341 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
590292 CGAGTCATGC
590302 ATATTTAATATTATA
1 ATATTTAATATTATA
*
590317 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
590334 ATATTTAA
1 ATATTTAA
590342 CATATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:591092 original size:22 final size:22
Alignment explanation
Indices: 591064--591111 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
591054 TCATCATCTT
*
591064 GAATGGGATCAAGAGTTGGCAA
1 GAATGGGATCAAAAGTTGGCAA
591086 GAATGGGATCAAAAGTTGGCAA
1 GAATGGGATCAAAAGTTGGCAA
591108 GAAT
1 GAAT
591112 AAAACCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (22 bp):
GAATGGGATCAAAAGTTGGCAA
Found at i:595984 original size:12 final size:12
Alignment explanation
Indices: 595969--596000 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
595959 TAGTTGTCTC
595969 TGGTGTTGTTGT
1 TGGTGTTGTTGT
595981 TGGTGTTGTTGT
1 TGGTGTTGTTGT
*
595993 TGTTGTTG
1 TGGTGTTG
596001 ATGGTGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (12 bp):
TGGTGTTGTTGT
Found at i:596108 original size:15 final size:15
Alignment explanation
Indices: 596088--596134 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
596078 TGCTTTTGCT
*
596088 GGCGGTGGTTGTGGC
1 GGCGGTGGTGGTGGC
*
596103 GGCGGTGGTGGTGAC
1 GGCGGTGGTGGTGGC
*
596118 GACGGTGGTGGTGGC
1 GGCGGTGGTGGTGGC
596133 GG
1 GG
596135 TGACGGTGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.04, C:0.13, G:0.62, T:0.21
Consensus pattern (15 bp):
GGCGGTGGTGGTGGC
Found at i:596139 original size:18 final size:18
Alignment explanation
Indices: 596118--596171 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
596108 TGGTGGTGAC
*
596118 GACGGTGGTGGTGGCGGT
1 GACGGTGATGGTGGCGGT
*
596136 GACGGTGACGGTGGCGGT
1 GACGGTGATGGTGGCGGT
*
596154 GATGGTGATGGTGGCGGT
1 GACGGTGATGGTGGCGGT
596172 TGCTGTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.09, C:0.11, G:0.57, T:0.22
Consensus pattern (18 bp):
GACGGTGATGGTGGCGGT
Found at i:596142 original size:12 final size:12
Alignment explanation
Indices: 596118--596160 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
596108 TGGTGGTGAC
*
596118 GACGGTGGTGGT
1 GACGGTGGCGGT
* *
596130 GGCGGTGACGGT
1 GACGGTGGCGGT
596142 GACGGTGGCGGT
1 GACGGTGGCGGT
*
596154 GATGGTG
1 GACGGTG
596161 ATGGTGGCGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.09, C:0.12, G:0.58, T:0.21
Consensus pattern (12 bp):
GACGGTGGCGGT
Found at i:596214 original size:18 final size:18
Alignment explanation
Indices: 596170--596222 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
596160 GATGGTGGCG
596170 GTTGCTGTTCCTGTT-CC
1 GTTGCTGTTCCTGTTGCC
* **
596187 GATTGTTGTTCCTGTTGTT
1 G-TTGCTGTTCCTGTTGCC
*
596206 GTTGCTGTTGCTGTTGC
1 GTTGCTGTTCCTGTTGC
596223 TGTGGTGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.28, T:0.51
Consensus pattern (18 bp):
GTTGCTGTTCCTGTTGCC
Found at i:596233 original size:6 final size:6
Alignment explanation
Indices: 596224--596395 Score: 137
Period size: 6 Copynumber: 28.7 Consensus size: 6
596214 TGCTGTTGCT
* * * * * * *
596224 GTGGTG GTGGTG GTTGCG GTGGCG GTGGCT GTGGCT GTGGCT GTGGCT
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG
* * * * * **
596272 GTGGCG GTGGCT GTGGCT GTGGCT GTGGCG GTGGCT GTGGCT GTGGTT
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG
* * * * * * *
596320 GTGGCA GTGGCG GTGGCT GTGGCT GTGGCT GTGGTG GTGGCT GTGGCT
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG
* *
596368 GTGGCT GTGGCT GTGGCG GTGGCG GTGG
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGG
596396 TTGTTCCTGT
Statistics
Matches: 148, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 148 1.00
ACGTcount: A:0.01, C:0.14, G:0.56, T:0.30
Consensus pattern (6 bp):
GTGGCG
Found at i:596239 original size:24 final size:24
Alignment explanation
Indices: 596209--596395 Score: 216
Period size: 24 Copynumber: 7.8 Consensus size: 24
596199 TGTTGTTGTT
* * *
596209 GCTGTTGCTGTTGCTGTGGTGGTG
1 GCTGTGGCTGTGGCTGTGGCGGTG
* * * *
596233 G-TGGTTGCGGTGGCGGTGGCTGTG
1 GCT-GTGGCTGTGGCTGTGGCGGTG
596257 GCTGTGGCTGTGGCTGTGGCGGTG
1 GCTGTGGCTGTGGCTGTGGCGGTG
596281 GCTGTGGCTGTGGCTGTGGCGGTG
1 GCTGTGGCTGTGGCTGTGGCGGTG
* *
596305 GCTGTGGCTGTGGTTGTGGCAGTG
1 GCTGTGGCTGTGGCTGTGGCGGTG
* *
596329 GCGGTGGCTGTGGCTGTGGCTGTG
1 GCTGTGGCTGTGGCTGTGGCGGTG
*
596353 G-TGGTGGCTGTGGCTGTGGCTGTG
1 GCT-GTGGCTGTGGCTGTGGCGGTG
* *
596377 GCTGTGGCGGTGGCGGTGG
1 GCTGTGGCTGTGGCTGTGG
596396 TTGTTCCTGT
Statistics
Matches: 142, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.01
24 139 0.98
25 2 0.01
ACGTcount: A:0.01, C:0.14, G:0.54, T:0.31
Consensus pattern (24 bp):
GCTGTGGCTGTGGCTGTGGCGGTG
Found at i:596255 original size:30 final size:30
Alignment explanation
Indices: 596215--596395 Score: 224
Period size: 30 Copynumber: 6.0 Consensus size: 30
596205 TGTTGCTGTT
* *
596215 GCTGTTGCTGTGG-TGGTGGTGGTTGCGGTG
1 GCTGTGGCTGTGGCT-GTGGTGGTGGCGGTG
* *
596245 GCGGTGGCTGTGGCTGTGGCT-GTGGCTGTG
1 GCTGTGGCTGTGGCTGTGG-TGGTGGCGGTG
*
596275 GCGGTGGCTGTGGCTGTGGCT-GTGGCGGTG
1 GCTGTGGCTGTGGCTGTGG-TGGTGGCGGTG
* **
596305 GCTGTGGCTGTGGTTGTGGCAGTGGCGGTG
1 GCTGTGGCTGTGGCTGTGGTGGTGGCGGTG
*
596335 GCTGTGGCTGTGGCTGTGGTGGTGGCTGTG
1 GCTGTGGCTGTGGCTGTGGTGGTGGCGGTG
*
596365 GCTGTGGCTGTGGCTGTGGCGGTGGCGGTG
1 GCTGTGGCTGTGGCTGTGGTGGTGGCGGTG
596395 G
1 G
596396 TTGTTCCTGT
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
30 132 0.99
31 2 0.01
ACGTcount: A:0.01, C:0.14, G:0.55, T:0.30
Consensus pattern (30 bp):
GCTGTGGCTGTGGCTGTGGTGGTGGCGGTG
Found at i:596257 original size:12 final size:12
Alignment explanation
Indices: 596242--596395 Score: 220
Period size: 12 Copynumber: 12.8 Consensus size: 12
596232 GGTGGTTGCG
*
596242 GTGGCGGTGGCT
1 GTGGCTGTGGCT
596254 GTGGCTGTGGCT
1 GTGGCTGTGGCT
*
596266 GTGGCTGTGGCG
1 GTGGCTGTGGCT
596278 GTGGCTGTGGCT
1 GTGGCTGTGGCT
*
596290 GTGGCTGTGGCG
1 GTGGCTGTGGCT
596302 GTGGCTGTGGCT
1 GTGGCTGTGGCT
* *
596314 GTGGTTGTGGCA
1 GTGGCTGTGGCT
*
596326 GTGGCGGTGGCT
1 GTGGCTGTGGCT
596338 GTGGCTGTGGCT
1 GTGGCTGTGGCT
596350 GTGG-TGGTGGCT
1 GTGGCT-GTGGCT
596362 GTGGCTGTGGCT
1 GTGGCTGTGGCT
*
596374 GTGGCTGTGGCG
1 GTGGCTGTGGCT
*
596386 GTGGCGGTGG
1 GTGGCTGTGG
596396 TTGTTCCTGT
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
11 1 0.01
12 125 0.98
13 1 0.01
ACGTcount: A:0.01, C:0.15, G:0.55, T:0.29
Consensus pattern (12 bp):
GTGGCTGTGGCT
Found at i:599501 original size:15 final size:16
Alignment explanation
Indices: 599468--599502 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
599458 CCATATTTCA
599468 TGTTTGATATGTATTT
1 TGTTTGATATGTATTT
*
599484 TGTTTGATA-GTGTTT
1 TGTTTGATATGTATTT
599499 TGTT
1 TGTT
599503 AACGGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (16 bp):
TGTTTGATATGTATTT
Found at i:600055 original size:21 final size:21
Alignment explanation
Indices: 600031--600072 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
600021 AGTTGATTGT
*
600031 TGAGAAGATGTTGTAGTAGGG
1 TGAGAAGATGTTGTAGCAGGG
*
600052 TGAGAAGTTGTTGTAGCAGGG
1 TGAGAAGATGTTGTAGCAGGG
600073 GCTTGAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.43, T:0.29
Consensus pattern (21 bp):
TGAGAAGATGTTGTAGCAGGG
Found at i:601501 original size:20 final size:20
Alignment explanation
Indices: 601478--601531 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
601468 TACTGAACCC
* *
601478 TTGGTATCGATACCCACATG
1 TTGGTATCAATACCCACATA
*
601498 TTGGTATCAATACTCACATA
1 TTGGTATCAATACCCACATA
601518 TTGGTATCAATACC
1 TTGGTATCAATACC
601532 TTCTAACTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGGTATCAATACCCACATA
Found at i:607814 original size:2 final size:2
Alignment explanation
Indices: 607807--607834 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
607797 ACTGTTTTAA
607807 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
607835 CATGAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:608803 original size:32 final size:33
Alignment explanation
Indices: 608743--608807 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
608733 CGGAAGTTAG
608743 GTTCAACAATTGAAGTATAAAAAAACACCTTAC
1 GTTCAACAATTGAAGTATAAAAAAACACCTTAC
608776 GTTCAACAATTGAAGTAT-AAAAAACACCTTAC
1 GTTCAACAATTGAAGTATAAAAAAACACCTTAC
608808 CACTCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (33 bp):
GTTCAACAATTGAAGTATAAAAAAACACCTTAC
Found at i:609367 original size:18 final size:18
Alignment explanation
Indices: 609344--609402 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
609334 TATTAACATG
*
609344 TTATTAAAGTGTATCATT
1 TTATTAAAGTGTATCACT
*
609362 TTATT--AGTTTA-CTACT
1 TTATTAAAGTGTATC-ACT
*
609378 TTATTAAAGTGTATTACT
1 TTATTAAAGTGTATCACT
609396 TTATTAA
1 TTATTAA
609403 TTTACTACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 1 0.03
16 12 0.36
18 20 0.61
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATTAAAGTGTATCACT
Done.