Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008314.1 Hibiscus syriacus cultivar Beakdansim tig00111008_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: 2414839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:457658 original size:61 final size:61
Alignment explanation
Indices: 457532--457676 Score: 152
Period size: 61 Copynumber: 2.4 Consensus size: 61
457522 TCATCCTCAT
* **
457532 ACTTTTGAATATTCCAA-TTTCATCCCTAAACTATGACTCTCAATCTAAATTAATACTTAA
1 ACTTTTGAATATTCTAATTTTCATCCCTAAACTATGACTCTCAATCTAAATTAATACCCAA
* * * ** *
457592 ACTTTTGATTATTCTAATTTTTATCCCTAAACTATGACTCT-ATTTCTAAATTGGTTCCCAA
1 ACTTTTGAATATTCTAATTTTCATCCCTAAACTATGACTCTCA-ATCTAAATTAATACCCAA
* * *
457653 GCTTTTAAATAGTCTAA-TTTCATC
1 ACTTTTGAATATTCTAATTTTCATC
457677 TTCAAATTCA
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
60 22 0.32
61 47 0.68
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.43
Consensus pattern (61 bp):
ACTTTTGAATATTCTAATTTTCATCCCTAAACTATGACTCTCAATCTAAATTAATACCCAA
Found at i:458543 original size:15 final size:15
Alignment explanation
Indices: 458523--458575 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
458513 TTCCAGAAAA
458523 TGAATTACTGGAATT
1 TGAATTACTGGAATT
458538 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
458553 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
458568 TGAATTAC
1 TGAATTAC
458576 ATTTCTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:458589 original size:20 final size:20
Alignment explanation
Indices: 458560--458627 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
458550 ATTTGAATTA
458560 CTGGAAAATGAATTACATTT
1 CTGGAAAATGAATTACATTT
*
458580 CTGTAAAATGAATTACATTT
1 CTGGAAAATGAATTACATTT
458600 CTGGAAAATGAATTACATTT
1 CTGGAAAATGAATTACATTT
458620 CTGGAAAA
1 CTGGAAAA
458628 CATCTGGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
CTGGAAAATGAATTACATTT
Found at i:458829 original size:28 final size:28
Alignment explanation
Indices: 458797--458859 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
458787 TTACTAAAAT
* *
458797 ATTATTGAAA-ATATAAATAATATTATTC
1 ATTATT-AAATATATAAAAAAAATTATTC
458825 ATTATTAAATATATAAAAAAAATTATT-
1 ATTATTAAATATATAAAAAAAATTATTC
458852 ATATATTA
1 AT-TATTA
458860 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTATTAAATATATAAAAAAAATTATTC
Found at i:458870 original size:24 final size:23
Alignment explanation
Indices: 458825--458884 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
458815 AATATTATTC
*
458825 ATTATTAAATA-TA-TAAAAAAA
1 ATTATTATATATTATTAAAAAAA
458846 ATTATTATATATTATTAAAATAAA
1 ATTATTATATATTATTAAAA-AAA
* * *
458870 AATATAATATCTTAT
1 ATTATTATATATTAT
458885 ATTATTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.31
22 2 0.06
23 5 0.16
24 15 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTATATATTATTAAAAAAA
Found at i:458937 original size:22 final size:23
Alignment explanation
Indices: 458912--458955 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
458902 GATTATTTTA
458912 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
458934 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
458956 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:458960 original size:22 final size:22
Alignment explanation
Indices: 458916--458972 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
458906 ATTTTATATA
* *
458916 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
458937 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
458959 ATATTTTAAATATT
1 ATATTATAAATATT
458973 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:458971 original size:52 final size:51
Alignment explanation
Indices: 458852--458972 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
458842 AAAAATTATT
**
458852 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
458903 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
458957 ATATATTTTAAATATT
1 ATATATTTTAAATATT
458973 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:459220 original size:42 final size:42
Alignment explanation
Indices: 459161--459280 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
459151 ATGAATTACA
*
459161 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
459203 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
459245 TTCCGGAAAATGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
459281 TTCGGGGAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:466493 original size:38 final size:38
Alignment explanation
Indices: 466449--466529 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
466439 GGTTTATTTA
*
466449 AATTAAATT-TAAAATTATCATTTTACTAATCAAAATAT
1 AATTAAATTGTAAAATTATAATTTT-CTAATCAAAATAT
** * *
466487 AATTAAATTGTAACTTTATAATTTTTTAATCATAATAT
1 AATTAAATTGTAAAATTATAATTTTCTAATCAAAATAT
466525 AATTA
1 AATTA
466530 TATGATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (38 bp):
AATTAAATTGTAAAATTATAATTTTCTAATCAAAATAT
Found at i:473462 original size:38 final size:38
Alignment explanation
Indices: 473393--473471 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
473383 AATTTTATAC
* *
473393 CTTTTAAATTTTTAATATAACTTCTTTAAAAATTTACA
1 CTTTTAAACTTTTAATATAACATCTTTAAAAATTTACA
* *
473431 CTTTCTAAACTTTTAATTTAACATC-TTAAAAATTTAGA
1 CTTT-TAAACTTTTAATATAACATCTTTAAAAATTTACA
473469 CTT
1 CTT
473472 ATAATATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 19 0.53
39 17 0.47
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.48
Consensus pattern (38 bp):
CTTTTAAACTTTTAATATAACATCTTTAAAAATTTACA
Found at i:478548 original size:19 final size:19
Alignment explanation
Indices: 478524--478586 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
478514 CCCCTTATGC
*
478524 CTCTCAAGTGTATCTTCGA
1 CTCTCAAGTTTATCTTCGA
*
478543 CTCTCAAGTTTCTCTTCGA
1 CTCTCAAGTTTATCTTCGA
*
478562 CTCTATCAAGTTTTTCTTCGA
1 CTC--TCAAGTTTATCTTCGA
478583 CTCT
1 CTCT
478587 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 21 0.54
21 18 0.46
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (19 bp):
CTCTCAAGTTTATCTTCGA
Found at i:478572 original size:21 final size:20
Alignment explanation
Indices: 478527--478587 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
478517 CTTATGCCTC
*
478527 TCAAGTGTATCTTCGACTC-
1 TCAAGTTTATCTTCGACTCT
*
478546 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTATCTTCGACTCT
*
478566 ATCAAGTTTTTCTTCGACTCT
1 -TCAAGTTTATCTTCGACTCT
478587 T
1 T
478588 GATTGTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.18, C:0.26, G:0.11, T:0.44
Consensus pattern (20 bp):
TCAAGTTTATCTTCGACTCT
Found at i:481124 original size:21 final size:21
Alignment explanation
Indices: 481098--481138 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
481088 AAGACAATCA
481098 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
481119 AGAGTCGAAGAGAAACTTGA
1 AGAGTCGAAGAGAAACTTGA
481139 GAGACATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:483363 original size:199 final size:199
Alignment explanation
Indices: 482979--483414 Score: 757
Period size: 199 Copynumber: 2.2 Consensus size: 199
482969 TGTTGATACT
* *
482979 TTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGA
1 TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAAAGAATAGGTCTAAATAATGTATCGA
*
483044 CACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACATAAAG
66 CACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGACAAACAGGGTGCAACATAAAG
* * *
483109 TGTCGATCCATATATAAAAAGTGTCGATCCGATAAATATCGAAACTCATAAGTATAATGTAATAG
131 TGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACTCAAAAGTATAATGTAATAG
483174 GTAA
196 GTAA
* *
483178 TTTTTCAATATAACCGGTACAAGTATACCGGTTTTATGAAAGAATATGTCTAAATAATGTATCGA
1 TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAAAGAATAGGTCTAAATAATGTATCGA
*
483243 CATTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGACAAACAGGGTGCAACAATAAA
66 CACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGACAAACAGGGTGCAAC-ATAAA
*
483308 GTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAC-CAAAAGTATAATGTATTA
130 GTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACTCAAAAGTATAATGTAATA
483372 GGTAA
195 GGTAA
*
483377 TTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATG
1 TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
483415 GGAGAATTGA
Statistics
Matches: 224, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
199 175 0.78
200 49 0.22
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (199 bp):
TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAAAGAATAGGTCTAAATAATGTATCGA
CACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGACAAACAGGGTGCAACATAAAG
TGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACTCAAAAGTATAATGTAATAG
GTAA
Found at i:484960 original size:18 final size:18
Alignment explanation
Indices: 484924--484977 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
484914 ACCAAGCGGT
*
484924 CAATGAAGATGAAGCTGA
1 CAATGAAGATGAAGATGA
*
484942 CAATGAAGATGACGATGA
1 CAATGAAGATGAAGATGA
* * *
484960 CAACGATGATGATGATGA
1 CAATGAAGATGAAGATGA
484978 TGATCCAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.19
Consensus pattern (18 bp):
CAATGAAGATGAAGATGA
Found at i:498834 original size:59 final size:59
Alignment explanation
Indices: 498706--498851 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 59
498696 GCATCATATG
* *
498706 TCCCTAAACTAT-AATCCTCATTTTAAATTAGTTCTTAAACTTTTTAATATTTCAATTCCA
1 TCCCTAAACTATGAAT-CTCATTCTAAA-TAGTTCTTAAACTTTTGAATATTTCAATTCCA
* * *
498766 TCCCCAAACTATGACTCTCATTCTAAATAG-TCTTTAAACTTTTGAATA-TTCTAATTTCA
1 TCCCTAAACTATGAATCTCATTCTAAATAGTTC-TTAAACTTTTGAATATTTC-AATTCCA
* * *
498825 TTCCTAAACTATG-TTCTCTTTCTAAAT
1 TCCCTAAACTATGAATCTCATTCTAAAT
498852 TGGTCCCCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
58 17 0.23
59 34 0.46
60 21 0.28
61 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (59 bp):
TCCCTAAACTATGAATCTCATTCTAAATAGTTCTTAAACTTTTGAATATTTCAATTCCA
Found at i:504758 original size:2 final size:2
Alignment explanation
Indices: 504751--504784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
504741 ACCATATAAG
504751 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
504785 TCATATTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508891 original size:11 final size:11
Alignment explanation
Indices: 508875--508900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
508865 TTTTAGTAAT
508875 TGAAATTAAAA
1 TGAAATTAAAA
508886 TGAAATTAAAA
1 TGAAATTAAAA
508897 TGAA
1 TGAA
508901 TGATGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (11 bp):
TGAAATTAAAA
Found at i:512098 original size:15 final size:16
Alignment explanation
Indices: 512064--512108 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 16
512054 GTTGTGGTTA
512064 AAATAAAAAATATGAATT
1 AAAT-AAAAA-ATGAATT
512082 AAATAAAAAAT-AATT
1 AAATAAAAAATGAATT
512097 AAATAAACAAAT
1 AAATAAA-AAAT
512109 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.42
16 6 0.23
17 5 0.19
18 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATAAAAAATGAATT
Found at i:512821 original size:64 final size:64
Alignment explanation
Indices: 512696--512821 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
512686 TAAAACATCT
* * *
512696 TAAATCCTAATTAAAACACTTAAAATTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACACTTAAAAATATTTAAACTAAAATACCTAAAAAAAAATAAAATATTC
*
512760 TAAATCCTAATTAAAATAC-TAAAACATATTTAAACTAAAATA-C-AAAGAAAAAGATAAAATAT
1 TAAATCCTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACCTAAA-AAAAA-ATAAAATAT
512822 AAAAATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
62 3 0.05
63 10 0.18
64 42 0.76
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (64 bp):
TAAATCCTAATTAAAACACTTAAAAATATTTAAACTAAAATACCTAAAAAAAAATAAAATATTC
Found at i:512904 original size:76 final size:75
Alignment explanation
Indices: 512751--512893 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 75
512741 AAAAAATAAT
* * *
512751 ATAATATTCTAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGAAAAAGATA
1 ATAATATCCTAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGAAAAAGATA
512816 AAATATAAAA
66 AAATATAAAA
* * * *
512826 ATAATATCTTAAAACTTAATTAAAATACTAAAAACCTATTTAAATTAAAATACAAAGATAAAATA
1 ATAATATCCTAAAACTTAATTAAAATACT-AAAACATATTTAAACTAAAATACAAAGA-AAAAGA
512891 TAA
64 TAA
512894 TGTTTAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 25 0.42
76 26 0.44
77 8 0.14
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (75 bp):
ATAATATCCTAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGAAAAAGATA
AAATATAAAA
Found at i:514723 original size:20 final size:20
Alignment explanation
Indices: 514685--514731 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
514675 AAGTTTGCTA
514685 AAAAATAAAAAAAATAAAAC
1 AAAAATAAAAAAAATAAAAC
*
514705 GAAAAT-AAAAAAATAAAAAC
1 AAAAATAAAAAAAAT-AAAAC
514725 AAAAATA
1 AAAAATA
514732 TAACGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAATAAAAAAAATAAAAC
Found at i:514728 original size:19 final size:20
Alignment explanation
Indices: 514686--514722 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
514676 AGTTTGCTAA
514686 AAAATAAAAAAAATAAAACG
1 AAAATAAAAAAAATAAAACG
514706 AAAAT-AAAAAAATAAAA
1 AAAATAAAAAAAATAAAA
514723 ACAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAATAAAAAAAATAAAACG
Found at i:516649 original size:13 final size:13
Alignment explanation
Indices: 516631--516661 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
516621 CCTTAATAAA
516631 CCTGCGGTAAAAT
1 CCTGCGGTAAAAT
516644 CCTGCGGTAAAAT
1 CCTGCGGTAAAAT
516657 CCTGC
1 CCTGC
516662 ATAGCCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGCGGTAAAAT
Found at i:520203 original size:11 final size:11
Alignment explanation
Indices: 520186--520252 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
520176 AAAGATATAT
520186 TAAAATAAAAGA
1 TAAAATAAAA-A
520198 -AAAATAAAAA
1 TAAAATAAAAA
520208 TAAAAT-AAAA
1 TAAAATAAAAA
*
520218 TATAATAATAAA
1 TAAAATAA-AAA
* *
520230 TATTAATAATAA
1 TA-AAATAAAAA
520242 TAAATATAAAA
1 TAAA-ATAAAA
520253 GGGGGATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
10 10 0.22
11 16 0.35
12 14 0.30
13 6 0.13
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:520217 original size:16 final size:17
Alignment explanation
Indices: 520189--520252 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
520179 GATATATTAA
* *
520189 AATAAAAGAAAAATAAA
1 AATAAAATAAAAATAAT
520206 AATAAAATAAAATATAAT
1 AATAAAATAAAA-ATAAT
**
520224 AAT-AAATATTAATAAT
1 AATAAAATAAAAATAAT
520240 AATAAATATAAAA
1 AATAAA-ATAAAA
520253 GGGGGATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.21
17 19 0.50
18 11 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAAAATAAAAATAAT
Found at i:520229 original size:13 final size:13
Alignment explanation
Indices: 520200--520241 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
520190 ATAAAAGAAA
520200 AATAAAA-ATAA-
1 AATAAAATATAAT
520211 AATAAAATATAAT
1 AATAAAATATAAT
520224 AAT-AAATATTAAT
1 AATAAAATA-TAAT
520237 AATAA
1 AATAA
520242 TAAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.26
12 9 0.33
13 10 0.37
14 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAAATATAAT
Found at i:521039 original size:75 final size:76
Alignment explanation
Indices: 520960--521108 Score: 237
Period size: 75 Copynumber: 2.0 Consensus size: 76
520950 CTAAAATACC
* * * *
520960 TAAAAAATAAATATAATATTCTAAATCCTAATTAAAATACT-AAAATCTATTTAAACTAAAATAC
1 TAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
521024 AAAGATAAAGA
66 AAAGATAAAGA
* *
521035 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
521100 AAAGATAAA
66 AAAGATAAA
521109 ATATAATGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 36 0.54
76 31 0.46
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (76 bp):
TAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
AAAGATAAAGA
Found at i:521124 original size:76 final size:75
Alignment explanation
Indices: 520967--521135 Score: 232
Period size: 76 Copynumber: 2.2 Consensus size: 75
520957 ACCTAAAAAA
* * *
520967 TAAATATAATATTCTAAATCCTAATTAAAATACTAAAATCTATTTAAACTAAAATACAAAGATAA
1 TAAA-ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAA
521032 AGATAAAATAT
65 AGATAAAATAT
* *
521043 AAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAA
1 TAAAATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAA
* *
521108 A-ATATAATGTT
65 AGATAAAAT-AT
*
521119 TAAAATATTATCCTAAA
1 TAAAATAATATCCTAAA
521136 TTTGAGTTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
75 32 0.39
76 50 0.61
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (75 bp):
TAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA
GATAAAATAT
Found at i:531196 original size:109 final size:109
Alignment explanation
Indices: 531005--531231 Score: 445
Period size: 109 Copynumber: 2.1 Consensus size: 109
530995 ATTATCTAAT
531005 ATAAATATTGATCCTAGCTTACGTCTCAATCTTCGCCAATGGGCTTTCAGATTACTTTGGTGATA
1 ATAAATATTGATCCTAGCTTACGTCTCAATCTTCGCCAATGGGCTTTCAGATTACTTTGGTGATA
*
531070 GGAATAGTCCGAGTCAACCTAGAGTGTGACATATTTCCATCTTA
66 GGAATAGTCCAAGTCAACCTAGAGTGTGACATATTTCCATCTTA
531114 ATAAATATTGATCCTAGCTTACGTCTCAATCTTCGCCAATGGGCTTTCAGATTACTTTGGTGATA
1 ATAAATATTGATCCTAGCTTACGTCTCAATCTTCGCCAATGGGCTTTCAGATTACTTTGGTGATA
531179 GGAATAGTCCAAGTCAACCTAGAGTGTGACATATTTCCATCTTA
66 GGAATAGTCCAAGTCAACCTAGAGTGTGACATATTTCCATCTTA
531223 ATAAATATT
1 ATAAATATT
531232 TAGCTTAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 117 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (109 bp):
ATAAATATTGATCCTAGCTTACGTCTCAATCTTCGCCAATGGGCTTTCAGATTACTTTGGTGATA
GGAATAGTCCAAGTCAACCTAGAGTGTGACATATTTCCATCTTA
Found at i:532677 original size:42 final size:43
Alignment explanation
Indices: 532619--532805 Score: 290
Period size: 43 Copynumber: 4.4 Consensus size: 43
532609 AGTAAAAGAG
* *
532619 CCTGGGGAAACTGTAAGGCTTACCATTGCACACAGCAAAGGAA
1 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
*
532662 CCT-GGGAAACTGTAAGGCTTATCCTTGCACACAGCAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
*
532704 CCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
1 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
*
532747 CCTGGGGGAAA-TGTAAGGCTTACCCTTGCACACAGCAAATGGA
1 CCT-GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
532790 CCTAGGGG-AACTGTAA
1 CCT-GGGGAAACTGTAA
532806 CAGTAATTAA
Statistics
Matches: 133, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
42 41 0.31
43 86 0.65
44 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.18
Consensus pattern (43 bp):
CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
Found at i:532690 original size:85 final size:85
Alignment explanation
Indices: 532588--532805 Score: 273
Period size: 85 Copynumber: 2.5 Consensus size: 85
532578 GTAAAAACGA
* *
532588 TAAGGTCTTATACTTGCACATAGTAAAAGAG-CCTGGGGAAACTGTAAGGCTTACCATTGCACAC
1 TAAGG-CTTATCCTTGCACACAG-AAAAGAGACCTGGGGAAACTGTAAGGCTTACCATTGCACAC
532652 AGCAAAGGAACCT-GGGAAACTG
64 AGCAAAGGAACCTGGGGAAA-TG
* * * *
532674 TAAGGCTTATCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTATCCTTGCACACAGAAAAGAGACCTGGGGAAACTGTAAGGCTTACCATTGCACACAG
*
532739 CAAAGGGACCTGGGGGAAATG
66 CAAAGGAACCT-GGGGAAATG
* *
532760 TAAGGCTTACCCTTGCACACAGCAAATG-GACCTAGGGG-AACTGTAA
1 TAAGGCTTATCCTTGCACACAG-AAAAGAGACCT-GGGGAAACTGTAA
532806 CAGTAATTAA
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
84 5 0.04
85 58 0.50
86 41 0.35
87 13 0.11
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (85 bp):
TAAGGCTTATCCTTGCACACAGAAAAGAGACCTGGGGAAACTGTAAGGCTTACCATTGCACACAG
CAAAGGAACCTGGGGAAATG
Found at i:534768 original size:17 final size:18
Alignment explanation
Indices: 534737--534772 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
534727 AAACTAACAT
*
534737 TTTTTATGCACATCAATA
1 TTTTTATGCAAATCAATA
534755 TTTTTAT-CAAATCAATA
1 TTTTTATGCAAATCAATA
534772 T
1 T
534773 GTCTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTTATGCAAATCAATA
Found at i:537008 original size:19 final size:19
Alignment explanation
Indices: 536984--537028 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
536974 TTTGAATTTA
536984 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
* *
537003 AAAAAATCATAAAAATTAC
1 AAAAAATCAGAAAAAATAC
537022 AAAAAAT
1 AAAAAAT
537029 TAGTATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:537120 original size:19 final size:19
Alignment explanation
Indices: 537096--537139 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
537086 CTTGAATTTA
537096 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
* *
537115 AAAAAATCATAAAAATTAC
1 AAAAAATCAGAAAAAATAC
537134 AAAAAA
1 AAAAAA
537140 ATTAGTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:537209 original size:112 final size:112
Alignment explanation
Indices: 536969--537219 Score: 391
Period size: 113 Copynumber: 2.3 Consensus size: 112
536959 TCTAATAAAT
536969 ATCTATTTGAATTTAAAAAAATCAGAAAAAATACAAAAAATCATAAAAATTACAAAAAATTAGTA
1 ATCTATTTGAATTTAAAAAAATCAGAAAAAATACAAAAAATCATAAAAATTACAAAAAATTAGTA
* * * *
537034 TGTTTATTTATCTAATTTCAATGTATTTTTATTTATCTTGCAAATTA
66 TGTTTATATATATAATTTCAATGTATTTTCATCTATCTTGCAAATTA
*
537081 ATCTACTTGAATTTAAAAAAATCAGAAAAAATACAAAAAATCATAAAAATTACAAAAAAATTAGT
1 ATCTATTTGAATTTAAAAAAATCAGAAAAAATACAAAAAATCATAAAAATTAC-AAAAAATTAGT
** *
537146 ATGTTTATATATATAATTTCAATGTATTTTCATCTATCTTTTAATTTA
65 ATGTTTATATATATAATTTCAATGTATTTTCATCTATCTTGCAAATTA
*
537194 ATTTATTTGAA-TT-AAAAAA-CAGAAAA
1 ATCTATTTGAATTTAAAAAAATCAGAAAA
537220 TTATAGCGCA
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
110 7 0.05
111 6 0.05
112 54 0.42
113 61 0.48
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (112 bp):
ATCTATTTGAATTTAAAAAAATCAGAAAAAATACAAAAAATCATAAAAATTACAAAAAATTAGTA
TGTTTATATATATAATTTCAATGTATTTTCATCTATCTTGCAAATTA
Found at i:538926 original size:24 final size:23
Alignment explanation
Indices: 538880--538927 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
538870 TACATGTGTA
*
538880 TTTTATACTATTTTTAACTTATT
1 TTTTATAATATTTTTAACTTATT
538903 TTTTATAAATATTTTTAGAC-TATT
1 TTTTAT-AATATTTTTA-ACTTATT
538927 T
1 T
538928 ATTAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 14 0.64
25 2 0.09
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTATAATATTTTTAACTTATT
Found at i:545886 original size:23 final size:23
Alignment explanation
Indices: 545855--545899 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
545845 CATTTCCTGA
* *
545855 TTCCCTGAGTTGAGCTCAGTGCT
1 TTCCATGAGATGAGCTCAGTGCT
545878 TTCCATGAGATGAGCTCAGTGC
1 TTCCATGAGATGAGCTCAGTGC
545900 AAAATTCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
TTCCATGAGATGAGCTCAGTGCT
Found at i:551606 original size:2 final size:2
Alignment explanation
Indices: 551599--551629 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
551589 CTATTATTCT
551599 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 T
551630 GATTTCCCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:559453 original size:22 final size:21
Alignment explanation
Indices: 559420--559462 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
559410 AGATTATCGT
559420 TAATTTTTAACAAAAAAATAA
1 TAATTTTTAACAAAAAAATAA
* *
559441 TAATTTTTGAACATATAAATAA
1 TAATTTTT-AACAAAAAAATAA
559463 GCGGTTGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATTTTTAACAAAAAAATAA
Found at i:560262 original size:19 final size:18
Alignment explanation
Indices: 560240--560287 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
560230 TAAGAGGGCG
*
560240 AAAAAATAAATTATTAATA
1 AAAAAATAAATAATTAA-A
* *
560259 AAAATATAAAAAATTAAA
1 AAAAAATAAATAATTAAA
*
560277 AAAAATTAAAT
1 AAAAAATAAAT
560288 GATAAATCGC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAAATAAATAATTAAA
Found at i:567881 original size:7 final size:7
Alignment explanation
Indices: 567871--567895 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
567861 ATGAAAAGCC
567871 AAAAGAG
1 AAAAGAG
567878 AAAAGAG
1 AAAAGAG
567885 AAAAGAG
1 AAAAGAG
567892 AAAA
1 AAAA
567896 TAGGTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:568194 original size:19 final size:20
Alignment explanation
Indices: 568153--568203 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
568143 AACGCGATCC
568153 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
568173 CCAGAATCGCAAATCA-TTT
1 CCAGAATCGCAAATCAGTTT
*
568192 CCAAAATCGCAA
1 CCAGAATCGCAA
568204 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:568269 original size:20 final size:20
Alignment explanation
Indices: 568189--568289 Score: 58
Period size: 20 Copynumber: 5.0 Consensus size: 20
568179 TCGCAAATCA
568189 TTTCCAAAATCGCAACGCGAT
1 TTTCC-AAATCGCAACGCGAT
** * *
568210 TCTTGAAAATCGCGATGCGAT
1 T-TTCCAAATCGCAACGCGAT
** * * **
568231 AGTACAATTCGCATTGCGAT
1 TTTCCAAATCGCAACGCGAT
*
568251 TTTCCAAATCGCAACGCGAA
1 TTTCCAAATCGCAACGCGAT
* **
568271 TATGAAAATCGCAACGCGA
1 TTTCCAAATCGCAACGCGA
568290 ACACATAAAT
Statistics
Matches: 58, Mismatches: 21, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
20 42 0.72
21 14 0.24
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
TTTCCAAATCGCAACGCGAT
Found at i:568290 original size:20 final size:20
Alignment explanation
Indices: 568256--568447 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
568246 GCGATTTTCC
* ** *
568256 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
568276 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
568296 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
568316 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
568336 AAATCGCAACGCGTAT-GGT
1 AAATCGCAACGCGTATCCGT
*
568355 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
568375 ATATCGCAACGCGTATCCGA
1 AAATCGCAACGCGTATCCGT
* * *
568395 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
568415 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
568435 AAATCGCAACGCG
1 AAATCGCAACGCG
568448 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 19 0.13
20 122 0.85
21 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:568861 original size:32 final size:33
Alignment explanation
Indices: 568819--568888 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
568809 TTCACTTAGA
568819 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
568852 TTTCA-TTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
568884 TTTCA
1 TTTCA
568889 AGTTGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:568993 original size:21 final size:19
Alignment explanation
Indices: 568967--569050 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
568957 TGCAGAAGAG
568967 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATG-AAA
* *
568988 TCGCAACGAGAGAATGACA
1 TCGCAACGAGAAAATGAAA
569007 TCGCAACGAG---A-G-AA
1 TCGCAACGAGAAAATGAAA
*
569021 TCGCAACGCG-AAATGGAAA
1 TCGCAACGAGAAAAT-GAAA
569040 TCGCAACGAGA
1 TCGCAACGAGA
569051 GAATCGCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
18 1 0.02
19 23 0.44
20 4 0.08
21 11 0.21
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAAATGAAA
Found at i:569011 original size:19 final size:20
Alignment explanation
Indices: 568967--569021 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
568957 TGCAGAAGAG
*
568967 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
*
568988 TCGCAACGAGAGAATG-ACA
1 TCGCAACGAGAGAATGAAAA
569007 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
569022 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 4 0.12
21 11 0.34
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:569025 original size:14 final size:14
Alignment explanation
Indices: 569006--569061 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
568996 AGAGAATGAC
569006 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
569020 ATCGCAACGCGAAATGGAA
1 ATCGCAA--CGAGA--G-A
569039 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
569053 ATCGCAACG
1 ATCGCAACG
569062 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 17 0.49
15 1 0.03
16 4 0.11
17 4 0.11
18 1 0.03
19 8 0.23
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:569028 original size:33 final size:33
Alignment explanation
Indices: 568986--569066 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
568976 GATAAATGAA
*
568986 AATCGCAACGAGAGAAT-GACATCGCAACGAGAG
1 AATCGCAACGAGA-AATGGAAATCGCAACGAGAG
*
569019 AATCGCAACGCGAAATGGAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGGAAATCGCAACGAGAG
*
569052 AATCGCAACGCGAAA
1 AATCGCAACGAGAAA
569067 CCAAAAATCG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 3 0.07
33 42 0.93
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.09
Consensus pattern (33 bp):
AATCGCAACGAGAAATGGAAATCGCAACGAGAG
Found at i:569101 original size:19 final size:18
Alignment explanation
Indices: 569074--569191 Score: 64
Period size: 14 Copynumber: 7.1 Consensus size: 18
569064 AAACCAAAAA
*
569074 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
569093 TCGCGTTGCGA---TC--
1 TCGCGTTGCGATTTTCAT
*
569106 TCTCGTTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCA-T
569126 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
569140 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
569158 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
569173 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
569191 T
1 T
569192 TCAACCAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 33
0.65 0.07 0.28
Matches are distributed among these distances:
13 10 0.13
14 20 0.27
16 7 0.09
17 7 0.09
18 1 0.01
19 20 0.27
20 10 0.13
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:569127 original size:33 final size:33
Alignment explanation
Indices: 569079--569193 Score: 196
Period size: 33 Copynumber: 3.5 Consensus size: 33
569069 AAAAATCGCA
569079 TTGCGATTTTCATTTCGCGTTGCGA-TCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
569111 TTGCGATTTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGA-TTTTCATTTCGCGTTGCGATTCTCTCG
* *
569145 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
569178 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
569194 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
32 6 0.08
33 58 0.75
34 13 0.17
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:569148 original size:14 final size:14
Alignment explanation
Indices: 569129--569185 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
569119 TTTCATTTCG
569129 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
569143 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
569160 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
569176 CGTTGCGATT
1 CGTTGCGATT
569186 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:571154 original size:91 final size:91
Alignment explanation
Indices: 570867--571229 Score: 657
Period size: 91 Copynumber: 4.0 Consensus size: 91
570857 TTGCTTAGTA
570867 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
570932 TCTTTGTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTGTCTTTTGGTTGAAAGT
570958 AATTTGTTCGG-TGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATA-TATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
571020 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTG-TTTGTCTTTTGGTTGAAAGT
571047 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TT
1 -AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
571111 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
65 GTCTTTG-TTTGTCTTTTGGTTGAAAGT
571139 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAT-GTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
571203 TCTTTGTTT-TCTTTTGGTTGAAAGT
66 TCTTTGTTTGTCTTTTGGTTGAAAGT
571228 AA
1 AA
571230 ATTTATCCAT
Statistics
Matches: 266, Mismatches: 0, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
88 12 0.05
89 67 0.25
90 33 0.12
91 93 0.35
92 59 0.22
93 2 0.01
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (91 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTGTCTTTTGGTTGAAAGT
Found at i:571218 original size:181 final size:181
Alignment explanation
Indices: 570863--571233 Score: 685
Period size: 181 Copynumber: 2.0 Consensus size: 181
570853 TAGATTGCTT
570863 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
570928 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTGCTGCCAATTCTGCTAACTGTGT
66 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTGCTGCCAATTCTGCTAACTGTGT
570993 ATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 ATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
571044 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
571109 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAATTTGTTCGG-TGCTGCCAATTCTGCT-AACTG
*
571173 TGTATTCTTTAACACTGTGAAATGTATTTGTCTTTG-TTT-TCTTTTGGTTGAA
128 TGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
571225 AGTAAATTT
1 AGTAAATTT
571234 ATCCATTCAA
Statistics
Matches: 186, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
180 9 0.05
181 118 0.63
182 19 0.10
183 40 0.22
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (181 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTGCTGCCAATTCTGCTAACTGTGT
ATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:571317 original size:19 final size:19
Alignment explanation
Indices: 571277--571405 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
571267 TAGTTTACTT
* *
571277 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
571297 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
571316 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
571335 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
571349 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
571368 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
571382 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
571401 TCGCA
1 TCGCA
571406 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:571356 original size:33 final size:32
Alignment explanation
Indices: 571313--571405 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
571303 CGCGAAACCA
**
571313 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
571345 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
571378 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
571406 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:571403 original size:52 final size:52
Alignment explanation
Indices: 571277--571405 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
571267 TAGTTTACTT
**
571277 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
571329 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
571382 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
571406 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:571442 original size:14 final size:14
Alignment explanation
Indices: 571423--571479 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
571413 TTTCATTTCG
571423 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
571437 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
571454 CGCATTGCGATTATGT
1 CG--TTGCGATTCTTT
571470 CGTTGCGATT
1 CGTTGCGATT
571480 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:571448 original size:33 final size:33
Alignment explanation
Indices: 571406--571498 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
571396 CAAAATCGCA
* *
571406 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
*
571439 TTGCGATTTTCATTTCGCATTGCGATTATGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
571472 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
571499 TTGGTTTTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
Found at i:571509 original size:20 final size:19
Alignment explanation
Indices: 571401--571536 Score: 121
Period size: 19 Copynumber: 7.6 Consensus size: 19
571391 GAAACCAAAA
*
571401 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
571420 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
571436 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
571453 TCGCATTGCGA--TT-ATG
1 TCGCGTTGCGATTTTCATT
571469 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
571486 TCGCGTTGCGATTTTGGTTT
1 TCGCGTTGCGATTTT-CATT
*
571506 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
571526 TCGTGTTGCGA
1 TCGCGTTGCGA
571537 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 29 0.31
20 29 0.31
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:573375 original size:34 final size:36
Alignment explanation
Indices: 573336--573404 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
573326 AATTGATTGT
573336 TTTTTGATTGTTT-A-ATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATATTTGTAAAAGTTGATTCAA
573370 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATT
1 TTTTTGATTGTTTAA-T-ATTTGTAAAAGTTGATT
573405 TGTGTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 13 0.42
35 1 0.03
38 17 0.55
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (36 bp):
TTTTTGATTGTTTAATATTTGTAAAAGTTGATTCAA
Found at i:573530 original size:19 final size:19
Alignment explanation
Indices: 573514--573614 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
573504 AAAAATGACT
573514 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
573533 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
573552 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
573566 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
573584 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
573604 ATCGCAATGCG
1 ATCGCAATGCG
573615 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 34 0.47
20 12 0.16
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:573661 original size:52 final size:51
Alignment explanation
Indices: 573605--573878 Score: 220
Period size: 52 Copynumber: 5.2 Consensus size: 51
573595 GAAATGAAAA
* *
573605 TCGCAATGCGTTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGTTT-TCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
573657 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* * *
573709 TCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATT
1 TCGCATTGCGTTTTCATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATT
** * * *
573765 TCGCATTGCGATTATGTCGGTTCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TT-T-TCATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATT
* * *
573817 TCGCATTGCG-ATTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGTTTTCATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATT
573869 TCGCATTGCG
1 TCGCATTGCG
573879 ATTCTCTCGT
Statistics
Matches: 183, Mismatches: 22, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
45 3 0.02
46 1 0.01
47 3 0.02
48 4 0.02
49 1 0.01
50 2 0.01
51 18 0.10
52 101 0.55
53 5 0.03
54 7 0.04
56 25 0.14
57 1 0.01
58 3 0.02
59 9 0.05
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (51 bp):
TCGCATTGCGTTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:573663 original size:33 final size:33
Alignment explanation
Indices: 573621--573948 Score: 210
Period size: 33 Copynumber: 9.5 Consensus size: 33
573611 TGCGTTTATA
573621 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
573654 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
573690 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
573724 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
573762 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
573795 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
573835 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
573866 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
573899 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
573933 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
573949 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 20, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 97 0.39
34 34 0.14
35 22 0.09
36 15 0.06
37 28 0.11
38 28 0.11
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:573667 original size:19 final size:19
Alignment explanation
Indices: 573643--573948 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
573633 GATTATCTCG
573643 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
573662 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
573681 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
573695 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
573714 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
573732 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
573751 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
573770 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
573785 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
573803 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
573822 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
573836 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
573855 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
573874 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
573888 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
573908 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
573922 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
573941 TTGCGATT
1 TTGCGATT
573949 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.13
17 28 0.11
18 23 0.09
19 119 0.48
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:573879 original size:52 final size:52
Alignment explanation
Indices: 573643--573920 Score: 361
Period size: 52 Copynumber: 5.2 Consensus size: 52
573633 GATTATCTCG
*
573643 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
573695 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
573751 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
573803 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
573855 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
573908 TTGCGATTTTCAT
1 TTGCGATTTTCAT
573921 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 21 0.10
52 133 0.63
53 22 0.10
54 8 0.04
55 3 0.01
56 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:574624 original size:12 final size:12
Alignment explanation
Indices: 574607--574631 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
574597 TCTTCGGGGA
574607 CTTTTTCTTCTT
1 CTTTTTCTTCTT
574619 CTTTTTCTTCTT
1 CTTTTTCTTCTT
574631 C
1 C
574632 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:574840 original size:24 final size:24
Alignment explanation
Indices: 574806--574852 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
574796 CTGAAACATC
574806 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
574830 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
574853 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:575553 original size:20 final size:20
Alignment explanation
Indices: 575525--575893 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
575515 AAATTTCAGT
* * * *
575525 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
575545 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
575565 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
575585 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
575605 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
575625 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
575645 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
575665 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
575685 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
575705 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
575725 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
575745 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
575765 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
575785 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
575805 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
575825 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
575845 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
575865 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
575885 GTTGCGATT
1 GTTGCGATT
575894 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:577711 original size:20 final size:20
Alignment explanation
Indices: 577673--577712 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
577663 AATAATAAAT
*
577673 TATACATACATATACACATA
1 TATACATACATAAACACATA
* *
577693 TATACATACTTAAATACATA
1 TATACATACATAAACACATA
577713 CATTATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (20 bp):
TATACATACATAAACACATA
Found at i:577802 original size:19 final size:19
Alignment explanation
Indices: 577778--577823 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
577768 AATTATAATG
*
577778 CATACATTAATAAAATAGA
1 CATACATAAATAAAATAGA
* * *
577797 CATACATAAATTATATATA
1 CATACATAAATAAAATAGA
577816 CATACATA
1 CATACATA
577824 CATACATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (19 bp):
CATACATAAATAAAATAGA
Found at i:577804 original size:23 final size:23
Alignment explanation
Indices: 577778--577830 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
577768 AATTATAATG
577778 CATACATTA-ATA-AAATAGACATA
1 CATACATTATATATAAAT--ACATA
* *
577801 CATAAATTATATATACATACATA
1 CATACATTATATATAAATACATA
577824 CATACAT
1 CATACAT
577831 ACATACATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 19 0.76
24 3 0.12
25 3 0.12
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (23 bp):
CATACATTATATATAAATACATA
Found at i:577820 original size:4 final size:4
Alignment explanation
Indices: 577813--577872 Score: 86
Period size: 4 Copynumber: 14.8 Consensus size: 4
577803 TAAATTATAT
*
577813 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA- GTAC ATATC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC
577861 ATAC ATATC ATA
1 ATAC ATA-C ATA
577873 GTTTAATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
3 2 0.04
4 41 0.80
5 8 0.16
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:579629 original size:23 final size:23
Alignment explanation
Indices: 579594--579667 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
579584 TAAATTAACA
579594 TAAAGTGAATATGTTTGTGAATAT
1 TAAA-TGAATATGTTTGTGAATAT
* * *
579618 TAATTGAATATGTTTGCGAATGT
1 TAAATGAATATGTTTGTGAATAT
* *
579641 TAAATAAATGTGTTTGTGAATAT
1 TAAATGAATATGTTTGTGAATAT
579664 TAAA
1 TAAA
579668 CAAACGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (23 bp):
TAAATGAATATGTTTGTGAATAT
Found at i:580502 original size:6 final size:6
Alignment explanation
Indices: 580491--580528 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
580481 GATTTTCAGG
*
580491 TTTTTA TTTTTA -TTTTA TTTTTA TCTTTTA TATTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA TT
580529 ACTTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:580521 original size:13 final size:12
Alignment explanation
Indices: 580491--580528 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
580481 GATTTTCAGG
580491 TTTTTATTTTTA
1 TTTTTATTTTTA
580503 -TTTTATTTTTA
1 TTTTTATTTTTA
*
580514 TCTTTTATATTTA
1 T-TTTTATTTTTA
580527 TT
1 TT
580529 ACTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 11 0.48
12 1 0.04
13 11 0.48
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:588239 original size:13 final size:13
Alignment explanation
Indices: 588221--588254 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
588211 TAGGAACCAC
588221 ATGAAGGCAACAA
1 ATGAAGGCAACAA
588234 ATGAAGGCAACAA
1 ATGAAGGCAACAA
*
588247 ACGAAGGC
1 ATGAAGGC
588255 TAATATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.06
Consensus pattern (13 bp):
ATGAAGGCAACAA
Found at i:591693 original size:15 final size:15
Alignment explanation
Indices: 591673--591707 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
591663 CAACTGGTAA
591673 ATTAGCATTTAATAT
1 ATTAGCATTTAATAT
591688 ATTAGCATTTAATAT
1 ATTAGCATTTAATAT
591703 ATTAG
1 ATTAG
591708 AGACGGTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (15 bp):
ATTAGCATTTAATAT
Found at i:613340 original size:21 final size:21
Alignment explanation
Indices: 613316--613356 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
613306 ATAAAAGTCG
613316 AGTCAAACTTA-TTAAATTTAA
1 AGTCAAA-TTATTTAAATTTAA
613337 AGTCAAATTATTTAAATTTA
1 AGTCAAATTATTTAAATTTA
613357 TGTTAATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
AGTCAAATTATTTAAATTTAA
Found at i:622472 original size:30 final size:30
Alignment explanation
Indices: 622407--622472 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
622397 CAATGCTACG
* *
622407 GTCTTCCTAAAGTCGTCGAGTGATCCATAC
1 GTCTTCCTAAAGTCGTCAAGTGATCCAGAC
* * *
622437 ATCTTCCTAAAGTCGTCAAGTGATTCGGAC
1 GTCTTCCTAAAGTCGTCAAGTGATCCAGAC
622467 GTCTTC
1 GTCTTC
622473 TATCATGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (30 bp):
GTCTTCCTAAAGTCGTCAAGTGATCCAGAC
Found at i:627924 original size:20 final size:20
Alignment explanation
Indices: 627854--627920 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
627844 TTCCTAATTT
627854 GCAATGCAAATACGTAAATC
1 GCAATGCAAATACGTAAATC
* *
627874 GTAATGCAAAT-C-TGACTATC
1 GCAATGCAAATACGT-A-AATC
*
627894 GCAATGCGAATACGTAAATC
1 GCAATGCAAATACGTAAATC
627914 GCAATGC
1 GCAATGC
627921 GAATCTGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 2 0.05
20 32 0.84
21 2 0.05
22 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
GCAATGCAAATACGTAAATC
Found at i:627934 original size:20 final size:20
Alignment explanation
Indices: 627871--627942 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
627861 AAATACGTAA
* *
627871 ATCGTAATGCAAATCTGACT
1 ATCGCAATGCGAATCTGACT
*
627891 ATCGCAATGCGAATAC-GTA-A
1 ATCGCAATGCGAAT-CTG-ACT
627911 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
627931 ATCGCAATGCGA
1 ATCGCAATGCGA
627943 TTTACATAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:627941 original size:40 final size:40
Alignment explanation
Indices: 627854--627942 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
627844 TTCCTAATTT
* *
627854 GCAATGCAAATACGTAAATCGTAATGCAAATCTGACTATC
1 GCAATGCGAATACGTAAATCGCAATGCAAATCTGACTATC
*
627894 GCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATC
1 GCAATGCGAATACGTAAATCGCAATGCAAATCTGACTATC
627934 GCAATGCGA
1 GCAATGCGA
627943 TTTACATAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (40 bp):
GCAATGCGAATACGTAAATCGCAATGCAAATCTGACTATC
Found at i:628536 original size:20 final size:20
Alignment explanation
Indices: 628511--628559 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
628501 CAACGAGTGA
628511 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
628531 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
628551 ATCGCAACG
1 ATCGCAACG
628560 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:628642 original size:20 final size:20
Alignment explanation
Indices: 628572--628658 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
628562 AGAATCGCAA
628572 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
628591 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
* ** *
628611 TGTGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
628631 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
628651 TGCAATTT
1 TGCGATTT
628659 AAAGTTTCAG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 9 0.16
20 47 0.84
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:628666 original size:20 final size:20
Alignment explanation
Indices: 628623--628666 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
628613 TGATAGTCAT
* ** *
628623 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCAATTTAAAG
628643 TTTCGTGTTGCAATTTAAAG
1 TTTCGTGTTGCAATTTAAAG
628663 TTTC
1 TTTC
628667 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTAAAG
Found at i:630554 original size:20 final size:20
Alignment explanation
Indices: 630529--630595 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
630519 ATAATAGTTT
630529 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
630549 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
630569 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
630589 ACTATCG
1 ACTATCG
630596 TAACGAGAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:630664 original size:34 final size:34
Alignment explanation
Indices: 630626--630744 Score: 141
Period size: 34 Copynumber: 3.4 Consensus size: 34
630616 GAAATGAAAA
630626 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
* ** *
630660 TCGCATTGCGATAGTCATTTTCGCGTTGCGATTTTC-ATT
1 TCGCATTGCGAT--TC----TCTCGTTGCGATAGTCAAAT
630699 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
630733 TCGCATTGCGAT
1 TCGCATTGCGAT
630745 AATCATTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
33 13 0.19
34 26 0.37
36 2 0.03
37 2 0.03
39 14 0.20
40 13 0.19
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
Found at i:630670 original size:20 final size:20
Alignment explanation
Indices: 630645--630795 Score: 145
Period size: 20 Copynumber: 7.9 Consensus size: 20
630635 GATTCTCTCG
*
630645 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
630665 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
**
630685 TTGCGATTTTC-ATTTCGCA
1 TTGCGATAGTCAATTTCGCA
*
630704 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCAATTTCGCA
*
630718 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
630738 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
630758 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
*
630778 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCAATTTCG
630796 TGTTGTGATT
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.06
17 2 0.02
18 3 0.03
19 13 0.12
20 78 0.72
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:630690 original size:73 final size:73
Alignment explanation
Indices: 630607--630763 Score: 233
Period size: 73 Copynumber: 2.2 Consensus size: 73
630597 AACGAGAGCA
*
630607 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
*
630672 AGTCATTT
66 AATCATTT
* ** ** **
630680 TCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
630745 AATCATTT
66 AATCATTT
630753 TCGCATTGCGA
1 TCGCATTGCGA
630764 TAGTTATTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (73 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGAT
AATCATTT
Found at i:630764 original size:73 final size:74
Alignment explanation
Indices: 630626--630784 Score: 268
Period size: 73 Copynumber: 2.2 Consensus size: 74
630616 GAAATGAAAA
* *
630626 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGA
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATCATTTTCGCATTGCGA
*
630691 T-TTTCA-TT
66 TAGTT-ATTT
630699 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATCATTTTCGCATTGCGA
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATCATTTTCGCATTGCGA
630764 TAGTTATTT
66 TAGTTATTT
630773 TCGCATTGCGAT
1 TCGCATTGCGAT
630785 AGTCATTTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
73 65 0.80
74 16 0.20
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (74 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATCATTTTCGCATTGCGA
TAGTTATTT
Found at i:631384 original size:42 final size:42
Alignment explanation
Indices: 631313--631394 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
631303 CTCCCCTATC
*
631313 GTTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACT
* ** *
631355 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
631395 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:632767 original size:14 final size:14
Alignment explanation
Indices: 632748--632783 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
632738 ATTGTTTAAT
632748 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
632762 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
632776 TGATTTGT
1 TGATTTGT
632784 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:632973 original size:34 final size:33
Alignment explanation
Indices: 632885--632980 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
632875 AAAACAGACT
* **
632885 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
**
632919 ATCGCAATGCGAAATGAAAATCGCAACGAGTTA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
632952 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
632981 CGAAACTACG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:633018 original size:20 final size:20
Alignment explanation
Indices: 632989--633097 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 20
632979 CGCGAAACTA
*
632989 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
633009 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
633029 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
633049 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
* *
633069 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
633089 CGTTGCGAT
1 CGTTGCGAT
633098 TTCCGCGTTG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 76 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:636480 original size:20 final size:20
Alignment explanation
Indices: 636444--636490 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
636434 CAGAATCTCG
636444 TTGCGATTTACAGATTCACA
1 TTGCGATTTACAGATTCACA
*
636464 TTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCACA
636484 TTGCGAT
1 TTGCGAT
636491 AGTCAGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCACA
Found at i:636500 original size:20 final size:19
Alignment explanation
Indices: 636423--636509 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 19
636413 GAAATTCAGT
* *
636423 ATTGCGATAGTCAGAATCTC
1 ATTGCGAT-GTCAGATTCGC
* * *
636443 GTTGCGATTTACAGATTCAC
1 ATTGCGATGT-CAGATTCGC
*
636463 ATTGCGAT-TTACGTATTCGC
1 ATTGCGATGTCA-G-ATTCGC
636483 ATTGCGATAGTCAGATTCGC
1 ATTGCGAT-GTCAGATTCGC
*
636503 GTTGCGA
1 ATTGCGA
636510 ATCTGGAAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 46 0.87
21 1 0.02
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (19 bp):
ATTGCGATGTCAGATTCGC
Found at i:637219 original size:2 final size:2
Alignment explanation
Indices: 637214--637241 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
637204 AAAAATATTC
637214 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
637242 CATTATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:640411 original size:17 final size:18
Alignment explanation
Indices: 640377--640416 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
640367 AATATTATGT
640377 ATTTAATTTATTTAAATA
1 ATTTAATTTATTTAAATA
* *
640395 TTTTACTTTATTT-AATA
1 ATTTAATTTATTTAAATA
640412 ATTTA
1 ATTTA
640417 TTAATATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATTTATTTAAATA
Found at i:642121 original size:18 final size:18
Alignment explanation
Indices: 642098--642153 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
642088 CAGCAGCCAC
*
642098 CGCAGCCATTTATGATGT
1 CGCAGCCATATATGATGT
642116 CGCAGCCATATATGATGT
1 CGCAGCCATATATGATGT
*
642134 CGCAGCCATATATTATGT
1 CGCAGCCATATATGATGT
642152 CG
1 CG
642154 TTGCCTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:642703 original size:26 final size:24
Alignment explanation
Indices: 642632--642703 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
642622 TTATATTTGT
642632 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
642657 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
642679 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
642704 GTTGAACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:646119 original size:16 final size:16
Alignment explanation
Indices: 646107--646140 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
646097 TCAAATAATC
646107 ATAATAAACAATAAGT
1 ATAATAAACAATAAGT
646123 ATAATAAA-AA-AAGT
1 ATAATAAACAATAAGT
646137 ATAA
1 ATAA
646141 CAAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAATAAACAATAAGT
Found at i:646138 original size:14 final size:15
Alignment explanation
Indices: 646107--646145 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
646097 TCAAATAATC
646107 ATAATAAACAATAAGT
1 ATAATAAA-AATAAGT
646123 ATAATAAAAA-AAGT
1 ATAATAAAAATAAGT
*
646137 ATAACAAAA
1 ATAATAAAA
646146 TTTATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:665332 original size:15 final size:17
Alignment explanation
Indices: 665306--665339 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
665296 TATTTAAAAC
665306 AAAATATTTATTAT-TT
1 AAAATATTTATTATATT
665322 AAAAT-TTTATTATATT
1 AAAATATTTATTATATT
665338 AA
1 AA
665340 TTGGGCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATATTTATTATATT
Found at i:683711 original size:23 final size:23
Alignment explanation
Indices: 683685--683735 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
683675 TCAATTTATT
* *
683685 TTTATTTTTTAAAATTTAATAAG
1 TTTATTTTATAAAATTTAATAAA
* *
683708 TTTATTTTATAAGATTTTATAAA
1 TTTATTTTATAAAATTTAATAAA
683731 TTTAT
1 TTTAT
683736 CATTGTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTATTTTATAAAATTTAATAAA
Found at i:685470 original size:17 final size:18
Alignment explanation
Indices: 685437--685470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
685427 ATTAAGTGAA
*
685437 GAAAGAAAGATGGAAAAG
1 GAAAAAAAGATGGAAAAG
685455 GAAAAAAAGA-GGAAAA
1 GAAAAAAAGATGGAAAA
685471 TTCAACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (18 bp):
GAAAAAAAGATGGAAAAG
Found at i:686328 original size:3 final size:3
Alignment explanation
Indices: 686320--686355 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
686310 ATGAAAAAAG
686320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
686356 GAAAGAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:687623 original size:21 final size:21
Alignment explanation
Indices: 687603--687672 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
687593 AAAAGAAATA
687603 AATAAATAAGAA-AA-AATAAT
1 AATAAA-AAGAATAATAATAAT
*
687623 AATTAAAAGAATAATAATAAT
1 AATAAAAAGAATAATAATAAT
*
687644 AAT-AAAA-TATAATATATAAT
1 AATAAAAAGAATAATA-ATAAT
687664 ATATAAAAA
1 A-ATAAAAA
687673 TATTTTCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.26
20 17 0.40
21 11 0.26
22 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (21 bp):
AATAAAAAGAATAATAATAAT
Found at i:687625 original size:3 final size:3
Alignment explanation
Indices: 687617--687674 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
687607 AATAAGAAAA
*
687617 AAT AAT AATT AA- AAG AAT AAT AAT AAT AAT AA- AAT -AT AAT ATAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
687661 AAT ATAT AAA AAT A
1 AAT A-AT AAT AAT A
687675 TTTTCAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
2 6 0.13
3 31 0.67
4 9 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:687660 original size:7 final size:7
Alignment explanation
Indices: 687633--687669 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
687623 AATTAAAAGA
687633 ATAATA-
1 ATAATAT
687639 ATAATA-
1 ATAATAT
*
687645 ATAAAAT
1 ATAATAT
687652 ATAATAT
1 ATAATAT
687659 ATAATAT
1 ATAATAT
687666 ATAA
1 ATAA
687670 AAATATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
ATAATAT
Found at i:687675 original size:22 final size:19
Alignment explanation
Indices: 687617--687671 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
687607 AATAAGAAAA
*
687617 AATAATAATTAAAAGAATAAT
1 AATAATAA-TAAAA-TATAAT
687638 AATAATAATAAAATATAAT
1 AATAATAATAAAATATAAT
687657 ATATAATATATAAAA
1 A-ATAATA-ATAAAA
687672 ATATTTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.19
20 11 0.35
21 14 0.45
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAATAATAAAATATAAT
Found at i:687688 original size:24 final size:25
Alignment explanation
Indices: 687661--687709 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
687651 TATAATATAT
687661 AATATATA-AAAATATTTTCAAAAA
1 AATATATATAAAATATTTTCAAAAA
* *
687685 AATATATATAATATATTTTTAAAAA
1 AATATATATAAAATATTTTCAAAAA
687710 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATATAAAATATTTTCAAAAA
Found at i:687695 original size:33 final size:33
Alignment explanation
Indices: 687655--687768 Score: 108
Period size: 33 Copynumber: 3.4 Consensus size: 33
687645 ATAAAATATA
687655 ATATATAATATATAAAAATATTTTCAAAAAAAT
1 ATATATAATATATAAAAATATTTTCAAAAAAAT
*
687688 ATATATAATATATTTTTAAAAATA-TTT-AAAAAACT
1 ATATATAATATA----TAAAAATATTTTCAAAAAAAT
* * *
687723 ATATATTATATATTTAAAAATATTTTC-CAAAATT
1 ATATA-TA-ATATATAAAAATATTTTCAAAAAAAT
*
687757 ATATATTATATA
1 ATATATAATATA
687769 ATTTTCAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
32 4 0.06
33 21 0.31
34 13 0.19
35 12 0.18
36 5 0.07
37 12 0.18
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATATAATATATAAAAATATTTTCAAAAAAAT
Found at i:687719 original size:35 final size:35
Alignment explanation
Indices: 687667--688047 Score: 157
Period size: 36 Copynumber: 10.9 Consensus size: 35
687657 ATATAATATA
*
687667 TAAAAATATTTTCAAAAAAATATATATAATATATTTT
1 TAAAAATATTTT-AAAAAATTATATAT-ATATATTTT
* *
687704 TAAAAATA-TTTAAAAAACTATATAT-TATATATT
1 TAAAAATATTTTAAAAAATTATATATATATATTTT
**
687737 TAAAAATATTTTCCAAAATTATATATTATATAATTTT
1 TAAAAATATTTTAAAAAATTATATA-TATAT-ATTTT
* * *
687774 CAAAAATGTTTT--AAAATTATATAT-TACATGTTT
1 TAAAAATATTTTAAAAAATTATATATATATAT-TTT
* ***
687807 TCAAAAATGTTTTTTTTAAA-TATATAT-TATA--TT
1 T-AAAAAT-ATTTTAAAAAATTATATATATATATTTT
*
687840 TAAAAATGATTTT--AAAA--CTATATATATA-TTT
1 TAAAAAT-ATTTTAAAAAATTATATATATATATTTT
* * * *
687871 TCAAAATGTTTT-CAAAATTATATATATATATATATA
1 TAAAAATATTTTAAAAAATTATATATATATAT-T-TT
* * * * * * *
687907 TATATATATATATATATATATATATATATATATATATA
1 TAAAAATAT-TTTA-AAAAAT-TATATATATATATTTT
* * * * * *
687945 TATTAAATGTTTTCAAAAATCATATATATATGTTTC
1 TA-AAAATATTTTAAAAAATTATATATATATATTTT
* *
687981 CAAAAA-AGTTTTCCAAAAATTATATAATATATATTTT
1 TAAAAATA-TTTT-AAAAAATTATAT-ATATATATTTT
* ** *
688018 CAAAAACCGTTTT-CAAAATTATATATATAT
1 TAAAAA-TATTTTAAAAAATTATATATATAT
688048 TATATGTATT
Statistics
Matches: 270, Mismatches: 47, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
29 5 0.02
30 11 0.04
31 12 0.04
32 13 0.05
33 33 0.12
34 20 0.07
35 43 0.16
36 56 0.21
37 46 0.17
38 10 0.04
39 8 0.03
40 13 0.05
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (35 bp):
TAAAAATATTTTAAAAAATTATATATATATATTTT
Found at i:687855 original size:29 final size:29
Alignment explanation
Indices: 687820--687901 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 29
687810 AAAATGTTTT
687820 TTTTAAATATATAT-TATATTTAAAAATG
1 TTTTAAATATATATATATATTTAAAAATG
*
687848 ATTTTAAA-ACTATATATATATTTTCAAAATG
1 -TTTTAAATA-TATATATATA-TTTAAAAATG
687879 TTTTCAAAATTATATATATATAT
1 TTTT--AAA-TATATATATATAT
687902 ATATATATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.02
29 12 0.27
30 8 0.18
31 9 0.20
32 4 0.09
33 10 0.22
34 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TTTTAAATATATATATATATTTAAAAATG
Found at i:687877 original size:31 final size:31
Alignment explanation
Indices: 687683--687899 Score: 147
Period size: 31 Copynumber: 6.5 Consensus size: 31
687673 TATTTTCAAA
* * *
687683 AAAATATATATAATATATTTTTAAAAATATTTAA
1 AAAAT-TATAT-ATATATTTTCAAAAATGTTT-T
* *
687717 AAAACTATATATTATATATTT-AAAAATATTTT
1 AAAATTATATA-TATAT-TTTCAAAAATGTTTT
687749 CCAAAATTATATATTATATAATTTTCAAAAATGTTTT
1 --AAAA-T-TATA-TATAT-ATTTTCAAAAATGTTTT
*
687786 AAAATTATATATTACATGTTTTCAAAAATGTTTTTTT
1 AAAATTATATA-T--ATATTTTCAAAAATG---TTTT
*
687823 TAAA-TATATAT-TATATTT-AAAAATGATTTT
1 AAAATTATATATATAT-TTTCAAAAATG-TTTT
*
687853 AAAACTATATATATATTTTC-AAAATGTTTT
1 AAAATTATATATATATTTTCAAAAATGTTTT
687883 CAAAATTATATATATAT
1 -AAAATTATATATATAT
687900 ATATATATAT
Statistics
Matches: 153, Mismatches: 10, Indels: 43
0.74 0.05 0.21
Matches are distributed among these distances:
30 11 0.07
31 31 0.20
32 15 0.10
33 28 0.18
34 24 0.16
35 7 0.05
36 16 0.10
37 21 0.14
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (31 bp):
AAAATTATATATATATTTTCAAAAATGTTTT
Found at i:687895 original size:33 final size:32
Alignment explanation
Indices: 687682--687901 Score: 164
Period size: 33 Copynumber: 6.6 Consensus size: 32
687672 ATATTTTCAA
* * *
687682 AAAAATATATATAATATATTTTTAAAAATATTTAA
1 AAAATTATATAT-ATATA-TTTTAAAAATGTTT-T
* *
687717 AAAACTATATAT-TATATATTTAAAAATATTTT
1 AAAATTATATATATATAT-TTTAAAAATGTTTT
687749 CCAAAATTATATATTATATAATTTTCAAAAATGTTTT
1 --AAAATTATATA-TATAT-ATTTT-AAAAATGTTTT
* *
687786 AAAATTATATATTACATGTTTTCAAAAATGTTTTTTT
1 AAAATTATATA-TATATATTTT-AAAAATG---TTTT
*
687823 TAAA-TATATAT-TATA-TTTAAAAATGATTTT
1 AAAATTATATATATATATTTTAAAAATG-TTTT
* *
687853 AAAA--CTATATATATATTTTCAAAATGTTTT
1 AAAATTATATATATATATTTTAAAAATGTTTT
687883 CAAAATTATATATATATAT
1 -AAAATTATATATATATAT
687902 ATATATATAT
Statistics
Matches: 156, Mismatches: 14, Indels: 32
0.77 0.07 0.16
Matches are distributed among these distances:
29 5 0.03
30 15 0.10
31 13 0.08
32 8 0.05
33 31 0.20
34 24 0.15
35 29 0.19
36 12 0.08
37 19 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (32 bp):
AAAATTATATATATATATTTTAAAAATGTTTT
Found at i:687896 original size:2 final size:2
Alignment explanation
Indices: 687889--687947 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
687879 TTTTCAAAAT
687889 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
687931 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
687948 TAAATGTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.