Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 6 of 21
Found at i:540865 original size:32 final size:33
Alignment explanation
Indices: 540829--540897 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 33
540819 ATATTAAAAA
540829 TAAAATA-ATTATAATATAAA-TATATAAAT-TTT
1 TAAAATATA-TATAATATAAATTAT-TAAATATTT
*
540861 TAAAATTTATATAATATAAATTATTAAATATTT
1 TAAAATATATATAATATAAATTATTAAATATTT
540894 TAAA
1 TAAA
540898 TACGATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TAAAATATATATAATATAAATTATTAAATATTT
Found at i:542493 original size:45 final size:52
Alignment explanation
Indices: 542439--542550 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 52
542429 CATAATTAAT
542439 AAAAAAATATTTTT-A-TATT-AATATAT-ATTTT-A-TAAT-TAAATT-TAA
1 AAAAAAATATTTTTAATTATTAAATAT-TCATTTTGACTAATCTAAATTATAA
*
542484 ATAAAAATATTTTTTAATTATTAAATATTCATTTTGACTAATCTAAATTGATAA
1 AAAAAAATA-TTTTTAATTATTAAATATTCATTTTGACTAATCTAAATT-ATAA
542538 AAAAAAATATTTT
1 AAAAAAATATTTT
542551 AAAGTAATCC
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
45 8 0.15
46 5 0.09
47 1 0.02
48 5 0.09
49 10 0.18
50 1 0.02
51 4 0.07
52 6 0.11
53 4 0.07
54 11 0.20
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (52 bp):
AAAAAAATATTTTTAATTATTAAATATTCATTTTGACTAATCTAAATTATAA
Found at i:546843 original size:19 final size:20
Alignment explanation
Indices: 546806--546843 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
546796 AAATTTAAAT
* *
546806 TAATTTAAATTATTATTTAA
1 TAATTAAAAATATTATTTAA
546826 TAATTAAAAATATT-TTTA
1 TAATTAAAAATATTATTTA
546844 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTAAAAATATTATTTAA
Found at i:547250 original size:20 final size:22
Alignment explanation
Indices: 547211--547253 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
547201 TATTTCAATT
547211 TTATTTAATATTAATAAATAAA
1 TTATTTAATATTAATAAATAAA
*
547233 TTATTTAAT-TT-TTAAATAAA
1 TTATTTAATATTAATAAATAAA
547253 T
1 T
547254 CTAATCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTAATATTAATAAATAAA
Found at i:547662 original size:13 final size:13
Alignment explanation
Indices: 547625--547663 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
547615 GATATATTCA
*
547625 TTTTCTGATTTTT
1 TTTTTTGATTTTT
*
547638 TTTTTTACATTTTT
1 TTTTTT-GATTTTT
547652 TTTTTTGATTTT
1 TTTTTTGATTTT
547664 CTTATAAGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTGATTTTT
Found at i:548626 original size:10 final size:11
Alignment explanation
Indices: 548596--548638 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
548586 TTGGTTAAAT
*
548596 AAGAAAGAAAG
1 AAGAAAAAAAG
*
548607 AAGATGAAAAAG
1 AAGA-AAAAAAG
548619 AA-AAAAAAAG
1 AAGAAAAAAAG
548629 AAGAAAAAAA
1 AAGAAAAAAA
548639 CATATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.30
11 12 0.44
12 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:548634 original size:19 final size:20
Alignment explanation
Indices: 548596--548636 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
548586 TTGGTTAAAT
* *
548596 AAGAAAGAAAGAAGATGAAA
1 AAGAAAGAAAAAAGAAGAAA
548616 AAGAAA-AAAAAAGAAGAAA
1 AAGAAAGAAAAAAGAAGAAA
548635 AA
1 AA
548637 AACATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAAAAAGAAGAAA
Found at i:551586 original size:14 final size:13
Alignment explanation
Indices: 551550--551586 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
551540 TAAAAATTTA
551550 TTAAATTTAATAT
1 TTAAATTTAATAT
551563 TTAAATTTTAATAT
1 TTAAA-TTTAATAT
551577 TTATAATTTA
1 TTA-AATTTA
551587 TTTTTATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:551823 original size:77 final size:77
Alignment explanation
Indices: 551696--551849 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
551686 TTGGTGGAAG
551696 AGAAAGAATAATTTAGTGTGGAGAAATTCTATGGTGCTTATAATTTTTTATGTGATTTTTTTTTT
1 AGAAAGAATAATTTAGTGTGGAGAAATTCTATGGTGCTTATAATTTTTTATGTGATTTTTTTTTT
551761 GAAACTTGCTTT
66 GAAACTTGCTTT
551773 AGAAAGAATAATTTAGTGTGGAGAAATTCTATGGTGCTTATAATTTTTTATGTGATTTTTTTTTT
1 AGAAAGAATAATTTAGTGTGGAGAAATTCTATGGTGCTTATAATTTTTTATGTGATTTTTTTTTT
551838 GAAACTTGCTTT
66 GAAACTTGCTTT
551850 CTAATGAGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (77 bp):
AGAAAGAATAATTTAGTGTGGAGAAATTCTATGGTGCTTATAATTTTTTATGTGATTTTTTTTTT
GAAACTTGCTTT
Found at i:552317 original size:23 final size:23
Alignment explanation
Indices: 552291--552336 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
552281 AAAAATAAAA
552291 AACATGTTATTTTTATTTAATCT
1 AACATGTTATTTTTATTTAATCT
*
552314 AACATTTTATTTTTATTTAATCT
1 AACATGTTATTTTTATTTAATCT
552337 TTGACCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (23 bp):
AACATGTTATTTTTATTTAATCT
Found at i:552699 original size:2 final size:2
Alignment explanation
Indices: 552692--552735 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
552682 TCATTGCATC
552692 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
552734 AT
1 AT
552736 CAACGTTCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:553236 original size:2 final size:2
Alignment explanation
Indices: 553200--553224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
553190 AAATTAATTT
553200 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 T
553225 GATCACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:554751 original size:2 final size:2
Alignment explanation
Indices: 554746--554785 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
554736 GTATATAAAA
* * *
554746 AT AT AT AG AT GT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
554786 TCTGTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554759 original size:20 final size:20
Alignment explanation
Indices: 554734--554772 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
554724 TGAGGGGATA
554734 ATGTATATAAAAATATATAG
1 ATGTATATAAAAATATATAG
* *
554754 ATGTATATATATATATATA
1 ATGTATATAAAAATATATA
554773 TATATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
ATGTATATAAAAATATATAG
Found at i:555486 original size:2 final size:2
Alignment explanation
Indices: 555479--555566 Score: 71
Period size: 2 Copynumber: 45.5 Consensus size: 2
555469 ATATTTCTAG
* *
555479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AG AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
555521 A- AGT A- AT A- ACT -T A- AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
555560 AC AT AT A
1 AT AT AT A
555567 AATTAACAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
1 6 0.08
2 63 0.88
3 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:558257 original size:2 final size:2
Alignment explanation
Indices: 558250--558285 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
558240 GTCATTTTCG
558250 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
558286 TAAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561508 original size:2 final size:2
Alignment explanation
Indices: 561503--561528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
561493 TTTTTTTTTC
561503 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
561529 TGATATTGAA
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:562080 original size:9 final size:8
Alignment explanation
Indices: 562065--562098 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
562055 TAAAATATAA
562065 ATTTTTTT
1 ATTTTTTT
*
562073 ACTTTTTT
1 ATTTTTTT
562081 ATTTTTTTT
1 A-TTTTTTT
562090 ATTTTTTT
1 ATTTTTTT
562098 A
1 A
562099 ATCACGATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:562086 original size:17 final size:17
Alignment explanation
Indices: 562066--562098 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
562056 AAAATATAAA
562066 TTTTTTTACTTTTTTAT
1 TTTTTTTACTTTTTTAT
*
562083 TTTTTTTATTTTTTTA
1 TTTTTTTACTTTTTTA
562099 ATCACGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTACTTTTTTAT
Found at i:562212 original size:24 final size:24
Alignment explanation
Indices: 562164--562232 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
562154 AACGTAATTG
562164 ATAATATTATA-TATTAATATATTA
1 ATAAT-TTATATTATTAATATATTA
*
562188 ATAATTTATATTATATAA-ATTTTA
1 ATAATTTATATTAT-TAATATATTA
* *
562212 AT-ATTTTTATATATTTATATA
1 ATAATTTATAT-TATTAATATA
562233 ATATTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 14 0.38
24 20 0.54
25 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATAATTTATATTATTAATATATTA
Found at i:562343 original size:2 final size:2
Alignment explanation
Indices: 562336--562361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
562326 TTGAAATGAT
562336 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
562362 GCTTATTCAA
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):
TA
Found at i:564619 original size:21 final size:22
Alignment explanation
Indices: 564570--564619 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
564560 TTTTTATATA
564570 AATTTTA-ATAAATTAATAATT
1 AATTTTATATAAATTAATAATT
* *
564591 AATATTATATAAATT-TTAATT
1 AATTTTATATAAATTAATAATT
*
564612 TATTTTAT
1 AATTTTAT
564620 TATATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTATATAAATTAATAATT
Found at i:564988 original size:19 final size:18
Alignment explanation
Indices: 564960--565010 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
564950 AAATTCACCT
564960 TAAA-TTATTTATTATTAA
1 TAAATTTATTTATT-TTAA
*
564978 -AATATTTATTTAATTTAA
1 TAA-ATTTATTTATTTTAA
564996 TAAATTTAATTTATT
1 TAAATTT-ATTTATT
565011 CGAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.07
18 9 0.33
19 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTTATTTATTTTAA
Found at i:565108 original size:47 final size:48
Alignment explanation
Indices: 565057--565151 Score: 106
Period size: 47 Copynumber: 2.0 Consensus size: 48
565047 AGTTAGAATT
* * * *
565057 AATATTTAATAATTAAAATAATA-TTTTTATTTAAATT-TT-ATTATAAA
1 AATATATAATAA-TAAAAAAATAGATTTTAATT-AATTATTAATTATAAA
*
565104 AATATATATTAATAAAAAAATAGATTTTAATTAATTATTAATTATAAA
1 AATATATAATAATAAAAAAATAGATTTTAATTAATTATTAATTATAAA
565152 TATGAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
46 13 0.32
47 19 0.47
48 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (48 bp):
AATATATAATAATAAAAAAATAGATTTTAATTAATTATTAATTATAAA
Found at i:565133 original size:18 final size:18
Alignment explanation
Indices: 565091--565134 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
565081 TTTTATTTAA
* * *
565091 ATTTTATTATAAAAATAT
1 ATTTTAATAAAAAAATAG
*
565109 ATATTAATAAAAAAATAG
1 ATTTTAATAAAAAAATAG
565127 ATTTTAAT
1 ATTTTAAT
565135 TAATTATTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTTTAATAAAAAAATAG
Found at i:565193 original size:16 final size:17
Alignment explanation
Indices: 565172--565205 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
565162 ATGAATAAAT
*
565172 TAAA-TTAAATCAAAAA
1 TAAATTTAAATAAAAAA
565188 TAAATTTAAATAAAAAA
1 TAAATTTAAATAAAAAA
565205 T
1 T
565206 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATTTAAATAAAAAA
Found at i:568137 original size:22 final size:22
Alignment explanation
Indices: 568084--568144 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
568074 AAACAGTAAA
568084 AAATAAAAAAT-AT-ATATTTT
1 AAATAAAAAATAATAATATTTT
*
568104 AAA-AAATTAATAAGTAAT-TTTT
1 AAATAAA-AAATAA-TAATATTTT
568126 AAATAAAAAATAATTAATA
1 AAATAAAAAATAA-TAATA
568145 ACAAAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 1 0.03
22 17 0.53
23 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAAAAAATAATAATATTTT
Found at i:571084 original size:17 final size:17
Alignment explanation
Indices: 571062--571115 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 17
571052 ATAATACATA
571062 TAATATTTTTATTTAAT
1 TAATATTTTTATTTAAT
571079 TAATATGTTTAATAATTTATAT
1 TAATAT-TTT--T-ATTTA-AT
571101 T-ATATTTTTATTTAA
1 TAATATTTTTATTTAA
571116 ATCATTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 1 0.03
17 11 0.34
18 4 0.12
20 4 0.12
21 9 0.28
22 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATATTTTTATTTAAT
Found at i:572933 original size:9 final size:9
Alignment explanation
Indices: 572916--572954 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
572906 TTTATATTCG
572916 TAAATATAA
1 TAAATATAA
*
572925 TAGATATAA
1 TAAATATAA
572934 TATAATTATAA
1 TA-AA-TATAA
572945 TAAATATAA
1 TAAATATAA
572954 T
1 T
572955 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 16 0.62
10 3 0.12
11 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
TAAATATAA
Found at i:572965 original size:20 final size:19
Alignment explanation
Indices: 572917--572965 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
572907 TTATATTCGT
* *
572917 AAATATAATAGATATAATA
1 AAATTTAATAAATATAATA
*
572936 TAATTATAATAAATATAATTA
1 AAATT-TAATAAATATAA-TA
572957 AAATTTAAT
1 AAATTTAAT
572966 TAAAAGCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATTTAATAAATATAATA
Found at i:573421 original size:16 final size:17
Alignment explanation
Indices: 573402--573449 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
573392 ATAATTATTT
*
573402 TTTTATA-TAATTTTAA
1 TTTTATATTAATATTAA
573418 TTTT-TATTAATATTAA
1 TTTTATATTAATATTAA
573434 TATTTATGATTAATAT
1 T-TTTAT-ATTAATAT
573450 ATATTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 13 0.48
17 3 0.11
18 1 0.04
19 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATATTAATATTAA
Found at i:573479 original size:24 final size:23
Alignment explanation
Indices: 573444--573521 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 23
573434 TATTTATGAT
573444 TAATATA-T-ATTATAATTAATAA
1 TAATATATTAATTAT-ATTAATAA
*
573466 TAATATATTAATTATATTTATAA
1 TAATATATTAATTATATTAATAA
*
573489 T--TATATTAAATATGATATAATTAA
1 TAATATATTAATTAT-AT-TAA-TAA
*
573513 AAATATATT
1 TAATATATT
573522 CATATCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
21 11 0.24
22 9 0.20
23 11 0.24
24 8 0.18
26 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
TAATATATTAATTATATTAATAA
Found at i:573497 original size:35 final size:33
Alignment explanation
Indices: 573422--573497 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
573412 TTTTAATTTT
*
573422 TATTAATATTAATATTTATGATTAATATATATTA
1 TATTAATAATAATATTTA-GATTAATATATATTA
*
573456 TAATTAATAATAATATATTA-ATTATATTTATAATTA
1 T-ATTAATAATAATAT-TTAGATTA-ATATAT-ATTA
573492 TATTAA
1 TATTAA
573498 ATATGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
34 5 0.14
35 23 0.64
36 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TATTAATAATAATATTTAGATTAATATATATTA
Found at i:573501 original size:30 final size:32
Alignment explanation
Indices: 573438--573511 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
573428 TATTAATATT
573438 TATGATTAA-TATATATTATAATTAATAATAA
1 TATGATTAATTATATATTATAATTAATAATAA
*
573469 TAT-ATTAATTATAT-TTATAATT-ATATTAAA
1 TATGATTAATTATATATTATAATTAATAAT-AA
573499 TATGATATAATTA
1 TATGAT-TAATTA
573512 AAAATATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 4 0.11
30 18 0.47
31 10 0.26
32 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TATGATTAATTATATATTATAATTAATAATAA
Found at i:573507 original size:20 final size:20
Alignment explanation
Indices: 573438--573511 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
573428 TATTAATATT
573438 TATGAT-TAATATATATTATAA
1 TATGATATAAT-TATATTA-AA
*
573459 T-TAATAATAA-TATATTAATTA
1 TATGAT-ATAATTATATTAA--A
*
573480 TAT-TTATAATTATATTAAA
1 TATGATATAATTATATTAAA
573499 TATGATATAATTA
1 TATGATATAATTA
573512 AAAATATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
19 5 0.12
20 22 0.51
21 12 0.28
22 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATGATATAATTATATTAAA
Found at i:574837 original size:19 final size:20
Alignment explanation
Indices: 574808--574862 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
574798 TAAATTTATT
*
574808 TTTAT-TTATTTTAATCA-A
1 TTTATATTATTTTAATAATA
*
574826 TTTATATTATTTTATTAATA
1 TTTATATTATTTTAATAATA
574846 TTTATA-TATTTT-ATAAT
1 TTTATATTATTTTAATAAT
574863 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 9 0.28
19 16 0.50
20 7 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATATTATTTTAATAATA
Found at i:574864 original size:22 final size:20
Alignment explanation
Indices: 574824--574924 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 20
574814 TATTTTAATC
574824 AATTTATATTATTTT--ATTA
1 AATTTATA-TATTTTAAATTA
574843 ATATTTATATATTTTATAATTA
1 A-ATTTATATATTTTA-AATTA
*
574865 AATTTA-AAATTTTTAATTATTA
1 AATTTATATA-TTTTAA--ATTA
*
574887 AA--TAT-TATTTTAAATCA
1 AATTTATATATTTTAAATTA
* *
574904 AATTAATATAATTTAAATTA
1 AATTTATATATTTTAAATTA
574924 A
1 A
574925 CAAAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
17 5 0.08
19 15 0.23
20 24 0.37
21 10 0.15
22 11 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTATATATTTTAAATTA
Found at i:575433 original size:12 final size:11
Alignment explanation
Indices: 575404--575444 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
575394 TATAAATATT
575404 ATTAAAAAATA
1 ATTAAAAAATA
*
575415 ATTAAAATATA
1 ATTAAAAAATA
575426 ACTTAAAAAATA
1 A-TTAAAAAATA
575438 ATATAAA
1 AT-TAAA
575445 TATAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
ATTAAAAAATA
Found at i:575435 original size:23 final size:22
Alignment explanation
Indices: 575390--575449 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
575380 AATATATTAC
*
575390 ATAATATAAATATTATTAAAAA
1 ATAATATAAATATAATTAAAAA
575412 ATAAT-TAAAATATAACTTAAAAA
1 ATAATAT-AAATATAA-TTAAAAA
575435 ATAATATAAATATAA
1 ATAATATAAATATAA
575450 AAATTCCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.35
23 20 0.59
24 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATATAAATATAATTAAAAA
Found at i:575740 original size:4 final size:4
Alignment explanation
Indices: 575731--575755 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
575721 AAAACCACTC
575731 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
575756 TTCAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:575771 original size:8 final size:8
Alignment explanation
Indices: 575754--575786 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
575744 ATAAATAAAT
575754 AATTCAAAA
1 AATTC-AAA
575763 AATTC-AA
1 AATTCAAA
575770 AATTCAAA
1 AATTCAAA
575778 AATTCAAA
1 AATTCAAA
575786 A
1 A
575787 TGTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 11 0.48
9 5 0.22
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTCAAA
Found at i:575780 original size:15 final size:15
Alignment explanation
Indices: 575754--575797 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
575744 ATAAATAAAT
575754 AATTCAAAAAATTCAA
1 AATTC-AAAAATTCAA
575770 AATTCAAAAATTCAA
1 AATTCAAAAATTCAA
*
575785 AATGTAAAAAATT
1 AAT-TCAAAAATT
575798 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.27
Consensus pattern (15 bp):
AATTCAAAAATTCAA
Found at i:577405 original size:23 final size:25
Alignment explanation
Indices: 577371--577440 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
577361 AATAAAAATT
577371 AGCCACCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTGACAAACAACA
*
577395 AGCCA-CAATTTTTGACAAACAAAA
1 AGCCACCAATTTTTGACAAACAACA
577419 AGAAACCACC-ATTTTTGACAAA
1 AG---CCACCAATTTTTGACAAA
577441 TACAAAGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 3 0.08
24 21 0.52
27 15 0.38
28 1 0.03
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (25 bp):
AGCCACCAATTTTTGACAAACAACA
Found at i:577435 original size:27 final size:26
Alignment explanation
Indices: 577373--577469 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
577363 TAAAAATTAG
* *
577373 CCACCAATTTTGACAAACAACAAG--
1 CCACCATTTTTGACAAACAAAAAGAA
*
577397 CCACAATTTTTGACAAACAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAG-AA
* *
577424 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAG-AA
* *
577451 CCACTATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
577470 CATGGTGGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 21 0.35
27 39 0.65
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (26 bp):
CCACCATTTTTGACAAACAAAAAGAA
Found at i:577488 original size:24 final size:25
Alignment explanation
Indices: 577457--577514 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
577447 GTAACCACTA
*
577457 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
577481 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
577507 TTGTTGAC
1 TTGTTGAC
577515 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:582002 original size:23 final size:25
Alignment explanation
Indices: 581968--582037 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
581958 AATAAAAATT
581968 AGCCACCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTGACAAACAACA
* *
581992 AGCCA-CAATTTTTGATAAACAAAA
1 AGCCACCAATTTTTGACAAACAACA
582016 AGAAACCACC-ATTTTTGACAAA
1 AG---CCACCAATTTTTGACAAA
582038 TACAAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.08
24 20 0.53
27 14 0.37
28 1 0.03
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTTGACAAACAACA
Found at i:582030 original size:27 final size:26
Alignment explanation
Indices: 581970--582066 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
581960 TAAAAATTAG
* *
581970 CCACCAATTTTGACAAACAACAAG--
1 CCACCATTTTTGACAAACAAAAAGAA
* *
581994 CCACAATTTTTGATAAACAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAG-AA
* *
582021 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAG-AA
*
582048 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
582067 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 20 0.34
27 39 0.66
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (26 bp):
CCACCATTTTTGACAAACAAAAAGAA
Found at i:582085 original size:24 final size:25
Alignment explanation
Indices: 582054--582111 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
582044 GTAACCACCA
582054 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAATGGTGGCTT
582078 TTGTTGACAAACACAAATGGTGGCTT
1 TTGTTGACAAACAC-AATGGTGGCTT
582104 TTGTTGAC
1 TTGTTGAC
582112 TAACCACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 14 0.44
26 18 0.56
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAATGGTGGCTT
Found at i:583985 original size:16 final size:16
Alignment explanation
Indices: 583953--583996 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
583943 TAAATAAATT
*
583953 TTTATTTGTATTT--A
1 TTTATTTATATTTAAA
*
583967 TTTATTTATTTTTAAA
1 TTTATTTATATTTAAA
583983 TTTATTTATATTTA
1 TTTATTTATATTTA
583997 GTTCATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTATTTATATTTAAA
Found at i:585328 original size:13 final size:13
Alignment explanation
Indices: 585310--585335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585300 CAATTTTTTG
585310 TGTATCGATACAT
1 TGTATCGATACAT
585323 TGTATCGATACAT
1 TGTATCGATACAT
585336 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:585347 original size:32 final size:33
Alignment explanation
Indices: 585290--585353 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
585280 TACAAGCCAA
**
585290 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
585323 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
585354 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:593433 original size:13 final size:13
Alignment explanation
Indices: 593415--593440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
593405 CAATTTTTTG
593415 TGTATCGATACAT
1 TGTATCGATACAT
593428 TGTATCGATACAT
1 TGTATCGATACAT
593441 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:593452 original size:32 final size:33
Alignment explanation
Indices: 593395--593458 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
593385 TACAAGCCCA
**
593395 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
593428 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
593459 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:594016 original size:12 final size:13
Alignment explanation
Indices: 593994--594036 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
593984 ATATTTTTTG
593994 TAATTAATTATAA
1 TAATTAATTATAA
*
594007 TAA-TATTTATTATA
1 TAATTAATTA-TA-A
594021 TAATTAATTATAA
1 TAATTAATTATAA
594034 TAA
1 TAA
594037 ACACGAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 6 0.24
15 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTAATTATAA
Found at i:594028 original size:27 final size:25
Alignment explanation
Indices: 593982--594036 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
593972 TTTTCGTTGT
*
593982 TAATATTTTTTGTAATTAATTATAA
1 TAATATTTTTTATAATTAATTATAA
594007 TAATATTTATTATATAATTAATTATAA
1 TAATATTT-TT-TATAATTAATTATAA
594034 TAA
1 TAA
594037 ACACGAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.30
26 2 0.07
27 17 0.63
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TAATATTTTTTATAATTAATTATAA
Found at i:596177 original size:19 final size:18
Alignment explanation
Indices: 596153--596188 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
596143 TTGATAATTT
*
596153 ATATATTTATATCATATTA
1 ATATATTCATAT-ATATTA
596172 ATATATTCATATATATT
1 ATATATTCATATATATT
596189 TTTATTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATTCATATATATTA
Found at i:596883 original size:18 final size:19
Alignment explanation
Indices: 596851--596888 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
596841 TTGATAATTC
596851 ATATATTTATATCATATTA
1 ATATATTTATATCATATTA
596870 ATATATTT-TATCATATTA
1 ATATATTTATATCATATTA
596888 A
1 A
596889 CTTTACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATTTATATCATATTA
Found at i:596924 original size:17 final size:17
Alignment explanation
Indices: 596902--596949 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
596892 TACTTAAATT
596902 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
596919 ATTTTAATATATTA-ATAA
1 ATTTT-ATAT-TTATATAA
*
596937 TTTTTAT-TTTATA
1 ATTTTATATTTATA
596950 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 7 0.26
18 12 0.44
19 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:596936 original size:18 final size:18
Alignment explanation
Indices: 596902--596956 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
596892 TACTTAAATT
596902 ATTTT-ATATTTATATAA
1 ATTTTAATATTTATATAA
596919 ATTTTAATATATTA-AT-A
1 ATTTTAATAT-TTATATAA
596936 ATTTT--TATTT-TAT-A
1 ATTTTAATATTTATATAA
596950 ATTTTAA
1 ATTTTAA
596957 AATATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
14 10 0.30
15 3 0.09
17 11 0.33
18 6 0.18
19 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAATATTTATATAA
Found at i:599229 original size:21 final size:21
Alignment explanation
Indices: 599205--599249 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
599195 TAAAAATAAA
599205 TAATAAATATA-ATTATATATT
1 TAATAAATATATATT-TATATT
* *
599226 TAATACATATATATTTATTTT
1 TAATAAATATATATTTATATT
599247 TAA
1 TAA
599250 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAAATATATATTTATATT
Found at i:600927 original size:38 final size:38
Alignment explanation
Indices: 600863--600941 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
600853 TCTAATACTA
* * * *
600863 TATGTTGTTTGTAGTTTTTTTTAATAAAAATAAGAAAGT
1 TATGATGTGTGTAGTTTTTTTAAATAAAAATAA-AAAAT
600902 TATGATGTGTGTAG-TTTTTTAAATAAAAATAAAAAAT
1 TATGATGTGTGTAGTTTTTTTAAATAAAAATAAAAAAT
600939 TAT
1 TAT
600942 ATTTTCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 7 0.19
38 17 0.47
39 12 0.33
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (38 bp):
TATGATGTGTGTAGTTTTTTTAAATAAAAATAAAAAAT
Found at i:603245 original size:31 final size:30
Alignment explanation
Indices: 603177--603246 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
603167 GAAAAAAAGT
* * *
603177 TAAAAGTTGAATATAAAGTACATATCTTAA
1 TAAAAATTAAATATAAAGCACATATCTTAA
603207 TAAAAAATTAAATATAAAGCACAATATCTTAA
1 T-AAAAATTAAATATAAAGCAC-ATATCTTAA
603239 TAAAAATT
1 TAAAAATT
603247 TATCTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 24 0.69
32 10 0.29
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (30 bp):
TAAAAATTAAATATAAAGCACATATCTTAA
Found at i:605867 original size:28 final size:29
Alignment explanation
Indices: 605798--605869 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
605788 ATAATAATTG
605798 ATATTAT-ATAA-ATTTTAAAATATTTAT
1 ATATTATAATAATATTTTAAAATATTTAT
* * * *
605825 ATATT-TATTTTATATTTT-AATTATTTTT
1 ATATTATA-ATAATATTTTAAAATATTTAT
605853 ATATTATAATAATATTT
1 ATATTATAATAATATTT
605870 AACATTGGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.03
27 5 0.14
28 22 0.63
29 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTATAATAATATTTTAAAATATTTAT
Found at i:606045 original size:34 final size:34
Alignment explanation
Indices: 606001--606068 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
605991 GCTCGCATAA
*
606001 TTTTTAAGTCAAAGGTTACATTTCATTGCAATAC
1 TTTTAAAGTCAAAGGTTACATTTCATTGCAATAC
606035 TTTTAAAGTCAAAGGTTACATTTCATTGCAATAC
1 TTTTAAAGTCAAAGGTTACATTTCATTGCAATAC
606069 AATATTGGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (34 bp):
TTTTAAAGTCAAAGGTTACATTTCATTGCAATAC
Found at i:606605 original size:19 final size:18
Alignment explanation
Indices: 606573--606611 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
606563 AAAAATTAAT
* *
606573 TAAAATATATTATAAAATA
1 TAAAAAATAATAT-AAATA
606592 TAAAAAATAATATAAATA
1 TAAAAAATAATATAAATA
606610 TA
1 TA
606612 TGAATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAATAATATAAATA
Found at i:606663 original size:17 final size:18
Alignment explanation
Indices: 606636--606685 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
606626 TTTTTATAAC
*
606636 ATAAATTATTTATTATTA
1 ATAATTTATTTATTATTA
*
606654 A-AATTTATTTA-TATCA
1 ATAATTTATTTATTATTA
606670 ATAATTTATTT-TTATT
1 ATAATTTATTTATTATT
606686 TTTAAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.19
17 21 0.78
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAATTTATTTATTATTA
Found at i:606665 original size:33 final size:31
Alignment explanation
Indices: 606618--606685 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
606608 TATATGAATA
606618 TATTAAAATTTTTATAAC-ATAAATTATTTAT
1 TATTAAAATTTTTATAACAATAAATTATTT-T
* *
606649 TATTAAAATTTATTTATATCAATAATTTATTTT
1 TATTAAAA-TT-TTTATAACAATAAATTATTTT
606682 TATT
1 TATT
606686 TTTAAATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.25
32 2 0.06
33 12 0.38
34 10 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTAAAATTTTTATAACAATAAATTATTTT
Found at i:607172 original size:17 final size:16
Alignment explanation
Indices: 607141--607176 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
607131 ATTATATTTT
*
607141 TATATTCGTATTTAAA
1 TATATTCGAATTTAAA
607157 TATATATCGAATTTAAA
1 TATAT-TCGAATTTAAA
607174 TAT
1 TAT
607177 TAAATACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (16 bp):
TATATTCGAATTTAAA
Found at i:607655 original size:27 final size:27
Alignment explanation
Indices: 607625--607688 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
607615 TAGTCACCAA
*
607625 TTTTGACAAACAAAAAAGAACTATC-AT
1 TTTTGACAAACAAAAAAGAACCA-CAAT
* *
607652 TTTTGACAAACACAAAGGAACCACAAT
1 TTTTGACAAACAAAAAAGAACCACAAT
607679 TTTTGACAAA
1 TTTTGACAAA
607689 TACAAAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.25
Consensus pattern (27 bp):
TTTTGACAAACAAAAAAGAACCACAAT
Found at i:609595 original size:21 final size:21
Alignment explanation
Indices: 609569--609610 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
609559 ATCTGTTGAA
* *
609569 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTATGGAGTAT
609590 ACTCCACCTGCTATGGAGTAT
1 ACTCCACCTGCTATGGAGTAT
609611 TACTTGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
ACTCCACCTGCTATGGAGTAT
Found at i:612175 original size:27 final size:27
Alignment explanation
Indices: 612126--612217 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
612116 CCTATTTTGT
** *
612126 AATAAAAATTAATCATCAATTTTGAAA
1 AATAAAAAAGAATCATCATTTTTGAAA
612153 AATAAAAAAGAA--ATACTATTTTT-AATA
1 AATAAAAAAGAATCAT-C-ATTTTTGAA-A
* *
612180 AATACAAAAGAATCATCATTTTTGACA
1 AATAAAAAAGAATCATCATTTTTGAAA
612207 AATATAAAAAG
1 AATA-AAAAAG
612218 TGATTTTTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 38 0.73
28 7 0.13
29 2 0.04
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (27 bp):
AATAAAAAAGAATCATCATTTTTGAAA
Found at i:613814 original size:26 final size:24
Alignment explanation
Indices: 613768--613815 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
613758 TTTATAAAAA
*
613768 TTTATATAAAATAAATTATTAAAT
1 TTTATATAAAATAAATAATTAAAT
613792 TTTATATAAATATATAATAATTAA
1 TTTATATAAA-ATA-AATAATTAA
613816 TATATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATATAAAATAAATAATTAAAT
Found at i:613845 original size:20 final size:18
Alignment explanation
Indices: 613777--613857 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 18
613767 ATTTATATAA
*
613777 AATAAATTATTAAAT-TTT
1 AATAAA-TATTAAATAATT
613795 ATATAAATA-TATAATAATT
1 A-ATAAATATTA-AATAATT
*
613814 AATATATAATTACAATAATTT
1 AATAAAT-ATTA-AATAA-TT
613835 AATAAATATTAAATTAATT
1 AATAAATATTAAA-TAATT
613854 AATA
1 AATA
613858 CGATATTACT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.04
18 11 0.21
19 17 0.33
20 14 0.27
21 8 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATATTAAATAATT
Found at i:613978 original size:27 final size:26
Alignment explanation
Indices: 613916--614009 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
613906 TAAATACGAA
*
613916 ATAAT-AAAT-TAATTAAATAAAAAT
1 ATAATAAAATATAAATAAATAAAAAT
613940 -TAA-AAAATTATAAATAAATTAAAAAT
1 ATAATAAAA-TATAAATAAA-TAAAAAT
*
613966 ATAATAAAATATAATTAAAATATAAAA-
1 ATAATAAAATATAAAT-AAATA-AAAAT
*
613993 ATAATATAATATAAATA
1 ATAATAAAATATAAATA
614010 TTTAAATTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
23 6 0.10
24 1 0.02
25 7 0.12
26 8 0.14
27 25 0.43
28 11 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATAAAATATAAATAAATAAAAAT
Found at i:613988 original size:11 final size:11
Alignment explanation
Indices: 613945--613990 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
613935 AAAATTAAAA
613945 AATTATAAATA-
1 AATTA-AAATAT
613956 AATTAAAAATAT
1 AATT-AAAATAT
613968 AA-TAAAATAT
1 AATTAAAATAT
613978 AATTAAAATAT
1 AATTAAAATAT
613989 AA
1 AA
613991 AAATAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.28
11 20 0.62
12 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAAAATAT
Found at i:613995 original size:19 final size:18
Alignment explanation
Indices: 613936--613996 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 18
613926 AATTAAATAA
* *
613936 AAATTAAAAAATTATAAAT
1 AAATTAAAATA-TAAAAAT
613955 AAATTAAAAATATAATAAAAT
1 AAATT-AAAATAT-A-AAAAT
613976 ATAATTAAAATATAAAAAT
1 A-AATTAAAATATAAAAAT
613995 AA
1 AA
613997 TATAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 1 0.03
19 12 0.33
20 7 0.19
21 12 0.33
22 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTAAAATATAAAAAT
Found at i:613998 original size:11 final size:10
Alignment explanation
Indices: 613961--614010 Score: 64
Period size: 11 Copynumber: 4.7 Consensus size: 10
613951 AAATAAATTA
613961 AAAATATAAT
1 AAAATATAAT
613971 AAAATATAATT
1 AAAATATAA-T
*
613982 AAAATATAAA
1 AAAATATAAT
613992 AATAATATAAT
1 AA-AATATAAT
614003 ATAAATAT
1 A-AAATAT
614011 TTAAATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.31
11 23 0.66
12 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATATAAT
Found at i:614016 original size:22 final size:22
Alignment explanation
Indices: 613952--614007 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
613942 AAAAATTATA
*
613952 AATA-AATTAAAAATATAATAA-
1 AATATAATT-AAAATATAAAAAT
613973 AATATAATTAAAATATAAAAAT
1 AATATAATTAAAATATAAAAAT
613995 AATATAATATAAA
1 AATATAAT-TAAA
614008 TATTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 15 0.48
22 12 0.39
23 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATAATTAAAATATAAAAAT
Found at i:616749 original size:11 final size:11
Alignment explanation
Indices: 616733--616807 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
616723 AAATATTTAA
616733 ATATTTATATT
1 ATATTTATATT
* *
616744 ATATTTGTTTTTT
1 ATA-TT-TATATT
*
616757 ATATTTATAAT
1 ATATTTATATT
616768 ATATTT-TATAT
1 ATATTTATAT-T
* *
616779 AAATTTTAAATT
1 ATA-TTTATATT
*
616791 ATTTTTATATT
1 ATATTTATATT
616802 ATATTT
1 ATATTT
616808 GGGTTTGAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
10 2 0.04
11 27 0.57
12 9 0.19
13 9 0.19
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:617764 original size:3 final size:3
Alignment explanation
Indices: 617751--617813 Score: 117
Period size: 3 Copynumber: 20.7 Consensus size: 3
617741 TAAATGAAGA
617751 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
617797 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
617814 ATATAAATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:618537 original size:19 final size:19
Alignment explanation
Indices: 618515--618556 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
618505 GGTTGATATT
618515 ATTTAAATATATTT-TTTAA
1 ATTT-AATATATTTATTTAA
*
618534 ATTTAATATTTTTATTTAA
1 ATTTAATATATTTATTTAA
618553 ATTT
1 ATTT
618557 TTATAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTAATATATTTATTTAA
Found at i:618996 original size:20 final size:20
Alignment explanation
Indices: 618941--618996 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
618931 TAAATAACAA
* *
618941 AATTATATATTAAAAAATTT
1 AATTAAATATTAAAATATTT
*
618961 AATTAAAT-TCATAAATATTGT
1 AATTAAATATTA-AAATATT-T
618982 AA-TAAATATTAAAAT
1 AATTAAATATTAAAAT
618997 TTATTTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTAAATATTAAAATATTT
Found at i:619396 original size:20 final size:21
Alignment explanation
Indices: 619354--619398 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
619344 AGTTATATTT
*
619354 TTATATTTTATTATATTATAA
1 TTATATTTTATAATATTATAA
619375 TTATATTTATATAATA-TA-AA
1 TTATATTT-TATAATATTATAA
619395 TTAT
1 TTAT
619399 TAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATTTTATAATATTATAA
Found at i:619402 original size:27 final size:26
Alignment explanation
Indices: 619368--619426 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
619358 ATTTTATTAT
* *
619368 ATTATAATTATATTTATA-TAATATAA
1 ATTATAATT-TATTAAAATTAATATAA
619394 ATTATTAATTTATTAAAATTAATATAA
1 ATTA-TAATTTATTAAAATTAATATAA
619421 A-TATAA
1 ATTATAA
619427 AATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 3 0.10
26 12 0.41
27 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTATAATTTATTAAAATTAATATAA
Found at i:619439 original size:16 final size:16
Alignment explanation
Indices: 619418--619475 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
619408 AAAATTAATA
619418 TAAATATAAAATATTT
1 TAAATATAAAATATTT
*
619434 TAAATAT--AAT-TAT
1 TAAATATAAAATATTT
* *
619447 AAAATAATAAAATA-TA
1 TAAAT-ATAAAATATTT
619463 TAAATATAAAATA
1 TAAATATAAAATA
619476 AGTTCACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
15 8 0.24
16 14 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:619458 original size:8 final size:7
Alignment explanation
Indices: 619414--619475 Score: 56
Period size: 7 Copynumber: 8.6 Consensus size: 7
619404 TATTAAAATT
619414 AATAT-A
1 AATATAA
619420 AATATAA
1 AATATAA
*
619427 AATATTTTA
1 AATA--TAA
619436 AATAT-A
1 AATATAA
*
619442 ATTATAA
1 AATATAA
619449 AATAATAA
1 AAT-ATAA
619457 AATATATA
1 AATATA-A
619465 AATATAA
1 AATATAA
619472 AATA
1 AATA
619476 AGTTCACAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 10 0.21
7 17 0.36
8 14 0.30
9 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AATATAA
Found at i:619739 original size:42 final size:45
Alignment explanation
Indices: 619649--619810 Score: 132
Period size: 38 Copynumber: 3.7 Consensus size: 45
619639 CAAAGTATTG
*
619649 AATATAATAT-AATTAT-AA-AATATAAAAA-AT-TAATTAA--T-
1 AATATAATATAAATAATAAATAATATAAAAATATATAA-TAATTTA
* *
619687 AATATAATAT-AATAATAAATAATATAAAAATATTTTA-AATTT-
1 AATATAATATAAATAATAAATAATATAAAAATATATAATAATTTA
* * *
619729 TATATAATATAAATTATAAATATATTAAAATAAATATATAATAATTTA
1 AATATAATATAAATAATAAATA-A-TATAA-AAATATATAATAATTTA
619777 AATATAATTATAATATAATAAAT-ATATAAAAATA
1 AATATAA-TATAA-ATAATAAATAATATAAAAATA
619811 ACATAAATAC
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
38 15 0.15
39 2 0.02
40 12 0.12
41 2 0.02
42 12 0.12
43 10 0.10
44 1 0.01
45 4 0.04
46 13 0.13
47 9 0.09
48 7 0.07
49 5 0.05
50 8 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (45 bp):
AATATAATATAAATAATAAATAATATAAAAATATATAATAATTTA
Found at i:619797 original size:36 final size:37
Alignment explanation
Indices: 619732--619810 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 37
619722 TAAATTTTAT
*
619732 ATAATATAAATTATAAATATATTAAAATAAATATATA
1 ATAATATAAATTATAAATATAATAAAATAAATATATA
* * *
619769 ATAATTTAAA-TATAATTATAATATAATAAATATATA
1 ATAATATAAATTATAAATATAATAAAATAAATATATA
*
619805 AAAATA
1 ATAATA
619811 ACATAAATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
ATAATATAAATTATAAATATAATAAAATAAATATATA
Found at i:619799 original size:20 final size:20
Alignment explanation
Indices: 619649--619802 Score: 90
Period size: 20 Copynumber: 7.5 Consensus size: 20
619639 CAAAGTATTG
619649 AATATAATATAATTATAAAATAT
1 AATA-AATATAATTAT--AATAT
*
619672 AAAAAAT-TAATTAATAATAT
1 AATAAATATAATT-ATAATAT
619692 AATATAATAATAA--ATAATAT
1 AATA-AAT-ATAATTATAATAT
* *
619712 AA-AAATAT-TTTA-AATTT
1 AATAAATATAATTATAATAT
*
619729 TATATAATATAAATTATAAATAT
1 AATA-AATAT-AATTAT-AATAT
*
619752 ATTAAA-ATAAATATATAATA-
1 AATAAATAT-AAT-TATAATAT
*
619772 ATTTAAATATAATTATAATAT
1 A-ATAAATATAATTATAATAT
619793 AATAAATATA
1 AATAAATATA
619803 TAAAAATAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
17 7 0.07
18 5 0.05
19 6 0.06
20 33 0.31
21 30 0.29
22 12 0.11
23 12 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAATATAATTATAATAT
Found at i:619810 original size:14 final size:15
Alignment explanation
Indices: 619744--619811 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 15
619734 AATATAAATT
*
619744 ATAAATATATTA-AA
1 ATAAATATATAATAA
619758 ATAAATATATAATAA
1 ATAAATATATAATAA
*
619773 TTTAAATATAATTATAATATA
1 -AT-AA-AT-A-TATAATA-A
619794 ATAAATATATAA-AA
1 ATAAATATATAATAA
619808 ATAA
1 ATAA
619812 CATAAATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
14 16 0.36
15 3 0.07
16 6 0.14
17 3 0.07
18 4 0.09
19 3 0.07
20 8 0.18
21 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATATATAATAA
Found at i:619977 original size:27 final size:25
Alignment explanation
Indices: 619927--619978 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
619917 TTGTGTAGTC
*
619927 TAATAAATATAAAAAATTGATAATT
1 TAATAAATATAAAAAATTAATAATT
619952 TAATAAATCCATAAAAAA-TAATTAATT
1 TAATAAAT--ATAAAAAATTAA-TAATT
619979 ACTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
26 2 0.09
27 13 0.57
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
TAATAAATATAAAAAATTAATAATT
Found at i:620106 original size:20 final size:19
Alignment explanation
Indices: 620068--620110 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
620058 TTAGTTATAT
620068 ATTAAAGATAATATTATTA
1 ATTAAAGATAATATTATTA
* *
620087 ATTAAATATATATTTTATTA
1 ATTAAAGATA-ATATTATTA
620107 ATTA
1 ATTA
620111 TTAATTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAAAGATAATATTATTA
Found at i:620131 original size:27 final size:27
Alignment explanation
Indices: 620080--620135 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
620070 TAAAGATAAT
*
620080 ATTATTAATTAAATATATATTTTATTA
1 ATTATTAATTAAATATATATATTATTA
620107 ATTATTAATTATACATA-ATA-ATTATTA
1 ATTATTAATTA-A-ATATATATATTATTA
620134 AT
1 AT
620136 ATCAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 19 0.73
28 4 0.15
29 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATTAATTAAATATATATATTATTA
Found at i:620810 original size:18 final size:19
Alignment explanation
Indices: 620782--620821 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
620772 TTAAATTATA
620782 AAAAGTTTAAACTTAATTT
1 AAAAGTTTAAACTTAATTT
* *
620801 AAAA-TTTAAAGTTATTTT
1 AAAAGTTTAAACTTAATTT
620819 AAA
1 AAA
620822 CTAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAAGTTTAAACTTAATTT
Found at i:634740 original size:21 final size:20
Alignment explanation
Indices: 634705--634748 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
634695 TAATATTAAT
*
634705 AAATAGTAAAAATAGAATAA
1 AAATAGTAAAAATAGAAAAA
*
634725 AAATATTAATAAATAGAAAAA
1 AAATAGTAA-AAATAGAAAAA
634746 AAA
1 AAA
634749 CTATATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATAGTAAAAATAGAAAAA
Found at i:634746 original size:20 final size:20
Alignment explanation
Indices: 634705--634747 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
634695 TAATATTAAT
634705 AAATAGTAAAAATAGAATAA
1 AAATAGTAAAAATAGAATAA
*
634725 AAATATTAATAAATAGAA-AA
1 AAATAGTAA-AAATAGAATAA
634745 AAA
1 AAA
634748 ACTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAATAGTAAAAATAGAATAA
Found at i:635919 original size:12 final size:12
Alignment explanation
Indices: 635902--635932 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
635892 TTAATAAAAA
635902 ATTAATTTTTAT
1 ATTAATTTTTAT
635914 ATTAATTTTTAT
1 ATTAATTTTTAT
635926 -TTAATTT
1 ATTAATTT
635933 AATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTAATTTTTAT
Found at i:636092 original size:24 final size:24
Alignment explanation
Indices: 636043--636092 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
636033 TTTTTTTGTT
* **
636043 TAAATTTAAATTTGATCTAATTAA
1 TAAATTTAAATTTCATCTAAAAAA
636067 TAAATTTAAATTATCAT-TAAAAAA
1 TAAATTTAAATT-TCATCTAAAAAA
636091 TA
1 TA
636093 TTAAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATTTAAATTTCATCTAAAAAA
Found at i:636138 original size:22 final size:21
Alignment explanation
Indices: 636110--636162 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
636100 ATTAAAAATT
636110 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTA-A
636132 TATTTTTATAATTAAATTTAA
1 TATTTTTATAATTAAATTTAA
636153 TAATTTTTAT
1 T-ATTTTTAT
636163 TTTATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTATAATTAAATTTAA
Found at i:636170 original size:23 final size:23
Alignment explanation
Indices: 636110--636171 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
636100 ATTAAAAATT
*
636110 TATTTTTATATTA-ATATTTATA
1 TATTTTTATATTATAAATTTATA
*
636132 TATTTTTATAAT-TAAATTTA-A
1 TATTTTTATATTATAAATTTATA
*
636153 TAATTTTTATTTTATAAAT
1 T-ATTTTTATATTATAAAT
636172 AATTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 2 0.06
22 26 0.79
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTTTATATTATAAATTTATA
Found at i:636436 original size:16 final size:16
Alignment explanation
Indices: 636417--636447 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
636407 CATTTATTTT
636417 ATTAGAATAAAATAAA
1 ATTAGAATAAAATAAA
*
636433 ATTATAATAAAATAA
1 ATTAGAATAAAATAA
636448 TTATTCTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATTAGAATAAAATAAA
Found at i:636561 original size:18 final size:19
Alignment explanation
Indices: 636529--636565 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
636519 AGAATATTAT
*
636529 AAAATTAATTTTTTTAAAA
1 AAAATTAATTATTTTAAAA
636548 AAAATTAA-TATTTTAAAA
1 AAAATTAATTATTTTAAAA
636566 TAATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTAATTATTTTAAAA
Found at i:638006 original size:26 final size:25
Alignment explanation
Indices: 637954--638013 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
637944 TTGATTCGAG
* * *
637954 AAAATATTTTTATTTTTATTTTTAA
1 AAAATATTTTTATTTATAATTTGAA
637979 AAAATAATTTTTATTTATAATTTGAA
1 AAAAT-ATTTTTATTTATAATTTGAA
*
638005 AATATATTT
1 AAAATATTT
638014 GATTTAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AAAATATTTTTATTTATAATTTGAA
Found at i:639924 original size:23 final size:21
Alignment explanation
Indices: 639898--639959 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 21
639888 GTATTATCAC
639898 TATTTAAAATAAAATTTATAAAT
1 TATTT-AAATAAAATTTAT-AAT
* * *
639921 TATTTTTATTAATATTTATAAT
1 TA-TTTAAATAAAATTTATAAT
639943 TAAATTTAAATAAAATT
1 T--ATTTAAATAAAATT
639960 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 4 0.13
23 22 0.73
24 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTAAATAAAATTTATAAT
Found at i:643252 original size:33 final size:33
Alignment explanation
Indices: 643196--643260 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
643186 TACAAGCCAA
* *
643196 TGTATCGATACAATTTTTTGTGTATCAATACAT
1 TGTATCGATACAATCTTTGGTGTATCAATACAT
*
643229 TGTATCGATAC-ATACTTTGGTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCAATACA
643261 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCAATACAT
Found at i:647094 original size:11 final size:11
Alignment explanation
Indices: 647070--647099 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
647060 TTTAATTTAT
647070 TAAAATAA-AA
1 TAAAATAATAA
647080 TAAAATAATAA
1 TAAAATAATAA
647091 TAAAATAAT
1 TAAAATAAT
647100 TATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:647684 original size:16 final size:16
Alignment explanation
Indices: 647634--647686 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
647624 TTTAAGATAT
647634 TTTATATT-TATATAAA
1 TTTATATTATATA-AAA
*
647650 TTT-TAATATATTAATAA
1 TTTATATTATA-TAA-AA
647667 TTTATATTATATAAAA
1 TTTATATTATATAAAA
647683 TTTA
1 TTTA
647687 AAATATGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 10 0.32
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:647754 original size:19 final size:20
Alignment explanation
Indices: 647719--647756 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
647709 ATATTTTAAT
647719 TATTTTATATATCTATATCA
1 TATTTTATATATCTATATCA
647739 TATTTGTATA-AT-TATATC
1 TATTT-TATATATCTATATC
647757 TAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTTTATATATCTATATCA
Found at i:648283 original size:11 final size:11
Alignment explanation
Indices: 648267--648296 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
648257 TAATTTTGAG
648267 TATGATATGAA
1 TATGATATGAA
648278 TATGATATGAA
1 TATGATATGAA
*
648289 TATAATAT
1 TATGATAT
648297 ATTTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (11 bp):
TATGATATGAA
Found at i:649531 original size:34 final size:34
Alignment explanation
Indices: 649486--649703 Score: 235
Period size: 34 Copynumber: 6.4 Consensus size: 34
649476 TAAAAACCAC
* *
649486 CATTTAATCAACAATGGCAACCTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
* *
649520 CATTTAGTCAACAATGGTAAGCC-ACCAAATCACC
1 CATTTAATCAACAATGGTAA-CCTACCAAATCACT
** * * **
649554 CATTTAATCAACAAAAGTAAGCTATCAAATTTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
* * *
649588 TATTTAATCAACAATGGTAAGCTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
* * *
649622 CATTTAGTCAACAATGGCAAACC-ACCAAATCACC
1 CATTTAATCAACAATGG-TAACCTACCAAATCACT
* *
649656 CATTTAATCAACAATGGTAAACTACTAAATCACT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
649690 -ATTTAATCAACAAT
1 CATTTAATCAACAAT
649704 TCTCCACTTG
Statistics
Matches: 152, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
33 18 0.12
34 129 0.85
35 5 0.03
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAACCTACCAAATCACT
Found at i:649599 original size:68 final size:68
Alignment explanation
Indices: 649485--649703 Score: 260
Period size: 68 Copynumber: 3.2 Consensus size: 68
649475 GTAAAAACCA
* * *
649485 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAAT
649550 CAC
66 CAC
** * * * * *
649553 CCATTTAATCAACAAAAGTAAGCTATCAAATTTCTTATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAAT
*
649618 CTC
66 CAC
* * * * * * *
649621 TCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAAT
649686 CA-
66 CAC
*
649688 CTATTTAATCAACAAT
1 CCATTTAATCAACAAT
649704 TCTCCACTTG
Statistics
Matches: 123, Mismatches: 28, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
67 13 0.11
68 110 0.89
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:649663 original size:102 final size:101
Alignment explanation
Indices: 649487--649703 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 101
649477 AAAAACCACC
* *
649487 ATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAAATCA
* **
649552 CCCATTTAATCAACAAAAGTAAGCTA-TCAAATTTCTT
66 CCCATTTAATCAACAAAAGTAAACTACT-AAATCAC-T
* *
649589 ATTTAATCAACAATGGTAAGCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAAATCA
**
649654 CCCATTTAATCAACAATGGTAAACTACTAAATCACT
66 CCCATTTAATCAACAAAAGTAAACTACTAAATCACT
649690 ATTTAATCAACAAT
1 ATTTAATCAACAAT
649704 TCTCCACTTG
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
101 15 0.14
102 89 0.85
103 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAAATCA
CCCATTTAATCAACAAAAGTAAACTACTAAATCACT
Found at i:653397 original size:19 final size:19
Alignment explanation
Indices: 653370--653413 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
653360 TCACGTGTAC
* *
653370 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
653389 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
653408 AGTACC
1 AGTACC
653414 TCGACAACCA
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:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:653764 original size:34 final size:33
Alignment explanation
Indices: 653720--653935 Score: 218
Period size: 34 Copynumber: 6.4 Consensus size: 33
653710 AAAAATTACT
*
653720 ATTTAATCAACAATGGCAACTTACCAAATCTCCC
1 ATTTAATCAACAATGGTAAC-TACCAAATCTCCC
* * *
653754 ATTTAGTCAACAATGGTAAGCCACCAAATCACCC
1 ATTTAATCAACAATGGTAA-CTACCAAATCTCCC
* * * *
653788 ATTTAATCAACAATGATAAATTACCAAATTTCTC
1 ATTTAATCAACAATGGT-AACTACCAAATCTCCC
*
653822 ATTTAATTAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAA-CTACCAAATCTCCC
* * * *
653856 ATTTAGTCAACAATGGCAAACTACCAAATCACTC
1 ATTTAATCAACAATGG-TAACTACCAAATCTCCC
* * **
653890 ATTTAATCAACAATGATAAACTACTAAAT-TATC
1 ATTTAATCAACAATGGT-AACTACCAAATCTCCC
653923 ATTTAATCAACAA
1 ATTTAATCAACAA
653936 CAAGATCTCA
Statistics
Matches: 150, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
33 17 0.11
34 128 0.85
35 5 0.03
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.28
Consensus pattern (33 bp):
ATTTAATCAACAATGGTAACTACCAAATCTCCC
Found at i:653834 original size:68 final size:68
Alignment explanation
Indices: 653720--653935 Score: 272
Period size: 68 Copynumber: 3.2 Consensus size: 68
653710 AAAAATTACT
* * * *
653720 ATTTAATCAACAATGGCAACTTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAAATTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAATCA
653785 CCC
66 CCC
** * * *
653788 ATTTAATCAACAATGATAAATTACCAAATTTCTCATTTAATTAACAATGGTAAGCTACCAAATCT
1 ATTTAATCAACAATGGCAAATTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAATCA
653853 CCC
66 CCC
* * * * * * *
653856 ATTTAGTCAACAATGGCAAACTACCAAATCACTCATTTAATCAACAATGATAAACTACTAAATTA
1 ATTTAATCAACAATGGCAAATTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAATCA
*
653921 -TC
66 CCC
653923 ATTTAATCAACAA
1 ATTTAATCAACAA
653936 CAAGATCTCA
Statistics
Matches: 125, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
67 13 0.10
68 112 0.90
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.28
Consensus pattern (68 bp):
ATTTAATCAACAATGGCAAATTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAATCA
CCC
Found at i:653896 original size:102 final size:102
Alignment explanation
Indices: 653712--653935 Score: 328
Period size: 102 Copynumber: 2.2 Consensus size: 102
653702 GGTTTGGTAA
* * *
653712 AAATTACT-ATTTAATCAACAATGGCAACTTACCAAATCTCCCATTTAGTCAACAATGGTAAGCC
1 AAATTTCTCATTTAATCAACAATGGCAACTTACCAAATCTCCCATTTAGTCAACAATGGCAAACC
*
653776 ACCAAATCACCCATTTAATCAACAATGATAAATTACC
66 ACCAAATCACCCATTTAATCAACAATGATAAACTACC
* *
653813 AAATTTCTCATTTAATTAACAATGGTAAGC-TACCAAATCTCCCATTTAGTCAACAATGGCAAAC
1 AAATTTCTCATTTAATCAACAATGGCAA-CTTACCAAATCTCCCATTTAGTCAACAATGGCAAAC
* * *
653877 TACCAAATCACTCATTTAATCAACAATGATAAACTACT
65 CACCAAATCACCCATTTAATCAACAATGATAAACTACC
*
653915 AAA-TTATCATTTAATCAACAA
1 AAATTTCTCATTTAATCAACAA
653936 CAAGATCTCA
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 23 0.21
102 86 0.78
103 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (102 bp):
AAATTTCTCATTTAATCAACAATGGCAACTTACCAAATCTCCCATTTAGTCAACAATGGCAAACC
ACCAAATCACCCATTTAATCAACAATGATAAACTACC
Found at i:654801 original size:20 final size:20
Alignment explanation
Indices: 654778--654821 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
654768 TCAAATAAAG
*
654778 TAAAATATATT-TAATAATT
1 TAAAATATATTATAAAAATT
*
654797 TTAAATATATTATAAAAATT
1 TAAAATATATTATAAAAATT
654817 TAAAA
1 TAAAA
654822 CTAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATATATTATAAAAATT
Found at i:654802 original size:19 final size:20
Alignment explanation
Indices: 654780--654817 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
654770 AAATAAAGTA
*
654780 AAATATATT-TAATAATTTT
1 AAATATATTATAAAAATTTT
654799 AAATATATTATAAAAATTT
1 AAATATATTATAAAAATTT
654818 AAAACTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATATTATAAAAATTTT
Found at i:654848 original size:44 final size:45
Alignment explanation
Indices: 654800--654909 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
654790 AATAATTTTA
* * *
654800 AATATA-TT-ATAAAAATTTAAAACTAATATAATAGTACATATTAT
1 AATATATTTAATAAAAATATAAAAATAATATAATA-TACATAATAT
* *
654844 AATATATTTAAATATAAATATAAAAATAATATAATATTCATAATAT
1 AATATATTT-AATAAAAATATAAAAATAATATAATATACATAATAT
* *
654890 AATATTTTTAAATATAAATA
1 AATATATTT-AATAAAAATA
654910 ATAGGAAGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 6 0.11
45 2 0.04
46 27 0.47
47 22 0.39
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (45 bp):
AATATATTTAATAAAAATATAAAAATAATATAATATACATAATAT
Found at i:654886 original size:14 final size:14
Alignment explanation
Indices: 654869--654895 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
654859 AAATATAAAA
654869 ATAATATAATATTC
1 ATAATATAATATTC
654883 ATAATATAATATT
1 ATAATATAATATT
654896 TTTAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATAATATTC
Done.