Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006607.1 Hibiscus syriacus cultivar Beakdansim tig00016212_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: 1995858
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:534428 original size:115 final size:115
Alignment explanation
Indices: 534226--534456 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
534216 CATATCCCCG
534226 AATGGTTCCTTTCACAATGTGGACATTGTCTGACTTGGCTTGGGTTAGATCTCCTAGCTCCAGAT
1 AATGGTTCCTTTCACAATGTGGACATTGTCTGACTTGGCTTGGGTTAGATCTCCTAGCTCCAGAT
534291 CCCACTGACTTTGTCTGTTGACCCCTCATCTGATTTGATCCCCTTGCAGA
66 CCCACTGACTTTGTCTGTTGACCCCTCATCTGATTTGATCCCCTTGCAGA
534341 AATGGTTCCTTTCACAATGTGGACATTGTCTGACTTGGCTTGGGTTAGATCTCCTAGCTCCAGAT
1 AATGGTTCCTTTCACAATGTGGACATTGTCTGACTTGGCTTGGGTTAGATCTCCTAGCTCCAGAT
534406 CCCACTGACTTTGTCTGTTGACCCCTCATCTGATTTGATCCCCTTGCAGA
66 CCCACTGACTTTGTCTGTTGACCCCTCATCTGATTTGATCCCCTTGCAGA
534456 A
1 A
534457 GATGCAACTG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.35
Consensus pattern (115 bp):
AATGGTTCCTTTCACAATGTGGACATTGTCTGACTTGGCTTGGGTTAGATCTCCTAGCTCCAGAT
CCCACTGACTTTGTCTGTTGACCCCTCATCTGATTTGATCCCCTTGCAGA
Found at i:536130 original size:18 final size:18
Alignment explanation
Indices: 536087--536132 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
536077 TTTGTCCCAG
*
536087 AGGACCAATATGTCCCGA
1 AGGACCACTATGTCCCGA
536105 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
536123 AGGACCACTA
1 AGGACCACTA
536133 ATAATCCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:536862 original size:64 final size:64
Alignment explanation
Indices: 536746--536867 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
536736 ACATAAATCC
* * * * *
536746 CATTTGATGTTTGTATTTTAAGGGGGTGCATCAATGCACTACTTGTACATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTACATCGATACACTGATGG
* * * **
536810 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGTATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTACATCGATACAC
536868 CTTGAATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTACATCGATACACTGATGG
Found at i:539518 original size:58 final size:58
Alignment explanation
Indices: 539427--539559 Score: 198
Period size: 58 Copynumber: 2.3 Consensus size: 58
539417 AATTAATTAG
* * * *
539427 TTAATTAATCATGTTCAAT--AAATAAATTGTTTTAACTTTTAATGATTATAATTAAT
1 TTAATTAATCATATTCAATGCCAATAAATTATTTTAACTTGTAATGATTATAATTAAT
*
539483 TTAATTATTCATATTCAATGCCAATAAATTATTTTAACTTGTAATGATTATAATTAAT
1 TTAATTAATCATATTCAATGCCAATAAATTATTTTAACTTGTAATGATTATAATTAAT
*
539541 TTAATTAATCATGTTCAAT
1 TTAATTAATCATATTCAAT
539560 AAATAAATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 17 0.25
58 51 0.75
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (58 bp):
TTAATTAATCATATTCAATGCCAATAAATTATTTTAACTTGTAATGATTATAATTAAT
Found at i:539687 original size:20 final size:21
Alignment explanation
Indices: 539641--539692 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
539631 TAATAAGTAA
* * *
539641 ATTTATTAATTTAATTATCAT
1 ATTTAATAATTTAATTATAAC
*
539662 AATTAATAATTT-ATTATAAC
1 ATTTAATAATTTAATTATAAC
*
539682 ATTTAAAAATT
1 ATTTAATAATT
539693 AATCATATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAATAATTTAATTATAAC
Found at i:540610 original size:21 final size:20
Alignment explanation
Indices: 540582--540657 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 20
540572 AAATGCCTGA
540582 GGGTATCGATACCTAAGTAGG
1 GGGTATCGATACCTAA-TAGG
*
540603 GGGAATCGATACC-ATATCATGG
1 GGGTATCGATACCTA-AT-A-GG
*
540625 GGGTATCGATACCTACTAGG
1 GGGTATCGATACCTAATAGG
*
540645 GGGTATCGGTACC
1 GGGTATCGATACC
540658 ATCTGAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 16 0.34
21 15 0.32
22 15 0.32
23 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCTAATAGG
Found at i:540632 original size:22 final size:21
Alignment explanation
Indices: 540582--540659 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
540572 AAATGCCTGA
*
540582 GGGTATCGATACC-TAAGTAGG
1 GGGTATCGATACCAT-ACTAGG
*
540603 GGGAATCGATACCATA-TCATGG
1 GGGTATCGATACCATACT-A-GG
540625 GGGTATCGATACC-TACTAGG
1 GGGTATCGATACCATACTAGG
*
540645 GGGTATCGGTACCAT
1 GGGTATCGATACCAT
540660 CTGAGCATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 15 0.31
21 18 0.37
22 16 0.33
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (21 bp):
GGGTATCGATACCATACTAGG
Found at i:540721 original size:20 final size:20
Alignment explanation
Indices: 540696--540733 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
540686 CAAAATATTC
540696 ATAGGGGGTATCGGTACCCT
1 ATAGGGGGTATCGGTACCCT
540716 ATAGGGGGTATCGGTACC
1 ATAGGGGGTATCGGTACC
540734 ATCCGAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (20 bp):
ATAGGGGGTATCGGTACCCT
Found at i:540722 original size:76 final size:76
Alignment explanation
Indices: 540619--540811 Score: 275
Period size: 76 Copynumber: 2.6 Consensus size: 76
540609 CGATACCATA
* *
540619 TCAT-GGGGGTATCGATA-CCTACTAGGGGGTATCGGTACCATCTGAGCATTATGTTATTTCTCG
1 TCATAGGGGGTATCGGTACCCTA-TAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCG
*
540682 GAATCAAAATAT
65 GAACCAAAATAT
* *
540694 TCATAGGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTTGG
1 TCATAGGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGG
*
540759 AACCAAAATGT
66 AACCAAAATAT
* *
540770 TCATA-GGGGTATCAGTACCCTATATGGGGGTATCGATACCAT
1 TCATAGGGGGTATCGGTACCCTATA-GGGGGTATCGGTACCAT
540812 ACTAAATAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
75 22 0.21
76 81 0.76
77 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (76 bp):
TCATAGGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGG
AACCAAAATAT
Found at i:540828 original size:76 final size:76
Alignment explanation
Indices: 540619--540833 Score: 183
Period size: 76 Copynumber: 2.9 Consensus size: 76
540609 CGATACCATA
* * * **
540619 TCAT-GGGGGTATC-GATA-CCTACTAGGGGGTATCGGTACCAT-CTGAGCATTATGTTATTTCT
1 TCATAGGGGGTATCAG-TACCCTA-TAGGGGGTATCGATACCATAC-GAGAATAAACTTATTTCT
* *
540680 CGGAATCAAAATAT
63 TGGAACCAAAATAT
* * * * ****
540694 TCATAGGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTTGG
1 TCATAGGGGGTATCAGTACCCTATAGGGGGTATCGATACCATACGAGAATAAACTTATTTCTTGG
*
540759 AACCAAAATGT
66 AACCAAAATAT
*
540770 TCATA-GGGGTATCAGTACCCTATATGGGGGTATCGATACCATACTA-AATAAAACTTATTT-TT
1 TCATAGGGGGTATCAGTACCCTATA-GGGGGTATCGATACCATACGAGAAT-AAACTTATTTCTT
540832 GG
64 GG
540834 CTCGAATATG
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
75 28 0.23
76 87 0.72
77 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (76 bp):
TCATAGGGGGTATCAGTACCCTATAGGGGGTATCGATACCATACGAGAATAAACTTATTTCTTGG
AACCAAAATAT
Found at i:543429 original size:44 final size:45
Alignment explanation
Indices: 543371--543481 Score: 131
Period size: 44 Copynumber: 2.5 Consensus size: 45
543361 TATCGATACC
*
543371 ATCAGGGGGTATCGATACTC-ATTCAAA-GAGGGAATCGATACCTAT
1 ATCA-GGGGTATCGATACTCTATTCAAATG-GGGAATCGATACATAT
* * *
543416 -TCAATGGGTATCGATAC-CTATTCAAATGGGGTATCGATACATGT
1 ATC-AGGGGTATCGATACTCTATTCAAATGGGGAATCGATACATAT
543460 ATCAGGGGTATCGATACTCTAT
1 ATCAGGGGTATCGATACTCTAT
543482 GCACATAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
43 1 0.02
44 47 0.84
45 8 0.14
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (45 bp):
ATCAGGGGTATCGATACTCTATTCAAATGGGGAATCGATACATAT
Found at i:543430 original size:21 final size:21
Alignment explanation
Indices: 543357--543481 Score: 114
Period size: 21 Copynumber: 5.8 Consensus size: 21
543347 AACCCGACAG
*
543357 GGGGTATCGATACC-A-TCAG
1 GGGGTATCGATACCTATTCAA
543376 GGGGTATCGATA-CTCATTCAAA
1 GGGGTATCGATACCT-ATTC-AA
*
543398 GAGGGAATCGATACCTATTCAA
1 G-GGGTATCGATACCTATTCAA
*
543420 TGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTC-AA
* *
543442 TGGGGTATCGATACATGTATC-A
1 -GGGGTATCGATACCTAT-TCAA
543464 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
543482 GCACATAAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.01
19 12 0.14
20 1 0.01
21 32 0.37
22 9 0.10
23 28 0.32
24 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGGTATCGATACCTATTCAA
Found at i:547109 original size:22 final size:21
Alignment explanation
Indices: 547067--547106 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
547057 GAGTTTATTT
*
547067 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
547088 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
547107 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:549023 original size:22 final size:21
Alignment explanation
Indices: 548974--549051 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
548964 CCCCTTCATA
* *
548974 GGGTATCGGTACC-TAAGTAGG
1 GGGTATCGATACCAT-ACTAGG
*
548995 GAGTATCGATACCATA-TCATGG
1 GGGTATCGATACCATACT-A-GG
549017 GGGTATCGATACC-TACTAGG
1 GGGTATCGATACCATACTAGG
*
549037 GGGTATCGGTACCAT
1 GGGTATCGATACCAT
549052 CCGAGCATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 15 0.31
21 17 0.35
22 16 0.33
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCATACTAGG
Found at i:549141 original size:76 final size:74
Alignment explanation
Indices: 549011--549203 Score: 280
Period size: 76 Copynumber: 2.5 Consensus size: 74
549001 CGATACCATA
* *
549011 TCATGGGGGTATCGATA-CCTACTAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGG
1 TCATAGGGGTATCG-TACCCTA-TAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCAG
*
549075 AATCAAAATAT
64 AACCAAAATAT
549086 TCATAGGGGTATCAGTACCCTATAGGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCAG
1 TCATAGGGGTATC-GTACCCTATA-GGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCAG
*
549151 AACCAAAATGT
64 AACCAAAATAT
*
549162 TCATAGGGGTATCGGTACCCTATATGGGGGTATCGATACCAT
1 TCATAGGGGTATC-GTACCCTATA-GGGGGTATCGGTACCAT
549204 ACTAAATAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 16 0.15
76 92 0.85
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (74 bp):
TCATAGGGGTATCGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCAGAA
CCAAAATAT
Found at i:549220 original size:76 final size:76
Alignment explanation
Indices: 549064--549221 Score: 183
Period size: 76 Copynumber: 2.1 Consensus size: 76
549054 GAGCATTCTG
* * * *
549064 TTATTTCTCGGAATCAAAATATTCATAGGGGTATCAGTACCCTATAGGGGGGTATCGGTACCATC
1 TTATTTCTCAGAACCAAAATATTCATAGGGGTATCAGTACCCTATAGGGGGGTATCGATACCATA
* ****
549129 CGAGCATTCTG
66 CGAGAATAAAC
* * *
549140 TTATTTCTCAGAACCAAAATGTTCATAGGGGTATCGGTACCCTATATGGGGGTATCGATACCATA
1 TTATTTCTCAGAACCAAAATATTCATAGGGGTATCAGTACCCTATAGGGGGGTATCGATACCATA
*
549205 CTA-AATAAAAC
66 CGAGAAT-AAAC
549216 TTATTT
1 TTATTT
549222 TTGGCTCGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
75 2 0.03
76 66 0.97
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (76 bp):
TTATTTCTCAGAACCAAAATATTCATAGGGGTATCAGTACCCTATAGGGGGGTATCGATACCATA
CGAGAATAAAC
Found at i:550067 original size:73 final size:70
Alignment explanation
Indices: 549968--550105 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 70
549958 TTCCTAGAAG
549968 ACTTAATTTATCTAAACTTTTTAACCACTATGTTATAAATATA-GCATTTACATAAAATATAAAA
1 ACTTAATTTATCTAAACTTTTTAACCACTATGTTATAAATATATGCATTTACATAAAATATAAAA
550032 ATATT
66 ATATT
*
550037 ACTTAATTTACTCATAAACTTTTTTTAACCACTATGTTATAAATATATGCATTTACATATAATAT
1 ACTTAATTTA-TC-TAAAC--TTTTTAACCACTATGTTATAAATATATGCATTTACATAAAATAT
550102 AAAA
62 AAAA
550106 TCTTAAATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
69 10 0.16
70 2 0.03
71 5 0.08
73 26 0.41
74 20 0.32
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (70 bp):
ACTTAATTTATCTAAACTTTTTAACCACTATGTTATAAATATATGCATTTACATAAAATATAAAA
ATATT
Found at i:550119 original size:2 final size:2
Alignment explanation
Indices: 550112--550156 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
550102 AAAATCTTAA
550112 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550152 AT AT A
1 AT AT A
550157 ATTAAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:550126 original size:25 final size:27
Alignment explanation
Indices: 550093--550157 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
550083 ATGCATTTAC
*
550093 ATATA-ATATAAA-ATCTTAAATATATA
1 ATATATATATAAATAT-ATAAATATATA
* * *
550119 TTATATATATATATATATATATATATA
1 ATATATATATAAATATATAAATATATA
550146 ATATATATATAA
1 ATATATATATAA
550158 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.13
27 25 0.81
28 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATATATAAATATATAAATATATA
Found at i:551063 original size:20 final size:20
Alignment explanation
Indices: 551038--551104 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
551028 TTTTCCCAAT
551038 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
551058 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
551079 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
551099 TCGCAA
1 TCGCAA
551105 CACGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:551081 original size:21 final size:21
Alignment explanation
Indices: 551055--551121 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
551045 GCGAATAAGT
551055 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
551076 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
551096 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
551117 AAATC
1 AAATC
551122 ATAATGCGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:551083 original size:41 final size:41
Alignment explanation
Indices: 551038--551130 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
551028 TTTTCCCAAT
*
551038 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
551079 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
**
551120 TCATAATGCGA
1 TCGCAATGCGA
551131 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:551425 original size:22 final size:22
Alignment explanation
Indices: 551397--551440 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
551387 CTCTCTCTCA
551397 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
551419 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
551441 TATCCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:551722 original size:18 final size:19
Alignment explanation
Indices: 551699--551734 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
551689 CGATTCTCTC
551699 GTTGCGA-TATCATTTTCG
1 GTTGCGATTATCATTTTCG
*
551717 GTTGCGATTTTCATTTTC
1 GTTGCGATTATCATTTTC
551735 AGAAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (19 bp):
GTTGCGATTATCATTTTCG
Found at i:553074 original size:17 final size:18
Alignment explanation
Indices: 553037--553080 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
553027 TCCACTTCGG
*
553037 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGACCA
*
553055 GAGCTATCACCTC-ACCA
1 GAGCCATCACCTCGACCA
553072 GAGCCATCA
1 GAGCCATCA
553081 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCGACCA
Found at i:553607 original size:19 final size:20
Alignment explanation
Indices: 553564--553619 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
553554 TTCGCACACA
553564 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
553584 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
553603 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
553620 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:553627 original size:14 final size:14
Alignment explanation
Indices: 553608--553665 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
553598 ATGCGAAATG
553608 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
553622 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
553638 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
553654 AAAATCGCAACG
1 AAAATCGCAACG
553666 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:553650 original size:32 final size:33
Alignment explanation
Indices: 553592--553682 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
553582 GGAAATGGCT
553592 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
553625 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
553657 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
553683 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:553676 original size:19 final size:19
Alignment explanation
Indices: 553592--553687 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
553582 GGAAATGGCT
553592 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
553611 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
553625 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
553643 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
553657 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553676 ATCGCAATGCGA
1 ATCGCAATGCGA
553688 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:553722 original size:14 final size:14
Alignment explanation
Indices: 553699--553756 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
553689 TTGTGTTTCG
553699 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
553713 CGTTGTGATTTCATTT
1 CGTTGCGATTT--TGT
553729 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
553745 CGTTGCGATTTT
1 CGTTGCGATTTT
553757 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:553730 original size:32 final size:33
Alignment explanation
Indices: 553694--553772 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
553684 GCGATTTGTG
*
553694 TTTCGCGTTGCGATTTTGTCGTTGTGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
553726 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
553759 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
553773 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:553771 original size:19 final size:19
Alignment explanation
Indices: 553756--553811 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
553746 GTTGCGATTT
553756 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
553775 CCATTTCCGTATTGCGATAG
1 TCATTT-CGCATTGCGATAG
*
553795 TCATTTCGCGTTGCGAT
1 TCATTTCGCATTGCGAT
553812 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:556215 original size:31 final size:31
Alignment explanation
Indices: 556117--556207 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
556107 CAATTTAAGG
556117 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
556148 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
556179 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
556208 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:556306 original size:18 final size:18
Alignment explanation
Indices: 556272--556336 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 18
556262 AATGTTTTTA
*
556272 TGAATAGTAATTTACTATT
1 TGAACAGTAA-TTACTATT
556291 TGAACAGTAATTACTA-T
1 TGAACAGTAATTACTATT
* *
556308 TGAACAGTAAATCACTGTT
1 TGAACAGT-AATTACTATT
556327 TGAACAGTAA
1 TGAACAGTAA
556337 CCCGAGACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 9 0.22
18 14 0.34
19 18 0.44
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (18 bp):
TGAACAGTAATTACTATT
Found at i:556466 original size:21 final size:21
Alignment explanation
Indices: 556440--556481 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
556430 ATTTGAATAT
*
556440 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
556461 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
556482 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:556543 original size:21 final size:21
Alignment explanation
Indices: 556510--556549 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
556500 TTTGAGTAGA
*
556510 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
556532 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
556550 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:556796 original size:34 final size:32
Alignment explanation
Indices: 556752--556822 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 32
556742 TCCTTTTGTA
* *
556752 AGGGGAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
556786 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
556818 AGGGA
1 AGGGA
556823 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.21
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:558017 original size:33 final size:32
Alignment explanation
Indices: 557980--558079 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 32
557970 GCAACGAGAT
557980 AATGAGAATCGCAACGCGGAAATGACTATCGCA
1 AATGAGAATCGCAACGC-GAAATGACTATCGCA
558013 AATGAGAAATCGCAACGCGAAATGACTATCGCGA
1 AATGAG-AATCGCAACGCGAAATGACTATCGC-A
* * **
558047 CCA-GACAATCGCAACGCGAAATGAAAATCGCA
1 -AATGAGAATCGCAACGCGAAATGACTATCGCA
558079 A
1 A
558080 CCGCGAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
32 1 0.02
33 43 0.73
34 14 0.24
35 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (32 bp):
AATGAGAATCGCAACGCGAAATGACTATCGCA
Found at i:558075 original size:19 final size:19
Alignment explanation
Indices: 557959--558135 Score: 139
Period size: 19 Copynumber: 9.8 Consensus size: 19
557949 TCTTTTGGTT
*
557959 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
557977 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
* *
557997 GGAAATG---A-C-TATCGC
1 -GAAATGAAAATCGCAACGC
558012 -AAATGAGAAATCGCAACGC
1 GAAATGA-AAATCGCAACGC
** *
558031 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
558049 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
558064 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
558084 GAAATAAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
558101 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
558120 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
558136 TGAGATTTTG
Statistics
Matches: 127, Mismatches: 14, Indels: 35
0.72 0.08 0.20
Matches are distributed among these distances:
13 5 0.04
14 10 0.08
15 6 0.05
16 1 0.01
17 18 0.14
18 5 0.04
19 42 0.33
20 38 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:558113 original size:37 final size:37
Alignment explanation
Indices: 558053--558135 Score: 132
Period size: 36 Copynumber: 2.2 Consensus size: 37
558043 GCGACCAGAC
558053 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAAC-CGAAATGAAAATCGCAA-CGCGAAATAAA
*
558092 AATCGCAA-CGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACCGAAATGAAAATCGCAACGCGAAATAAA
558128 AATCGCAA
1 AATCGCAA
558136 TGAGATTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
36 18 0.42
37 17 0.40
39 8 0.19
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (37 bp):
AATCGCAACCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:558161 original size:19 final size:19
Alignment explanation
Indices: 558139--558180 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
558129 ATCGCAATGA
*
558139 GATTTTGGTTTCGCGTTGC
1 GATTTTGATTTCGCGTTGC
*
558158 GATTTTTATTTCGCGTTGC
1 GATTTTGATTTCGCGTTGC
558177 GATT
1 GATT
558181 ATCTCGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.26, T:0.50
Consensus pattern (19 bp):
GATTTTGATTTCGCGTTGC
Found at i:558746 original size:20 final size:20
Alignment explanation
Indices: 558721--558760 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
558711 GCGCTATGTA
558721 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
558741 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
558761 TCCGTTGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:558768 original size:17 final size:19
Alignment explanation
Indices: 558722--558770 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
558712 CGCTATGTAA
558722 ATCGCGTTGCGAAAGTCAG
1 ATCGCGTTGCGAAAGTCAG
558741 AATCGCGTTGCGAAAGTCAG
1 -ATCGCGTTGCGAAAGTCAG
558761 -TC-CGTTGCGA
1 ATCGCGTTGCGA
558771 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.28
18 2 0.07
20 19 0.66
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
ATCGCGTTGCGAAAGTCAG
Found at i:558923 original size:21 final size:21
Alignment explanation
Indices: 558883--558923 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
558873 ATTGTATACC
**
558883 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
558904 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
558924 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:562918 original size:31 final size:31
Alignment explanation
Indices: 562876--562934 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
562866 AATTTAAAAG
* *
562876 AGTTTTGCAATACAGAGATTTAAATAATTTT
1 AGTTTTACAATACAGAAATTTAAATAATTTT
*
562907 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACAGAAATTTAAATAAT
562935 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTTTACAATACAGAAATTTAAATAATTTT
Found at i:563013 original size:54 final size:54
Alignment explanation
Indices: 562949--563453 Score: 353
Period size: 54 Copynumber: 9.6 Consensus size: 54
562939 ACAACTACAA
* *
562949 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAGTCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
563003 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
563057 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT-T
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * * * * *
563114 TTTTAAAATAAAT-CAATCAATCCATACAAATACATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATAC
*** * * *
563173 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
** * *
563226 T-AT--A-T-TTTAAAATAAATCAAT-CA-ATCCATACAAATAAAT-TAT--TTA-
1 TAATAAATTATTTAAAATAAATCAATCCATAT-TTTA-AAATAAATCAATCCATAC
* * * * * *
563271 AAATAAATCAATCTATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 TAATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
563321 -AACTACA--A--T--AATAAACCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
563369 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
563423 TAATAAATTATTTAAAATAAATTAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
563454 CTAATAAATT
Statistics
Matches: 347, Mismatches: 66, Indels: 76
0.71 0.13 0.16
Matches are distributed among these distances:
43 2 0.01
44 5 0.01
45 2 0.01
46 13 0.04
47 14 0.04
48 45 0.13
49 8 0.02
50 11 0.03
51 5 0.01
52 3 0.01
53 2 0.01
54 155 0.45
55 5 0.01
56 10 0.03
57 14 0.04
58 32 0.09
59 12 0.03
60 9 0.03
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:563019 original size:32 final size:30
Alignment explanation
Indices: 562981--563080 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 30
562971 CAATCCATAT
562981 TTTAAAATAAATCAGTCTATACTAATAAATTA
1 TTTAAAATAAATCA-T-TATACTAATAAATTA
*
563013 TTTAAAATAAATCA--AT-C-CAT--A-T-
1 TTTAAAATAAATCATTATACTAATAAATTA
563035 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATC-ATT-ATACTAATAAATTA
563067 TTTAAAATAAATCA
1 TTTAAAATAAATCA
563081 ATCCATACAA
Statistics
Matches: 56, Mismatches: 2, Indels: 21
0.71 0.03 0.27
Matches are distributed among these distances:
22 13 0.23
23 2 0.04
24 1 0.02
26 4 0.07
27 2 0.04
28 4 0.07
30 1 0.02
31 2 0.04
32 27 0.48
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (30 bp):
TTTAAAATAAATCATTATACTAATAAATTA
Found at i:563039 original size:22 final size:22
Alignment explanation
Indices: 563013--563055 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
563003 TAATAAATTA
563013 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
563035 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
563056 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:563064 original size:22 final size:22
Alignment explanation
Indices: 563015--563063 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
563005 ATAAATTATT
**
563015 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
563037 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
563060 TAAA
1 TAAA
563064 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:563081 original size:32 final size:32
Alignment explanation
Indices: 563035--563475 Score: 313
Period size: 32 Copynumber: 15.3 Consensus size: 32
563025 CAATCCATAT
*
563035 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563067 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
563097 --T--AATAAATCAATCCAT-TTTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
563122 --T-AAATCAATCAATCCATACAAATACATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563151 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563183 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
563213 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
563238 --T-AAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563267 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563299 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
563329 --T--AATAAACCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
563347 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
563379 TTTAAAATAAATC-A---AT-C-AAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
563401 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
563433 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
563465 TTTAAAATAAA
1 TTTAAAATAAA
563476 ATTTTTTAAA
Statistics
Matches: 330, Mismatches: 35, Indels: 88
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.00
22 26 0.08
23 3 0.01
24 3 0.01
25 11 0.03
26 77 0.23
27 9 0.03
28 8 0.02
29 2 0.01
30 4 0.01
31 10 0.03
32 176 0.53
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:563118 original size:80 final size:82
Alignment explanation
Indices: 563018--563172 Score: 242
Period size: 84 Copynumber: 1.9 Consensus size: 82
563008 AATTATTTAA
*
563018 AATAAATCAATCCATATTTTAAAATAAATCAAT-T-CATACTAATAAATTATTTAAAATAAATCA
1 AATAAATCAATCCATATTTTAAAATAAATCAATATCCATACAAATAAATTATTTAAAATAAATCA
563081 ATCCATACAACTACAAT
66 ATCCATACAACTACAAT
* *
563098 AATAAATCAATCCATTTTTTAAAATAAATCAATCAATCCATACAAATACATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAAT--ATCCATACAAATAAATTATTTAAAATAAAT
*
563163 CAATTCATAC
64 CAATCCATAC
563173 TAATAAATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
80 32 0.48
83 1 0.01
84 34 0.51
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (82 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATATCCATACAAATAAATTATTTAAAATAAATCA
ATCCATACAACTACAAT
Found at i:563125 original size:116 final size:114
Alignment explanation
Indices: 562949--563360 Score: 465
Period size: 116 Copynumber: 3.6 Consensus size: 114
562939 ACAACTACAA
* ** * **
562949 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAGT-C-TATACT--AA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
*
563006 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
66 TAAATCA-TTAAAATAAATCAAT-CATATTTTAAAATAAATCAATTCATAC
*
563057 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATTTTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
* * **
563122 TAAATCAAT-CAATCCATACAAATACAT-TATTTAAAATAAATCAATTCATAC
66 TAAATCATTAAAATAAAT-C-AAT-CATAT-TTTAAAATAAATCAATTCATAC
*
563173 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
* * *
563238 TAAATCAATCAATCCATACAAATAAAT--TA-TTTAAAATAAATCAA-TCTATAC
66 TAAATC-ATTAA---A-ATAAATCAATCATATTTTAAAATAAATCAATTC-ATAC
*
563289 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAACCAATCCATATTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
563354 TAAATCA
66 TAAATCA
563361 ATCCATACTA
Statistics
Matches: 261, Mismatches: 24, Indels: 31
0.83 0.08 0.10
Matches are distributed among these distances:
108 30 0.11
111 4 0.02
112 10 0.04
113 1 0.00
114 8 0.03
115 6 0.02
116 193 0.74
117 2 0.01
120 3 0.01
121 1 0.00
122 3 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (114 bp):
TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
TAAATCATTAAAATAAATCAATCATATTTTAAAATAAATCAATTCATAC
Found at i:563276 original size:14 final size:14
Alignment explanation
Indices: 563257--563310 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
563247 CAATCCATAC
563257 AAATAAATTATTTA
1 AAATAAATTATTTA
*
563271 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
563288 CTAATAAATTATTTA
1 -AAATAAATTATTTA
563303 AAATAAAT
1 AAATAAAT
563311 CAATCCATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:563361 original size:116 final size:116
Alignment explanation
Indices: 563035--563394 Score: 631
Period size: 116 Copynumber: 3.1 Consensus size: 116
563025 CAATCCATAT
563035 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
* *
563100 TAAATCAATCCATTTTTTAAAATAAATCAATCAATCCATACAAATACATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
563151 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
*
563216 TAAATCAATCTATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
563267 TTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
1 TTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
* *
563331 ATAAACCAATCCATATTTTAAAAT--A--AATCAATCCATACTAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
563379 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
563395 CAATATTTTA
Statistics
Matches: 236, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
112 37 0.16
114 1 0.00
115 2 0.01
116 196 0.83
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (116 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
Found at i:563376 original size:22 final size:23
Alignment explanation
Indices: 563301--563375 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
563291 ATAAATTATT
563301 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
563323 CTACAATAATAAACCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
563349 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
563372 TAAA
1 TAAA
563376 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:563430 original size:22 final size:22
Alignment explanation
Indices: 563381--563429 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
563371 ATAAATTATT
**
563381 TAAAATAAATCAATCAATATTT
1 TAAAATAAATCAATCAATATAA
*
563403 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCAATA-TAA
563426 TAAA
1 TAAA
563430 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:563461 original size:18 final size:18
Alignment explanation
Indices: 563406--563464 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
563396 AATATTTTAA
*
563406 AATAAATCAATCCATACT
1 AATAAATTAATCCATACT
* *
563424 AATAAATT-AT--TTA-A
1 AATAAATTAATCCATACT
563438 AATAAATTAATCCATACT
1 AATAAATTAATCCATACT
563456 AATAAATTA
1 AATAAATTA
563465 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
17 4 0.12
18 16 0.50
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAATTAATCCATACT
Found at i:563483 original size:15 final size:15
Alignment explanation
Indices: 563456--563612 Score: 150
Period size: 15 Copynumber: 10.5 Consensus size: 15
563446 AATCCATACT
563456 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
563470 AATAAAATT-TTTTAA
1 AAT-AAATTATTTTAA
*
563485 AATAAATCAATTCATATTTTAT
1 AAT--A--AATT---ATTTTAA
*
563507 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
563522 AATAAATTATTTTAT
1 AATAAATTATTTTAA
563537 AATAAATTATTTTAA
1 AATAAATTATTTTAA
563552 AAT--A--A--TTAA
1 AATAAATTATTTTAA
*
563561 AATAAATTATTTTAT
1 AATAAATTATTTTAA
563576 AATAAATTATTTTAA
1 AATAAATTATTTTAA
563591 AATAAATTATTTTAA
1 AATAAATTATTTTAA
563606 AATAAAT
1 AATAAAT
563613 AACCTTATTA
Statistics
Matches: 120, Mismatches: 8, Indels: 29
0.76 0.05 0.18
Matches are distributed among these distances:
9 7 0.06
11 2 0.02
13 2 0.02
14 3 0.03
15 88 0.73
16 2 0.02
18 7 0.06
20 1 0.01
22 8 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:563484 original size:47 final size:48
Alignment explanation
Indices: 563424--563599 Score: 140
Period size: 54 Copynumber: 3.5 Consensus size: 48
563414 AATCCATACT
* *
563424 AATAAATTATTTAAAATAAATTAATCCATA-CTAATAAATTA-TTTAA
1 AATAAATTTTTTAAAATAAATTAATCCATATATAATAAATTATTTTAA
* * *
563470 AATAAAATTTTTTAAAATAAATCAATTCATATTTTATAATAATTTATTTTAA
1 AAT-AAATTTTTTAAAATAAATTAATCCATA---TATAATAAATTATTTTAA
* * ** * *
563522 AATAAATTATTTTATAATAAATTATTTTAAAATAATTAAAATAAATTATTTTAT
1 AATAAATT-TTTTAAAATAAATTA--AT-CCAT-A-TATAATAAATTATTTTAA
563576 AATAAATTATTTTAAAATAAATTA
1 AATAAATT-TTTTAAAATAAATTA
563600 TTTTAAAATA
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
46 3 0.03
47 24 0.23
51 14 0.13
52 21 0.20
54 40 0.38
55 2 0.02
56 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (48 bp):
AATAAATTTTTTAAAATAAATTAATCCATATATAATAAATTATTTTAA
Found at i:563572 original size:39 final size:39
Alignment explanation
Indices: 563518--563595 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
563508 ATAATTTATT
563518 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
1 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
563557 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
1 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
563596 ATTATTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
Found at i:563572 original size:54 final size:54
Alignment explanation
Indices: 563456--563610 Score: 192
Period size: 54 Copynumber: 2.9 Consensus size: 54
563446 AATCCATACT
* * * * * *
563456 AATAAATTA-TTTAAAATAAAATT-TTTTAAAATAAATCA-ATTCATAT-TTTAT
1 AATAAATTATTTTAAAAT-AAATTATTTTAAAATAAATTATTTTAAAATAATTAA
* *
563507 AATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTTAAAATAATTAA
1 AATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTAAAATAATTAA
*
563561 AATAAATTATTTTATAATAAATTATTTTAAAATAAATTATTTTAAAATAA
1 AATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTAAAATAA
563611 ATAACCTTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
51 13 0.15
52 21 0.24
53 5 0.06
54 50 0.56
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (54 bp):
AATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTAAAATAATTAA
Found at i:563574 original size:69 final size:66
Alignment explanation
Indices: 563456--563612 Score: 217
Period size: 69 Copynumber: 2.3 Consensus size: 66
563446 AATCCATACT
* ** *
563456 AATAAATTA-TTTAAAATAAAATTTTTTAAAATAAATCAATTCATATTTTATAATAATTTATTTT
1 AATAAATTATTTTAAAAT-AAATTTTTTAAAATAAATAAATAAATATTTTATAATAAATTATTTT
563520 AA
65 AA
* *
563522 AATAAATTATTTTATAATAAATTATTTTAAAATAATTAAAATAAATTATTTTATAATAAATTATT
1 AATAAATTATTTTAAAATAAATT-TTTTAAAATAAAT-AAATAAA-TATTTTATAATAAATTATT
563587 TTAA
63 TTAA
563591 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
563613 AACCTTATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
66 14 0.17
67 19 0.24
68 4 0.05
69 43 0.54
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (66 bp):
AATAAATTATTTTAAAATAAATTTTTTAAAATAAATAAATAAATATTTTATAATAAATTATTTTA
A
Found at i:565468 original size:51 final size:49
Alignment explanation
Indices: 565413--565542 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 49
565403 TTCAAACATT
**
565413 GAAAAACAATTTTCTAAAAATATTTTTCAACTATCAAACAC-AGAAAAATGA
1 GAAAAA-AATTTTCT-AAAATATTTTTCAACTAAAAAACACAAG-AAAATGA
* * *
565464 GAAAAATATTTGTCCGAAAATA-TTTTCAACTAAAAAACATAAGAAAATGA
1 GAAAAAAATTT-T-CTAAAATATTTTTCAACTAAAAAACACAAGAAAATGA
*
565514 GAAAAATATTTTTCGTAAAATATTTTTCA
1 GAAAAA-AATTTTC-TAAAATATTTTTCA
565543 GCGTCAAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
49 1 0.02
50 39 0.60
51 24 0.37
52 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (49 bp):
GAAAAAAATTTTCTAAAATATTTTTCAACTAAAAAACACAAGAAAATGA
Found at i:565511 original size:50 final size:50
Alignment explanation
Indices: 565429--565539 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
565419 CAATTTTCTA
** *
565429 AAAATATTTTTCAACTATCAAACACAGAAAAATGAGAAAAATATTTGTCCG-
1 AAAATA-TTTTCAACTAAAAAACAAAGAAAAATGAGAAAAATATTT-TCCGT
*
565480 AAAATATTTTCAACTAAAAAACATAAG-AAAATGAGAAAAATATTTTTCGT
1 AAAATATTTTCAACTAAAAAACA-AAGAAAAATGAGAAAAATATTTTCCGT
565530 AAAATATTTT
1 AAAATATTTT
565540 TCAGCGTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 3 0.06
50 43 0.80
51 8 0.15
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (50 bp):
AAAATATTTTCAACTAAAAAACAAAGAAAAATGAGAAAAATATTTTCCGT
Found at i:566531 original size:43 final size:44
Alignment explanation
Indices: 566463--566980 Score: 654
Period size: 43 Copynumber: 12.1 Consensus size: 44
566453 GCAAAATCGA
* *
566463 TAAGGTCTTATCCTTGCACATAGCAAAAGAG-CCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
*
566507 TAAGGCTTACCCTTGCACACAGCAAAGGA-ACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* * *
566549 TAAGGCTTACCCATGCACACAACAAAGGA-ACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
*
566591 TAAGGCTTACCCTTGCACACAGCAAAGGA-ACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCT-GGGGAAACTG
* * * *
566635 TAAGGCCTACCCTTGCACACAGC-ACAGGGACCTGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* *
566678 TAAGGCTTACCCTTGCACACAAC-AAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* *
566721 TAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* *
566764 TAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* * *
566807 TAAGGCTTACCCTTGCACACAGC-AAAGGGACTTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* *
566850 TAAGGCTTACCCTTGCACATAGCAAAGGA-ACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* * *
566892 TAAGGCTTACCTTTGCACACAGCAAAGGA-ACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
* *
566935 TAAGGCTTACCCTTGCACACA--ATAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCA-AAAGAGACCTGGGGAAACTG
566978 TAA
1 TAA
566981 CGGTAATTAA
Statistics
Matches: 436, Mismatches: 30, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.00
42 122 0.28
43 270 0.62
44 43 0.10
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.17
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAGCAAAAGAGACCTGGGGAAACTG
Found at i:566715 original size:86 final size:86
Alignment explanation
Indices: 566463--566980 Score: 765
Period size: 86 Copynumber: 6.0 Consensus size: 86
566453 GCAAAATCGA
* * *
566463 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
566527 AGCAAAGGAACCT-GGGAAACTG
64 AGCAAAGGAACCTGGGGAAACTG
* * *
566549 TAAGGCTTACCCATGCACACAACAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
566613 CAAAGGAACCTGGGGGAAACTG
66 CAAAGGAACCT-GGGGAAACTG
* * * *
566635 TAAGGCCTACCCTTGCACACAGCACAGGGACCTGGGAAAACTGTAAGGCTTACCCTTGCACACAA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
566700 CAAAGGGACCTGGGGAAACTG
66 CAAAGGAACCTGGGGAAACTG
*
566721 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* *
566786 CAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTG
* * *
566807 TAAGGCTTACCCTTGCACACAGCAAAGGGACTTGGGGGAACTGTAAGGCTTACCCTTGCACATAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
566872 CAAAGGAACCT-GGGAAACTG
66 CAAAGGAACCTGGGGAAACTG
* * * *
566892 TAAGGCTTACCTTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * *
566957 TAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTG
566978 TAA
1 TAA
566981 CGGTAATTAA
Statistics
Matches: 395, Mismatches: 32, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
84 42 0.11
85 97 0.25
86 217 0.55
87 39 0.10
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.17
Consensus pattern (86 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGAACCTGGGGAAACTG
Found at i:566766 original size:129 final size:129
Alignment explanation
Indices: 566463--566980 Score: 799
Period size: 129 Copynumber: 4.0 Consensus size: 129
566453 GCAAAATCGA
* * * *
566463 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
* *
566528 GCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCATGCACACAACAAAGGAACCT-GGGAAACTG
65 GCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
*
566591 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTACCCTTGCACACA
* * *
566656 GCACAGGGACCTGGGAAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
65 GCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
* *
566721 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * * * *
566786 CAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACTTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
* *
566850 TAAGGCTTACCCTTGCACATAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCTTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * *
566914 CAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAATAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
566978 TAA
1 TAA
566981 CGGTAATTAA
Statistics
Matches: 360, Mismatches: 27, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
127 24 0.07
128 137 0.38
129 158 0.44
130 41 0.11
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.17
Consensus pattern (129 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
Found at i:569499 original size:18 final size:18
Alignment explanation
Indices: 569472--569546 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
569462 CGGGTCAACA
*
569472 GGTCGAGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
569490 GGTCGGGTCAACGGG-C-
1 GGTCGGGTCAACGGGTCG
* *
569506 ---CTGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
* *
569521 AGTCGGATCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
569539 GGTCGGGT
1 GGTCGGGT
569547 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
17 1 0.02
18 32 0.73
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.17
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:569500 original size:31 final size:30
Alignment explanation
Indices: 569462--569539 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
569452 CAACAGTCAA
* * *
569462 CGGGTCAACAGGTCGAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCG-GTAAACGGGTCGAGT
*
569493 CGGGTCAACGGGCCTGGTAAACGGGTCGAGT
1 CGGGTCAACGGGTC-GGTAAACGGGTCGAGT
*
569524 CGGATCAACGGGTCGG
1 CGGGTCAACGGGTCGG
569540 GTCGGGTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 37 0.93
32 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (30 bp):
CGGGTCAACGGGTCGGTAAACGGGTCGAGT
Found at i:571622 original size:43 final size:43
Alignment explanation
Indices: 571554--572072 Score: 696
Period size: 43 Copynumber: 12.1 Consensus size: 43
571544 GCAAAAACGA
* *
571554 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGAGA-CCTGGGGAAACTG
571598 TAAGGCTTACCCTTGCACACAGCAAAG-GAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
*
571640 TAAGGCTTACCCATGCACACAGCAAAG-GAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
571682 TAAGGCTTACCCTTGCACACAGCAAAG-GAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCT-GGGGAAACTG
* * *
571726 TAAGGCCTACCCTTGCACACAGCAAAGGGACCTGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* *
571769 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* *
571812 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* * *
571855 TAAGGCTTACCCTTGCACATAGCAAAGGGACCTGGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCT-GGGGAAACTG
* * *
571899 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
*
571942 TAAGGCTTACCCTTGCACACAGTAAAG-GAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
* * *
571984 TAAGGGTTACCTTTGCACACAGCAAAG-GAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
* *
572027 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
572070 TAA
1 TAA
572073 CGGTAATTAA
Statistics
Matches: 445, Mismatches: 21, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
42 121 0.27
43 236 0.53
44 87 0.20
45 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
Found at i:571764 original size:86 final size:87
Alignment explanation
Indices: 571554--572072 Score: 784
Period size: 86 Copynumber: 6.0 Consensus size: 87
571544 GCAAAAACGA
* * *
571554 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
571618 AGCAAAGGAACCT--GGGAAACTG
64 AGCAAAGGAACCTGGGGGAAACTG
* *
571640 TAAGGCTTACCCATGCACACAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
571704 CAAAGGAACCTGGGGGAAACTG
66 CAAAGGAACCTGGGGGAAACTG
* *
571726 TAAGGCCTACCCTTGCACACAGCAAAGGGACCTGGGAAAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
571791 CAAAGGGACCTGGGGG-AACTG
66 CAAAGGAACCTGGGGGAAACTG
* *
571812 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACATAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* *
571877 CAAAGGGACCTGGGGGGAACTG
66 CAAAGGAACCTGGGGGAAACTG
* *
571899 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
571964 TAAAGGAACCT--GGGAAACTG
66 CAAAGGAACCTGGGGGAAACTG
* * * *
571984 TAAGGGTTACCTTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
572049 CAAAGGGACCTGGGGG-AACTG
66 CAAAGGAACCTGGGGGAAACTG
572070 TAA
1 TAA
572073 CGGTAATTAA
Statistics
Matches: 401, Mismatches: 25, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
84 42 0.10
85 99 0.25
86 135 0.34
87 125 0.31
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (87 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGAACCTGGGGGAAACTG
Found at i:572002 original size:215 final size:215
Alignment explanation
Indices: 571554--572072 Score: 812
Period size: 215 Copynumber: 2.4 Consensus size: 215
571544 GCAAAAACGA
* * * *
571554 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGGAACTGTAAGGCTTACCCTTGCACAC
* *
571618 AGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCATGCACACAGCAAAGGAACCTGGGAAACTG
64 AGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCATGCACACAGCAAAGGAACCTGGGAAACTG
*
571682 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACA
129 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACA
*
571747 GCAAAGGGACCTGGGAAAACTG
194 GCAAAGGAACCTGGGAAAACTG
571769 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
* * * *
571834 CAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACATAGCAAAGGGACCTGGGGGGAACTG
66 CAAAGGGACCTGGGGGAACTGTAAGGCTTACCCATGCACACAGCAAAGGAACCT--GGGAAACTG
* *
571899 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG-AACTGTAAGGCTTACCCTTGCACACA
129 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACA
*
571963 GTAAAGGAACCTGGG-AAACTG
194 GCAAAGGAACCTGGGAAAACTG
* * *
571984 TAAGGGTTACCTTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
572049 CAAAGGGACCTGGGGGAACTGTAA
66 CAAAGGGACCTGGGGGAACTGTAA
572073 CGGTAATTAA
Statistics
Matches: 282, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
214 63 0.22
215 137 0.49
216 38 0.13
217 44 0.16
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (215 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGGACCTGGGGGAACTGTAAGGCTTACCCATGCACACAGCAAAGGAACCTGGGAAACTGTA
AGGCTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACAGC
AAAGGAACCTGGGAAAACTG
Found at i:573096 original size:15 final size:15
Alignment explanation
Indices: 573076--573111 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
573066 GGTCAACGCC
573076 GGTCAACAATCAACG
1 GGTCAACAATCAACG
**
573091 GGTCAACGGTCAACG
1 GGTCAACAATCAACG
573106 GGTCAA
1 GGTCAA
573112 TGGGTCGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14
Consensus pattern (15 bp):
GGTCAACAATCAACG
Found at i:573098 original size:8 final size:8
Alignment explanation
Indices: 573085--573117 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
573075 CGGTCAACAA
573085 TCAACGGG
1 TCAACGGG
573093 TCAAC-GG
1 TCAACGGG
573100 TCAACGGG
1 TCAACGGG
*
573108 TCAATGGG
1 TCAACGGG
573116 TC
1 TC
573118 GAGTCAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (8 bp):
TCAACGGG
Found at i:582515 original size:2 final size:2
Alignment explanation
Indices: 582508--582564 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
582498 TAATATAATG
* *
582508 TA TA TA TA T- TA TA -A TG TA TA TA TA T- TA TA -A TG 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
582546 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
582565 GTTATTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:582522 original size:16 final size:16
Alignment explanation
Indices: 582501--582564 Score: 103
Period size: 16 Copynumber: 4.0 Consensus size: 16
582491 TATGTGATAA
582501 TATAATGTATATATAT
1 TATAATGTATATATAT
582517 TATAATGTATATATAT
1 TATAATGTATATATAT
582533 TATAATGTATATATA-
1 TATAATGTATATATAT
*
582548 TATATATATATATATAT
1 TATA-ATGTATATATAT
582565 GTTATTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 4 0.09
16 41 0.91
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TATAATGTATATATAT
Found at i:583690 original size:3 final size:3
Alignment explanation
Indices: 583668--583729 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
583658 ATTTTCCTAT
* * * * * * *
583668 TTA TTT TTA TTG TAA TTA TTA TTA TTA TTA TTA TTT TTA ATG TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
583716 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
583730 CCTTATATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:583723 original size:6 final size:6
Alignment explanation
Indices: 583638--583729 Score: 62
Period size: 6 Copynumber: 15.5 Consensus size: 6
583628 TCATTTTACA
* * ** * * *
583638 ATTATT TTTATT TTTATT -TTATT -TTCCT ATTTATT TTTATT GTAATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT A-TTATT ATTATT ATTATT
* * * *
583685 ATTATT ATTATT ATTATT TTTAAT GTTAAT ATTATT ATTATT ATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATT
583730 CCTTATATAT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 8 0.12
6 58 0.84
7 3 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (6 bp):
ATTATT
Found at i:583850 original size:53 final size:53
Alignment explanation
Indices: 583781--583882 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
583771 ATATTTTTTT
* *
583781 CTTTCTATTTTTATTTTTATTA-TTAT-TATCATTATTATTATTGATTTTTAAGC
1 CTTTCTATTTATATTTTCATTATTTATAT-TCATT-TTATTATTGATTTTTAAGC
* * *
583834 CTTTTTATTTATATTTTCATTATTTATATTTATTTTATTTTTGATTTTT
1 CTTTCTATTTATATTTTCATTATTTATATTCATTTTATTATTGATTTTT
583883 TTTTCTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 33 0.79
54 8 0.19
55 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (53 bp):
CTTTCTATTTATATTTTCATTATTTATATTCATTTTATTATTGATTTTTAAGC
Found at i:583871 original size:15 final size:14
Alignment explanation
Indices: 583835--583884 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
583825 TTTTTAAGCC
583835 TTTTTATTTATATT
1 TTTTTATTTATATT
*
583849 TTCATTATTTATATT
1 TT-TTTATTTATATT
*
583864 TATTTTATTTTTGATT
1 T-TTTTATTTAT-ATT
583880 TTTTT
1 TTTTT
583885 TTCTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.07
15 23 0.77
16 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:583882 original size:7 final size:6
Alignment explanation
Indices: 583776--583911 Score: 60
Period size: 6 Copynumber: 21.2 Consensus size: 6
583766 TATGTATATT
* * * * * * *
583776 TTTTTC TTTCTA TTTTTA TTTTTA TTATTA TTATCA TTATTA TTATTGA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
* * *
583825 TTTTTAA GCCTTTTTA TTTATA TTTTCA TTATTTA TATTTA -TTTTA TTTTTGA
1 TTTTT-A ---TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTT-A
*
583878 TTTTT- TTTTCTAA TTTTCTA ATTTTA TTTATTA T
1 TTTTTA TTTT-T-A TTTT-TA TTTTTA TTT-TTA T
583912 GTGCTTATTC
Statistics
Matches: 101, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
5 8 0.08
6 58 0.57
7 23 0.23
8 6 0.06
9 1 0.01
10 5 0.05
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTTTA
Found at i:583980 original size:23 final size:24
Alignment explanation
Indices: 583943--583993 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
583933 ATTTCATGTG
583943 TTTATTATCTTG-TTTACTCTTTCT
1 TTTATTATCTTGTTTTA-TCTTTCT
* *
583967 TTTATTGT-TTGTTTTATCTTTTT
1 TTTATTATCTTGTTTTATCTTTCT
583990 TTTA
1 TTTA
583994 CTTCCTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTATTATCTTGTTTTATCTTTCT
Found at i:585763 original size:159 final size:159
Alignment explanation
Indices: 585474--585792 Score: 638
Period size: 159 Copynumber: 2.0 Consensus size: 159
585464 TGAAAGCCAG
585474 AGATGCAATCATTCGAGATTTTTTGGATCAAGTAGCTCGTCACTTGCACATTTTAGCCAAAGGAG
1 AGATGCAATCATTCGAGATTTTTTGGATCAAGTAGCTCGTCACTTGCACATTTTAGCCAAAGGAG
585539 CTTTAACGGTGCGACTGGGTATTCAACCGGTGACAGAAAAAAGATGGAAGACGAATCAACTTGTC
66 CTTTAACGGTGCGACTGGGTATTCAACCGGTGACAGAAAAAAGATGGAAGACGAATCAACTTGTC
585604 ATAGGCTGTTTGGGATCTATACCATCAAA
131 ATAGGCTGTTTGGGATCTATACCATCAAA
585633 AGATGCAATCATTCGAGATTTTTTGGATCAAGTAGCTCGTCACTTGCACATTTTAGCCAAAGGAG
1 AGATGCAATCATTCGAGATTTTTTGGATCAAGTAGCTCGTCACTTGCACATTTTAGCCAAAGGAG
585698 CTTTAACGGTGCGACTGGGTATTCAACCGGTGACAGAAAAAAGATGGAAGACGAATCAACTTGTC
66 CTTTAACGGTGCGACTGGGTATTCAACCGGTGACAGAAAAAAGATGGAAGACGAATCAACTTGTC
585763 ATAGGCTGTTTGGGATCTATACCATCAAA
131 ATAGGCTGTTTGGGATCTATACCATCAAA
585792 A
1 A
585793 TGTTTTTTAT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (159 bp):
AGATGCAATCATTCGAGATTTTTTGGATCAAGTAGCTCGTCACTTGCACATTTTAGCCAAAGGAG
CTTTAACGGTGCGACTGGGTATTCAACCGGTGACAGAAAAAAGATGGAAGACGAATCAACTTGTC
ATAGGCTGTTTGGGATCTATACCATCAAA
Found at i:588179 original size:96 final size:96
Alignment explanation
Indices: 588060--588250 Score: 276
Period size: 96 Copynumber: 2.0 Consensus size: 96
588050 TACTATTATA
* * * * *
588060 TATACAATAAAGCTTGACCTATCCTTCT-AGAGCAATTGGTTAAACGCCTCGGTTTTATGGATAA
1 TATACAATAAAGCTGGACCTATCCCTCTAAG-GAAATTGGTTAAACGCCCCGGCTTTATGGATAA
*
588124 GATTCAACTAGCCTGATAAAAGTGATTATATC
65 GATTCAACTAACCTGATAAAAGTGATTATATC
*
588156 TATACAATAAAGCTGGAGCTATCCCTCTAAGGAAATTGGTTAAACGCCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTGGACCTATCCCTCTAAGGAAATTGGTTAAACGCCCCGGCTTTATGGATAAG
* * *
588221 ATTCAGCTAACCTGATAAAGGTGTTTATAT
66 ATTCAACTAACCTGATAAAAGTGATTATAT
588251 ATTGAGTTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 82 0.98
97 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (96 bp):
TATACAATAAAGCTGGACCTATCCCTCTAAGGAAATTGGTTAAACGCCCCGGCTTTATGGATAAG
ATTCAACTAACCTGATAAAAGTGATTATATC
Found at i:590198 original size:36 final size:36
Alignment explanation
Indices: 590140--590236 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
590130 TCGATCTCCT
* *
590140 TTGAGACATTTTCTCTTAAAACAAATTTTGTCTATC
1 TTGAGACAGTTTCCCTTAAAACAAATTTTGTCTATC
* *
590176 TTGAGACAGTTTCCCTTTAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTAAAACAAATTTTGTCTATC
*
590212 TTGAGACAGTTTCCCTTGAAACAAA
1 TTGAGACAGTTTCCCTTAAAACAAA
590237 ATCTTTGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTAAAACAAATTTTGTCTATC
Found at i:590384 original size:36 final size:36
Alignment explanation
Indices: 590331--590437 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
590321 AAATTTTGTC
* * *
590331 TTTGTCTCTCGTAAGACATTTTCTCTTGAAACAAAT
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
* * * * *
590367 TTTATCTCTATTGAGACAGTTTCCCTGGACACAAAT
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
*
590403 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
590438 ATCTGTGAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
Found at i:590488 original size:201 final size:205
Alignment explanation
Indices: 590143--590734 Score: 827
Period size: 216 Copynumber: 2.9 Consensus size: 205
590133 ATCTCCTTTG
* * *
590143 AGACATTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTTAAACAAATTTTGTC
1 AGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTC
* *
590208 TCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTACATT-AAACAAATTTTGT
66 TCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTT-CCTTGAAACAAATTTTGT
590272 CTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA-AA-C-AAAT-TTTGTCTT
130 CTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGACAATCTAAATATTTGTCTT
590333 TGTCTCTCGTA
195 TGTCTCTCGTA
* * ** *
590344 AGACATTTTCTCTTGAAACAAATTTTATCTCTATTGAGACAGTTTCCCTGGACACAAATTTTGTC
1 AGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTC
* * *
590409 TCTCTTGAGACAATTTCTCTTGAAACAAAATCTGTGAATATGTTTTCCTTGAAACAAATTTCGTC
66 TCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGTC
590474 TCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAATAA
131 TCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTT--GACAA----TC-T-AAAT--
* *
590539 ACTTTGTCTTTGTCTCTCTTG
186 A-TTTGTCTTTGTCTCTCGTA
* * *
590560 AGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGCC
1 AGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTC
* * **
590625 TCTCTTGAGACAGTTT-TCCTTCAAACAAAATCTTTGAATCTGTTTTCCTTGAAACCGATTTTGT
66 TCTCTTGAGACAGTTTCT-CTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGT
590689 CTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
130 CTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
590735 GATAGTTTCC
Statistics
Matches: 345, Mismatches: 29, Indels: 21
0.87 0.07 0.05
Matches are distributed among these distances:
200 3 0.01
201 157 0.46
203 2 0.01
204 2 0.01
209 1 0.00
212 4 0.01
214 2 0.01
215 1 0.00
216 173 0.50
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (205 bp):
AGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTC
TCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGTC
TCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGACAATCTAAATATTTGTCTTT
GTCTCTCGTA
Found at i:590564 original size:42 final size:42
Alignment explanation
Indices: 590505--590622 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 42
590495 GGAACTAAGT
*
590505 TTTGTCTCTCTTGAGACAATTTCTCTTGAAATAAACTTTGTC
1 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAACTTTGTC
*
590547 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA-----T-
1 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAACTTTGTC
* * *
590583 TTTGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTG
1 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAACTTTG
590623 CCTCTCTTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
36 32 0.48
37 1 0.02
42 33 0.50
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (42 bp):
TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAACTTTGTC
Found at i:590587 original size:36 final size:36
Alignment explanation
Indices: 590550--590653 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
590540 CTTTGTCTTT
*
590550 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* *
590586 GTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* * *
590622 GCCTCTCTTGAGACAGTTT-TCCTTCAAACAAA
1 GTCTCTCTTGAGACAATTTCT-CTTGAAACAAA
590654 ATCTTTGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
Found at i:590593 original size:21 final size:21
Alignment explanation
Indices: 590568--590632 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
590558 TGAGACAGTT
590568 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
590589 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
* *
590606 -C-CTTAAAACAAATTTTGCC
1 TCTCTTGAAACAAATTTTGTC
590625 TCTCTTGA
1 TCTCTTGA
590633 GACAGTTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 2 0.06
18 4 0.12
19 1 0.03
20 3 0.09
21 14 0.42
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:590599 original size:216 final size:215
Alignment explanation
Indices: 590310--590791 Score: 697
Period size: 216 Copynumber: 2.3 Consensus size: 215
590300 AAGTTTTGTC
* * *
590310 TCTCTTGAAACAAATTTTGTCTTTGTCTCTCGTAAGACATTTTCTCTTGAAACAAATTTTATCTC
1 TCTCTTGAAACAAA-TTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTC
* * * * *
590375 TATTGAGACAGTTTCCCTGGACACAAATTTTGTCTCTCTTGAGACAA-TTTCTCTTGAAACAAAA
65 TATTGAGACAATTTCCCTGAAAACAAATTTTGCCTCTCTTGAGACAATTTTC-CTTCAAACAAAA
590439 TCTGTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
129 TCTGTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
590504 TTTTGTCTCTCTTGAGACAATT
194 TTTTGTCTCTCTTGAGACAATT
* *
590526 TCTCTTGAAATAAACTTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTC
1 TCTCTTGAAACAAA-TTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTC
* * *
590591 TCTTGAGACAATTTCCCTTAAAACAAATTTTGCCTCTCTTGAGACAGTTTTCCTTCAAACAAAAT
65 TATTGAGACAATTTCCCTGAAAACAAATTTTGCCTCTCTTGAGACAATTTTCCTTCAAACAAAAT
* * ** *
590656 CTTTGAATCTGTTTTCCTTGAAACCGATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
130 CTGTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
* *
590721 TTTGTCTCTCTTGAGATAGTT
195 TTTGTCTCTCTTGAGACAATT
* *
590742 TCCCTTGAAACAAA----T-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTTGAAACAAATTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
590792 ATCTTTGAAT
Statistics
Matches: 241, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
210 34 0.14
211 1 0.00
216 202 0.84
217 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (215 bp):
TCTCTTGAAACAAATTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCT
ATTGAGACAATTTCCCTGAAAACAAATTTTGCCTCTCTTGAGACAATTTTCCTTCAAACAAAATC
TGTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTT
TTGTCTCTCTTGAGACAATT
Found at i:590767 original size:36 final size:36
Alignment explanation
Indices: 590666--590791 Score: 162
Period size: 36 Copynumber: 3.5 Consensus size: 36
590656 CTTTGAATCT
* ** *
590666 GTTTTCCTTGAAACCGATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * *
590702 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
590739 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
590775 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
590792 ATCTTTGAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
36 47 0.63
37 28 0.37
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:590794 original size:138 final size:138
Alignment explanation
Indices: 590547--590929 Score: 588
Period size: 138 Copynumber: 2.8 Consensus size: 138
590537 AAACTTTGTC
* * * * * *
590547 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCCCTTA
1 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
590611 AAACAAATTTTGCCTCTCTTGAGACAGTTTTCCTTCAAACAAAATCTTTGAATCTGTTTTCCTTG
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGTTTTCCTTG
*
590676 AAACCGAT
131 AAACCAAT
*
590684 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
590749 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGTTTTCCTTG
*
590814 AAACTAAT
131 AAACCAAT
* * * * *
590822 TTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTTTCTCTCTTGACACAGTTTCTCTTG
1 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
590887 AAACAAATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACAAA
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
590930 GTTTTATCTC
Statistics
Matches: 225, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
137 29 0.13
138 196 0.87
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (138 bp):
TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGTTTTCCTTG
AAACCAAT
Found at i:590908 original size:36 final size:36
Alignment explanation
Indices: 590806--590964 Score: 167
Period size: 37 Copynumber: 4.4 Consensus size: 36
590796 TTGAATCTGT
* * * *
590806 TTTC-CTTGAAACTAATTTCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * * *
590841 TTTCTTTTGGAACTAAGTTTTTTCTCTCTTGACACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
590878 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
590914 TTTCCCTTAAAACAAAGTTTTATCTCTCTTGAGAGAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
590951 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
590965 CCAATCTTGG
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
35 4 0.04
36 40 0.40
37 56 0.56
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:590932 original size:73 final size:73
Alignment explanation
Indices: 590806--590964 Score: 194
Period size: 73 Copynumber: 2.2 Consensus size: 73
590796 TTGAATCTGT
* * ** ** * *
590806 TTTC-CTTGAAACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTTTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAAACAATTTCCCTTAAAACAAAGTTTTATCTCTCT
590870 TGACACAG
66 TGACACAG
* * *
590878 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACAAAGTTTTATCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAAACAATTTCCCTTAAAACAAAGTTTTATCTCTCT
* *
590943 TGAGAGAG
66 TGACACAG
590951 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
590965 CCAATCTTGG
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 4 0.05
73 69 0.95
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAAACAATTTCCCTTAAAACAAAGTTTTATCTCTCT
TGACACAG
Found at i:591063 original size:35 final size:35
Alignment explanation
Indices: 591017--591106 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 35
591007 CCTTGAGACA
** * *
591017 GTTTCTCTTGAAACATAAAAAATTCTTTTGAAATT
1 GTTTCTCTTGAAACATAAAAAACCCCTTTGAAAAT
*
591052 GTTTCTCTTGAAACACAAAAAACCCCTTTGAAAAT
1 GTTTCTCTTGAAACATAAAAAACCCCTTTGAAAAT
*
591087 GTTTCTCTTAAAACATAAAA
1 GTTTCTCTTGAAACATAAAA
591107 CCTTCGAGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (35 bp):
GTTTCTCTTGAAACATAAAAAACCCCTTTGAAAAT
Found at i:591311 original size:83 final size:84
Alignment explanation
Indices: 591103--591299 Score: 254
Period size: 84 Copynumber: 2.4 Consensus size: 84
591093 CTTAAAACAT
* * * *
591103 AAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGTTTAAGGCGAT
1 AAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCGAG
591168 AAGGGCTATCTTCCAACCA
66 AAGGGCTATCTTCCAACCA
* * *
591187 AATACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCATTTACAGCTTAGCTCAAGGCGAG
1 AAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCGAG
* * *
591252 AAGGGTTATGTAT-CAA-TA
66 AAGGGCTATCT-TCCAACCA
* * *
591270 AAAACCTTCGAGTTCGGTTCCATTCAGCTC
1 AAAACCTTCGAGTTCGATTACACTCAGCTC
591300 GATGACACAT
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
83 27 0.28
84 70 0.71
85 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (84 bp):
AAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCGAG
AAGGGCTATCTTCCAACCA
Found at i:591881 original size:16 final size:17
Alignment explanation
Indices: 591858--591901 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
591848 AATATGTGAT
591858 TATATAATGTATATATA
1 TATATAATGTATATATA
*
591875 T-TATAATGTGTATATA
1 TATATAATGTATATATA
591891 TATATATATGT
1 TATATA-ATGT
591902 TATTTATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 15 0.62
17 5 0.21
18 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
TATATAATGTATATATA
Found at i:593048 original size:3 final size:3
Alignment explanation
Indices: 593034--593064 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
593024 TCATTGTAAC
*
593034 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
593065 CTTCTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:593108 original size:35 final size:35
Alignment explanation
Indices: 593054--593121 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
593044 ATTATTATTA
*
593054 TTATTATTATTCTTCTTTATATA-TTTTTTATTTGT
1 TTATTATTATTCTTCTTTAT-TACCTTTTTATTTGT
*
593089 TTATT-TTATTCTTGTTTTATTACCTTTTTATTT
1 TTATTATTATTCTT-CTTTATTACCTTTTTATTT
593122 TTGTTTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (35 bp):
TTATTATTATTCTTCTTTATTACCTTTTTATTTGT
Found at i:593144 original size:2 final size:2
Alignment explanation
Indices: 593137--593171 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
593127 TACAAATTAT
593137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
593172 GTTTTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:593301 original size:25 final size:25
Alignment explanation
Indices: 593271--593318 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
593261 TTTAAGCCTT
593271 TTTATTTGTATTTTC-ATTATTTTCA
1 TTTATTT-TATTTTCGATTATTTTCA
*
593296 TTTATTTTATTTTCGATTGTTTT
1 TTTATTTTATTTTCGATTATTTT
593319 TTTCTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTATTTTATTTTCGATTATTTTCA
Found at i:599006 original size:87 final size:87
Alignment explanation
Indices: 598860--599044 Score: 334
Period size: 87 Copynumber: 2.1 Consensus size: 87
598850 TTTAATGATC
*
598860 TGATTTGCTTCCTTTTGAACAAGTAGTAGGATGAAGAAATTCGAATCAGATCAAACTGATTCTTG
1 TGATTTGCTTCCTTTTGAACAAGTAGTAGGATGAAGAAATTCGAATCAAATCAAACTGATTCTTG
*
598925 TGTTTATTGAGTCAGTTTAACA
66 TGTTCATTGAGTCAGTTTAACA
*
598947 TGATTTGCTTCCTTTTGAACAAGTAGTAGGATGAAGAAATTCGATTCAAATCAAACTGATTCTTG
1 TGATTTGCTTCCTTTTGAACAAGTAGTAGGATGAAGAAATTCGAATCAAATCAAACTGATTCTTG
599012 TGTTCATTGAGTCAGTTTAACA
66 TGTTCATTGAGTCAGTTTAACA
*
599034 TGACTTGCTTC
1 TGATTTGCTTC
599045 TGCTGCAAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 94 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (87 bp):
TGATTTGCTTCCTTTTGAACAAGTAGTAGGATGAAGAAATTCGAATCAAATCAAACTGATTCTTG
TGTTCATTGAGTCAGTTTAACA
Found at i:599756 original size:14 final size:15
Alignment explanation
Indices: 599737--599767 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
599727 ATAATTAAAA
599737 TAAATTGTA-AAATT
1 TAAATTGTATAAATT
599751 TAAATTGTATAAATT
1 TAAATTGTATAAATT
599766 TA
1 TA
599768 TATTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
TAAATTGTATAAATT
Found at i:600676 original size:24 final size:23
Alignment explanation
Indices: 600615--600676 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
600605 ATATGTTCAT
600615 GAACATGTTCATTTAAAGTTTAC
1 GAACATGTTCATTTAAAGTTTAC
*
600638 GAACATGTTCATTTAGAGTTTAC
1 GAACATGTTCATTTAAAGTTTAC
*
600661 GAACATAGTTCGTTTA
1 GAACAT-GTTCATTTA
600677 TGTGTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 28 0.78
24 8 0.22
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (23 bp):
GAACATGTTCATTTAAAGTTTAC
Found at i:603246 original size:48 final size:49
Alignment explanation
Indices: 603190--603285 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
603180 AATCATTCAA
*
603190 AACTTCAAAGTTGAAATTAGAATATTTAAAAGTTT-GGGATCAATATAG
1 AACTTCAAAGTTGAAATTAGAATATCTAAAAGTTTGGGGATCAATATAG
* *
603238 AACTTCAAAGTTGAAGTTTGAATATCTAAAAGTTTGGGGATCAATATA
1 AACTTCAAAGTTGAAATTAGAATATCTAAAAGTTTGGGGATCAATATA
603286 AAATTAGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 32 0.73
49 12 0.27
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (49 bp):
AACTTCAAAGTTGAAATTAGAATATCTAAAAGTTTGGGGATCAATATAG
Found at i:618829 original size:27 final size:26
Alignment explanation
Indices: 618768--618820 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
618758 ATTATTAATT
618768 AATATTTTACTACACCCAAAAATCAA
1 AATATTTTACTACACCCAAAAATCAA
618794 AATATTTTACTACACCCAAAAATCAA
1 AATATTTTACTACACCCAAAAATCAA
618820 A
1 A
618821 CTCTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (26 bp):
AATATTTTACTACACCCAAAAATCAA
Found at i:619095 original size:32 final size:33
Alignment explanation
Indices: 619051--619112 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
619041 CAACGAACTT
*
619051 AACGAGCAACGAGTCGAACAACAAAATTTTTTA
1 AACGAGCAACGAGTAGAACAACAAAATTTTTTA
619084 AACGAG-AACGAGTAGAACAACAAAATTTT
1 AACGAGCAACGAGTAGAACAACAAAATTTT
619113 AACAAGCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (33 bp):
AACGAGCAACGAGTAGAACAACAAAATTTTTTA
Found at i:624368 original size:12 final size:13
Alignment explanation
Indices: 624331--624370 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 13
624321 CAAACATACA
624331 AAAATTATAGATCAT
1 AAAATTATA-AT-AT
624346 AAAATTATAATAT
1 AAAATTATAATAT
624359 AAAA-TATAATAT
1 AAAATTATAATAT
624371 TTAGGCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.32
13 6 0.24
14 2 0.08
15 9 0.36
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (13 bp):
AAAATTATAATAT
Found at i:625544 original size:60 final size:60
Alignment explanation
Indices: 625476--625589 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
625466 TTATATTTAT
* * *
625476 CATTCTAAATTAGTCCTTAAA-GTATTGAACATTTCAATTTCATCCCTAAACTATGAACCG
1 CATTCTAAATTAATCCTCAAACGTATTGAACATTCCAATTTCATCCC-AAACTATGAACCG
* * * *
625536 CATTCTAAATTAATCCTCAAACTTTTTTAACATTCCAATTTCATCTCAAACTAT
1 CATTCTAAATTAATCCTCAAACGTATTGAACATTCCAATTTCATCCCAAACTAT
625590 ACATAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 26 0.57
61 20 0.43
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (60 bp):
CATTCTAAATTAATCCTCAAACGTATTGAACATTCCAATTTCATCCCAAACTATGAACCG
Found at i:626586 original size:23 final size:20
Alignment explanation
Indices: 626539--626586 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
626529 AATAGTGTTA
626539 TATTATATTTTTAAAATATT
1 TATTATATTTTTAAAATATT
* *
626559 AATTAGTATATTTTAAATATCTT
1 TATTA-TAT-TTTTAAA-ATATT
626582 TATTA
1 TATTA
626587 AAATATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 7 0.32
23 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTATATTTTTAAAATATT
Found at i:626605 original size:19 final size:20
Alignment explanation
Indices: 626581--626651 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
626571 TTAAATATCT
*
626581 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTAAA
* *
626600 TTATT-ATATTAATATTAAA
1 TTATTAATAATATTATTAAA
* *
626619 TATATAAATAATATTATT-CA
1 T-TATTAATAATATTATTAAA
626639 TTATTAATAATAT
1 TTATTAATAATAT
626652 AATATTATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 5 0.12
21 9 0.22
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATTAATAATATTATTAAA
Found at i:626837 original size:50 final size:49
Alignment explanation
Indices: 626752--626851 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 49
626742 TTATTATAAT
* *
626752 ATAATTGATTATTTTATTAAAAAAATAATATAATATTATTAGAAATATTA
1 ATAATTGAATATTTTATTAAAAAAATAATAAAATATT-TTAGAAATATTA
** * **
626802 ATAATT-AATATTTTGATTAAAATGATATTAAAATATTTTATTAATATTA
1 ATAATTGAATATTTT-ATTAAAAAAATAATAAAATATTTTAGAAATATTA
626851 A
1 A
626852 ATTCATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
49 18 0.43
50 24 0.57
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (49 bp):
ATAATTGAATATTTTATTAAAAAAATAATAAAATATTTTAGAAATATTA
Found at i:627805 original size:16 final size:16
Alignment explanation
Indices: 627784--627815 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
627774 CGGACGGGTC
627784 ACTTTTATATATTGTA
1 ACTTTTATATATTGTA
627800 ACTTTTATATATTGTA
1 ACTTTTATATATTGTA
627816 TGTGACATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
ACTTTTATATATTGTA
Found at i:628595 original size:27 final size:27
Alignment explanation
Indices: 628562--628614 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
628552 AAACAAATTA
628562 TTAATTATGATTATTAGATTAATAAAG
1 TTAATTATGATTATTAGATTAATAAAG
628589 TTAATTATGATTATTAGATTAATAAA
1 TTAATTATGATTATTAGATTAATAAA
628615 TTTACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (27 bp):
TTAATTATGATTATTAGATTAATAAAG
Found at i:628858 original size:63 final size:62
Alignment explanation
Indices: 628693--628965 Score: 367
Period size: 62 Copynumber: 4.4 Consensus size: 62
628683 GAGGATTTCC
* *
628693 ATTTTAAAATTTCACCAAAATTTTAAAAACTAGGGAG-G-AGAAAGAAGAGGGAA-GATTTAA
1 ATTTTAAAATTTCACTAAAATTTTAAAAACTAGGGAGAGAAGAAAGAAGAGGGAATG-TTTTA
* * * *
628753 ATTTTAAAATTTTAGTAAAATTTTAAAAATTAGGGAGAGAAGAAAGAAGAGGCAATGTTTTA
1 ATTTTAAAATTTCACTAAAATTTTAAAAACTAGGGAGAGAAGAAAGAAGAGGGAATGTTTTA
* * *
628815 ATATTAAAATTTCACTAAAATTTTAAAAAACTAGGGAGGGAAGAAAGAAAAGGGAATGTTTTA
1 ATTTTAAAATTTCACTAAAATTTT-AAAAACTAGGGAGAGAAGAAAGAAGAGGGAATGTTTTA
* * *
628878 ATTTTAAAATCTCACTAAAATTTTAAAAACTAGGGAGAGTAGAAAG-AGTAGGGAAGGTTTTA
1 ATTTTAAAATTTCACTAAAATTTTAAAAACTAGGGAGAGAAGAAAGAAG-AGGGAATGTTTTA
*
628940 GTTTTAAAATTT-ACTAAAATTTTAAA
1 ATTTTAAAATTTCACTAAAATTTTAAA
628966 TTTTAAAAAC
Statistics
Matches: 187, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
60 33 0.18
61 16 0.09
62 81 0.43
63 57 0.30
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (62 bp):
ATTTTAAAATTTCACTAAAATTTTAAAAACTAGGGAGAGAAGAAAGAAGAGGGAATGTTTTA
Found at i:629019 original size:144 final size:141
Alignment explanation
Indices: 628862--629244 Score: 440
Period size: 137 Copynumber: 2.7 Consensus size: 141
628852 GGGAAGAAAG
* * *
628862 AAAAGGGAATGTTTTAATTTT-AAAATCTCACTAAAATTTTAAAAACTAGGGAGAGTAGAAAGAG
1 AAAAGAGAATGTTTTAATTTTAAAAAT-TCAATAAAATTTTAAAAACTAGGGAG-GAAGAAAGA-
*
628926 TAGGGAAGGTTTTAGTTTTAAAATTTACTAAAATTTTAAATTTTAAAAACTACGGAGGGAAGATA
63 -AGGGAAGGTTTTAGTTTTAAAATTTACTAAAATTTTAAATTTTAAAAACTACGGAGGGAAGACA
628991 GAAGAGGGACA-AGAT
127 GAAGAGGGA-ATAGAT
* * * * * *
629006 AAAAGTGATTGTTTTAATTTTAAAAATTCAATAACATTTTAAAAACTAAGGAGGGCATAAAGAAA
1 AAAAGAGAATGTTTTAATTTTAAAAATTCAATAAAATTTTAAAAACTAGGGA-GGAAGAAAG-AA
** *
629071 GGGAAGGTTTTAGTTTTAAAATTT-C-ACCA----AAATTTTAAAAACTATGGAGGGAAGACAGA
64 GGGAAGGTTTTAGTTTTAAAATTTACTAAAATTTTAAATTTTAAAAACTACGGAGGGAAGACAGA
629130 AGAGGGAATAGAT
129 AGAGGGAATAGAT
* * *
629143 AAGAGAGAATGTTTTAATTTTAAAAATTCAATAAAAATTTAAAAACTAGGTAGGAATGAAAGAAG
1 AAAAGAGAATGTTTTAATTTTAAAAATTCAATAAAATTTTAAAAACTAGGGAGGAA-GAAAGAAG
* * *
629208 TGAAAGTGTTTTAATTTTAAATTTTCACTAAAATTTT
65 -GGAAG-GTTTTAGTTTTAAAATTT-ACTAAAATTTT
629245 GAAAACTAAG
Statistics
Matches: 200, Mismatches: 25, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
136 7 0.04
137 92 0.46
138 16 0.08
140 1 0.00
141 4 0.02
142 1 0.00
143 25 0.12
144 47 0.23
145 7 0.04
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (141 bp):
AAAAGAGAATGTTTTAATTTTAAAAATTCAATAAAATTTTAAAAACTAGGGAGGAAGAAAGAAGG
GAAGGTTTTAGTTTTAAAATTTACTAAAATTTTAAATTTTAAAAACTACGGAGGGAAGACAGAAG
AGGGAATAGAT
Found at i:629280 original size:55 final size:55
Alignment explanation
Indices: 629202--629379 Score: 164
Period size: 61 Copynumber: 3.1 Consensus size: 55
629192 GTAGGAATGA
629202 AAGA-AGTGAAAGTGTTTTAATTTTAAATTTTCACTAAAATTTTGAAAACTAAGGAGGG
1 AAGAGAGTGAAAGT-TTTT-ATTTTAAA-TTTCACTAAAATTTT-AAAACTAAGGAGGG
* *
629260 AAGAG-G-GAAAGTTTTTATTTTACAATTTCACTAAAATTTTAAAAATTAGTGAGGG
1 AAGAGAGTGAAAGTTTTTATTTTA-AATTTCACTAAAATTTTAAAACTAAG-GAGGG
* ** * *
629315 AAAAAGAAGAGTGGAAGTTTGAATTTTAAAATTTAACTAAAATTTTAAAAACTAGGGAGGG
1 ---AAG-AGAGTGAAAGTTTTTATTTT-AAATTTCACTAAAATTTT-AAAACTAAGGAGGG
629376 AAGA
1 AAGA
629380 AAGAAGAGGA
Statistics
Matches: 100, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
54 7 0.07
55 26 0.26
56 6 0.06
57 7 0.07
58 11 0.11
59 2 0.02
60 1 0.01
61 33 0.33
62 7 0.07
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (55 bp):
AAGAGAGTGAAAGTTTTTATTTTAAATTTCACTAAAATTTTAAAACTAAGGAGGG
Found at i:629324 original size:61 final size:62
Alignment explanation
Indices: 629259--629618 Score: 200
Period size: 61 Copynumber: 6.2 Consensus size: 62
629249 ACTAAGGAGG
* * * *
629259 GAAGAGGGAAAGTTTTTATTTTACAATTTCACTAAAATTTTAAAAATTAGTGAGGGAA-AAA
1 GAAGAGGGAAAGTTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
* *
629320 GAAGAGTGG-AAGTTTGAATTTTAAAATTTAACTAAAATTTTAAAAACTAGGGAGGGAAGAAA
1 GAAGAG-GGAAAGTTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
* * * *
629382 GAAGA-GGAACG-----A-TTT---ATGTT---TAA-ATTTTAAAAATTGGGGAGGAAAAAAAGA
1 GAAGAGGGAAAGTTTTAATTTTAAAAT-TTAACTAAAATTTTAAAAATTAGGGAGG-GAAGAA-A
* * *** * * * * * * *
629433 -AGAG-CGAATGTTTTAATTTTAAAATTTTACC-AAAATTTTAAAAACTAGGAAGGGAAGAAA
1 GA-AGAGGGAAAGTTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
*
629493 G-AGA-GGAAAGATTTTAATTTTAAAATTTAACTAATATTTTAAAAATTAGGGAGGGAAG-AA
1 GAAGAGGGAAAG-TTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
* * * * **
629553 G--GA---ACA-TTTTTATTTTAAAATTTCACTAAAATTCTAAAAATTAGAAAGGGAAGAAA
1 GAAGAGGGAAAGTTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
*
629609 GGAGAGGGAA
1 GAAGAGGGAA
629619 TATAACATCA
Statistics
Matches: 225, Mismatches: 43, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
49 17 0.08
50 8 0.04
51 5 0.02
52 2 0.01
53 2 0.01
55 44 0.20
56 4 0.02
57 4 0.02
58 2 0.01
59 8 0.04
60 22 0.10
61 81 0.36
62 26 0.12
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.29
Consensus pattern (62 bp):
GAAGAGGGAAAGTTTTAATTTTAAAATTTAACTAAAATTTTAAAAATTAGGGAGGGAAGAAA
Found at i:629516 original size:111 final size:110
Alignment explanation
Indices: 629293--629506 Score: 315
Period size: 111 Copynumber: 1.9 Consensus size: 110
629283 AATTTCACTA
* * * *
629293 AAATTTTAAAAATTAGTGAGGGAAAAAGAAGAGTGGAAGTTTGAATTTTAAAATTTAACTAAAAT
1 AAATTTTAAAAATTAGGGAGGAAAAAAGAAGAGTCGAAGTTTGAATTTTAAAATTTAACCAAAAT
* *
629358 TTTAAAAACTAGGGAGGGAAGAAAGAAGAGGAACGATTTATGTTT
66 TTTAAAAACTAGGAAGGGAAGAAAGAAGAGGAAAGATTTATGTTT
* * *
629403 AAATTTTAAAAATTGGGGAGGAAAAAAAGAAGAG-CGAATGTTTTAATTTTAAAATTTTACCAAA
1 AAATTTTAAAAATTAGGGAGG-AAAAAAGAAGAGTCGAA-GTTTGAATTTTAAAATTTAACCAAA
629467 ATTTTAAAAACTAGGAAGGGAAGAAAG-AGAGGAAAGATTT
64 ATTTTAAAAACTAGGAAGGGAAGAAAGAAGAGGAAAGATTT
629507 TAATTTTAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
110 34 0.37
111 59 0.63
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (110 bp):
AAATTTTAAAAATTAGGGAGGAAAAAAGAAGAGTCGAAGTTTGAATTTTAAAATTTAACCAAAAT
TTTAAAAACTAGGAAGGGAAGAAAGAAGAGGAAAGATTTATGTTT
Done.