Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008308.1 Hibiscus syriacus cultivar Beakdansim tig00110998_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: 1044366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:464802 original size:16 final size:15
Alignment explanation
Indices: 464760--464819 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
464750 AAAGAAAACT
*
464760 AATAAAATATAAAAA
1 AATAAAATAAAAAAA
**
464775 AATGTTAA-AAAAAAA
1 AAT-AAAATAAAAAAA
*
464790 AATAAAAGTAAAACAA
1 AATAAAA-TAAAAAAA
464806 AATAAAATAAAAAA
1 AATAAAATAAAAAA
464820 TGGGAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 2 0.06
15 18 0.51
16 15 0.43
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (15 bp):
AATAAAATAAAAAAA
Found at i:464828 original size:36 final size:36
Alignment explanation
Indices: 464788--464866 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
464778 GTTAAAAAAA
464788 AAAATAAAAG-TAAAACAAAATAAAATAAAAAATGGG
1 AAAATAAAAGATAAAACAAAATAAAATAAAAAA-GGG
* *
464824 AAAAT-AAAGATAAAACAAAATAAGATGAAAAAGGG
1 AAAATAAAAGATAAAACAAAATAAAATAAAAAAGGG
464859 AAATATAA
1 AAA-ATAA
464867 TAAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 10 0.26
36 27 0.71
37 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.13, T:0.14
Consensus pattern (36 bp):
AAAATAAAAGATAAAACAAAATAAAATAAAAAAGGG
Found at i:464944 original size:18 final size:18
Alignment explanation
Indices: 464923--464965 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
464913 GTTGTTTTTA
* *
464923 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
464941 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
464959 AAATAAA
1 AAATAAA
464966 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:466783 original size:6 final size:6
Alignment explanation
Indices: 466772--466825 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
466762 CGTTTGTTTA
* * * *
466772 ATTTTT ATTTTT ATTTTA AATTTT ATTTTT CTAATTT ATTTTT -TTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTTTT ATTTTT
466820 ATTTTT
1 ATTTTT
466826 CTCTGATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 5 0.13
6 29 0.76
7 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:466809 original size:25 final size:24
Alignment explanation
Indices: 466781--466827 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
466771 AATTTTTATT
466781 TTTATTTTAAATTTTATTTTTCTAA
1 TTTATTTT-AATTTTATTTTTCTAA
**
466806 TTTATTTTTTTTTTATTTTTCT
1 TTTATTTTAATTTTATTTTTCT
466828 CTGATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTATTTTAATTTTATTTTTCTAA
Found at i:467076 original size:31 final size:28
Alignment explanation
Indices: 467000--467076 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
466990 GAAATACACT
* *
467000 GTTCGGACAGTGCAGAAAAACTGATTTG
1 GTTCGAACAGTGCAGAAAAACTGACTTG
* *
467028 GTT-GAATAGTGGAGAAAAACAATAGACTTG
1 GTTCGAACAGTGCAGAAAAAC--T-GACTTG
467058 GTTCGAACAGTGCAGAAAA
1 GTTCGAACAGTGCAGAAAA
467077 TACACAGCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 14 0.36
28 3 0.08
29 1 0.03
30 8 0.21
31 13 0.33
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (28 bp):
GTTCGAACAGTGCAGAAAAACTGACTTG
Found at i:469156 original size:20 final size:22
Alignment explanation
Indices: 469133--469172 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
469123 TTTTAAGTAT
469133 TTTA-ATTAGGATT-TATTTTC
1 TTTATATTAGGATTATATTTTC
*
469153 TTTATTTTAGGATTATATTT
1 TTTATATTAGGATTATATTT
469173 ACCTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTATATTAGGATTATATTTTC
Found at i:469164 original size:21 final size:22
Alignment explanation
Indices: 469138--469190 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
469128 AGTATTTTAA
*
469138 TTAGGATTTATTT-TCTT-TATT
1 TTAGGATTTATTTACCTTGT-TT
469159 TTAGGATTATATTTACCTTGTTT
1 TTAGGATT-TATTTACCTTGTTT
469182 TTAGGATTT
1 TTAGGATTT
469191 TGAAGGCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.29
22 6 0.21
23 13 0.46
24 1 0.04
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (22 bp):
TTAGGATTTATTTACCTTGTTT
Found at i:470055 original size:12 final size:12
Alignment explanation
Indices: 470038--470062 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
470028 AAACAATTTA
470038 TATTTTATTATT
1 TATTTTATTATT
470050 TATTTTATTATT
1 TATTTTATTATT
470062 T
1 T
470063 TATTCTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:470626 original size:31 final size:31
Alignment explanation
Indices: 470566--470630 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
470556 AGTTCACATC
* *
470566 TTAATTAAATAAAAACGATATTGAACAAATA
1 TTAATTAAATAAAAACGAAAGTGAACAAATA
*
470597 TTAATTAAATAAAAATC-AAAGTGACCAAATA
1 TTAATTAAATAAAAA-CGAAAGTGAACAAATA
470628 TTA
1 TTA
470631 TATTTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTGAACAAATA
Found at i:474358 original size:30 final size:30
Alignment explanation
Indices: 474322--474381 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
474312 CCTAAAATTC
* *
474322 GAAAATTACCCATTTGGTCCTTGAACTTTT
1 GAAAATTACCCATTTAGTCCTTAAACTTTT
* *
474352 GAAAATTATCCTTTTAGTCCTTAAACTTTT
1 GAAAATTACCCATTTAGTCCTTAAACTTTT
474382 CAAACTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.43
Consensus pattern (30 bp):
GAAAATTACCCATTTAGTCCTTAAACTTTT
Found at i:474398 original size:30 final size:30
Alignment explanation
Indices: 474338--474417 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
474328 TACCCATTTG
* * *
474338 GTCCTTGAACTTTTGAAAATTATCCTTTTA
1 GTCCTTAAACTTTTCAAAATTATACTTTTA
*
474368 GTCCTTAAACTTTTCAAACTTCATAC-TTTA
1 GTCCTTAAACTTTTCAAAATT-ATACTTTTA
*
474398 GACAC-TAAAC-TTTCAAAATT
1 GTC-CTTAAACTTTTCAAAATT
474418 TATGTTTTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 9 0.21
30 29 0.69
31 4 0.10
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (30 bp):
GTCCTTAAACTTTTCAAAATTATACTTTTA
Found at i:474440 original size:25 final size:25
Alignment explanation
Indices: 474412--474468 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
474402 CTAAACTTTC
* *
474412 AAAATTTATGTTTTGGTCACTAATT
1 AAAATTTATATTTTGGTCACTAACT
474437 AAAATTTATATTTTGGTCACTAACT
1 AAAATTTATATTTTGGTCACTAACT
474462 AAAATTT
1 AAAATTT
474469 GGGGATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (25 bp):
AAAATTTATATTTTGGTCACTAACT
Found at i:474742 original size:32 final size:33
Alignment explanation
Indices: 474667--474743 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
474657 GTATAAAATT
*
474667 TTAAATT-TTAAATATAAACAATTATTAAAAAA
1 TTAAATTATTAAATATAAACAATTACTAAAAAA
*
474699 TT-AATACATTAAATATAAA-AA-TACTACAAAAA
1 TTAAAT-TATTAAATATAAACAATTACTA-AAAAA
474731 TTAAATTATTAAA
1 TTAAATTATTAAA
474744 AAATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 7 0.18
32 17 0.45
33 14 0.37
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (33 bp):
TTAAATTATTAAATATAAACAATTACTAAAAAA
Found at i:476914 original size:23 final size:23
Alignment explanation
Indices: 476889--476985 Score: 104
Period size: 23 Copynumber: 4.2 Consensus size: 23
476879 AAGTGACACA
* *
476889 TAGAAATGTCCCGAAGGACCACA
1 TAGAAATATCCCGAAGGACCACG
* * * *
476912 TAGTATTATCCCGGAGGACCGCG
1 TAGAAATATCCCGAAGGACCACG
*
476935 TAGAAATATCCTGAAGGACCACG
1 TAGAAATATCCCGAAGGACCACG
* * *
476958 TAGAATTGTCCCGAAAGACCACG
1 TAGAAATATCCCGAAGGACCACG
476981 TAGAA
1 TAGAA
476986 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
TAGAAATATCCCGAAGGACCACG
Found at i:476941 original size:46 final size:46
Alignment explanation
Indices: 476889--476985 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
476879 AAGTGACACA
* * * * *
476889 TAGAAATGTCCCGAAGGACCACATAGTATTATCCCGGAGGACCGCG
1 TAGAAATATCCCGAAGGACCACATAGAATTATCCCGAAAGACCACG
* * *
476935 TAGAAATATCCTGAAGGACCACGTAGAATTGTCCCGAAAGACCACG
1 TAGAAATATCCCGAAGGACCACATAGAATTATCCCGAAAGACCACG
476981 TAGAA
1 TAGAA
476986 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (46 bp):
TAGAAATATCCCGAAGGACCACATAGAATTATCCCGAAAGACCACG
Found at i:477091 original size:16 final size:15
Alignment explanation
Indices: 477069--477109 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
477059 TTTTGATAGC
477069 TTATCACATAA-CCA
1 TTATCACATAACCCA
477083 TGTATTCACATAACCCA
1 T-TA-TCACATAACCCA
477100 TTATCACATA
1 TTATCACATA
477110 GCTTATGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 10 0.42
17 4 0.17
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (15 bp):
TTATCACATAACCCA
Found at i:480702 original size:54 final size:54
Alignment explanation
Indices: 480644--480982 Score: 480
Period size: 54 Copynumber: 6.3 Consensus size: 54
480634 TTTTGTACCT
* ** * * * *
480644 TGCACACCTAGTGTTGAAACGGATATTCATCCTCATAGGATAAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
480698 TGCACACTTAGTACCGAAACGGTTATCCATCCATATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
480752 TGCACACTTAGTGTCGAAACAGTTATTCATCCACATAAGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
480806 TGCATACTTAGTGCCGAAACGGTTATTCATCCATATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
480860 TGCAAACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGATA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
480914 TGGACACTTAGTACCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
480968 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
480983 TATTGGGTAC
Statistics
Matches: 252, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 252 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:487579 original size:54 final size:52
Alignment explanation
Indices: 487496--487796 Score: 408
Period size: 53 Copynumber: 5.7 Consensus size: 52
487486 TATTGATTCT
*
487496 CATAGGATGAATTCGTGAAATGCACACTTAGTGTCGAAACAGTTATTCATCCA
1 CATAGGATGAATTCGTGAAATGCACACTTAGTG-CGAAACGGTTATTCATCCA
*
487549 CATAGGATGAATTTCGTGAAATGCGCACTTAGTGTCG-AACGGTTATTCATCCA
1 CATAGGATGAA-TTCGTGAAATGCACACTTAGTG-CGAAACGGTTATTCATCCA
* *
487602 CATAAGATGAATTAGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
1 CATAGGATGAATTCGTGAAATGCACACTTAGTG-CGAAACGGTTATTCATCCA
*
487655 CATAGTATGAATTCTGTGAAATGCACACTTAGTGCTGAAACGGTTATTCATCCA
1 CATAGGATGAATTC-GTGAAATGCACACTTAGTGC-GAAACGGTTATTCATCCA
* * *
487709 CATAGGATGAATTCCGTG-AATGCATACTTAATGCTGAAACGGTTATTCGTCCA
1 CATAGGATGAATT-CGTGAAATGCACACTTAGTGC-GAAACGGTTATTCATCCA
** *
487762 TGTAGGTTGAATTCCGTGAAATGCACACTTAGTGC
1 CATAGGATGAATT-CGTGAAATGCACACTTAGTGC
487797 CTATTGGGTA
Statistics
Matches: 224, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
52 22 0.10
53 111 0.50
54 90 0.40
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (52 bp):
CATAGGATGAATTCGTGAAATGCACACTTAGTGCGAAACGGTTATTCATCCA
Found at i:487710 original size:29 final size:29
Alignment explanation
Indices: 487624--487710 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 29
487614 TAGTGAAATG
*
487624 CACACTTAGTGCCGAAACGGTTATTCATC
1 CACACTTAGTGCTGAAACGGTTATTCATC
* * * * * *
487653 CACA--TAGT-ATGAATTCTGTGA--AATG
1 CACACTTAGTGCTGAA-ACGGTTATTCATC
487678 CACACTTAGTGCTGAAACGGTTATTCATC
1 CACACTTAGTGCTGAAACGGTTATTCATC
487707 CACA
1 CACA
487711 TAGGATGAAT
Statistics
Matches: 39, Mismatches: 13, Indels: 12
0.61 0.20 0.19
Matches are distributed among these distances:
25 6 0.15
26 3 0.08
27 16 0.41
28 4 0.10
29 10 0.26
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (29 bp):
CACACTTAGTGCTGAAACGGTTATTCATC
Found at i:487748 original size:107 final size:107
Alignment explanation
Indices: 487496--487796 Score: 407
Period size: 107 Copynumber: 2.8 Consensus size: 107
487486 TATTGATTCT
* *
487496 CATAGGATGAATTCGTGAAATGCACACTTAGTG-TCGAAACAGTTATTCATCCACATAGGATGAA
1 CATAGGATGAATTCGTGAAATGCACACTTAGTGCT-GAAACGGTTATTCATCCACATAGTATGAA
*
487560 TT-TCGTGAAATGCGCACTTAGTG-TCGAACGGTTATTCATCCA
65 TTCT-GTGAAATGCACACTTAGTGCTCGAACGGTTATTCATCCA
* * *
487602 CATAAGATGAATTAGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGTATGAAT
1 CATAGGATGAATTCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCATCCACATAGTATGAAT
487667 TCTGTGAAATGCACACTTAGTGCT-GAAACGGTTATTCATCCA
66 TCTGTGAAATGCACACTTAGTGCTCG-AACGGTTATTCATCCA
* * * **
487709 CATAGGATGAATTCCGTG-AATGCATACTTAATGCTGAAACGGTTATTCGTCCATGTAGGT-TGA
1 CATAGGATGAATT-CGTGAAATGCACACTTAGTGCTGAAACGGTTATTCATCCACATA-GTATGA
*
487772 ATTCCGTGAAATGCACACTTAGTGC
64 ATTCTGTGAAATGCACACTTAGTGC
487797 CTATTGGGTA
Statistics
Matches: 174, Mismatches: 15, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
106 79 0.45
107 90 0.52
108 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (107 bp):
CATAGGATGAATTCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCATCCACATAGTATGAAT
TCTGTGAAATGCACACTTAGTGCTCGAACGGTTATTCATCCA
Found at i:488319 original size:95 final size:95
Alignment explanation
Indices: 488136--488320 Score: 221
Period size: 95 Copynumber: 1.9 Consensus size: 95
488126 ATACCTATAC
* * * * **
488136 CATGGTATCGATACTACCCTACTATGGTATCGATACCCCCTTCTGGTATCGGTACCAAAATTATT
1 CATGGTATCGATACTACCATACTAGGGTATCGATACCCCCTTCCGGTATCGATACCAAAATTAGG
* * *
488201 TTTGATGTGCCTTGCTATTGATACCCTCAT
66 TTCGATGTACCTTGCTATCGATACCCTCAT
* * *
488231 CATGGTATCGATACTACTATGCTAGGGT-GCTGATACCCCCTTCCGGTATCGATACCAAAATTAG
1 CATGGTATCGATACTACCATACTAGGGTATC-GATACCCCCTTCCGGTATCGATACCAAAATTAG
*
488295 GTTCGATGTTACC-TGGTATCGATACC
65 GTTCGATG-TACCTTGCTATCGATACC
488321 TCCCCATCAG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 71 0.95
96 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (95 bp):
CATGGTATCGATACTACCATACTAGGGTATCGATACCCCCTTCCGGTATCGATACCAAAATTAGG
TTCGATGTACCTTGCTATCGATACCCTCAT
Found at i:494451 original size:53 final size:53
Alignment explanation
Indices: 494393--494666 Score: 413
Period size: 53 Copynumber: 5.1 Consensus size: 53
494383 CTTGCATACC
** * *
494393 TAGTGCCGAAACGGACATTCATCCTCATAGGATGAATTCATGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACT
* * *
494446 TAGTGCCGAAACAGTTATTCATCCACATATGATGAATTTGTGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACT
* *
494499 TAGTGTCGAAACGGTTATTCATCCACATAAGATGAATTCCGTGAAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATT-CGTGAAATGCACACT
*
494553 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGTACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATT-CGTGAAATGCACACT
* * *
494607 TAGTGTCGAAAAGGTTATTCATCCACATAGGATGAATTCGTGAAATGTACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACT
494660 TAGTGCC
1 TAGTGCC
494667 TATTGGGTAC
Statistics
Matches: 203, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 102 0.50
54 101 0.50
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (53 bp):
TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACT
Found at i:494558 original size:107 final size:107
Alignment explanation
Indices: 494393--494666 Score: 424
Period size: 107 Copynumber: 2.6 Consensus size: 107
494383 CTTGCATACC
* ** * *
494393 TAGTGCCGAAACGGACATTCATCCTCATAGGATGAATTCATGAAATGCACACTTAGTGCCGAAAC
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACTTAGTGCCGAAAC
* *
494458 AGTTATTCATCCACATATGATGAATT-TGTGAAATGCACACT
66 AGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACT
*
494499 TAGTGTCGAAACGGTTATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATT-CGTGAAATGCACACTTAGTGCCGAAA
* *
494564 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGTACACT
65 CAGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACT
* *
494607 TAGTGTCGAAAAGGTTATTCATCCACATAGGATGAATTCGTGAAATGTACACTTAGTGCC
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACTTAGTGCC
494667 TATTGGGTAC
Statistics
Matches: 153, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
106 33 0.22
107 71 0.46
108 49 0.32
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (107 bp):
TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCGTGAAATGCACACTTAGTGCCGAAAC
AGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACT
Found at i:499779 original size:24 final size:24
Alignment explanation
Indices: 499752--499800 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
499742 CACCGCAGCT
* * *
499752 CGTATAAATTGCACTGAAGTGCCA
1 CGTAGAAATTGCACTAAAGTACCA
499776 CGTAGAAATTGCACTAAAGTACCA
1 CGTAGAAATTGCACTAAAGTACCA
499800 C
1 C
499801 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTGCACTAAAGTACCA
Found at i:499808 original size:24 final size:24
Alignment explanation
Indices: 499757--499808 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
499747 CAGCTCGTAT
* * * *
499757 AAATTGCACTGAAGTGCCACGTAG
1 AAATTGCACTAAAGTACCACATAA
499781 AAATTGCACTAAAGTACCACATAA
1 AAATTGCACTAAAGTACCACATAA
499805 AAAT
1 AAAT
499809 ATCCAGAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (24 bp):
AAATTGCACTAAAGTACCACATAA
Found at i:499857 original size:23 final size:23
Alignment explanation
Indices: 499831--499885 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
499821 CACATAGTAT
*
499831 TGTCCCGAAGGACCGTGTAGAAA
1 TGTCCCGAAGGACCATGTAGAAA
* * *
499854 TGTCTCAAAGGACCATGTAGAAT
1 TGTCCCGAAGGACCATGTAGAAA
499877 TGTCCCGAA
1 TGTCCCGAA
499886 AGATCACGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (23 bp):
TGTCCCGAAGGACCATGTAGAAA
Found at i:501887 original size:2 final size:2
Alignment explanation
Indices: 501880--501912 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
501870 CAATAAAATA
501880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
501913 ATTTATACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:503147 original size:22 final size:22
Alignment explanation
Indices: 503122--503165 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
503112 ACACTTAGTG
503122 AAACATTATC-AAATATAAAATA
1 AAACA-TATCGAAATATAAAATA
*
503144 AAACATATCGATATATAAAATA
1 AAACATATCGAAATATAAAATA
503166 TCACATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.27
Consensus pattern (22 bp):
AAACATATCGAAATATAAAATA
Found at i:504550 original size:217 final size:220
Alignment explanation
Indices: 504175--504613 Score: 857
Period size: 217 Copynumber: 2.0 Consensus size: 220
504165 AAAGCATATG
504175 TTAGTACCACACTAACATAGGCATAAGCTAGTAATTAAATTTATAAAAATTCTTCTAACATTTGT
1 TTAGTACCACACTAACATAGGCATAAGCTAGTAATTAAATTTATAAAAATTCTTCTAACATTTGT
504240 GCGATACTAAACCATATCACAAAATAAATCTTGACTTTTATTCTTCAAAATAACATGTTACGTCC
66 GCGATACTAAACCATATCACAAAATAAATCTTGACTTTTATTCTTCAAAATAACATGTTACGTCC
504305 TTTACTATTCATATTCACAACTGTTCACCTGACATTTCAAATTTCACATTTCAA-C-CTAATATA
131 TTTACTATTCATATTCACAACTGTTCACCTGACATTTCAAATTTCACATTTCAACCACTAATATA
504368 AATTATG-TAGAATTCATCTCAACT
196 AATTATGTTAGAATTCATCTCAACT
504392 TTAGTACCACACTAACATAGGCATAAGCTAGTAATTAAATTTATAAAAATTCTTCTAACATTTGT
1 TTAGTACCACACTAACATAGGCATAAGCTAGTAATTAAATTTATAAAAATTCTTCTAACATTTGT
504457 GCGATACTAAACCATATCACAAAATAAATCTTGACTTTTATTCTTCAAAATAACATGTTACGTCC
66 GCGATACTAAACCATATCACAAAATAAATCTTGACTTTTATTCTTCAAAATAACATGTTACGTCC
504522 TTTACTATTCATATTCACAACTGTTCACCTGACATTTCAAATTTCACATTTCAACCACTAATATA
131 TTTACTATTCATATTCACAACTGTTCACCTGACATTTCAAATTTCACATTTCAACCACTAATATA
504587 AATTATGTTAGAATTCATCTCAACT
196 AATTATGTTAGAATTCATCTCAACT
504612 TT
1 TT
504614 TTAAATTTAT
Statistics
Matches: 219, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
217 184 0.84
218 1 0.00
219 15 0.07
220 19 0.09
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (220 bp):
TTAGTACCACACTAACATAGGCATAAGCTAGTAATTAAATTTATAAAAATTCTTCTAACATTTGT
GCGATACTAAACCATATCACAAAATAAATCTTGACTTTTATTCTTCAAAATAACATGTTACGTCC
TTTACTATTCATATTCACAACTGTTCACCTGACATTTCAAATTTCACATTTCAACCACTAATATA
AATTATGTTAGAATTCATCTCAACT
Found at i:508060 original size:31 final size:31
Alignment explanation
Indices: 508025--508083 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
508015 TTTAATCACA
*
508025 TTATCGTTTTATTAGGTTTTGGCCACTTATG
1 TTATCGTTTTATTAAGTTTTGGCCACTTATG
*
508056 TTATCGTTTTATTAAGTTTTGGTCACTT
1 TTATCGTTTTATTAAGTTTTGGCCACTT
508084 GGACGTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (31 bp):
TTATCGTTTTATTAAGTTTTGGCCACTTATG
Found at i:509508 original size:31 final size:31
Alignment explanation
Indices: 509441--509509 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
509431 ATTCAATGTC
** * *
509441 CAAGTGACCAAAACTTAATACAACGATAACA
1 CAAGTGACCAAAACACAATAAAACAATAACA
* *
509472 TAAGTGACCAAAACACAATAAAACAATAACG
1 CAAGTGACCAAAACACAATAAAACAATAACA
509503 CAAGTGA
1 CAAGTGA
509510 TTAAAAGTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.14
Consensus pattern (31 bp):
CAAGTGACCAAAACACAATAAAACAATAACA
Found at i:511309 original size:20 final size:21
Alignment explanation
Indices: 511281--511320 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
511271 TCGAGGGTTC
511281 TATGCGGTCCTTC-GGACATA
1 TATGCGGTCCTTCTGGACATA
*
511301 TATGTGGTCCTTCTGGACAT
1 TATGCGGTCCTTCTGGACAT
511321 TCTATATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGCGGTCCTTCTGGACATA
Found at i:525644 original size:81 final size:81
Alignment explanation
Indices: 525547--525707 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
525537 TGGCAAGGAT
*
525547 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATGTGGCAGCTATAATCAAATATGCA
1 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
525612 TGTGGCAGTGGAAGAC
66 TGTGGCAGTGGAAGAC
525628 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
1 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
*
525693 TGTGGTAGTGGAAGA
66 TGTGGCAGTGGAAGA
525708 TATAATGGTG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (81 bp):
AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
TGTGGCAGTGGAAGAC
Found at i:531609 original size:23 final size:21
Alignment explanation
Indices: 531575--531622 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
531565 CTAAAAATCT
531575 TAAAAACAAAGAAAAGATAATTCC
1 TAAAAACAAAG---AGATAATTCC
531599 TAAAAAC-AAGAGATAATTCC
1 TAAAAACAAAGAGATAATTCC
531619 TAAA
1 TAAA
531623 GATAATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.58
23 3 0.12
24 7 0.29
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.19
Consensus pattern (21 bp):
TAAAAACAAAGAGATAATTCC
Found at i:536563 original size:184 final size:184
Alignment explanation
Indices: 536298--536672 Score: 610
Period size: 184 Copynumber: 2.0 Consensus size: 184
536288 TATAAAAATT
* *
536298 AAATGTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AAAT-TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
536363 TTCAGATAAATTTTTTAATTAATTAATATAGATTTAGATTTAAAAGTTATTGGATCTTAAATTAT
65 TTCAGATAAATTTTTTAATTAATTAATATAGATTTAGATTTAAAAGTTATTGGATCTTAAATTAT
* *
536428 TAATT-AGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTA
130 TAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTA
*
536482 ATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAA
1 AAATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAA
* * * *
536547 TTT-ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
64 TTTCAGATAAATTTTTTAATTAATTAATATAGATTTAGATTTAAAAGTTATTGGATCTTAAATTA
* *
536611 TTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTA
129 TTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTA
536667 AAATTT
1 AAATTT
536673 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
183 15 0.09
184 103 0.59
185 58 0.33
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (184 bp):
AAATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
TCAGATAAATTTTTTAATTAATTAATATAGATTTAGATTTAAAAGTTATTGGATCTTAAATTATT
AATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTA
Found at i:538575 original size:23 final size:23
Alignment explanation
Indices: 538505--538578 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
538495 ACATATAGGT
*
538505 CAATGAAAGCAGAACCATCTGAA-
1 CAATGAAAGCAGAACCATC-AAAC
* **
538528 CAACGAAATTA-AACCACATACAAAC
1 CAATGAAAGCAGAA-C-CAT-CAAAC
538553 CAATGAAAGCAGAACCATCAAAC
1 CAATGAAAGCAGAACCATCAAAC
538576 CAA
1 CAA
538579 CAAGCACTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
22 2 0.05
23 17 0.44
24 8 0.21
25 10 0.26
26 2 0.05
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.11
Consensus pattern (23 bp):
CAATGAAAGCAGAACCATCAAAC
Found at i:540544 original size:32 final size:33
Alignment explanation
Indices: 540498--540560 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
540488 TTTATTTTGT
* *
540498 TCGGGTCGG-GTTTTTTAAGTGTGATATTCGAG
1 TCGGGTCGGATTTTTTTAAGTATGATATTCGAG
540530 TCGGGTCGGATTTTTTTAAGTATGATATTCG
1 TCGGGTCGGATTTTTTTAAGTATGATATTCG
540561 GGTTTGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.17, C:0.10, G:0.30, T:0.43
Consensus pattern (33 bp):
TCGGGTCGGATTTTTTTAAGTATGATATTCGAG
Found at i:544860 original size:20 final size:20
Alignment explanation
Indices: 544835--544924 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
544825 TTAGTTTCCA
544835 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
544855 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
544875 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCGAATATGT
*
544895 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCGAATATGT
544915 AAATCGCAAC
1 AAATCGCAAC
544925 ACATAAGTCA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:544941 original size:20 final size:20
Alignment explanation
Indices: 544918--544963 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
544908 AATCTGTAAA
* *
544918 TCGCAACACATAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
544938 TCGCAACAAAGAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
*
544958 TTGCAA
1 TCGCAA
544964 AACGCGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.20
Consensus pattern (20 bp):
TCGCAACAAAGAAGTCAAAT
Found at i:544942 original size:40 final size:39
Alignment explanation
Indices: 544835--544944 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 39
544825 TTAGTTTCCA
* *
544835 AAATCGCAACGCGAATATGTAAATCGCAACGCGAATATGT
1 AAATCGCAACAC-AATAAGTAAATCGCAACGCGAATATGT
* ** *
544875 AAATCGCAACGCGAATCTGTAAATCGCAACGCGAATCTGT
1 AAATCGCAACAC-AATAAGTAAATCGCAACGCGAATATGT
544915 AAATCGCAACAC-ATAAGTCAAATTCGCAAC
1 AAATCGCAACACAATAAGT-AAA-TCGCAAC
544945 AAAGAAGTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
38 4 0.06
39 3 0.05
40 56 0.89
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (39 bp):
AAATCGCAACACAATAAGTAAATCGCAACGCGAATATGT
Found at i:545146 original size:22 final size:22
Alignment explanation
Indices: 545118--545168 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
545108 CTACGGCGAC
**
545118 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
545140 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
545162 ATCCGTC
1 ATCCGTC
545169 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:545558 original size:19 final size:20
Alignment explanation
Indices: 545534--545587 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
545524 AAATGGCAAC
545534 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
545553 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
545573 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
545588 AGAAACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:547338 original size:21 final size:21
Alignment explanation
Indices: 547314--547363 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
547304 TGGTGCATGG
547314 CGTGATGAGGTACA-GTCTTTA
1 CGTGATGAGGTACAGGT-TTTA
* *
547335 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTACAGGTTTTA
*
547356 CGCGATGA
1 CGTGATGA
547364 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTACAGGTTTTA
Found at i:547725 original size:21 final size:21
Alignment explanation
Indices: 547670--547735 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
547660 GCCTGATTCA
547670 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
547691 TCTCAT-ATCCTTCAAGAGGCC
1 CCT-GTCATCGTTCAAGAGGCC
*
547712 CCTGTCATCGTTCAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
547733 CCT
1 CCT
547736 CCCACCGTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:547744 original size:21 final size:21
Alignment explanation
Indices: 547678--547750 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
547668 CACCTGTCAT
* **
547678 CGTTCAAGAGGCCTCTCATATC
1 CGTTCAAGAGGCCCCTCCCA-C
** *
547700 C-TTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
*
547720 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
547741 CGTTCGAGAG
1 CGTTCAAGAG
547751 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:549158 original size:63 final size:64
Alignment explanation
Indices: 549058--549205 Score: 208
Period size: 63 Copynumber: 2.3 Consensus size: 64
549048 AAATTGATGT
549058 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * * *** * *
549121 ATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTTCTTGTTTAATTT
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
*
549185 ATCTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
549206 GTTTTAAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 39 0.53
64 35 0.47
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:549329 original size:20 final size:20
Alignment explanation
Indices: 549306--549360 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
549296 TTTTCGCGTT
* *
549306 GCGATAGTCAAATTCGCAAG
1 GCGAAAGTCAAATTCGCAAC
*
549326 GCGAAAGTTAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
549346 GCGAAAGTCAAATTC
1 GCGAAAGTCAAATTC
549361 ACGTTGCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:549377 original size:14 final size:14
Alignment explanation
Indices: 549358--549387 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
549348 GAAAGTCAAA
549358 TTCACGTTGCGATT
1 TTCACGTTGCGATT
549372 TTCACGTTGCGATT
1 TTCACGTTGCGATT
549386 TT
1 TT
549388 GCGTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (14 bp):
TTCACGTTGCGATT
Found at i:549644 original size:18 final size:18
Alignment explanation
Indices: 549621--549656 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
549611 AAGCCGGTTG
*
549621 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
549639 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
549657 CATTTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:549663 original size:18 final size:18
Alignment explanation
Indices: 549623--549660 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
549613 GCCGGTTGTG
* *
549623 ATTGGGATTTTGATTTTG
1 ATTGCGATTTTGATTTTC
549641 ATTGCGATTTTGA-TTTC
1 ATTGCGATTTTGATTTTC
549658 ATT
1 ATT
549661 TGCTTGGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (18 bp):
ATTGCGATTTTGATTTTC
Found at i:549883 original size:16 final size:15
Alignment explanation
Indices: 549861--549899 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
549851 GAAATCATTG
549861 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
549877 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
549892 AAAAATTA
1 AAAAATTA
549900 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:550100 original size:20 final size:20
Alignment explanation
Indices: 550056--550209 Score: 111
Period size: 20 Copynumber: 7.7 Consensus size: 20
550046 AATAAAACCT
*
550056 GTTGCGAAATT-AAAATTCGTA
1 GTTGCGAATTTGAAAA-TCG-A
*
550077 -TTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATCGA
*
550096 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATCGA
* *
550116 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAAATC-GA
* *
550137 GTTGTGAATTTGTAAATCGCA
1 GTTGCGAATTTGAAAATCG-A
**
550158 -ACGCGAATTTGAAAATC-A
1 GTTGCGAATTTGAAAATCGA
* *
550176 CGTTGCGAATTTGGAAATCGC
1 -GTTGCGAATTTGAAAATCGA
*
550197 GTTGTGAATTTGA
1 GTTGCGAATTTGA
550210 CTTCTGTGTT
Statistics
Matches: 103, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 76 0.74
21 23 0.22
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGA
Found at i:552183 original size:17 final size:18
Alignment explanation
Indices: 552144--552190 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
552134 TGTTTCTGAG
552144 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
552162 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
*
552179 GGAATTGGAATC
1 GGAATTAGAATC
552191 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:553624 original size:49 final size:48
Alignment explanation
Indices: 553547--553642 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 48
553537 TTTTATGTTA
553547 CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
1 CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
*
553595 CCAATAGAATGATATTATGTGTACGAATCTTAACTTCAATCAATCAAT
1 CCAATAGAATGATA-CATGTGTACGAATCTTAACTTCAATCAATCAAT
553643 CACACATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 14 0.30
49 32 0.70
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (48 bp):
CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
Found at i:558290 original size:54 final size:53
Alignment explanation
Indices: 558204--558725 Score: 626
Period size: 54 Copynumber: 9.8 Consensus size: 53
558194 TGCATTTTTA
* * *
558204 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGACACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* *
558258 TATCGGCACTATGTGTGCAACCCACAACATTCATAACGAGTTTGTGAATTACCG
1 TATCGACACTATGTGTGCAACCCACAA-ATTCATAATGAGTTTGTGAATTACCG
* *
558312 TATCGAAACTATGTGTGCAACCCACGAAATTTATAATGAGTTTGTGAATTACCG
1 TATCGACACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* * * *
558366 TATCGGCACTATATGTGCAACCCACAGAATTCGTAATGAGTTTGTGAATTATCG
1 TATCGACACTATGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCG
* * *
558420 TATCAACACTATATGTGCAACCCACATAATTCATAATGAGTTTTTGAATTACCG
1 TATCGACACTATGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCG
* *
558474 TATCGACACTATGTCTTCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
1 TATCGACACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* *
558528 TATCGACACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGACACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* * * *
558582 TATC-AGTACTATGCGTGCAACGCACAGAATTCATAATGAGTTTGTAAATTACCG
1 TATCGA-CACTATGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCG
* * * *
558636 TATCGACACTATGTGTGCAA--CTC----TCATAATAAGTTTGTGAATAACTG
1 TATCGACACTATGTGTGCAACCCACAAATTCATAATGAGTTTGTGAATTACCG
* * ** *
558683 TATCGACACTATGTGTACAATCCATGGAATTCATAATAAGTTT
1 TATCGACACTATGTGTGCAACCCA-CAAATTCATAATGAGTTT
558726 ATGATTTTCC
Statistics
Matches: 410, Mismatches: 44, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
47 39 0.10
49 1 0.00
52 2 0.00
53 3 0.01
54 361 0.88
55 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (53 bp):
TATCGACACTATGTGTGCAACCCACAAATTCATAATGAGTTTGTGAATTACCG
Found at i:558471 original size:162 final size:161
Alignment explanation
Indices: 558204--558725 Score: 700
Period size: 162 Copynumber: 3.3 Consensus size: 161
558194 TGCATTTTTA
*
558204 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
* *
558269 TGTGTGCAACCCACAACATTCATAACGAGTTTGTGAATTACCGTATCGAAACTATGTGTGCAACC
66 TGTGTGCAACCCACAA-ATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
* *
558334 CACGAAATTTATAATGAGTTTGTGAATTACCG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* * * * * *
558366 TATCGGCACTATATGTGCAACCCACAGAATTCGTAATGAGTTTGTGAATTATCGTATCAACACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
* * * *
558431 TATGTGCAACCCACATAATTCATAATGAGTTTTTGAATTACCGTATCGACACTATGTCTTCAACC
66 TGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
558496 CACAAAATTCATAATGAGTTTGTGAATTACCG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* *
558528 TATCGACACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGTACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
* * *
558593 TGCGTGCAACGCACAGAATTCATAATGAGTTTGTAAATTACCGTATCGACACTATGTGTGCAA--
66 TGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
* * * *
558656 CTC-----TCATAATAAGTTTGTGAATAACTG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* * * *
558683 TATCGACACTATGTGTACAA-TCCATGGAATTCATAATAAGTTT
1 TATCGGCACTATGTGTGCAACT-CACGGAATTCATAATGAGTTT
558726 ATGATTTTCC
Statistics
Matches: 320, Mismatches: 38, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
154 1 0.00
155 59 0.18
160 2 0.01
162 257 0.80
163 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (161 bp):
TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
TGTGTGCAACCCACAAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCC
ACAAAATTCATAATGAGTTTGTGAATTACCG
Found at i:564015 original size:6 final size:6
Alignment explanation
Indices: 564001--564068 Score: 88
Period size: 6 Copynumber: 11.5 Consensus size: 6
563991 AATAAAAATT
*
564001 AAAATG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACTTG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAAC--G
564051 AAAA-G AAAA-G AAAA-G AAA
1 AAAACG AAAACG AAAACG AAA
564069 GGAAACAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
5 14 0.24
6 40 0.68
8 5 0.08
ACGTcount: A:0.69, C:0.10, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAACG
Found at i:577799 original size:24 final size:23
Alignment explanation
Indices: 577747--577793 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
577737 TTAGCATGTT
577747 TAAAAATAAAACTTAAAATGAAA
1 TAAAAATAAAACTTAAAATGAAA
577770 TAAAAATGAAAACTTGAAAA-GAAA
1 TAAAAAT-AAAACTT-AAAATGAAA
577794 AGAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (23 bp):
TAAAAATAAAACTTAAAATGAAA
Found at i:577808 original size:4 final size:4
Alignment explanation
Indices: 577787--577820 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
577777 GAAAACTTGA
577787 AAAG AAAAG AAA- AAAG AAAG AAAG AAAG AAAG AA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
577821 CTTTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:580494 original size:45 final size:45
Alignment explanation
Indices: 580444--580699 Score: 211
Period size: 45 Copynumber: 5.7 Consensus size: 45
580434 TCCCATTATT
* *
580444 CTTTAAT-AATTATTCATTATATTCATTTATGGCATCCTTTCATGC
1 CTTTAATGAATCATTCATCAT-TTCATTTATGGCATCCTTTCATGC
* * * *
580489 CTTTAATGCA-GAGTT-GTGCATTCCATTTATGGCATCCTTTCATGC
1 CTTTAATGAATCA-TTCAT-CATTTCATTTATGGCATCCTTTCATGC
** * * *
580534 CTTTAATTCACCGTT-ATGCATTTCATTTATGGCATCATTTCATGC
1 CTTTAATGAATCATTCAT-CATTTCATTTATGGCATCCTTTCATGC
* * * *
580579 CTCTAATGCACCATT-ATGCATTTCATTTATGACATCCTTTCATGC
1 CTTTAATGAATCATTCAT-CATTTCATTTATGGCATCCTTTCATGC
* * * *
580624 CTTTAATGCACCGTT-ATGCATTTCATTTATGGCATCATTTCATGC
1 CTTTAATGAATCATTCAT-CATTTCATTTATGGCATCCTTTCATGC
* *
580669 CTTTAATGCATCGTT-ATGCATTTCATTTATG
1 CTTTAATGAATCATTCAT-CATTTCATTTATG
580700 TAATGAAAAC
Statistics
Matches: 186, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
45 181 0.97
46 5 0.03
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (45 bp):
CTTTAATGAATCATTCATCATTTCATTTATGGCATCCTTTCATGC
Found at i:580575 original size:90 final size:90
Alignment explanation
Indices: 580465--580699 Score: 375
Period size: 90 Copynumber: 2.6 Consensus size: 90
580455 ATTCATTATA
* * * * *
580465 TTCATTTATGGCATCCTTTCATGCCTTTAATGCAGAGTTGTGCATTCCATTTATGGCATCCTTTC
1 TTCATTTATGGCATCATTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGACATCCTTTC
*
580530 ATGCCTTTAATTCACCGTTATGCAT
66 ATGCCTTTAATGCACCGTTATGCAT
*
580555 TTCATTTATGGCATCATTTCATGCCTCTAATGCACCA-TTATGCATTTCATTTATGACATCCTTT
1 TTCATTTATGGCATCATTTCATGCCTTTAATGCA-CAGTTATGCATTTCATTTATGACATCCTTT
580619 CATGCCTTTAATGCACCGTTATGCAT
65 CATGCCTTTAATGCACCGTTATGCAT
580645 TTCATTTATGGCATCATTTCATGCCTTTAATGCATC-GTTATGCATTTCATTTATG
1 TTCATTTATGGCATCATTTCATGCCTTTAATGCA-CAGTTATGCATTTCATTTATG
580700 TAATGAAAAC
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
90 133 0.99
91 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.43
Consensus pattern (90 bp):
TTCATTTATGGCATCATTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGACATCCTTTC
ATGCCTTTAATGCACCGTTATGCAT
Found at i:581065 original size:20 final size:20
Alignment explanation
Indices: 581040--581085 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
581030 AGACTCAATA
581040 GTATCGGTACCCCTACCATG
1 GTATCGGTACCCCTACCATG
581060 GTATCGGTACCCCTACCATG
1 GTATCGGTACCCCTACCATG
581080 GTATCG
1 GTATCG
581086 ATACTTCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.26
Consensus pattern (20 bp):
GTATCGGTACCCCTACCATG
Found at i:581189 original size:54 final size:54
Alignment explanation
Indices: 581119--581238 Score: 222
Period size: 54 Copynumber: 2.2 Consensus size: 54
581109 TACGCCCTTC
*
581119 TAGTATCGATATCATTTCTACATTCTATAATTCATGGTATCGATACATTTCTCT
1 TAGTATCGATACCATTTCTACATTCTATAATTCATGGTATCGATACATTTCTCT
*
581173 TAGTATCGATACCATTTCTACATTCTGTAATTCATGGTATCGATACATTTCTCT
1 TAGTATCGATACCATTTCTACATTCTATAATTCATGGTATCGATACATTTCTCT
581227 TAGTATCGATAC
1 TAGTATCGATAC
581239 TTCTATACTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (54 bp):
TAGTATCGATACCATTTCTACATTCTATAATTCATGGTATCGATACATTTCTCT
Found at i:586394 original size:137 final size:135
Alignment explanation
Indices: 586108--586490 Score: 549
Period size: 137 Copynumber: 2.8 Consensus size: 135
586098 AGGTAAACCA
586108 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGACATCATCCGACAGAGGGAGCAA-AA-TTC
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAC-TCATCCGACAGAGGGAG-AAGAAGTTC
* * * *
586171 ATAATAAGAAGAACTTG-TTGACATATTGCTTGATTCACT-TCATTTTGAATCAGCAACACCTCA
64 ATAATGAGAAGAACTTGTTTGACCTATTGCTAGATTCA-TGACATTTTGAATCAGCAACACCTCA
586234 CTTAAGGG
128 CTTAAGGG
* *
586242 ATTAACATTTCCAATGGAGAGTTTATAATGAGAAGATCTCATCCGACAGAGGGAGAAGAAGTTTA
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGA-CTCATCCGACAGAGGGAGAAGAAGTTCA
* *
586307 TAATGAGAAGAACTTGTTTGACCTATTTGCTCGATTCATGACATTTTGAATCAGCAACACCTCGC
65 TAATGAGAAGAACTTGTTTGACCTA-TTGCTAGATTCATGACATTTTGAATCAGCAACACCTCAC
*
586372 TTGAGGG
129 TTAAGGG
* *
586379 ATTAATATTTCCAATGGAGAGTTCATAATGAGAACAGCTCATCCGACAGAGGGAGAAGAAGTTCA
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGA-CTCATCCGACAGAGGGAGAAGAAGTTCA
* ** *
586444 TAATGAGAAGAACATGTTCAACCTATTGCTAGATTCATGGCATTTTG
65 TAATGAGAAGAACTTGTTTGACCTATTGCTAGATTCATGACATTTTG
586491 TTCATAATGA
Statistics
Matches: 225, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
133 2 0.01
134 54 0.24
135 19 0.08
136 28 0.12
137 122 0.54
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (135 bp):
ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGACTCATCCGACAGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTTGACCTATTGCTAGATTCATGACATTTTGAATCAGCAACACCTCACTT
AAGGG
Found at i:586559 original size:91 final size:91
Alignment explanation
Indices: 586399--586579 Score: 254
Period size: 91 Copynumber: 2.0 Consensus size: 91
586389 CCAATGGAGA
* * * *
586399 GTTCATAATGAGAACAGCTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACATGTTCA
1 GTTCATAATGAGAACAGCTCATCCAACAGAAGGAGAAAAAGTTCAAAATGAGAAGAACATGTTCA
*
586464 ACCTATTGCTAGATTCATGGCATTTT
66 ACCTATTGCTAGATTCACGGCATTTT
* * * * **
586490 GTTCATAATGAGAAGAGCTCATGCAACAGAAGGAGAAAAAGTTCAAAATGAGAATAACTTGTTTG
1 GTTCATAATGAGAACAGCTCATCCAACAGAAGGAGAAAAAGTTCAAAATGAGAAGAACATGTTCA
*
586555 ACCTATTGCTTGATTCACGGCATTT
66 ACCTATTGCTAGATTCACGGCATTT
586580 CGAATCAGCA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (91 bp):
GTTCATAATGAGAACAGCTCATCCAACAGAAGGAGAAAAAGTTCAAAATGAGAAGAACATGTTCA
ACCTATTGCTAGATTCACGGCATTTT
Found at i:586817 original size:12 final size:12
Alignment explanation
Indices: 586800--586841 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
586790 CTAAACCAAC
586800 CCCAAAATAAAA
1 CCCAAAATAAAA
*
586812 CCCAAACTAAAA
1 CCCAAAATAAAA
* *
586824 CCC-AATTAATA
1 CCCAAAATAAAA
586835 CCCAAAA
1 CCCAAAA
586842 CCTGATCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.57, C:0.31, G:0.00, T:0.12
Consensus pattern (12 bp):
CCCAAAATAAAA
Found at i:589635 original size:24 final size:24
Alignment explanation
Indices: 589585--589671 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
589575 TGTGAAATTT
*
589585 TCCCGAAGGACCTCTG-TA-TATG
1 TCCCGAAGGACCTATGTTACTATG
589607 TCCCGAAGGACCTATGTTACTATG
1 TCCCGAAGGACCTATGTTACTATG
* *
589631 TCCCGAATGACCTGTGTTACTATG
1 TCCCGAAGGACCTATGTTACTATG
*
589655 TCCCGAATGACCTATGT
1 TCCCGAAGGACCTATGT
589672 AACCCTCGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 15 0.25
23 2 0.03
24 42 0.71
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (24 bp):
TCCCGAAGGACCTATGTTACTATG
Found at i:593469 original size:3 final size:3
Alignment explanation
Indices: 593461--593489 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
593451 ATATTAATGT
593461 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
593490 TTAAGCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:594532 original size:19 final size:19
Alignment explanation
Indices: 594496--594544 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
594486 AACTCTGTTT
*
594496 ATATATTTAGTACATATAC
1 ATATATGTAGTACATATAC
*
594515 ATATATGTAGATACTATATCAA
1 ATATATGTAG-TAC-ATAT-AC
594537 ATATATGT
1 ATATATGT
594545 TATAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 3 0.12
21 4 0.16
22 9 0.36
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATATGTAGTACATATAC
Found at i:594896 original size:5 final size:5
Alignment explanation
Indices: 594627--594893 Score: 401
Period size: 5 Copynumber: 53.6 Consensus size: 5
594617 AAATATTTTA
594627 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
594677 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
* * * *
594727 AATGT -ATGT AATGT AGTGT AATGT AATGT AGTGT AATGT AGTGT AGTGT
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
* * * * * * *
594776 AGTGT AGTGT AGTGT AGTGT AGTGT AATGT AGTGT AATGT AGTGT AATGT
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
* *
594826 AGTGT AATGT AGTGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT
*
594876 AATGT AATGT AATAT AAT
1 AATGT AATGT AATGT AAT
594894 ATATACCGGA
Statistics
Matches: 246, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
4 4 0.02
5 242 0.98
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (5 bp):
AATGT
Found at i:603027 original size:17 final size:17
Alignment explanation
Indices: 603005--603040 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
602995 AAAAGTTCTG
603005 AAATATGT-TCGAATGAA
1 AAATATGTAT-GAATGAA
603022 AAATATGTATGAATGAA
1 AAATATGTATGAATGAA
603039 AA
1 AA
603041 GAATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (17 bp):
AAATATGTATGAATGAA
Found at i:605084 original size:25 final size:25
Alignment explanation
Indices: 605055--605133 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
605045 AGGGGCACCG
605055 TTTTTCAAAATTCTTTCATCAAACA
1 TTTTTCAAAATTCTTTCATCAAACA
*
605080 TTTTTCAAAATTCTTTCATAAAACA
1 TTTTTCAAAATTCTTTCATCAAACA
*
605105 -TTTTCAAAACTTC-TTCATCAAACT
1 TTTTTCAAAA-TTCTTTCATCAAACA
605129 TTTTT
1 TTTTT
605134 TTGACCTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
24 18 0.37
25 31 0.63
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTTCAAAATTCTTTCATCAAACA
Found at i:606054 original size:40 final size:40
Alignment explanation
Indices: 605999--606075 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
605989 CTCTAAAATA
* * *
605999 TGACTATATGTCCTCAATATGAAGGAACAATGTCATCCAC
1 TGACTAGATCTCCTCAACATGAAGGAACAATGTCATCCAC
* * *
606039 TGACTAGATCTCCTCAACATGACGGAGCAATTTCATC
1 TGACTAGATCTCCTCAACATGAAGGAACAATGTCATC
606076 ATCAGGTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (40 bp):
TGACTAGATCTCCTCAACATGAAGGAACAATGTCATCCAC
Found at i:606839 original size:3 final size:3
Alignment explanation
Indices: 606831--606856 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
606821 ATATTAATGT
606831 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
606857 TACATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:608315 original size:2 final size:2
Alignment explanation
Indices: 608308--608333 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
608298 TTTTAAATTA
608308 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
608334 GGTAGTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:609018 original size:21 final size:21
Alignment explanation
Indices: 608990--609041 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
608980 AGGATCGCAA
*
608990 TTTAAATTTCGAATTC-AAGT
1 TTTAAATTTCGAATTCAAAAT
*
609010 TTGTAAATTTTGAATTCAAAAT
1 TT-TAAATTTCGAATTCAAAAT
609032 TTTAAATTTC
1 TTTAAATTTC
609042 CGGTACTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (21 bp):
TTTAAATTTCGAATTCAAAAT
Found at i:612667 original size:2 final size:2
Alignment explanation
Indices: 612660--612690 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
612650 AACCTTGAGC
612660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
612691 GCTTAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:619903 original size:30 final size:30
Alignment explanation
Indices: 619811--619895 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
619801 ATCATATTCG
* *
619811 ATTTAAAGAACCAAAATAGCAAAAACAAAA
1 ATTTAAAGGACTAAAATAGCAAAAACAAAA
* * * *
619841 ACTTAAAGGATTAAAATATCAAAAACATAA
1 ATTTAAAGGACTAAAATAGCAAAAACAAAA
*
619871 ATTTAAAGGACTAAAATAGGAAAAA
1 ATTTAAAGGACTAAAATAGCAAAAA
619896 TAGAAATTCG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGCAAAAACAAAA
Found at i:624248 original size:33 final size:33
Alignment explanation
Indices: 624206--624294 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
624196 ATAACACATG
* *
624206 GTAATAAAGTTTCATTGGAACCATCCTATCATA
1 GTAATAAAGTTCCATTAGAACCATCCTATCATA
* *
624239 GTAATAAAGTTCCATTAGAACCATCCTCTCATG
1 GTAATAAAGTTCCATTAGAACCATCCTATCATA
624272 GTAATAAAGTTCCATTAGAACCA
1 GTAATAAAGTTCCATTAGAACCA
624295 AGAAAACAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.30
Consensus pattern (33 bp):
GTAATAAAGTTCCATTAGAACCATCCTATCATA
Found at i:626420 original size:55 final size:54
Alignment explanation
Indices: 626252--626439 Score: 251
Period size: 55 Copynumber: 3.6 Consensus size: 54
626242 TAAACATATT
*** * *
626252 ATGAATTCCGTGTTTTGCACACATAGTGCCGAAACAGTTATTCATCCACATACG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
*
626306 ATGAATT-CGTGAAATGCACACTTAGTGCCGAAAC-G---GTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
* * *
626355 ATGAAATCCGTAAAATGCACACTTAGTGCCGAAAACAGTTATTCATCCATATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCG-AAACAGTTATTCATCCACATAGG
626410 ATGAATTCCGTGAAATGCACACTTAGTGCC
1 ATGAATTCCGTGAAATGCACACTTAGTGCC
626440 TATTTGGTAA
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
49 18 0.16
50 22 0.19
51 4 0.03
52 2 0.02
53 23 0.20
54 7 0.06
55 40 0.34
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
Found at i:631818 original size:3 final size:3
Alignment explanation
Indices: 631810--631848 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
631800 TTAGTTTACA
*
631810 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT ATAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TA
631849 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:633201 original size:2 final size:2
Alignment explanation
Indices: 633196--633251 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
633186 TTATATAGTC
633196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
633238 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
633252 TTATTTGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:633572 original size:158 final size:156
Alignment explanation
Indices: 633249--633641 Score: 418
Period size: 158 Copynumber: 2.6 Consensus size: 156
633239 TATATATATA
* * *
633249 TATTTATTTGTTTA-TTTTATATATAAAGAAAATGACAGTCTTAAAGCAACTAGATGTCCTATTA
1 TATTTATTTATTTATTTTTAAATATAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCTATTA
*
633313 TGATATTTTAAAAATAAATAAATATCATACTTATAAAAACCAGACAATACATATTGTTTTATTTA
66 TGATATTTTAAAAATAAATAAATATCATACTTAT-AAAA-CAGA-AATACATATTGTCTTATTTA
*
633378 AATTATTTTCTTAGGAAAATTATTATTTT
128 AATTATTTTCTTAGAAAAATTATTATTTT
* * * * *
633407 TA-ATATTTATTTATTTTTCAAATATTAAG-AAAGGACATTCTTAAATCAACTAGATGTCTTATT
1 TATTTATTTATTTATTTTT-AAATATAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCTATT
* * * * *
633470 CTGATATTTTAAAAAATAAATAAATATCATGCTTAT-AAA-TG-TATATATATT-TACTTAGTTT
65 ATGATATTTT-AAAAATAAATAAATATCATACTTATAAAACAGAAATACATATTGT-CTTA-TTT
** * *
633531 TTATTATTTT-TTAGAAAAATTAATATATT
127 AAATTATTTTCTTAGAAAAATTATTATTTT
* * *
633560 CATTTATTTATTTA---TT-AATTTAAAGAAAAGG-CAGTCTTAAAGCAACTAGATGTCCTTTTA
1 TATTTATTTATTTATTTTTAAATATAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCTATTA
*
633620 TGATATTTT-TAAATAAATAAAT
66 TGATATTTTAAAAATAAATAAAT
633642 GTTATATTTA
Statistics
Matches: 199, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
147 12 0.06
149 40 0.20
150 5 0.03
151 2 0.01
152 1 0.01
153 28 0.14
154 21 0.11
155 1 0.01
157 12 0.06
158 45 0.23
159 32 0.16
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (156 bp):
TATTTATTTATTTATTTTTAAATATAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCTATTA
TGATATTTTAAAAATAAATAAATATCATACTTATAAAACAGAAATACATATTGTCTTATTTAAAT
TATTTTCTTAGAAAAATTATTATTTT
Found at i:633664 original size:149 final size:148
Alignment explanation
Indices: 633246--633668 Score: 394
Period size: 149 Copynumber: 2.8 Consensus size: 148
633236 ATATATATAT
* * * *
633246 ATATATTTATTTGTTTA-TTTTATATATAAAGAAAATGACAGTCTTAAAGCAACTAGATGTCCTA
1 ATATATTTATTTATTTATTTTTA-ATTTAAAGAAAA-GGCAGTCTTAAAGCAACTAGATGTCCTT
* * *
633310 TTATGATATTTTAAAAATAAATAAATATCATACTTATAAAAACCAGACAATACATATTGTTTTAT
64 TTATGATATTTTAAAAATAAATAAATATCATA-TT-TAAAAACC---CTATATATATTGTCTTAT
*
633375 TTAAATTATTTTCTTAGGAAAATTA
124 TTAAATTATTTTCTTAGAAAAATTA
* * * *
633400 TTATTTTTAATATTTATTTATTTTTCAAATATT-AAG-AAAGGACATTCTTAAATCAACTAGATG
1 ATA-TATT--TATTTATTTATTTTT--AAT-TTAAAGAAAAGG-CAGTCTTAAAGCAACTAGATG
* ** * **
633463 T-CTTATTCTGATATTTTAAAAAATAAATAAATATCATGCTTATAAA-TGTATATATATT-TACT
59 TCCTT-TTATGATATTTT-AAAAATAAATAAATATCATATTTAAAAACCCTATATATATTGT-CT
**
633525 TAGTTTTTATTATTTT-TTAGAAAAATTA
121 TA-TTTAAATTATTTTCTTAGAAAAATTA
*
633553 ATATATTCATTTATTTATTTATTAATTTAAAGAAAAGGCAGTCTTAAAGCAACTAGATGTCCTTT
1 ATATATTTATTTATTTATTT-TTAATTTAAAGAAAAGGCAGTCTTAAAGCAACTAGATGTCCTTT
* * *
633618 TATGATATTTT-TAAATAAATAAATGTTATATTTACAAAACCCTATATATAT
65 TATGATATTTTAAAAATAAATAAATATCATATTTA-AAAACCCTATATATAT
633669 ATATATATAT
Statistics
Matches: 217, Mismatches: 34, Indels: 41
0.74 0.12 0.14
Matches are distributed among these distances:
147 18 0.08
148 5 0.02
149 46 0.21
150 20 0.09
151 2 0.01
152 4 0.02
153 24 0.11
154 13 0.06
155 3 0.01
157 17 0.08
158 39 0.18
159 24 0.11
160 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (148 bp):
ATATATTTATTTATTTATTTTTAATTTAAAGAAAAGGCAGTCTTAAAGCAACTAGATGTCCTTTT
ATGATATTTTAAAAATAAATAAATATCATATTTAAAAACCCTATATATATTGTCTTATTTAAATT
ATTTTCTTAGAAAAATTA
Found at i:635701 original size:35 final size:34
Alignment explanation
Indices: 635646--635715 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
635636 CATTCACATA
* *
635646 TTTACATTTGCATTTTCATTTTGCATTTTTGTATT
1 TTTACATTTGCATTTACATTTT-CATTTTTGCATT
* *
635681 TTTACGTTTGTATTTACATTTTCATTTTTGCATT
1 TTTACATTTGCATTTACATTTTCATTTTTGCATT
635715 T
1 T
635716 GCATCTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTTCATTTTTGCATT
Found at i:643151 original size:22 final size:22
Alignment explanation
Indices: 643126--643177 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
643116 TACGCTCTTT
643126 AAAGATGATAGATTCACTCTCC
1 AAAGATGATAGATTCACTCTCC
* * *
643148 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCACTCTCC
643170 AAAGATGA
1 AAAGATGA
643178 AAGCTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (22 bp):
AAAGATGATAGATTCACTCTCC
Found at i:644056 original size:116 final size:116
Alignment explanation
Indices: 643849--644341 Score: 738
Period size: 116 Copynumber: 4.2 Consensus size: 116
643839 CTATTTCCCA
* * * * * *
643849 CATCTTTAAGACCTACAGTGCATGATGTTTTCAAAACCTTC-GGGTCATCTATAAGACCTACAGT
1 CATCTGTAAGACCTACAGTGCAAGATG--AT-AAGACC-TCAGGGCCATCCATAAGACCTACAGT
* * *
643913 GCAAGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAACCTCTGGGT
62 GCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* *
643968 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTTCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAT
*
644033 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTAGATATTTAAAGCCTCCGGGT
66 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* *
644084 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCATGGCCATCTATAAGACCTACAGTGCAT
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAT
* *
644149 GATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATATTTAAAGCCTCTGGGT
66 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
*
644200 CATCTGTAA-ACCTACAGTGCAAGATGATAAGACCTCAGGACCATCCATAAGACCTACAGTGCAT
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAT
* * * *
644264 GATGTTTTCAAAAAGCCTTCGGAAGTTTTTTGATCTTTAAAGCCTCCGGGT
66 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
*
644315 CATCTGTAAGACCTACAGTGCATGATG
1 CATCTGTAAGACCTACAGTGCAAGATG
644342 TTTTCAAAAA
Statistics
Matches: 345, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
115 109 0.32
116 210 0.61
117 1 0.00
119 25 0.07
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (116 bp):
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAT
GATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
Found at i:644118 original size:22 final size:22
Alignment explanation
Indices: 644090--644152 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
644080 GGGTCATCTG
644090 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGCAAGATGA
* **
644112 TAAGACCT-CA-TGGCCATCT-A
1 TAAGACCTACAGT-GCAAGATGA
*
644132 TAAGACCTACAGTGCATGATG
1 TAAGACCTACAGTGCAAGATG
644153 TTTTCAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
20 10 0.33
21 11 0.37
22 9 0.30
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (22 bp):
TAAGACCTACAGTGCAAGATGA
Found at i:644309 original size:231 final size:232
Alignment explanation
Indices: 643894--644341 Score: 781
Period size: 231 Copynumber: 1.9 Consensus size: 232
643884 ACCTTCGGGT
*
643894 CATCTATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAA
1 CATCTATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATATTTAAAA
*
643959 CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCT
66 CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGACCATCCATAAGACCT
* * *
644024 ACAGTTCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTAGATATTTAAAGCCTCCGGGTCATCT
131 ACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTAGATATTTAAAGCCTCCGGGTCATCT
644089 GTAAGACCTACAGTGCAAGATGATAAGACCTCATGGC
196 GTAAGACCTACAGTGCAAGATGATAAGACCTCATGGC
* *
644126 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATATTTAAAG
1 CATCTATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATATTTAAAA
644191 CCTCTGGGTCATCTGTAA-ACCTACAGTGCAAGATGATAAGACCTCAGGACCATCCATAAGACCT
66 CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGACCATCCATAAGACCT
* * * *
644255 ACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGTTTTTTGATCTTTAAAGCCTCCGGGTCATCT
131 ACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTAGATATTTAAAGCCTCCGGGTCATCT
*
644320 GTAAGACCTACAGTGCATGATG
196 GTAAGACCTACAGTGCAAGATG
644342 TTTTCAAAAA
Statistics
Matches: 204, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
231 124 0.61
232 80 0.39
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (232 bp):
CATCTATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGATATTTAAAA
CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGACCATCCATAAGACCT
ACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTAGATATTTAAAGCCTCCGGGTCATCT
GTAAGACCTACAGTGCAAGATGATAAGACCTCATGGC
Found at i:644368 original size:74 final size:74
Alignment explanation
Indices: 644247--644475 Score: 359
Period size: 74 Copynumber: 3.1 Consensus size: 74
644237 GGACCATCCA
* *
644247 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGTTTTTTGATCTTTAAAGCCTCCG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTAAAGCCTCCG
644312 GGTCATCTG
66 GGTCATCTG
* *
644321 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGCAGCTTTTTGATATTTAAAGCCTCTG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTAAAGCCTCCG
644386 GGTCATCTG
66 GGTCATCTG
* * * * * *
644395 TAAGACCTATAGTGCAGGATCTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAATCCTCCG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTAAAGCCTCCG
*
644460 GGTCATCTA
66 GGTCATCTG
644469 TAAGACC
1 TAAGACC
644476 CATAGTACAA
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 143 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (74 bp):
TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTG
Found at i:644670 original size:3 final size:3
Alignment explanation
Indices: 644662--644700 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
644652 TTCAGTTTAC
644662 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
644701 GAATAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:646490 original size:147 final size:148
Alignment explanation
Indices: 646085--646493 Score: 390
Period size: 147 Copynumber: 2.7 Consensus size: 148
646075 ATAAATAAAT
* * *
646085 ATTTATTT-TT-TTATATA-TAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCTATTCTGAT
1 ATTTATTTATTATTAAATATTAAAGAAAATGACAGTCTTAAAGCAACTAGATGT-CTTTTCTGAT
* *
646147 ATTTTAAAAATAAATAAATATCCTACTTATAAAAACCAAACAATATATATTGTTTTATTTAAATT
65 ATTTT-AAAATAAATAAATATCATA-TT-TAAAAA-C---C-ATATATATTGTCTTATTTAAATT
* * *
646212 ATTTTCTTAGGAAAATTATTATTTTAAT
122 ATTTTCTTAGGAAAATTAATATATT-AC
* * *
646240 ATTTATTTATTTTTCAAATATT-AAG-AAATGACAGTCTTAAAGCAATTAGATGTCTTATTATGA
1 ATTTATTTATTATT-AAATATTAAAGAAAATGACAGTCTTAAAGCAACTAGATGTCTT-TTCTGA
* ** * ** *
646303 TATTTTAAAAAATAATAAATATCATGCTTATAAATTATATATATT-TACTTAGTTT-TATTATTT
64 TATTTTAAAATA-AATAAATATCATATTTAAAAACCATATATATTGT-CTTA-TTTAAATTATTT
646366 T-TTAGGAAAATTAATATATT-C
126 TCTTAGGAAAATTAATATATTAC
*
646387 ATTTATTTATTAATT-AATATTAAAGAAAATG-CAGTCTTAAAGCAACTAGATGTCATTTTCTAA
1 ATTTATTTATT-ATTAAATATTAAAGAAAATGACAGTCTTAAAGCAACTAGATGTC-TTTTCTGA
* *
646450 TATTTTTAAATAAATAAATGTCATATTTACAAAACCATATATAT
64 TATTTTAAAATAAATAAATATCATATTTA-AAAACCATATATAT
646494 ATATTTAATA
Statistics
Matches: 212, Mismatches: 29, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
146 20 0.09
147 61 0.29
148 9 0.04
149 18 0.08
150 20 0.09
151 3 0.01
155 13 0.06
156 10 0.05
157 50 0.24
158 7 0.03
159 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (148 bp):
ATTTATTTATTATTAAATATTAAAGAAAATGACAGTCTTAAAGCAACTAGATGTCTTTTCTGATA
TTTTAAAATAAATAAATATCATATTTAAAAACCATATATATTGTCTTATTTAAATTATTTTCTTA
GGAAAATTAATATATTAC
Found at i:648198 original size:54 final size:55
Alignment explanation
Indices: 648140--648290 Score: 151
Period size: 55 Copynumber: 2.8 Consensus size: 55
648130 CCATACAGTC
** ** * * *
648140 ATTCATAAACATATTATGAATTTTGTGTTTTGCACACATAGTG-CCAAAACGGTT
1 ATTCATAAACATAGGATGAATTCCGTGATATACACACATAGTGTCCAAAACGGTT
** * *
648194 ATTCATCCACATAGGATGAATTCCGTGATATACACACTTAGTGTCCGAAACGGTT
1 ATTCATAAACATAGGATGAATTCCGTGATATACACACATAGTGTCCAAAACGGTT
** * * *
648249 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGT
1 ATTCATAAACATAGGATGAATTCCGTGATATACACACATAGT
648291 ACCTATTTGG
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
54 33 0.40
55 50 0.60
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (55 bp):
ATTCATAAACATAGGATGAATTCCGTGATATACACACATAGTGTCCAAAACGGTT
Found at i:648260 original size:55 final size:54
Alignment explanation
Indices: 648172--648290 Score: 193
Period size: 55 Copynumber: 2.2 Consensus size: 54
648162 TTGTGTTTTG
* *
648172 CACACATAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGATATA
1 CACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
* *
648226 CACACTTAGTGTCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATG
1 CACACTTAGTG-CCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
648281 CACACTTAGT
1 CACACTTAGT
648291 ACCTATTTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 10 0.17
55 50 0.83
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (54 bp):
CACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
Found at i:652059 original size:9 final size:9
Alignment explanation
Indices: 652028--652079 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
652018 ATTTTATTTA
652028 TTTAAT-AT
1 TTTAATAAT
652036 TTTAATATCAT
1 TTTAATA--AT
652047 TTTAATAAT
1 TTTAATAAT
652056 TTTAATAAT
1 TTTAATAAT
* *
652065 ATT-ATATT
1 TTTAATAAT
652073 TTTAATA
1 TTTAATA
652080 TTATATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 12 0.32
9 16 0.43
11 9 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTAATAAT
Found at i:652141 original size:18 final size:17
Alignment explanation
Indices: 652099--652158 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
652089 TATATACTCA
652099 AATATATTATAA-TAAT
1 AATATATTATAATTAAT
*
652115 ATATGATATTATAATTTAGT
1 A-AT-ATATTATAA-TTAAT
* *
652135 AATATATAATAAATTATT
1 AATATATTAT-AATTAAT
652153 AATATA
1 AATATA
652159 ATTAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 25 0.69
19 4 0.11
20 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATATATTATAATTAAT
Found at i:652592 original size:28 final size:30
Alignment explanation
Indices: 652531--652593 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
652521 AAATGTATTT
*
652531 CATTTTACGTAAAACAGTATTCACATAATT
1 CATTTTACGTAAAACAGTATTCACATAATC
* **
652561 CATTTT-CGTAAAA-AGTTTTCAGGTAATC
1 CATTTTACGTAAAACAGTATTCACATAATC
652589 CATTT
1 CATTT
652594 AACATAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.55
29 7 0.24
30 6 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (30 bp):
CATTTTACGTAAAACAGTATTCACATAATC
Found at i:660898 original size:24 final size:23
Alignment explanation
Indices: 660840--660924 Score: 89
Period size: 24 Copynumber: 3.6 Consensus size: 23
660830 AAACGGAGAT
* *
660840 ATCAGAAATCAAAACAGAATTTAG
1 ATCAGAAATCAGAACA-AAATTAG
* * *
660864 GTCATATATCAGAACAAAATCTAG
1 ATCAGAAATCAGAACAAAAT-TAG
*
660888 ATCAGAAATCAGAACAAAATTCAA
1 ATCAGAAATCAGAACAAAATT-AG
660912 ATCAGAAATCAGA
1 ATCAGAAATCAGA
660925 TAAAACACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
23 4 0.08
24 46 0.92
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (23 bp):
ATCAGAAATCAGAACAAAATTAG
Found at i:664373 original size:20 final size:20
Alignment explanation
Indices: 664348--664392 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
664338 GTTGGATTCA
664348 AGTTTGAGAGTGATCGAATG
1 AGTTTGAGAGTGATCGAATG
*
664368 AGTTTGAGAGTGATCTAATG
1 AGTTTGAGAGTGATCGAATG
664388 AGTTT
1 AGTTT
664393 AAATGTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (20 bp):
AGTTTGAGAGTGATCGAATG
Found at i:665021 original size:27 final size:27
Alignment explanation
Indices: 664991--665048 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
664981 AGATTGAAGG
*
664991 AAATGACCAAAATGCCCCCGAAGTGTA
1 AAATGACCAAAATGCCCCCGAAGCGTA
* *
665018 AAATGACCAAAATGCTCCTGAAGCGTA
1 AAATGACCAAAATGCCCCCGAAGCGTA
665045 AAAT
1 AAAT
665049 AACCCAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCCGAAGCGTA
Found at i:669828 original size:70 final size:70
Alignment explanation
Indices: 669740--669881 Score: 212
Period size: 70 Copynumber: 2.0 Consensus size: 70
669730 AGTTGATGAA
* * *
669740 TAACCGTACAGGCACTATGCATGAAAATCCATGGAATTCATCATGAGTTGATGAATAATCGTACA
1 TAACCGTACAGGCACTATGCATGAAAATCCACGGAATTCATCATGAGTTGATAAATAATCGTAAA
669805 TGCAC
66 TGCAC
* ** * *
669810 TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAATAATCGTAAA
1 TAACCGTACAGGCACTATGCATGAAAATCCACGGAATTCATCATGAGTTGATAAATAATCGTAAA
669875 TGCAC
66 TGCAC
669880 TA
1 TA
669882 TGTGTGCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (70 bp):
TAACCGTACAGGCACTATGCATGAAAATCCACGGAATTCATCATGAGTTGATAAATAATCGTAAA
TGCAC
Found at i:669844 original size:27 final size:26
Alignment explanation
Indices: 669814--669897 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
669804 ATGCACTAAC
669814 CGTACATGCACTATGTGTGCAAATCCA
1 CGTA-ATGCACTATGTGTGCAAATCCA
* * * *
669841 CGTAATTCA-TCATGAGTTGATAAAT-AA
1 CGTAATGCACT-ATGTG-TG-CAAATCCA
669868 TCGTAAATGCACTATGTGTGCAAATCCA
1 -CGT-AATGCACTATGTGTGCAAATCCA
669896 CG
1 CG
669898 AAATTCATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
25 1 0.02
26 8 0.19
27 13 0.31
28 10 0.24
29 9 0.21
30 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (26 bp):
CGTAATGCACTATGTGTGCAAATCCA
Found at i:669901 original size:26 final size:26
Alignment explanation
Indices: 669819--669901 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
669809 CTAACCGTAC
*
669819 ATGCACTATGTGTGCAAATCCACGTA
1 ATGCACTATGTGTGCAAATCCACGAA
* * * *
669845 ATTCA-TCATGAGTTGATAAAT-AATCGTAA
1 ATGCACT-ATGTG-TG-CAAATCCA-CG-AA
669874 ATGCACTATGTGTGCAAATCCACGAA
1 ATGCACTATGTGTGCAAATCCACGAA
669900 AT
1 AT
669902 TCATCATGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
25 1 0.02
26 12 0.29
27 9 0.22
28 9 0.22
29 9 0.22
30 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (26 bp):
ATGCACTATGTGTGCAAATCCACGAA
Found at i:669903 original size:55 final size:55
Alignment explanation
Indices: 669810--670161 Score: 453
Period size: 55 Copynumber: 6.5 Consensus size: 55
669800 GTACATGCAC
* *
669810 TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
* *
669865 TAATCGTAAATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
* *
669920 TAACCGTACAGGCACTATGTGT--AAATCCACGAAATTCATCATGAGTTGATAAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
*
669973 TAACTGTACATGCACTATGTGTGCAAATCCAC-AGAATTCATCATGAGTTGATGAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAA
* * * ** *
670028 TAATCGTACAAGCACTATATGTGCAAATCCACGGGATTCATCATTAGTTGATGAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
* * * * * *
670083 TAACCATACAGGCACGATGTGTGC-AATGCACGGAATTCATTATGAGTTGATGAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
* * *
670137 CT-ACCATATAGGCACTATGTGTGCA
1 -TAACCGTACATGCACTATGTGTGCA
670162 TCTTAATAAA
Statistics
Matches: 262, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
53 50 0.19
54 47 0.18
55 165 0.63
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (55 bp):
TAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
Found at i:669913 original size:125 final size:125
Alignment explanation
Indices: 669691--669936 Score: 350
Period size: 125 Copynumber: 2.0 Consensus size: 125
669681 CTATGTGTAC
* *
669691 TACATGCACTAAGTGTGCAAATCCATAGAATTCATCAGGAGTTGATGAATAACCGTACAGGCACT
1 TACATGCACTAAGTGTGCAAATCCATAGAATTCATCAGGAGTTGATAAATAACCGTAAAGGCACT
* * * *
669756 ATGCATGAAAATCCATGGAATTCATCATGAGTTGATGAATAATCGTACATGCACTAACCG
66 ATGCATGAAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCACTAACCG
* * * * *
669816 TACATGCACTATGTGTGCAAATCCA-CGTAATTCATCATGAGTTGATAAATAATCGTAAATGCAC
1 TACATGCACTAAGTGTGCAAATCCATAG-AATTCATCAGGAGTTGATAAATAACCGTAAAGGCAC
** *
669880 TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCACTA
65 TATGCATGAAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCACTA
669937 TGTGTAAATC
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
124 1 0.01
125 105 0.99
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (125 bp):
TACATGCACTAAGTGTGCAAATCCATAGAATTCATCAGGAGTTGATAAATAACCGTAAAGGCACT
ATGCATGAAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCACTAACCG
Found at i:670001 original size:108 final size:108
Alignment explanation
Indices: 669810--670158 Score: 436
Period size: 108 Copynumber: 3.2 Consensus size: 108
669800 GTACATGCAC
* * *
669810 TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAATAA-TCGTAA
1 TAACCGTACAGGCACTATGTGT--AAATCCACGAAATTCATCATGAGTTGATAAATAACT-GTAC
669874 ATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
63 ATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
669920 TAACCGTACAGGCACTATGTGTAAATCCACGAAATTCATCATGAGTTGATAAATAACTGTACATG
1 TAACCGTACAGGCACTATGTGTAAATCCACGAAATTCATCATGAGTTGATAAATAACTGTACATG
669985 CACTATGTGTGCAAATCCAC-AGAATTCATCATGAGTTGATGAA
66 CACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAA
* * * ** * * **
670028 TAATCGTACAAGCACTATATGTGCAAATCCACGGGATTCATCATTAGTTGATGAATAACCATACA
1 TAACCGTACAGGCAC--TATGTGTAAATCCACGAAATTCATCATGAGTTGATAAATAACTGTACA
* * * * *
670093 GGCACGATGTGTGC-AATGCACGGAATTCATTATGAGTTGATGAA
64 TGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
* *
670137 CT-ACCATATAGGCACTATGTGT
1 -TAACCGTACAGGCACTATGTGT
670159 GCATCTTAAT
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
107 7 0.03
108 93 0.44
109 36 0.17
110 75 0.36
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (108 bp):
TAACCGTACAGGCACTATGTGTAAATCCACGAAATTCATCATGAGTTGATAAATAACTGTACATG
CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
Found at i:670085 original size:163 final size:164
Alignment explanation
Indices: 669810--670161 Score: 505
Period size: 163 Copynumber: 2.2 Consensus size: 164
669800 GTACATGCAC
669810 TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAATAATCGTAAA
1 TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAATAATCGTAAA
* * *
669875 TGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGT
66 TGCACTATATGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAGGCACGATGT
669940 GT-AAATCCACGAAATTCATCATGAGTTGATAAA
131 GTGAAATCCACGAAATTCATCATGAGTTGATAAA
* *
669973 TAACTGTACATGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTTGATGAATAATCGTAC
1 TAACCGTACATGCACTATGTGTGCAAATCCAC-GTAATTCATCATGAGTTGATAAATAATCGTA-
** *
670037 AA-GCACTATATGTGCAAATCCACGGGATTCATCATTAGTTGATGAATAACCATACAGGCACGAT
64 AATGCACTATATGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAGGCACGAT
* * * * *
670101 GTGTGCAATGCACGGAATTCATTATGAGTTGATGAAC
129 GTGTGAAATCCACGAAATTCATCATGAGTTGAT-AAA
* * *
670138 T-ACCATATAGGCACTATGTGTGCA
1 TAACCGTACATGCACTATGTGTGCA
670162 TCTTAATAAA
Statistics
Matches: 168, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
163 119 0.71
164 46 0.27
165 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (164 bp):
TAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATAAATAATCGTAAA
TGCACTATATGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAGGCACGATGT
GTGAAATCCACGAAATTCATCATGAGTTGATAAA
Found at i:673660 original size:54 final size:55
Alignment explanation
Indices: 673457--673690 Score: 249
Period size: 55 Copynumber: 4.3 Consensus size: 55
673447 GTGTACTACA
* * * * *
673457 GGCACTACGTGTGCAAATCCACAGAATTCACCATGAGTTTATGAATAACCGTATA
1 GGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTATT
* * * * *
673512 GACACTATGTGTGCAAATTCACGAAATTCATCATGAGTTTATGAATAACCGTACAT
1 GGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTA-TT
* * * *
673568 -GCACTATGTTTGCAAATCCACGGGATTCATCATTAGTTGGTGAATAACCGTATT
1 GGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTATT
* * * *
673622 GGCACGATGTGTGCAACT-CACGGAATTCATCTTGAGTTGATGAACT-ACCGTATA
1 GGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTATT
* *
673676 AGCACTACGTGTGCA
1 GGCACTATGTGTGCA
673691 TCTTAATAAA
Statistics
Matches: 148, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
54 42 0.28
55 106 0.72
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (55 bp):
GGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTATT
Found at i:674397 original size:54 final size:55
Alignment explanation
Indices: 674193--674466 Score: 286
Period size: 55 Copynumber: 5.0 Consensus size: 55
674183 TGTGTACTAC
* * * * * * *
674193 AGGCACTACGTGTACAAATCCACAGAATTCACCATGAGTTGATGAATAACAGTAT
1 AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAATAACCGTAT
* * * * ** * *
674248 AGACACTATGTGTACAATTCCACAAAATTCATCATGAGTTTATGAATAACCGTAC
1 AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAATAACCGTAT
* * * * *
674303 ATGCACTATGTGTGCAAATCCACGGGATTCATCATTAGTTGATGAATAACCGTAT
1 AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAATAACCGTAT
*
674358 AGGCACGATGCGTGCAACT-CACGGAATTCATCATGAGTTGATGAACT-ACCGTAT
1 AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAA-TAACCGTAT
* * *
674412 AGGCACGATGTGTGCAACT-CATGGAATTCATCATAAGTTCATGAACT-ACCGTAT
1 AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAA-TAACCGTAT
674466 A
1 A
674467 AGCAATACGT
Statistics
Matches: 190, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
54 82 0.43
55 108 0.57
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (55 bp):
AGGCACGATGTGTGCAACTCCACGGAATTCATCATGAGTTGATGAATAACCGTAT
Found at i:674696 original size:10 final size:10
Alignment explanation
Indices: 674681--674710 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
674671 ATCAAAGTAA
674681 GGAGATCATC
1 GGAGATCATC
674691 GGAGATCATC
1 GGAGATCATC
*
674701 GGACATCATC
1 GGAGATCATC
674711 AAGCAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (10 bp):
GGAGATCATC
Found at i:677158 original size:92 final size:92
Alignment explanation
Indices: 676992--677164 Score: 276
Period size: 92 Copynumber: 1.9 Consensus size: 92
676982 AAAAATTAGT
*
676992 GAATTTGTTGAAATCCTTAGTGGTCGAAAGCTAAGGTAGTGGATGTAGACTTTGGTTGAGAAAGT
1 GAATTTGTTGAAATCCTTAGTAGTCGAAAGCTAAGGTAGTGGATGTAGACTTTGGTTGAGAAAGT
*
677057 TGAACCACTATAAATTAATTTGTTCGA
66 TAAACCACTATAAATTAATTTGTTCGA
* * *
677084 GAATTTGTTGAAATCCTTGGTAGTGGAAAGCTAAGGTAGTGTATGTAGACTTTGGTTGAGAAA-T
1 GAATTTGTTGAAATCCTTAGTAGTCGAAAGCTAAGGTAGTGGATGTAGACTTTGGTTGAGAAAGT
*
677148 TCAAATCACTATAAATT
66 T-AAACCACTATAAATT
677165 TATTGTCTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 2 0.03
92 72 0.97
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (92 bp):
GAATTTGTTGAAATCCTTAGTAGTCGAAAGCTAAGGTAGTGGATGTAGACTTTGGTTGAGAAAGT
TAAACCACTATAAATTAATTTGTTCGA
Found at i:677362 original size:18 final size:18
Alignment explanation
Indices: 677339--677377 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
677329 TTCCTATTCA
677339 ACTGAGAAGATGACTTCC
1 ACTGAGAAGATGACTTCC
*
677357 ACTGAGAATATGACTTCC
1 ACTGAGAAGATGACTTCC
677375 ACT
1 ACT
677378 TCCGACTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (18 bp):
ACTGAGAAGATGACTTCC
Found at i:683366 original size:3 final size:3
Alignment explanation
Indices: 683358--683404 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
683348 CCAGTTAATA
*
683358 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
683405 AATAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:684718 original size:9 final size:9
Alignment explanation
Indices: 684706--684759 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
684696 ATTTAATCAC
684706 TATATTTAT
1 TATATTTAT
684715 TATATTTAT
1 TATATTTAT
684724 TAT-TTTA-
1 TATATTTAT
684731 -ATCATTTAT
1 TAT-ATTTAT
*
684740 T-TATATACT
1 TATATTTA-T
684749 TATATTTAT
1 TATATTTAT
684758 TA
1 TA
684760 CTAGAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
6 2 0.05
8 12 0.32
9 18 0.49
10 5 0.14
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (9 bp):
TATATTTAT
Found at i:684733 original size:30 final size:27
Alignment explanation
Indices: 684691--684755 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
684681 TTTTGTATTT
* *
684691 TTATAATTTAATCACTATATTTATTATAT
1 TTATATTTTAATCA-TATATTTA-TATAC
*
684720 TTATTATTTTAATCATTTATTTATATAC
1 TTA-TATTTTAATCATATATTTATATAC
684748 TTATATTT
1 TTATATTT
684756 ATTACTAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.16
28 7 0.22
29 10 0.31
30 10 0.31
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATATTTTAATCATATATTTATATAC
Found at i:687878 original size:23 final size:22
Alignment explanation
Indices: 687823--687880 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
687813 CATTGCACAG
* *
687823 TTTGCATTTCAATTTCTGCATT
1 TTTGCATTGCATTTTCTGCATT
* *
687845 TTCGCATTTGCATTTTTTGCATTT
1 TTTGCA-TTGCATTTTCTGCA-TT
687869 TTTGCATTGCAT
1 TTTGCATTGCAT
687881 AACATATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.17
23 17 0.59
24 7 0.24
ACGTcount: A:0.16, C:0.17, G:0.12, T:0.55
Consensus pattern (22 bp):
TTTGCATTGCATTTTCTGCATT
Found at i:689067 original size:2 final size:2
Alignment explanation
Indices: 689060--689124 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
689050 TTAATTTGTT
689060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
689102 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
689125 TAACCAACAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:690003 original size:21 final size:21
Alignment explanation
Indices: 689974--690015 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
689964 TTTTACAAAA
*
689974 AATGCCGCAACAGATAAGTAC
1 AATGCCGCAACAAATAAGTAC
* *
689995 AATGTCGCAACAAATTAGTAC
1 AATGCCGCAACAAATAAGTAC
690016 TTTAGTGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (21 bp):
AATGCCGCAACAAATAAGTAC
Found at i:694262 original size:9 final size:10
Alignment explanation
Indices: 694248--694350 Score: 63
Period size: 10 Copynumber: 10.0 Consensus size: 10
694238 AGCCGAAGCT
694248 GAAGCA-AGA
1 GAAGCAGAGA
694257 GAAGCAGAGA
1 GAAGCAGAGA
*
694267 GAGTAGCA-CGA
1 GA--AGCAGAGA
*
694278 GAAGTAGAGA
1 GAAGCAGAGA
694288 G-AGCAACGAGA
1 GAAGC-A-GAGA
*
694299 GAAGTAGAGA
1 GAAGCAGAGA
694309 G-AGCAGCGAGA
1 GAAGCA--GAGA
*
694320 GAAGTAGAGA
1 GAAGCAGAGA
694330 G-AGCAGCGAGA
1 GAAGCA--GAGA
694341 GAAGCAGAGA
1 GAAGCAGAGA
694351 CAAAAGCAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 25
0.69 0.08 0.24
Matches are distributed among these distances:
9 17 0.23
10 23 0.32
11 20 0.27
12 13 0.18
ACGTcount: A:0.46, C:0.11, G:0.40, T:0.04
Consensus pattern (10 bp):
GAAGCAGAGA
Done.