Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007729.1 Hibiscus syriacus cultivar Beakdansim tig00109980_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: 1111098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:836340 original size:32 final size:32
Alignment explanation
Indices: 836295--836355 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
836285 AGGTATACTG
836295 TCCATATGCCCCGAAAGACATAGGTAATTTTA
1 TCCATATGCCCCGAAAGACATAGGTAATTTTA
*
836327 TCCATATGTCCCGAAAGACATAGGTAATT
1 TCCATATGCCCCGAAAGACATAGGTAATT
836356 GTCCATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (32 bp):
TCCATATGCCCCGAAAGACATAGGTAATTTTA
Found at i:844370 original size:12 final size:12
Alignment explanation
Indices: 844355--844412 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
844345 GATACATGAC
844355 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
844367 CTGATTTCTGAT
1 CTGAATTCTGTT
844379 CT-AGATTCTGTT
1 CTGA-ATTCTGTT
844391 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
844403 TTGATTTCTG
1 CTGAATTCTG
844413 ATATCTCCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.16, C:0.16, G:0.17, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:850420 original size:18 final size:20
Alignment explanation
Indices: 850397--850436 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
850387 TTCTCATCAA
850397 TTTTATT-CC-CTGGTAATC
1 TTTTATTCCCACTGGTAATC
850415 TTTTATTCCCACTGGTAATC
1 TTTTATTCCCACTGGTAATC
850435 TT
1 TT
850437 ACATTCCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTATTCCCACTGGTAATC
Found at i:850442 original size:20 final size:20
Alignment explanation
Indices: 850406--850443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
850396 ATTTTATTCC
**
850406 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
850426 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
850444 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:856684 original size:20 final size:20
Alignment explanation
Indices: 856652--856689 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
856642 TTAGTTAGCG
*
856652 AAAATAACTTTTTCGGTAAA
1 AAAATAACTTTTTAGGTAAA
856672 AAAATAA-TGTTTTAGGTA
1 AAAATAACT-TTTTAGGTA
856690 GCGCTTTATT
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:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
AAAATAACTTTTTAGGTAAA
Found at i:858677 original size:21 final size:21
Alignment explanation
Indices: 858648--858688 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
858638 AAATCAAAGT
*
858648 TATTATTTAAC-TTATATAAA
1 TATTATTTAACATTAAATAAA
858668 TATTAATTTAACATTAAATAA
1 TATT-ATTTAACATTAAATAA
858689 TTTCTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTATTTAACATTAAATAAA
Found at i:859227 original size:10 final size:10
Alignment explanation
Indices: 859188--859227 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
859178 TTATTAGTTG
*
859188 ATTAAAATTA
1 ATTAAAAATA
859198 ATTAAATAATA
1 ATTAAA-AATA
859209 ATATAAAAATA
1 AT-TAAAAATA
859220 ATTAAAAA
1 ATTAAAAA
859228 ATACCATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 12 0.44
11 11 0.41
12 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:869007 original size:17 final size:18
Alignment explanation
Indices: 868971--869011 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
868961 ATATTATGTA
*
868971 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
868989 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
869006 TTTACT
1 TTTACT
869012 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:870716 original size:18 final size:18
Alignment explanation
Indices: 870689--870724 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
870679 ACAGTAGCCA
* *
870689 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
870707 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
870725 TCGTCTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:879408 original size:18 final size:19
Alignment explanation
Indices: 879385--879443 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 19
879375 ATTTGGTGCA
*
879385 GAGGGAATCGA-TCCCCCT
1 GAGGGAACCGATTCCCCCT
879403 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
879424 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
879444 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:879469 original size:19 final size:20
Alignment explanation
Indices: 879426--879463 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
879416 CCCCCTTTGA
*
879426 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
879446 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
879464 CTGGGGTTCT
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:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:896402 original size:21 final size:20
Alignment explanation
Indices: 896372--896425 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
896362 GATAGACACT
*
896372 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
896393 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
896416 TTACATTATA
1 TTACATTATA
896426 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:896413 original size:23 final size:23
Alignment explanation
Indices: 896387--896449 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
896377 ATATAACCAT
896387 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
896410 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
896433 TACCTATTACATCATAT
1 TACCTATTACATTATAT
896450 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:896829 original size:21 final size:20
Alignment explanation
Indices: 896799--896852 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
896789 GATAGACACT
*
896799 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
896820 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
896843 TTACATTATA
1 TTACATTATA
896853 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:896840 original size:23 final size:23
Alignment explanation
Indices: 896814--896876 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
896804 ATATAACCAT
896814 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
896837 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
896860 TACCTATTACATCATAT
1 TACCTATTACATTATAT
896877 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:899739 original size:184 final size:184
Alignment explanation
Indices: 899430--900283 Score: 1622
Period size: 184 Copynumber: 4.7 Consensus size: 184
899420 TTTTAAATGG
* *
899430 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
899495 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
899560 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
899614 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
899679 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
899744 GATGTGT-AAATGTCGACAC-TTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
899796 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
899861 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
899926 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
899980 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
900045 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
900110 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
900164 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
900229 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
900284 ATGTTGAAAG
Statistics
Matches: 659, Mismatches: 9, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
182 169 0.26
183 24 0.04
184 466 0.71
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:900102 original size:366 final size:368
Alignment explanation
Indices: 899430--900283 Score: 1622
Period size: 366 Copynumber: 2.3 Consensus size: 368
899420 TTTTAAATGG
* *
899430 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
899495 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
899560 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
899625 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
899690 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGT-AAA
261 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAA
*
899754 TGTCGACAC-TTTTTAAATTGTATCGACACATTTTTCTTCCAA
326 TGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
899796 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
899861 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
899926 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
*
899991 AGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
900056 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAA
261 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAA
900121 TGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
326 TGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
900164 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
900229 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
900284 ATGTTGAAAG
Statistics
Matches: 478, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
366 316 0.66
367 12 0.03
368 150 0.31
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (368 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAA
TGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:901659 original size:3 final size:3
Alignment explanation
Indices: 901651--901737 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
901641 ACTTGTTTGG
* * * **
901651 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
901699 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
901738 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:901674 original size:18 final size:18
Alignment explanation
Indices: 901651--901752 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
901641 ACTTGTTTGG
901651 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
901669 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
901687 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
901705 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
901723 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
901741 AGCTTCATCTTC
1 ATCATCATCTTC
901753 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:901718 original size:42 final size:42
Alignment explanation
Indices: 901659--901749 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
901649 GGATCATCAT
*
901659 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
901701 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
901743 CTTCATC
1 CTTCATC
901750 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:903561 original size:197 final size:199
Alignment explanation
Indices: 903214--904251 Score: 1669
Period size: 199 Copynumber: 5.1 Consensus size: 199
903204 TTTAAATTAG
* *
903214 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
903279 A-TGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
903341 CGACACGTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTTATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
903405 AAAA
196 AAAA
903409 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
903473 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
903538 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
903603 AAAA
196 AAAA
* *
903607 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
903672 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
903737 CGACACTTTTTATATATGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG
131 CGACACTTTTTATATATGGATCGACAC----T-T-TATGGGT-G-CAC---CTTG-T-----TT-
* *
903802 TTT-TTAATTCATTCTGGAAAAAAAA
178 TTTATTCATTC--T-GGGAA-AAAAA
903827 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
903892 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
903957 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
904022 AAAA
196 AAAA
* *
904026 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
904091 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
904154 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
904219 AAAA
196 AAAA
*
904223 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
904252 TGACCCTTAA
Statistics
Matches: 791, Mismatches: 24, Indels: 54
0.91 0.03 0.06
Matches are distributed among these distances:
194 47 0.06
195 32 0.04
196 22 0.03
197 182 0.23
198 64 0.08
199 221 0.28
200 4 0.01
201 1 0.00
202 3 0.00
203 9 0.01
204 1 0.00
205 6 0.01
206 1 0.00
207 3 0.00
208 1 0.00
209 3 0.00
210 3 0.00
211 1 0.00
212 3 0.00
213 1 0.00
214 6 0.01
215 1 0.00
216 9 0.01
217 3 0.00
218 1 0.00
219 4 0.01
220 159 0.20
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAA
AAAA
Found at i:903759 original size:21 final size:21
Alignment explanation
Indices: 903733--903787 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
903723 GATGATTTTG
903733 GGATCGACACTTTTTATATAT
1 GGATCGACACTTTTTATATAT
903754 GGATCGACACTTTTTATATAT
1 GGATCGACACTTTTTATATAT
903775 GGATCGACACTTT
1 GGATCGACACTTT
903788 ATTGATGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
GGATCGACACTTTTTATATAT
Found at i:903916 original size:220 final size:220
Alignment explanation
Indices: 903534--904183 Score: 997
Period size: 220 Copynumber: 3.1 Consensus size: 220
903524 GATGATTTTG
* *
903534 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGG
* * *
903599 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAA
66 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
903664 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
131 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
903729 TTTGGGATCGACACTTTTTATATAT
196 TTTGGGATCGACACTTTTTATATAT
*
903754 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGG
903819 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
66 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
*
903884 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
131 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
903949 TTTGGGATCGACACTTTTTATATAT
196 TTTGGGATCGACACTTTTTATATAT
* * * *
903974 GGATCGACAC----T-T-TATGGGT-G-CAC-CT-T-G-T-----TT-TTTATTCATTC--T-GG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTT-TTAATTCATTCTG
* * *
904018 GAAAAAAAT-ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAA
65 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAA
904082 ACCGGTATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATAC-TTTGGGTTCGATGA
130 ACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
904145 TTTTGGGATCGACACTTTTTATATAT
195 TTTTGGGATCGACACTTTTTATATAT
904171 GGATCGACACTTT
1 GGATCGACACTTT
904184 ATTGATGCAC
Statistics
Matches: 412, Mismatches: 14, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
197 50 0.12
198 23 0.06
199 79 0.19
200 9 0.02
201 1 0.00
202 3 0.01
203 8 0.02
208 1 0.00
209 1 0.00
210 1 0.00
211 1 0.00
212 3 0.01
213 1 0.00
214 6 0.01
215 1 0.00
216 1 0.00
220 223 0.54
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (220 bp):
GGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGG
AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
TTTGGGATCGACACTTTTTATATAT
Found at i:904359 original size:19 final size:19
Alignment explanation
Indices: 904332--904376 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
904322 TATTCACATA
*
904332 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
904351 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
904370 AAAATTA
1 AAAATTA
904377 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:906203 original size:33 final size:33
Alignment explanation
Indices: 906166--906231 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
906156 CATCTTAATA
*
906166 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
906199 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
906232 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:908554 original size:20 final size:19
Alignment explanation
Indices: 908508--908554 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
908498 TCCGGTATCA
*
908508 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
908527 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
908548 TTTTACC
1 TTTTACC
908555 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:908701 original size:21 final size:20
Alignment explanation
Indices: 908675--908722 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
908665 ACACTTTTAA
*
908675 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
908695 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
908716 TTTTACC
1 TTTTACC
908723 TGGTATATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:918191 original size:23 final size:23
Alignment explanation
Indices: 918165--918233 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
918155 CACCACAGCT
*
918165 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
918188 CGTAGAATTACACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
918211 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
918234 TATAAAATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:919301 original size:374 final size:374
Alignment explanation
Indices: 918612--919363 Score: 1504
Period size: 374 Copynumber: 2.0 Consensus size: 374
918602 TCTTTATCAC
918612 ATAACTTATTTCATATTCTTATATAATCACAAATCTCATAGCTCAATCACTTATACATGTATTCT
1 ATAACTTATTTCATATTCTTATATAATCACAAATCTCATAGCTCAATCACTTATACATGTATTCT
918677 TATAATTTCTTATCATATCATATAATTTATATCATCATAACATAACATGTGTTCACATCAATCAT
66 TATAATTTCTTATCATATCATATAATTTATATCATCATAACATAACATGTGTTCACATCAATCAT
918742 ATAAACACATATAATCACATAACTTGTCATTTCTTATGAGATCACTTATGTCATATAACATATAT
131 ATAAACACATATAATCACATAACTTGTCATTTCTTATGAGATCACTTATGTCATATAACATATAT
918807 ATAGTTTATATCATTTCTCATATTTTCACCTAATTCCTTATATTTATCATATAAACATATACTCT
196 ATAGTTTATATCATTTCTCATATTTTCACCTAATTCCTTATATTTATCATATAAACATATACTCT
918872 TATAGATAATTTATATTATATAACCTATATCTTAGTTTCACATAATCACTATATCTCATATATTC
261 TATAGATAATTTATATTATATAACCTATATCTTAGTTTCACATAATCACTATATCTCATATATTC
918937 ATATACCACATGAACCAATAATTTCTTATGTAAATATCATATAACTTAT
326 ATATACCACATGAACCAATAATTTCTTATGTAAATATCATATAACTTAT
918986 ATAACTTATTTCATATTCTTATATAATCACAAATCTCATAGCTCAATCACTTATACATGTATTCT
1 ATAACTTATTTCATATTCTTATATAATCACAAATCTCATAGCTCAATCACTTATACATGTATTCT
919051 TATAATTTCTTATCATATCATATAATTTATATCATCATAACATAACATGTGTTCACATCAATCAT
66 TATAATTTCTTATCATATCATATAATTTATATCATCATAACATAACATGTGTTCACATCAATCAT
919116 ATAAACACATATAATCACATAACTTGTCATTTCTTATGAGATCACTTATGTCATATAACATATAT
131 ATAAACACATATAATCACATAACTTGTCATTTCTTATGAGATCACTTATGTCATATAACATATAT
919181 ATAGTTTATATCATTTCTCATATTTTCACCTAATTCCTTATATTTATCATATAAACATATACTCT
196 ATAGTTTATATCATTTCTCATATTTTCACCTAATTCCTTATATTTATCATATAAACATATACTCT
919246 TATAGATAATTTATATTATATAACCTATATCTTAGTTTCACATAATCACTATATCTCATATATTC
261 TATAGATAATTTATATTATATAACCTATATCTTAGTTTCACATAATCACTATATCTCATATATTC
919311 ATATACCACATGAACCAATAATTTCTTATGTAAATATCATATAACTTAT
326 ATATACCACATGAACCAATAATTTCTTATGTAAATATCATATAACTTAT
919360 ATAA
1 ATAA
919364 TTACTTATAT
Statistics
Matches: 378, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
374 378 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (374 bp):
ATAACTTATTTCATATTCTTATATAATCACAAATCTCATAGCTCAATCACTTATACATGTATTCT
TATAATTTCTTATCATATCATATAATTTATATCATCATAACATAACATGTGTTCACATCAATCAT
ATAAACACATATAATCACATAACTTGTCATTTCTTATGAGATCACTTATGTCATATAACATATAT
ATAGTTTATATCATTTCTCATATTTTCACCTAATTCCTTATATTTATCATATAAACATATACTCT
TATAGATAATTTATATTATATAACCTATATCTTAGTTTCACATAATCACTATATCTCATATATTC
ATATACCACATGAACCAATAATTTCTTATGTAAATATCATATAACTTAT
Found at i:919902 original size:64 final size:65
Alignment explanation
Indices: 919795--919935 Score: 212
Period size: 64 Copynumber: 2.2 Consensus size: 65
919785 ACACTAATTA
* * **
919795 CATTCGATATTTTCAATTTCAATGGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCCTGG
1 CATTCGATGTTTTCAATTTAAATGGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGG
* *
919860 CATTCGATGTTTTTATTTTAAAT-GGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGG
1 CATTCGATGTTTTCAATTTAAATGGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGG
*
919924 CATTCTATGTTT
1 CATTCGATGTTT
919936 CTTCTTTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 50 0.72
65 19 0.28
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (65 bp):
CATTCGATGTTTTCAATTTAAATGGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGG
Found at i:919944 original size:64 final size:63
Alignment explanation
Indices: 919819--919954 Score: 202
Period size: 64 Copynumber: 2.1 Consensus size: 63
919809 AATTTCAATG
** *
919819 GGGTGCATCGATGCACTAACTGTGCATCGGTACACTCCTGGCATTCGATGTTTTTATTTTAAA
1 GGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTTTTACTTTAAA
*
919882 TGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGGCATTCTATGTTTCTT-CTTTAAA
1 -GGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTT-TTACTTTAAA
*
919946 GAGTGCATC
1 GGGTGCATC
919955 AGTACACTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
63 8 0.12
64 56 0.85
65 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (63 bp):
GGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTTTTACTTTAAA
Found at i:925566 original size:24 final size:24
Alignment explanation
Indices: 925508--925617 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
925498 AATGTTTTAA
* *
925508 CTGATTTCTGATTTGAATTCTGTT
1 CTGATTTCTGATATGAATTATGTT
* ** *
925532 CTAATACCTGATATGAATTCTGTT
1 CTGATTTCTGATATGAATTATGTT
* * * *
925556 ATGATTTCTGATCTGGATTATTTT
1 CTGATTTCTGATATGAATTATGTT
*
925580 CTGATATCTGA-ACTGAATTATGTT
1 CTGATTTCTGATA-TGAATTATGTT
* *
925604 TTGATTTATGATAT
1 CTGATTTCTGATAT
925618 CTCTGTTTAC
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
24 63 0.98
25 1 0.02
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (24 bp):
CTGATTTCTGATATGAATTATGTT
Found at i:925597 original size:48 final size:48
Alignment explanation
Indices: 925509--925615 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
925499 ATGTTTTAAC
* * *
925509 TGATTTCTGATTTGAATTCTGTTCTAATACCTGATATGAATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTCTAATACCTGATATGAATTATGTTA
* * * * *
925557 TGATTTCTGATCTGGATTATTTTCTGATATCTGA-ACTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTCTAATACCTGATA-TGAATTATGTTA
*
925605 TGATTTATGAT
1 TGATTTCTGAT
925616 ATCTCTGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (48 bp):
TGATTTCTGATCTGAATTATGTTCTAATACCTGATATGAATTATGTTA
Found at i:927948 original size:21 final size:21
Alignment explanation
Indices: 927924--927972 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
927914 GGTGTTACAT
927924 ATACA-CTATGAATGTGTACCG
1 ATACATCT-TGAATGTGTACCG
*
927945 ATACATTCCTTGAATGTGTATCG
1 ATACA-T-CTTGAATGTGTACCG
927968 ATACA
1 ATACA
927973 ATCCTAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (21 bp):
ATACATCTTGAATGTGTACCG
Found at i:927959 original size:23 final size:23
Alignment explanation
Indices: 927932--927977 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
927922 ATATACACTA
*
927932 TGAATGTGTACCGATACATTCCT
1 TGAATGTGTACCGATACAATCCT
*
927955 TGAATGTGTATCGATACAATCCT
1 TGAATGTGTACCGATACAATCCT
927978 AGGTGTATCG
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:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (23 bp):
TGAATGTGTACCGATACAATCCT
Found at i:934389 original size:18 final size:19
Alignment explanation
Indices: 934357--934397 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
934347 ATGATAAAAC
934357 ATAA-TATCATAATCTCAA
1 ATAATTATCATAATCTCAA
*
934375 ATAATTATCAT-ATCTCAG
1 ATAATTATCATAATCTCAA
934393 ATAAT
1 ATAAT
934398 ATGTTAACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAATTATCATAATCTCAA
Found at i:941111 original size:37 final size:36
Alignment explanation
Indices: 941052--941134 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
941042 TGGTAACCAA
941052 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
941087 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
941124 -GTTGAAAAATG
1 CTTTGAAAAATG
941135 ATAATGGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.14
36 14 0.33
37 23 0.53
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:941533 original size:12 final size:12
Alignment explanation
Indices: 941516--941540 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
941506 ATTTTTTGCG
941516 AGGTTACTATTC
1 AGGTTACTATTC
941528 AGGTTACTATTC
1 AGGTTACTATTC
941540 A
1 A
941541 CGTGAATAGT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:945698 original size:37 final size:36
Alignment explanation
Indices: 945639--945721 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
945629 TGGTAACCAA
945639 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
945674 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
945711 -GTTGAAAAATG
1 CTTTGAAAAATG
945722 ATAATGGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.14
36 14 0.33
37 23 0.53
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:946121 original size:12 final size:12
Alignment explanation
Indices: 946104--946128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
946094 ATTTTTTGCG
946104 AGGTTACTATTC
1 AGGTTACTATTC
946116 AGGTTACTATTC
1 AGGTTACTATTC
946128 A
1 A
946129 CGTGAATAGT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:950287 original size:37 final size:36
Alignment explanation
Indices: 950228--950310 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
950218 TGGTAACCAA
950228 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
950263 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
950300 -GTTGAAAAATG
1 CTTTGAAAAATG
950311 ATAATGGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.14
36 14 0.33
37 23 0.53
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:954226 original size:21 final size:22
Alignment explanation
Indices: 954202--954254 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
954192 TTTAAATTAA
*
954202 TTTTATATTTTTATTT-ATATT
1 TTTTATATTTTAATTTGATATT
*
954223 TTTTATAATTTAATTTGATATT
1 TTTTATATTTTAATTTGATATT
954245 TTTATATATT
1 TTT-TATATT
954255 AAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 14 0.52
22 8 0.30
23 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTATATTTTAATTTGATATT
Found at i:958560 original size:3 final size:3
Alignment explanation
Indices: 958547--958595 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
958537 TTAGGCCTGG
* ** *
958547 AAT AGT AAT AAT AAT TTT AAT AAT AAT AAT AAT AAC AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
958594 AA
1 AA
958596 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:959013 original size:136 final size:138
Alignment explanation
Indices: 958849--959212 Score: 466
Period size: 136 Copynumber: 2.6 Consensus size: 138
958839 AATCTAGCAA
*
958849 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAA-ATTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * *
958914 AAACTCCT-TCTGGAAATGCTGAT-CCTCAAAAGAGGTATC-GT-TGATTCAACTTCATATGTGA
65 GAACT-CTATCTGGAAATGTTGATCCCTCAAAAGAGGT-TCTCTCTAATTCAACTCCATAAGTGA
* **
958975 TGAATTAAGGC
128 CGAACCAAGGC
*
958986 AAGGTTGAACAAACTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
1 AAGGTTGAACAAATTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
* * * * *
959051 AACTTTCTCTCGAAATGTTGATCCCTCGAATGAGGTTCTTCTCTAATTCAACTCCATAAGTGACG
66 AACTCTATCTGGAAATGTTGATCCCTCAAAAGAGGTTC-TCTCTAATTCAACTCCATAAGTGACG
**
959116 AACCAAGTT
130 AACCAAGGC
** *
959125 AAGGTCAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAATT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
959190 GAACTCTATCTGGAAATGTTGAT
65 GAACTCTATCTGGAAATGTTGAT
959213 GCTAATATAT
Statistics
Matches: 197, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
135 1 0.01
136 69 0.35
137 23 0.12
138 1 0.01
139 34 0.17
140 69 0.35
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (138 bp):
AAGGTTGAACAAATTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
AACTCTATCTGGAAATGTTGATCCCTCAAAAGAGGTTCTCTCTAATTCAACTCCATAAGTGACGA
ACCAAGGC
Found at i:959259 original size:123 final size:123
Alignment explanation
Indices: 959132--959581 Score: 701
Period size: 123 Copynumber: 3.7 Consensus size: 123
959122 GTTAAGGTCA
959132 AACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATTATGAACTC
* * * * * *
959196 TATCTGGAAATGTTGATGCTAATATATCTCATTCTGTGATAGAGTTAAGTAAAAGGTTG
65 TACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTTGAGCAAAAGGTTG
*
959255 AACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATTATGAACTC
* *
959319 TACCTGGCAATGTTGATACTGATCTATCTCATTCTATGATAGAGTTGAGCAAAAGGTTG
65 TACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTTGAGCAAAAGGTTG
* * *
959378 AACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTCATATGAGTTCTTCTCATTATGAACTAT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGTTCTTCTCATTATGAACTCT
* *
959443 ACCT-GACAATGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCGAGCAAAAGGTTG
66 ACCTGGA-AATGTTGATGCTGATCTATCTCATTCTATGATAGAGTTGAGCAAAAGGTTG
959501 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGTTCTTCTCATTATGAACTCT
*
959566 -CTTTGGAAATGTTGAT
66 AC-CTGGAAATGTTGAT
959582 CAATCGAGTG
Statistics
Matches: 302, Mismatches: 21, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
122 2 0.01
123 296 0.98
124 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGTTCTTCTCATTATGAACTCT
ACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTTGAGCAAAAGGTTG
Found at i:959416 original size:24 final size:22
Alignment explanation
Indices: 959384--959429 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
959374 GTTGAACAAG
959384 TTCTTCTCATTATGAACTTCTTCT
1 TTCTTCTCA-TATG-ACTTCTTCT
*
959408 TTCTTCTCATATGAGTTCTTCT
1 TTCTTCTCATATGACTTCTTCT
959430 CATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.54
Consensus pattern (22 bp):
TTCTTCTCATATGACTTCTTCT
Found at i:959428 original size:15 final size:16
Alignment explanation
Indices: 959408--959437 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
959398 AACTTCTTCT
959408 TTCTTCTCA-TATGAG
1 TTCTTCTCATTATGAG
959423 TTCTTCTCATTATGA
1 TTCTTCTCATTATGA
959438 ACTATACCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (16 bp):
TTCTTCTCATTATGAG
Found at i:966567 original size:17 final size:18
Alignment explanation
Indices: 966520--966572 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
966510 TAAATTTATG
*
966520 AAATAAATATAATGAATGT
1 AAAT-AATATAAAGAATGT
*
966539 AAATAATGTAAA-AATGT
1 AAATAATATAAAGAATGT
966556 AAA-AAGTATAAAGAATG
1 AAATAA-TATAAAGAATG
966573 AGTGCCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 10 0.34
19 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.26
Consensus pattern (18 bp):
AAATAATATAAAGAATGT
Found at i:977232 original size:35 final size:33
Alignment explanation
Indices: 977181--977253 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 33
977171 TCTGGGTTGA
977181 TATTATTATTACTATTATATATAAATA-TATATA
1 TATTATTATTACTATTATATATAAATATTAT-TA
* *
977214 TATTATGCTATTATTATTATATATTAATATTATTA
1 TATTAT--TATTACTATTATATATAAATATTATTA
977249 TATTA
1 TATTA
977254 CAAATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 6 0.17
35 26 0.74
36 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
TATTATTATTACTATTATATATAAATATTATTA
Found at i:977244 original size:19 final size:20
Alignment explanation
Indices: 977180--977249 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
977170 ATCTGGGTTG
*
977180 ATATTATTATTA-CTATTAT
1 ATATTATTATTATATATTAT
* *
977199 ATATAAATATATATATATTAT
1 ATATTATTAT-TATATATTAT
*
977220 GCTATTATTATTATATATTA-
1 -ATATTATTATTATATATTAT
977240 ATATTATTAT
1 ATATTATTAT
977250 ATTACAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 17 0.41
20 2 0.05
21 15 0.37
22 7 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATTATTATTATATATTAT
Found at i:977246 original size:16 final size:16
Alignment explanation
Indices: 977193--977251 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
977183 TTATTATTAC
*
977193 TATTATATATAAATA-
1 TATTATATATTAATAT
*
977208 TATATATATTATGCTATTAT
1 TAT-TATA-TAT--TAATAT
977228 TATTATATATTAATAT
1 TATTATATATTAATAT
977244 TATTATAT
1 TATTATAT
977252 TACAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.08
16 17 0.47
17 3 0.08
18 3 0.08
19 7 0.19
20 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTATATATTAATAT
Found at i:980963 original size:55 final size:57
Alignment explanation
Indices: 980889--981050 Score: 229
Period size: 57 Copynumber: 2.9 Consensus size: 57
980879 TGACGGGGAA
980889 GAATACTTGCAGGTTCCTCGGC-TTGTGCTGAGAGCC-TACTGTTCGTGACGGAGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGAGTT
* * *
980944 GAATACTTGCAAGTTCCTCGGCTTTGTGTTGAGAGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGAGTT
* * * * * *
981001 GATTACTTGCAGGTTTCTTGGCTTTATGCTTAGGGCCTTACTGTTCGTGA
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGA
981051 TGGGGGGTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 21 0.22
56 13 0.14
57 60 0.64
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGAGTT
Found at i:985530 original size:24 final size:24
Alignment explanation
Indices: 985498--985543 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
985488 CTTGCCCCAG
985498 CAAATTTTGTCCCTGATGAATTTA
1 CAAATTTTGTCCCTGATGAATTTA
985522 CAAATTTTGTCCCTGATGAATT
1 CAAATTTTGTCCCTGATGAATT
985544 GGCTTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (24 bp):
CAAATTTTGTCCCTGATGAATTTA
Found at i:992148 original size:2 final size:2
Alignment explanation
Indices: 992141--992173 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
992131 TAATTTATTT
992141 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
992174 CCCTTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:992298 original size:9 final size:8
Alignment explanation
Indices: 992286--992529 Score: 58
Period size: 9 Copynumber: 30.2 Consensus size: 8
992276 ATTTTTTTTC
992286 ATTTATCTT
1 ATTTAT-TT
992295 ATTTTATTT
1 A-TTTATTT
*
992304 ATTT-TAT
1 ATTTATTT
*
992311 ATGTA-TT
1 ATTTATTT
992318 ATTT-TTT
1 ATTTATTT
*
992325 A-CTATTT
1 ATTTATTT
992332 -TTTATTTT
1 ATTTA-TTT
992340 ATTTTATTAT
1 A-TTTATT-T
*
992350 TTTTATTT
1 ATTTATTT
992358 ATTT-TTT
1 ATTTATTT
992365 -TCTTATTT
1 AT-TTATTT
992373 -TCTTATTT
1 AT-TTATTT
*
992381 -TTATCTTT
1 ATT-TATTT
992389 ATTTCATTT
1 ATTT-ATTT
*
992398 -GTT-TTT
1 ATTTATTT
*
992404 ATTTTCTTT
1 A-TTTATTT
992413 ATTT-TTAT
1 ATTTATT-T
*
992421 TTTTATTGT
1 ATTTATT-T
992430 ATTTATCTT
1 ATTTAT-TT
992439 ATTTA--T
1 ATTTATTT
992445 ATTTATTT
1 ATTTATTT
992453 -TATT-TTT
1 AT-TTATTT
*
992460 ATCTTTTTT
1 AT-TTATTT
992469 ATCTTATCTT
1 AT-TTAT-TT
*
992479 TTTTATTT
1 ATTTATTT
*
992487 CATTTGTTT
1 -ATTTATTT
992496 -TTTCATCTT
1 ATTT-AT-TT
992505 ATTTATTT
1 ATTTATTT
992513 -TTATATTT
1 ATT-TATTT
*
992521 CTTT-TTT
1 ATTTATTT
992528 AT
1 AT
992530 CTAACACATT
Statistics
Matches: 181, Mismatches: 22, Indels: 66
0.67 0.08 0.25
Matches are distributed among these distances:
6 11 0.06
7 38 0.21
8 55 0.30
9 60 0.33
10 17 0.09
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (8 bp):
ATTTATTT
Found at i:992344 original size:20 final size:18
Alignment explanation
Indices: 992296--992362 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
992286 ATTTATCTTA
992296 TTTTATTTATTTTA-TAT
1 TTTTATTTATTTTACTAT
*
992313 GTATTA-TT-TTTTACTATT
1 -TTTTATTTATTTTACTA-T
*
992331 TTTTATTTTATTTTATTAT
1 TTTTA-TTTATTTTACTAT
992350 TTTTATTTATTTT
1 TTTTATTTATTTT
992363 TTTCTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 5 0.12
17 8 0.20
18 13 0.32
19 8 0.20
20 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (18 bp):
TTTTATTTATTTTACTAT
Found at i:992350 original size:30 final size:31
Alignment explanation
Indices: 992287--992442 Score: 101
Period size: 30 Copynumber: 5.0 Consensus size: 31
992277 TTTTTTTTCA
*
992287 TTTATCTTATTTTATTTATTTTATATGTATTATTT
1 TTTATC-TA-TTT-TTTATTTTAT-TTTATTATTT
992322 TTTA-CTATTTTTTATTTTATTTTATTA-TT
1 TTTATCTATTTTTTATTTTATTTTATTATTT
* * *
992351 TTTATTTATTTTTT-TCTTATTTTCTTA-TT
1 TTTATCTATTTTTTATTTTATTTTATTATTT
* *
992380 TTTATCT-TTATTTCATTTGT-TTTTATT-TTC
1 TTTATCTATT-TTTTATTT-TATTTTATTATTT
* * * *
992410 TTTATTTTTATTTTTATTGTATTTATCTTATTT
1 TTTATCTAT-TTTTTATTTTATTT-TATTATTT
992443 ATATTTATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
28 2 0.02
29 28 0.29
30 30 0.31
31 21 0.22
32 7 0.07
33 4 0.04
34 1 0.01
35 4 0.04
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (31 bp):
TTTATCTATTTTTTATTTTATTTTATTATTT
Found at i:992355 original size:6 final size:6
Alignment explanation
Indices: 992330--992466 Score: 67
Period size: 6 Copynumber: 22.8 Consensus size: 6
992320 TTTTTACTAT
*
992330 TTTTTA -TTTTA -TTTTA TTATTT- TTATTTA TTTTT- TTCTTA TTTTCTTA
1 TTTTTA TTTTTA TTTTTA TT-TTTA TT-TTTA TTTTTA TTTTTA -TTT-TTA
* *
992378 TTTTTA TCTTTA -TTTCA TTTGTT- TTTATT- TTCTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTT-TTA TT-TTTA TTTTTA TTTTTA
* * * *
992426 -TTGTA TTTATC TTATTTA TATTTA -TTTTA TTTTTA TCTTTT
1 TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA T-TTTT
992467 TTATCTTATC
Statistics
Matches: 103, Mismatches: 14, Indels: 27
0.72 0.10 0.19
Matches are distributed among these distances:
5 25 0.24
6 54 0.52
7 21 0.20
8 3 0.03
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:992406 original size:35 final size:34
Alignment explanation
Indices: 992330--992433 Score: 129
Period size: 36 Copynumber: 3.0 Consensus size: 34
992320 TTTTTACTAT
* * *
992330 TTTTTATTTTATT-TTATTATTTTTATTTATTTT
1 TTTTTATTTTCTTATTTTTATTTTTATTTATTTG
*
992363 TTTCTTATTTTCTTATTTTTATCTTTATTTCATTTG
1 TTT-TTATTTTCTTATTTTTATTTTTATTT-ATTTG
992399 TTTTTATTTTCTTTATTTTTATTTTTATTGTATTT
1 TTTTTATTTTC-TTATTTTTATTTTTATT-TATTT
992434 ATCTTATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
33 3 0.05
34 9 0.15
35 21 0.34
36 27 0.44
37 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (34 bp):
TTTTTATTTTCTTATTTTTATTTTTATTTATTTG
Found at i:992441 original size:35 final size:34
Alignment explanation
Indices: 992338--992486 Score: 134
Period size: 35 Copynumber: 4.4 Consensus size: 34
992328 ATTTTTTATT
992338 TTATTTTA-TTATTTTTA--TTTATTT-TTT-TC
1 TTATTTTATTTATTTTTATTTTTATTTATTTATC
* * * *
992367 TTATTTT-CTTATTTTTATCTTTATTTCATTTGTTT
1 TTATTTTATTTATTTTTATTTTTATTT-ATTT-ATC
*
992402 TTATTTTCTTTATTTTTATTTTTATTGTATTTATC
1 TTATTTTATTTATTTTTATTTTTATT-TATTTATC
*
992437 TTATTTATATTTA-TTTTATTTTTATCTTTTTTATC
1 TTATTT-TATTTATTTTTATTTTTAT-TTATTTATC
992472 TTATCTTT-TTTATTT
1 TTAT-TTTATTTATTT
992487 CATTTGTTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
29 16 0.16
31 7 0.07
33 3 0.03
34 4 0.04
35 41 0.41
36 28 0.28
37 1 0.01
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (34 bp):
TTATTTTATTTATTTTTATTTTTATTTATTTATC
Found at i:992482 original size:29 final size:29
Alignment explanation
Indices: 992450--992531 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
992440 TTTATATTTA
992450 TTTTATTTTTATCTTTTTTATCTTATCT-T
1 TTTTATTTTT-TCTTTTTTATCTTATCTAT
* *
992479 TTTTATTTCATTTGTTTTTTCATCTTATTTAT
1 TTTTATTT--TTTCTTTTTT-ATCTTATCTAT
*
992511 TTTTA-TATTTCTTTTTTATCT
1 TTTTATTTTTTCTTTTTTATCT
992532 AACACATTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 7 0.16
31 11 0.24
32 6 0.13
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTTATTTTTTCTTTTTTATCTTATCTAT
Found at i:992504 original size:40 final size:40
Alignment explanation
Indices: 992410--992510 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 40
992400 TTTTATTTTC
*
992410 TTTATTTTTATTTTTATTGTAT-TTATCTTATTTATATTTAT
1 TTTATTTTTA-TCTTATT-TATCTTATCTTATTTATATTTAT
*
992451 TTTATTTTTATCTTTTTTATCTTATCTT-TTT-TATTTCAT
1 TTTATTTTTATCTTATTTATCTTATCTTATTTATATTT-AT
992490 TTGT-TTTTTCATCTTATTTAT
1 TT-TATTTTT-ATCTTATTTAT
992511 TTTTATATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
38 5 0.09
39 15 0.28
40 23 0.43
41 10 0.19
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (40 bp):
TTTATTTTTATCTTATTTATCTTATCTTATTTATATTTAT
Found at i:992872 original size:3 final size:3
Alignment explanation
Indices: 992864--992917 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
992854 TTCCGAAATA
992864 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
992912 TAT TAT
1 TAT TAT
992918 CTTAAGTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:994053 original size:15 final size:15
Alignment explanation
Indices: 994035--994065 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
994025 AAATTCTAAA
994035 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
994050 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
994065 T
1 T
994066 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:997483 original size:2 final size:2
Alignment explanation
Indices: 997476--997501 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
997466 TTTACATTCT
997476 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
997502 ATAATGACCT
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):
TA
Found at i:1002299 original size:24 final size:24
Alignment explanation
Indices: 1002262--1002323 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1002252 CATTTAAATG
*
1002262 ATAAACGAATACAAATGAACAAAC
1 ATAAACGAACACAAATGAACAAAC
* * *
1002286 ATAAACAAACACAAATGAACGAAT
1 ATAAACGAACACAAATGAACAAAC
*
1002310 GTAAACGAACACAA
1 ATAAACGAACACAA
1002324 TAAATGAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACAAAC
Found at i:1002570 original size:24 final size:24
Alignment explanation
Indices: 1002527--1002609 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
1002517 AATTTGACTA
* * *
1002527 AACATAAACGAACGACTATAAATG
1 AACATAAATGAACGAATATAAACG
*
1002551 AACATAAATGAATGAATATAAACG
1 AACATAAATGAACGAATATAAACG
* * *
1002575 AATATAAATAAACGAATATAAACA
1 AACATAAATGAACGAATATAAACG
1002599 AACATAAATGA
1 AACATAAATGA
1002610 CTGAACATAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (24 bp):
AACATAAATGAACGAATATAAACG
Found at i:1002592 original size:14 final size:14
Alignment explanation
Indices: 1002568--1002601 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1002558 ATGAATGAAT
1002568 ATAAACGAATATAA
1 ATAAACGAATATAA
1002582 ATAAACGAATATAA
1 ATAAACGAATATAA
*
1002596 ACAAAC
1 ATAAAC
1002602 ATAAATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (14 bp):
ATAAACGAATATAA
Found at i:1007111 original size:19 final size:19
Alignment explanation
Indices: 1007087--1007123 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1007077 ATGACCAACA
*
1007087 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1007106 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1007124 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1007223 original size:20 final size:20
Alignment explanation
Indices: 1007200--1007288 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
1007190 GAATATGTAA
1007200 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
1007220 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
1007240 AATCGCAACTCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
1007261 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1007281 GTCGCAAC
1 ATCGCAAC
1007289 ACTGAATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 41 0.69
21 14 0.24
22 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1008136 original size:24 final size:24
Alignment explanation
Indices: 1008109--1008162 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1008099 GTATTCAAAA
1008109 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1008133 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1008157 TTTGAT
1 TTTGAT
1008163 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1010429 original size:18 final size:18
Alignment explanation
Indices: 1010397--1010431 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1010387 AGCAAAAGGC
**
1010397 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
1010415 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1010432 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1010741 original size:140 final size:140
Alignment explanation
Indices: 1010489--1010771 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
1010479 GTAAACGTTG
* *
1010489 TATTATGTGTATTTTATGTGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
*
1010554 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGTAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1010619 CGAATTTGAC
131 CGAATTTGAC
1010629 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
*
1010694 TTGAACTTTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1010759 CGAATTTGAC
131 CGAATTTGAC
1010769 TAT
1 TAT
1010772 CGCAACGCGA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1010767 original size:20 final size:20
Alignment explanation
Indices: 1010742--1010836 Score: 145
Period size: 20 Copynumber: 4.8 Consensus size: 20
1010732 TTACACATTC
*
1010742 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1010762 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1010782 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1010802 ATTTGATTATTGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1010822 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
1010837 AGAGAAAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1010902 original size:20 final size:20
Alignment explanation
Indices: 1010877--1010920 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1010867 GCAACGCGAA
**
1010877 TTGACTTTCGTGTTGCGATT
1 TTGACTTTCGCATTGCGATT
1010897 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
1010917 TTGA
1 TTGA
1010921 GTTTAACGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:1010932 original size:20 final size:20
Alignment explanation
Indices: 1010888--1010934 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1010878 TGACTTTCGT
**
1010888 GTTGCGATTTTGACTTTCGC
1 GTTGCGATTTTGACTTTAAC
* *
1010908 ATTGCGATTTTGAGTTTAAC
1 GTTGCGATTTTGACTTTAAC
1010928 GTTGCGA
1 GTTGCGA
1010935 AAGTGTACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43
Consensus pattern (20 bp):
GTTGCGATTTTGACTTTAAC
Found at i:1011094 original size:13 final size:13
Alignment explanation
Indices: 1011044--1011098 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
1011034 TTATTTACAC
1011044 ATCAATTAAACAA
1 ATCAATTAAACAA
**
1011057 ATCAACTTTTACAA
1 ATCAA-TTAAACAA
*
1011071 ATAAGAATTAAACAA
1 AT--CAATTAAACAA
1011086 ATCAATTAAACAA
1 ATCAATTAAACAA
1011099 GCAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 15 0.45
14 8 0.24
15 8 0.24
16 2 0.06
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:1013745 original size:3 final size:3
Alignment explanation
Indices: 1013727--1013777 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1013717 TTGTAATATT
* * *
1013727 TAA TAAA TAA TAAA TAA TAT TAC TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1013774 TAA T
1 TAA T
1013778 TTAAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1014059 original size:76 final size:76
Alignment explanation
Indices: 1013933--1014467 Score: 937
Period size: 76 Copynumber: 7.0 Consensus size: 76
1013923 GGTCTTATGA
* *
1013933 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
1013997 CAGGACTTACAG
65 AAGGACTTACAG
* * *
1014009 ATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1014074 AGGACTTACAG
66 AGGACTTACAG
1014085 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1014150 AGGACTTACAG
66 AGGACTTACAG
* *
1014161 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
1014226 AGGGCTTACAG
66 AGGACTTACAG
*
1014237 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1014302 AGGACTTACAG
66 AGGACTTACAG
*
1014313 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1014378 AGGACTTACAG
66 AGGACTTACAG
* *
1014389 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1014454 AGGACTTACAG
66 AGGACTTACAG
1014465 ATG
1 ATG
1014468 TAGGAAATAG
Statistics
Matches: 442, Mismatches: 16, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
76 442 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:1015180 original size:22 final size:22
Alignment explanation
Indices: 1015152--1015206 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1015142 CATAAAGTTT
*
1015152 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* *
1015174 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
1015196 TCATCTTTGAA
1 TCATCTTTGAA
1015207 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:1015648 original size:54 final size:54
Alignment explanation
Indices: 1015566--1015721 Score: 222
Period size: 54 Copynumber: 2.9 Consensus size: 54
1015556 AGAATAGCAG
* ***
1015566 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
** * * *
1015620 GTTCGTAAAACATTTGACAACACATTCATTTTTTCCTGTGGTTTATGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
1015674 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1015722 CAAGATTTCT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1017925 original size:114 final size:114
Alignment explanation
Indices: 1017713--1017932 Score: 305
Period size: 114 Copynumber: 1.9 Consensus size: 114
1017703 GATCATGCAG
* * *
1017713 TTCATCTTTCAATTCCAATGATCGATTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
1017778 ACACTTACAGAAGATGCTATTGGGCCTCCTTATTTATACTATGAGTAAA
66 ACACTTACAAAAGATGCTATTGAGCCTCATTATTTATACTATGAGTAAA
* * * * *
1017827 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATATCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * * *
1017892 ACACTTCCAAAAGATGCTATTGAGTCTTATTATTTTTACTA
66 ACACTTACAAAAGATGCTATTGAGCCTCATTATTTATACTA
1017933 CGAGAACGTG
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTACAAAAGATGCTATTGAGCCTCATTATTTATACTATGAGTAAA
Found at i:1027131 original size:3 final size:3
Alignment explanation
Indices: 1027113--1027184 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
1027103 TTGTAATATT
* * *
1027113 TAA TAAA TAA TAAA TAA TAT TAC TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** **
1027160 TAA TTT TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1027185 TTAAAATGAA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1028161 original size:42 final size:42
Alignment explanation
Indices: 1028102--1028224 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
1028092 GTGAATCGGG
* *
1028102 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
** * *
1028144 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGT
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
* * *
1028186 CTCTTGAACGATAGAAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGG
1028225 TGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:1028162 original size:21 final size:21
Alignment explanation
Indices: 1028102--1028216 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
1028092 GTGAATCGGG
* *
1028102 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
1028123 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1028144 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* ** *
1028165 CTCTTG-AGGGATGATAGGGGT
1 CTCTTGAACGG-TGGGAGGGGC
* * * *
1028186 CTCTTGAACGATAGAAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
1028207 CTCTTGAACG
1 CTCTTGAACG
1028217 ATGACAGGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1028725 original size:20 final size:20
Alignment explanation
Indices: 1028700--1028743 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1028690 AATAGTTTCT
1028700 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1028720 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1028740 GAAA
1 GAAA
1028744 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1028753 original size:20 final size:20
Alignment explanation
Indices: 1028730--1028797 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
1028720 GAAACTTAAA
1028730 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1028750 ATCGCAATGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1028770 ATCGCAACGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
1028790 ATCGCAAC
1 ATCGCAAC
1028798 AAGATAATCG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1028827 original size:19 final size:19
Alignment explanation
Indices: 1028803--1028860 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
1028793 GCAACAAGAT
*
1028803 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
1028822 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
*
1028841 AATCGTAACGCGAAACTAAA
1 AATCGCAACGCGAAA-TAAA
1028861 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1028924 original size:20 final size:20
Alignment explanation
Indices: 1028899--1028946 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1028889 CGATTATCTT
1028899 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
1028919 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
1028939 GTTGCGAT
1 GTTGCGAT
1028947 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:1028956 original size:20 final size:20
Alignment explanation
Indices: 1028899--1028965 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1028889 CGATTATCTT
*
1028899 GTTGCGATAGTCAA-ATTCGC
1 GTTGCGATAGT-AAGTTTCGC
* *
1028919 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTAAGTTTCGC
** *
1028939 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATAGTAAGTTTCGC
1028959 GTTGCGA
1 GTTGCGA
1028966 CTATTCTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTAAGTTTCGC
Found at i:1030689 original size:25 final size:25
Alignment explanation
Indices: 1030661--1030725 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1030651 ATACCAAGTT
*
1030661 AGATATACCAAAAACTACACTGTGA
1 AGATATACCAAAAACGACACTGTGA
1030686 AGATATACCAAAAACGACACTGTGA
1 AGATATACCAAAAACGACACTGTGA
1030711 AGATATACCAAAAAC
1 AGATATACCAAAAAC
1030726 AATAATAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACGACACTGTGA
Found at i:1030913 original size:20 final size:20
Alignment explanation
Indices: 1030873--1030978 Score: 101
Period size: 20 Copynumber: 5.4 Consensus size: 20
1030863 TCTGAAACTT
*
1030873 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACGCG-AAAATG
*
1030894 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
1030914 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
1030934 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
1030953 -AAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1030971 AAAATCGC
1 AAAATCGC
1030979 GTTGCGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.15
19 13 0.18
20 35 0.48
21 14 0.19
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1031387 original size:20 final size:21
Alignment explanation
Indices: 1031362--1031426 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
1031352 TCTGAGAGAT
1031362 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
1031382 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
1031404 AGAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
1031426 G
1 G
1031427 TAGAGAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.16
22 31 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1031396 original size:22 final size:22
Alignment explanation
Indices: 1031369--1031426 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1031359 GATGGAGATA
1031369 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1031391 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1031413 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1031427 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1031589 original size:20 final size:20
Alignment explanation
Indices: 1031564--1031608 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1031554 GCGCTTTGAA
1031564 AATCGCAACGCAATAGTCAG
1 AATCGCAACGCAATAGTCAG
*** *
1031584 AATCGCGTTGCGATAGTCAG
1 AATCGCAACGCAATAGTCAG
1031604 AATCG
1 AATCG
1031609 TGTTGCGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCAATAGTCAG
Found at i:1031613 original size:20 final size:20
Alignment explanation
Indices: 1031576--1031679 Score: 104
Period size: 20 Copynumber: 5.1 Consensus size: 20
1031566 TCGCAACGCA
1031576 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
*
1031596 ATAGTCAGAATCGTGTTGCG
1 ATAGTCAGAATCGCGTTGCG
**
1031616 ATTATGT-ATTATCGCGTTGCG
1 A-TA-GTCAGAATCGCGTTGCG
**
1031637 ATTATGT-ATTATCGCGTTGCG
1 A-TA-GTCAGAATCGCGTTGCG
*
1031658 ATAGTCAGAATCGCATTGCG
1 ATAGTCAGAATCGCGTTGCG
1031678 AT
1 AT
1031680 TTACATATTC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 35 0.47
21 35 0.47
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
ATAGTCAGAATCGCGTTGCG
Found at i:1031634 original size:21 final size:21
Alignment explanation
Indices: 1031605--1031659 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1031595 GATAGTCAGA
*
1031605 ATCGTGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
1031626 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
1031647 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1031660 AGTCAGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1031719 original size:21 final size:21
Alignment explanation
Indices: 1031695--1031735 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1031685 TATTCGCATT
* *
1031695 GCGATTTTCTAAAATCGCAAC
1 GCGAATTTCGAAAATCGCAAC
*
1031716 GCGAATTTGGAAAATCGCAA
1 GCGAATTTCGAAAATCGCAA
1031736 TGCCATAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTCGAAAATCGCAAC
Found at i:1033049 original size:34 final size:34
Alignment explanation
Indices: 1033006--1033137 Score: 110
Period size: 34 Copynumber: 3.7 Consensus size: 34
1032996 GAATGAATTG
1033006 TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
1 TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
* * *
1033040 TAGTCACGA--CC-CATTAGAAAAGAGGTAAGGAA-TGAA
1 TAGTTACGACCCCTCATTAG--TA-A-GT-AGCAACTG-A
*
1033076 TTGTAGTTACGACCCCTCACTAGTAAGTAGCAACTGA
1 ---TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
*
1033113 TAGTTACAACCCCTCATTAGTAAGT
1 TAGTTACGACCCCTCATTAGTAAGT
1033138 TCAAAATCAA
Statistics
Matches: 76, Mismatches: 9, Indels: 26
0.68 0.08 0.23
Matches are distributed among these distances:
31 6 0.08
32 2 0.03
33 1 0.01
34 32 0.42
35 4 0.05
36 5 0.07
37 5 0.07
38 4 0.05
39 9 0.12
40 1 0.01
41 2 0.03
42 5 0.07
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (34 bp):
TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
Found at i:1033100 original size:73 final size:73
Alignment explanation
Indices: 1032980--1033116 Score: 265
Period size: 73 Copynumber: 1.9 Consensus size: 73
1032970 GAATAGAGTG
*
1032980 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCATTAGTAAGTAGCAACTGATAGTC
1 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCACTAGTAAGTAGCAACTGATAGTC
1033045 ACGACCCA
66 ACGACCCA
1033053 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCACTAGTAAGTAGCAACTGATAGT
1 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCACTAGTAAGTAGCAACTGATAGT
1033117 TACAACCCCT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (73 bp):
TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCACTAGTAAGTAGCAACTGATAGTC
ACGACCCA
Found at i:1035852 original size:21 final size:22
Alignment explanation
Indices: 1035828--1035869 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1035818 TAGCATTTTT
1035828 ATATTT-AATT-TTTTATATTTC
1 ATATTTAAATTATTTT-TATTTC
1035849 ATATTTAAATTATTTTTATTT
1 ATATTTAAATTATTTTTATTT
1035870 TTTCCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATTTAAATTATTTTTATTTC
Found at i:1037475 original size:59 final size:58
Alignment explanation
Indices: 1037357--1037477 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 58
1037347 TTTGGTGACT
* * * *
1037357 ATTTTATAACTTTTAATAGTCGAATACTCAACAAAGCAACTGCCTATAGCCGGAAATC
1 ATTTTATAACTTTTAATAGTCGAAGACTCAACAAAACAACTACCTATAACCGGAAATC
* * *
1037415 ATTTTATAACTTTTAATAGTTGAAAGACTCAACAAAATAA-TACTCTATAATC-GAAGATC
1 ATTTTATAACTTTTAATAGTCG-AAGACTCAACAAAACAACTAC-CTATAACCGGAA-ATC
1037474 ATTT
1 ATTT
1037478 GTGAACTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
58 26 0.49
59 27 0.51
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (58 bp):
ATTTTATAACTTTTAATAGTCGAAGACTCAACAAAACAACTACCTATAACCGGAAATC
Found at i:1039091 original size:17 final size:16
Alignment explanation
Indices: 1039065--1039096 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1039055 ATATATTTGT
1039065 AAATTTTAATTAATTA
1 AAATTTTAATTAATTA
1039081 AAATATTTAATTAATT
1 AAAT-TTTAATTAATT
1039097 TCAAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTAATTAATTA
Found at i:1050504 original size:15 final size:15
Alignment explanation
Indices: 1050484--1050518 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1050474 CATTTTTATT
*
1050484 TTATTATTATTGTTA
1 TTATTAATATTGTTA
1050499 TTATTAATATTGTTA
1 TTATTAATATTGTTA
1050514 TTATT
1 TTATT
1050519 TTTACAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATTAATATTGTTA
Found at i:1050765 original size:2 final size:2
Alignment explanation
Indices: 1050758--1050816 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1050748 CCCCTGTTCA
1050758 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
1050800 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1050817 ATCAATCAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1051492 original size:31 final size:32
Alignment explanation
Indices: 1051457--1051516 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1051447 GTAAAATCAT
*
1051457 AAAACAATTTATA-ATTAACATACA-AGTTCGG
1 AAAACAATTCATATATT-ACATACAGAGTTCGG
*
1051488 AAAACCATTCATATATTACATACAGAGTT
1 AAAACAATTCATATATTACATACAGAGTT
1051517 AAAGTCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (32 bp):
AAAACAATTCATATATTACATACAGAGTTCGG
Found at i:1054686 original size:30 final size:30
Alignment explanation
Indices: 1054650--1054709 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1054640 CGTCTTATAG
1054650 GTTGGGTTTATGTTAAATTGTCATCACTGA
1 GTTGGGTTTATGTTAAATTGTCATCACTGA
1054680 GTTGGGTTTATGTTAAATTGTCATCACTGA
1 GTTGGGTTTATGTTAAATTGTCATCACTGA
1054710 ATGATGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (30 bp):
GTTGGGTTTATGTTAAATTGTCATCACTGA
Found at i:1054919 original size:32 final size:32
Alignment explanation
Indices: 1054883--1054961 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
1054873 AAAACCAATA
* * *
1054883 GATCCGATATTGACCCGAATAGAAAATTGATT
1 GATCCGATATTGACCCAAATAGAAAATCGAAT
* * *
1054915 GATCCGATATTAACCTAAATCGAAAATCGAAT
1 GATCCGATATTGACCCAAATAGAAAATCGAAT
*
1054947 GATTCGATATTGACC
1 GATCCGATATTGACC
1054962 TGACTCGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (32 bp):
GATCCGATATTGACCCAAATAGAAAATCGAAT
Found at i:1055722 original size:15 final size:16
Alignment explanation
Indices: 1055692--1055728 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1055682 ATAAAAAATT
1055692 TTAT-TTATAATATTG
1 TTATGTTATAATATTG
1055707 TTATGTTATAAT-TTG
1 TTATGTTATAATATTG
1055722 TT-TGTTA
1 TTATGTTA
1055729 CGTTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (16 bp):
TTATGTTATAATATTG
Found at i:1056441 original size:22 final size:22
Alignment explanation
Indices: 1056416--1056459 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1056406 CTGTTTATTA
* *
1056416 ATTAATAATTTAGTAATATTTT
1 ATTAATAAATTAATAATATTTT
* *
1056438 ATTAGTAAATTAATAATTTTTT
1 ATTAATAAATTAATAATATTTT
1056460 TGAATGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTAATAAATTAATAATATTTT
Found at i:1056450 original size:34 final size:31
Alignment explanation
Indices: 1056381--1056451 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1056371 GTAGTAAAAT
**
1056381 ATTAATTAATAATTTAATATTTTTACTGTTT
1 ATTAATTAATAATTTAATATTTTTACTGTAA
* *
1056412 ATTAATTAATAATTTAGTAATATTTTATTAGTAA
1 ATTAATTAATAATTTAAT-AT-TTTTACT-GTAA
1056446 ATTAAT
1 ATTAAT
1056452 AATTTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 17 0.52
32 2 0.06
33 6 0.18
34 8 0.24
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (31 bp):
ATTAATTAATAATTTAATATTTTTACTGTAA
Found at i:1057487 original size:28 final size:27
Alignment explanation
Indices: 1057451--1057527 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
1057441 ACTATATTTT
*
1057451 TAAAAAATATAAAATAATATATAACTA
1 TAAAAAATATAAAATAATATATAAATA
*
1057478 CTAAAAAATAT-AATTAATATTATAAATA
1 -TAAAAAATATAAAATAATA-TATAAATA
*
1057506 TAAAATAATTATAACATAATAT
1 TAAAA-AA-TATAAAATAATAT
1057528 TTTATAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 12 0.29
28 19 0.46
29 4 0.10
30 6 0.15
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAAAATATAAAATAATATATAAATA
Found at i:1058181 original size:43 final size:44
Alignment explanation
Indices: 1058120--1058300 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 44
1058110 TAGGGTCTCT
* *
1058120 ATTTTTTTAAT-ATCACTTTCTATCTTTATAACT-A-ATGCCCTTA
1 ATTTTTTCAATCATCACTTTCTACCTTTATAACTGAGAT-CCC-TA
*
1058163 ATTTTTTCAATCA-CACTTTCTACCTTTATAATTGAGATCCCTA
1 ATTTTTTCAATCATCACTTTCTACCTTTATAACTGAGATCCCTA
* * *
1058206 ATTTTTTCAATC-TCTCATTT-TACCTTTATAATTGAG-GCCTCTA
1 ATTTTTTCAATCATCAC-TTTCTACCTTTATAACTGAGATCC-CTA
* * * * **
1058249 ACTTTTT-AAT-ATCACTTTTTACCTTTATAATTAAGGCCCCTA
1 ATTTTTTCAATCATCACTTTCTACCTTTATAACTGAGATCCCTA
1058291 A-TTTTTCAAT
1 ATTTTTTCAAT
1058301 TCCATAAAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
41 8 0.07
42 30 0.25
43 71 0.60
44 8 0.07
45 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.48
Consensus pattern (44 bp):
ATTTTTTCAATCATCACTTTCTACCTTTATAACTGAGATCCCTA
Found at i:1058386 original size:3 final size:3
Alignment explanation
Indices: 1058378--1058414 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1058368 AATCTAATCA
1058378 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1058415 TTCGGATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1065192 original size:21 final size:21
Alignment explanation
Indices: 1065168--1065213 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1065158 AGACAAATGA
* *
1065168 TGTTCTCTCATCTCAAAATTC
1 TGTTATCTCATCTCAAAACTC
* *
1065189 TGTTATTTCATCTGAAAACTC
1 TGTTATCTCATCTCAAAACTC
1065210 TGTT
1 TGTT
1065214 GAGTTTTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (21 bp):
TGTTATCTCATCTCAAAACTC
Found at i:1071667 original size:232 final size:231
Alignment explanation
Indices: 1070940--1072339 Score: 2509
Period size: 231 Copynumber: 6.0 Consensus size: 231
1070930 AAGGGGCAAA
*
1070940 AACAATTTTTAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1071005 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG--AAAAAAAAC
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
*
1071068 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATTGC
131 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
* *
1071133 AAAGCAGCACAATCTAAAATTATTATTGTCAAAAAT
196 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
1071169 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
* * * *
1071234 CACGAGTATAGAAGGTTATACAAACAATAAAGTTTGGCGAATATCAACGAATTGAAAAAAAAAAC
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
1071299 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
131 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
1071364 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
196 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
1071400 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
*
1071465 CACGAGTATAGAAGGTTATGCAAATAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAA
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG-AAAAAAAAAA
1071530 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
130 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
1071595 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
195 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
*
1071632 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCCTAAACTG
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA-CCCTAAAATG
1071697 ACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAA
65 ACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAA
1071762 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
130 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
1071827 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
195 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
1071864 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
* **
1071929 CATGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGGGAAAAAAAAC
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
*
1071994 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGT
131 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
1072059 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
196 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
1072095 AACAATTTTCAATAGAAAATACAAAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA
1 AACAATTTTC-------AAT----AGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA
*
1072160 CCCTAAACTGACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG
55 CCCTAAAATGACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG
1072225 -AAAAAAAAACCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGAC
120 AAAAAAAAAACCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGAC
* *
1072289 TGTTATATAGCAGAGTGGCACAATCTAAAATTACTATTGTCAAAAAT
185 TGTTATATAGCAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
1072336 AACA
1 AACA
1072340 GTGGATAATA
Statistics
Matches: 1130, Mismatches: 26, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
229 114 0.10
231 403 0.36
232 332 0.29
233 63 0.06
238 3 0.00
241 111 0.10
242 104 0.09
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (231 bp):
AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
Found at i:1072124 original size:11 final size:11
Alignment explanation
Indices: 1072108--1072137 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1072098 AATTTTCAAT
1072108 AGAAAATACAA
1 AGAAAATACAA
1072119 AGAAAATACAA
1 AGAAAATACAA
1072130 AGAAAATA
1 AGAAAATA
1072138 TCTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (11 bp):
AGAAAATACAA
Found at i:1073613 original size:60 final size:60
Alignment explanation
Indices: 1073500--1073614 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
1073490 ATAGTCGGGT
* *
1073500 GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAGTTCTTTATAGTTGAAG
1 GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAATTCTCTATAGTTGAAG
1073560 GATCATTTTGTAACTTTTAATAGTC-A-GGTAACTCAATAAAATAATAT-TCTATAGT
1 GATCATTTTGTAACTTTTAATAGTCGATGG--ACTCAATAAAATAAT-TCTCTATAGT
1073615 GGGGGGCCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
58 2 0.04
59 1 0.02
60 46 0.92
61 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAATTCTCTATAGTTGAAG
Found at i:1077055 original size:129 final size:129
Alignment explanation
Indices: 1076898--1077130 Score: 322
Period size: 129 Copynumber: 1.8 Consensus size: 129
1076888 CTGTTGACTA
* * * * * * *
1076898 TTGACTTTGACCAAAAAGTTAAATTTTTCGACATGTCATATTTTATGTTTTTTGACGTACTAAAT
1 TTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAAT
* *
1076963 CCGATTCCGAAGTCCAATTTGCCAAATTCGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
66 CCGATTCAGAAGTCCAATTTGCCAAATTAGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
* * *
1077027 TTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATATTTTATGTTTTTCGATGTCCTGAAT
1 TTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAAT
* ** *
1077092 CTGATTCAGAAGTCCGTTTTGCCAAATTATAACCCGAAA
66 CCGATTCAGAAGTCCAATTTGCCAAATTAGAACCCGAAA
1077131 ACCCCGAATT
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
129 88 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (129 bp):
TTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAAT
CCGATTCAGAAGTCCAATTTGCCAAATTAGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
Found at i:1079032 original size:21 final size:20
Alignment explanation
Indices: 1079008--1079056 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1078998 CTCAAAATCA
* *
1079008 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
1079028 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
1079048 CTTTT-AAAA
1 TTTTTCAAAA
1079057 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Done.