Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007713.1 Hibiscus syriacus cultivar Beakdansim tig00109937_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: 584604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:227562 original size:2 final size:2
Alignment explanation
Indices: 227555--227584 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
227545 CCTTTTTCTC
227555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227585 GGGGTAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228622 original size:22 final size:22
Alignment explanation
Indices: 228597--228638 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
228587 TTTGTTGTTA
* * *
228597 CATTTATAAAATTTTAAAATTT
1 CATTTAAAAAACTTAAAAATTT
228619 CATTTAAAAAACTTAAAAAT
1 CATTTAAAAAACTTAAAAAT
228639 ATATATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
CATTTAAAAAACTTAAAAATTT
Found at i:229708 original size:19 final size:20
Alignment explanation
Indices: 229672--229714 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
229662 TTTCGTTGTA
229672 TATTTTTTTAACGAAAAAAT
1 TATTTTTTTAACGAAAAAAT
229692 TATTTTTATTAA-G-AAAAAT
1 TATTTTT-TTAACGAAAAAAT
229711 TATT
1 TATT
229715 AGTACATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TATTTTTTTAACGAAAAAAT
Found at i:235040 original size:55 final size:55
Alignment explanation
Indices: 234962--235255 Score: 394
Period size: 55 Copynumber: 5.3 Consensus size: 55
234952 TTATGTGGGT
* * * * *
234962 TGCACAC-ATAGTACCTATACGGTGATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACGA-AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
* ** *
235017 TGGACAC-AAGGTGTTTGTACGGTGATTCATCAACTCATGATGAATTCTGTGAATA
1 TGCACACGAA-GTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
* * * *
235072 TGCACACGAAGTGCCTTTACAGTGATTCATCAACTCATGATAAATTCCATGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
* *
235127 TGCACACGAAGTGCCTGTACGGTGATTCATTAACTCATGATGTATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
*
235182 TGCACACGAAGTGCCTGTACGGTGATTCATAAACTCATGATGAATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
* *
235237 TGCACATGAAGTGCTTGTA
1 TGCACACGAAGTGCCTGTA
235256 GTACACATAT
Statistics
Matches: 212, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 1 0.00
55 209 0.99
56 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (55 bp):
TGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATA
Found at i:235751 original size:95 final size:97
Alignment explanation
Indices: 235625--235817 Score: 255
Period size: 95 Copynumber: 2.0 Consensus size: 97
235615 TACTTCTATA
*** * * * * *
235625 CTATGGTACCGATACCCCCTTTGGGTATCGATACTAAAAATAGGTTCGATGTTGGTTGGTATCGA
1 CTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCAATATTGCTTGGTATCGA
*
235690 TA-CCCTTACCATGGTATCGATACTACC-CTT
66 TACCCCTTACCATGATATCGATACTACCTCTT
* * *
235720 CTATGGTACTGATACCCCCTACCGGTATCGATACCAAAATTAGATTCAATATTTCTTGGTATCGA
1 CTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCAATATTGCTTGGTATCGA
*
235785 TACCCCTTATCATGATATCGATACTACCTCTT
66 TACCCCTTACCATGATATCGATACTACCTCTT
235817 C
1 C
235818 GGTATCGATA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 56 0.67
96 23 0.28
97 4 0.05
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (97 bp):
CTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCAATATTGCTTGGTATCGA
TACCCCTTACCATGATATCGATACTACCTCTT
Found at i:243325 original size:24 final size:25
Alignment explanation
Indices: 243298--243360 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
243288 ATATATATAT
243298 ATAATATTA-ATAAATTTAATTTAA
1 ATAATATTATATAAATTTAATTTAA
* *
243322 ATAA-AATATATATATTTAATTTAA
1 ATAATATTATATAAATTTAATTTAA
243346 ATATATATATATATA
1 ATA-ATAT-TATATA
243361 CCCGGCCCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.09
24 21 0.66
25 1 0.03
26 1 0.03
27 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAATATTATATAAATTTAATTTAA
Found at i:243340 original size:19 final size:19
Alignment explanation
Indices: 243316--243355 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
243306 AATAAATTTA
243316 ATTTAAATAAAATATATAT
1 ATTTAAATAAAATATATAT
* *
243335 ATTTAATTTAAATATATAT
1 ATTTAAATAAAATATATAT
243354 AT
1 AT
243356 ATATACCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAAATATATAT
Found at i:243401 original size:12 final size:12
Alignment explanation
Indices: 243378--243422 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
243368 CGATTCCCAG
243378 CCAATA-CCGAC
1 CCAATACCCGAC
243389 CCAATACCCGAC
1 CCAATACCCGAC
*
243401 CCAATACCCGGC
1 CCAATACCCGAC
243413 CCAATACCCG
1 CCAATACCCG
243423 TTTAAATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 6 0.19
12 26 0.81
ACGTcount: A:0.31, C:0.49, G:0.11, T:0.09
Consensus pattern (12 bp):
CCAATACCCGAC
Found at i:264646 original size:2 final size:2
Alignment explanation
Indices: 264639--264671 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
264629 TGGCTGTCCC
264639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
264672 CAATATCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:266316 original size:26 final size:26
Alignment explanation
Indices: 266280--266349 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
266270 ATTCATCTAC
266280 TTTATCAGAGATATAAATCGAATATA
1 TTTATCAGAGATATAAATCGAATATA
*
266306 TTTATCAGAGATATAAATTGAATATA
1 TTTATCAGAGATATAAATCGAATATA
*
266332 TTTATCATAGATATAAAT
1 TTTATCAGAGATATAAAT
266350 GAAAGCTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (26 bp):
TTTATCAGAGATATAAATCGAATATA
Found at i:278454 original size:13 final size:14
Alignment explanation
Indices: 278436--278473 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
278426 ATAAATATCA
278436 TAAACCCTAAAT-T
1 TAAACCCTAAATAT
*
278449 TAAACCCTGAATAT
1 TAAACCCTAAATAT
*
278463 TAAACTCTAAA
1 TAAACCCTAAA
278474 ATCTAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAACCCTAAATAT
Found at i:278793 original size:27 final size:26
Alignment explanation
Indices: 278746--278816 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 26
278736 CTTGTTAGGG
*
278746 TTAGAATTTAGAA-TTTGGGGTTTAAGAT
1 TTAG-ATTTA-AAGTTTAGGGTTTAAG-T
278774 TTA-ACTTTAAAGTTTAGGGTTTAAGT
1 TTAGA-TTTAAAGTTTAGGGTTTAAGT
278800 TTAGGATTTAAAGTTTA
1 TTA-GATTTAAAGTTTA
278817 AGATCTAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 7 0.18
27 27 0.71
28 4 0.11
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (26 bp):
TTAGATTTAAAGTTTAGGGTTTAAGT
Found at i:278813 original size:14 final size:14
Alignment explanation
Indices: 278779--278837 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
278769 AAGATTTAAC
*
278779 TTTAAAGTTTAGGG
1 TTTAAAGTTTAGGA
278793 TTT-AAGTTTAGGA
1 TTTAAAGTTTAGGA
*
278806 TTTAAAGTTTAAGA
1 TTTAAAGTTTAGGA
* *
278820 TCTAGAATTTTAGGA
1 TTTA-AAGTTTAGGA
278835 TTT
1 TTT
278838 GGTGTATACG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 12 0.32
14 15 0.41
15 10 0.27
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (14 bp):
TTTAAAGTTTAGGA
Found at i:282604 original size:21 final size:21
Alignment explanation
Indices: 282580--282619 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
282570 TTATTTTAAT
* *
282580 TTAAAATCTAAATCTTAAACC
1 TTAAAATATAAACCTTAAACC
*
282601 TTAAACTATAAACCTTAAA
1 TTAAAATATAAACCTTAAA
282620 TAAGACAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACCTTAAACC
Found at i:282605 original size:14 final size:15
Alignment explanation
Indices: 282588--282620 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
282578 ATTTAAAATC
282588 TAAATCT-TAAACCT
1 TAAATCTATAAACCT
282602 TAAA-CTATAAACCT
1 TAAATCTATAAACCT
282616 TAAAT
1 TAAAT
282621 AAGACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATCTATAAACCT
Found at i:283140 original size:12 final size:10
Alignment explanation
Indices: 283114--283142 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
283104 TCACACCAAA
283114 TTCTCTCAAT
1 TTCTCTCAAT
283124 TTCTCTCAAT
1 TTCTCTCAAT
283134 TTCTCTCAA
1 TTCTCTCAA
283143 ATAATCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:283228 original size:17 final size:18
Alignment explanation
Indices: 283191--283229 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
283181 ATATTATGTA
283191 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
283209 TTTATTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
283226 TTTA
1 TTTA
283230 CTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:284933 original size:18 final size:18
Alignment explanation
Indices: 284906--284943 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
284896 ACAGCACCCA
* *
284906 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
284924 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
284942 CC
1 CC
284944 TCCATCGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:285565 original size:35 final size:33
Alignment explanation
Indices: 285526--285610 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
285516 ATATTTCAGT
285526 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
285561 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
285596 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
285611 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:291195 original size:18 final size:20
Alignment explanation
Indices: 291165--291208 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
291155 TACTATTTTT
291165 TTTTTTGTAATTTTTCTT-A
1 TTTTTTGTAATTTTTCTTAA
291184 TTTTTTGT-ATTTTTCTTAA
1 TTTTTTGTAATTTTTCTTAA
291203 TTTTTT
1 TTTTTT
291209 TTTAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTTTGTAATTTTTCTTAA
Found at i:291217 original size:109 final size:112
Alignment explanation
Indices: 291093--291305 Score: 285
Period size: 118 Copynumber: 1.9 Consensus size: 112
291083 TTCGTGCTAC
* *
291093 AATTTTTTTTTAATTCAAG-TA-GA-TT-AA-AT-TACAAAAATACATTGAAATTAGATAAATAA
1 AATTTTTTTTTAATTCAAGATATAATTTCAAGATAGACAAAAATACATTGAAATTAGATAAATAA
**
291152 ACATACTATTTTTTTTTTTGTAATTTTTCTTATTTTTTGTATTTTTCTT
66 ACATACTA-ACTTTTTTTTGTAATTTTT-TTATTTTTTGTATTTTTCTT
*
291201 AATTTTTTTTTAAATTCAAGTATATTAATTTGCAAGATAGATAAAAATACATTGAAATTAGATAA
1 AATTTTTTTTT-AATTCAAG-ATA-TAATTT-CAAGATAGACAAAAATACATTGAAATTAGATAA
291266 ATAAACATACTAACTTTTTTTTGTAATTTTTTTATTTTTT
62 ATAAACATACTAACTTTTTTTTGTAATTTTTTTATTTTTT
291306 TTAAAATTCA
Statistics
Matches: 90, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
108 11 0.12
109 8 0.09
111 2 0.02
113 1 0.01
114 2 0.02
116 11 0.12
117 19 0.21
118 36 0.40
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (112 bp):
AATTTTTTTTTAATTCAAGATATAATTTCAAGATAGACAAAAATACATTGAAATTAGATAAATAA
ACATACTAACTTTTTTTTGTAATTTTTTTATTTTTTGTATTTTTCTT
Found at i:291836 original size:65 final size:64
Alignment explanation
Indices: 291723--291884 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 64
291713 AATTAAATTG
* * *
291723 AACATCGAATGCATTTTATGCATCGATGCACTTACCATACACCAATGCACTAAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAACATACACCAATGCACTAAGGATATTT-TG-
291787 A
64 A
* * * ** *
291788 AACATCGAATGCATTTGATGCATCGATGCAC-CAGACATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-ACATACACCAATGCACTAAGGATATTTTGA
* *
291852 AACATCGAATGCAATTGATGCATCGGTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
291885 TTAGTGCACT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 31 0.37
65 49 0.59
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAACATACACCAATGCACTAAGGATATTTTGA
Found at i:297725 original size:24 final size:24
Alignment explanation
Indices: 297697--297776 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
297687 CACTTAACAA
297697 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
297721 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
297742 TGCACCGATGCA-CACC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
297765 TGCATCGATGCA
1 TGCATCGATGCA
297777 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:300574 original size:64 final size:65
Alignment explanation
Indices: 300419--300580 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
300409 AATTAAATTG
* * *
300419 AACATCGAATGCATTTTATGCATCGATGCACTTACCATACACCGATGCACTAAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAACATACACCGATGCACTAAGGATTTTATGAA
* * ** *
300484 AACATCGAATGCATTTGATGCATCGATGCA-TCAGACATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-ACATACACCGATGCACTAAGGAT-TTTATG
300547 -A
64 AA
*
300548 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
300581 TTAGTGCACT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 32 0.38
65 50 0.59
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAACATACACCGATGCACTAAGGATTTTATGAA
Found at i:303136 original size:19 final size:19
Alignment explanation
Indices: 303112--303150 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
303102 GGCATTTACT
*
303112 CAACGGACAACCACTTCCC
1 CAACGGACAAACACTTCCC
303131 CAACGGACAAACACTTCCC
1 CAACGGACAAACACTTCCC
303150 C
1 C
303151 CTTCAGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.46, G:0.10, T:0.10
Consensus pattern (19 bp):
CAACGGACAAACACTTCCC
Found at i:307374 original size:4 final size:4
Alignment explanation
Indices: 307365--307389 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
307355 GTCTAATCAG
307365 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
307390 CAAGGAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:310244 original size:21 final size:21
Alignment explanation
Indices: 310218--310259 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
310208 TTTTTTGTAA
310218 AGAAAAGAGTTACAGATGCTG
1 AGAAAAGAGTTACAGATGCTG
310239 AGAAAAGAGTTACAGATGCTG
1 AGAAAAGAGTTACAGATGCTG
310260 GGATTCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.19
Consensus pattern (21 bp):
AGAAAAGAGTTACAGATGCTG
Found at i:321346 original size:19 final size:21
Alignment explanation
Indices: 321301--321352 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
321291 ACCCTCATGA
321301 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TT-AAG
321324 GGGAACCGATTCCCCC-T-AG
1 GGGAACCGATTCCCCCTTAAG
*
321343 GGGAATCGAT
1 GGGAACCGAT
321353 ACCCACCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
21 1 0.04
23 16 0.57
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTTAAG
Found at i:326801 original size:30 final size:30
Alignment explanation
Indices: 326744--326802 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
326734 TAATTTTAAA
* *
326744 AAAATTAAAATTTAAGTACTAAAACATATT
1 AAAACTAAAATTTAAATACTAAAACATATT
326774 AAAACTAATAATTTAAATACT-AAACATAT
1 AAAACTAA-AATTTAAATACTAAAACATAT
326803 AATTCACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAACTAAAATTTAAATACTAAAACATATT
Found at i:331039 original size:20 final size:21
Alignment explanation
Indices: 331014--331105 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
331004 TTTCCCCAAT
*
331014 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
331034 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
331055 TCGC-ATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
331074 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
331095 TCGCAATGCGA
1 TCGCAATGCGA
331106 TACTGACTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
19 9 0.16
20 23 0.41
21 24 0.43
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:331063 original size:40 final size:41
Alignment explanation
Indices: 331014--331105 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 41
331004 TTTCCCCAAT
331014 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
331055 TCGC-ATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
331095 TCGCAATGCGA
1 TCGCAATGCGA
331106 TACTGACTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 40 0.80
41 10 0.20
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:331118 original size:41 final size:41
Alignment explanation
Indices: 331033--331166 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
331023 GAATAAGTAA
* *
331033 ATCGCAACGCGAATTGGGAAAATCGC-ATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
331073 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
331114 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
331155 TTCGCAACGCGA
1 ATCGCAACGCGA
331167 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
40 30 0.38
41 47 0.59
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:331119 original size:20 final size:20
Alignment explanation
Indices: 331094--331187 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
331084 AATTGGGAAA
*
331094 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
331114 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
331135 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
331155 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
331175 TTCGC-ACGCGATA
1 ATCGCAACGCGATA
331188 ATACATAATC
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
19 8 0.13
20 38 0.63
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:339630 original size:32 final size:33
Alignment explanation
Indices: 339589--339659 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
339579 TATTGAGATC
*
339589 AATTT-AAATAACTTTTTT-TTATAAAAAA-TAT
1 AATTTAAAATAACTTTTTTAATA-AAAAAAGTAT
339620 AATTTAAAATAACTTTTTTAATAAAAAAAGTAT
1 AATTTAAAATAACTTTTTTAATAAAAAAAGTAT
339653 AATTTAA
1 AATTTAA
339660 GGGATTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 5 0.14
32 19 0.53
33 12 0.33
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (33 bp):
AATTTAAAATAACTTTTTTAATAAAAAAAGTAT
Found at i:339638 original size:33 final size:32
Alignment explanation
Indices: 339589--339659 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
339579 TATTGAGATC
**
339589 AATTT-AAATAACTTTTTTTTATAAAAAA-TAT
1 AATTTAAAATAACTTTTTAATA-AAAAAAGTAT
339620 AATTTAAAATAACTTTTTTAATAAAAAAAGTAT
1 AATTTAAAATAAC-TTTTTAATAAAAAAAGTAT
339653 AATTTAA
1 AATTTAA
339660 GGGATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.14
32 13 0.37
33 17 0.49
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (32 bp):
AATTTAAAATAACTTTTTAATAAAAAAAGTAT
Found at i:343201 original size:73 final size:73
Alignment explanation
Indices: 343057--343193 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
343047 TTTTAAGTTT
* * * ** *
343057 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTCAAATATTTTAAAATATGATAATTTAA
1 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCAA
343122 TGGACCCC
66 TGGACCCC
343130 AATAATTAAAAAATATTTTTAAACATCA-TTTTTTATTTAAAAAACTCGAAAATATGATAATTCA
1 AATAATTAAAAAATATTTTTAAACAT-ATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCA
343194 GTTGACCCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 56 0.98
74 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (73 bp):
AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATGATAATTCAA
TGGACCCC
Found at i:361544 original size:4 final size:4
Alignment explanation
Indices: 361535--361559 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
361525 CAGGTTATAT
361535 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
361560 CTAACTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:361785 original size:14 final size:14
Alignment explanation
Indices: 361745--361790 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
361735 ATTATTCATT
*
361745 TATACATACATACA
1 TATACATACATATA
* *
361759 TACACACACATATA
1 TATACATACATATA
*
361773 TATACATATATATA
1 TATACATACATATA
361787 TATA
1 TATA
361791 TATGTGTGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
TATACATACATATA
Found at i:363384 original size:11 final size:11
Alignment explanation
Indices: 363368--363397 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
363358 AGATAATTTG
363368 AAAAAAAGAAA
1 AAAAAAAGAAA
363379 AAAAAAAGAAA
1 AAAAAAAGAAA
363390 AAGAAAAA
1 AA-AAAAA
363398 TATAGGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:366157 original size:53 final size:52
Alignment explanation
Indices: 366084--366218 Score: 157
Period size: 53 Copynumber: 2.5 Consensus size: 52
366074 GTTTTATTTT
*
366084 AATAATATATAATAAATTATTAATAAAATTTATATTATTTATTAATTTCATAGA
1 AATAATATATAATAAATTATTAATAAAATTAATATTATTTA-T-ATTTCATAGA
* * *
366138 AATAATAT-TATTAAATTATTAATAATATTAATATTATTTATATTTCATATTA
1 AATAATATATAATAAATTATTAATAAAATTAATATTATTTATATTTCATA-GA
*
366190 ATATAATAATCTAATAATATT-TTAATAAA
1 A-ATAAT-ATATAATAA-ATTATTAATAAA
366219 GATATTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
51 8 0.11
52 3 0.04
53 34 0.49
54 10 0.14
55 12 0.17
56 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (52 bp):
AATAATATATAATAAATTATTAATAAAATTAATATTATTTATATTTCATAGA
Found at i:366238 original size:23 final size:23
Alignment explanation
Indices: 366212--366259 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
366202 AATAATATTT
366212 TAATAAAGATATTTAAAATATAA
1 TAATAAAGATATTTAAAATATAA
* * *
366235 TAATTAATATTTTTAAAATATAA
1 TAATAAAGATATTTAAAATATAA
366258 TA
1 TA
366260 TAACACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAA
Found at i:367057 original size:19 final size:19
Alignment explanation
Indices: 366992--367069 Score: 93
Period size: 21 Copynumber: 3.9 Consensus size: 19
366982 CCGTTAGACA
*
366992 GGGGGAATCGGTATCCCCTG
1 GGGGGAATCTGTA-CCCCTG
* *
367012 GAGGGAAATCTGTTCCCCCTGG
1 G-GGGGAATCTG-TACCCCT-G
367034 GGGGGAATCTGTACCCCTG
1 GGGGGAATCTGTACCCCTG
367053 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
367070 CTGGACAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 18 0.36
20 7 0.14
21 22 0.44
22 3 0.06
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.21
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:368492 original size:23 final size:21
Alignment explanation
Indices: 368459--368519 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
368449 TTTAAATCAA
*
368459 AATTTTGTTTTTCAAAACTAT
1 AATTTTTTTTTTCAAAACTAT
* * *
368480 CAATTTTTATTTTTGAAAGCTCT
1 -AATTTTT-TTTTTCAAAACTAT
*
368503 AATTTCTTTTTTCAAAA
1 AATTTTTTTTTTCAAAA
368520 TTTCATTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 8 0.26
22 12 0.39
23 11 0.35
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.52
Consensus pattern (21 bp):
AATTTTTTTTTTCAAAACTAT
Found at i:368554 original size:19 final size:20
Alignment explanation
Indices: 368511--368558 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
368501 CTAATTTCTT
*
368511 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
368531 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
368550 TTTTCAAAA
1 TTTTCAAAA
368559 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:370426 original size:32 final size:31
Alignment explanation
Indices: 370390--370465 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 31
370380 CGGGGCCATG
*
370390 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
370422 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
370453 -GACCTACCTAAGA
1 GGGCCTACCTAAGA
370466 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 10 0.27
31 13 0.35
32 14 0.38
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:370451 original size:31 final size:32
Alignment explanation
Indices: 370390--370453 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
370380 CGGGGCCATG
* *
370390 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCCAAGAACACATCTCAGGGCCGCA
* *
370422 GGGCCTACCCGAGAATA-ATCTCAGGGCCGCA
1 GGGCCTACCCAAGAACACATCTCAGGGCCGCA
370453 G
1 G
370454 ACCTACCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.27, C:0.31, G:0.28, T:0.14
Consensus pattern (32 bp):
GGGCCTACCCAAGAACACATCTCAGGGCCGCA
Found at i:371376 original size:22 final size:22
Alignment explanation
Indices: 371348--371390 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
371338 AACGGTCAAT
371348 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
371370 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
371391 AGACCGGTCA
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:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:371411 original size:19 final size:19
Alignment explanation
Indices: 371387--371515 Score: 129
Period size: 19 Copynumber: 6.7 Consensus size: 19
371377 GGTCGGGTCG
*
371387 GGTCAGACCGG-TCAAACC
1 GGTCAAACCGGTTCAAACC
* *
371405 GATTCAGACCGG-TCAAACC
1 G-GTCAAACCGGTTCAAACC
*
371424 GGTTCAAACCGGTTGAAACC
1 GG-TCAAACCGGTTCAAACC
*
371444 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
*
371463 GGTTGAAACCGG-TCAAACC
1 GG-TCAAACCGGTTCAAACC
*
371482 GGTCAGAACCGGTTGAAAACC
1 GGTCA-AACCGGTT-CAAACC
371503 GGTCAAACCGGTT
1 GGTCAAACCGGTT
371516 TCCAGCAGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
18 3 0.03
19 56 0.60
20 25 0.27
21 10 0.11
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:371430 original size:10 final size:10
Alignment explanation
Indices: 371393--371515 Score: 132
Period size: 10 Copynumber: 12.7 Consensus size: 10
371383 GTCGGGTCAG
371393 ACCGG-TCAA
1 ACCGGTTCAA
* *
371402 ACCGATTCAG
1 ACCGGTTCAA
371412 ACCGG-TCAA
1 ACCGGTTCAA
371421 ACCGGTTCAA
1 ACCGGTTCAA
*
371431 ACCGGTTGAA
1 ACCGGTTCAA
371441 ACCGG-TCAA
1 ACCGGTTCAA
*
371450 ACCGGTTCGA
1 ACCGGTTCAA
*
371460 ACCGGTTGAA
1 ACCGGTTCAA
371470 ACCGG-TCAA
1 ACCGGTTCAA
371479 ACCGG-TCAGA
1 ACCGGTTCA-A
*
371489 ACCGGTTGAAA
1 ACCGGTT-CAA
371500 ACCGG-TCAA
1 ACCGGTTCAA
371509 ACCGGTT
1 ACCGGTT
371516 TCCAGCAGCC
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
9 38 0.40
10 49 0.52
11 7 0.07
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.16
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:371444 original size:29 final size:28
Alignment explanation
Indices: 371412--371515 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 28
371402 ACCGATTCAG
* *
371412 ACCGGTCAAACCGGTTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTGAAACCGG-TCAA
*
371441 ACCGGTCAAACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTT-GAAACCGG-TCAA
* *
371470 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTGA-AACCGG-T-CAA
371500 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
371516 TCCAGCAGCC
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
28 1 0.01
29 49 0.73
30 16 0.24
31 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTGAAACCGGTCAA
Found at i:377751 original size:31 final size:31
Alignment explanation
Indices: 377724--377799 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
377714 CGGGGCCGTG
377724 GGGCCTACCTAAGAACACATCT-AGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
377755 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
377786 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
377800 GTCACATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:377782 original size:62 final size:63
Alignment explanation
Indices: 377677--377799 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 63
377667 CCCTAAGGGA
* * ** *
377677 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
377740 ACATC-TAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
377800 GTCACATTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
61 1 0.02
62 42 0.82
63 8 0.16
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.16
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:378698 original size:5 final size:5
Alignment explanation
Indices: 378688--378745 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
378678 AACGGTCAAC
* * *
378688 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGCCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
378737 GGTCG GGTC
1 GGTCG GGTC
378746 AGACCGGTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.07, C:0.24, G:0.52, T:0.17
Consensus pattern (5 bp):
GGTCG
Found at i:378709 original size:22 final size:22
Alignment explanation
Indices: 378681--378745 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
378671 AACGGTCAAC
378681 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
378703 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
378725 GGCCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
378746 AGACCGGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.25, G:0.49, T:0.17
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:378799 original size:29 final size:31
Alignment explanation
Indices: 378767--378841 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
378757 ACCGATTCAG
*
378767 ACCGGTCAAATCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
378796 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
378826 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
378842 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.55
30 16 0.38
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:378808 original size:9 final size:9
Alignment explanation
Indices: 378742--378840 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
378732 GGTCGGGTCG
*
378742 GGTCAGACC
1 GGTCAAACC
*
378751 GGTAAAACC
1 GGTCAAACC
* *
378760 GATTCAGACC
1 G-GTCAAACC
*
378770 GGTCAAATC
1 GGTCAAACC
*
378779 GGTTCGAACC
1 GG-TCAAACC
*
378789 GGTTGAAACC
1 GG-TCAAACC
378799 GGTCAAACC
1 GGTCAAACC
378808 GGTCAGAACC
1 GGTCA-AACC
*
378818 GGTTGAAAACC
1 GG-T-CAAACC
378829 GGTCAAACC
1 GGTCAAACC
378838 GGT
1 GGT
378841 TTCCAGCAGC
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
9 34 0.49
10 28 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:378839 original size:20 final size:21
Alignment explanation
Indices: 378803--378841 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
378793 GAAACCGGTC
378803 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
378824 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
378842 TCCAGCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:379637 original size:19 final size:21
Alignment explanation
Indices: 379596--379651 Score: 89
Period size: 19 Copynumber: 2.8 Consensus size: 21
379586 CGTTAGATAA
*
379596 GGGGAATCGGTACCCCTTGGG
1 GGGGAATCTGTACCCCTTGGG
379617 GGGGAATCTGTACCCC-T-GG
1 GGGGAATCTGTACCCCTTGGG
379636 GGGGAATCTGTACCCC
1 GGGGAATCTGTACCCC
379652 CTGGACAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.53
20 1 0.03
21 15 0.44
ACGTcount: A:0.16, C:0.27, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCTTGGG
Found at i:379975 original size:20 final size:20
Alignment explanation
Indices: 379942--379981 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
379932 TTATAAAATT
379942 ATAAAAAAAATATTTTAATA
1 ATAAAAAAAATATTTTAATA
* *
379962 ATAAATAAATTATTTTAATA
1 ATAAAAAAAATATTTTAATA
379982 TTTTAAAAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAATA
Found at i:380159 original size:21 final size:21
Alignment explanation
Indices: 380129--380168 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
380119 GTTTTCCAGA
* *
380129 AATTTTTTTTTCAAAAAATGT
1 AATTTATTTTACAAAAAATGT
*
380150 AATTTATTTTACAGAAAAT
1 AATTTATTTTACAAAAAAT
380169 ATTTTCCGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
AATTTATTTTACAAAAAATGT
Found at i:380761 original size:25 final size:25
Alignment explanation
Indices: 380716--380767 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
380706 TGTATATCTC
*
380716 AATAACATATGACATGTACAGAAAT
1 AATAACATATGACATGCACAGAAAT
* *
380741 AATAATATATGATC-TGCACAGAGAT
1 AATAACATATGA-CATGCACAGAAAT
380766 AA
1 AA
380768 AGAGATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (25 bp):
AATAACATATGACATGCACAGAAAT
Found at i:383029 original size:16 final size:17
Alignment explanation
Indices: 383003--383035 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
382993 ATAGGAGCAC
383003 GTTAGGCTTAGATTCAT
1 GTTAGGCTTAGATTCAT
*
383020 GTTA-GCTTAGTTTCAT
1 GTTAGGCTTAGATTCAT
383036 ACGTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (17 bp):
GTTAGGCTTAGATTCAT
Found at i:383324 original size:22 final size:23
Alignment explanation
Indices: 383299--383348 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
383289 TGTTTAATAT
383299 TATATAT-ATAGTA-ATTTAAAAA
1 TATATATAATA-TATATTTAAAAA
383321 TATA-ATAATATATATTTAAAAA
1 TATATATAATATATATTTAAAAA
383343 -ATATAT
1 TATATAT
383349 CAACTAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATATATAATATATATTTAAAAA
Found at i:383346 original size:23 final size:25
Alignment explanation
Indices: 383294--383347 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
383284 AGAGTTGTTT
*
383294 AATATTATATATATAGTAATTTAAA
1 AATATAATATATATAGTAATTTAAA
383319 AATATAATA-ATATA-T-ATTTAAAA
1 AATATAATATATATAGTAATTT-AAA
383342 AATATA
1 AATATA
383348 TCAACTAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 10 0.37
24 5 0.19
25 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AATATAATATATATAGTAATTTAAA
Found at i:384464 original size:23 final size:24
Alignment explanation
Indices: 384434--384485 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
384424 AAAATTTATT
* *
384434 AAAATTCATA-AAAATATATTTAA
1 AAAATTCAAACAAAATATATTGAA
384457 AAAATTCAAACAAAATATATTGAA
1 AAAATTCAAACAAAATATATTGAA
384481 AAAAT
1 AAAAT
384486 AATTATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTCAAACAAAATATATTGAA
Found at i:387524 original size:20 final size:20
Alignment explanation
Indices: 387501--387538 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
387491 AAAAAAAATT
387501 AAAACAAAGA-AAAACTTTGG
1 AAAACAAA-ATAAAACTTTGG
*
387521 AAAAGAAAATAAAACTTT
1 AAAACAAAATAAAACTTT
387539 TTCAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.63, C:0.08, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAACAAAATAAAACTTTGG
Found at i:391167 original size:40 final size:38
Alignment explanation
Indices: 391084--391167 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 38
391074 ATATTTTAGG
391084 AACCAAAGATGAAATTCTCATGTGCAAAGTTGACCACC
1 AACCAAAGATGAAATTCTCATGTGCAAAGTTGACCACC
* * *
391122 TACCAAAGATGAATTTTCTCATGTGTACAAGTT-AGCCACC
1 AACCAAAGATGAA-ATTCTCATGTGCA-AAGTTGA-CCACC
391162 AACCAA
1 AACCAA
391168 CTTGTCAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 12 0.31
39 12 0.31
40 15 0.38
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (38 bp):
AACCAAAGATGAAATTCTCATGTGCAAAGTTGACCACC
Found at i:394531 original size:14 final size:14
Alignment explanation
Indices: 394514--394566 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
394504 CATCATGCTA
394514 TGCAATACATGTTG
1 TGCAATACATGTTG
*
394528 TGCAATACATGCTG
1 TGCAATACATGTTG
394542 TGCAATACATGTTG
1 TGCAATACATGTTG
394556 TGCAATACATG
1 TGCAATACATG
394567 CATCTGGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (14 bp):
TGCAATACATGTTG
Found at i:394539 original size:28 final size:28
Alignment explanation
Indices: 394507--394567 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
394497 TCATTTGCAT
394507 CATGCTATGCAATACATGTTGTGCAATA
1 CATGCTATGCAATACATGTTGTGCAATA
*
394535 CATGCTGTGCAATACATGTTGTGCAATA
1 CATGCTATGCAATACATGTTGTGCAATA
394563 CATGC
1 CATGC
394568 ATCTGGAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (28 bp):
CATGCTATGCAATACATGTTGTGCAATA
Found at i:403737 original size:16 final size:18
Alignment explanation
Indices: 403709--403746 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
403699 ATCGCCGACA
403709 AAATTTCACTATTCACG-
1 AAATTTCACTATTCACGT
403726 AAATTT-ACTATTCACGT
1 AAATTTCACTATTCACGT
403743 AAAT
1 AAAT
403747 AGTAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTTCACTATTCACGT
Found at i:407260 original size:3 final size:3
Alignment explanation
Indices: 407252--407286 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
407242 AAAATTATAT
407252 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
407287 ATTATTATTA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:407634 original size:85 final size:85
Alignment explanation
Indices: 407516--407721 Score: 218
Period size: 87 Copynumber: 2.4 Consensus size: 85
407506 TCCCATTTTT
* * * *
407516 TTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCATCTTGTACACTTATAA-TTAAGC
1 TTTTTACCTTTATAATTGA-GGTCCTAATTTTTTCAATCCCAT-TTGTACACATATAAGTTAAGC
* ** *
407580 TCCTGCTT-TTTTCAATCTCAC
64 CCCTAATTGTTTTCAATATCAC
* * *
407601 TTTTTACCTTTATAATTGAGGTCTCTAATTTTTTTCAATCCCATTTTTACTCATATAAGTTAGGC
1 TTTTTACCTTTATAATTGAGGTC-CTAA-TTTTTTCAATCCCATTTGTACACATATAAGTTAAGC
*
407666 CCCTAATTGTTTTTAATATCAC
64 CCCTAATTGTTTTCAATATCAC
* * *
407688 TTTTTACCTTTAAAATTGATGTCCCTATTTTTTT
1 TTTTTACCTTTATAATTGAGGT-CCTAATTTTTT
407722 AATATCACTT
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
84 3 0.03
85 33 0.33
86 30 0.30
87 34 0.34
88 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (85 bp):
TTTTTACCTTTATAATTGAGGTCCTAATTTTTTCAATCCCATTTGTACACATATAAGTTAAGCCC
CTAATTGTTTTCAATATCAC
Found at i:407693 original size:44 final size:42
Alignment explanation
Indices: 407586--407776 Score: 129
Period size: 43 Copynumber: 4.5 Consensus size: 42
407576 AAGCTCCTGC
* * * * * *
407586 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCTCTAA
1 TTTTTTTAATATCACTTTTTACCTATAAAATTGAGGCCCCT-A
* * *
407629 TTTTTTTCA-ATCCCATTTTTA-CTCATATAAGTT-AGGCCCCTAA
1 TTTTTTTAATATCAC-TTTTTACCT-ATA-AAATTGAGGCCCCT-A
* * *
407672 TTGTTTTTAATATCACTTTTTACCTTTAAAATTGATGTCCCTA
1 TT-TTTTTAATATCACTTTTTACCTATAAAATTGAGGCCCCTA
* * * *
407715 TTTTTTTAATATCACTTTTTACCTTTATAATTGGGGTCCCTAA
1 TTTTTTTAATATCACTTTTTACCTATAAAATTGAGGCCCCT-A
*
407758 TTTTTTCAATCAT-ACTTTT
1 TTTTTTTAAT-ATCACTTTT
407777 ACTTTTATAG
Statistics
Matches: 120, Mismatches: 19, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
42 41 0.34
43 48 0.40
44 25 0.21
45 6 0.05
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (42 bp):
TTTTTTTAATATCACTTTTTACCTATAAAATTGAGGCCCCTA
Found at i:407775 original size:43 final size:44
Alignment explanation
Indices: 407425--407785 Score: 211
Period size: 42 Copynumber: 8.3 Consensus size: 44
407415 TAATTTTAGT
* * *
407425 TTTTTATCC-TTATAATTGAGGTCCTTAATTTTTGT-AACCCT-AC
1 TTTTTA-CCTTTATAATTGAGGTCCCTAATTTTT-TCAATCATCAC
* * * ***
407468 TTTTTATCTTTATAATGGAGG-CCCTTAATTTTTTTCATTCCCATTTTT
1 TTTTTACCTTTATAATTGAGGTCCC-TAA-TTTTTTCAAT--CA-TCAC
* * * *
407516 TTTTTACATTTATAATTGATGAT-CCTAAGTTTTTCAATC-CCA-
1 TTTTTACCTTTATAATTGA-GGTCCCTAATTTTTTCAATCATCAC
* * * **
407558 TCTTGTACAC-TTATAATTAAGCT-CCTGCTTTTTTCAATC-TCAC
1 T-TTTTAC-CTTTATAATTGAGGTCCCTAATTTTTTCAATCATCAC
* *
407601 TTTTTACCTTTATAATTGAGGTCTCTAATTTTTTTCAATC-CCA-
1 TTTTTACCTTTATAATTGAGGTCCCTAA-TTTTTTCAATCATCAC
* * *
407644 TTTTTA-CTCATATAAGTT-AGGCCCCTAATTGTTTTTAAT-ATCAC
1 TTTTTACCT-TTATAA-TTGAGGTCCCTAATT-TTTTCAATCATCAC
* * *
407688 TTTTTACCTTTAAAATTGATGTCCCT-ATTTTTTTAAT-ATCAC
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCATCAC
*
407730 TTTTTACCTTTATAATTGGGGTCCCTAATTTTTTCAATCAT-AC
1 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCATCAC
*
407773 -TTTTACTTTTATA
1 TTTTTACCTTTATA
407786 GTTTAAGCCC
Statistics
Matches: 247, Mismatches: 46, Indels: 51
0.72 0.13 0.15
Matches are distributed among these distances:
41 1 0.00
42 89 0.36
43 83 0.34
44 39 0.16
45 3 0.01
46 1 0.00
47 9 0.04
48 19 0.08
49 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (44 bp):
TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCATCAC
Found at i:408715 original size:20 final size:20
Alignment explanation
Indices: 408692--408743 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
408682 AACGCGATCC
408692 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
408712 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
408732 CCAAAATCGCAA
1 CCAGAATCGCAA
408744 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:408760 original size:21 final size:20
Alignment explanation
Indices: 408733--408831 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
408723 AATCAGTTTC
408733 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
408754 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
408775 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
408795 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
408816 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
408832 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:408860 original size:20 final size:20
Alignment explanation
Indices: 408798--408991 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
408788 CGATTTTCCA
* ** *
408798 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
408818 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
408838 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
408858 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
408878 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
408898 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
408918 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
408938 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
408958 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
408979 AAATCGCAACGCG
1 AAATCGCAACGCG
408992 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:408882 original size:60 final size:60
Alignment explanation
Indices: 408798--408991 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
408788 CGATTTTCCA
* ** * *
408798 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
408858 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
408918 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
408979 AAATCGCAACGCG
1 AAATCGCAACGCG
408992 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:409410 original size:33 final size:33
Alignment explanation
Indices: 409371--409441 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
409361 TTCACTTAGA
*
409371 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
409404 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
409437 TTTCA
1 TTTCA
409442 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:409629 original size:33 final size:33
Alignment explanation
Indices: 409562--409632 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
409552 AGAATGACTG
* ***
409562 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACAAGAGAATCGCAACGCGAAACCAAAA
409595 TCGCAACAAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACAAGAGAATCGCAACGCGAAACCAAAA
409628 TCGCA
1 TCGCA
409633 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACAAGAGAATCGCAACGCGAAACCAAAA
Found at i:409650 original size:19 final size:19
Alignment explanation
Indices: 409628--409725 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
409618 GAAACCAAAA
*
409628 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
409647 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
409661 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
409680 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
409694 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
409713 TCGCGTTGCGATT
1 TCGCGTTGCGATT
409726 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:409669 original size:14 final size:14
Alignment explanation
Indices: 409650--409739 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
409640 TTTCATTTCG
409650 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
409664 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
409683 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
409697 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
409714 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
409730 CGTTGCGATT
1 CGTTGCGATT
409740 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:409675 original size:33 final size:33
Alignment explanation
Indices: 409633--409747 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
409623 CAAAATCGCA
409633 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
409666 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
409699 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
409732 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
409748 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:411675 original size:185 final size:186
Alignment explanation
Indices: 411445--411826 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
411435 TAGATTGCTT
411445 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411510 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
411575 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
411630 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411695 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
411760 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
411816 AGTAAATTTAT
1 AGTAAATTTAT
411827 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:411759 original size:93 final size:93
Alignment explanation
Indices: 411445--411824 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
411435 TAGATTGCTT
*
411445 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411510 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
411538 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411602 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
411630 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411695 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
411723 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
411788 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
411816 AGTAAATTT
1 AGTAAATTT
411825 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:411908 original size:19 final size:19
Alignment explanation
Indices: 411868--411996 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
411858 TAGTTTACTT
* *
411868 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
411888 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
411907 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
411926 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
411940 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
411959 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
411973 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
411992 TCGCA
1 TCGCA
411997 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:411947 original size:33 final size:32
Alignment explanation
Indices: 411904--411996 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
411894 CGCGAAACCA
**
411904 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
411936 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
411969 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
411997 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:411994 original size:52 final size:52
Alignment explanation
Indices: 411868--411996 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
411858 TAGTTTACTT
**
411868 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
411920 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
411973 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
411997 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:412014 original size:19 final size:19
Alignment explanation
Indices: 411992--412126 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
411982 GAAACCAAAA
*
411992 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
412011 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
412027 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
412044 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
412060 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
412077 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
412096 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
412116 TCGTGTTGCGA
1 TCGCGTTGCGA
412127 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:412033 original size:14 final size:14
Alignment explanation
Indices: 412014--412070 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
412004 TTTCATTTCG
412014 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
412028 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
412045 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
412061 CGTTGCGATT
1 CGTTGCGATT
412071 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:412039 original size:33 final size:33
Alignment explanation
Indices: 411997--412089 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
411987 CAAAATCGCA
*
411997 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
412030 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
412063 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
412090 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:413986 original size:38 final size:38
Alignment explanation
Indices: 413943--414015 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
413933 TAATTGATTG
*
413943 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
413981 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
414016 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:414002 original size:19 final size:19
Alignment explanation
Indices: 413939--414002 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
413929 AGTTTAATTG
413939 ATTG-TTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
413957 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
413975 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
413995 ATTGATTT
1 ATTGATTT
414003 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:414016 original size:14 final size:14
Alignment explanation
Indices: 413997--414032 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
413987 ATTGTTTAAT
413997 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
414011 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
414025 TGATTTGT
1 TGATTTGT
414033 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:414155 original size:19 final size:19
Alignment explanation
Indices: 414139--414240 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
414129 AAAAATGACT
414139 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
414158 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
414177 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
414191 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
414210 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
414230 ATCGCAATGCG
1 ATCGCAATGCG
414241 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:414289 original size:33 final size:36
Alignment explanation
Indices: 414247--414565 Score: 320
Period size: 33 Copynumber: 9.1 Consensus size: 36
414237 TGCGTTTATA
*
414247 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
414280 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
414316 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
414351 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
414389 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
414425 -TCTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTC
*
414459 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
414492 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
414528 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTC
414564 AT
1 AT
414566 GTTGGGATTT
Statistics
Matches: 252, Mismatches: 10, Indels: 44
0.82 0.03 0.14
Matches are distributed among these distances:
32 18 0.07
33 85 0.34
34 13 0.05
35 29 0.12
36 28 0.11
37 7 0.03
38 72 0.29
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:414293 original size:19 final size:19
Alignment explanation
Indices: 414269--414593 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
414259 GATTATCTCG
414269 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
414288 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
414307 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
414321 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
414340 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
414359 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
414378 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
414397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
414416 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
414430 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
414448 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
414467 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
414481 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
414500 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
414519 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
414533 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
414553 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
414567 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
414586 TTGCGATT
1 TTGCGATT
414594 GTATTTTCCG
Statistics
Matches: 268, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
15 3 0.01
16 32 0.12
17 24 0.09
18 9 0.03
19 153 0.57
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:414309 original size:52 final size:52
Alignment explanation
Indices: 414247--414565 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
414237 TGCGTTTATA
*
414247 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
414299 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
414351 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
414408 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
414459 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
414511 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
414564 AT
1 AT
414566 GTTGGGATTT
Statistics
Matches: 255, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
51 50 0.20
52 130 0.51
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:416915 original size:12 final size:12
Alignment explanation
Indices: 416898--416922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
416888 TCTTCGGGGA
416898 CTTTTTCTTCTT
1 CTTTTTCTTCTT
416910 CTTTTTCTTCTT
1 CTTTTTCTTCTT
416922 C
1 C
416923 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:417131 original size:24 final size:24
Alignment explanation
Indices: 417097--417143 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
417087 CTGAAACATC
417097 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
417121 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
417144 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:417845 original size:20 final size:20
Alignment explanation
Indices: 417817--418265 Score: 573
Period size: 20 Copynumber: 22.4 Consensus size: 20
417807 AAATTTCAGT
* * * *
417817 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
417837 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
417857 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
417877 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
417897 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
417917 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
417937 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
417957 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
417977 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
417997 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
418017 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
418037 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
418057 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
418077 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
418097 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
418117 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
418137 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
418157 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
418177 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
418197 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
418217 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
418237 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
418257 GTTGCGATT
1 GTTGCGATT
418266 ATGGAAAATC
Statistics
Matches: 379, Mismatches: 42, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
19 5 0.01
20 369 0.97
21 5 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:423221 original size:27 final size:27
Alignment explanation
Indices: 423181--423232 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
423171 AAATCGTAGA
*
423181 ATATAAACACTAATGATATATATATAT
1 ATATAAACACTAATAATATATATATAT
* * *
423208 ATATAATCATTAATAATATTTATAT
1 ATATAAACACTAATAATATATATAT
423233 GATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATAAACACTAATAATATATATATAT
Found at i:426107 original size:18 final size:19
Alignment explanation
Indices: 426086--426127 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
426076 TAATTATTTC
*
426086 AATAAATATA-AAATTCAA
1 AATAAATAAAGAAATTCAA
*
426104 AAT-AATAAAGAAATTCGA
1 AATAAATAAAGAAATTCAA
426122 AATAAA
1 AATAAA
426128 ACCATATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAAATAAAGAAATTCAA
Found at i:428011 original size:3 final size:3
Alignment explanation
Indices: 427991--428031 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
427981 CTCTTCACTC
*
427991 TCA TCA TCT TCA GT-A TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA -TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
428032 GACCCCAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:429503 original size:64 final size:62
Alignment explanation
Indices: 429435--429643 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 62
429425 TTTCACTAAG
429435 AGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGG-T
* * * * * *
429499 AGTGCATCGATGCATCAAATGCATTCGAAGTTTTCATAAA-ACTCTGAGTGTATCAATGCATAGT
1 AGTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-CAGAGTGCATCGATGCATGGT
* *
429563 ATGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG
1 A-GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG
429626 ATT
62 --T
* *
429629 GGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
429644 TACTTTGAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.39
65 64 0.54
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (62 bp):
AGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGT
Found at i:430098 original size:2 final size:2
Alignment explanation
Indices: 430091--430139 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
430081 TAGCCAATTG
430091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
430133 AT AT AT A
1 AT AT AT A
430140 GCTTAAACTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430747 original size:21 final size:21
Alignment explanation
Indices: 430723--430766 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
430713 GTACCGGAGG
* *
430723 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
430744 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
430765 AG
1 AG
430767 CTCCCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:438122 original size:29 final size:29
Alignment explanation
Indices: 438080--438144 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
438070 GGGAGCGTCA
438080 GTGCATCGATGCATACCCAAGGTGCATTG
1 GTGCATCGATGCATACCCAAGGTGCATTG
438109 GTGCATCGATGCATACCCAAGGTGCATTG
1 GTGCATCGATGCATACCCAAGGTGCATTG
438138 GTGCATC
1 GTGCATC
438145 AAGTGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (29 bp):
GTGCATCGATGCATACCCAAGGTGCATTG
Found at i:438298 original size:46 final size:46
Alignment explanation
Indices: 438199--438323 Score: 184
Period size: 46 Copynumber: 2.7 Consensus size: 46
438189 CGGTGCACTA
438199 AGAGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCC
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCC
*
438244 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-C
* *
438290 TGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTT
438324 CAATTTATTC
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
45 32 0.43
46 39 0.53
47 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (46 bp):
AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCC
Found at i:438361 original size:20 final size:20
Alignment explanation
Indices: 438336--438391 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
438326 ATTTATTCCA
438336 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
438356 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
438376 TGGTGCATCGATGCAT
1 TGGTGCATCGATGCAT
438392 TACTTTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:438805 original size:16 final size:16
Alignment explanation
Indices: 438784--438824 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
438774 CTCAACAATA
438784 GCATAACAGATATAAG
1 GCATAACAGATATAAG
*
438800 GCATAACAAATATAAG
1 GCATAACAGATATAAG
*
438816 GCACAACAG
1 GCATAACAG
438825 TCAGTCATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (16 bp):
GCATAACAGATATAAG
Found at i:439058 original size:21 final size:21
Alignment explanation
Indices: 439032--439078 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
439022 GAGTAATCAA
439032 ATATCTTCTAATTTATAAGAG
1 ATATCTTCTAATTTATAAGAG
*
439053 ATATCTTCTAATTTATAAGGG
1 ATATCTTCTAATTTATAAGAG
439074 ATATC
1 ATATC
439079 AAGATGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (21 bp):
ATATCTTCTAATTTATAAGAG
Found at i:439975 original size:18 final size:17
Alignment explanation
Indices: 439919--439976 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
439909 TATATGAATT
*
439919 AAAATTTGAAAAAATATTA
1 AAAATTTTAAAAAA-A-TA
*
439938 AAAATATTAAAATAAATA
1 AAAATTTTAAAA-AAATA
439956 AAAATTTTAAAAAAAGTA
1 AAAATTTTAAAAAAA-TA
439974 AAA
1 AAA
439977 TAACATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 3 0.09
18 18 0.53
19 11 0.32
20 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATTTTAAAAAAATA
Found at i:443444 original size:3 final size:3
Alignment explanation
Indices: 443367--443424 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
443357 CACTTAGCAG
443367 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
443415 TAT TAT TAT T
1 TAT TAT TAT T
443425 TTGTTGATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:446215 original size:20 final size:21
Alignment explanation
Indices: 446187--446225 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
446177 GTTTTCAAAA
*
446187 ATGA-TTTTTAAAAATATTAT
1 ATGAGTTTTCAAAAATATTAT
*
446207 ATGAGTTTTCCAAAATATT
1 ATGAGTTTTCAAAAATATT
446226 TTTAAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (21 bp):
ATGAGTTTTCAAAAATATTAT
Found at i:446232 original size:33 final size:32
Alignment explanation
Indices: 446172--446240 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
446162 ACTATATACC
446172 ATATAGTTTTCAAAAATGATTTTTAAAAATATT
1 ATATAGTTTTCAAAAATGATTTTTAAAAATA-T
* *
446205 ATATGAGTTTTCCAAAAT-ATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATGATTTTTAAAAATAT
446237 ATAT
1 ATAT
446241 TATATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 5 0.15
33 16 0.48
34 12 0.36
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (32 bp):
ATATAGTTTTCAAAAATGATTTTTAAAAATAT
Found at i:446330 original size:35 final size:36
Alignment explanation
Indices: 446286--446369 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
446276 TATACATTAT
446286 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATGATTTCAAAATATATATTG-TATATA
* *
446321 ATTTTCAAAATGTTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGATTTCAAAA--TATATATTGTATATA
446359 AGTTTTCAAAA
1 A-TTTTCAAAA
446370 ACGTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 19 0.45
38 12 0.29
39 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
ATTTTCAAAATGATTTCAAAATATATATTGTATATA
Found at i:446406 original size:41 final size:39
Alignment explanation
Indices: 446346--446449 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 39
446336 TTAAAACTTA
* **
446346 TATATTGTATATAAGTTTTCAAAAACGTTTTTTTAAAAAAAC
1 TATATTGTATAT-ATTTTTCAAAAACCATTTTTT--AAAAAC
* * **
446388 TATATTATATATATTTTTCAGAAACCATTTTTTGTAAAC
1 TATATTGTATATATTTTTCAAAAACCATTTTTTAAAAAC
446427 TATA-TGT-TATATTTTTCAAAAAC
1 TATATTGTATATATTTTTCAAAAAC
446450 ACTTTCAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
37 15 0.28
38 2 0.04
39 8 0.15
41 17 0.32
42 11 0.21
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (39 bp):
TATATTGTATATATTTTTCAAAAACCATTTTTTAAAAAC
Found at i:447503 original size:68 final size:68
Alignment explanation
Indices: 447428--447558 Score: 244
Period size: 68 Copynumber: 1.9 Consensus size: 68
447418 CTTGAAGAAG
*
447428 GGTGATTCATAATCTTATCTTGGCTCAAGCTAACTAAGATTAGAGTGCTTAAAGATTGGCTCTTG
1 GGTGATTCATAATCTTACCTTGGCTCAAGCTAACTAAGATTAGAGTGCTTAAAGATTGGCTCTTG
447493 AAT
66 AAT
*
447496 GGTGATTCATAATCTTACCTTGGCTCAAGCTAACTAAGATTAGAGTGCTTGAAGATTGGCTCT
1 GGTGATTCATAATCTTACCTTGGCTCAAGCTAACTAAGATTAGAGTGCTTAAAGATTGGCTCT
447559 GGGAAATAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (68 bp):
GGTGATTCATAATCTTACCTTGGCTCAAGCTAACTAAGATTAGAGTGCTTAAAGATTGGCTCTTG
AAT
Found at i:453027 original size:29 final size:29
Alignment explanation
Indices: 452985--453098 Score: 219
Period size: 29 Copynumber: 3.9 Consensus size: 29
452975 GCCCAACACA
452985 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
453014 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
453043 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
453072 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
453099 ACCCTCGCTC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.11, C:0.38, G:0.31, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Done.