Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 78
Found at i:5143678 original size:39 final size:38
Alignment explanation
Indices: 5143635--5143724 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
5143625 GCGACCAGAC
* *
5143635 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA-CGCGAAATGAA
5143674 AATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAA
5143712 AATCGCAATGCGA
1 AATCGCAATGCGA
5143725 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 23 0.47
39 26 0.53
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (38 bp):
AATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAA
Found at i:5143753 original size:19 final size:19
Alignment explanation
Indices: 5143720--5143764 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5143710 AAAATCGCAA
*
5143720 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
5143739 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
5143758 TGCGATT
1 TGCGATT
5143765 ATCTCGTTGC
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:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:5144405 original size:20 final size:20
Alignment explanation
Indices: 5144320--5144413 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
5144310 CGCTAAGTAA
*
5144320 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
5144340 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
5144360 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
5144381 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
5144401 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
5144414 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:5144432 original size:41 final size:41
Alignment explanation
Indices: 5144402--5144497 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
5144392 ATAGTCAGTA
* * *
5144402 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
*
5144443 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTAC-TAAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGT-AT
5144484 TCGCATTGCGAATT
1 TCGCATTGCGAATT
5144498 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:5144446 original size:20 final size:20
Alignment explanation
Indices: 5144402--5144494 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
5144392 ATAGTCAGTA
* *
5144402 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTAAT
* *
5144423 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
5144443 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
*
5144464 TCGCGTTGCGATTTACTAAT
1 TCGCATTGCGATTTACTAAT
5144484 TCGCATTGCGA
1 TCGCATTGCGA
5144495 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 33 0.56
21 26 0.44
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:5145230 original size:26 final size:26
Alignment explanation
Indices: 5145201--5145254 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
5145191 TTCAAGTTAG
* * *
5145201 AATTCAACTTTATCGATTTAAGTTTT
1 AATTCAAATTAATCGATTTAAGATTT
* *
5145227 AATTTAAATTAATTGATTTAAGATTT
1 AATTCAAATTAATCGATTTAAGATTT
5145253 AA
1 AA
5145255 GAGAAAGAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (26 bp):
AATTCAAATTAATCGATTTAAGATTT
Found at i:5146072 original size:18 final size:17
Alignment explanation
Indices: 5146035--5146068 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5146025 ATAAATTAAT
* *
5146035 TAATATTTAATATCAAA
1 TAATATTTAAAATAAAA
5146052 TAATATTTAAAATAAAA
1 TAATATTTAAAATAAAA
5146069 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATTTAAAATAAAA
Found at i:5146497 original size:11 final size:11
Alignment explanation
Indices: 5146483--5146514 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5146473 TAAAGAGTAT
5146483 GAAACAAAAAC
1 GAAACAAAAAC
5146494 GAAACAAAAAC
1 GAAACAAAAAC
*
5146505 AAAACAAAAA
1 GAAACAAAAA
5146515 ATCTAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (11 bp):
GAAACAAAAAC
Found at i:5147317 original size:18 final size:18
Alignment explanation
Indices: 5147286--5147320 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5147276 CAGAATTATA
*
5147286 ATTAAATTTTAATAAATG
1 ATTAAATTTAAATAAATG
*
5147304 ATTAACTTTAAATAAAT
1 ATTAAATTTAAATAAAT
5147321 CCTTATACTT
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:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTTAAATAAATG
Found at i:5151838 original size:21 final size:21
Alignment explanation
Indices: 5151809--5151863 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5151799 GAGTTACCCG
*
5151809 CGACGGCCGCAATAGCGTCCA
1 CGACGGCCGCAATAGCGCCCA
* * * *
5151830 CGACAGCCGTAACAGCGCCCG
1 CGACGGCCGCAATAGCGCCCA
5151851 CGACGGCCGCAAT
1 CGACGGCCGCAAT
5151864 CACGGTAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.40, G:0.29, T:0.07
Consensus pattern (21 bp):
CGACGGCCGCAATAGCGCCCA
Found at i:5158106 original size:42 final size:42
Alignment explanation
Indices: 5158060--5158180 Score: 179
Period size: 42 Copynumber: 2.9 Consensus size: 42
5158050 CAATCGAATC
**
5158060 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAAGATTATTAAAAGT
* *
5158102 ATTAGGTGAATCATTGAAATTTCCAATAAGATTATTATAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAAGATTATTAAAAGT
* **
5158144 ATTAGGTGAATCATTAGAATTTCCAATCGGATTATTA
1 ATTAGGTGAATCATTGGAATTTCCAATAAGATTATTA
5158181 GAAGGTTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAAGATTATTAAAAGT
Found at i:5158367 original size:28 final size:28
Alignment explanation
Indices: 5158309--5158367 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
5158299 ACATATTTAA
* *
5158309 AAGTAATCAATAAAACAAATATAGTATC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
5158337 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
5158365 AAG
1 AAG
5158368 GAAAGATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.22
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:5158754 original size:28 final size:28
Alignment explanation
Indices: 5158722--5158776 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
5158712 ATGCTAAGTT
5158722 TGCCGACTAAACATG-AAAGAAATGAGTG
1 TGCCGACTAAACATGCAAA-AAATGAGTG
5158750 TGCCGACTAAACATGCAAAAAATGAGT
1 TGCCGACTAAACATGCAAAAAATGAGT
5158777 AAGTTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (28 bp):
TGCCGACTAAACATGCAAAAAATGAGTG
Found at i:5161235 original size:26 final size:26
Alignment explanation
Indices: 5161206--5161260 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5161196 ATTTTAGTTC
*
5161206 AAGTTAGAATTCAACTTAATCGATTT
1 AAGTTAGAATTCAAATTAATCGATTT
** * *
5161232 AAGTTTTAATTTAAATTAATTGATTT
1 AAGTTAGAATTCAAATTAATCGATTT
5161258 AAG
1 AAG
5161261 ATTTAAGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (26 bp):
AAGTTAGAATTCAAATTAATCGATTT
Found at i:5161396 original size:28 final size:30
Alignment explanation
Indices: 5161360--5161423 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
5161350 ATGTTATTAA
* *
5161360 AATTTAATTATAA-TTTTAATAGAAAT-AT
1 AATTAAATTATAATTTTTAATAAAAATAAT
*
5161388 AATTAAATTATAATTTTTATTAAAAATAAT
1 AATTAAATTATAATTTTTAATAAAAATAAT
5161418 AATTAA
1 AATTAA
5161424 TTTGAGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.39
29 11 0.35
30 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
AATTAAATTATAATTTTTAATAAAAATAAT
Found at i:5162081 original size:3 final size:3
Alignment explanation
Indices: 5162073--5162114 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5162063 TTTGTCCCGC
5162073 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5162115 AATAATTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5165678 original size:14 final size:14
Alignment explanation
Indices: 5165661--5165696 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5165651 TTCTTATTTA
*
5165661 TGCATTTTCGTATT
1 TGCATTTTCGCATT
5165675 TGCATTTTCGCATT
1 TGCATTTTCGCATT
*
5165689 TACATTTT
1 TGCATTTT
5165697 TTTCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (14 bp):
TGCATTTTCGCATT
Found at i:5167311 original size:34 final size:30
Alignment explanation
Indices: 5167273--5167341 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
5167263 TTGATATAAC
5167273 AATTTAAGGCAAAATGGATTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GATTTTGGACTT-AATTG
*
5167307 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGATTTTGGACTTAATTG
5167336 AATTTA
1 AATTTA
5167342 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGATTTTGGACTTAATTG
Found at i:5167352 original size:29 final size:30
Alignment explanation
Indices: 5167282--5167341 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
5167272 CAATTTAAGG
*
5167282 CAAAATGGATTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
5167313 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
5167342 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:5167582 original size:21 final size:21
Alignment explanation
Indices: 5167556--5167595 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5167546 ATTTGAATTT
5167556 TATGAAGGGGTACCGATACCA
1 TATGAAGGGGTACCGATACCA
*
5167577 TATGAATGGGTACCGATAC
1 TATGAAGGGGTACCGATAC
5167596 GCCCTGTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (21 bp):
TATGAAGGGGTACCGATACCA
Found at i:5170772 original size:34 final size:30
Alignment explanation
Indices: 5170734--5170802 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
5170724 TTGATATAAC
5170734 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
5170768 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
5170797 AATTTA
1 AATTTA
5170803 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:5170813 original size:29 final size:30
Alignment explanation
Indices: 5170743--5170802 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5170733 CAATTTAAGG
5170743 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
5170774 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
5170803 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:5171022 original size:21 final size:21
Alignment explanation
Indices: 5170996--5171036 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5170986 ATTTGAATTT
5170996 TATGAA-GGGATACCGATACCA
1 TATGAATGGG-TACCGATACCA
*
5171017 TATGAATGGGTATCGATACC
1 TATGAATGGGTACCGATACC
5171037 CCCTGTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (21 bp):
TATGAATGGGTACCGATACCA
Found at i:5174823 original size:38 final size:38
Alignment explanation
Indices: 5174667--5174815 Score: 212
Period size: 38 Copynumber: 3.9 Consensus size: 38
5174657 TAGTAAATCT
* *
5174667 TTGACTTCCT-AGTAAAGAGAAATCAA-CTTTGTTATCC
1 TTGACTTCCTCA-TGAAGAGAAGTCAACCTTTGTTATCC
5174704 TTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATCC
1 TTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATCC
* * * *
5174742 TTGACTTCTTCTTGAAGAAAAGTCAACCTTTGTTATCA
1 TTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATCC
*
5174780 TTGACTTCCTCACGAAGAGAAGTCAACCTTTGTTAT
1 TTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTAT
5174816 TTCTGACTCC
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 22 0.22
38 78 0.78
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (38 bp):
TTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATCC
Found at i:5174877 original size:62 final size:62
Alignment explanation
Indices: 5174776--5175059 Score: 229
Period size: 62 Copynumber: 4.5 Consensus size: 62
5174766 AACCTTTGTT
*** * *
5174776 ATCATTGACTTCCTCACGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAGAGGAGCCA
1 ATCATTGACTTCCTCGTAAAGAGAAGTCAACTTTTGTTATTTCTGACTCCTCAGAGGAGTCA
* * *
5174838 ATCTTTGACTTTCTCGTAAAGAAAAGTCAACTTTTGTTATTTCTTGACTCC-CTAGTA-GAGTCA
1 ATCATTGACTTCCTCGTAAAGAGAAGTCAACTTTTGTTATTTC-TGACTCCTC-AG-AGGAGTCA
* * * * *
5174901 ATCATTGATTTTCTCTTGAAA-AGAAGTCCA-TATTTGTTATTTCTGACTCCCTTGTAAAGAGGA
1 ATCATTGACTTCCTCGT-AAAGAGAAGTCAACT-TTTGTTATTTCTGACT-CC---T-CAGAGGA
5174964 GTCA
59 GTCA
* * * * * * *
5174968 AT-TTTATACTTCCTCATGAATAGAAGTCAACTTTTGTTATTTCTGACTCCCCA-ATAGAGTCA
1 ATCATT-GACTTCCTCGTAAAGAGAAGTCAACTTTTGTTATTTCTGACTCCTCAGA-GGAGTCA
*
5175030 ATCATTGACTTCCTCGTGAAGAGAAGTCAA
1 ATCATTGACTTCCTCGTAAAGAGAAGTCAA
5175060 TATTGTAGAT
Statistics
Matches: 177, Mismatches: 28, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
61 1 0.01
62 73 0.41
63 50 0.28
64 4 0.02
66 7 0.04
67 41 0.23
68 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (62 bp):
ATCATTGACTTCCTCGTAAAGAGAAGTCAACTTTTGTTATTTCTGACTCCTCAGAGGAGTCA
Found at i:5175055 original size:129 final size:125
Alignment explanation
Indices: 5174776--5175063 Score: 337
Period size: 129 Copynumber: 2.3 Consensus size: 125
5174766 AACCTTTGTT
* ** *
5174776 ATCATTGACTTCCTCACGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAGAGGAGCCAATC
1 ATCATTGACTTCCTCATGAAGAGAAGTCAATATTTGTTATTTCTGACTCCTAAGAGGAGCCAATC
* * * *
5174841 TTTGACTTTCTCGTAAAGAAAAGTCAACTTTTGTTATTTCTTGACTCCCTAGTAGAGTCA
66 TTTGACTTCCTCATAAAGAAAAGTCAACTTTTGTTATTTCTTGACTCCCCAATAGAGTCA
* * * * * *
5174901 ATCATTGATTTTCTCTTGAAAAGAAGTCCATATTTGTTATTTCTGACTCCCTTGTAAAGAGGAGT
1 ATCATTGACTTCCTCATGAAGAGAAGTCAATATTTGTTATTTCTGACT-CC---T-AAGAGGAGC
* * * *
5174966 CAAT-TTTATACTTCCTCATGAATAGAAGTCAACTTTTGTTATTTC-TGACTCCCCAATAGAGTC
61 CAATCTTT-GACTTCCTCATAAAGAAAAGTCAACTTTTGTTATTTCTTGACTCCCCAATAGAGTC
5175029 A
125 A
*
5175030 ATCATTGACTTCCTCGTGAAGAGAAGTCAATATT
1 ATCATTGACTTCCTCATGAAGAGAAGTCAATATT
5175064 GTAGATTTGG
Statistics
Matches: 134, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
125 40 0.30
126 2 0.01
129 50 0.37
130 42 0.31
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (125 bp):
ATCATTGACTTCCTCATGAAGAGAAGTCAATATTTGTTATTTCTGACTCCTAAGAGGAGCCAATC
TTTGACTTCCTCATAAAGAAAAGTCAACTTTTGTTATTTCTTGACTCCCCAATAGAGTCA
Found at i:5175250 original size:36 final size:36
Alignment explanation
Indices: 5175203--5175599 Score: 526
Period size: 36 Copynumber: 11.0 Consensus size: 36
5175193 AACTCGAATC
*
5175203 TAAGCCTTCACGAAAGAGTAGTGAAGCAAATCAATT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
* *
5175239 TAAGCCTTCACGGAAGAGTAATGAAGCAAATCAACT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
* *
5175275 TAAGCCTTCACGGAAGA-TAGTGAAACAAATCAATC
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
* *
5175310 TAATCCTTCACGGAAGAGTAGTGAAGCAAATCAACT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
** * *
5175346 TAAGCCTTCACATAAGATTAGTGAAGCAAATCAACT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
** * * * *
5175382 TAAGCCTTCACATAATAGTAGTTAAACAAATCAATC
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
* * *
5175418 TAAGCCTTTACGGAAGAGTAGTGAATCAAATCAATC
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
*
5175454 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATC
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
*
5175490 TAAACCTTCACGGAAGAGTAGTGAAGCAAATCAATT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
*
5175526 TAAGCCTTCACGGAAGAGTAATGAAGCAAATCAATCT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAAT-T
* * * * *
5175563 TATGCCTTCACGGAAGAATAGTGGAGCAGATCCATT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
5175599 T
1 T
5175600 TACAAAGATT
Statistics
Matches: 320, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
35 30 0.09
36 260 0.81
37 30 0.09
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (36 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
Found at i:5175758 original size:102 final size:102
Alignment explanation
Indices: 5175576--5176054 Score: 557
Period size: 102 Copynumber: 4.7 Consensus size: 102
5175566 GCCTTCACGG
* * *
5175576 AAGAATAGTGGAGCAGATCCATTTTACAAAGATTTCTTGAGTCTTAT-ATCCCTAAAAGAAGAGT
1 AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCA-CCCTAAAAGAAGAGT
* * * **
5175640 TGAGTAGATTTATCTTCCCTTGGATCGTATCTCCCTGA
65 GGAGCAAATTCGTCTTCCCTTGGATCGTATCTCCCTGA
* * *
5175678 AATAAGAGTGGAGCAGATCCATTTTACAAATATTTCTCGAGTCTTATCACCCTAAAAGAAGAGTG
1 AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCACCCTAAAAGAAGAGTG
*
5175743 GAGCAAATTTGTCTTCCCTTGGATCGTATCTCCCTGA
66 GAGCAAATTCGTCTTCCCTTGGATCGTATCTCCCTGA
* ** * * *
5175780 AATAAGAGTGGAGCATATCTGTTTTACATAGATTTCTCGTGTCTTAT-ATCCCTGAAAGAAGAGT
1 AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCA-CCCTAAAAGAAGAGT
* * * *
5175844 GAAACAAATTCGTCTTCCTTTGGATCATATCTCCCTGA
65 GGAGCAAATTCGTCTTCCCTTGGATCGTATCTCCCTGA
* * * * * *
5175882 AAGAATAGTGAAGCATATCAACTTTACAAAGATTTCTCGAGTCTTATCTCCCTAAAACAAGAGTG
1 AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCACCCTAAAAGAAGAGTG
* * *
5175947 GAGCAGATTCGTCTTCCTTTGGATCTTATCTCCCTGA
66 GAGCAAATTCGTCTTCCCTTGGATCGTATCTCCCTGA
* * * * * * * * *
5175984 AAGAAGATTGGAGCATATCCGTTTTACAAAGATCTCTTGAGTCTAATCTCCCCTTAATGAATAGT
1 AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATC-ACCCTAAAAGAAGAGT
5176049 GGAGCA
65 GGAGCA
5176055 TACATGTCTT
Statistics
Matches: 324, Mismatches: 49, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
101 1 0.00
102 305 0.94
103 18 0.06
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (102 bp):
AAGAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCACCCTAAAAGAAGAGTG
GAGCAAATTCGTCTTCCCTTGGATCGTATCTCCCTGA
Found at i:5177086 original size:18 final size:18
Alignment explanation
Indices: 5177055--5177089 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5177045 CAGAATTATA
*
5177055 ATTAAATTTTAATAAATG
1 ATTAAATTTAAATAAATG
*
5177073 ATTAACTTTAAATAAAT
1 ATTAAATTTAAATAAAT
5177090 CCTTATACTT
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:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTTAAATAAATG
Found at i:5181600 original size:21 final size:21
Alignment explanation
Indices: 5181571--5181625 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5181561 GAGTTACCCG
*
5181571 CGACGGCCGCAATAGCGTCCA
1 CGACGGCCGCAATAGCGCCCA
* * * *
5181592 CGACAGCCGTAACAGCGCCCG
1 CGACGGCCGCAATAGCGCCCA
5181613 CGACGGCCGCAAT
1 CGACGGCCGCAAT
5181626 CACGGTAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.40, G:0.29, T:0.07
Consensus pattern (21 bp):
CGACGGCCGCAATAGCGCCCA
Found at i:5197446 original size:32 final size:32
Alignment explanation
Indices: 5197345--5197451 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 32
5197335 TAGATCCCGA
* * * *
5197345 AGAACCTAGGTAA-AATGTCCATATGTTCCTT
1 AGAACATAGGTAATACTATCCATATGTTCCGT
*
5197376 AGAACATAGGT-ATACTGTCCATATG-TCTCG-
1 AGAACATAGGTAATACTATCCATATGTTC-CGT
* *
5197406 AAAGACATAGGTAATTCTATCCATATGTTCCGT
1 AGA-ACATAGGTAATACTATCCATATGTTCCGT
5197439 AGAACATAGGTAA
1 AGAACATAGGTAA
5197452 ACCCTCTACT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
30 5 0.08
31 30 0.48
32 24 0.38
33 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AGAACATAGGTAATACTATCCATATGTTCCGT
Found at i:5199459 original size:75 final size:76
Alignment explanation
Indices: 5199350--5199491 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 76
5199340 CCTTAAATCC
* ** *
5199350 GAATTTTCTTCGGTTATTTATTTATTTTACTGATGGTATTC-CCCTGAAATTTTATTTGTGCCCA
1 GAATTTTCTTCGGTTAATTACCTATTTTACTGATGGTATTCACCCTAAAATTTTATTTGTGCCCA
5199414 CCTTGATACAT
66 CCTTGATACAT
* * * *
5199425 GAATTTTCTTCGGTTAATTACCTATTTTACTGATGTTTTTCATCCTAAAATTTTATTTGTGTCCA
1 GAATTTTCTTCGGTTAATTACCTATTTTACTGATGGTATTCACCCTAAAATTTTATTTGTGCCCA
5199490 CC
66 CC
5199492 CCAATAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 36 0.62
76 22 0.38
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.49
Consensus pattern (76 bp):
GAATTTTCTTCGGTTAATTACCTATTTTACTGATGGTATTCACCCTAAAATTTTATTTGTGCCCA
CCTTGATACAT
Found at i:5204456 original size:20 final size:20
Alignment explanation
Indices: 5204431--5204469 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5204421 AGAATATGAT
5204431 AAAAATTATACGATGTTATC
1 AAAAATTATACGATGTTATC
5204451 AAAAATTATACGATGTTAT
1 AAAAATTATACGATGTTAT
5204470 ACACCATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAAATTATACGATGTTATC
Found at i:5207825 original size:17 final size:16
Alignment explanation
Indices: 5207805--5207842 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5207795 TATTATCAAC
5207805 AAATATATTTTTTATAT
1 AAATATA-TTTTTATAT
*
5207822 AAATA-ATTTTTATTT
1 AAATATATTTTTATAT
5207837 AAATAT
1 AAATAT
5207843 TTAGAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 13 0.68
16 1 0.05
17 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATATTTTTATAT
Found at i:5208060 original size:20 final size:20
Alignment explanation
Indices: 5208004--5208061 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5207994 ATCCTATTCC
*
5208004 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTTTATTTCTA
5208024 CTGATAATCTTTTATTTCTA
1 CTGATAATCTTTTATTTCTA
*
5208044 CTGATAATCTTATATTTC
1 CTGATAATCTTTTATTTC
5208062 GTGAATCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (20 bp):
CTGATAATCTTTTATTTCTA
Found at i:5209352 original size:24 final size:24
Alignment explanation
Indices: 5209325--5209393 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
5209315 GTGACATATA
*
5209325 AAATTGTCCTGAAGGACCACGTAG
1 AAATTGTCCTGAAGGACCACATAG
5209349 AAA-TGTCCCTG-AGGACCACATAG
1 AAATTGT-CCTGAAGGACCACATAG
* * *
5209372 -AATTCTCCTTAAAGACCACATA
1 AAATTGTCCTGAAGGACCACATA
5209394 TATATTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.13
23 26 0.68
24 7 0.18
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (24 bp):
AAATTGTCCTGAAGGACCACATAG
Found at i:5211478 original size:16 final size:16
Alignment explanation
Indices: 5211459--5211539 Score: 90
Period size: 16 Copynumber: 4.9 Consensus size: 16
5211449 TATTAGTATA
*
5211459 CATACATATATACATG
1 CATACATACATACATG
*
5211475 CATACATGCATACATG
1 CATACATACATACATG
* *
5211491 CATATACATGCATACAGG
1 C--ATACATACATACATG
*
5211509 CATACATGCATACATG
1 CATACATACATACATG
*
5211525 CATACATGCATACAT
1 CATACATACATACAT
5211540 ATATTTCAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
16 44 0.75
18 15 0.25
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (16 bp):
CATACATACATACATG
Found at i:5211479 original size:8 final size:8
Alignment explanation
Indices: 5211468--5211539 Score: 117
Period size: 8 Copynumber: 8.8 Consensus size: 8
5211458 ACATACATAT
5211468 ATACATGC
1 ATACATGC
5211476 ATACATGC
1 ATACATGC
5211484 ATACATGC
1 ATACATGC
5211492 ATATACATGC
1 --ATACATGC
*
5211502 ATACAGGC
1 ATACATGC
5211510 ATACATGC
1 ATACATGC
5211518 ATACATGC
1 ATACATGC
5211526 ATACATGC
1 ATACATGC
5211534 ATACAT
1 ATACAT
5211540 ATATTTCAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
8 52 0.87
10 8 0.13
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (8 bp):
ATACATGC
Found at i:5213086 original size:3 final size:4
Alignment explanation
Indices: 5211719--5214172 Score: 4006
Period size: 4 Copynumber: 627.0 Consensus size: 4
5211709 GGTCCGCCCC
5211719 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5211767 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT- TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5211814 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5211862 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5211910 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5211958 TGTA TGTA TGTA TGTA TGGTA TGTA TGTA TGTA TGTA TGTA GGTA TG-A
1 TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212006 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212054 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212102 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA
*
5212151 TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212197 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5212244 TGTA TG-- TGTA TGTA TGTA TGTA GGTA TGTA TGTA TGTA TGTA TTGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA
* *
5212291 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGGA TGTA TGGGA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA
5212340 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212388 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5212436 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTC TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5212482 GGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5212530 TGTA TGTA TGGA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212576 TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5212623 TGTA TGTC TGTA TGTA TGTA TGTA TGTA TGTA TGT- TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212670 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT-
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212717 TGTA TGTA TGGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TG-A TGTA
1 TGTA TGTA T-GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
5212764 TGTA TGTA TGTA TGTA TGTA GGTA TG-G TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212811 TGTA TGTA TAGGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA T--GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
5212861 TGTA TGTA -GTA TGTA TGTA TGTA TGTA TTTA TGTC TGTA TGTA GTATA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA
5212909 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5212957 TGTA TGTA TGTA TGTA TGTA TGTA T-TA TGTA TGTAA TGTA TGTA TGT-
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT-A TGTA TGTA TGTA
* *
5213004 TGTA TGTA TGTA GGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTG TAGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA
5213051 TGTA TGTA TG-A TGTA -GTA TGTA TGTA TGTA -GTA -GTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213095 TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213139 TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA GGTA --TA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
5213184 TGTA TGTA TGTA TGGA TGTA TGTA TGTA --TA TGTA TGGA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213230 TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213277 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATGA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT-A
*
5213326 TGTA TGT- TGTA TGTA TG-- TGTA TGTA TGTA TGTA TG-- TGTA GGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213369 TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGGA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213414 TGTA TGT- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213461 TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213508 TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA GGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213555 TGTA TGTA TGTA TGGGTA TGTA TGTA GGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA T--GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213605 TGTA TGTA TGT- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213651 TGTA TGTA TGTA -GTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213696 -GTA TG-A TGTA TGTA TGTA TGGTA TGTA TGTA TGTA -GTA TGTA TGTC
1 TGTA TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213742 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGGA TGTA TGTA -GTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213789 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213836 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213884 TGGTA TGTA TGTA TGTA TGT- TGTA TGTA TGTA TGTA TGTA TGTA TG-A
1 T-GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5213931 TGTA TGTAA TGTA TGT- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGT-A TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5213979 TGTA TGTA TGTA TGTA TGTA TGT- TGTA GGTA TGTA TG-- TGTA T-TA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5214023 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5214069 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5214116 TGTA TGTA TGGTA TGTA TGTA -GTA TGTA TGTA GGT- TGTA TGTA TG--
1 TGTA TGTA T-GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5214161 TGTA TGTA TGTA
1 TGTA TGTA TGTA
5214173 AAGGGTTGCA
Statistics
Matches: 2308, Mismatches: 55, Indels: 174
0.91 0.02 0.07
Matches are distributed among these distances:
2 32 0.01
3 115 0.05
4 2105 0.91
5 48 0.02
6 8 0.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:5214462 original size:4 final size:4
Alignment explanation
Indices: 5214443--5214571 Score: 119
Period size: 4 Copynumber: 33.0 Consensus size: 4
5214433 TCCACCCATG
*
5214443 CATA CATA TATA -ATA CATA CATA CATA CTATA -ATA CATA -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA CATA
* *
5214489 TATA CATA CATA CATA CATA CATA CATA CATA C-TA CAT- -ATA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
5214534 CATA TATTGCA CATA -ATA CATA CACA TATA CATA CATA
1 CATA CA-T--A CATA CATA CATA CATA CATA CATA CATA
5214572 TATATATATA
Statistics
Matches: 103, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
2 2 0.02
3 15 0.15
4 79 0.77
5 4 0.04
6 1 0.01
7 2 0.02
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:5214540 original size:12 final size:12
Alignment explanation
Indices: 5214443--5214662 Score: 126
Period size: 12 Copynumber: 18.0 Consensus size: 12
5214433 TCCACCCATG
5214443 CATACATATATA
1 CATACATATATA
*
5214455 -ATACATACATA
1 CATACATATATA
5214466 CATAC-TATAATA
1 CATACATAT-ATA
5214478 CATAATACATATATA
1 C---ATACATATATA
*
5214493 CATACATACATA
1 CATACATATATA
*
5214505 CATACATACATA
1 CATACATATATA
*
5214517 CATACTACATATA
1 CATAC-ATATATA
* *
5214530 CAGACATATATTG
1 CATACATATA-TA
5214543 C--ACATA-ATA
1 CATACATATATA
*
5214552 CATACACATATA
1 CATACATATATA
5214564 CATACATATATA
1 CATACATATATA
* * *
5214576 TATATATCTATA
1 CATACATATATA
* *
5214588 TATATTATATATA
1 CATA-CATATATA
* *
5214601 TATATATATATA
1 CATACATATATA
* *
5214613 TATATATATATA
1 CATACATATATA
* *
5214625 TATATTATATATA
1 CATA-CATATATA
* *
5214638 TATATATTATATA
1 CATACA-TATATA
* *
5214651 TATATATATATA
1 CATACATATATA
5214663 GAATATATAA
Statistics
Matches: 179, Mismatches: 15, Indels: 28
0.81 0.07 0.13
Matches are distributed among these distances:
9 2 0.01
10 1 0.01
11 21 0.12
12 98 0.55
13 46 0.26
15 8 0.04
16 3 0.02
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (12 bp):
CATACATATATA
Found at i:5214576 original size:2 final size:2
Alignment explanation
Indices: 5214559--5214671 Score: 162
Period size: 2 Copynumber: 58.5 Consensus size: 2
5214549 ATACATACAC
* * *
5214559 AT AT AC AT AC AT AT AT AT AT AT AT CT AT AT AT AT -T 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
5214600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
*
5214641 AT AT -T AT AT AT AT AT AT AT AT AG A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5214672 ATAAATATTT
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
1 4 0.04
2 96 0.96
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5215951 original size:16 final size:16
Alignment explanation
Indices: 5215926--5215956 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5215916 TTTGATGAGT
*
5215926 TTAACTAACAACAAGC
1 TTAACGAACAACAAGC
5215942 TTAACGAACAACAAG
1 TTAACGAACAACAAG
5215957 TTTCAAGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.16
Consensus pattern (16 bp):
TTAACGAACAACAAGC
Found at i:5217275 original size:64 final size:64
Alignment explanation
Indices: 5217144--5217298 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
5217134 TACACTTGGG
* * * * * **
5217144 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAGAGCCAGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAAACCAGGAGTGCATCGATACATGGAAT
* *
5217208 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAATCATGAGTGCATCGATACAT-GAAT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAA-AAAACCAGGAGTGCATCGATACATGGAAT
* * *
5217272 GTGCATCGTTACACAAAATGTATTCGA
1 GTGCATCGGTACATAAAATGCATTCGA
5217299 ATTAGGTTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 57 0.74
65 19 0.25
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAAAACCAGGAGTGCATCGATACATGGAAT
Found at i:5217946 original size:21 final size:23
Alignment explanation
Indices: 5217910--5217952 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5217900 GCACCGTAAT
5217910 ACCACATAGAATGTCCC-AAATG
1 ACCACATAGAATGTCCCGAAATG
5217932 ACCACATAG-ATGTCCCGAAAT
1 ACCACATAGAATGTCCCGAAAT
5217953 ACCGCGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (23 bp):
ACCACATAGAATGTCCCGAAATG
Found at i:5218824 original size:3 final size:3
Alignment explanation
Indices: 5218816--5218863 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5218806 CTCAAGGGGA
5218816 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5218864 CTAGACTTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5221079 original size:22 final size:22
Alignment explanation
Indices: 5221050--5221163 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 22
5221040 CACCGTAGTG
5221050 CCACATAGAATGTCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
5221072 CCATATAG-ATGTCCCCAAAGGA
1 CCACATAGAATGT-CCCGAAGGA
* * * *
5221094 CCGCGTAGAAATTATCCCGAAAGA
1 CCACATAG-AA-TGTCCCGAAGGA
5221118 -CATCATAGAATTGTCCCGAAGGA
1 CCA-CATAGAA-TGTCCCGAAGGA
* *
5221141 CCACATA-TATATCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
5221162 CC
1 CC
5221164 GCGTAGAACC
Statistics
Matches: 72, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
21 17 0.24
22 21 0.29
23 18 0.25
24 14 0.19
25 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:5221084 original size:21 final size:21
Alignment explanation
Indices: 5221054--5221163 Score: 60
Period size: 21 Copynumber: 4.9 Consensus size: 21
5221044 GTAGTGCCAC
5221054 ATAGAATGTCCCGAAGGACCAT
1 ATAG-ATGTCCCGAAGGACCAT
* *
5221076 ATAGATGTCCCCAAAGGACCGCGT
1 ATAGATGT-CCCGAAGGA-C-CAT
* * * *
5221100 AGAAATTATCCCGAAAGA-CAT
1 ATAGA-TGTCCCGAAGGACCAT
*
5221121 CATAGAATTGTCCCGAAGGACCAC
1 -ATAG-A-TGTCCCGAAGGACCAT
* *
5221145 ATATATATCCCGAAGGACC
1 ATAGATGTCCCGAAGGACC
5221164 GCGTAGAACC
Statistics
Matches: 66, Mismatches: 15, Indels: 15
0.69 0.16 0.16
Matches are distributed among these distances:
21 19 0.29
22 15 0.23
23 16 0.24
24 14 0.21
25 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
ATAGATGTCCCGAAGGACCAT
Found at i:5222136 original size:20 final size:20
Alignment explanation
Indices: 5222111--5222159 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5222101 TTACCTTATG
*
5222111 GTATCGATATTGTTCATCTA
1 GTATCGATAGTGTTCATCTA
5222131 GTATCGATAGTGTTCATCTA
1 GTATCGATAGTGTTCATCTA
5222151 GTATCGATA
1 GTATCGATA
5222160 CTCAGACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
GTATCGATAGTGTTCATCTA
Found at i:5228794 original size:2 final size:2
Alignment explanation
Indices: 5228787--5228868 Score: 155
Period size: 2 Copynumber: 40.5 Consensus size: 2
5228777 AGCGACCAAC
5228787 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
5228829 AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5228869 AAATGGCTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 77 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5235887 original size:36 final size:36
Alignment explanation
Indices: 5235840--5235915 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
5235830 CATGCACTAA
*
5235840 GACCACCACTGGTTTCGTCGGTTTGTCCAAATGGGT
1 GACCACCACTGGTTTCGTCGGTTTCTCCAAATGGGT
*
5235876 GACCACCACTGGTTTTGTCGGTTTCTCCAAATGGGT
1 GACCACCACTGGTTTCGTCGGTTTCTCCAAATGGGT
5235912 GACC
1 GACC
5235916 TTTTTTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (36 bp):
GACCACCACTGGTTTCGTCGGTTTCTCCAAATGGGT
Found at i:5239004 original size:25 final size:23
Alignment explanation
Indices: 5238953--5239013 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 23
5238943 TTTGTATTTT
* * *
5238953 TGGCACATATTCTTTTGCCTTTC
1 TGGCACATTTTTTTTTGCCTTTA
*
5238976 TGGCACGTATTTTTTTTTGCTTTTA
1 TGGCAC--ATTTTTTTTTGCCTTTA
5239001 TGGCACATTTTTT
1 TGGCACATTTTTT
5239014 CTATGCCGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 13 0.41
25 19 0.59
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (23 bp):
TGGCACATTTTTTTTTGCCTTTA
Found at i:5239010 original size:23 final size:22
Alignment explanation
Indices: 5238949--5239013 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
5238939 TAATTTTGTA
* *
5238949 TTTTTGGCACATATTCTTTTGCC
1 TTTTTGGCACATTTTTTTTTG-C
*
5238972 TTTCTGGCACGTATTTTTTTTTGC
1 TTTTTGGCAC--ATTTTTTTTTGC
5238996 TTTTATGGCACATTTTTT
1 TTTT-TGGCACATTTTTT
5239014 CTATGCCGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.46
24 4 0.11
25 15 0.43
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTTTGGCACATTTTTTTTTGC
Found at i:5239574 original size:65 final size:66
Alignment explanation
Indices: 5239482--5239622 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 66
5239472 AGCGGTTTTT
* * * * * *
5239482 ATAAAAAA-ATT-TTAAATTATACTAATTATTTATCAAAATAAGTATATTA-TATTATATTATTA
1 ATAAAAAATATTATT-AGTTATACTAATTACTCATCAAAATAAGAATATTATTATAATAATATTA
5239544 AA
65 AA
* * *
5239546 ATAATAAATATTATTAGTTATATTAATTACTCATTAAAATAAGAATATTATTATAATAATATTAA
1 ATAAAAAATATTATTAGTTATACTAATTACTCATCAAAATAAGAATATTATTATAATAATATTAA
5239611 A
66 A
5239612 ATAAAAAATAT
1 ATAAAAAATAT
5239623 CATATTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 7 0.11
65 32 0.50
66 25 0.39
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (66 bp):
ATAAAAAATATTATTAGTTATACTAATTACTCATCAAAATAAGAATATTATTATAATAATATTAA
A
Found at i:5239801 original size:10 final size:10
Alignment explanation
Indices: 5239786--5239826 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
5239776 TATTAATAAT
5239786 TTATTATATA
1 TTATTATATA
5239796 TTATTAAAATATA
1 TTATT---ATATA
5239809 TTATTATATA
1 TTATTATATA
5239819 TTATTATA
1 TTATTATA
5239827 AAATAGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTATTATATA
Found at i:5239809 original size:13 final size:13
Alignment explanation
Indices: 5239791--5239831 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5239781 ATAATTTATT
5239791 ATATATTATTAAA
1 ATATATTATTAAA
*
5239804 ATATATTATT-AT
1 ATATATTATTAAA
5239816 ATATTATTA-TAAA
1 ATA-TATTATTAAA
5239829 ATA
1 ATA
5239832 GCTTAGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATTATTAAA
Found at i:5239828 original size:25 final size:24
Alignment explanation
Indices: 5239786--5239867 Score: 85
Period size: 25 Copynumber: 3.4 Consensus size: 24
5239776 TATTAATAAT
5239786 TTATTATATATTAT-TAAAATATA
1 TTATTATATATTATATAAAATATA
**
5239809 TTATTATATATTATTATAAAATAGC
1 TTATTATATATTA-TATAAAATATA
* * *
5239834 TTAGTATATCTAATATTAAAATATA
1 TTATTATATATTATA-TAAAATATA
*
5239859 ATATTATAT
1 TTATTATAT
5239868 TATAACTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 13 0.28
24 3 0.06
25 31 0.66
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATTATATATTATATAAAATATA
Found at i:5240293 original size:25 final size:25
Alignment explanation
Indices: 5240265--5240357 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 25
5240255 ATTAATAATT
5240265 TATTATATATTATTAAAAAATATAA
1 TATTATATATTATTAAAAAATATAA
* *
5240290 TATTATATATTATTATAAAATA-ACT
1 TATTATATATTATTAAAAAATATA-A
*
5240315 TAGTATATCATTATAATATTAAAAATATAA
1 TATTATAT-ATTAT--TA--AAAAATATAA
5240345 TATTATATTATTA
1 TATTATA-TATTA
5240358 AACTTATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
24 1 0.02
25 28 0.52
26 5 0.09
28 2 0.04
30 16 0.30
31 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTATATATTATTAAAAAATATAA
Found at i:5240429 original size:12 final size:12
Alignment explanation
Indices: 5240368--5240429 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
5240358 AACTTATTTA
*
5240368 TAAATA-TATTT
1 TAAATATTATAT
* *
5240379 TAAATATTTTAA
1 TAAATATTATAT
* *
5240391 TAATTATTTTAT
1 TAAATATTATAT
5240403 TAAA-ATTATATT
1 TAAATATTATA-T
5240415 TAAATATTATAT
1 TAAATATTATAT
5240427 TAA
1 TAA
5240430 TACTAAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
11 11 0.27
12 24 0.59
13 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:5242322 original size:2 final size:2
Alignment explanation
Indices: 5242315--5242346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5242305 GCACCTCAAC
5242315 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
5242347 TGAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5247471 original size:2 final size:2
Alignment explanation
Indices: 5247464--5247502 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5247454 CAATTTTGTA
5247464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5247503 AATTTTATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5251041 original size:16 final size:16
Alignment explanation
Indices: 5251020--5251062 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
5251010 ACATAACCTC
5251020 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
5251036 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
5251052 TGAATCATTCA
1 TGAATCATTCA
5251063 ACGCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:5254301 original size:12 final size:12
Alignment explanation
Indices: 5254284--5254312 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5254274 AGTATATAAT
5254284 CTATGTGAAATG
1 CTATGTGAAATG
5254296 CTATGTGAAATG
1 CTATGTGAAATG
5254308 CTATG
1 CTATG
5254313 AGTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (12 bp):
CTATGTGAAATG
Found at i:5254416 original size:57 final size:59
Alignment explanation
Indices: 5254296--5254423 Score: 170
Period size: 57 Copynumber: 2.2 Consensus size: 59
5254286 ATGTGAAATG
* * * * *
5254296 CTATGTGAAATGCTATGAGTATATATATTCTATGTAAATAAATGATAATTTGAGTAATG
1 CTATGTGAAATACTATGAGTATATATATTATATGTAAATAAATGATAATTTAAATAATA
* * *
5254355 CTATGTGAAATACTATGAGTA-AT-TGTTATATGTGAATAAATGGTAATTTAAATAATA
1 CTATGTGAAATACTATGAGTATATATATTATATGTAAATAAATGATAATTTAAATAATA
5254412 CTATGTGAAATA
1 CTATGTGAAATA
5254424 ATTATATGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 39 0.64
58 2 0.03
59 20 0.33
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (59 bp):
CTATGTGAAATACTATGAGTATATATATTATATGTAAATAAATGATAATTTAAATAATA
Found at i:5254530 original size:23 final size:23
Alignment explanation
Indices: 5254504--5254580 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
5254494 TTCTACGCGA
5254504 TCCTTCGGGATAATTCTATGTGG
1 TCCTTCGGGATAATTCTATGTGG
* **
5254527 TCCTTCGAGATAATTCTACCTGG
1 TCCTTCGGGATAATTCTATGTGG
*
5254550 TCCTTCGGGGA-AAATCTATGTGG
1 TCCTTC-GGGATAATTCTATGTGG
5254573 -CACTTCGG
1 TC-CTTCGG
5254581 TGTATATTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.07
23 39 0.87
24 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (23 bp):
TCCTTCGGGATAATTCTATGTGG
Found at i:5254596 original size:24 final size:24
Alignment explanation
Indices: 5254538--5254617 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
5254528 CCTTCGAGAT
* *
5254538 AATTCTACCTGGTC-CTTCGG-GGA
1 AATTCTACGTGG-CACTTCGGTGCA
* * *
5254561 AAATCTATGTGGCACTTCGGTGTA
1 AATTCTACGTGGCACTTCGGTGCA
*
5254585 TATTCTACGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
5254609 AATTCTACG
1 AATTCTACG
5254618 CTGCATTTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.02
23 15 0.33
24 30 0.65
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTGCA
Found at i:5259458 original size:14 final size:14
Alignment explanation
Indices: 5259439--5259465 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5259429 TGTTAAGGTG
5259439 AGTAAAATTTAAGA
1 AGTAAAATTTAAGA
5259453 AGTAAAATTTAAG
1 AGTAAAATTTAAG
5259466 TAGATTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
AGTAAAATTTAAGA
Found at i:5260313 original size:27 final size:29
Alignment explanation
Indices: 5260275--5260329 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 29
5260265 TTGATTCCAT
5260275 TGCTATGAGTATATA-A-TCTATGTAAAA
1 TGCTATGAGTATATATATTCTATGTAAAA
5260302 TGCTATGAGTATATATATTCTATGTAAA
1 TGCTATGAGTATATATATTCTATGTAAA
5260330 CAAATGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 15 0.58
28 1 0.04
29 10 0.38
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (29 bp):
TGCTATGAGTATATATATTCTATGTAAAA
Found at i:5260415 original size:57 final size:58
Alignment explanation
Indices: 5260287--5260417 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 58
5260277 CTATGAGTAT
* * *
5260287 ATAATCTATGTAAAATGCTATGAGTATATATATTCTATGTAAACAAATGATAATTTGA
1 ATAATCTATGTGAAATGCTATGAGTATATATATTATATGTAAACAAATGATAATTTAA
* * * * * * *
5260345 GTAATGTTGTGTGAAATGTTATGAGTA-ATA-ATTATATGTGAATAAATGGTAATTTAA
1 ATAAT-CTATGTGAAATGCTATGAGTATATATATTATATGTAAACAAATGATAATTTAA
5260402 ATAATACTATGTGAAA
1 ATAAT-CTATGTGAAA
5260418 AAATTATATG
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
57 34 0.59
58 7 0.12
59 17 0.29
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (58 bp):
ATAATCTATGTGAAATGCTATGAGTATATATATTATATGTAAACAAATGATAATTTAA
Found at i:5260644 original size:23 final size:23
Alignment explanation
Indices: 5260491--5260633 Score: 232
Period size: 23 Copynumber: 6.2 Consensus size: 23
5260481 GAGTCGAGGG
* *
5260491 TTCTACGCGGTCATTCGAGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * *
5260514 TTCTATGTGGTCATTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
5260537 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
5260560 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
5260583 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
5260606 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
*
5260629 ATCTA
1 TTCTA
5260634 TGTGGCACTT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 113 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.28
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:5260679 original size:24 final size:24
Alignment explanation
Indices: 5260626--5260688 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
5260616 TCCTTCGGGA
*
5260626 CAAA-TCTATGTGGCACTTCAGTG
1 CAAATTCTACGTGGCACTTCAGTG
* *
5260649 CATATTCTACGTGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCAGTG
* *
5260673 TAAATTCTACGCGGCA
1 CAAATTCTACGTGGCA
5260689 GTTTCGACTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 3 0.09
24 30 0.91
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCAGTG
Found at i:5270390 original size:29 final size:29
Alignment explanation
Indices: 5270358--5270413 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
5270348 ATTAATTCTT
5270358 AAACTTTTGAACA-TTCTAATTTCATCCCC
1 AAACTTTTGAACATTTC-AATTTCATCCCC
*
5270387 AAACTTTTGAATATTTCAATTTCATCC
1 AAACTTTTGAACATTTCAATTTCATCC
5270414 AAATATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
AAACTTTTGAACATTTCAATTTCATCCCC
Found at i:5270651 original size:60 final size:59
Alignment explanation
Indices: 5270571--5270682 Score: 179
Period size: 60 Copynumber: 1.9 Consensus size: 59
5270561 TTGGGGGACC
*
5270571 AATTTAGAATGAATGTCATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTGAAGACT
1 AATTTAGAATGAATATCATAGTTTAGGGATGAAATTAAAATATT-AAAAGTTTGAAGACT
* * *
5270631 AATTTAGAATTATTATCATAGTTTTGGGATGAAATTAAAATATTAAAAGTTT
1 AATTTAGAATGAATATCATAGTTTAGGGATGAAATTAAAATATTAAAAGTTT
5270683 AAGGATGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 8 0.17
60 40 0.83
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (59 bp):
AATTTAGAATGAATATCATAGTTTAGGGATGAAATTAAAATATTAAAAGTTTGAAGACT
Found at i:5271935 original size:30 final size:29
Alignment explanation
Indices: 5271901--5272000 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 29
5271891 ACATTAACAT
*
5271901 AAACTTAAAGGAATAAAATAGCAAAAATAG
1 AAACTTAAAGGACTAAAATAGC-AAAATAG
*
5271931 AAACTTAAAGGACTAAAATAGCCAAAACA-
1 AAACTTAAAGGACTAAAATAG-CAAAATAG
* *
5271960 AAATGTTAAAGGACTAAAATAGCAAACTAG
1 AAA-CTTAAAGGACTAAAATAGCAAAATAG
*
5271990 AAAGTTAAAGG
1 AAACTTAAAGG
5272001 GATGAACTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 16 0.26
30 45 0.73
31 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (29 bp):
AAACTTAAAGGACTAAAATAGCAAAATAG
Found at i:5273291 original size:3 final size:3
Alignment explanation
Indices: 5273276--5273319 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
5273266 ATGTAAATTT
* *
5273276 ATA ATA TTA ATA ATA ATA ACA ATA ATA ATA ATA ATTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA A
5273320 ACTAATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5273325 original size:15 final size:14
Alignment explanation
Indices: 5273286--5273330 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
5273276 ATAATATTAA
5273286 TAATAATAAC-AA-
1 TAATAATAACTAAT
5273298 TAATAATAA-TAAT
1 TAATAATAACTAAT
5273311 TAATAATAAACTAAT
1 TAATAAT-AACTAAT
5273326 TAATA
1 TAATA
5273331 TATATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 2 0.07
15 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAATAACTAAT
Found at i:5273329 original size:19 final size:16
Alignment explanation
Indices: 5273283--5273340 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 16
5273273 TTTATAATAT
*
5273283 TAATAATAATAA-CAA
1 TAATAATAATAATTAA
5273298 TAATAATAATAATTAA
1 TAATAATAATAATTAA
*
5273314 TAATAA-ACTAATTAA
1 TAATAATAATAATTAA
*
5273329 TATATATTAATA
1 TA-ATAATAATA
5273341 TTTTTGTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 22 0.61
16 11 0.31
17 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAATAATAATTAA
Found at i:5273329 original size:25 final size:25
Alignment explanation
Indices: 5273288--5273340 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
5273278 AATATTAATA
5273288 ATAATAACAATAATAATAATAATTA
1 ATAATAACAATAATAATAATAATTA
*
5273313 ATAATAA-ACTAATTAAT-ATATATTA
1 ATAATAACAATAA-TAATAATA-ATTA
5273338 ATA
1 ATA
5273341 TTTTTGTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAATAACAATAATAATAATAATTA
Found at i:5273647 original size:39 final size:40
Alignment explanation
Indices: 5273545--5273647 Score: 95
Period size: 43 Copynumber: 2.5 Consensus size: 40
5273535 AGGGGTGATA
*
5273545 ACACGGTTCCTATGCGATGAGGATGGCTGGTTATCTAGGGGTG
1 ACACGGTTCCTACGCGATGAGGATGGCTGG-T-TC-AGGGGTG
* * **
5273588 AAACGGCTCCTACATGATGAGG-TGGTCTGG-TC-GGGGATG
1 ACACGGTTCCTACGCGATGAGGATGG-CTGGTTCAGGGG-TG
5273627 ACACGGTTCCTACGCGATGAG
1 ACACGGTTCCTACGCGATGAG
5273648 AATGACAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
38 4 0.08
39 19 0.39
40 2 0.04
42 3 0.06
43 21 0.43
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.24
Consensus pattern (40 bp):
ACACGGTTCCTACGCGATGAGGATGGCTGGTTCAGGGGTG
Found at i:5274076 original size:133 final size:131
Alignment explanation
Indices: 5273706--5274086 Score: 494
Period size: 132 Copynumber: 2.9 Consensus size: 131
5273696 GATGACACGT
* *
5273706 CTCCTACGTGATGAGGAGATATGGTCGAGGGATGACACAACTCATACGTGATGAAGAGTTCTGGT
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACGTGATGAAGAGTTCTGGT
* * * * ** *
5273771 CATCTTTAAGAATGGTGATAACACGGTTCCTACGCGATGGGGATGACTGATTATCAGGGTGACAC
66 CATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGA-GGTTGGTTATCAGGGTGACAC
**
5273836 GG
130 AA
* *
5273838 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGC
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACGTGATGAAGAGTTCTGGT
* * *
5273903 CATCTTTAGGGAGGGTGATAACACGGTTCCTACACAATGAGGACGGTTGGTTATCAAGGTTGACA
66 CATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGA-GGTTGGTTATC-AGGGTGACA
5273968 CAA
129 CAA
* * **
5273971 CTCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACAACTCATAAC-TGATGAAGAGTTCTTA
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCAT-ACGTGATGAAGAGTTCTGG
* ** *
5274035 TCATCTTTAGGGAGGGTGATAGCATAGTTCCTACGTGATGAGGAGGTCTGGT
65 TCATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGAGGT-TGGT
5274087 CGGGGGATGA
Statistics
Matches: 217, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
132 109 0.50
133 106 0.49
134 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (131 bp):
CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACGTGATGAAGAGTTCTGGT
CATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGAGGTTGGTTATCAGGGTGACACA
A
Found at i:5274488 original size:33 final size:33
Alignment explanation
Indices: 5274441--5274506 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
5274431 GTTGAATCCC
5274441 CAAAAATGCTCCAATATTCGATATTGATTGCTT
1 CAAAAATGCTCCAATATTCGATATTGATTGCTT
* *
5274474 CAAAGATGCTCCAATATTCGATGTTGATTGCTT
1 CAAAAATGCTCCAATATTCGATATTGATTGCTT
5274507 TAACATTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
CAAAAATGCTCCAATATTCGATATTGATTGCTT
Found at i:5275576 original size:11 final size:11
Alignment explanation
Indices: 5275552--5275647 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
5275542 TCTTGTCTTC
5275552 TTTTTCTTTGT
1 TTTTTCTTTGT
*
5275563 TTTTTGTTT-T
1 TTTTTCTTTGT
*
5275573 TTTTTCTTTGC
1 TTTTTCTTTGT
* *
5275584 TCTTTCATTTGC
1 TTTTTC-TTTGT
*
5275596 TTTTTCTTTGCCC
1 TTTTTCTTTG--T
*
5275609 TTTTTCCTTGAT
1 TTTTTCTTTG-T
* *
5275621 TTTTTCCTTAT
1 TTTTTCTTTGT
**
5275632 TTACTCTTTGT
1 TTTTTCTTTGT
5275643 TTTTT
1 TTTTT
5275648 TCCCTTTTCT
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
10 9 0.14
11 28 0.42
12 19 0.29
13 10 0.15
ACGTcount: A:0.04, C:0.17, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTCTTTGT
Found at i:5284159 original size:20 final size:20
Alignment explanation
Indices: 5284134--5284214 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
5284124 TATTTGGAAG
* *
5284134 AGGGAATCGATACCCCCATA
1 AGGGAACCGATACCCCCTTA
*
5284154 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATACCCCC-TT-A
*
5284176 ATGGGAACCGATTCCCTCCTTA
1 A-GGGAACCGATACCC-CCTTA
* *
5284198 GGGGAATCGATACCCCC
1 AGGGAACCGATACCCCC
5284215 CACGGGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 17 0.33
21 13 0.25
22 3 0.06
23 16 0.31
24 2 0.04
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (20 bp):
AGGGAACCGATACCCCCTTA
Found at i:5284202 original size:21 final size:22
Alignment explanation
Indices: 5284155--5284214 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
5284145 ACCCCCATAA
*
5284155 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTT-AAG
5284178 GGGAACCGATTCCCTCC-TT-AG
1 GGGAACCGATTCCC-CCTTTAAG
* *
5284199 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
5284215 CACGGGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
23 16 0.48
24 2 0.06
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTTAAG
Found at i:5288139 original size:29 final size:29
Alignment explanation
Indices: 5288044--5288144 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
5288034 GACATTAACG
* *
5288044 GAAACTTAAAGGAATAAATTAG-AAATATCA
1 GAAACTTAAAGGACTAAAATAGCAAA-A-CA
* *
5288074 GAAACTTAAAGGACAAAAATAGCCAAAATA
1 GAAACTTAAAGGACTAAAATAG-CAAAACA
* *
5288104 TAAAGTTAAAGGACTAAAATAGCAAAACA
1 GAAACTTAAAGGACTAAAATAGCAAAACA
*
5288133 GAAAGTTAAAGG
1 GAAACTTAAAGG
5288145 GATGAACTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 17 0.28
30 39 0.65
31 1 0.02
32 3 0.05
ACGTcount: A:0.57, C:0.09, G:0.16, T:0.18
Consensus pattern (29 bp):
GAAACTTAAAGGACTAAAATAGCAAAACA
Found at i:5289405 original size:3 final size:3
Alignment explanation
Indices: 5289397--5289454 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
5289387 AAATATATAG
* *
5289397 TAA TAA TAA TAA TAA CAA CAA TAA TAA TAA TTAA TAA -AA TAA TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-AA
*
5289443 TATA TAT TAA TA
1 TA-A TAA TAA TA
5289455 TTTTTGTAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 2 0.04
3 36 0.77
4 9 0.19
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5299309 original size:16 final size:16
Alignment explanation
Indices: 5299288--5299321 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5299278 TTTTTGTTCC
*
5299288 CGTAAACGAGTCTAGT
1 CGTAAACGAGTCGAGT
5299304 CGTAAACGAGTCGAGT
1 CGTAAACGAGTCGAGT
5299320 CG
1 CG
5299322 AACTCGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (16 bp):
CGTAAACGAGTCGAGT
Found at i:5306837 original size:23 final size:23
Alignment explanation
Indices: 5306803--5306871 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
5306793 CACCACAGCT
*
5306803 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
5306826 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
5306849 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
5306872 TATAATAATG
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:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:5310340 original size:12 final size:13
Alignment explanation
Indices: 5310307--5310344 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
5310297 ACATAATATG
5310307 ATTTTTTC-AAAT
1 ATTTTTTCAAAAT
5310319 ATTGTTTTCAAAAT
1 ATT-TTTTCAAAAT
5310333 A-TTTTTCAAAAT
1 ATTTTTTCAAAAT
5310345 TTTCCCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.54
13 6 0.25
14 5 0.21
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTTTTTCAAAAT
Found at i:5311855 original size:19 final size:21
Alignment explanation
Indices: 5311824--5311867 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
5311814 ATATATATAT
*
5311824 ATTTGGTTTTGATT-GTTTGA
1 ATTTGGTTTTGATTAGTTTAA
5311844 ATTTGG-TTTGATTAGTTTAA
1 ATTTGGTTTTGATTAGTTTAA
5311864 ATTT
1 ATTT
5311868 ATATTGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
ATTTGGTTTTGATTAGTTTAA
Found at i:5320087 original size:24 final size:24
Alignment explanation
Indices: 5320055--5320118 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
5320045 CCATTAAATG
5320055 GTATCGATACTACTCTATATAGTA
1 GTATCGATACTACTCTATATAGTA
5320079 GTATCGATACTACTCTATATAGTA
1 GTATCGATACTACTCTATATAGTA
*
5320103 GTATCGATACTCCTCT
1 GTATCGATACTACTCT
5320119 GACAGTATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (24 bp):
GTATCGATACTACTCTATATAGTA
Found at i:5330659 original size:18 final size:18
Alignment explanation
Indices: 5330638--5330672 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5330628 AGGGATTATC
5330638 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
5330656 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5330673 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5332714 original size:408 final size:406
Alignment explanation
Indices: 5331907--5332722 Score: 1350
Period size: 408 Copynumber: 2.0 Consensus size: 406
5331897 GGATTTGTGG
* **
5331907 AAGCTCGAATCGACAATCGAAGGGGTGCGCCAAGAGGGGTTGAGTCAGTTCTTGTGTTTAGGGAG
1 AAGCTCGAATCGACAACCGAAGGGGAACGCCAAGAGGGGTTGAGTCAGTTCTTGTGTTTAGGGAG
5331972 TAAGGAGATTGAAAGATAGAAAATTTGCACAGCGATTTATAGTGGTTCGACTTCTCAACCAAGTC
66 TAAGGAGATTGAAAGATAGAAAATTTGCACAGCGATTTATAGTGGTTCGACTTCTCAACCAAGTC
* *
5332037 TACATCCACTACCTTATCTCTTCACCAAGGATGTTCCAACAAATTCACTAATTTTTTTTTCTTTT
131 TACATCCACAACCTTAGCTCTTCACCAAGGATGTTCCAACAAATTCACTAATTTTTTTTTCTTTT
*
5332102 TAAGGACAAAGAGATAATCTTTACAAACTCCCTAGTTTTTCACGGGCTAAACTAGAACCTTTCCC
196 TAAGGACAAAGAGATAACCTTTACAAACTCCCTAGTTTTTCACGGGCTAAACTAGAACCTTTCCC
* *
5332167 TAGCTTTTCACGGGCTCAGATAGAACCAAAACCCCTTTACAATGGAAGGAAATGTAAACAAGAAA
261 TAGCTTTTCACGGGCTCAGATAGAACCAAAACCCCTTTACAATGAAAGGAAATATAAACAAGAAA
* *
5332232 ACCTTTCTAAGGTAGGTGTTTACAAGAATTAAGCTCACAAGAATAAAAATATTTACAAGAGAAAG
326 ACCTCTCTAAGGTAGGTGTTTACAAGAATTAAGCTCACAAGAACAAAAATATTTACAAGAGAAAG
*
5332297 ATGAAATAAGAATGAA
391 ATAAAATAAGAATGAA
*
5332313 AAGCTCGAATCGATAACCGAAGGGGAACGCCAAGAGGGGTTGAGTCA-TTCTTGTGTTTAGGGAG
1 AAGCTCGAATCGACAACCGAAGGGGAACGCCAAGAGGGGTTGAGTCAGTTCTTGTGTTTAGGGAG
* *
5332377 TAAGGAGATTGAAAGATAGAAAATTTTCACAGCGATTTATAGTGGTTTGACTTCTCAACCAAGTC
66 TAAGGAGATTGAAAGATAGAAAATTTGCACAGCGATTTATAGTGGTTCGACTTCTCAACCAAGTC
* * * *
5332442 TACATCCACAACCTTCGCTCCTT-ACCAAGGATTTTCCAATAAATTCACTAATTTGTTCTTTTTT
131 TACATCCACAACCTTAGCT-CTTCACCAAGGATGTTCCAACAAATTCACTAATTT-TT-TTTTCT
*
5332506 TTTTCATA-GACAAAGAGATAACCTTTACAAACTCCCTAGTTTTTCACTGGCTAAACTAGAACCT
193 TTTT-A-AGGACAAAGAGATAACCTTTACAAACTCCCTAGTTTTTCACGGGCTAAACTAGAACCT
* * *
5332570 TTCCCTAGCTTTTTAGGGGCTCAGCTAGAACCAAAACCCCTTTACAATGAAAGGAAATATAAACA
256 TTCCCTAGCTTTTCACGGGCTCAGATAGAACCAAAACCCCTTTACAATGAAAGGAAATATAAACA
* *
5332635 AGAAAACCTCTCTAATGTATGTGTTTACAAGAATTAAGCTCACAAGAACAAAAATATTTACAAGA
321 AGAAAACCTCTCTAAGGTAGGTGTTTACAAGAATTAAGCTCACAAGAACAAAAATATTTACAAGA
5332700 GAAAGATAAAATAAGAATGAA
386 GAAAGATAAAATAAGAATGAA
5332721 AA
1 AA
5332723 ACTCTTCTCT
Statistics
Matches: 381, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
405 125 0.33
406 48 0.13
407 9 0.02
408 198 0.52
409 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (406 bp):
AAGCTCGAATCGACAACCGAAGGGGAACGCCAAGAGGGGTTGAGTCAGTTCTTGTGTTTAGGGAG
TAAGGAGATTGAAAGATAGAAAATTTGCACAGCGATTTATAGTGGTTCGACTTCTCAACCAAGTC
TACATCCACAACCTTAGCTCTTCACCAAGGATGTTCCAACAAATTCACTAATTTTTTTTTCTTTT
TAAGGACAAAGAGATAACCTTTACAAACTCCCTAGTTTTTCACGGGCTAAACTAGAACCTTTCCC
TAGCTTTTCACGGGCTCAGATAGAACCAAAACCCCTTTACAATGAAAGGAAATATAAACAAGAAA
ACCTCTCTAAGGTAGGTGTTTACAAGAATTAAGCTCACAAGAACAAAAATATTTACAAGAGAAAG
ATAAAATAAGAATGAA
Found at i:5333591 original size:12 final size:12
Alignment explanation
Indices: 5333574--5333599 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5333564 ATAAATTTAA
5333574 CATTTGAAAAAT
1 CATTTGAAAAAT
5333586 CATTTGAAAAAT
1 CATTTGAAAAAT
5333598 CA
1 CA
5333600 AAGCTCCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (12 bp):
CATTTGAAAAAT
Found at i:5336769 original size:2 final size:2
Alignment explanation
Indices: 5336656--5336755 Score: 191
Period size: 2 Copynumber: 49.5 Consensus size: 2
5336646 CACATATGCA
5336656 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
5336698 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
5336740 AT AT AT AT CAT AT AT A
1 AT AT AT AT -AT AT AT A
5336756 AAACATACAT
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 95 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5337093 original size:23 final size:23
Alignment explanation
Indices: 5337067--5337135 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
5337057 CACCACAGCT
*
5337067 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
5337090 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
5337113 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
5337136 TATAAGGTTG
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:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:5342246 original size:42 final size:41
Alignment explanation
Indices: 5342174--5342253 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
5342164 AATTTAAGAT
*
5342174 TTAACCATTGTATTTCAATTCAACACAATTTGATTCTTTTTC
1 TTAACCATTGCATTTCAATTCAACACAATTTGA-TCTTTTTC
* * * *
5342216 TTAATCATTGCATTTCAGTTTAACATAATTTGATCTTT
1 TTAACCATTGCATTTCAATTCAACACAATTTGATCTTT
5342254 CTGTCTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 5 0.15
42 28 0.85
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (41 bp):
TTAACCATTGCATTTCAATTCAACACAATTTGATCTTTTTC
Found at i:5342318 original size:32 final size:32
Alignment explanation
Indices: 5342281--5342344 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5342271 ATAGTTAGTC
5342281 AAAATTATTAACACCATTAATTACCCTAGTTA
1 AAAATTATTAACACCATTAATTACCCTAGTTA
*
5342313 AAAATTATTAACACCATTAATTATCCTAGTTA
1 AAAATTATTAACACCATTAATTACCCTAGTTA
5342345 GAACGAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (32 bp):
AAAATTATTAACACCATTAATTACCCTAGTTA
Found at i:5342867 original size:20 final size:20
Alignment explanation
Indices: 5342844--5342909 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
5342834 AATCTGTAAA
5342844 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
5342864 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
5342884 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
5342904 TCGCAA
1 TCGCAA
5342910 TGCGGAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 2 0.05
20 38 0.93
21 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:5342888 original size:40 final size:40
Alignment explanation
Indices: 5342819--5342931 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 40
5342809 ACACAGTTTC
* *
5342819 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACAAAAGT
5342859 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* *
5342899 CAAATTCGCAATGCGGA-ATTTCAAATTCGCAAC
1 CAAATTCGCAACGC-GATA-GTCAAATTCGCAAC
5342932 TGAATTTCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 43 0.66
41 15 0.23
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:5342964 original size:20 final size:19
Alignment explanation
Indices: 5342898--5342989 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 19
5342888 AACACAAAAG
*
5342898 TCAAATTCGCAATGCGGAATT
1 TCAAATTCGCAA--CTGAATT
5342919 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
5342938 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
5342958 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
5342978 T-AATTTCGCAAC
1 TCAAATTCGCAAC
5342990 AGGTTTTAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 29 0.47
20 21 0.34
21 12 0.19
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:5342977 original size:40 final size:40
Alignment explanation
Indices: 5342844--5343015 Score: 122
Period size: 40 Copynumber: 4.4 Consensus size: 40
5342834 AATCTGTAAA
** **
5342844 TCGCAACACAGAA-GTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACAC-GAATGTCAAATTCGCAACTAGATTTTCAAAT
* * * *
5342884 TCGCAACACAAAAGTCAAATTCGCAA-TGCGGAATTTCAAAT
1 TCGCAACACGAATGTCAAATTCGCAACT--AGATTTTCAAAT
* * *
5342925 TCGCAAC-TGAATTTCAAATTCGCAACTAGATTTTCGAAT
1 TCGCAACACGAATGTCAAATTCGCAACTAGATTTTCAAAT
* * * **
5342964 TCGCAACACGAAT-TTAATTTCGCAAC-AGGTTTT-AGTT
1 TCGCAACACGAATGTCAAATTCGCAACTAGATTTTCAAAT
*
5343001 TCGCAACACAAATGT
1 TCGCAACACGAATGT
5343016 TTTGGGTATA
Statistics
Matches: 105, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
37 13 0.12
38 7 0.07
39 29 0.28
40 40 0.38
41 16 0.15
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (40 bp):
TCGCAACACGAATGTCAAATTCGCAACTAGATTTTCAAAT
Found at i:5342990 original size:19 final size:19
Alignment explanation
Indices: 5342963--5343009 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5342953 GATTTTCGAA
5342963 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
5342982 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
5343000 TTCGCAACAC
1 TTCGCAACAC
5343010 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:5346536 original size:20 final size:20
Alignment explanation
Indices: 5346507--5346555 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5346497 ATGTTGCGAT
5346507 CAATGCGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
*
5346527 CAATGTGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
5346547 CAATGCGAA
1 CAATGCGAA
5346556 TTTACCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (20 bp):
CAATGCGAAAGTCAAATTCG
Found at i:5346693 original size:25 final size:25
Alignment explanation
Indices: 5346665--5346713 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5346655 AAATCAATTA
*
5346665 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
*
5346690 AACATTGTTATGGGTACATTATTT
1 AACATTATTATGGGTACATTATTT
5346714 CCAAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:5347103 original size:24 final size:25
Alignment explanation
Indices: 5347076--5347130 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
5347066 TTTCAAATTC
*
5347076 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
5347100 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
5347124 ATTTCAA
1 ATTTCAA
5347131 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:5347116 original size:18 final size:18
Alignment explanation
Indices: 5347095--5347131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5347085 GTAATTGGAG
5347095 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5347113 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5347131 T
1 T
5347132 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5347138 original size:24 final size:24
Alignment explanation
Indices: 5347087--5347139 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5347077 TTTCATATGT
* * *
5347087 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
5347111 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
5347135 AATTT
1 AATTT
5347140 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:5350160 original size:21 final size:21
Alignment explanation
Indices: 5350099--5350217 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 21
5350089 ATGAATCGGG
* * *
5350099 CTCTTGAACGATGGGCGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
5350120 CTCTTGAACAATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
5350141 CTCTTGAACGGTGGGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
* *
5350162 TTCTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGATGAGAGGGGC
*
5350183 CTCTTGAACGAT-ATGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
*
5350204 CTCTTGAATGATGA
1 CTCTTGAACGATGA
5350218 TAGGTGCATC
Statistics
Matches: 75, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.03
21 71 0.95
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:5352828 original size:22 final size:22
Alignment explanation
Indices: 5352771--5352821 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5352761 GATAGAGATA
*
5352771 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
5352793 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
5352815 GACGGAT
1 GACGGAT
5352822 GTTGTCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:5352986 original size:40 final size:40
Alignment explanation
Indices: 5352937--5353012 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
5352927 TGTGTTTCGC
5352937 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTAT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTAT
* *
5352977 GTTGTGAATTTGGCTATCGCGTTGCGAATTTGACTT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT
5353013 ATGTATTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.42
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTAT
Found at i:5353023 original size:20 final size:20
Alignment explanation
Indices: 5352933--5353011 Score: 104
Period size: 20 Copynumber: 4.0 Consensus size: 20
5352923 ATATTGTGTT
5352933 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
5352953 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
*** * *
5352973 TTATGTTGTGAATTTGGCTA
1 TCGCGTTGCGAATTTGACTA
5352993 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
5353012 TATGTATTGC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:5353080 original size:20 final size:21
Alignment explanation
Indices: 5353029--5353084 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
5353019 TGCGATTTAC
5353029 AAATTCGCGTTGCGAAATTGG
1 AAATTCGCGTTGCGAAATTGG
* *
5353050 AAAAT-GGGTTGCGAAATTGG
1 AAATTCGCGTTGCGAAATTGG
*
5353070 -AGTTCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
5353085 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.07
20 23 0.79
21 4 0.14
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (21 bp):
AAATTCGCGTTGCGAAATTGG
Found at i:5359078 original size:15 final size:15
Alignment explanation
Indices: 5359058--5359108 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
5359048 TTTCGGAGAA
*
5359058 TGAATTACTGTAATT
1 TGAATTACTGGAATT
**
5359073 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
5359088 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
5359103 TAAATT
1 TGAATT
5359109 CTGAAAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:5359092 original size:30 final size:29
Alignment explanation
Indices: 5359056--5359124 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
5359046 TTTTTCGGAG
* * *
5359056 AATGAATTACTGTAATTTGAATTACTGGAA
1 AATGAATTACTGGAATTTAAATT-CTGAAA
5359086 AATGAATTACTGGAATTTAAATTCTGAAA
1 AATGAATTACTGGAATTTAAATTCTGAAA
5359115 AATGAATTAC
1 AATGAATTAC
5359125 ATTTCTGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.35
Consensus pattern (29 bp):
AATGAATTACTGGAATTTAAATTCTGAAA
Found at i:5359538 original size:28 final size:28
Alignment explanation
Indices: 5359497--5359661 Score: 107
Period size: 27 Copynumber: 6.0 Consensus size: 28
5359487 TTAATATCTT
*
5359497 TATTAAATA-TATTAAATATATAAATAA
1 TATTATATATTATTAAATATATAAATAA
**
5359524 TATTAT-TCATTATT-AATATATAAATTTT
1 TATTATAT-ATTATTAAATATATAAA-TAA
*
5359552 TATTATATATTATTAAA-ATAAAAATAA
1 TATTATATATTATTAAATATATAAATAA
* * *
5359579 TATCT-TATATTATTATA-ATATAATTGAT
1 TAT-TATATATTATTAAATATATAAAT-AA
* *
5359607 TATTTTTATAATATTAAA-A-ATAATATAA
1 TA-TTATATATTATTAAATATATAA-ATAA
5359635 TATTATA-ATTA-TAAATATTAATAAATA
1 TATTATATATTATTAAATA-T-ATAAATA
5359662 TTTTTAAATA
Statistics
Matches: 108, Mismatches: 16, Indels: 27
0.72 0.11 0.18
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 41 0.38
28 38 0.35
29 20 0.19
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTATATATTATTAAATATATAAATAA
Found at i:5359554 original size:25 final size:26
Alignment explanation
Indices: 5359503--5359563 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
5359493 TCTTTATTAA
5359503 ATATATTAAATATATAAATAATATTATT
1 ATATATT-AATATATAAAT-ATATTATT
*
5359531 CAT-TATTAATATATAAAT-TTTTATT
1 -ATATATTAATATATAAATATATTATT
5359556 ATATATTA
1 ATATATTA
5359564 TTAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 2 0.07
25 11 0.37
27 11 0.37
28 4 0.13
29 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATATTAATATATAAATATATTATT
Found at i:5359610 original size:55 final size:54
Alignment explanation
Indices: 5359496--5359640 Score: 134
Period size: 56 Copynumber: 2.6 Consensus size: 54
5359486 TTTAATATCT
* * *
5359496 TTATTAAATATATTAAATATATAAATAATATTATTCATTATTAATATATAAATTT
1 TTATTATATATATTAAA-ATAAAAATAATATTATTCATTATTAATATATAAATTA
* **
5359551 TTATTATATATTATTAAAATAAAAATAATATCTTATATTATTA-TAATATAATTGATTA
1 TTATTATATA-TATTAAAATAAAAATAATA--TTAT-TCATTATTAATAT-ATAAATTA
* *
5359609 TTTTTATA-ATATTAAAA-ATAATATAATATTAT
1 TTATTATATATATTAAAATA-AAAATAATATTAT
5359641 AATTATAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
54 4 0.05
55 21 0.28
56 23 0.30
57 11 0.14
58 17 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (54 bp):
TTATTATATATATTAAAATAAAAATAATATTATTCATTATTAATATATAAATTA
Found at i:5359635 original size:17 final size:17
Alignment explanation
Indices: 5359613--5359661 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5359603 TGATTATTTT
5359613 TATAATATTAAAAATAA
1 TATAATATTAAAAATAA
* *
5359630 TATAATATT-ATAATTA
1 TATAATATTAAAAATAA
5359646 TA-AATATTAATAAATA
1 TATAATATTAA-AAATA
5359662 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 12 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATATTAAAAATAA
Found at i:5359635 original size:33 final size:33
Alignment explanation
Indices: 5359593--5359661 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
5359583 TTATATTATT
**
5359593 ATAATATAATTGATTATTTTTAT-AATATTAA-AA
1 ATAATATAA-T-ATTATAATTATAAATATTAATAA
5359626 ATAATATAATATTATAATTATAAATATTAATAA
1 ATAATATAATATTATAATTATAAATATTAATAA
5359659 ATA
1 ATA
5359662 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 9 0.28
32 9 0.28
33 14 0.44
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAATATAATATTATAATTATAAATATTAATAA
Done.