Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005397.1 Hibiscus syriacus cultivar Beakdansim tig00012370_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: 1218879
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:358112 original size:15 final size:16
Alignment explanation
Indices: 358089--358122 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
358079 AGAGAAACGG
358089 AAAGAAAAGAAAAAAA
1 AAAGAAAAGAAAAAAA
358105 AAAG-AAAGAAAAAAA
1 AAAGAAAAGAAAAAAA
358120 AAA
1 AAA
358123 TAACAACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAAA
Found at i:371038 original size:12 final size:12
Alignment explanation
Indices: 371021--371046 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
371011 ATTATGCTTG
371021 AAGAGAATAAAA
1 AAGAGAATAAAA
371033 AAGAGAATAAAA
1 AAGAGAATAAAA
371045 AA
1 AA
371047 ACCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAGAGAATAAAA
Found at i:372279 original size:82 final size:82
Alignment explanation
Indices: 372180--373033 Score: 1539
Period size: 82 Copynumber: 10.4 Consensus size: 82
372170 TGTGATATCC
372180 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
372245 TATCTGACCTGGTTTAC
66 TATCTGACCTGGTTTAG
372262 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372327 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
* * *
372344 CAGAACATTCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372409 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
* * *
372426 CAGAACATTCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372491 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
*
372508 CAGAACATTCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372573 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
* * *
372590 CAGAACATTCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372655 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
*
372672 CAGAACAATCATTGAATTTAGAAGATGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372737 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
372754 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372819 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
372836 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
372901 TATCTGACCTGGTTTAG
66 TATCTGACCTGGTTTAG
*
372918 CAGAACAATCATTGAATTTAGGAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* *
372983 TATCTGATCTGG-TTGG
66 TATCTGACCTGGTTTAG
* *
372999 ATAGAACAATCATTGAATTTGGAAGATGAATTTGC
1 -CAGAACAATCATTGAATTTAGAAGATGAATTTGC
373034 TCATAGTAAA
Statistics
Matches: 752, Mismatches: 19, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
81 3 0.00
82 749 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (82 bp):
CAGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGACCTGGTTTAG
Found at i:373883 original size:113 final size:113
Alignment explanation
Indices: 373680--374323 Score: 1139
Period size: 113 Copynumber: 5.7 Consensus size: 113
373670 ATTAACATTG
* *
373680 CCAGGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
373745 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
66 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
373793 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
*
373858 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATTATCTTTT
66 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
373906 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
373971 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
66 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
374019 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
374084 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGAACATTTTTT
66 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
*
374132 CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
374197 ATTTGTTCAACCTTTTACCTGAATCCATCAATTGATGGATTATCTTTT
66 ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
* * *
374245 CCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
374309 ACTTGTTCAA-CTTTT
66 ATTTATTCAACCTTTT
374324 GGCATAATTC
Statistics
Matches: 513, Mismatches: 18, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
111 5 0.01
112 65 0.13
113 443 0.86
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTATTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTT
Found at i:374650 original size:3 final size:3
Alignment explanation
Indices: 374642--374751 Score: 193
Period size: 3 Copynumber: 36.7 Consensus size: 3
374632 TTTTTATCCA
* * *
374642 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
374690 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
374738 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
374752 AATATATTAA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:374793 original size:20 final size:19
Alignment explanation
Indices: 374751--374794 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
374741 TATTATTATT
* * *
374751 AAATATATTAAATACATAT
1 AAATATATTAAAAACAAAC
374770 AAATATTATTAAAAACAAAC
1 AAATA-TATTAAAAACAAAC
374790 AAATA
1 AAATA
374795 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATATTAAAAACAAAC
Found at i:375311 original size:12 final size:13
Alignment explanation
Indices: 375289--375322 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
375279 CAGAGAAACG
*
375289 GAAAGAAAAGAAA
1 GAAAAAAAAGAAA
375302 -AAAAAAAAGAAA
1 GAAAAAAAAGAAA
375314 GAAAAAAAA
1 GAAAAAAAA
375323 ATAACAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:375316 original size:16 final size:17
Alignment explanation
Indices: 375290--375323 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
375280 AGAGAAACGG
375290 AAAGAAAAGAAAAAAAA
1 AAAGAAAAGAAAAAAAA
375307 AAAG-AAAGAAAAAAAA
1 AAAGAAAAGAAAAAAAA
375323 A
1 A
375324 TAACAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAAAAA
Found at i:380805 original size:19 final size:19
Alignment explanation
Indices: 380783--380824 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
380773 ACTTTAGAAT
*
380783 ATATT-TAATATATTAAATA
1 ATATTATAATATAATAAA-A
*
380802 ATATTATAATGTAATAAAA
1 ATATTATAATATAATAAAA
380821 ATAT
1 ATAT
380825 AATATATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATATTATAATATAATAAAA
Found at i:384837 original size:68 final size:68
Alignment explanation
Indices: 384728--384866 Score: 242
Period size: 68 Copynumber: 2.0 Consensus size: 68
384718 AGAATGGGAC
* * *
384728 TGTACCTCCTCATCCAATCCACTCCCGCAACCGTATCGTTGCCTTGCATTTGTAATACCCTAAAA
1 TGTACCTCCTCATCCAATCCACTCCCACAACCATATCGTTGCCTCGCATTTGTAATACCCTAAAA
384793 TCA
66 TCA
*
384796 TGTACCTCTTCATCCAATCCACTCCCACAACCATATCGTTGCCTCGCATTTGTAATACCCTAAAA
1 TGTACCTCCTCATCCAATCCACTCCCACAACCATATCGTTGCCTCGCATTTGTAATACCCTAAAA
384861 TCA
66 TCA
384864 TGT
1 TGT
384867 TGAAAGATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.30
Consensus pattern (68 bp):
TGTACCTCCTCATCCAATCCACTCCCACAACCATATCGTTGCCTCGCATTTGTAATACCCTAAAA
TCA
Found at i:394930 original size:27 final size:28
Alignment explanation
Indices: 394873--394930 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
394863 AGAGGTTCAC
394873 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATCCGAATATCCGATTTTGGG-AA
*
394902 AAAATATCCGAA-A-CCGGATTTT-GGAA
1 AAAAAATCCGAATATCC-GATTTTGGGAA
394928 AAA
1 AAA
394931 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:395034 original size:24 final size:24
Alignment explanation
Indices: 395000--395088 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 24
394990 AAATTGAACG
* *
395000 ACCGGTATTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
395024 ACCGGTTTTTTTTTAAACCGGATAAAAA
1 ACCGG--TTTTTTT--ACCGGATAAAAA
*
395052 ACCGG-TTTTTTATCC-GAAAAAAA
1 ACCGGTTTTTTTA-CCGGATAAAAA
395075 ATCCGGTTTTTTTA
1 A-CCGGTTTTTTTA
395089 AAAAACTGGA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
23 9 0.16
24 11 0.20
25 13 0.24
26 6 0.11
28 16 0.29
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:395091 original size:41 final size:40
Alignment explanation
Indices: 395046--395144 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 40
395036 TTAAACCGGA
395046 TAAAAAACCGGTTTTTTATCCGAAAAAAAATCCGG-TTTTTT
1 TAAAAAACCGGTTTTTTATCCG--AAAAAATCCGGTTTTTTT
* *
395087 TAAAAAACTGGATTTTTATCCGAAAAAATCCGGTTTTTTTT
1 TAAAAAACCGGTTTTTTATCCGAAAAAATCCGG-TTTTTTT
395128 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
395145 GCAAACCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 11 0.21
41 41 0.79
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (40 bp):
TAAAAAACCGGTTTTTTATCCGAAAAAATCCGGTTTTTTT
Found at i:395093 original size:19 final size:18
Alignment explanation
Indices: 395070--395144 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 18
395060 TTTATCCGAA
395070 AAAAAATCCGG-TTTTTTT
1 AAAAAA-CCGGATTTTTTT
* *
395088 AAAAAACTGGATTTTTATCCG
1 AAAAAACCGGATTTTT-T--T
*
395109 AAAAAATCCGGTTTTTTTTT
1 AAAAAA-CCGG-ATTTTTTT
395129 AAAAAACCGG-TTTTTT
1 AAAAAACCGGATTTTTT
395145 GCAAACCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 9 0.20
18 11 0.24
19 5 0.11
20 6 0.13
21 6 0.13
22 4 0.09
23 5 0.11
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (18 bp):
AAAAAACCGGATTTTTTT
Found at i:403108 original size:26 final size:26
Alignment explanation
Indices: 403078--403129 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
403068 TAATGCACTG
*
403078 AAAGTGCATTAGTTGGCAGTAATGAT
1 AAAGTGCATTAGTTGGCAGCAATGAT
403104 AAAGTGCATTAGTTGGCAGCAATGAT
1 AAAGTGCATTAGTTGGCAGCAATGAT
403130 TCAATGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (26 bp):
AAAGTGCATTAGTTGGCAGCAATGAT
Found at i:406791 original size:20 final size:20
Alignment explanation
Indices: 406762--406801 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
406752 CACAACGAGT
406762 CTTCTCCTTTATACAGTAAC
1 CTTCTCCTTTATACAGTAAC
* *
406782 CTTCTTCTTTATACCGTAAC
1 CTTCTCCTTTATACAGTAAC
406802 AATCGTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (20 bp):
CTTCTCCTTTATACAGTAAC
Found at i:408554 original size:30 final size:32
Alignment explanation
Indices: 408486--408566 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 32
408476 CACCACATTG
* * *
408486 ATATTTTAACTAAAATTTAAGTGTCAAAAATG
1 ATATTTTATCTAAAATTTAAGCGTCAAAAATA
* *
408518 ATATTTTATCTAAAGTTTAA-CGTC-AAATTA
1 ATATTTTATCTAAAATTTAAGCGTCAAAAATA
408548 ATATTTTATCTAAAATTTA
1 ATATTTTATCTAAAATTTA
408567 GGTATAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 22 0.51
31 3 0.07
32 18 0.42
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (32 bp):
ATATTTTATCTAAAATTTAAGCGTCAAAAATA
Found at i:414277 original size:13 final size:13
Alignment explanation
Indices: 414259--414284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
414249 AATTTTTTAA
414259 AATATATAATTTT
1 AATATATAATTTT
414272 AATATATAATTTT
1 AATATATAATTTT
414285 TTCGAATCAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATATAATTTT
Found at i:415195 original size:20 final size:20
Alignment explanation
Indices: 415159--415196 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
415149 ATCCTATTCC
**
415159 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
415179 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
415197 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:415622 original size:21 final size:23
Alignment explanation
Indices: 415578--415623 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
415568 AAATCTAAAA
415578 TATATGTTTAATTTCAAAATGTT
1 TATATGTTTAATTTCAAAATGTT
* *
415601 TATAT-TTTAGTTTC-ATATGTT
1 TATATGTTTAATTTCAAAATGTT
415622 TA
1 TA
415624 CAGTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
TATATGTTTAATTTCAAAATGTT
Found at i:428707 original size:2 final size:2
Alignment explanation
Indices: 428700--428726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
428690 CATATCCATT
428700 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 T
428727 CAATTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:429063 original size:15 final size:15
Alignment explanation
Indices: 429034--429096 Score: 103
Period size: 15 Copynumber: 4.3 Consensus size: 15
429024 AAATAATTTT
429034 AAATAATTTA--ATA
1 AAATAATTTATTATA
*
429047 AAATAATTTATTTTA
1 AAATAATTTATTATA
429062 AAATAATTTATTATA
1 AAATAATTTATTATA
429077 AAATAATTTATTATA
1 AAATAATTTATTATA
429092 AAATA
1 AAATA
429097 TGGATTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.22
15 36 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATAATTTATTATA
Found at i:429149 original size:54 final size:52
Alignment explanation
Indices: 429052--429164 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 52
429042 TAATAAAATA
*
429052 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGAGTG
* * * *
429104 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGAGTG
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTATAAAATATGGAGTG
429158 ATTTATT
1 ATTTATT
429165 ATTGTAGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
51 13 0.25
52 11 0.21
54 29 0.55
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (52 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGAGTG
Found at i:429215 original size:32 final size:32
Alignment explanation
Indices: 429174--429281 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
429164 TATTGTAGTT
429174 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429206 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429229 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429260 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
429282 ATATGAATGA
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 14 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 36 0.55
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:429232 original size:22 final size:22
Alignment explanation
Indices: 429207--429249 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
429197 AATTTATTAG
429207 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
429229 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
429250 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:429243 original size:54 final size:54
Alignment explanation
Indices: 429175--433135 Score: 3127
Period size: 54 Copynumber: 73.6 Consensus size: 54
429165 ATTGTAGTTG
429175 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
429229 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
429283 TAT-GAATGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A
** ** * ** * * *
429339 GTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 -TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
*
429394 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
429448 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGTTTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
429502 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * * * *
429556 TGTGAATTGATTTATTATT--GTAGTTGTA-T-GAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAA
** ** * ** * * *
429614 TATGGATTGATTTATTTTAAAATAA-GGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* ** ** * ** * * *
429668 CATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
429722 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
429776 TATGGATTGATTTA--TT--AT--TTTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
* * * * * *
429823 TA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAA
** * * * * *
429877 TAATTTATTAGTATGTATTGTT--TTATTTTA-AAATATGGATTGATTTAATTTAAATAATTTAT
1 T-ATGGATT-G-ATTTATT-TTAAATAATTTATTAGTATGGATTGATTT-ATTT---TAA---A-
429939 TA
54 -A
* ** ** * ** * * *
429941 GTGTGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 -TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
** ** * ** * * *
429996 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTA-AAA
* * * * * *
430049 TATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTATTTTAAATAATTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTT--AT-TTTA-AAA
** ** * ** * * *
430102 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
** ** * ** * * *
430156 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
430210 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430264 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
430318 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430372 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * ***
430425 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTTTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGA--T-TTATTTTA-AAA
430484 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
430537 -ATGGATTGATTTATTTTAAATAA-TTATTAGTATGTATTGA-TTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430587 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430641 TATGGATTGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
430694 TATGGATTGATTTATTTT-AATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430747 TATGGATTGATTTATTTTAAATAATTTATTAGTA-GGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430799 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT-TTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ***
430852 TTATTAGTATAAATTGATTTATTTT-AA-AATGTGA--A-T-T-GATT-A-TTATTGTAGTTG
1 -TA-T-G----GATTGATTTATTTTAAATAAT-TTATTAGTATGGATTGATTTATTTTA-AAA
*
430906 TATGAATTGATTTA-TTTAAATAATTTATTAG--TGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
430957 TATGGATTGATTTTTTATTTTAAATAATTT-TTAGTA-GGATTGA-TTATTTTAAAA
1 TATGGATTGA---TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431011 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GGATTGATTTATTTTAAAA
* * ** * * ** * ***
431065 TA---ATTTA-TTAGTATGGATTGATTTATTTTAAAATAGATTGATTTATTATTTTAGTTG
1 TATGGATTGATTTA-TTTTAAATAATTTA--TTAGTATGGATTGA--T-TTATTTTA-AAA
*
431122 TATGGATTGA-TT-TTTTAAATAATTTA-TAGTATAGATTGATTTA-TTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
431172 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTA-TGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431225 TATGGATTGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
431278 TATGGA-TGA-TT-TTTTAAATAA-TTATTAGTATGGATTGA-TTATTTAAATAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA-AA
* * * * *
431328 TTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATAATTTA
1 --TA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A
* ** ** * ** * * *
431386 GTATGGA-TGATTTATTTTAAATTATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* *
431440 TATGGAATGATTTATTTTAAATAATTT-TT-GTATGGATTAATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
431491 TATGGATTGA-TTA--TT--AT--TGTAGTT-GTATAGA-TGATTTATTTTAAATAATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT--A-AA--A
** ** * ** * * *
431542 TTAGTAGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 -TA-T-GGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
431599 TATGGATTGATTTATTTTAAATAATTT-TT-GTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431651 TATGGATTGATTTATTTTAAAT-ATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431704 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA-TGATTTA-TTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431755 TATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * * ***
431807 TA---ATTTATTAGTATGGATTGATTTATTTA-AAATATGGATTGATTTATATTTTAGTTG
1 TATGGATTGATT--TAT--TTTAAATAATTTATTAGTATGGATTGA-TT-TATTTTA-AAA
431864 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
431918 TATGGATTGA-TTATTTTAAATAA-TT-TTAGTATGTA-TGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
431968 TATGGATTGATTTATTTT--A-AA--TATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432017 TATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
432070 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATGATTTA-TTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432122 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432176 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * ** * * ** ***
432229 TA---ATTTA-TTAGTATGGATTGATTTATTTTAAAATGTGAATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-TTTTAAATAATTTA--TTAGTATG-G-ATTGATTTA-T-TT-TA-AAA
*
432288 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432342 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTA-TTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432394 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT---TAA---A--A
* * ***
432457 GTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTTTAGTTG
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
*
432506 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
432560 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
432614 TATGGATTGATTTATTTT-AAT--TTTATTAGTATGGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A
432671 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
432726 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
432780 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGAATGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * ** *
432833 TA---ATTTATTTGTATGGATTAATTTATTTTAAAATATGGATTGATTTATTATTGTAG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATT-TTAAAA
*
432889 T-TGTATAGATGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGAT---TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
432944 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT---TAA---A---A
* * * ***
433007 TATGGATTGATTTATTTT-AA-AA--TA-T-GGAT-GATTTA-TTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
433054 TATGGATTGA-TTATTTTAAATAATTTATTAGTATGGATTGA-TT-TTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
433105 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
433136 TTGTAGTTTT
Statistics
Matches: 3267, Mismatches: 332, Indels: 618
0.77 0.08 0.15
Matches are distributed among these distances:
43 3 0.00
44 6 0.00
45 11 0.00
46 20 0.01
47 51 0.02
48 78 0.02
49 53 0.02
50 161 0.05
51 181 0.06
52 347 0.11
53 500 0.15
54 1177 0.36
55 159 0.05
56 75 0.02
57 71 0.02
58 119 0.04
59 51 0.02
60 45 0.01
61 55 0.02
62 38 0.01
63 39 0.01
64 26 0.01
65 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:429348 original size:32 final size:32
Alignment explanation
Indices: 429307--433027 Score: 535
Period size: 32 Copynumber: 120.7 Consensus size: 32
429297 TATTGTAGTT
429307 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429339 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429362 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429393 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429425 GCATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429448 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429479 GTATGGTTTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429502 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429533 GTATGGATTGATTTATTTTAAAATGTGAATTGATT-
1 GTATGGATTGATTTATTTT-AAA--T-AATTTATTA
* * * * * * *
429568 -TAT-TATTGTAGTTGTATGAATTGATTTATT-
1 GTATGGATTG-ATTTATTTTAAATAATTTATTA
* * * * * *
429598 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
* *
429635 ATAAGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429667 GCATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429690 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429721 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
429753 GTATGGATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * * *
429784 G-ATTTATT-ATTTTAGTTGTATGGATTGATTTATT-
1 GTATGGATTGA-TTTA-TT-T-T-AAATAATTTATTA
* * * * *
429818 -T-T-AAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-TA-AATAATTTA--TT--A
*
429855 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
429887 GTATGTATTGTTTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429910 -TATGGATTGATTTAATTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
429941 GTGTGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429964 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
429995 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * * ** * * *
430021 GGATTGATTTATTTA-AATAATTTA-TTAGTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * * * *
430051 TGGATTGATT--TAT-TTTAAAATATGGATTGATTTA
1 -GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * * * *
430085 -TTTTAAAT-AATTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
430123 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430155 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430178 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430209 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430241 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430264 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430295 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430318 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430349 GTATGGATTGATTTA-TTT---TAA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430372 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430403 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
430435 GTATGGATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * * *
430466 G-ATTTATT-ATTTTAGTTGTATGGATTGATTTATT-
1 GTATGGATTGA-TTTA-TT-T-T-AAATAATTTATTA
* * * * * *
430500 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TTA
**
430535 AAATGGATTGATTTATTTTAAATAA-TTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
430566 GTATGTATTGA-TTATTTTAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * * * *
430601 -TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
430640 ATATGGATTGATTTATTTTAAATAA-TTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
430671 GTATGGATTGATTTATTTTAAAATATGGATTGATT-
1 GTATGGATTGATTTATTTT-AAATA---ATTTATTA
** * * * *
430706 -TATTTTAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 GTA-TGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
430746 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
430778 GTA-GGATTGATTTATTTTAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * * * *
430813 -TTTTAAATAATTTATTAGTATGGATTGATTT-TT-
1 GTATGGATTGATTTATT--T-T-AAATAATTTATTA
* ** * * *
430846 TTA-AAATT-A-TTAGTATAAATTGATTTATTTTA
1 GTATGGATTGATTTATTTTAAA-TAATTTA--TTA
** *
430878 AAATGTGAATTGA-TTA--TT--AT--TGTAGTT-
1 GTATG-G-ATTGATTTATTTTAAATAATTTA-TTA
*
430905 GTATGAATTGATTTA-TTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430936 G--TGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * *
430960 GGATTGATT-TTTTATTTTAAATAATTT-TTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
430990 GTA-GGATTGA-TTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431011 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431042 GTATGGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GGATTGATTTATTTTAAATAATTTATTA
431075 GTATGGATTGATTTATTTTAAAATAGATTGATTTATTA
1 GTATGGATTGATTTATTTT-AAAT--A---ATTTATTA
* * * *
431113 TTTTAGTTGTATGGATTGATTTTTTAAATAATTTA-TA
1 --GTA--TGGATTGATTTATTTT--AAATAATTTATTA
* * *
431150 GTATAGATTGATTTATTTAAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * ** *
431186 -TTTTAAATAATTTATTAGTATGTATGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-TAAATAATTTA--TT--A
*
431224 ATATGGATTGATTTATTTTAAATAA-TTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
431255 GTATGGATTGATTTATTTTAAA-ATATGGA-T-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
*** * * * * * *
431285 G-ATTTTTTAAATAATTATTAGTATGGATTGATTA
1 GTATGGATTGATTTATT-TTA-AAT-AATTTATTA
** * * * * *
431319 -T-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
431357 ATATGGATTGATTTATTTTAAATAA--T-TTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431386 GTATGGA-TGATTTA-TTT---TAA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431408 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
431439 GTATGGAATGATTTATTTTAAATAATTT-TT-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
431469 GTATGGATTAATTTATTTTAAATATGGATTGATTA
1 GTATGGATTGATTTATTTTAAATA---ATTTATTA
* * ** ** * *
431504 TTATTGTAGTTGTATAGATGATTTATTTTAAATAATTA
1 GTA-TGGA-TTG-ATTTAT--TTTA-AATAATTTATTA
* * * * *
431542 TTA-GTA-GGATTGA-TTT--AT--TTTA-AA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
431566 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431598 GTATGGATTGATTTATTTTAAATAATTT-TT-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431628 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431651 -TATGGATTGATTTATTTTAAAT-ATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431681 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431704 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
431735 GTATGGA-TGATTTATTTAAATATGGATGATTTATT-
1 GTATGGATTGATTTATTTTAA-AT--A--ATTTATTA
* * * * * *
431770 -T-T-AAATAATTTATTAGTATGGATTGATTTATT-
1 GTATGGATTGATTTATT--T-T-AAATAATTTATTA
* * * * * *
431802 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA-TT--A
*
431838 ATATGGATTGATTTA---T--AT--TTTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
431863 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
431895 GTATGGATTGATTTATTTTAAAATATGGATTGATTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTATTA
* ** * * * * ** *
431931 -TTTTAAATAATTTTAGTATGTATGATTTATTTTAAA
1 GTATGGATTGA-TTTATTTTAAATAATTTA--TT--A
*
431967 ATATGGATTGATTTATTTT--A-AA--TATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
431994 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * ** * * *
432020 GGAT-GATTTATTT-TAAATAATTTA-TTAGTA
1 GTATGGATTGATTTAT-TTTAAATAATTTATTA
* * * * *
432050 TGGATTGATT--TAT-TTTAAAATATGGATTGATTTA
1 -GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * * *
432084 -TTTTAAATAATTTATTAGTATGAATGATTTATTTAAA
1 GTATGGATTGATTTATT--T-TAAATAATTTA-TT--A
*
432121 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432153 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432176 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432207 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
432239 GTATGGATTGATTTATTTTAAAATGTGAATTGATT-
1 GTATGGATTGATTTATTTT-AAA--T-AATTTATTA
* * * * * * *
432274 -TAT-TATTGTAGTTGTATGAATTGATTTATT-
1 GTATGGATTG-ATTTATTTTAAATAATTTATTA
* * * * * *
432304 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
432341 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
432373 GTATGGATTGA-TTATTTAAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTTAAATA---ATTTA-TTA
* ** * * * * *
432408 -TTTTAAATAATTTATTAGTATGGATTGATTTATT-
1 GTATGGATTGATTTATT--T-T-AAATAATTTATTA
* * * * * *
432442 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
* *
432479 ATATAGATTGATTTA--TT--AT--TTTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
432505 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
432537 GTATAGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432560 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
432591 GTATGTATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * *
432614 -TATGGATTGATTTATTTTAATTTTA-TTAGTA
1 GTATGGATTGATTTATTTTAA-ATAATTTATTA
* * *
432645 TGGATTGATTTATTT-T---AAATAA--T-TTA
1 -GTATGGATTGATTTATTTTAAATAATTTATTA
432671 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432703 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432726 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432757 GTATGGATTGATTTA-TTT---TAA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
432780 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
432811 GTATGGAATGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
432843 GTATGGATTAATTTATTTTAAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTA-TTA
* * ** ** * *
432880 TTATTGTAGTTGTATAGATGATTTATTTTAAATAATTA
1 GTA-TGGA-TTG-ATTTAT--TTTA-AATAATTTATTA
* * * * *
432918 TTA-GTATGGATTGA-TTT--AT--TTTA-AA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
432943 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
432975 GTATGGATTGATTTA-TTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
433006 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
433028 ATATGGATGA
Statistics
Matches: 2748, Mismatches: 416, Indels: 1050
0.65 0.10 0.25
Matches are distributed among these distances:
20 2 0.00
21 14 0.01
22 240 0.09
23 72 0.03
24 10 0.00
25 76 0.03
26 115 0.04
27 45 0.02
28 99 0.04
29 98 0.04
30 119 0.04
31 271 0.10
32 824 0.30
33 138 0.05
34 112 0.04
35 112 0.04
36 134 0.05
37 37 0.01
38 83 0.03
39 38 0.01
40 81 0.03
41 6 0.00
42 18 0.01
43 4 0.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:429365 original size:22 final size:22
Alignment explanation
Indices: 429340--429382 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
429330 AATTTATTAG
429340 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
429362 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
429383 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:429452 original size:22 final size:22
Alignment explanation
Indices: 429427--429468 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
429417 ATTTATTAGC
429427 ATGGATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAAT
429449 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
429469 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAT
Found at i:429505 original size:22 final size:22
Alignment explanation
Indices: 429480--429522 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
429470 AATTTATTAG
*
429480 TATGGTTTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
429502 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
429523 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:429694 original size:22 final size:22
Alignment explanation
Indices: 429669--429710 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
429659 ATTTATTAGC
429669 ATGGATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAAT
429691 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
429711 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAT
Found at i:429913 original size:22 final size:22
Alignment explanation
Indices: 429888--429930 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
429878 AATTTATTAG
* * *
429888 TATGTATTGTTTTATTTTAAAA
1 TATGGATTGATTTAATTTAAAA
429910 TATGGATTGATTTAATTTAAA
1 TATGGATTGATTTAATTTAAA
429931 TAATTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTAATTTAAAA
Found at i:430021 original size:22 final size:22
Alignment explanation
Indices: 429996--430144 Score: 91
Period size: 22 Copynumber: 6.0 Consensus size: 22
429986 AATTTATTAG
429996 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
430018 TATGGATTGATTTATTTAAATAA
1 TATGGATTGATTTATTTTAA-AA
* *
430041 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGA----TTTATTTTAAAA
430071 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* *
430095 TTATTAGTATGGATTGATTTATTTTAAAA
1 -TA-T-GGATTGA----TTTATTTTAAAA
430124 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
430145 TAATTTATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 36
0.68 0.07 0.25
Matches are distributed among these distances:
22 38 0.38
23 4 0.04
24 2 0.02
25 4 0.04
26 12 0.12
27 12 0.12
28 4 0.04
29 2 0.02
30 4 0.04
31 17 0.17
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:430181 original size:22 final size:22
Alignment explanation
Indices: 430156--430198 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
430146 AATTTATTAG
430156 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
430178 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
430199 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:430267 original size:22 final size:22
Alignment explanation
Indices: 430242--430284 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
430232 AATTTATTAG
430242 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
430264 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
430285 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:430321 original size:22 final size:22
Alignment explanation
Indices: 430296--430338 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
430286 AATTTATTAG
430296 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
430318 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
430339 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:430375 original size:22 final size:22
Alignment explanation
Indices: 430350--430393 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
430340 AATTTATTAG
430350 TATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAAT
430372 TATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAAT
430394 AATTTATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAT
Found at i:430603 original size:21 final size:20
Alignment explanation
Indices: 430567--430663 Score: 77
Period size: 22 Copynumber: 5.1 Consensus size: 20
430557 TAATTATTAG
*
430567 TATGTATTGATTATTTTAAA
1 TATGGATTGATTATTTTAAA
430587 TATGGATTGATTTATTTTAAA
1 TATGGATTGA-TTATTTTAAA
*
430608 TA---A-T--TTA--TT-AG
1 TATGGATTGATTATTTTAAA
430619 TATGGATTGATTTATTTTAAAA
1 TATGGATTGA-TTATTTT-AAA
430641 TATGGATTGATTTATTTTAAA
1 TATGGATTGA-TTATTTTAAA
430662 TA
1 TA
430664 ATTATTAGTA
Statistics
Matches: 62, Mismatches: 3, Indels: 23
0.70 0.03 0.26
Matches are distributed among these distances:
11 3 0.05
12 2 0.03
14 4 0.06
15 1 0.02
17 1 0.02
18 4 0.06
20 11 0.18
21 17 0.27
22 19 0.31
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (20 bp):
TATGGATTGATTATTTTAAA
Found at i:430644 original size:22 final size:22
Alignment explanation
Indices: 430619--430713 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
430609 AATTTATTAG
430619 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
430641 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* *
430665 TTATTAGTATGGATTGATTTATTTTAAAA
1 -TA-T-GGATTGA----TTTATTTTAAAA
430694 TATGGATTGATTTATTTTAA
1 TATGGATTGATTTATTTTAA
430714 TAATTTATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
22 28 0.47
23 2 0.03
24 2 0.03
25 2 0.03
26 6 0.10
27 6 0.10
28 2 0.03
29 2 0.03
30 2 0.03
31 8 0.13
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:430750 original size:22 final size:22
Alignment explanation
Indices: 430725--430767 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
430715 AATTTATTAG
430725 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
430747 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
430768 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:430805 original size:21 final size:21
Alignment explanation
Indices: 430781--430821 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
430771 TTTATTAGTA
430781 GGATTGATTTATTTTAAATAT
1 GGATTGATTTATTTTAAATAT
430802 GGATTGATTTATTTTAAATA
1 GGATTGATTTATTTTAAATA
430822 ATTTATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
GGATTGATTTATTTTAAATAT
Found at i:431099 original size:33 final size:32
Alignment explanation
Indices: 431011--431096 Score: 163
Period size: 33 Copynumber: 2.7 Consensus size: 32
431001 TATTTTAAAA
431011 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
431043 TATGGGATTGATTTATTTTAAATAATTTATTAG
1 TAT-GGATTGATTTATTTTAAATAATTTATTAG
431076 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
431097 ATAGATTGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 21 0.40
33 32 0.60
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:431179 original size:21 final size:21
Alignment explanation
Indices: 431155--431194 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
431145 TTATAGTATA
431155 GATTGATTTATTTAAAATATG
1 GATTGATTTATTTAAAATATG
*
431176 GATTGATTTATTTTAAATA
1 GATTGATTTATTTAAAATA
431195 ATTTATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
GATTGATTTATTTAAAATATG
Found at i:431361 original size:22 final size:22
Alignment explanation
Indices: 431336--431428 Score: 107
Period size: 22 Copynumber: 4.0 Consensus size: 22
431326 AATTTATTAG
431336 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
431358 TATGGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTT--A-AA---A
*
431386 GTATGGA-TGATTTATTTTAAAT
1 -TATGGATTGATTTATTTTAAAA
431408 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
431429 TAATTTATTA
Statistics
Matches: 62, Mismatches: 1, Indels: 16
0.78 0.01 0.20
Matches are distributed among these distances:
21 6 0.10
22 32 0.52
24 1 0.02
25 4 0.06
26 1 0.02
28 12 0.19
29 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:431655 original size:22 final size:22
Alignment explanation
Indices: 431629--431671 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
431619 ATAATTTTTG
431629 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
431651 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
431672 TATTTATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:431707 original size:22 final size:22
Alignment explanation
Indices: 431682--431724 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
431672 TATTTATTAG
431682 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
431704 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
431725 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:431921 original size:22 final size:22
Alignment explanation
Indices: 431896--432036 Score: 142
Period size: 22 Copynumber: 6.0 Consensus size: 22
431886 AATTTATTAG
431896 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
431918 TATGGATTGA-TTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* *
431941 TTTTAGTATGTATGATTTATTTTAAAA
1 -TAT-GGA--T-TGATTTATTTTAAAA
431968 TATGGATTGATTTATTTTAAATATTA
1 TATGGATTGATTTATTTT-AA-A--A
431994 GTATGGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAAA
432017 TATGGA-TGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432037 TAATTTATTA
Statistics
Matches: 102, Mismatches: 4, Indels: 27
0.77 0.03 0.20
Matches are distributed among these distances:
21 21 0.21
22 29 0.28
23 6 0.06
24 3 0.03
25 5 0.05
26 5 0.05
27 21 0.21
28 5 0.05
29 7 0.07
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432073 original size:22 final size:22
Alignment explanation
Indices: 432048--432090 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432038 AATTTATTAG
432048 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432070 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432091 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432179 original size:22 final size:22
Alignment explanation
Indices: 432154--432196 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432144 AATTTATTAG
432154 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432176 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432197 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432345 original size:22 final size:22
Alignment explanation
Indices: 432320--432362 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432310 AATTTATTAG
432320 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432342 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432363 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432399 original size:20 final size:21
Alignment explanation
Indices: 432374--432416 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
432364 AATTTATTAG
432374 TATGGATTGA-TTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
432394 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
432415 TA
1 TA
432417 ATTTATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:432608 original size:22 final size:22
Alignment explanation
Indices: 432592--432633 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
432582 AATTTATTAG
*
432592 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432614 TATGGATTGATTTATTTTAA
1 TATGGATTGATTTATTTTAA
432634 TTTTATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432729 original size:22 final size:22
Alignment explanation
Indices: 432704--432746 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432694 AATTTATTAG
432704 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432726 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432747 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:432783 original size:22 final size:22
Alignment explanation
Indices: 432758--432801 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
432748 AATTTATTAG
432758 TATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAAT
432780 TATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAAT
432802 AATTTATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAT
Found at i:432808 original size:14 final size:14
Alignment explanation
Indices: 432789--432842 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
432779 TTATGGATTG
432789 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
432803 ATTTATTAGTATGGAATG
1 ATTTATT--T-T-AAATA
432821 ATTTATTTTAAATA
1 ATTTATTTTAAATA
432835 ATTTATTT
1 ATTTATTT
432843 GTATGGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:432950 original size:22 final size:22
Alignment explanation
Indices: 432922--432964 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432912 TAATTATTAG
432922 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
432944 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
432965 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:433110 original size:20 final size:21
Alignment explanation
Indices: 433085--433127 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
433075 AATTTATTAG
433085 TATGGATTGATTT-TTTAAAA
1 TATGGATTGATTTATTTAAAA
*
433105 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
433126 TA
1 TA
433128 ATTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:433185 original size:31 final size:31
Alignment explanation
Indices: 433150--433208 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
433140 AGTTTTATGG
* *
433150 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
433181 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
433209 CTTTTGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:433561 original size:2 final size:2
Alignment explanation
Indices: 433554--433595 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
433544 CATATCCATT
433554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
433595 T
1 T
433596 CAATTAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:435338 original size:5 final size:5
Alignment explanation
Indices: 435328--435356 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
435318 TTTTGAAGAC
435328 AATAA AATAA AATAA AATAA AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATA
435357 CAACTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:436994 original size:12 final size:12
Alignment explanation
Indices: 436979--437044 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
436969 GTTATTTAAA
436979 CGGGTATTGGGC
1 CGGGTATTGGGC
*
436991 CGGGTATTGGGT
1 CGGGTATTGGGC
*
437003 CGGGTATTGGGT
1 CGGGTATTGGGC
437015 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
437026 CGGGAATCGGGC
1 CGGGTATTGGGC
*
437038 TGGGTAT
1 CGGGTAT
437045 ATATATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.21
12 37 0.79
ACGTcount: A:0.11, C:0.14, G:0.48, T:0.27
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:437006 original size:24 final size:24
Alignment explanation
Indices: 436979--437044 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
436969 GTTATTTAAA
*
436979 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
437003 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* * *
437026 CGGGAATCGGGCTGGGTAT
1 CGGGTATTGGGCCGGGTAT
437045 ATATATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.11, C:0.14, G:0.48, T:0.27
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:437100 original size:24 final size:25
Alignment explanation
Indices: 437044--437124 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 25
437034 GGGCTGGGTA
437044 TATATATATTTAAATTAAATATATAT
1 TATAT-TATTTAAATTAAATATATAT
*
437070 T-TTTTATTTAAATTAAAT-T-TAT
1 TATATTATTTAAATTAAATATATAT
* * *
437092 TAATATTATATATA-TATATATATA-
1 T-ATATTATTTAAATTAAATATATAT
437116 TA-ATTATTT
1 TATATTATTT
437125 TTAATATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 10 0.22
23 6 0.13
24 24 0.53
25 4 0.09
26 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATTATTTAAATTAAATATATAT
Found at i:438932 original size:2 final size:2
Alignment explanation
Indices: 438925--438967 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
438915 ATTTAAATTA
* * *
438925 AT AT AT AT AT AT AT AT AT AT AT TT A- AT TT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
438966 AT
1 AT
438968 CCGGCCCGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:447086 original size:29 final size:29
Alignment explanation
Indices: 447044--447101 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
447034 TCCCATGGAT
447044 TCCATCGCAAAACAGGTCTCTTGTCTCGA
1 TCCATCGCAAAACAGGTCTCTTGTCTCGA
447073 TCCATCGCAAAACAGGTCTCTTGTCTCGA
1 TCCATCGCAAAACAGGTCTCTTGTCTCGA
447102 GAAATGGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (29 bp):
TCCATCGCAAAACAGGTCTCTTGTCTCGA
Found at i:447787 original size:14 final size:14
Alignment explanation
Indices: 447768--447824 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
447758 CAATGTATTA
*
447768 CATCGTGCCTCCGC
1 CATCGTGCATCCGC
* *
447782 CATCGTGCA-CAATGG
1 CATCGTGCATC--CGC
447797 CATCGTGCATCCGC
1 CATCGTGCATCCGC
447811 CATCGTGCATCCGC
1 CATCGTGCATCCGC
447825 ACGCCTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.03
14 23 0.66
15 10 0.29
16 1 0.03
ACGTcount: A:0.16, C:0.40, G:0.23, T:0.21
Consensus pattern (14 bp):
CATCGTGCATCCGC
Found at i:451254 original size:60 final size:60
Alignment explanation
Indices: 451180--451306 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
451170 CATGGTTCTC
* * * *
451180 CGACTATATGATATTAT-TTTGTT-AAGTCTCTTGACTATTAAAAGTTACAAAATAGTCCCT
1 CGACTATAGGATATT-TCTTTGTTGAA-TCCCTCGACTATTAAAAGTTACAAAATAGTCACT
*
451240 CGACTATAGGATATTTCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGGTCACT
1 CGACTATAGGATATTTCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATAGTCACT
*
451300 TGACTAT
1 CGACTAT
451307 TTATTATGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 1 0.02
60 56 0.95
61 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (60 bp):
CGACTATAGGATATTTCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATAGTCACT
Found at i:451635 original size:60 final size:60
Alignment explanation
Indices: 451517--451649 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
451507 TCAGTTGACT
* * * * *
451517 ATTTTGTAACTTTTAATAGTCGAATGACTCAAAAAAGTAATATCCTATAATTGAAGGACC
1 ATTTTGTAACTTTTAATAGTCGAAGGACTCAAAAAAGCAACATCATATAATCGAAGGACC
* * *
451577 ATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAA-CAACATCATATAGTCGGAGGACC
1 ATTTTGTAACTTTTAATAGTCGAAGGACTCAA-AAAAGCAACATCATATAATCGAAGGACC
451637 ATTTT-TATACTTT
1 ATTTTGTA-ACTTT
451650 ATCCTATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 57 0.90
61 4 0.06
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAAGGACTCAAAAAAGCAACATCATATAATCGAAGGACC
Found at i:451792 original size:25 final size:23
Alignment explanation
Indices: 451764--451818 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
451754 CCAATATTGT
*
451764 CTAAAATTTAGAAGTTCAATTGAAG
1 CTAAAATTT-G-AGCTCAATTGAAG
451789 CTAAAAATTTGAGCTCAATTGAAG
1 CT-AAAATTTGAGCTCAATTGAAG
*
451813 CGAAAA
1 CTAAAA
451819 AATAGTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 3 0.11
26 7 0.26
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (23 bp):
CTAAAATTTGAGCTCAATTGAAG
Found at i:460425 original size:2 final size:2
Alignment explanation
Indices: 460420--460451 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
460410 ATATATATAC
*
460420 GT GT GT GT GT GT TT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
460452 TTATACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
GT
Found at i:461673 original size:21 final size:21
Alignment explanation
Indices: 461647--461688 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
461637 TTATGATTCA
461647 TTTTTAAAATTATAAAAGTAT
1 TTTTTAAAATTATAAAAGTAT
*
461668 TTTTTAATATTATAAAAGTAT
1 TTTTTAAAATTATAAAAGTAT
461689 CTCTATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTTAAAATTATAAAAGTAT
Found at i:463142 original size:5 final size:5
Alignment explanation
Indices: 463132--463157 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
463122 TGACTTAGAA
463132 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
463158 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:463567 original size:23 final size:23
Alignment explanation
Indices: 463541--463586 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
463531 ATTTTAAATT
*
463541 TATATACTTTTTAATAAAATTTA
1 TATATAATTTTTAATAAAATTTA
*
463564 TATATAATTTTTTATAAAATTTA
1 TATATAATTTTTAATAAAATTTA
463587 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATAATTTTTAATAAAATTTA
Found at i:463594 original size:24 final size:23
Alignment explanation
Indices: 463548--463594 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
463538 ATTTATATAC
* *
463548 TTTTTAATAAAATTTATATATAA
1 TTTTTAATAAAATTTAAAGATAA
*
463571 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
463595 ATGGATAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTAATAAAATTTAAAGATAA
Found at i:467184 original size:2 final size:2
Alignment explanation
Indices: 467177--467202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
467167 TACAAATAGG
467177 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
467203 CAAACCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:468740 original size:28 final size:28
Alignment explanation
Indices: 468705--468763 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
468695 TTCCAACATA
468705 ATAGTGAGGGTGGAACCATAATTATAAC
1 ATAGTGAGGGTGGAACCATAATTATAAC
468733 ATAGTGAGGGTGGAACCATAATTATAAC
1 ATAGTGAGGGTGGAACCATAATTATAAC
468761 ATA
1 ATA
468764 ATACTGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (28 bp):
ATAGTGAGGGTGGAACCATAATTATAAC
Found at i:471941 original size:21 final size:22
Alignment explanation
Indices: 471900--471953 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
471890 TCATTCTAGC
*
471900 TGTTATTGTTTTTAGTCGTTAT
1 TGTTATTGTTTTTAATCGTTAT
471922 TGTTATTGTTTTTAAT-GTTAT
1 TGTTATTGTTTTTAATCGTTAT
*
471943 TATTATTGTTT
1 TGTTATTGTTT
471954 CTGATTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.67
Consensus pattern (22 bp):
TGTTATTGTTTTTAATCGTTAT
Found at i:474183 original size:20 final size:20
Alignment explanation
Indices: 474160--474200 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
474150 AAGATAAAGG
474160 AAAAAAATAGGTTAGAAAAA
1 AAAAAAATAGGTTAGAAAAA
* *
474180 AAAACACTAGGTTAGAAAAA
1 AAAAAAATAGGTTAGAAAAA
474200 A
1 A
474201 TAGGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAAAATAGGTTAGAAAAA
Found at i:475867 original size:2 final size:2
Alignment explanation
Indices: 475860--475899 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
475850 ATTCAGAAAT
475860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475900 ATTTTTATGA
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):
TA
Found at i:476212 original size:23 final size:23
Alignment explanation
Indices: 476156--476231 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
476146 CATTTAAATG
*
476156 ATAAACGAACACAAACGAACGAAC
1 ATAAACGAACATAAACGAAC-AAC
*
476180 ATAAATGAACATAAACGAAC-AC
1 ATAAACGAACATAAACGAACAAC
476202 AATAAACGAACATAAACGAACAAC
1 -ATAAACGAACATAAACGAACAAC
*
476226 ACAAAC
1 ATAAAC
476232 ACAAAAAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.04
23 24 0.52
24 20 0.43
ACGTcount: A:0.61, C:0.22, G:0.09, T:0.08
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACAAC
Found at i:476505 original size:14 final size:14
Alignment explanation
Indices: 476486--476520 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
476476 GCCCTCTGTT
476486 CGAACATAAATGAA
1 CGAACATAAATGAA
476500 CGAACATAAATGAA
1 CGAACATAAATGAA
476514 CGAACAT
1 CGAACAT
476521 GTAATCGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:478736 original size:14 final size:14
Alignment explanation
Indices: 478717--478766 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
478707 TTACTTTTAT
478717 TTAGGGTTTAAAGG
1 TTAGGGTTTAAAGG
478731 TTAGGGTTTAAAGG
1 TTAGGGTTTAAAGG
*
478745 TTAGCGTTTAAAGG
1 TTAGGGTTTAAAGG
*
478759 TTATGGTT
1 TTAGGGTT
478767 ATGGTTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (14 bp):
TTAGGGTTTAAAGG
Found at i:478781 original size:28 final size:29
Alignment explanation
Indices: 478716--478787 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
478706 TTTACTTTTA
478716 TTTAGGGTTTAAAGGTTAGGGTTTAAAGG
1 TTTAGGGTTTAAAGGTTAGGGTTTAAAGG
* * *
478745 -TTAGCGTTTAAAGGTTATGG-TT-ATGG
1 TTTAGGGTTTAAAGGTTAGGGTTTAAAGG
478771 TTTAGGGGTTT-AAGGTT
1 TTTA-GGGTTTAAAGGTT
478788 TAGAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 3 0.08
27 11 0.30
28 23 0.62
ACGTcount: A:0.24, C:0.01, G:0.33, T:0.42
Consensus pattern (29 bp):
TTTAGGGTTTAAAGGTTAGGGTTTAAAGG
Found at i:479119 original size:3 final size:3
Alignment explanation
Indices: 479113--479147 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
479103 AATATTCCTT
479113 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
479148 TTGTGTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:505382 original size:20 final size:21
Alignment explanation
Indices: 505344--505383 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
505334 CTGATTGAAA
* *
505344 AAAATTAAAAATTTGATAATC
1 AAAATTAAAAATATAATAATC
505365 AAAA-TAAAAATATAATAAT
1 AAAATTAAAAATATAATAAT
505384 TAACTGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATTAAAAATATAATAATC
Found at i:510107 original size:22 final size:22
Alignment explanation
Indices: 510082--510162 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 22
510072 GAGAAGAGAG
510082 AGAGAAGAGAAGGAAAGGAAAA
1 AGAGAAGAGAAGGAAAGGAAAA
* *
510104 AGAGGAG-GAAAGAGAAGG-AAA
1 AGAGAAGAGAAGGA-AAGGAAAA
* *
510125 AGAAAAGGAGAA-GAAGAGGAAAG
1 AGAGAA-GAGAAGGAA-AGGAAAA
510148 AGA-AAGAG-AGGAAAG
1 AGAGAAGAGAAGGAAAG
510163 CAAAGAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 3 0.06
21 19 0.40
22 18 0.38
23 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (22 bp):
AGAGAAGAGAAGGAAAGGAAAA
Found at i:510144 original size:32 final size:30
Alignment explanation
Indices: 510070--510151 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 30
510060 GAGAAAGAGG
*
510070 AAGAGAAGAGAGAGAGAAGAGAAGGAAAGGAA
1 AAGAGAAGAGAG-GA-AAGAGAAGGAAAAGAA
510102 AA-AG-AG-GAGGAAAGAGAAGGAAAAGAA
1 AAGAGAAGAGAGGAAAGAGAAGGAAAAGAA
510129 AAGGAGAAGAAGAGGAAAGAGAA
1 AA-GAGAAG-AGAGGAAAGAGAA
510152 AGAGAGGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
27 17 0.39
28 2 0.05
29 5 0.11
30 4 0.09
31 2 0.05
32 14 0.32
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (30 bp):
AAGAGAAGAGAGGAAAGAGAAGGAAAAGAA
Found at i:510153 original size:27 final size:27
Alignment explanation
Indices: 510083--510154 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 27
510073 AGAAGAGAGA
*
510083 GAGAAG-AGAAGGAAAG-GAAA-AAGAG
1 GAGAAGAAG-AGGAAAGAGAAAGAAAAG
* *
510108 GAGGA-AAGA-GAAGGA-AAAGAAAAG
1 GAGAAGAAGAGGAAAGAGAAAGAAAAG
510132 GAGAAGAAGAGGAAAGAGAAAGA
1 GAGAAGAAGAGGAAAGAGAAAGA
510155 GAGGAAAGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
23 7 0.19
24 9 0.25
25 10 0.28
26 5 0.14
27 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (27 bp):
GAGAAGAAGAGGAAAGAGAAAGAAAAG
Found at i:510153 original size:38 final size:35
Alignment explanation
Indices: 510058--510178 Score: 99
Period size: 33 Copynumber: 3.4 Consensus size: 35
510048 GGAGAGGAGG
* * *
510058 AGGAGAAAGAGGAAGAGAAGAGAGAGAGAAGAGAAGGAA
1 AGGAAAAAGAGGAAGAGAA-AGAGA-AG--GAAAAGAAA
510097 AGGAAAAAGAGG-AG-GAAAGAGAAGGAAAAGAAA
1 AGGAAAAAGAGGAAGAGAAAGAGAAGGAAAAGAAA
*
510130 AGGAGAAGAAGAGGAAAGAGAAAGAG-AGG-AAAGCAA
1 AGGA-AA-AAGAGG-AAGAGAAAGAGAAGGAAAAGAAA
510166 A-GAAAAAGGAGGA
1 AGGAAAAA-GAGGA
510179 CAAGTTAGAG
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
33 14 0.19
34 8 0.11
35 10 0.14
36 12 0.17
37 8 0.11
38 9 0.12
39 11 0.15
ACGTcount: A:0.60, C:0.01, G:0.40, T:0.00
Consensus pattern (35 bp):
AGGAAAAAGAGGAAGAGAAAGAGAAGGAAAAGAAA
Found at i:510156 original size:21 final size:19
Alignment explanation
Indices: 510123--510171 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
510113 AAGAGAAGGA
*
510123 AAAGAAAAGGAGAAGAAGAGG
1 AAAGAAAA-GAGAAGAA-AGC
*
510144 AAAGAGAAAGAGAGGAAAGC
1 AAAGA-AAAGAGAAGAAAGC
510164 AAAGAAAA
1 AAAGAAAA
510172 AGGAGGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 7 0.28
21 12 0.48
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (19 bp):
AAAGAAAAGAGAAGAAAGC
Found at i:512475 original size:24 final size:24
Alignment explanation
Indices: 512448--512504 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
512438 CTCTTTCTTA
512448 TGCTTCCTAACTTAGTGACCATTT
1 TGCTTCCTAACTTAGTGACCATTT
512472 TGCTTCCTAACTTAGTGACCATTT
1 TGCTTCCTAACTTAGTGACCATTT
*
512496 TGCTGCCTA
1 TGCTTCCTA
512505 TCTGTTGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (24 bp):
TGCTTCCTAACTTAGTGACCATTT
Found at i:512941 original size:2 final size:2
Alignment explanation
Indices: 512898--512923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
512888 ACACATTTTG
512898 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
512924 CGGGTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513887 original size:45 final size:45
Alignment explanation
Indices: 513823--514120 Score: 366
Period size: 45 Copynumber: 6.6 Consensus size: 45
513813 AATGGAAATG
* * * *
513823 GTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGAGAAG
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
* * * *
513868 GTATCGGGTACGGCGTTGGACAATCATGGGGACAATCAGGAGAAG
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
* * *
513913 GTACCGGATATGGCATTGGACAATCAGGGGGACAGTCAGGA-AATA
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAA-A
* *
513958 GTATGGGGTATGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
*
514003 GTATCGGATACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
* * * * * *
514048 GTTTTGGGTACGGCATTGGGCAATCAGGAGGACAGTTAGGA-ACTA
1 GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGA-AA
* *
514093 GCATTGGGTACGGCATTGGACAATCAGG
1 GTATCGGGTACGGCATTGGACAATCAGG
514121 AGGTCAATCA
Statistics
Matches: 223, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
44 3 0.01
45 218 0.98
46 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.19
Consensus pattern (45 bp):
GTATCGGGTACGGCATTGGACAATCAGGGGGACAGTCAGGAGAAA
Found at i:514063 original size:135 final size:135
Alignment explanation
Indices: 513816--514133 Score: 429
Period size: 135 Copynumber: 2.4 Consensus size: 135
513806 AATTGGCAAT
* * *
513816 GGAAATGGTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGAGAAGGTATCGGGTACGG
1 GGAAATAGTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGAGAAAGTATCGGATACGG
* * * * *
513881 CGTTGGACAATCATGGGGACAATCAGGAGAAGGTACCGGATATGGCATTGGACAATCAGGGGGAC
66 CATTGGACAATCAGGGGGACAATCAGGAGAAAGTACCGGATACGGCATTGGACAATCAGGAGGAC
513946 AGTCA
131 AGTCA
* *
513951 GGAAATAGTATGGGGTATGGCATTGGACAATCAGGGGGACAGTCAGGAGAAAGTATCGGATACGG
1 GGAAATAGTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGAGAAAGTATCGGATACGG
* *** * *
514016 CATTGGACAATCAGGGGGACAGTCAGGAGAAAGTTTTGGGTACGGCATTGGGCAATCAGGAGGAC
66 CATTGGACAATCAGGGGGACAATCAGGAGAAAGTACCGGATACGGCATTGGACAATCAGGAGGAC
*
514081 AGTTA
131 AGTCA
* * * * * *
514086 GGAACTAGCATTGGGTACGGCATTGGACAATCAGGAGGTCAATCAGGA
1 GGAAATAGTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGA
514134 AACAATGTCG
Statistics
Matches: 159, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
135 159 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.19
Consensus pattern (135 bp):
GGAAATAGTATAGGGTATGGCATTGGACAATCAGGGGGACAATCAGGAGAAAGTATCGGATACGG
CATTGGACAATCAGGGGGACAATCAGGAGAAAGTACCGGATACGGCATTGGACAATCAGGAGGAC
AGTCA
Found at i:517125 original size:45 final size:44
Alignment explanation
Indices: 516986--517354 Score: 224
Period size: 45 Copynumber: 8.3 Consensus size: 44
516976 AAATGGTATC
* * *
516986 GGATATGGTGTTGGACAATCAGGAGGTCAGTCAGGAAATA-GTAT
1 GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAAAATGT-T
* * * * *
517030 GGGATATGGTGCTGGACAATCGTGG-GGTAAATCGGGAAATAGTGTC
1 -GGATATGGTGTTGGACAATCG-GGAGGTCAATCAGGAAA-AATGTT
* *
517076 GGATATGGTGTTGGACAATCGGGGGGTCAATCAGGAAACAACGTT
1 GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAA-AATGTT
* * * **
517121 GGATATGGTATTGG--AATTGGCAATGG--AGAT--GGAGAAGGTGTT
1 GGATATGGTGTTGGACAATCGG-GA-GGTCA-ATCAGGA-AAAATGTT
* *
517163 GGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTT
1 GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAA-AATGTT
* * * * **
517208 GGATATGGTATTGG--AATTGGCAACGG-AAAT--GGAGAAGGTGTT
1 GGATATGGTGTTGGACAATCGG-GA-GGTCAATCAGGA-AAAATGTT
* * * *
517250 GGGTATGGTATTGGACAATCGGGAGGTCAATCAGGAAATAGTATT
1 GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAA-AATGTT
* ** *
517295 GGGTATGGTGTTGGACAATCGGGAGGTCCGTCAGGAAACAACGTT
1 GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAA-AATGTT
*
517340 GGATATGGTATTGGA
1 GGATATGGTGTTGGA
517355 ATTGGCAATG
Statistics
Matches: 248, Mismatches: 52, Indels: 48
0.71 0.15 0.14
Matches are distributed among these distances:
42 41 0.17
43 22 0.09
44 23 0.09
45 158 0.64
46 2 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.37, T:0.25
Consensus pattern (44 bp):
GGATATGGTGTTGGACAATCGGGAGGTCAATCAGGAAAAATGTT
Found at i:517214 original size:177 final size:177
Alignment explanation
Indices: 516894--517216 Score: 445
Period size: 177 Copynumber: 1.8 Consensus size: 177
516884 AATGGATATG
* * * * *
516894 GTGTCGGGTACGGCGTTGGACAATCTGGGGGTCAATTAGGAAACAGCGTTGGATATGGTATCGGT
1 GTGTCGGATACGGCGTTGGACAATCGGGGGGTCAATCAGGAAACAACGTTGGATATGGTATCGGA
* *
516959 ATTGGTAATGAAAATGGAAATGGTATCGGATATGGTGTTGGACAATCAGGAGGTCAGTCAGGAAA
66 ATTGGCAATGAAAATGGAAATGGTATCGGATATGGTGTTGGACAATCAGGAGGTCAATCAGGAAA
*
517024 TAGTATGGGATATGGTGCTGGACAATCGTGGGGTAAATCGGGAAATA
131 AAGTATGGGATATGGTGCTGGACAATCGTGGGGTAAATCGGGAAATA
* * *
517071 GTGTCGGATATGGTGTTGGACAATCGGGGGGTCAATCAGGAAACAACGTTGGATATGGTATTGGA
1 GTGTCGGATACGGCGTTGGACAATCGGGGGGTCAATCAGGAAACAACGTTGGATATGGTATCGGA
* * * * * *
517136 ATTGGCAATGGAGATGGAGAA-GGTGTTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAA
66 ATTGGCAATGAAAATGGA-AATGGTATCGGATATGGTGTTGGACAATCAGGAGGTCAATCAGGAA
517200 ACAACGT-T-GGATATGGT
130 A-AA-GTATGGGATATGGT
517217 ATTGGAATTG
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 120 0.95
178 4 0.03
179 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.37, T:0.25
Consensus pattern (177 bp):
GTGTCGGATACGGCGTTGGACAATCGGGGGGTCAATCAGGAAACAACGTTGGATATGGTATCGGA
ATTGGCAATGAAAATGGAAATGGTATCGGATATGGTGTTGGACAATCAGGAGGTCAATCAGGAAA
AAGTATGGGATATGGTGCTGGACAATCGTGGGGTAAATCGGGAAATA
Found at i:517297 original size:132 final size:132
Alignment explanation
Indices: 517161--517418 Score: 435
Period size: 132 Copynumber: 2.0 Consensus size: 132
517151 GGAGAAGGTG
517161 TTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTGGATATGGTATTGGAATT
1 TTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTGGATATGGTATTGGAATT
* * *
517226 GGCAACGGAAATGGAGAAGGTGTTGGGTATGGTATTGGACAATCGGGAGGTCAATCAGGAAATAG
66 GGCAACGGAAATGGAGAAGGTGTTGGGTACGGCATTGGACAATCAGGAGGTCAATCAGGAAATAG
517291 TA
131 TA
**
517293 TTGGGTATGGTGTTGGACAATCGGGAGGTCCGTCAGGAAACAACGTTGGATATGGTATTGGAATT
1 TTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTGGATATGGTATTGGAATT
* * * *
517358 GGCAATGGAGATGGAGAAGGTGTTGGGTACGGCGTTGGACAATCAGGAGGTCAGTCAGGAA
66 GGCAACGGAAATGGAGAAGGTGTTGGGTACGGCATTGGACAATCAGGAGGTCAATCAGGAA
517419 GCAATATTGG
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 117 1.00
ACGTcount: A:0.28, C:0.10, G:0.37, T:0.24
Consensus pattern (132 bp):
TTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTGGATATGGTATTGGAATT
GGCAACGGAAATGGAGAAGGTGTTGGGTACGGCATTGGACAATCAGGAGGTCAATCAGGAAATAG
TA
Found at i:517309 original size:87 final size:87
Alignment explanation
Indices: 516880--517287 Score: 419
Period size: 87 Copynumber: 4.7 Consensus size: 87
516870 GATATGGCGT
* * * * *
516880 TGGAAATGGATATGGTGTCGGGTACGGCGTTGGACAATCTGGG-GGTCAATTAGGAAACAGCGTT
1 TGGAAATGGAGAAGGTGTCGGGTATGGTGTTGGACAATC-GGGAGGTCAATCAGGAAACAGCGTT
* * *
516944 GGATATGGTATCGGTATTGGTAA
65 GGATATGGTATTGGAATTGGCAA
* * * * * * ** *
516967 TGAAAATGGA-AATGGTATCGGATATGGTGTTGGACAATCAGGAGGTCAGTCAGGAAATAGTATG
1 TGGAAATGGAGAA-GGTGTCGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAGCGTT
** * * **
517031 GGATATGGTGCTGGACAATCG-TG
65 GGATATGGTATTGGA-ATTGGCAA
* * * * *
517054 GGGTAAATCGG-GAAATAGTGTCGGATATGGTGTTGGACAATCGGGGGGTCAATCAGGAAACAAC
1 TGG-AAAT-GGAG-AA-GGTGTCGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAGC
517118 GTTGGATATGGTATTGGAATTGGCAA
62 GTTGGATATGGTATTGGAATTGGCAA
* * *
517144 TGGAGATGGAGAAGGTGTTGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTG
1 TGGAAATGGAGAAGGTGTCGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAGCGTTG
517209 GATATGGTATTGGAATTGGCAA
66 GATATGGTATTGGAATTGGCAA
* * *
517231 CGGAAATGGAGAAGGTGTTGGGTATGGTATTGGACAATCGGGAGGTCAATCAGGAAA
1 TGGAAATGGAGAAGGTGTCGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAA
517288 TAGTATTGGG
Statistics
Matches: 264, Mismatches: 48, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
86 3 0.01
87 182 0.69
88 11 0.04
89 9 0.03
90 59 0.22
ACGTcount: A:0.29, C:0.09, G:0.37, T:0.25
Consensus pattern (87 bp):
TGGAAATGGAGAAGGTGTCGGGTATGGTGTTGGACAATCGGGAGGTCAATCAGGAAACAGCGTTG
GATATGGTATTGGAATTGGCAA
Found at i:517385 original size:87 final size:85
Alignment explanation
Indices: 517293--517521 Score: 278
Period size: 87 Copynumber: 2.6 Consensus size: 85
517283 GGAAATAGTA
* * * *
517293 TTGGGTATGGTGTTGGACAATCGGGAGGTCCGTCAGGAAACAACGTTGGATATGGTATTGGAATT
1 TTGGGTACGGCGTTGGACAATCGGGAGGTCAGTCAGGAAACAACGTTGGATATGGCATTGGAATT
* * *
517358 GGCAATGGAGATGGAGAAGGTG
66 GGCAATGAAAAT-GAAAAGG-G
* * ** *
517380 TTGGGTACGGCGTTGGACAATCAGGAGGTCAGTCAGGAAGCAATATTGGATATGGCATTGGAGTT
1 TTGGGTACGGCGTTGGACAATCGGGAGGTCAGTCAGGAAACAACGTTGGATATGGCATTGGAATT
*
517445 GGGAATGAAAATGAAAAGGG
66 GGCAATGAAAATGAAAAGGG
* * *
517465 TATCGGATACGGCGTTGGACAATCGGGAGGTCAATCAGGAACCAACGTTGGATATGG
1 T-T-GGGTACGGCGTTGGACAATCGGGAGGTCAGTCAGGAAACAACGTTGGATATGG
517522 AGTTGGACAG
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 2 0.02
86 7 0.06
87 112 0.93
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (85 bp):
TTGGGTACGGCGTTGGACAATCGGGAGGTCAGTCAGGAAACAACGTTGGATATGGCATTGGAATT
GGCAATGAAAATGAAAAGGG
Found at i:517431 original size:219 final size:219
Alignment explanation
Indices: 517042--517575 Score: 714
Period size: 219 Copynumber: 2.4 Consensus size: 219
517032 GATATGGTGC
* * * * *
517042 TGGACAATCGTGG-GGTAAATCGGGAAATAGTGTCGGATATGGTGTTGGACAATCGGGGGGTCAA
1 TGGACAATCG-GGAGGTCAATCAGGAAATAGTGTTGGATATGGTGTTGGACAATCGGGAGGTCAG
*
517106 TCAGGAAACAACGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGGGTATGG
65 TCAGGAAACAACGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGGGTACGG
* * * * *
517171 TGTTGGACAATCGGGAGGTCAATCAGGAAACAACGTTGGATATGGTATTGGAATTGGCAACGGAA
130 CGTTGGACAATCAGGAGGTCAATCAGGAAACAACATTGGATATGGCATTGGAATTGGCAACGAAA
* * * *
517236 ATGGAGAAGGTGT-T-GGGTATGGTAT
195 AT-GAAAAGG-GTATCGGATACGGCAT
* * *
517261 TGGACAATCGGGAGGTCAATCAGGAAATAGTATTGGGTATGGTGTTGGACAATCGGGAGGTCCGT
1 TGGACAATCGGGAGGTCAATCAGGAAATAGTGTTGGATATGGTGTTGGACAATCGGGAGGTCAGT
517326 CAGGAAACAACGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGGGTACGGC
66 CAGGAAACAACGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGGGTACGGC
* * * * * *
517391 GTTGGACAATCAGGAGGTCAGTCAGGAAGCAATATTGGATATGGCATTGGAGTTGGGAATGAAAA
131 GTTGGACAATCAGGAGGTCAATCAGGAAACAACATTGGATATGGCATTGGAATTGGCAACGAAAA
*
517456 TGAAAAGGGTATCGGATACGGCGT
196 TGAAAAGGGTATCGGATACGGCAT
** ** * * *
517480 TGGACAATCGGGAGGTCAATCAGGAACCAACGTTGGATATGGAGTTGGACAGTCAGGAGGTCAGT
1 TGGACAATCGGGAGGTCAATCAGGAAATAGTGTTGGATATGGTGTTGGACAATCGGGAGGTCAGT
* *
517545 CTGGAAACAACGTTGGATATGGTATCGGAAT
66 CAGGAAACAACGTTGGATATGGTATTGGAAT
517576 CGGATCAGGA
Statistics
Matches: 275, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
217 2 0.01
218 9 0.03
219 264 0.96
ACGTcount: A:0.29, C:0.10, G:0.36, T:0.24
Consensus pattern (219 bp):
TGGACAATCGGGAGGTCAATCAGGAAATAGTGTTGGATATGGTGTTGGACAATCGGGAGGTCAGT
CAGGAAACAACGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGGGTACGGC
GTTGGACAATCAGGAGGTCAATCAGGAAACAACATTGGATATGGCATTGGAATTGGCAACGAAAA
TGAAAAGGGTATCGGATACGGCAT
Found at i:517539 original size:45 final size:45
Alignment explanation
Indices: 517469--517566 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
517459 AAAGGGTATC
* * * *
517469 GGATACGGCGTTGGACAATCGGGAGGTCAATCAGGAACCAACGTT
1 GGATATGGAGTTGGACAATCAGGAGGTCAATCAGGAAACAACGTT
* * *
517514 GGATATGGAGTTGGACAGTCAGGAGGTCAGTCTGGAAACAACGTT
1 GGATATGGAGTTGGACAATCAGGAGGTCAATCAGGAAACAACGTT
517559 GGATATGG
1 GGATATGG
517567 TATCGGAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.15, G:0.36, T:0.20
Consensus pattern (45 bp):
GGATATGGAGTTGGACAATCAGGAGGTCAATCAGGAAACAACGTT
Found at i:518585 original size:21 final size:21
Alignment explanation
Indices: 518561--518617 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
518551 GATAACTTAA
518561 CGACCTATGATCGATGAAACT
1 CGACCTATGATCGATGAAACT
518582 CGACCTATGATCGATGAAACT
1 CGACCTATGATCGATGAAACT
* *
518603 CGAACTATGAGCGAT
1 CGACCTATGATCGAT
518618 AACAAATCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
CGACCTATGATCGATGAAACT
Found at i:529388 original size:20 final size:22
Alignment explanation
Indices: 529348--529389 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
529338 TCACCTCTAT
529348 TTTATAGTATATATATTTAAAA
1 TTTATAGTATATATATTTAAAA
*
529370 TTTATA-TAT-TATTTTTAAAA
1 TTTATAGTATATATATTTAAAA
529390 AATATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTATAGTATATATATTTAAAA
Found at i:530574 original size:23 final size:23
Alignment explanation
Indices: 530547--530596 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
530537 TTAACGTTCT
530547 AAATTAAGTTTCTTTTTACCCTA
1 AAATTAAGTTTCTTTTTACCCTA
530570 AAATTAAGTTTCTTTTTACCCTA
1 AAATTAAGTTTCTTTTTACCCTA
530593 AAAT
1 AAAT
530597 GAAATATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTAAGTTTCTTTTTACCCTA
Found at i:530940 original size:2 final size:2
Alignment explanation
Indices: 530933--530979 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
530923 TAATAATTAT
530933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
530975 TA TA T
1 TA TA T
530980 GGCATGAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:531337 original size:60 final size:60
Alignment explanation
Indices: 531269--531407 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 60
531259 GTAAAGTACA
* * *
531269 AAAATGATC-CATTGACTATAGGATAA-TACTTTATTGAGTCTATTGACTATTAAAAGTTAT
1 AAAATGATCTC-TCGACTATAGGA-AATTACTTTATTGAGTCCATTGACTATTAAAAATTAT
** * * * *
531329 AAAATGATCTCTCGGTTATATGAAATTATTTTGTTGAGTCCCTTGACTATTAAAAATTAT
1 AAAATGATCTCTCGACTATAGGAAATTACTTTATTGAGTCCATTGACTATTAAAAATTAT
531389 AAAATGATCATC-CGACTAT
1 AAAATGATC-TCTCGACTAT
531408 TAATTATTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
59 2 0.03
60 60 0.92
61 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (60 bp):
AAAATGATCTCTCGACTATAGGAAATTACTTTATTGAGTCCATTGACTATTAAAAATTAT
Found at i:541153 original size:65 final size:64
Alignment explanation
Indices: 541078--541237 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 64
541068 TAATAAATTG
* * * *
541078 AACATCGAATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTGAGGGT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACAAT-CCATGCATCAATGCACTCAGGCTATTT-TG
541141 AA
64 -A
* *
541143 AACATTGAATGCATTTGATGCATCGATGCACAATCCATGCATCAATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACAATCCATGCATCAATGCACTCAGGCTATTTTGA
* *
541207 AACATCGAATGCACTTCATGCACCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
541238 TAAGGGTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.33
65 51 0.61
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAATCCATGCATCAATGCACTCAGGCTATTTTGA
Found at i:546939 original size:21 final size:21
Alignment explanation
Indices: 546915--546982 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
546905 AATCACTTGG
*
546915 ACTGCCACATCAACACCATGA
1 ACTGTCACATCAACACCATGA
* *
546936 ACTGTCACTTCAATACCATGA
1 ACTGTCACATCAACACCATGA
* * *
546957 ACTGTTACATCAACACCTTAA
1 ACTGTCACATCAACACCATGA
546978 ACTGT
1 ACTGT
546983 GTCGTCAGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.35, C:0.31, G:0.09, T:0.25
Consensus pattern (21 bp):
ACTGTCACATCAACACCATGA
Found at i:549962 original size:55 final size:55
Alignment explanation
Indices: 549878--549985 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
549868 TTCTTAAACT
*
549878 GGAGCAATTTTTTAGTCTATTAACGGATGGAGGGATCAATTCCTAATAACTTGCA
1 GGAGCAATTTTTTAGTCTATTAACGGATGGAGAGATCAATTCCTAATAACTTGCA
549933 GGAGCAATTTTTTAGTCTATTAACGGATGGAGAGATCAATTCCTAATAACTTG
1 GGAGCAATTTTTTAGTCTATTAACGGATGGAGAGATCAATTCCTAATAACTTG
549986 GATCAACTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (55 bp):
GGAGCAATTTTTTAGTCTATTAACGGATGGAGAGATCAATTCCTAATAACTTGCA
Found at i:553978 original size:33 final size:33
Alignment explanation
Indices: 553936--553999 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
553926 TAGACACATC
*
553936 TGAATAGATAGTT-TCGTTCACTAGAGTTCTATT
1 TGAATAGATAGTTCT-GTTCACTAGAATTCTATT
553969 TGAATAGATAGTTCTGTTCACTAGAATTCTA
1 TGAATAGATAGTTCTGTTCACTAGAATTCTA
554000 AAGAATTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (33 bp):
TGAATAGATAGTTCTGTTCACTAGAATTCTATT
Found at i:556575 original size:21 final size:22
Alignment explanation
Indices: 556551--556594 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
556541 AAATTGATTG
*
556551 CAGATATG-GATGTTCGAATAT
1 CAGATATGTGATATTCGAATAT
*
556572 CAGATTTGTTGATATTCGAATAT
1 CAGATATG-TGATATTCGAATAT
556595 GGATAGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
CAGATATGTGATATTCGAATAT
Found at i:556700 original size:17 final size:17
Alignment explanation
Indices: 556678--556713 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
556668 AAGAATCTTG
556678 AACCAGATCATGGAGTA
1 AACCAGATCATGGAGTA
556695 AACCAGATCATGGAGTA
1 AACCAGATCATGGAGTA
556712 AA
1 AA
556714 GGCAAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (17 bp):
AACCAGATCATGGAGTA
Found at i:561502 original size:39 final size:36
Alignment explanation
Indices: 561432--561503 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
561422 TTTTAATCAC
*
561432 CATAAATTATTTTATTATTGTTTATGTATGATGTGG
1 CATAAATTATTTTATTATTGTTTATATATGATGTGG
* *
561468 CATATATTATTATTATTATTTTATTAATATATGATG
1 CATAAATTATT-TTATTATTGT-TT-ATATATGATG
561504 AAAATAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 10 0.33
37 9 0.30
38 2 0.07
39 9 0.30
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (36 bp):
CATAAATTATTTTATTATTGTTTATATATGATGTGG
Found at i:563604 original size:615 final size:589
Alignment explanation
Indices: 562619--563810 Score: 1660
Period size: 615 Copynumber: 2.0 Consensus size: 589
562609 GACTCATGTG
**
562619 AAAGTGATATATATTGATGATATAGACCTTCCGTAGATAGCTTGGCTGGATAGGCTCAAATTTAG
1 AAAGTGATATATATTGATGATATAGACCTTCCGTAGATAGCTTGGCTGGATAGGCTCAAACGTAG
* * *
562684 GGATGACAAACGGGTTCTGATTTGATATGATATAGAGTCATATTTTTTAAAGGATGAAGTTGGGT
66 GGATGACAAACGGGTTCTGATTTGATATGATATAGAGTCAGATTTTTTAAAGGATGAAGTCGGAT
* *
562749 CTGGTTCGTGTAGAGGGTAAAAAATTCTGACCCGACTTAAATCGGGGATAATAATGTAATTTTTT
131 CTGGTTCGTGTAGAGGGTAAAAAATTCTGACCCGACTTAAATCAGGGATAATAATGTAATTTTCT
* *
562814 TTAAAAAATATTTATTTTTAAATTAAATCCTTAATTTGTGTCGGGTCGAAATTATACTCTAGAAA
196 TTAAAAAATATTTATTTTTAAATTAAATCCTTAATTTATGTCGGGTCGAAATTATACTCTAAAAA
* * *
562879 ATCGGGTGAGATCAGAGTCAGTGAAGGATATATATTTTACGGGGTAGGTCGGATCGGATGTAAGA
261 ATCGGGTCAGATCAGAATCAGTGAAGGATATATATTTTACGGGGTAGGTCGGATCGAATGTAAGA
* * * * * *
562944 TATAAAATTTTTAGATCGAATTCGAGTGGAGGGTGTATATTTTCGGGTTAGATCTGGTTGACCAA
326 TATAAAATTTTGAGATCGAATTCGAGTGGAAGCTGTATATTTTCGGATCAGATCGGGTTGACCAA
* *
563009 AAACTCAACCCGTTGCATCCCTACTCAAACTATATATGTAATTTTTTGTTGTTGTCCAAAAAGTC
391 AAACCCAACCCGTTGCATCCCTACTCAAACTATATAGGTAATTTTTTGTTGTTGTCCAAAAAGTC
*
563074 ATTATGGCCGAAAATAATAGTGAAAATTTCAATATAAAACGATACCAAATCATAATCCAACAAGT
456 ATTATGGCCGAAAATAATAGTGAAAAATTCAATATAAAACGATACCAAATCATAATCCAACAAGT
* *
563139 TTATGAACATGTCTAGACTGAAAGTAGTTTTTATTTAATGTCTATCATATATTTTATAAAACGAT
521 TTATGAACATGTCTAGACTGAAAGTAGTTTTTAATTAACGTCTATCATATATTTTATAAAACGAT
563204 ATCA
586 ATCA
563208 AAAGTGATATATATTGATGATATAGACCTTCCGTAGATAGCTTGGCTGGATAGGCTCAAACGTAG
1 AAAGTGATATATATTGATGATATAGACCTTCCGTAGATAGCTTGGCTGGATAGGCTCAAACGTAG
* *
563273 GGATGACAATTTTATCAGTATACGACGGGTTCTGATTTGATATGATTTAATCGGGTCAGATTTTT
66 GGATG--------A-C---A-A--ACGGGTTCTGATTTGATATGA--T-ATAGAGTCAGA-TTTT
* * *
563338 TTAAAGGATGAAGTCGGATC-GAGTTCGTGTGGAGGGTGAAAAAATT-TCGACTCGA-TCTAACT
112 TTAAAGGATGAAGTCGGATCTG-GTTCGTGTAGAGGGT-AAAAAATTCT-GACCCGACT-TAAAT
*
563400 CAGGGATAATAATGTAA-TTTCTTTAAAAATATTATTTGTTTTT-AATTAAATCCTTAATTTATA
173 CAGGGATAATAATGTAATTTTCTTTAAAAA-A-TATTTATTTTTAAATTAAATCCTTAA-TT-TA
* * * * *
563463 TCAGGTCGGGTTGAATTTATACTCTAAAAAATCGGGTCAGGTCAGAATCGGATGAAGGGTATATA
234 T---GTCGGGTCGAAATTATACTCTAAAAAATCGGGTCAGATCAGAATCAG-TGAAGGATATATA
* * *
563528 TTTTACGGGTTAGGTCAGGCT-GAATGTAGGATATAAAATTTTCGA-ATCGAATTCGAGTGGAAG
295 TTTTACGGGGTAGGTC-GGATCGAATGTAAGATATAAAATTTT-GAGATCGAATTCGAGTGGAAG
* *
563591 CTGTATATTTTCGGATCAGGTCGGGTTGACCAAAAACCCGACCCGTTGCATCCCTACTCAAACTA
358 CTGTATATTTTCGGATCAGATCGGGTTGACCAAAAACCCAACCCGTTGCATCCCTACTCAAACTA
* * *
563656 TATAGGTATTTTTTTTTTGTTGTCCAACAAGTCATTATGGCCGAAAATAATAGTGAAAAATTCAA
423 TATAGGTAATTTTTTGTTGTTGTCCAAAAAGTCATTATGGCCGAAAATAATAGTGAAAAATTCAA
563721 TATAAAACGATACCAAATCATAATCCAACAAGTTTATGAACATGTCTAGACTGAAAGTAGTTTTT
488 TATAAAACGATACCAAATCATAATCCAACAAGTTTATGAACATGTCTAGACTGAAAGTAGTTTTT
563786 AATTAACGTCTATCATATATTTTAT
553 AATTAACGTCTATCATATATTTTAT
563811 TATCCTAATG
Statistics
Matches: 528, Mismatches: 42, Indels: 40
0.87 0.07 0.07
Matches are distributed among these distances:
589 68 0.13
597 1 0.00
598 1 0.00
601 1 0.00
602 1 0.00
604 21 0.04
606 1 0.00
607 9 0.02
608 49 0.09
609 49 0.09
610 12 0.02
611 2 0.00
614 40 0.08
615 269 0.51
616 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (589 bp):
AAAGTGATATATATTGATGATATAGACCTTCCGTAGATAGCTTGGCTGGATAGGCTCAAACGTAG
GGATGACAAACGGGTTCTGATTTGATATGATATAGAGTCAGATTTTTTAAAGGATGAAGTCGGAT
CTGGTTCGTGTAGAGGGTAAAAAATTCTGACCCGACTTAAATCAGGGATAATAATGTAATTTTCT
TTAAAAAATATTTATTTTTAAATTAAATCCTTAATTTATGTCGGGTCGAAATTATACTCTAAAAA
ATCGGGTCAGATCAGAATCAGTGAAGGATATATATTTTACGGGGTAGGTCGGATCGAATGTAAGA
TATAAAATTTTGAGATCGAATTCGAGTGGAAGCTGTATATTTTCGGATCAGATCGGGTTGACCAA
AAACCCAACCCGTTGCATCCCTACTCAAACTATATAGGTAATTTTTTGTTGTTGTCCAAAAAGTC
ATTATGGCCGAAAATAATAGTGAAAAATTCAATATAAAACGATACCAAATCATAATCCAACAAGT
TTATGAACATGTCTAGACTGAAAGTAGTTTTTAATTAACGTCTATCATATATTTTATAAAACGAT
ATCA
Found at i:569335 original size:90 final size:90
Alignment explanation
Indices: 569176--569340 Score: 240
Period size: 90 Copynumber: 1.8 Consensus size: 90
569166 ATTAAATATA
* * *
569176 TAGTTTAGCAAGAGAATGATAGTGTAAGTTTAATAAAAATAAGGGTAAATTACGCGTTCAATACT
1 TAGTTTAGCAAGAGAATGATAATGTAAATTTAATAAAAATAAGGGTAAATTACGCGTTCAATACC
569241 TAATTTTGATTAGGTACTAAATACG
66 TAATTTTGATTAGGTACTAAATACG
* * * * ***
569266 TAGTTTATCAAGAGAATGTTAATGTAAATTTCATAAAAATAAGGGTAAATTATGCGTTTGGTACC
1 TAGTTTAGCAAGAGAATGATAATGTAAATTTAATAAAAATAAGGGTAAATTACGCGTTCAATACC
569331 TAATTTTGAT
66 TAATTTTGAT
569341 ACGTTTTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (90 bp):
TAGTTTAGCAAGAGAATGATAATGTAAATTTAATAAAAATAAGGGTAAATTACGCGTTCAATACC
TAATTTTGATTAGGTACTAAATACG
Found at i:572153 original size:31 final size:31
Alignment explanation
Indices: 572097--572170 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
572087 CCCTAAATTA
* * *
572097 TTTTGTTATTATTTTCAAATTACATGGATTT
1 TTTTATTATTATGTTCAAATGACATGGATTT
* *
572128 TTTTATTATTATGTTCATATGACATGGCTTT
1 TTTTATTATTATGTTCAAATGACATGGATTT
572159 TTCATTATTATT
1 TT--TTATTATT
572171 TAATATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 28 0.78
33 8 0.22
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.58
Consensus pattern (31 bp):
TTTTATTATTATGTTCAAATGACATGGATTT
Found at i:582718 original size:26 final size:23
Alignment explanation
Indices: 582672--582732 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 23
582662 AAGTTTAAAG
582672 TTTAAATATGTTATTAAAAATAGAT
1 TTTAAATAT-TTATTAAAAATA-AT
*
582697 ATTTAAATATTTATTATTAAATAAT
1 -TTTAAATATTTATTA-AAAATAAT
*
582722 TTAAAATATTT
1 TTTAAATATTT
582733 TAAAGAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.31
25 8 0.25
26 14 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TTTAAATATTTATTAAAAATAAT
Found at i:586872 original size:26 final size:28
Alignment explanation
Indices: 586830--586884 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
586820 AAGTGAATTA
*
586830 AAAATATTTAATTAA-TTAAT-TTATAT
1 AAAATATTTAATGAATTTAATGTTATAT
586856 AAAATA-TTAATCGAATTTAATGTTATAT
1 AAAATATTTAAT-GAATTTAATGTTATAT
586884 A
1 A
586885 TATTTCGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 5 0.20
26 8 0.32
27 5 0.20
28 7 0.28
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (28 bp):
AAAATATTTAATGAATTTAATGTTATAT
Found at i:588450 original size:36 final size:37
Alignment explanation
Indices: 588387--588456 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
588377 AAAATAGAAC
* * * *
588387 AAAGATGATAATCGTATATTAAGCGTATAGTTTACTT
1 AAAGATGATAACCGGATACTAAACGTATAGTTTACTT
588424 AAAG-TGATAACCGGATACTAAACGTATAGTTTA
1 AAAGATGATAACCGGATACTAAACGTATAGTTTA
588457 TCCTTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (37 bp):
AAAGATGATAACCGGATACTAAACGTATAGTTTACTT
Found at i:595717 original size:42 final size:41
Alignment explanation
Indices: 595656--595742 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 41
595646 AAATGATTTA
595656 TAATATTAATATCAACCGAATTAATACCAATTTTTTTTACTT
1 TAATATTAATATCAACCGAATTAATACCAA-TTTTTTTACTT
* * *
595698 TAATATTAATATTAGCCGAATTAATGCCAATTTTTTTACTT
1 TAATATTAATATCAACCGAATTAATACCAATTTTTTTACTT
595739 TAAT
1 TAAT
595743 TAAATAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.46
Consensus pattern (41 bp):
TAATATTAATATCAACCGAATTAATACCAATTTTTTTACTT
Done.