Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008613.1 Hibiscus syriacus cultivar Beakdansim tig00111569_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: 647085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:173448 original size:32 final size:32
Alignment explanation
Indices: 173407--173480 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
173397 TAAAGTCGGT
* * * * *
173407 TTGCTTTCGGTTCAGATTAATTTCTGTTTAGG
1 TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
*
173439 TTGCTTTCGGGTCGGATTAAATTCAGTTCAAG
1 TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
173471 TTGCTTTCGG
1 TTGCTTTCGG
173481 ATTGGGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (32 bp):
TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
Found at i:173550 original size:16 final size:15
Alignment explanation
Indices: 173529--173571 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
173519 AGTTTCTTTT
173529 GGTTCGGGTTGATTTC
1 GGTTCGGGTT-ATTTC
173545 GGTTCGGGTTAGTTTC
1 GGTTCGGGTTA-TTTC
*
173561 GGTTCAGGTTA
1 GGTTCGGGTTA
173572 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.09, C:0.12, G:0.37, T:0.42
Consensus pattern (15 bp):
GGTTCGGGTTATTTC
Found at i:174485 original size:14 final size:14
Alignment explanation
Indices: 174466--174495 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
174456 AATGAATTAT
174466 ATTTTCTGGAAAAC
1 ATTTTCTGGAAAAC
*
174480 ATTTTCTTGAAAAC
1 ATTTTCTGGAAAAC
174494 AT
1 AT
174496 CTTATGGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (14 bp):
ATTTTCTGGAAAAC
Found at i:174591 original size:19 final size:19
Alignment explanation
Indices: 174567--174603 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
174557 ATTTATTACA
174567 AATATTATATACAATAAAT
1 AATATTATATACAATAAAT
* *
174586 AATATTATTTATAATAAA
1 AATATTATATACAATAAA
174604 AATTTCATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTATATACAATAAAT
Found at i:174646 original size:22 final size:22
Alignment explanation
Indices: 174621--174672 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
174611 TATTATTATT
174621 TTTA-AAATATTAAAATAGTTTA
1 TTTATAAATATTAAAAT-GTTTA
* * *
174643 TTTATTATTATTAAAATGTTTT
1 TTTATAAATATTAAAATGTTTA
174665 TTCTATAA
1 TT-TATAA
174673 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTATAAATATTAAAATGTTTA
Found at i:179089 original size:2 final size:2
Alignment explanation
Indices: 179082--179108 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
179072 ATAGCTAGGG
179082 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
179109 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:179113 original size:2 final size:2
Alignment explanation
Indices: 179108--179152 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
179098 TCTCTCTCTC
179108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
179150 TA T
1 TA T
179153 TTGAGAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:181555 original size:74 final size:72
Alignment explanation
Indices: 181429--181579 Score: 275
Period size: 74 Copynumber: 2.1 Consensus size: 72
181419 GTAGATAGAT
181429 AACCCAAATTCATGTTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGTC
1 AACCCAAATTCATGTTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGTC
181494 GGAATTCA
66 -GAATTCA
*
181502 AACCCTAAATTCATGTTTTGGTAAAAAGTTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGT
1 AACCC-AAATTCATGTTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGT
181567 CGAATTCA
65 CGAATTCA
181575 AACCC
1 AACCC
181580 CAAACCTTCT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 17 0.22
74 59 0.78
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (72 bp):
AACCCAAATTCATGTTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGTC
GAATTCA
Found at i:193829 original size:15 final size:15
Alignment explanation
Indices: 193809--193838 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
193799 TAATTAATTT
*
193809 TCAAACAATAATCAA
1 TCAAACAAAAATCAA
193824 TCAAACAAAAATCAA
1 TCAAACAAAAATCAA
193839 AATTGATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (15 bp):
TCAAACAAAAATCAA
Found at i:199230 original size:8 final size:8
Alignment explanation
Indices: 199217--199257 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
199207 CTCATTTTCA
199217 GAGAATTT
1 GAGAATTT
199225 GAGAATTT
1 GAGAATTT
*
199233 -AGAGTTT
1 GAGAATTT
199240 G-GAAATTT
1 GAG-AATTT
199248 GAGAATTT
1 GAGAATTT
199256 GA
1 GA
199258 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 7 0.25
8 20 0.71
9 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:199259 original size:15 final size:15
Alignment explanation
Indices: 199217--199259 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
199207 CTCATTTTCA
199217 GAGAATTTGAGAATTT
1 GAGAATTTGA-AATTT
*
199233 -AGAGTTTGGAAATTT
1 GAGAATTT-GAAATTT
199248 GAGAATTTGAAA
1 GAGAATTTGAAA
199260 GATTGTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
GAGAATTTGAAATTT
Found at i:199700 original size:128 final size:128
Alignment explanation
Indices: 199328--199825 Score: 930
Period size: 128 Copynumber: 3.9 Consensus size: 128
199318 TAATCGGAGT
199328 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
199393 -ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
199455 ACTATTCACATTAAGGCGCATTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
199518 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
199581 ACTATTCACATGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
199646 CATTGCCTTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
199709 ACTATTCACATGAATGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
199774 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
199826 AATCAGGTAA
Statistics
Matches: 359, Mismatches: 9, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
125 34 0.09
126 89 0.25
127 26 0.07
128 210 0.58
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:200286 original size:33 final size:33
Alignment explanation
Indices: 200225--200323 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
200215 AAATTTAATG
*
200225 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAA-TTTGAATAATATAATTTATATTTTAAAT
* * * *
200259 TTAAATTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
* *
200292 TTAAATTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTGAATAATATAATTTATATTTTAAA
200324 AATATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 50 0.91
34 5 0.09
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:200931 original size:21 final size:21
Alignment explanation
Indices: 200843--200936 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
200833 TATGGTATAA
*
200843 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
200864 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
200885 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
200906 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
200927 AACCCTGCGG
1 AACCCTGCGG
200937 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:200966 original size:21 final size:21
Alignment explanation
Indices: 200940--200987 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
200930 CCTGCGGAGA
*
200940 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
200961 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
200982 GGGCAT
1 TGGCAT
200988 GAACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:202776 original size:30 final size:32
Alignment explanation
Indices: 202712--202789 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
202702 TTAATAATTC
*
202712 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
202746 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
202776 TATAAAAATAATAA
1 TA-AAAAATAATAA
202790 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 6 0.15
31 10 0.25
32 2 0.05
33 18 0.45
34 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:202813 original size:32 final size:34
Alignment explanation
Indices: 202747--202818 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
202737 TTATTTTAAT
* *
202747 AAAA-AATAATATTTACATAAATATATTAATATA
1 AAAATAATAATATTTACATAAATATACTAACATA
202780 AAAATAATAACTATTTA-A-AAA-ATACTAACATA
1 AAAATAATAA-TATTTACATAAATATACTAACATA
202812 AAAATAA
1 AAAATAA
202819 ATTTCTTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 16 0.46
33 7 0.20
34 6 0.17
35 6 0.17
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAATAATAATATTTACATAAATATACTAACATA
Found at i:207579 original size:24 final size:24
Alignment explanation
Indices: 207497--207591 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
207487 ATTTTTTATT
*
207497 TGAATTATGTTTTGACATCTGATC
1 TGAATTATGTTTTGATATCTGATC
* * * *
207521 TGAACTCTGTTTTGAT-TCCTAACC
1 TGAATTATGTTTTGATAT-CTGATC
* *
207545 T-AGATTCTGTTCTGATATCTGATC
1 TGA-ATTATGTTTTGATATCTGATC
*
207569 TGAATTATGTTTTGATTTCTGAT
1 TGAATTATGTTTTGATATCTGAT
207592 ATCTCCATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (24 bp):
TGAATTATGTTTTGATATCTGATC
Found at i:209543 original size:11 final size:12
Alignment explanation
Indices: 209519--209543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
209509 TTAAAATAAA
209519 TTTTGGGAATTT
1 TTTTGGGAATTT
209531 TTTTGGGAATTT
1 TTTTGGGAATTT
209543 T
1 T
209544 CCGACACCAT
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:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTTTGGGAATTT
Found at i:209663 original size:22 final size:22
Alignment explanation
Indices: 209621--209669 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
209611 TTAATTTCTG
209621 TTTGGGTGTTATTTGTTTAAA-A
1 TTTGGGTGTTATTTG-TTAAATA
209643 TTTGGGTGTTAGTTTCG-TAAATA
1 TTTGGGTGTTA-TTT-GTTAAATA
209666 TTTG
1 TTTG
209670 CAGAAGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 15 0.62
23 8 0.33
24 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.53
Consensus pattern (22 bp):
TTTGGGTGTTATTTGTTAAATA
Found at i:209769 original size:17 final size:17
Alignment explanation
Indices: 209733--209773 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
209723 ATGGTCGGCT
*
209733 GTTGACCGTTGACTTGC
1 GTTGACCGTTGACTCGC
209750 GTTGACCGTTGAC-CGAC
1 GTTGACCGTTGACTCG-C
209767 GTTGACC
1 GTTGACC
209774 ACTGTTGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (17 bp):
GTTGACCGTTGACTCGC
Found at i:212679 original size:609 final size:607
Alignment explanation
Indices: 209935--213574 Score: 5983
Period size: 607 Copynumber: 6.0 Consensus size: 607
209925 TTGACTTTGA
* * * **
209935 TTTTGACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTTGACGTCCAAAATTCGA
1 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAATTCGA
* ** * * *
210000 TTTTGATGTCCGTTTCTCCAAATTCGAACCTGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
66 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
** * *
210065 CGATATGTTTATCGTAATTAAGCTCCGTTTTTTTATGTTATTTCTGTTGATATGGATCCGAGGAA
131 CGATCCGTTTATCGCAATTAAGCTCCG-TTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAA
* * *
210130 ATATTGGAAGTTGAATTAAAGATGAAAGGCGTTCGAATGTAATTTATATGGTCGATCAATATGGA
195 ATATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGC
210195 ACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAAT
260 ACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAAT
*
210260 GCATAATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATAC
325 GCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATAC
* *
210325 AGTAAAAAGGTTCGGTAATTGATTATGATTCATATGACTTTTATAA-AAATTTGAGGGATTGTTA
390 AGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAA-TTGAGGGATTGTTA
* *
210389 GAATTAAATTACAAGTTATGTGTTTAGTGATAAAGAAATCAACATGGATCTGTAACTTATAATTT
454 GAATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTT
* * * * **
210454 ATTTTATCAGAGATTAAATGTTAAAGGTACTTAGATGAGAAATTATAAGAATAATTTGGTAGGGT
519 ATTTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGT
210519 AAAATTACGAAAATACCCTTATGT
584 AAAATTACGAAAATACCCTTATGT
* *
210543 TTTTGACCGAAAAGTCAAAATTTTTTGAAAAGTCATATTTTAGGTTTTTCGACATCCTG-ATCTC
1 TTTTTACCGAAAAGTCAAAA-TTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAAT-TC
* *
210607 GAATCCGATGTCGGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACTCGA
64 GAATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGA
*
210672 TTCGATCTGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGA
129 TTCGATCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGA
* *
210737 ATTATTGGAAGTTGAATTAAAGATCAAATGCGTTCGAATGGAATTTATATGGTCGATCAATATGG
194 AATATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGG
* *
210802 CACGAAAATCAAGGTAATACTTTACTACCTCTTTATACTTTATGGAACATGTGAATATTAGTAAA
259 CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAA
*
210867 TGCATGATTAAGATAATATTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATA
324 TGCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATA
* * * *
210932 CAGTAAAAAGGTTCGGTAATTGATAATGGTTCATATGACTTTTATAAGAAATTGAGGAATTTTTA
389 CAGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTA
* * * *
210997 GAATTAAATTACAAGTTATGTGCTTAGTGATAATGAAATTAACCTGGGTCTGTAACTTTTAATTT
454 GAATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTT
* *
211062 ATATCATCATAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGT
519 ATTTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGT
211127 AAAATTACGAAAATACCCTTATGT
584 AAAATTACGAAAATACCCTTATGT
*
211151 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCTTATTTTAGGTTTTTCGACATCCTGAATTCGA
1 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAATTCGA
* *
211216 ATCTGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTAATTAATCACCCGATT
66 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
* * *
211281 CGATCCGTTTATCGCAATTATGCTTCATTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAAA
131 CGATCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAAA
* *
211346 TATTGGAAGTTGAATTAAAGATCAAAGACGTTCAAATGGAATTTATATGGTCGATCAATATGGCA
196 TATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGCA
* * *
211411 C-AGAAATCAAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATATGAATATTGGTAAAT
261 CGA-AAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAAT
211475 GCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATAC
325 GCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATAC
* * * * *
211540 GGTAAAAAGGTTTAGTAATTTATTATGGTTTAGATGACTTTTATAAGAAATTGAGGGATTGTTAG
390 AGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTAG
*
211605 AATTAAATTACAAGTTATGTGCTTAGTGATAAATAAATCAACCTGGATCTGTAACTTATAATTTA
455 AATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTTA
* * * * *
211670 TTTCATCAAATATTAAATGTTAAAGGTACTTGGATGAGAAATTATAATAATACTCCGGTAGGATA
520 TTTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTA
*
211735 AAATTACGAAAATACCCTTATAT
585 AAATTACGAAAATACCCTTATGT
* *
211758 TTTTGACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCTTGAATTCGA
1 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAATTCGA
* * *
211823 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGATAAGTTGGTTTTCATTAATTAATCACCCGATT
66 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
* *
211888 C-ATTCTGTTTATCGCAATTAAGCTCTGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAA
131 CGA-TCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAA
211952 ATATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGC
195 ATATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGC
* * *
212017 ATGAAAATCGAGATAATAATTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAAT
260 ACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAAT
*
212082 GCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCAATCTGAATAC
325 GCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATAC
* * * *
212147 AGTAAAAAGGTTCGGTAATTGATTATGGTTCAAATGACTTTTATAAGAAATTGAGGAATTTTTAG
390 AGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTAG
*
212212 AATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATTAACCTGGATCTGTAACTTATAATTTA
455 AATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTTA
*
212277 TTTCATCATAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTA
520 TTTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTA
212342 AAATTACGAAAATACCCTTATGTTT
585 AAATTACGAAAATACCCTTATG--T
* * * *
212367 TTTTTACTGAAAAGTCAAAATTTTTGAAAAGTCATATTTTAGGTTTTTCGACGTCCTGAATTTGA
1 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAATTCGA
212432 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
66 ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
*
212497 CGATCCGTTTATCGCAATTAATCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAAA
131 CGATCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAAA
212562 TATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGCA
196 TATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGCA
* * *
212627 CGAAAATCGAGGCAATACTTTACTACCTCTTTATGCTTTATGGAATATGTGAATATTGGTAAATG
261 CGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAATG
212692 CATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATACA
326 CATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATACA
* * *
212757 TTAAAAAGGTTCAGTAATTGATTATGGTTTAGATGACTTTTATAAGAAATTGAGGGATTGTTAGA
391 GTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTAGA
* *
212822 ATTAAATTACAAGTTATGTGCTTAATAATAAAGAAATCAACCTGGATCTGTAACTTATAATTTAT
456 ATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTTAT
212887 TTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTAA
521 TTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTAA
*
212952 AATTATGAAAATACCCTTATGT
586 AATTACGAAAATACCCTTATGT
* * *
212974 TTTTTACCGAAAAGTCGAAATTTTTGAAAAGTCATATTTTAGGTTTTTCGACGA-CCTAAATTCG
1 TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGAC-ATCCTGAATTCG
* * *
213038 AATCCGATGCCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCATTGATTAATCACCTGAT
65 AATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGAT
*
213103 TCGATCCGTTTATCGCAATTAAGCTCCGTTTTTTTTGTAATTTCTGTTGATATGGATCCGAGGAA
130 TCGATCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAA
* * * * * *
213168 ATATTAGAAGTTGAATTAAATATCAAAGGTGTTTGAATGGAATTTATATGGTCGATCAATTTGGA
195 ATATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGC
* *
213233 AC-AGAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTTTGGAACATGTGAATATTGGTAAA
260 ACGA-AAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAA
* *
213297 TGCATGATTAAGATAATATTAGTCTCATTTGTGTAGTTAATTAATTTCTACAATCGATCTGAATA
324 TGCATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATA
*
213362 CGGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTA
389 CAGTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTA
* *
213427 GAATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGAATATGTAACTTAT-A---
454 GAATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTT
*
213488 A--T-ATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCTGGTAGGGT
519 ATTTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGT
213550 AAAATTACGAAAATACCCTTATGT
584 AAAATTACGAAAATACCCTTATGT
213574 T
1 T
213575 ATAAAAATAA
Statistics
Matches: 2841, Mismatches: 179, Indels: 32
0.93 0.06 0.01
Matches are distributed among these distances:
600 83 0.03
601 1 0.00
603 1 0.00
606 4 0.00
607 1591 0.56
608 462 0.16
609 698 0.25
610 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (607 bp):
TTTTTACCGAAAAGTCAAAATTTTCGAAAAGTCATATTTTAGGTTTTTCGACATCCTGAATTCGA
ATCCGATGTCTGTTTCGCCAAATTCGAACCCGGTAAGTTGGTTTTCACTGATTAATCACCCGATT
CGATCCGTTTATCGCAATTAAGCTCCGTTTTTTATGTAATTTCTGTTGATATGGATCCGAGGAAA
TATTGGAAGTTGAATTAAAGATCAAAGGCGTTCGAATGGAATTTATATGGTCGATCAATATGGCA
CGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAACATGTGAATATTAGTAAATG
CATGATTAAGATAATGTTAGTCTCATTTGTGTAGTTAATTAATTTCTACACTCGATCTGAATACA
GTAAAAAGGTTCAGTAATTGATTATGGTTCATATGACTTTTATAAGAAATTGAGGGATTGTTAGA
ATTAAATTACAAGTTATGTGCTTAGTGATAAAGAAATCAACCTGGATCTGTAACTTATAATTTAT
TTCATCAGAGATTAAATGTTAAAGGTACTTGGATGAGAAATTATGAGAATACTCCGGTAGGGTAA
AATTACGAAAATACCCTTATGT
Found at i:215445 original size:24 final size:24
Alignment explanation
Indices: 215383--215461 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
215373 CTATTTTGAC
* *
215383 ATCTGATCTAAAATATGTTCTGAT
1 ATCTGATCTGAATTATGTTCTGAT
* * *
215407 -TCCTAACCTGGATTATGTTCTGAT
1 AT-CTGATCTGAATTATGTTCTGAT
*
215431 ATCTGATCTGAATTATGTTTTGAT
1 ATCTGATCTGAATTATGTTCTGAT
*
215455 TTCTGAT
1 ATCTGAT
215462 ATCTTCGTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (24 bp):
ATCTGATCTGAATTATGTTCTGAT
Found at i:216664 original size:18 final size:18
Alignment explanation
Indices: 216625--216664 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
216615 TCAATTATAA
*
216625 TTTAAAATTTAGATTTTC
1 TTTAAAATTTAGATGTTC
216643 TTTAATAATTTAGATGTT-
1 TTTAA-AATTTAGATGTTC
216661 TTTA
1 TTTA
216665 TATTCCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTAAAATTTAGATGTTC
Found at i:220710 original size:20 final size:20
Alignment explanation
Indices: 220681--220774 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
220671 GAACCAAATA
*
220681 TTTGTCCCGAAGGACCA-TT
1 TTTGTCCCGAAGGACCACTG
* *
220700 TATTGTTCCGAAGAACCAC--
1 T-TTGTCCCGAAGGACCACTG
* *
220719 TATGTCCCGAAGGACAACTG
1 TTTGTCCCGAAGGACCACTG
220739 TTTGTCCCGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
220759 TTTGTCCCGAAGGACC
1 TTTGTCCCGAAGGACC
220775 GCTGCTAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
18 13 0.21
19 2 0.03
20 48 0.76
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (20 bp):
TTTGTCCCGAAGGACCACTG
Found at i:220726 original size:38 final size:39
Alignment explanation
Indices: 220683--220774 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 39
220673 ACCAAATATT
* *
220683 TGTCCCGAAGGACCA-TTTATTGTTCCGAAGAACCAC-TA
1 TGTCCCGAAGGACCACTGT-TTGTCCCGAAGAACCACGTA
* * *
220721 TGTCCCGAAGGACAACTGTTTGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCACTGTTTGTCCCGAAGAACCAC-GTA
220761 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
220775 GCTGCTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 29 0.64
39 2 0.04
40 14 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
TGTCCCGAAGGACCACTGTTTGTCCCGAAGAACCACGTA
Found at i:222631 original size:13 final size:13
Alignment explanation
Indices: 222613--222637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222603 ACGGGAGGAG
222613 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
222626 AGGAAGAAGAAG
1 AGGAAGAAGAAG
222638 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:222932 original size:24 final size:24
Alignment explanation
Indices: 222905--222958 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
222895 CTGAAACATC
*
222905 ATCAAAATTCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
*
222929 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
222953 ATCAAA
1 ATCAAA
222959 TTTCAAATAC
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:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:223734 original size:14 final size:16
Alignment explanation
Indices: 223699--223735 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
223689 GAAATCATTG
223699 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
223715 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
223729 AAAATTA
1 AAAATTA
223736 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:223920 original size:20 final size:20
Alignment explanation
Indices: 223872--223953 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 20
223862 CAAAACATTT
*
223872 GTGTTGCGAAACTAAAA--C
1 GTGTTGCGAAATTAAAATTC
*
223890 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
223910 GTGTTGTGAAACTAAAA--C
1 GTGTTGCGAAATTAAAATTC
*
223928 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
223948 GTGTTG
1 GTGTTG
223954 TGAGTTCGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 30 0.59
20 21 0.41
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:223923 original size:38 final size:38
Alignment explanation
Indices: 223872--223956 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
223862 CAAAACATTT
*
223872 GTGTTGCGAAACTAAAACCTGTTGCGAAATTAAAATTC
1 GTGTTGTGAAACTAAAACCTGTTGCGAAATTAAAATTC
223910 GTGTTGTGAAACTAAAACCTGTTGCGAAATTAAAATTC
1 GTGTTGTGAAACTAAAACCTGTTGCGAAATTAAAATTC
223948 GTGTTGTGA
1 GTGTTGTGA
223957 GTTCGAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (38 bp):
GTGTTGTGAAACTAAAACCTGTTGCGAAATTAAAATTC
Found at i:224039 original size:21 final size:21
Alignment explanation
Indices: 224014--224067 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
224004 AATCGAATTG
*
224014 CGAATTT-GAAATTCAGTGTTA
1 CGAATTTCGAAAATC-GTGTTA
* *
224035 CGAATTTGGAAAATCGTGTTG
1 CGAATTTCGAAAATCGTGTTA
224056 CGAATTTCGAAA
1 CGAATTTCGAAA
224068 CTGAGTTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (21 bp):
CGAATTTCGAAAATCGTGTTA
Found at i:225158 original size:323 final size:322
Alignment explanation
Indices: 224571--225219 Score: 1208
Period size: 323 Copynumber: 2.0 Consensus size: 322
224561 AAGCATCTTC
*
224571 AAATTTTAAGTATTTGATTATTTGACTATGTTGACTAACAGCCACTATTGTATTAAAAAAATGAT
1 AAATTTTAAGCATTTGATTATTTGACTATGTTGACTAACAGCCACTATTGTATTAAAAAAATGAT
* *
224636 ATTCTGATCACTTCCTTGTGTCCAGTTAATTCCTAGATTATTTGTCTACCAAAAAAATTACCTTT
66 ATTCTGATCACTTCCTTGTGTCCAGTTAATTCCTAGATTATTTGTCTACAAAAAAAATTACCTCT
*
224701 GATTTTTTTATAATTATTGAAAATGCACATATATTCTATAGATGCAATTATTCGAATTTTAGACT
131 GATTTTTTTATAATTATTGAAAATGCACATATATTCTATAGATGCAATTATTCAAATTTTAGACT
* *
224766 TTTTAAAAAATAATATTTCCTTTTATTATCGAAGTTGTTCAATGTAACTTTTTAAGGCTTAATAC
196 TCTAAAAAAATAATATTTCCTTTTATTATCGAAGTTGTTCAATGTAACTTTTTAAGGCTTAATAC
224831 AAAAATAAGTGCCTAAGTTATACTTCAAAAAACGTTTTAGTGCTTAAAGAATTTTTCGCTAA
261 AAAAATAAGTGCCTAAGTTATACTTCAAAAAACGTTTTAGTGCTTAAAGAATTTTTCGCTAA
* *
224893 AAATTTTAAGCATTTGATTGTTTGACTATGTTGACTAGCAGCCACTATTGTATTAAAAAAATGAT
1 AAATTTTAAGCATTTGATTATTTGACTATGTTGACTAACAGCCACTATTGTATTAAAAAAATGAT
224958 ATTCTGATCACTTCCTTGTGTCCAGTTAATTCCTAGATTATTTGTCTACAAAAAAAAATTACCTC
66 ATTCTGATCACTTCCTTGTGTCCAGTTAATTCCTAGATTATTTGTCTAC-AAAAAAAATTACCTC
*
225023 TGATTTTTTTATAATTATTGAAAATGCATATATATTCTATAGATGCAATTATTCAAATTTTAGAC
130 TGATTTTTTTATAATTATTGAAAATGCACATATATTCTATAGATGCAATTATTCAAATTTTAGAC
225088 TTCTAAAAAAATAATATTTCCTTTTATTATCGAAGTTGTTCAATGTAACTTTTTAAGGCTTAATA
195 TTCTAAAAAAATAATATTTCCTTTTATTATCGAAGTTGTTCAATGTAACTTTTTAAGGCTTAATA
225153 CAAAAATAAGTGCCTAAGTTATACTTCAAAAAACGTTTTAGTGCTTAAAGAATTTTTCGCTAA
260 CAAAAATAAGTGCCTAAGTTATACTTCAAAAAACGTTTTAGTGCTTAAAGAATTTTTCGCTAA
225216 AAAT
1 AAAT
225220 AAGTGTCTAA
Statistics
Matches: 317, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
322 111 0.35
323 206 0.65
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (322 bp):
AAATTTTAAGCATTTGATTATTTGACTATGTTGACTAACAGCCACTATTGTATTAAAAAAATGAT
ATTCTGATCACTTCCTTGTGTCCAGTTAATTCCTAGATTATTTGTCTACAAAAAAAATTACCTCT
GATTTTTTTATAATTATTGAAAATGCACATATATTCTATAGATGCAATTATTCAAATTTTAGACT
TCTAAAAAAATAATATTTCCTTTTATTATCGAAGTTGTTCAATGTAACTTTTTAAGGCTTAATAC
AAAAATAAGTGCCTAAGTTATACTTCAAAAAACGTTTTAGTGCTTAAAGAATTTTTCGCTAA
Found at i:225310 original size:25 final size:25
Alignment explanation
Indices: 225276--225324 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
225266 TTTTAATAAT
*
225276 AAAAATATTATCTTAATTA-AAAAAG
1 AAAAAAATTAT-TTAATTATAAAAAG
*
225301 AAAAAAATTATTTATTTATAAAAA
1 AAAAAAATTATTTAATTATAAAAA
225325 ACCTAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAAAAATTATTTAATTATAAAAAG
Found at i:225901 original size:16 final size:15
Alignment explanation
Indices: 225880--225910 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
225870 GTTGTGTTGT
225880 TTTTTTAATATTTTTA
1 TTTTTTAAT-TTTTTA
225896 TTTTTTAATTTTTTA
1 TTTTTTAATTTTTTA
225911 AAATAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTAATTTTTTA
Found at i:228263 original size:34 final size:34
Alignment explanation
Indices: 228225--228290 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
228215 AATTTATATG
* *
228225 TTAAATTTTGAATACCATAATTTGTATTTTAATT
1 TTAAATTTCGAATACCATAATTTGTATATTAATT
*
228259 TTAAATTTCGAATACTATAATTTGTATATTAA
1 TTAAATTTCGAATACCATAATTTGTATATTAA
228291 AAACATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (34 bp):
TTAAATTTCGAATACCATAATTTGTATATTAATT
Found at i:228824 original size:21 final size:21
Alignment explanation
Indices: 228806--228866 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
228796 CTAAAACCAT
228806 ACGGGCTAGGTATGTAACCTG
1 ACGGGCTAGGTATGTAACCTG
*
228827 GCGGGCTAGGTATGTAACCTG
1 ACGGGCTAGGTATGTAACCTG
* * *
228848 GCGAGCTAGGAATGTAACC
1 ACGGGCTAGGTATGTAACC
228867 CAAAGGGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (21 bp):
ACGGGCTAGGTATGTAACCTG
Found at i:230498 original size:16 final size:18
Alignment explanation
Indices: 230474--230507 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
230464 TCCTAAATAA
230474 TATACATT-ATAAAAATT
1 TATACATTAATAAAAATT
230491 TATA-ATTAATAAAAATT
1 TATACATTAATAAAAATT
230508 CATTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TATACATTAATAAAAATT
Found at i:230924 original size:20 final size:19
Alignment explanation
Indices: 230899--230952 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
230889 GCGAAATAAA
230899 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
230919 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
230939 AATCGCAACGCGAT
1 AATCGCAACGCGAT
230953 TATGAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:231014 original size:21 final size:21
Alignment explanation
Indices: 230899--231014 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
230889 GCGAAATAAA
*
230899 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
230919 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* ** *
230939 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTTTCCAG
* ** *
230960 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
** *
230980 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTTTCCAG
231002 AATCGCAACGCGA
1 AATCGCAACGCGA
231015 ACATATAAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 41 0.59
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:231070 original size:61 final size:60
Alignment explanation
Indices: 231002--231254 Score: 191
Period size: 61 Copynumber: 4.2 Consensus size: 60
230992 GATTTTCCAT
* * **
231002 AATCGCAACGCGAACATATAAATCGCAACGCAATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAACACATAAATCGCAACGCAATACGT-AAAATCGCAACGAGTATCCGT-A
* * * *
231063 AATCGCAACGCGTATC-CGTAAATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCG-AACACATAAATCGCAACG-CAATACGTAAAATCGCAACGAGTATCCGTA
* * * * *
231124 AATCGCAACGAGAATACATAAATCGCAACGC-GTATCTGT-AAAT---AACGAGAATACGTA
1 AATCGCAACGCGAACACATAAATCGCAACGCAATA-C-GTAAAATCGCAACGAGTATCCGTA
* * * * * *
231181 AATCGCAATGTGTATC-CGTAAATCGTAACGAAAATACGTAAAATCGCAAC-ACGTATCCGTA
1 AATCGCAACGCG-AACACATAAATCGCAACG-CAATACGTAAAATCGCAACGA-GTATCCGTA
231242 AATCGCAACGCGA
1 AATCGCAACGCGA
231255 TTTTTAAAGC
Statistics
Matches: 149, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
57 34 0.23
58 6 0.04
59 4 0.03
60 9 0.06
61 71 0.48
62 24 0.16
63 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGAACACATAAATCGCAACGCAATACGTAAAATCGCAACGAGTATCCGTA
Found at i:231087 original size:20 final size:20
Alignment explanation
Indices: 231043--231253 Score: 178
Period size: 20 Copynumber: 10.6 Consensus size: 20
231033 AATTCTGACT
*
231043 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
231064 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
231084 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
231105 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
231125 ATCGCAACGAGAATACATAA
1 ATCGCAACGCGTATCCGTAA
*
231145 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
231165 AT---AACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
231182 ATCGCAATGTGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *** *
231202 ATCGTAACGAAAATACGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
231223 ATCGCAACACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
231243 ATCGCAACGCG
1 ATCGCAACGCG
231254 ATTTTTAAAG
Statistics
Matches: 146, Mismatches: 37, Indels: 15
0.74 0.19 0.08
Matches are distributed among these distances:
17 13 0.09
20 86 0.59
21 47 0.32
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:231088 original size:41 final size:41
Alignment explanation
Indices: 231043--231251 Score: 284
Period size: 41 Copynumber: 5.2 Consensus size: 41
231033 AATTCTGACT
* *
231043 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
231084 ATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
231125 ATCGCAACGAGAATACAT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
231165 AT---AACGAGAATACGT-AAATCGCAATGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
231202 ATCGTAACGAAAATACGTAAAATCGCAACACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
231243 ATCGCAACG
1 ATCGCAACG
231252 CGATTTTTAA
Statistics
Matches: 147, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
37 33 0.22
40 34 0.23
41 80 0.54
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:231748 original size:11 final size:11
Alignment explanation
Indices: 231732--231773 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
231722 GAAGTTAGTA
231732 TTTGTCTTTGT
1 TTTGTCTTTGT
231743 TTTGTCTTTGT
1 TTTGTCTTTGT
231754 TTTGTCTTTGT
1 TTTGTCTTTGT
231765 TTTGTCTTT
1 TTTGTCTTT
231774 TGGTTGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.74
Consensus pattern (11 bp):
TTTGTCTTTGT
Found at i:231752 original size:6 final size:6
Alignment explanation
Indices: 231732--231773 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
231722 GAAGTTAGTA
231732 TTTGTC TTTGT- TTTGTC TTTGT- TTTGTC TTTGT- TTTGTC TTT
1 TTTGTC TTTGTC TTTGTC TTTGTC TTTGTC TTTGTC TTTGTC TTT
231774 TGGTTGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.74
Consensus pattern (6 bp):
TTTGTC
Found at i:231896 original size:21 final size:21
Alignment explanation
Indices: 231836--231913 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
231826 TTCTAAACTT
* *
231836 AAAATTGCAACATGA-AAATG
1 AAAATCGCAACAAGAGAAATG
231856 AAAATCGC-ACACA-A-AAATG
1 AAAATCGCAACA-AGAGAAATG
** *
231875 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACAAGAGAAATG
231896 AAAATCGCAACAAGAGAA
1 AAAATCGCAACAAGAGAA
231914 TCGCAATGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 16 0.35
20 10 0.22
21 20 0.43
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACAAGAGAAATG
Found at i:231929 original size:33 final size:33
Alignment explanation
Indices: 231890--231970 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
231880 CGCAACGAGA
*
231890 GAAATGAAAATCGCAACAAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
* * *
231923 GAAATGAAAATCACAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
**
231956 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
231971 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACAAGAGAATCGCAACGC
Found at i:231988 original size:19 final size:18
Alignment explanation
Indices: 231966--232123 Score: 81
Period size: 17 Copynumber: 9.1 Consensus size: 18
231956 GAAACCAAAA
231966 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
* *
231985 TCGCGTTGTGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
232001 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
* *
232018 TCGCTTTGTGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
232034 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
* *
232051 TCGCGTTGTGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
**
232067 TCG-TTGCGATAGTCATT
1 TCGCTTGCGATTTTCATT
232084 TCCGCGTTGCGATTTTCATT
1 T-CGC-TTGCGATTTTCATT
*
232104 CTC-TTTGCGATTTTCATT
1 -TCGCTTGCGATTTTCATT
232122 TC
1 TC
232124 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
14 15 0.14
16 20 0.19
17 21 0.20
18 16 0.15
19 19 0.18
20 13 0.12
21 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:232013 original size:33 final size:33
Alignment explanation
Indices: 231971--232123 Score: 216
Period size: 33 Copynumber: 4.5 Consensus size: 33
231961 CAAAATCGCA
231971 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
*
232004 TTGCGATTTTCATTTCGCTTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
232037 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
** * *
232070 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCT
1 TTGCGATTTTCATTT-CGCGTTGTGA--TTC--TCTCG
232108 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
232124 AACCAAAAGA
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
33 77 0.72
34 9 0.08
36 3 0.03
37 1 0.01
38 17 0.16
ACGTcount: A:0.10, C:0.22, G:0.19, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
Found at i:232102 original size:20 final size:20
Alignment explanation
Indices: 232068--232123 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
232058 GTGATTCTCT
**
232068 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
232088 CGTTGCGATTTTCA-TT-CT
1 CGTTGCGATTTTCATTTCCG
*
232106 CTTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
232124 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:235315 original size:14 final size:14
Alignment explanation
Indices: 235283--235317 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
235273 GATTGTTTAA
235283 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
235297 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
235311 TTGATTT
1 TTGATTT
235318 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:235498 original size:20 final size:19
Alignment explanation
Indices: 235421--235500 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 19
235411 AAAACAGACT
* *
235421 ATCGCAACGCGGAGATGAAA
1 ATCGCAATGC-GAAATGAAA
*
235441 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
235460 ATCGCAA--CG-AGTG--A
1 ATCGCAATGCGAAATGAAA
235474 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
235494 ATCGCAA
1 ATCGCAA
235501 CGGGAAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 8 0.17
16 5 0.10
17 2 0.04
18 3 0.06
19 14 0.29
20 16 0.33
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:235577 original size:19 final size:19
Alignment explanation
Indices: 235519--235598 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
235509 TAATTTCACG
235519 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
*
235539 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
*
235553 TTGCGATTTTCATTTCGGA
1 TTGCGATTTTCATTTCGCA
235572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
235591 TTGCGATT
1 TTGCGATT
235599 CTCTCGTTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 3 0.06
18 4 0.08
19 26 0.50
20 6 0.12
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:235605 original size:52 final size:53
Alignment explanation
Indices: 235517--235651 Score: 175
Period size: 52 Copynumber: 2.5 Consensus size: 53
235507 ACTAATTTCA
**
235517 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCG
*
235570 -GATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCG
1 CG-TTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCG
** *
235623 CGTTGCGATAGTCAATTCCGCATTGCGAT
1 CGTTGCGATTTTC-ATTTCGCATTGCGAT
235652 AGTCAAATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
52 34 0.47
53 23 0.32
54 15 0.21
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.41
Consensus pattern (53 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCG
Found at i:235628 original size:20 final size:20
Alignment explanation
Indices: 235603--235657 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
235593 GCGATTCTCT
*
235603 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
235623 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
235643 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
235658 ATGAATGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:235898 original size:19 final size:19
Alignment explanation
Indices: 235874--235965 Score: 104
Period size: 19 Copynumber: 5.1 Consensus size: 19
235864 AGAGGAAAAG
* *
235874 ATGAAAATTGTAATGCGAA
1 ATGAAAATCGCAATGCGAA
235893 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
235912 ATGAAAATCGCAA--CG-A
1 ATGAAAATCGCAATGCGAA
*
235928 GTG--AATCGCAATGCGAAA
1 ATGAAAATCGCAATGCG-AA
*
235946 ATGAAAATCGCAACGCGAA
1 ATGAAAATCGCAATGCGAA
235965 A
1 A
235966 CTAATTTCGC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
14 8 0.13
16 5 0.08
17 2 0.03
18 3 0.05
19 33 0.53
20 11 0.18
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.16
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:235991 original size:19 final size:19
Alignment explanation
Indices: 235969--236056 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
235959 CGCGAAACTA
*
235969 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
235988 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
236006 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
236022 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
236041 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
236057 CTTTCGTTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 3 0.05
18 4 0.07
19 28 0.47
20 12 0.20
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:236083 original size:53 final size:52
Alignment explanation
Indices: 235969--236109 Score: 174
Period size: 53 Copynumber: 2.7 Consensus size: 52
235959 CGCGAAACTA
* **
235969 ATTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCACTCGTTGCGATAGTC
** *
236022 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAGTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATAGTC
** *
236074 ATTTCCGCATTGCGATAGTCAATTCCGCATTGCGAT
1 ATTT-CGCATTGCGATTTTC-ATTTCGCATTGCGAT
236110 AGTCAAATGA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 31 0.40
53 32 0.42
54 14 0.18
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (52 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATAGTC
Found at i:236092 original size:20 final size:19
Alignment explanation
Indices: 235969--236114 Score: 105
Period size: 20 Copynumber: 8.1 Consensus size: 19
235959 CGCGAAACTA
* **
235969 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATAGTC
235988 ATTTTCGCATTGCGAT--TC
1 A-TTTCGCATTGCGATAGTC
* **
236006 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATAGTC
**
236022 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATAGTC
236041 ATTTCGCATTGCGAT--TC
1 ATTTCGCATTGCGATAGTC
*
236058 -TTTCG--TTGTGATAGTC
1 ATTTCGCATTGCGATAGTC
236074 ATTTCCGCATTGCGATAGTC
1 ATTT-CGCATTGCGATAGTC
*
236094 AATTCCGCATTGCGATAGTC
1 -ATTTCGCATTGCGATAGTC
236114 A
1 A
236115 AATGAATGTC
Statistics
Matches: 108, Mismatches: 6, Indels: 26
0.77 0.04 0.19
Matches are distributed among these distances:
14 13 0.12
16 13 0.12
17 8 0.07
18 5 0.05
19 28 0.26
20 38 0.35
21 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTC
Found at i:236292 original size:458 final size:457
Alignment explanation
Indices: 235435--236334 Score: 1656
Period size: 458 Copynumber: 2.0 Consensus size: 457
235425 CAACGCGGAG
235435 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCA
1 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCA
*
235500 ACGGGAAACTAATTTCACGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
66 ACGCGAAACTAATTTCACGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
* *
235565 TTTCGGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCG
131 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCG
235630 ATAGTCAATTCCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACTTATCA
196 ATAGTCAATTCCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACTTATCA
* * *
235695 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTCACATATAA
261 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAAATGAAAATGTTAAAAGTTCACACATAA
**
235760 TATACACATAATACAACGTTTTTATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGAAGCC
326 TATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGAAGCC
235825 GGTTGTGATTGGGATTTTGATGAGGATCCATATTTTGGTAGAGGAAAAGATGAAAATTGTAATGC
391 GGTTGTGATTGGGATTTTGATGAGGAT-CATATTTTGGTAGAGGAAAAGATGAAAATTGTAATGC
235890 GAA
455 GAA
*
235893 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCA
1 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCA
*
235958 ACGCGAAACTAATTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
66 ACGCGAAACTAATTTCACGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
* *
236023 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAGTCATTTCCGCATTGCG
131 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCG
*
236088 ATAGTCAATTCCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAATTTATCA
196 ATAGTCAATTCCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACTTATCA
236153 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAAATGAAAATGTTAAAAGTTCACACATAA
261 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAAATGAAAATGTTAAAAGTTCACACATAA
*
236218 TATACACATAATACAATGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGAAGCC
326 TATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGAAGCC
*
236283 GGTTGTGATTGGGGTTTTGATGAGGATCATATTTTGGTAGAGGAAAAGATGA
391 GGTTGTGATTGGGATTTTGATGAGGATCATATTTTGGTAGAGGAAAAGATGA
236335 TTGTGATGGC
Statistics
Matches: 427, Mismatches: 15, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
457 25 0.06
458 402 0.94
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (457 bp):
ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCA
ACGCGAAACTAATTTCACGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCG
ATAGTCAATTCCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACTTATCA
TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAAATGAAAATGTTAAAAGTTCACACATAA
TATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGAAGCC
GGTTGTGATTGGGATTTTGATGAGGATCATATTTTGGTAGAGGAAAAGATGAAAATTGTAATGCG
AA
Found at i:238557 original size:24 final size:24
Alignment explanation
Indices: 238523--238576 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
238513 CTGAAAAATC
238523 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
238547 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
238571 ATCAAA
1 ATCAAA
238577 TTTTGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:239465 original size:20 final size:19
Alignment explanation
Indices: 239436--239689 Score: 179
Period size: 20 Copynumber: 12.6 Consensus size: 19
239426 GTCAGAATCT
*
239436 CGTTGTGATTTACAGATTCG
1 CGTTGCGATTTAC-GATTCG
*
239456 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
* *
239476 CATTGCGATTTACGTATTTG
1 CGTTGCGATTTACG-ATTCG
* *
239496 CATTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
* * *
239516 CATTGTGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
239536 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCG
* * *
239556 CGTTGCGATATACATATTCT
1 CGTTGCGATTTAC-GATTCG
*
239576 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
*
239596 CGTTGCGATTTTACG-TGTTG
1 CGTTGCGA-TTTACGAT-TCG
*
239616 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
* *
239637 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTAC-GATTCG
*
239658 CGTTGCGATATT-CAGAATCG
1 CGTTGCGAT-TTAC-GATTCG
239678 CGTTGCGATTTA
1 CGTTGCGATTTA
239690 TATGTTAGTG
Statistics
Matches: 192, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
19 5 0.03
20 148 0.77
21 38 0.20
22 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTACGATTCG
Found at i:239519 original size:60 final size:60
Alignment explanation
Indices: 239436--239666 Score: 214
Period size: 60 Copynumber: 3.8 Consensus size: 60
239426 GTCAGAATCT
* * *
239436 CGTTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTTG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTTG
* * * * **
239496 CATTGCGATTTACGGATACGCATTGTGATTTACGTATTCTCGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTAC-GTATTTG
* * * * * * * *
239556 CGTTGCGATATACATATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT-GTTG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTTG
* * * * *
239616 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 -CGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCGCGTTGCGAT
239667 ATTCAGAATC
Statistics
Matches: 137, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
60 88 0.64
61 30 0.22
62 19 0.14
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTTG
Found at i:239661 original size:41 final size:40
Alignment explanation
Indices: 239436--239689 Score: 273
Period size: 40 Copynumber: 6.3 Consensus size: 40
239426 GTCAGAATCT
* * * * *
239436 CGTTGTGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACG
* *
239476 CATTGCGATTTACGTATT-TGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCT-CGTTGCGATTTACGGATACG
* * *
239516 CATTGTGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* *
239556 CGTTGCGATATACATATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* *
239596 CGTTGCGATTTTACGTGTTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
239637 CGTTGCGATTTTACGGATACTCGTTGCGATATT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACGGATA-CG
239678 CGTTGCGATTTA
1 CGTTGCGATTTA
239690 TATGTTAGTG
Statistics
Matches: 186, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 115 0.62
41 68 0.37
42 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:239806 original size:20 final size:19
Alignment explanation
Indices: 239757--239810 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
239747 ATTATTCATA
239757 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
239776 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
239797 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
239811 TTTATTTCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:243778 original size:64 final size:64
Alignment explanation
Indices: 243706--243911 Score: 170
Period size: 64 Copynumber: 3.2 Consensus size: 64
243696 GCATCAATCC
* *
243706 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGTATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
243769 T
64 T
** ** *** *
243770 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
* * * * * * * *
243834 ATGCACCGATGCACTCAGG-CT-ATTTTAAACATCGAATGCATTTTATGCATCGTTGCACACT-T
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
*
243896 AGTGCACCGATGCACT
1 A-TGCATCGATGCACT
243912 AAGTGTTCCA
Statistics
Matches: 117, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
62 3 0.03
63 53 0.45
64 59 0.50
65 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:243891 original size:63 final size:64
Alignment explanation
Indices: 243734--243912 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 64
243724 GAATAAATTG
* * * * * * *
243734 AACATCGAATGCATTTCATGTATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCAATGCACCGATGCACTAGGCTATTATTAA
**
243798 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TT-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCAATGCACCGATGCACT-AGGCTATTATTAA
* * * *
243861 AACATCGAATGCATTTTATGCATCGTTGCACACTTAGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCAATGCACCGATGCACTA
243913 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.01
63 46 0.46
64 47 0.47
65 5 0.05
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCAATGCACCGATGCACTAGGCTATTATTAA
Found at i:246022 original size:21 final size:21
Alignment explanation
Indices: 245996--246045 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
245986 CAAAAGTTCA
245996 TGATGATCATCAAAAGAAGAT
1 TGATGATCATCAAAAGAAGAT
246017 TGATGATCATCAAAAGAAGAT
1 TGATGATCATCAAAAGAAGAT
246038 TGATGATC
1 TGATGATC
246046 TTAAAACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (21 bp):
TGATGATCATCAAAAGAAGAT
Found at i:251519 original size:19 final size:19
Alignment explanation
Indices: 251478--251529 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
251468 AATGCATTTC
*** *
251478 ATGCATCGATGCACTCTCT
1 ATGCATCGATGCACAAGCA
251497 ATGCATCGATGCACAAGCA
1 ATGCATCGATGCACAAGCA
*
251516 ATGCACCGATGCAC
1 ATGCATCGATGCAC
251530 TCAGGCTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCA
Found at i:252677 original size:11 final size:10
Alignment explanation
Indices: 252663--253007 Score: 138
Period size: 10 Copynumber: 34.1 Consensus size: 10
252653 AAAAATATCT
252663 TTAACATATAA
1 TTAA-ATATAA
252674 TT-AATATAA
1 TTAAATATAA
*
252683 TTAGTATATCAAA
1 TTA-AATAT--AA
252696 CTTATAATATAA
1 -TTA-AATATAA
252708 -TATAATATAA
1 TTA-AATATAA
252718 -TATAATATAA
1 TTA-AATATAA
252728 -TATAATATAA
1 TTA-AATATAA
252738 -TATAATATAA
1 TTA-AATATAA
252748 -TATAATATAA
1 TTA-AATATAA
252758 -TATAATATAA
1 TTA-AATATAA
252768 -TATAATATAA
1 TTA-AATATAA
252778 -TATAATATAA
1 TTA-AATATAA
252788 -TATAATATAA
1 TTA-AATATAA
252798 -TATAATATAA
1 TTA-AATATAA
252808 -TATAATATAA
1 TTA-AATATAA
252818 -TATAATATAA
1 TTA-AATATAA
252828 -TATAATATAA
1 TTA-AATATAA
252838 -TATAATATAA
1 TTA-AATATAA
252848 -TATAATATAA
1 TTA-AATATAA
252858 -TATAATATAA
1 TTA-AATATAA
*
252868 -TATATATAA
1 TTAAATATAA
*
252877 TATATATATAA
1 T-TAAATATAA
252888 -TATAATAT-A
1 TTA-AATATAA
252897 TATAAATATAA
1 T-TAAATATAA
252908 -TATAATATAA
1 TTA-AATATAA
252918 -TATAATATAA
1 TTA-AATATAA
252928 -TATAATATAA
1 TTA-AATATAA
252938 -TATAATATAA
1 TTA-AATATAA
252948 -TATAATATAA
1 TTA-AATATAA
*
252958 -TATATATAA
1 TTAAATATAA
252967 -TATAATATAA
1 TTA-AATATAA
252977 -TATAATATAA
1 TTA-AATATAA
252987 -TATAATATAA
1 TTA-AATATAA
252997 -TATAATATAA
1 TTA-AATATAA
253007 T
1 T
253008 ATAATATTGT
Statistics
Matches: 313, Mismatches: 7, Indels: 28
0.90 0.02 0.08
Matches are distributed among these distances:
9 27 0.09
10 257 0.82
11 18 0.06
12 2 0.01
13 2 0.01
14 7 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAATATAA
Found at i:252708 original size:5 final size:5
Alignment explanation
Indices: 252698--253014 Score: 595
Period size: 5 Copynumber: 63.6 Consensus size: 5
252688 ATATCAAACT
252698 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
252748 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
252798 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
252848 TATAA TATAA TATAA TATAA TAT-A TATAA TATATA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA
252897 TATAAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TAT-AA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
252948 TATAA TATAA TAT-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
252997 TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TAT
253015 TGTAATCTCT
Statistics
Matches: 307, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.04
5 286 0.93
6 9 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:253063 original size:14 final size:15
Alignment explanation
Indices: 253036--253073 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
253026 GTGGACAAAT
*
253036 ATATTATTTTTAATA
1 ATATTATTTATAATA
253051 ATATT-TTTATAATA
1 ATATTATTTATAATA
*
253065 ATAATATTT
1 ATATTATTT
253074 TCATCTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTATTTATAATA
Found at i:253185 original size:3 final size:3
Alignment explanation
Indices: 253177--253201 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
253167 AAACTCTTTG
253177 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
253202 AGTTTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:257051 original size:27 final size:27
Alignment explanation
Indices: 257009--257076 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
256999 TTGTAGGAAT
257009 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
257034 TATAGAGATATGATTTGTTACCATTCG
1 TATAGAGATATGATTTGTTACCATTCC
257061 TATAGAGATATGATTT
1 TATAGAGATATGATTT
257077 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:261739 original size:27 final size:27
Alignment explanation
Indices: 261697--261764 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
261687 GTGTAGGAAT
261697 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
261722 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
261749 TATAGAGATATGATTT
1 TATAGAGATATGATTT
261765 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:263297 original size:30 final size:30
Alignment explanation
Indices: 263263--263325 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
263253 AAATGGCTCT
263263 TGACAATCTGAAAGAATCCAAGCAGAGTGA
1 TGACAATCTGAAAGAATCCAAGCAGAGTGA
263293 TGACAATCTGAAAGAATCCAAGCAGAGTGA
1 TGACAATCTGAAAGAATCCAAGCAGAGTGA
263323 TGA
1 TGA
263326 GCATGCCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (30 bp):
TGACAATCTGAAAGAATCCAAGCAGAGTGA
Found at i:264610 original size:12 final size:13
Alignment explanation
Indices: 264589--264620 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
264579 ATAGAAAAAA
264589 AAAT-AAATAA-T
1 AAATAAAATAATT
264600 AAATAAAATAATT
1 AAATAAAATAATT
264613 AAATAAAA
1 AAATAAAA
264621 CCAAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 6 0.32
13 9 0.47
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:264712 original size:16 final size:16
Alignment explanation
Indices: 264659--264722 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
264649 ATAAATAACC
* *
264659 TAAAGTAAAAAAAAGA
1 TAAAATAAAAAATAGA
* * *
264675 TAAAGTATCAAAATAAA
1 TAAAATA-AAAAATAGA
264692 TAAAATAAAAAATAGA
1 TAAAATAAAAAATAGA
264708 TAAAAAATAAAAAAT
1 T--AAAATAAAAAAT
264723 CAAACAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 15 0.38
17 12 0.31
18 12 0.31
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAAATAGA
Found at i:264900 original size:32 final size:33
Alignment explanation
Indices: 264836--264912 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
264826 AACAGTGATA
* *
264836 AAAAATAAA-AAAATAAAAAAAAATATCTAAAT
1 AAAAATAAAGAAAATAAAAAAAAACAACTAAAT
*
264868 AAAAATAAAGAAAATAAAAAAAACCAAC-AAAT
1 AAAAATAAAGAAAATAAAAAAAAACAACTAAAT
*
264900 AAAAA-GAAGAAAA
1 AAAAATAAAGAAAA
264913 AATACGAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 18 0.45
33 15 0.38
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.12
Consensus pattern (33 bp):
AAAAATAAAGAAAATAAAAAAAAACAACTAAAT
Found at i:264915 original size:33 final size:33
Alignment explanation
Indices: 264833--264916 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
264823 CATAACAGTG
* *
264833 ATAAAAA-ATAAAAAAATAAAAAAAAATATCTAA
1 ATAAAAAGA-AAAAAAATAAAAAAAAACAACTAA
* * *
264866 ATAAAAATAAAGAAAATAAAAAAAACCAAC-AA
1 ATAAAAAGAAAAAAAATAAAAAAAAACAACTAA
264898 ATAAAAAGAAGAAAAAATA
1 ATAAAAAGAA-AAAAAATA
264917 CGAAACTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 11 0.26
33 31 0.72
34 1 0.02
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.13
Consensus pattern (33 bp):
ATAAAAAGAAAAAAAATAAAAAAAAACAACTAA
Found at i:264994 original size:2 final size:2
Alignment explanation
Indices: 264987--265022 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
264977 AAGAAAGAAA
264987 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
265023 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267402 original size:2 final size:2
Alignment explanation
Indices: 267383--267440 Score: 80
Period size: 2 Copynumber: 28.0 Consensus size: 2
267373 ATATGTATGG
*
267383 AT AT AT GT AGT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
267427 AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT
267441 CTAATTCATG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:268435 original size:20 final size:20
Alignment explanation
Indices: 268407--268445 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
268397 GGATTATCAA
268407 TGGTACTTCAGGACAAATAG
1 TGGTACTTCAGGACAAATAG
* * *
268427 TGGTCCTTCGGGATAAATA
1 TGGTACTTCAGGACAAATA
268446 TTAAGTGCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (20 bp):
TGGTACTTCAGGACAAATAG
Found at i:272701 original size:21 final size:21
Alignment explanation
Indices: 272683--272725 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
272673 CTTATTTTAT
272683 TTTTTCATTTTTTTCTTTTTC
1 TTTTTCATTTTTTTCTTTTTC
* *
272704 TTTTTCCTTTTTTATTTTTTTC
1 TTTTTCATTTTTT-TCTTTTTC
272726 AATTTAGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCATTTTTTTCTTTTTC
Found at i:283033 original size:4 final size:4
Alignment explanation
Indices: 283013--283051 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
283003 AAAGTGTTAG
*
283013 ATAA AAAA ATGAA ATAA ATAA ATAA ATAAA ATAA ATAA A
1 ATAA ATAA AT-AA ATAA ATAA ATAA AT-AA ATAA ATAA A
283052 ACCAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:283039 original size:17 final size:17
Alignment explanation
Indices: 283013--283141 Score: 77
Period size: 17 Copynumber: 7.4 Consensus size: 17
283003 AAAGTGTTAG
*
283013 ATAAAAAAATGAAATAA
1 ATAAAAAAATAAAATAA
*
283030 ATAAATAAATAAAATAA
1 ATAAAAAAATAAAATAA
* *
283047 ATAAAACCAAGTAAAA-AG
1 ATAAAA--AAATAAAATAA
*
283065 A-AAAAAAATAATAGGTAA
1 ATAAAAAAATAA-A-ATAA
* *
283083 ATAAAAAACCTAAAGTAA
1 ATAAAAAA-ATAAAATAA
* *
283101 AAAAAGATAAAGTAACA-AA
1 ATAAA-A-AAA-TAAAATAA
283120 ATAAAAAAATAAAATAA
1 ATAAAAAAATAAAATAA
283137 A-AAAA
1 ATAAAA
283142 TAGATAAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
15 5 0.06
16 9 0.10
17 30 0.35
18 13 0.15
19 21 0.24
20 8 0.09
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (17 bp):
ATAAAAAAATAAAATAA
Found at i:283126 original size:21 final size:21
Alignment explanation
Indices: 283100--283143 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
283090 ACCTAAAGTA
* *
283100 AAAAAAGATAAAGTAACAAAAT
1 AAAAAA-ATAAAATAAAAAAAT
283122 AAAAAAATAAAATAAAAAAAT
1 AAAAAAATAAAATAAAAAAAT
283143 A
1 A
283144 GATAAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAAAATAAAATAAAAAAAT
Found at i:283148 original size:12 final size:13
Alignment explanation
Indices: 283013--283152 Score: 58
Period size: 13 Copynumber: 10.6 Consensus size: 13
283003 AAAGTGTTAG
*
283013 ATAAAAAAATGAA
1 ATAAAAAAATAAA
*
283026 ATAAATAAAT-AA
1 ATAAAAAAATAAA
283038 ATAAAATAAATAAA
1 ATAAAA-AAATAAA
* *
283052 ACCAAGTAAAAAGAAA
1 A-TAA--AAAAATAAA
*
283068 A-AAAATAATAGGTAA
1 ATAAAAAAATA---AA
*
283083 ATAAAAAACCTAAA
1 ATAAAAAA-ATAAA
* *
283097 GT--AAAAA-AAG
1 ATAAAAAAATAAA
** *
283107 ATAAAGTAACAAA
1 ATAAAAAAATAAA
283120 ATAAAAAAATAAA
1 ATAAAAAAATAAA
*
283133 ATAAAAAAAT-AG
1 ATAAAAAAATAAA
283145 ATAAAAAA
1 ATAAAAAA
283153 CCAAAAATCA
Statistics
Matches: 95, Mismatches: 19, Indels: 27
0.67 0.13 0.19
Matches are distributed among these distances:
10 3 0.03
12 28 0.29
13 35 0.37
14 8 0.08
15 5 0.05
16 12 0.13
17 4 0.04
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:283158 original size:38 final size:37
Alignment explanation
Indices: 283081--283158 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
283071 AATAATAGGT
* * *
283081 AAATAAAAAACCTAAAGTAAAAAAAGATAAAGTAACA
1 AAATAAAAAACATAAAATAAAAAAAGATAAAGAAACA
283118 AAATAAAAAA-ATAAAATAAAAAAATAGATAAA-AAACCA
1 AAATAAAAAACATAAAAT-AAAAAA-AGATAAAGAAA-CA
283156 AAA
1 AAA
283159 ATCAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.14
37 18 0.51
38 12 0.34
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (37 bp):
AAATAAAAAACATAAAATAAAAAAAGATAAAGAAACA
Found at i:283321 original size:16 final size:15
Alignment explanation
Indices: 283280--283319 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
283270 AAATTAAAAA
* *
283280 AAATAAAATATATAT
1 AAATAAAAAATGTAT
283295 AAATAAAAAATGTAT
1 AAATAAAAAATGTAT
283310 AAATAAAAAA
1 AAATAAAAAA
283320 ATAAAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAATAAAAAATGTAT
Found at i:283463 original size:18 final size:20
Alignment explanation
Indices: 283428--283465 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
283418 AATCATATGT
283428 ATATATATATATATAATAAA
1 ATATATATATATATAATAAA
*
283448 ATATA-ATATTTA-AATAAA
1 ATATATATATATATAATAAA
283466 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATATATATATAATAAA
Found at i:285042 original size:27 final size:27
Alignment explanation
Indices: 284955--285031 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
284945 ACATTATTAT
*
284955 TTTATCGGTTTTGTTATTATTGGCCGC
1 TTTACCGGTTTTGTTATTATTGGCCGC
*
284982 TTTACTGGTTTTGTTATTATTGGCCGC
1 TTTACCGGTTTTGTTATTATTGGCCGC
285009 TTTACCGGTTTTGTTATTATTGG
1 TTTACCGGTTTTGTTATTATTGG
285032 ATACTTTACC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.12, C:0.13, G:0.22, T:0.53
Consensus pattern (27 bp):
TTTACCGGTTTTGTTATTATTGGCCGC
Found at i:290137 original size:265 final size:253
Alignment explanation
Indices: 289825--290322 Score: 750
Period size: 265 Copynumber: 1.9 Consensus size: 253
289815 AATAAAGTTT
*
289825 ACCCGACTCGACCAGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
1 ACCCGACCCGACCAGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
289890 AAAAAAAATATATAGAG-GAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
66 AAAAAAAATATATAGAGTG-GTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-
* *
289954 TTTTTGGGTCGGGTCGGTCGGGTATTTTTCACCCTAAACCCGAACCCAACCCGACCCGAATATCA
129 TATTT---TC--G--GGTCGGGTATTTTTCACCCTAAACCCAAACCCAACCCGACCCGAATATCA
*
290019 CACTTAAAAAAACTGACTCGATCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAG
187 CACTT-AAAAAA---AC-CGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAG
290084 AAATCCG
247 AAATCCG
290091 ACCCGACCCGA-CACGAAATAAT-AAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGA
1 ACCCGACCCGACCA-GAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGA
**
290154 AAAAAATTATATATAGAGTGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
65 AAAAAAAAATATATAGAGTGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* * *
290219 ATTTTCGGGTCGGGTATTTTTCACCTTAAACCCAAACTCGACCCGACCCGAATATCACACTTAAA
130 ATTTTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCAACCCGACCCGAATATCACACTTAAA
*
290284 AAAACCGACCCGACCAAAATAAAGTTTCACTCGACCCGA
195 AAAACCGACCCGACCAAAATAAAGTTTCACCCGACCCGA
290323 CCCGACCCGA
Statistics
Matches: 220, Mismatches: 10, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
252 32 0.15
253 2 0.01
256 6 0.03
257 51 0.23
259 1 0.00
261 2 0.01
264 4 0.02
265 103 0.47
266 19 0.09
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (253 bp):
ACCCGACCCGACCAGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
AAAAAAAATATATAGAGTGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA
TTTTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCAACCCGACCCGAATATCACACTTAAAA
AAACCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCCG
Found at i:296989 original size:20 final size:19
Alignment explanation
Indices: 296951--296989 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
296941 TCTAAAATAA
* *
296951 TAAAATTATTTATTTTTTT
1 TAAAATTAATTAATTTTTT
296970 TAAAATGTAATTAATTTTTT
1 TAAAAT-TAATTAATTTTTT
296990 CGTATGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TAAAATTAATTAATTTTTT
Found at i:300192 original size:33 final size:30
Alignment explanation
Indices: 300155--300227 Score: 74
Period size: 33 Copynumber: 2.3 Consensus size: 30
300145 TGCAGATTCT
300155 TCACCAAAGGTTGTGGGACGGGTTGGAGTTTCA
1 TCACCAAAGGTTGTGGGA---GTTGGAGTTTCA
* * * *
300188 TCACCCAAGTTTGTGGTAGTTGGAGTTTCT
1 TCACCAAAGGTTGTGGGAGTTGGAGTTTCA
300218 TCAACCAAAG
1 TC-ACCAAAG
300228 TCGTCAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 13 0.38
31 6 0.18
33 15 0.44
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (30 bp):
TCACCAAAGGTTGTGGGAGTTGGAGTTTCA
Found at i:300438 original size:33 final size:33
Alignment explanation
Indices: 300401--300465 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
300391 TGGAAGCAGA
*
300401 GTAGGAGTTTCTTCC-CTGGAAGTTGGAGGAATT
1 GTAGGACTTTC-TCCACTGGAAGTTGGAGGAATT
* *
300434 GTAGGACTTTCTCCACTTGAGGTTGGAGGAAT
1 GTAGGACTTTCTCCACTGGAAGTTGGAGGAAT
300466 GGACCGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (33 bp):
GTAGGACTTTCTCCACTGGAAGTTGGAGGAATT
Found at i:300608 original size:60 final size:59
Alignment explanation
Indices: 300500--300951 Score: 460
Period size: 60 Copynumber: 7.6 Consensus size: 59
300490 TTCAGGATTA
* * * *
300500 GCTGGTGTCTCTTCGCCTAAGGTTCTAGGAATACTAGGGGGTTT-TTCTGCCAAGGGAATG
1 GCTGGAGTTTCTTCACC-AAGGTTCTGGGAATACTA-GGGGTTTCTTCTGCCAAGGGAATG
* * *
300560 GTTGGAGTTTCTTCACTCAGGGTTCTGGGAATACTGGGGGTTTCTTCTGCCAAGGGAATG
1 GCTGGAGTTTCTTCAC-CAAGGTTCTGGGAATACTAGGGGTTTCTTCTGCCAAGGGAATG
* * *
300620 GCAGGAGTTTCTTCATCCAAGGTTCTGGGAATGCTA-GGGTAGTCTTCTGCC-AGGGAAATG
1 GCTGGAGTTTCTTCA-CCAAGGTTCTGGGAATACTAGGGGT-TTCTTCTGCCAAGGG-AATG
* * * * *
300680 ACTGGTGTTTCTT--CC---GTTCTTGAAATACTAGGGGTTTCTTC-GACC-AGTGGAATA
1 GCTGGAGTTTCTTCACCAAGGTTCTGGGAATACTAGGGGTTTCTTCTG-CCAAG-GGAATG
* * * * * *
300734 GTTGGCGTTTCTTCAACCAAGGTTCTGGGAATACTAGTGGTTTCATCCGCCAAGGGAATA
1 GCTGGAGTTTCTTC-ACCAAGGTTCTGGGAATACTAGGGGTTTCTTCTGCCAAGGGAATG
* *
300794 GCTGGAGTTTCTTCACCTAAGGTTGTGGGAGTACTAGGGGTTTCTTCTGCCACAGGG-ATG
1 GCTGGAGTTTCTTCACC-AAGGTTCTGGGAATACTAGGGGTTTCTTCTGCCA-AGGGAATG
* *
300854 GCTGGAGTTTCTTCACCCAAGGTTCTGGGAACACTAGGGGTTTCTTC-GACCAAGGGAATA
1 GCTGGAGTTTCTTCA-CCAAGGTTCTGGGAATACTAGGGGTTTCTTCTG-CCAAGGGAATG
*
300914 GCTGGAGTTTCTTCACCTGAGGTTCTGGGAATACTAGG
1 GCTGGAGTTTCTTCACC-AAGGTTCTGGGAATACTAGG
300952 ATTTTCTGCT
Statistics
Matches: 328, Mismatches: 42, Indels: 44
0.79 0.10 0.11
Matches are distributed among these distances:
53 1 0.00
54 34 0.10
55 6 0.02
57 4 0.01
59 25 0.08
60 247 0.75
61 11 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (59 bp):
GCTGGAGTTTCTTCACCAAGGTTCTGGGAATACTAGGGGTTTCTTCTGCCAAGGGAATG
Found at i:301082 original size:63 final size:63
Alignment explanation
Indices: 301014--301149 Score: 220
Period size: 63 Copynumber: 2.2 Consensus size: 63
301004 GTGGGAATGC
*
301014 TTGAAGTTTCTTGACCTTCAGTAACGAAGT-CTGAATTTTCCTCACCCAAGCTTACATTAACCA
1 TTGAAGTTTCTTGACCTTCAGTAACGAA-TCCTGAATTTTCCTCAACCAAGCTTACATTAACCA
* * *
301077 TTGAAGTTTCTTGACCTTCGGTACCGAATCCTGAATTTTCCTCAACCAAGCTTACATTAACCG
1 TTGAAGTTTCTTGACCTTCAGTAACGAATCCTGAATTTTCCTCAACCAAGCTTACATTAACCA
301140 TTGAAGTTTC
1 TTGAAGTTTC
301150 CTCTCCCAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (63 bp):
TTGAAGTTTCTTGACCTTCAGTAACGAATCCTGAATTTTCCTCAACCAAGCTTACATTAACCA
Found at i:301453 original size:33 final size:33
Alignment explanation
Indices: 301353--301455 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
301343 TCAACATCGG
* * *
301353 TTGTAGCAATTGGCAATGTTTCCTCATACATGC
1 TTGTAGCAATGGGTAATGTCTCCTCATACATGC
* * ** *
301386 TCGTGGGGATGGGTAATGTTTCCTCATACATGC
1 TTGTAGCAATGGGTAATGTCTCCTCATACATGC
301419 TTGTAGCAATGGGTGAA-GTCTCCTCATACATGC
1 TTGTAGCAATGGGT-AATGTCTCCTCATACATGC
301452 TTGT
1 TTGT
301456 GTCGACGTCT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 56 0.97
34 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (33 bp):
TTGTAGCAATGGGTAATGTCTCCTCATACATGC
Found at i:304461 original size:12 final size:12
Alignment explanation
Indices: 304444--304469 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
304434 CCATCTAACA
304444 ACACCTTCTAAT
1 ACACCTTCTAAT
304456 ACACCTTCTAAT
1 ACACCTTCTAAT
304468 AC
1 AC
304470 TTTTTGTGGA
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:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (12 bp):
ACACCTTCTAAT
Found at i:305819 original size:26 final size:26
Alignment explanation
Indices: 305790--305874 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
305780 TAGATAAAGA
305790 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
* * *
305816 TAACT-CTTAGAAAG-TTAG-ATAAGGA-
1 TAACTACTAAG-TAGTTTAGTTTAA--AT
*
305841 TAACTACTACGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
*
305867 TAAATACT
1 TAACTACT
305875 TGTTCTCACC
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 22 0.50
27 3 0.07
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (26 bp):
TAACTACTAAGTAGTTTAGTTTAAAT
Found at i:305843 original size:51 final size:51
Alignment explanation
Indices: 305765--305869 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
305755 AATATAACAC
305765 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
* *
305816 TAACTCTTAGAAAGTTAGATAAGGATAACTACTACGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
305867 TAA
1 TAA
305870 ATACTTGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (51 bp):
TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
Found at i:305844 original size:25 final size:24
Alignment explanation
Indices: 305765--305845 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
305755 AATATAACAC
305765 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGAT-AAGA
* * *
305790 TAACTACTAAG-TAGTTTAGTTTAA-A
1 TAACT-CTTAGAAAG-TTAG-ATAAGA
305815 TTAACTCTTAGAAAGTTAGATAAGGA
1 -TAACTCTTAGAAAGTTAGATAA-GA
305841 TAACT
1 TAACT
305846 ACTACGTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 3 0.07
25 21 0.49
26 18 0.42
27 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (24 bp):
TAACTCTTAGAAAGTTAGATAAGA
Found at i:311719 original size:26 final size:26
Alignment explanation
Indices: 311690--311774 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
311680 TAGATAAAGA
311690 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
* * *
311716 TAACT-CTTAGAAAG-TTAG-ATAAGGA-
1 TAACTACTAAG-TAGTTTAGTTTAA--AT
311741 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
*
311767 TAAATACT
1 TAACTACT
311775 TGTTCTCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 23 0.51
27 3 0.07
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (26 bp):
TAACTACTAAGTAGTTTAGTTTAAAT
Found at i:311727 original size:51 final size:51
Alignment explanation
Indices: 311665--311769 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
311655 AATATAACAC
311665 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
*
311716 TAACTCTTAGAAAGTTAGATAAGGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
311767 TAA
1 TAA
311770 ATACTTGTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (51 bp):
TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
Found at i:311744 original size:25 final size:24
Alignment explanation
Indices: 311665--311745 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
311655 AATATAACAC
311665 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGAT-AAGA
* * *
311690 TAACTACTAAG-TAGTTTAGTTTAA-A
1 TAACT-CTTAGAAAG-TTAG-ATAAGA
311715 TTAACTCTTAGAAAGTTAGATAAGGA
1 -TAACTCTTAGAAAGTTAGATAA-GA
311741 TAACT
1 TAACT
311746 ACTAAGTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 3 0.07
25 21 0.49
26 18 0.42
27 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (24 bp):
TAACTCTTAGAAAGTTAGATAAGA
Found at i:311756 original size:25 final size:24
Alignment explanation
Indices: 311677--311756 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
311667 ACTCTTAGAA
311677 AGTTAGATAAAGATAACTACTAAGT
1 AGTTAGAT-AAGATAACTACTAAGT
* * *
311702 AGTTTAGTTTAA-ATTAACT-CTTAGAA
1 AG-TTAG-ATAAGA-TAACTACTAAG-T
311728 AGTTAGATAAGGATAACTACTAAGT
1 AGTTAGATAA-GATAACTACTAAGT
311753 AGTT
1 AGTT
311757 TAGTTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 3 0.07
25 20 0.48
26 18 0.43
27 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (24 bp):
AGTTAGATAAGATAACTACTAAGT
Found at i:322913 original size:28 final size:29
Alignment explanation
Indices: 322873--322937 Score: 114
Period size: 28 Copynumber: 2.3 Consensus size: 29
322863 CCCGTTGACC
322873 GGGTGCTATTCTGATAATTA-TTGGAAAA
1 GGGTGCTATTCTGATAATTATTTGGAAAA
*
322901 GGGTGCTATTCTGATAATTATTTTGAAAA
1 GGGTGCTATTCTGATAATTATTTGGAAAA
322930 GGGTGCTA
1 GGGTGCTA
322938 ATTTCGTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTGCTATTCTGATAATTATTTGGAAAA
Found at i:323020 original size:29 final size:30
Alignment explanation
Indices: 322969--323057 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
322959 TAATTTCTTG
*
322969 ATTTATTTTAAAAAT-ATGATATTTTAGTA
1 ATTTATTTTGAAAATGATGATATTTTAGTA
* *
322998 A-TTATTTTGAAAATGGTGATATTTTGGTA
1 ATTTATTTTGAAAATGATGATATTTTAGTA
* * * *
323027 ATTTTTTTTGGAAATGATGTTATTTTCGTA
1 ATTTATTTTGAAAATGATGATATTTTAGTA
323057 A
1 A
323058 AATGGTTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 12 0.24
29 14 0.28
30 24 0.48
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (30 bp):
ATTTATTTTGAAAATGATGATATTTTAGTA
Found at i:323786 original size:24 final size:24
Alignment explanation
Indices: 323753--323853 Score: 148
Period size: 24 Copynumber: 4.2 Consensus size: 24
323743 TATCTGATTT
* *
323753 TTGACCTGGATTTTGATATTATAC
1 TTGACATGGATTTTGATATGATAC
323777 TTGACATGGATTTTGATATGATAC
1 TTGACATGGATTTTGATATGATAC
* *
323801 TTGACCTGGATTTTTATATGATAC
1 TTGACATGGATTTTGATATGATAC
* *
323825 TTGACATGGATTCTGATATGCTAC
1 TTGACATGGATTTTGATATGATAC
323849 TTGAC
1 TTGAC
323854 CTGAATTATG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (24 bp):
TTGACATGGATTTTGATATGATAC
Found at i:323825 original size:48 final size:48
Alignment explanation
Indices: 323753--323856 Score: 172
Period size: 48 Copynumber: 2.2 Consensus size: 48
323743 TATCTGATTT
* *
323753 TTGACCTGGATTTTGATATTATACTTGACATGGATTTTGATATGATAC
1 TTGACCTGGATTTTGATATGATACTTGACATGGATTCTGATATGATAC
* *
323801 TTGACCTGGATTTTTATATGATACTTGACATGGATTCTGATATGCTAC
1 TTGACCTGGATTTTGATATGATACTTGACATGGATTCTGATATGATAC
323849 TTGACCTG
1 TTGACCTG
323857 AATTATGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (48 bp):
TTGACCTGGATTTTGATATGATACTTGACATGGATTCTGATATGATAC
Found at i:324353 original size:21 final size:21
Alignment explanation
Indices: 324329--324378 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
324319 TGGATTTATC
*
324329 TGTATTATTTATATTTTGTTA
1 TGTATTATTTATATTTTATTA
324350 TGTATTATTTATATTTTATTA
1 TGTATTATTTATATTTTATTA
324371 TGTATTAT
1 TGTATTAT
324379 ATTTAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (21 bp):
TGTATTATTTATATTTTATTA
Found at i:324390 original size:21 final size:21
Alignment explanation
Indices: 324329--324392 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
324319 TGGATTTATC
* * *
324329 TGTATTATTTATATTTTGTTA
1 TGTATTATTTATAATGTATTA
* *
324350 TGTATTATTTATATTTTATTA
1 TGTATTATTTATAATGTATTA
324371 TGTATTATATT-TAATGTATTA
1 TGTATTAT-TTATAATGTATTA
324392 T
1 T
324393 AAGTTGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TGTATTATTTATAATGTATTA
Found at i:324556 original size:45 final size:45
Alignment explanation
Indices: 324507--324619 Score: 154
Period size: 45 Copynumber: 2.5 Consensus size: 45
324497 AATGTCGAAG
* **
324507 AACAATTATGTCAATATTTTCTTCCCTTTGATTAAAATGTCAACA
1 AACAATGATGTCAATATCGTCTTCCCTTTGATTAAAATGTCAACA
* * * * *
324552 AACAATGATGTCATTATCGTCTTTCCTTTGATTCAAATGTCGACC
1 AACAATGATGTCAATATCGTCTTCCCTTTGATTAAAATGTCAACA
324597 AACAATGATGTCAATATCGTCTT
1 AACAATGATGTCAATATCGTCTT
324620 GAGATAGTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (45 bp):
AACAATGATGTCAATATCGTCTTCCCTTTGATTAAAATGTCAACA
Found at i:329946 original size:3 final size:3
Alignment explanation
Indices: 329938--329962 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
329928 AAATTTTGAT
329938 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
329963 ACAGGCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:338975 original size:7 final size:7
Alignment explanation
Indices: 338957--339010 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
338947 TTATCGGAGG
338957 GAAACAAA
1 GAAA-AAA
*
338965 GAAACAA
1 GAAAAAA
338972 GAAAAAA
1 GAAAAAA
338979 GAAAAAA
1 GAAAAAA
338986 GAAAAAA
1 GAAAAAA
338993 GAAAAAA
1 GAAAAAA
* *
339000 GGAAAAG
1 GAAAAAA
339007 GAAA
1 GAAA
339011 GGCAAAATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
7 37 0.90
8 4 0.10
ACGTcount: A:0.78, C:0.04, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:341624 original size:14 final size:14
Alignment explanation
Indices: 341601--341630 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
341591 AATACCAATA
*
341601 TTAAATATAAAAAT
1 TTAAAAATAAAAAT
341615 TTAAAAATAAAAAT
1 TTAAAAATAAAAAT
341629 TT
1 TT
341631 TGATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAATAAAAAT
Found at i:342181 original size:2 final size:2
Alignment explanation
Indices: 342174--342215 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
342164 TACCAAACGC
342174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
342216 CCAAAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:345045 original size:2 final size:2
Alignment explanation
Indices: 345038--345070 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
345028 CTCGATGTGA
*
345038 AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
345071 TTAATTCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:345581 original size:17 final size:15
Alignment explanation
Indices: 345549--345578 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
345539 CCATGTTTAG
345549 ATTTTTTTAAAAAAT
1 ATTTTTTTAAAAAAT
345564 ATTTATTTTAAAAAA
1 ATTT-TTTTAAAAAA
345579 ATAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTTTAAAAAAT
Done.