Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold77
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: 1374688
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.34
Warning! 47366 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:543596 original size:25 final size:27
Alignment explanation
Indices: 543562--543633 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
543552 TAAAAAAATA
543562 TAAATTTAATT-TTTATAATT-AATTT
1 TAAATTTAATTATTTATAATTAAATTT
*
543587 TAAATTTAATTATTTATATTTAAATTT
1 TAAATTTAATTATTTATAATTAAATTT
543614 T-AATTTAA--ATTTA-AATTAAA
1 TAAATTTAATTATTTATAATTAAA
543634 AATTTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.14
24 5 0.12
25 11 0.26
26 15 0.35
27 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAAATTTAATTATTTATAATTAAATTT
Found at i:543641 original size:27 final size:27
Alignment explanation
Indices: 543611--543662 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
543601 TATATTTAAA
* *
543611 TTTTAATTTAAATTTAAATTAAAAATT
1 TTTTAAATTAAATTTAAATAAAAAATT
**
543638 TTTTAAATTATTTTTAAATAAAAAA
1 TTTTAAATTAAATTTAAATAAAAAA
543663 ATTCTAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTTAAATTAAATTTAAATAAAAAATT
Found at i:550020 original size:2 final size:2
Alignment explanation
Indices: 550015--550075 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
550005 AAAAAATTAA
* * *
550015 AT AT AT TT AT GT AT AT A- AT AT AT TT AT AT CAT 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
*
550057 AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
550076 AAAGAAACAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:550536 original size:3 final size:3
Alignment explanation
Indices: 550528--550568 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
550518 TTTCAATTCA
550528 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
550569 ATTACAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:550701 original size:23 final size:23
Alignment explanation
Indices: 550675--550720 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
550665 AAATACGTGT
*
550675 TTAGTATTTGTGCTCCATATATA
1 TTAGTACTTGTGCTCCATATATA
550698 TTAGTACTTGTGCTCCATATATA
1 TTAGTACTTGTGCTCCATATATA
550721 CTCGGACATG
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:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (23 bp):
TTAGTACTTGTGCTCCATATATA
Found at i:550901 original size:22 final size:20
Alignment explanation
Indices: 550860--550904 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
550850 TTTTAAAATT
550860 TATTTTTATATTAATATAAA
1 TATTTTTATATTAATATAAA
*
550880 TATTTTTATAATTAAATTTAAA
1 TATTTTTAT-ATT-AATATAAA
550902 TAT
1 TAT
550905 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTATATTAATATAAA
Found at i:551090 original size:39 final size:37
Alignment explanation
Indices: 551022--551099 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 37
551012 CATTGGATAG
*
551022 ATTTAAAATATAATATAATTTTTTAAATATAAAAAAA
1 ATTTAAAATATAATATAATCTTTTAAATATAAAAAAA
*
551059 ATTTAAAATAATTAA-ATATATCTTTTAAATATATAAAAA
1 ATTTAAAAT-A-TAATATA-ATCTTTTAAATATAAAAAAA
551098 AT
1 AT
551100 ATAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
37 9 0.25
38 4 0.11
39 23 0.64
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (37 bp):
ATTTAAAATATAATATAATCTTTTAAATATAAAAAAA
Found at i:551799 original size:23 final size:24
Alignment explanation
Indices: 551764--551817 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
551754 TATTTAAAAT
*
551764 TTTATATTTTTATAATAT-ATTTA
1 TTTATATTTTTATAATATAATATA
*
551787 TTTAT-TTTGTTATATTATAATATA
1 TTTATATTT-TTATAATATAATATA
551811 TTTATAT
1 TTTATAT
551818 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 13 0.50
24 9 0.35
25 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATATTTTTATAATATAATATA
Found at i:551829 original size:28 final size:28
Alignment explanation
Indices: 551750--551843 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 28
551740 CATCTAAATT
* *
551750 TATTTATTTAAAATTTTATATTTTTATAATA
1 TATTTATAT-AAATTTTA-A-TATTATAATA
* * *
551781 TATTTAT-TTATTTTGTTATATTATAATA
1 TATTTATATAAATTT-TAATATTATAATA
551809 TATTTATATAAATTTTAATATT-TAATA
1 TATTTATATAAATTTTAATATTATAATA
551836 -ATTTATAT
1 TATTTATAT
551844 TATATAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 8 0.15
27 5 0.09
28 22 0.41
29 10 0.19
30 2 0.04
31 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
TATTTATATAAATTTTAATATTATAATA
Found at i:552707 original size:16 final size:16
Alignment explanation
Indices: 552685--552725 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
552675 ATTAATTTAA
552685 ATTTAATATTTAAATT
1 ATTTAATATTTAAATT
* *
552701 TTTTAAT-TTTAAGTT
1 ATTTAATATTTAAATT
552716 ATTT-ATATTT
1 ATTTAATATTT
552726 TAATCCGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.10
15 13 0.62
16 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTAATATTTAAATT
Found at i:552711 original size:22 final size:23
Alignment explanation
Indices: 552680--552726 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
552670 TTCGAATTAA
552680 TTTAAATTTAA-TATTTAAATTT
1 TTTAAATTTAAGTATTTAAATTT
* *
552702 TTTAATTTTAAGTTATTTATATTT
1 TTTAAATTTAAG-TATTTAAATTT
552726 T
1 T
552727 AATCCGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
24 11 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTAAATTTAAGTATTTAAATTT
Found at i:552720 original size:15 final size:15
Alignment explanation
Indices: 552685--552728 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
552675 ATTAATTTAA
552685 ATTTAATATTTAAATT
1 ATTTAAT-TTTAAATT
* *
552701 TTTTAATTTTAAGTT
1 ATTTAATTTTAAATT
552716 ATTTATATTTTAA
1 ATTTA-ATTTTAA
552729 TCCGTGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
ATTTAATTTTAAATT
Found at i:553533 original size:38 final size:35
Alignment explanation
Indices: 553463--553533 Score: 81
Period size: 38 Copynumber: 1.9 Consensus size: 35
553453 TAGATAAATA
**
553463 ATCTTAATTAATTAAATTTAAATAATTTAATTTTT
1 ATCTTAATTAATTAAATTTAAATAATAAAATTTTT
553498 ATCTTGAATTAAATTTAAATTTTAAA-AATAAAATTT
1 ATCTT-AATT-AA-TTAAA-TTTAAATAATAAAATTT
553534 AATCAATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
35 5 0.17
36 4 0.13
37 2 0.07
38 13 0.43
39 6 0.20
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
ATCTTAATTAATTAAATTTAAATAATAAAATTTTT
Found at i:553570 original size:23 final size:22
Alignment explanation
Indices: 553526--553571 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
553516 ATTTTAAAAA
*
553526 TAAAATTTAATCAATCTCAAAT
1 TAAAATTTAATCAAACTCAAAT
* *
553548 TAAATTTTAAATCAAACTTAAAT
1 TAAAATTT-AATCAAACTCAAAT
553571 T
1 T
553572 TCTTAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAATTTAATCAAACTCAAAT
Found at i:554063 original size:18 final size:18
Alignment explanation
Indices: 554019--554074 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
554009 TTATATAAAT
* *
554019 ATATAATATTTAAAATATA
1 ATATAAAATTAAAAAT-TA
554038 ATTATAAAATTAAAAATTA
1 A-TATAAAATTAAAAATTA
554057 ATATAAACA-TAAAAATTA
1 ATATAAA-ATTAAAAATTA
554075 TCAAATCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 15 0.45
19 5 0.15
20 13 0.39
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAAAATTAAAAATTA
Found at i:554195 original size:14 final size:14
Alignment explanation
Indices: 554171--554223 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
554161 TATTTAAAAT
554171 ATTTT-ATATATAA
1 ATTTTAATATATAA
554184 ATTTTAATATATTAATA
1 ATTTTAATATA-T-A-A
*
554201 ATTTTTATTATATAA
1 A-TTTTAATATATAA
554216 ATTTTAAT
1 ATTTTAAT
554224 TACGTACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.15
14 11 0.33
15 3 0.09
16 2 0.06
17 3 0.09
18 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTAATATATAA
Found at i:554213 original size:32 final size:32
Alignment explanation
Indices: 554159--554223 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 32
554149 TTATTATAAT
554159 TATATTTAAAATATTTTATATATAAATTTTAA
1 TATATTTAAAATATTTTATATATAAATTTTAA
554191 TATA-TTAATAAT-TTTTATTATATAAATTTTAA
1 TATATTTAA-AATATTTTA-TATATAAATTTTAA
554223 T
1 T
554224 TACGTACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATATTTAAAATATTTTATATATAAATTTTAA
Found at i:554220 original size:15 final size:15
Alignment explanation
Indices: 554167--554225 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
554157 ATTATATTTA
554167 AAATATTTTA-TATAT
1 AAAT-TTTTATTATAT
*
554182 AAA-TTTTAATATATT
1 AAATTTTTATTATA-T
554197 AATAATTTTTATTATAT
1 -A-AATTTTTATTATAT
*
554214 AAATTTTAATTA
1 AAATTTTTATTA
554226 CGTACTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 14 0.38
16 2 0.05
17 3 0.08
18 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTTTTATTATAT
Found at i:554247 original size:11 final size:11
Alignment explanation
Indices: 554231--554283 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
554221 AATTACGTAC
554231 TTATATTATAT
1 TTATATTATAT
554242 TTATATTTTATAT
1 TTATA--TTATAT
554255 TT-TAATTAT-T
1 TTAT-ATTATAT
*
554265 TTTTATTATAT
1 TTATATTATAT
554276 TTATATTA
1 TTATATTA
554284 AGATATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 8 0.22
11 18 0.50
12 1 0.03
13 9 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTATAT
Found at i:554279 original size:16 final size:18
Alignment explanation
Indices: 554231--554282 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
554221 AATTACGTAC
554231 TTATATTATATTTATATT
1 TTATATTATATTTATATT
* *
554249 TTATATTTTAATTAT-TT
1 TTATATTATATTTATATT
554266 TT-TATTATATTTATATT
1 TTATATTATATTTATATT
554283 AAGATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 10 0.34
17 6 0.21
18 13 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTATATTTATATT
Found at i:554284 original size:25 final size:28
Alignment explanation
Indices: 554242--554294 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
554232 TATATTATAT
*
554242 TTATATTTTATATTTTAA-TTATTTTTTA
1 TTATATTTTATA-TTTAAGATATTTTTTA
554270 TTATA-TTTATA-TTAAGATATTTTTT
1 TTATATTTTATATTTAAGATATTTTTT
554295 TAAGTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 8 0.35
27 6 0.26
28 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (28 bp):
TTATATTTTATATTTAAGATATTTTTTA
Found at i:554608 original size:33 final size:31
Alignment explanation
Indices: 554566--554644 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
554556 ATAATTATTT
*
554566 TTAAAATTTTATATTTATATAAATATTAATATA
1 TTAATATTTTATATTTATA-AAAT-TTAATATA
*
554599 TTAATATTTTATATATATAAAATTTAATATA
1 TTAATATTTTATATTTATAAAATTTAATATA
* *
554630 TTTATAATTTATATT
1 TTAATATTTTATATT
554645 ATTTTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 20 0.49
32 4 0.10
33 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAATATTTTATATTTATAAAATTTAATATA
Found at i:554628 original size:16 final size:16
Alignment explanation
Indices: 554567--554640 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
554557 TAATTATTTT
* *
554567 TAAAATTTTATATTTA
1 TAAAATTTAATATATA
554583 TATAAATATTAATATAT-
1 TA-AAAT-TTAATATATA
* *
554600 TAATATTTTATATATA
1 TAAAATTTAATATATA
*
554616 TAAAATTTAATATATT
1 TAAAATTTAATATATA
*
554632 TATAATTTA
1 TAAAATTTA
554641 TATTATTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.17
16 26 0.55
17 6 0.13
18 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTAATATATA
Found at i:554647 original size:16 final size:16
Alignment explanation
Indices: 554561--554648 Score: 51
Period size: 16 Copynumber: 5.5 Consensus size: 16
554551 ATATCATAAT
554561 TATT-TTTAAAATTTTA
1 TATTATTTAAAA-TTTA
* *
554577 TATTTATATAAATATTAA
1 TA-TTATTTAAA-ATTTA
*
554595 TA-TA-TTAATATTT-
1 TATTATTTAAAATTTA
*
554608 TATATATATAAAATTTA
1 TAT-TATTTAAAATTTA
*
554625 -ATATATTTATAATTTA
1 TAT-TATTTAAAATTTA
554641 TATTATTT
1 TATTATTT
554649 TTATATATTA
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
13 2 0.04
14 3 0.05
15 5 0.09
16 30 0.55
17 4 0.07
18 10 0.18
19 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTTA
Found at i:554651 original size:27 final size:26
Alignment explanation
Indices: 554520--554666 Score: 95
Period size: 27 Copynumber: 5.4 Consensus size: 26
554510 AAGTTTATTT
* *
554520 TATTTAT-TTTATTTTATTTTTAAAA
1 TATTTATATTTATATTATTTTTAATA
* *
554545 T-TTTATATATCATAATTATTTTTAAAA
1 TATTTATAT-TTAT-ATTATTTTTAATA
* * *
554572 T-TTTATATTTATATAAATATTAATA
1 TATTTATATTTATATTATTTTTAATA
* *
554597 TATTAATATTTTATATATATAAAATTTAATA
1 TATTTATA-TTTATAT-TAT---TTTTAATA
554628 TATTTATAATTTATATTATTTTTATATA
1 TATTTAT-ATTTATATTATTTTTA-ATA
554656 TTATTTA-ATTT
1 -TATTTATATTT
554667 TGCAAATGAG
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
24 5 0.05
25 12 0.12
26 11 0.11
27 35 0.36
28 4 0.04
29 6 0.06
30 3 0.03
31 19 0.20
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTATATTTATATTATTTTTAATA
Found at i:554877 original size:18 final size:17
Alignment explanation
Indices: 554850--554884 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
554840 AAAATTAAAA
*
554850 TTAAAATTTAATTTATT
1 TTAAAATTTAAATTATT
554867 TTAATAATTTAAATTATT
1 TTAA-AATTTAAATTATT
554885 ATTTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAAATTTAAATTATT
Found at i:556517 original size:21 final size:21
Alignment explanation
Indices: 556464--556518 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
556454 ATTTATATAT
556464 TTTATAATTAAATAAA-AATAA
1 TTTA-AATTAAATAAATAATAA
* *
556485 TTT---TTTATTAAATAATAA
1 TTTAAATTAAATAAATAATAA
556503 TTTAAATTAAATAAAT
1 TTTAAATTAAATAAAT
556519 TGATATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
21 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTAAATAAATAATAA
Found at i:557117 original size:50 final size:50
Alignment explanation
Indices: 557040--557298 Score: 217
Period size: 50 Copynumber: 5.2 Consensus size: 50
557030 AGGTGTTGTT
* *
557040 ATTGTTGACTA-TTTTTATCCA-CTTTTGATAATTGAGAAAGGTGATCGTA
1 ATTGTTGACTATTTTTTATCAATC-TTTGATAATCGAGAAAGGTGATCGTA
* * * *
557089 ATTGTTGACTATTTTTTATCAA-CTTTTGACAATCGA-AAGAGATGGTTGTA
1 ATTGTTGACTATTTTTTATCAATC-TTTGATAATCGAGAA-AGGTGATCGTA
* * * * * *
557139 ATTATTTACTATTCTTCATTAATCTTTGACAATCGA-AAGAGGTGATCGTA
1 ATTGTTGACTATTTTTTATCAATCTTTGATAATCGAGAA-AGGTGATCGTA
* * * * * *
557189 ATTGTTGACTATTCTTCACCAATCTTT-ACTAATCGAGATAGGTAATCATA
1 ATTGTTGACTATTTTTTATCAATCTTTGA-TAATCGAGAAAGGTGATCGTA
* * * *
557239 ATTGTTGATTATTTTTTA-CTAATATTTGATAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTTTTTATC-AATCTTTGATAATCGAGAAAGGTGATCGTA
557289 ATTGTTGACT
1 ATTGTTGACT
557299 CTAAGCAACT
Statistics
Matches: 172, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
49 15 0.09
50 154 0.90
51 3 0.02
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (50 bp):
ATTGTTGACTATTTTTTATCAATCTTTGATAATCGAGAAAGGTGATCGTA
Found at i:557703 original size:28 final size:27
Alignment explanation
Indices: 557667--557757 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 27
557657 CTTATTTTAA
557667 TTTTATCTTAATTTTGGAGACTTGAATT
1 TTTTATCTTAATTTTGGAGA-TTGAATT
* *
557695 TTTTTTCTTAATTTTGGA-ATAAATAAATT
1 TTTTATCTTAATTTTGGAGAT---TGAATT
557724 AATTTTATCTTAATTTTGGAGATTCGAATT
1 --TTTTATCTTAATTTTGGAGATT-GAATT
557754 TTTT
1 TTTT
557758 TCAATTTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 21 0.40
29 6 0.12
30 4 0.08
31 17 0.33
32 2 0.04
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (27 bp):
TTTTATCTTAATTTTGGAGATTGAATT
Found at i:557738 original size:31 final size:31
Alignment explanation
Indices: 557663--557743 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
557653 TAGACTTATT
** *
557663 TTAATTTTATCTTAATTTTGG-AGACTTGAA
1 TTAATTTTATCTTAATTTTGGAAGAAATAAA
* *
557693 TT--TTTTTTCTTAATTTTGGAATAAATAAA
1 TTAATTTTATCTTAATTTTGGAAGAAATAAA
557722 TTAATTTTATCTTAATTTTGGA
1 TTAATTTTATCTTAATTTTGGA
557744 GATTCGAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 16 0.38
29 7 0.17
30 2 0.05
31 17 0.40
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (31 bp):
TTAATTTTATCTTAATTTTGGAAGAAATAAA
Found at i:557849 original size:22 final size:22
Alignment explanation
Indices: 557821--557862 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
557811 ATTACAATAT
557821 TATTTTTAT-ATTAACATTTATA
1 TATTTTTATAATTAA-ATTTATA
557843 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
557863 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:559415 original size:20 final size:20
Alignment explanation
Indices: 559390--559469 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
559380 TTTAATAATA
559390 TAATAATTAAATATAAAAAT
1 TAATAATTAAATATAAAAAT
* *
559410 TAATAAATATATATAAATATAT
1 TAATAATTAAATATAAA-A-AT
*
559432 TAA-AATT-TATAT-AAAAT
1 TAATAATTAAATATAAAAAT
* *
559449 AAATTATTAAAATATATAAAA
1 TAATAATT-AAATATA-AAAA
559470 AAACTCCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 2 0.04
20 24 0.51
21 4 0.09
22 9 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATAATTAAATATAAAAAT
Found at i:559456 original size:24 final size:25
Alignment explanation
Indices: 559422--559471 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
559412 ATAAATATAT
* *
559422 ATAAATATATTAAAATTTATATAAA
1 ATAAATATATTAAAATATATAAAAA
559447 ATAAAT-TATTAAAATATATAAAAA
1 ATAAATATATTAAAATATATAAAAA
559471 A
1 A
559472 ACTCCTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAAATATATTAAAATATATAAAAA
Found at i:559796 original size:13 final size:13
Alignment explanation
Indices: 559778--559810 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
559768 TATACATGAT
559778 TATAATATATAAA
1 TATAATATATAAA
559791 TAT-A-ATATAAA
1 TATAATATATAAA
559802 TATAATATA
1 TATAATATA
559811 AATAGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.56
12 2 0.11
13 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAATATATAAA
Found at i:559800 original size:11 final size:11
Alignment explanation
Indices: 559784--559814 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
559774 TGATTATAAT
559784 ATATAAATATA
1 ATATAAATATA
559795 ATATAAATATA
1 ATATAAATATA
559806 ATATAAATA
1 ATATAAATA
559815 GATAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAAATATA
Found at i:560186 original size:24 final size:23
Alignment explanation
Indices: 560162--560209 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
560152 TATTAAAATT
560162 TTAAATATAAATATTATTTATATTTG
1 TTAAATAT-AATA-TATTTATA-TTG
*
560188 TTAAATATATTATATTTATATT
1 TTAAATATAATATATTTATATT
560210 AATATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 8 0.38
25 3 0.14
26 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTAAATATAATATATTTATATTG
Found at i:560224 original size:19 final size:19
Alignment explanation
Indices: 560202--560240 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
560192 ATATATTATA
560202 TTTATATTA-ATATTAAAAT
1 TTTATATTATAT-TTAAAAT
560221 TTTATATTATATTTAAAAT
1 TTTATATTATATTTAAAAT
560240 T
1 T
560241 ATCAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATATTATATTTAAAAT
Found at i:560236 original size:25 final size:26
Alignment explanation
Indices: 560188--560241 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
560178 TTTATATTTG
*
560188 TTAAATATATTATATTTATATTAATA
1 TTAAATATATTATATTTATATTAAAA
*
560214 TTAAA-ATTTTATA-TTATATTTAAAA
1 TTAAATATATTATATTTATA-TTAAAA
560239 TTA
1 TTA
560242 TCAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 15 0.60
26 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATATATTATATTTATATTAAAA
Found at i:561752 original size:16 final size:15
Alignment explanation
Indices: 561739--561773 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
561729 AATTTTTAAT
561739 TTATTTTGAATTTAGA
1 TTATTTT-AATTTAGA
561755 TTATTTTAATTTATGA
1 TTATTTTAATTTA-GA
561771 TTA
1 TTA
561774 AATAAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (15 bp):
TTATTTTAATTTAGA
Found at i:561783 original size:21 final size:21
Alignment explanation
Indices: 561759--561799 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
561749 TTTAGATTAT
*
561759 TTTAAT-TTATGATTAAATAAG
1 TTTAATATT-TGAGTAAATAAG
561780 TTTAATATTTGAGTAAATAA
1 TTTAATATTTGAGTAAATAA
561800 AATTTGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTAATATTTGAGTAAATAAG
Found at i:561980 original size:16 final size:16
Alignment explanation
Indices: 561953--561996 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
561943 ATTATTCGAT
*
561953 TCATTTTGAATTTAAA
1 TCATTTTAAATTTAAA
*
561969 TTATTTTAAATTTAAA
1 TCATTTTAAATTTAAA
561985 TCATTTTAAATT
1 TCATTTTAAATT
561997 ATTCGAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (16 bp):
TCATTTTAAATTTAAA
Found at i:562409 original size:3 final size:3
Alignment explanation
Indices: 562403--562431 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
562393 TTTGTTCTGA
562403 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
562432 TTACTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:564748 original size:37 final size:37
Alignment explanation
Indices: 564662--564749 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
564652 AATATGTTTA
*
564662 ATTAATTAATTATTTTTTTGAATTAAATAAAATAATGT
1 ATTAATTAA-TAATTTTTTGAATTAAATAAAATAATGT
*
564700 ATTAAAT-ATAATTTTTT-AATTAACAATAAAATAAT-T
1 ATTAATTAATAATTTTTTGAATT-A-AATAAAATAATGT
*
564736 TTTAATTAATAATT
1 ATTAATTAATAATT
564750 ATAGATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
35 4 0.09
36 15 0.35
37 18 0.42
38 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (37 bp):
ATTAATTAATAATTTTTTGAATTAAATAAAATAATGT
Found at i:564889 original size:21 final size:20
Alignment explanation
Indices: 564865--564903 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
564855 AATGATTAAT
564865 TTAATTTTGATTTAAATTTTG
1 TTAATTTT-ATTTAAATTTTG
*
564886 TTAATTTTTTTTAAATTT
1 TTAATTTTATTTAAATTT
564904 AGTTCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTAATTTTATTTAAATTTTG
Found at i:570260 original size:13 final size:14
Alignment explanation
Indices: 570217--570265 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
570207 GTTAAATTTA
570217 AAATTTAAAGAAGAT
1 AAATTTAAA-AAGAT
*
570232 AAA--TAAAAATATT
1 AAATTTAAAAAGA-T
570245 AAATTTAAAAA-AT
1 AAATTTAAAAAGAT
570258 AAATTTAA
1 AAATTTAA
570266 CTGAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 3 0.10
13 17 0.57
14 1 0.03
15 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATTTAAAAAGAT
Found at i:570653 original size:36 final size:35
Alignment explanation
Indices: 570588--570658 Score: 83
Period size: 34 Copynumber: 2.0 Consensus size: 35
570578 ATATAATTAA
*
570588 TTTAAAAATTATTAAAATTTTAATATAATACTTTTAC
1 TTTAAAAATTATT-AAATTTAAATATAATA-TTTTAC
570625 TTTAAAAA-TATT-AATTTAAATATTTAATATTTTA
1 TTTAAAAATTATTAAATTTAAATA--TAATATTTTA
570659 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
34 9 0.29
35 5 0.16
36 9 0.29
37 8 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTAAAAATTATTAAATTTAAATATAATATTTTAC
Found at i:570671 original size:17 final size:18
Alignment explanation
Indices: 570648--570708 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
570638 ATTTAAATAT
* *
570648 TTAATATTTTATTTTTTA
1 TTAATATTATATTATTTA
570666 -TAATATTATATTATTTA
1 TTAATATTATATTATTTA
* **
570683 TTAATAATATTATTAAATA
1 TTAATATTA-TATTATTTA
570702 TTAATAT
1 TTAATAT
570709 CATGATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 15 0.43
18 7 0.20
19 13 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTATATTATTTA
Found at i:570691 original size:21 final size:20
Alignment explanation
Indices: 570656--570695 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
570646 ATTTAATATT
*
570656 TTATTTTTTATAATATTATA
1 TTATTTTTAATAATATTATA
570676 TTATTTATTAATAATATTAT
1 TTATTT-TTAATAATATTAT
570696 TAAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTTAATAATATTATA
Found at i:570706 original size:16 final size:16
Alignment explanation
Indices: 570667--570708 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
570657 TATTTTTTAT
*
570667 AATATT-ATATTATTT
1 AATATTAATATTATTA
* *
570682 ATTAATAATATTATTA
1 AATATTAATATTATTA
570698 AATATTAATAT
1 AATATTAATAT
570709 CATGATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAATATTATTA
Found at i:571548 original size:15 final size:16
Alignment explanation
Indices: 571528--571558 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
571518 CATGTTCTAG
571528 ATCATATATA-ATATA
1 ATCATATATATATATA
571543 ATCATATATATATATA
1 ATCATATATATATATA
571559 TATATATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
ATCATATATATATATA
Found at i:571798 original size:28 final size:25
Alignment explanation
Indices: 571745--571799 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 25
571735 CTAAGGATAT
* *
571745 TTTATGTTTTTTTAATTATTTTTAA
1 TTTATGTTTTTTTAACTATTTATAA
571770 TTTATGTGTTTTAGTTAACTATTTATAA
1 TTTATGT-TTTT--TTAACTATTTATAA
571798 TT
1 TT
571800 GAAGCAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
28 14 0.56
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.65
Consensus pattern (25 bp):
TTTATGTTTTTTTAACTATTTATAA
Found at i:572144 original size:17 final size:18
Alignment explanation
Indices: 572114--572155 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
572104 TAATGAAAAA
*
572114 TAAT-TAAAATATAAT-T
1 TAATATAAAAAATAATAT
572130 TAATATAAAAAATAATAT
1 TAATATAAAAAATAATAT
*
572148 AAATATAA
1 TAATATAA
572156 TTTTTCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATATAAAAAATAATAT
Found at i:572550 original size:40 final size:41
Alignment explanation
Indices: 572497--572584 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 41
572487 AAAAATGACT
*
572497 ATTAAGAACATTTGATTAAAA-TATTTTTATAT-ATAATAA-AAA
1 ATTAA-AACATTTG--TAAAATTATATTTATATCA-AATAATAAA
572539 ATTAAAA-ATTTGTAAAATTATATTTATATCAAATAATAAA
1 ATTAAAACATTTGTAAAATTATATTTATATCAAATAATAAA
572579 ATTAAA
1 ATTAAA
572585 TAAATTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
38 5 0.12
39 15 0.36
40 15 0.36
41 2 0.05
42 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (41 bp):
ATTAAAACATTTGTAAAATTATATTTATATCAAATAATAAA
Found at i:572670 original size:37 final size:35
Alignment explanation
Indices: 572551--572744 Score: 164
Period size: 36 Copynumber: 5.4 Consensus size: 35
572541 TAAAAATTTG
* *
572551 TAAAATTATATTTATATCAAATAATAAAATTAAA-
1 TAAAATTATATTTATATTAAATAATAAAAATAAAT
* **
572585 T-AAATTATATTGT-TGTTAAATAATAATTAAAATTTAT
1 TAAAATTATATT-TATATTAAATAAT-A--AAAATAAAT
*
572622 TAAAATTATATTTATAATTAACTAATAAAACATAAAT
1 TAAAATTATATTTAT-ATTAAATAATAAAA-ATAAAT
* * * *
572659 TAAAATAATATTTATTTTAAATAATTACAAAT-TAT
1 TAAAATTATATTTATATTAAATAA-TAAAAATAAAT
*
572694 TAACAACTATATTTATATTAAATAAT-AAAATAATAAT
1 TAA-AATTATATTTATATTAAATAATAAAAAT-A-AAT
572731 TAAAATTATATTTA
1 TAAAATTATATTTA
572745 AAAATTTAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
33 19 0.15
34 7 0.06
35 6 0.05
36 45 0.36
37 29 0.23
38 12 0.10
39 8 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAAATTATATTTATATTAAATAATAAAAATAAAT
Found at i:572694 original size:72 final size:72
Alignment explanation
Indices: 572606--572744 Score: 194
Period size: 72 Copynumber: 1.9 Consensus size: 72
572596 GTTGTTAAAT
* *
572606 AATAATTAAAATTTATTAA-AATTATATTTATAATTAACTAATAAAAC-ATAAATTAAAATAATA
1 AATAATTAAAATTTATTAACAACTATATTTAT-ATTAAATAATAAAACAAT-AATTAAAATAATA
572669 TTTATTTTA
64 TTTATTTTA
* *
572678 AATAATTACAAA-TTATTAACAACTATATTTATATTAAATAATAAAATAATAATTAAAATTATAT
1 AATAATTA-AAATTTATTAACAACTATATTTATATTAAATAATAAAACAATAATTAAAATAATAT
572742 TTA
65 TTA
572745 AAAATTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
72 44 0.73
73 16 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (72 bp):
AATAATTAAAATTTATTAACAACTATATTTATATTAAATAATAAAACAATAATTAAAATAATATT
TATTTTA
Found at i:572715 original size:36 final size:33
Alignment explanation
Indices: 572528--572744 Score: 127
Period size: 36 Copynumber: 6.1 Consensus size: 33
572518 TATTTTTATA
* *
572528 TATAATAAAAAATTAAAAATT-TGTAAAATTATATT
1 TATATTAAATAATT-AAAATTAT-TAAAA-TATATT
* * *
572563 TATATCAAATAA-TAAAATTAAATAAATTATATT
1 TATATTAAATAATTAAAATT-ATTAAAATATATT
*
572596 GT-TGTTAAATAATAATTAAAATTTATTAAAATTATATT
1 -TATATT--A-AATAATTAAAA-TTATTAAAA-TATATT
* * *
572634 TATAATTAACTAATAAAACATAAATTAAAATAATATT
1 TAT-ATTAAATAATTAAA-AT-TATTAAAAT-ATATT
*
572671 TATTTTAAATAATTACAAATTATTAACAACTATATT
1 TATATTAAATAATTA-AAATTATTAA-AA-TATATT
572707 TATATTAAATAA-TAAAATAATAATTAAAATTATATT
1 TATATTAAATAATTAAAAT--T-ATTAAAA-TATATT
572743 TA
1 TA
572745 AAAATTTAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 39
0.71 0.09 0.19
Matches are distributed among these distances:
33 14 0.10
34 10 0.07
35 17 0.12
36 55 0.38
37 36 0.25
38 9 0.06
39 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
TATATTAAATAATTAAAATTATTAAAATATATT
Found at i:573677 original size:13 final size:13
Alignment explanation
Indices: 573659--573685 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
573649 ACATATTGCT
573659 TTGTATCGATACA
1 TTGTATCGATACA
573672 TTGTATCGATACA
1 TTGTATCGATACA
573685 T
1 T
573686 AATCTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:573783 original size:13 final size:13
Alignment explanation
Indices: 573765--573792 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
573755 CGATACATGG
573765 TATATTGTATCGA
1 TATATTGTATCGA
573778 TATATTGTATCGA
1 TATATTGTATCGA
573791 TA
1 TA
573793 CATAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
TATATTGTATCGA
Found at i:573794 original size:33 final size:33
Alignment explanation
Indices: 573749--573845 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
573739 CTACCACTGT
* **
573749 TTATATCGATACATGGT-ATATTGTATCGATATA
1 TTATATCGATACATAGTGA-AAAGTATCGATATA
*
573782 TTGTATCGATACATAGTGAAAAGTATCGATATA
1 TTATATCGATACATAGTGAAAAGTATCGATATA
573815 TTATATCGATACATAGTGAAAAGTATCGATA
1 TTATATCGATACATAGTGAAAAGTATCGATA
573846 CATTGTGCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 57 0.98
34 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (33 bp):
TTATATCGATACATAGTGAAAAGTATCGATATA
Found at i:573809 original size:20 final size:20
Alignment explanation
Indices: 573784--573848 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
573774 TCGATATATT
573784 GTATCGATACATAGTGAAAA
1 GTATCGATACATAGTGAAAA
*
573804 GTATCGAT--ATA-T---TA
1 GTATCGATACATAGTGAAAA
573818 -TATCGATACATAGTGAAAA
1 GTATCGATACATAGTGAAAA
573837 GTATCGATACAT
1 GTATCGATACAT
573849 TGTGCTCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 7 0.19
14 1 0.03
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
19 1 0.03
20 19 0.53
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACATAGTGAAAA
Found at i:575107 original size:30 final size:30
Alignment explanation
Indices: 575033--575111 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 30
575023 GCGGTTGGAA
*
575033 ACTCAAATTTATAAGCTTGAATGTTGACAT
1 ACTCAAATTTATAAGCTTGAATATTGACAT
*
575063 ACTCGTTAGTAATTTATAGGCTTGAATATTGACAT
1 ACTC---A--AATTTATAAGCTTGAATATTGACAT
575098 ACTCAAATTTATAA
1 ACTCAAATTTATAA
575112 ATTTAAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
30 12 0.29
32 1 0.02
33 1 0.02
35 27 0.66
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (30 bp):
ACTCAAATTTATAAGCTTGAATATTGACAT
Found at i:575234 original size:10 final size:10
Alignment explanation
Indices: 575216--575255 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
575206 CTTCATTTTG
575216 AAAAA-AAAA
1 AAAAAGAAAA
575225 AAAAAGAAAAA
1 AAAAAG-AAAA
575236 AAAAAGAAAA
1 AAAAAGAAAA
*
575246 GAAAAGAAAA
1 AAAAAGAAAA
575256 GGGGAAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 5 0.18
10 13 0.46
11 10 0.36
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:575237 original size:16 final size:16
Alignment explanation
Indices: 575216--575255 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
575206 CTTCATTTTG
575216 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
575232 AAAAAAAAAGAAAAGA
1 AAAAAAAAAAAAAAGA
575248 AAAGAAAA
1 AAA-AAAA
575256 GGGGAAACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:577655 original size:16 final size:16
Alignment explanation
Indices: 577624--577661 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
577614 TCTTAAATAA
*
577624 AAATTT-AAACTTTAT
1 AAATTTAAAAATTTAT
577639 AAATTTAAAAATTTAT
1 AAATTTAAAAATTTAT
*
577655 ATATTTA
1 AAATTTA
577662 TAACGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAAAAATTTAT
Found at i:580553 original size:21 final size:21
Alignment explanation
Indices: 580493--580557 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
580483 AATATTAAGA
*
580493 ATTAAATAATTTATATTATATT
1 ATTATATAA-TTATATTATATT
580515 AATT-T-TAATATATATTATATT
1 -ATTATATAAT-TATATTATATT
*
580536 ATTATATAATTATTTTAT-TT
1 ATTATATAATTATATTATATT
580556 AT
1 AT
580558 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 8 0.22
21 22 0.59
22 4 0.11
23 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATATAATTATATTATATT
Found at i:580564 original size:16 final size:15
Alignment explanation
Indices: 580501--580568 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 15
580491 GAATTAAATA
*
580501 ATTTATATTATAT-TA
1 ATTT-TATTATATATT
*
580516 ATTTTAATATATATT
1 ATTTTATTATATATT
*
580531 ATATTATTATATAATT
1 ATTTTATTATAT-ATT
*
580547 ATTTTATTTATATTTT
1 ATTTTA-TTATATATT
580563 ATTTTA
1 ATTTTA
580569 ATAAAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.16
15 15 0.34
16 16 0.36
17 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTATTATATATT
Found at i:580671 original size:8 final size:8
Alignment explanation
Indices: 580658--580718 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
580648 ATAATAATTA
580658 TTTTATAT
1 TTTTATAT
580666 TTTTATAT
1 TTTTATAT
*
580674 TTTTATAA
1 TTTTATAT
*
580682 ATTTATAT
1 TTTTATAT
*
580690 TATTAT-T
1 TTTTATAT
*
580697 TTTAATAAT
1 TTTTAT-AT
*
580706 ATTTATAT
1 TTTTATAT
580714 TTTTA
1 TTTTA
580719 ATTAATGTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 5 0.12
8 31 0.76
9 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAT
Found at i:580686 original size:24 final size:24
Alignment explanation
Indices: 580641--580718 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
580631 AGTATATAAA
*
580641 TTTTA-TTATAATAATTATTTTATAT
1 TTTTATTTTTAATAA-TA-TTTATAT
*
580666 TTTTATATTTTTATAA-ATTTATAT
1 TTTTAT-TTTTAATAATATTTATAT
*
580690 TATTATTTTTAATAATATTTATAT
1 TTTTATTTTTAATAATATTTATAT
580714 TTTTA
1 TTTTA
580719 ATTAATGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.18
24 24 0.53
25 6 0.13
27 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTATTTTTAATAATATTTATAT
Found at i:585359 original size:14 final size:15
Alignment explanation
Indices: 585335--585363 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
585325 ATGTTATTAA
585335 AATATTTTTTATATT
1 AATATTTTTTATATT
585350 AATA-TTTTTATATT
1 AATATTTTTTATATT
585364 TTTATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:585890 original size:19 final size:20
Alignment explanation
Indices: 585850--585911 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 20
585840 ATTATTTTTT
*
585850 ATTATTTATGATCATATTTA
1 ATTATTTATGATCATATATA
585870 ATTATTATAT-ATC-TATATA
1 ATTATT-TATGATCATATATA
585889 ATT-TTT-TGAT-ATAT-TA
1 ATTATTTATGATCATATATA
*
585905 ATAATTT
1 ATTATTT
585912 TTATTATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 5 0.14
17 9 0.25
18 2 0.06
19 8 0.22
20 9 0.25
21 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTATTTATGATCATATATA
Found at i:587292 original size:21 final size:18
Alignment explanation
Indices: 587264--587304 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
587254 ATTTTTATTT
587264 AAATTTAATTATAAAATATA
1 AAATTTAA-TATAAAA-ATA
587284 AAATATTAATATAAAAATA
1 AAAT-TTAATATAAAAATA
587303 AA
1 AA
587305 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAATATAAAAATA
Found at i:587308 original size:50 final size:50
Alignment explanation
Indices: 587238--587347 Score: 122
Period size: 50 Copynumber: 2.2 Consensus size: 50
587228 AGGTTTGAAT
* *
587238 TATTAAT-TAATAATATA-TTTTTATTTAAATTTAATT-ATAA-AATATAAAA
1 TATTAATATAAAAATAAATTTTTTA-TT-AATTT-ATTAATAATAATATAAAA
*
587287 TATTAATATAAAAATAAATTTTTTATTAATTTATTAATAATAATTTAAAA
1 TATTAATATAAAAATAAATTTTTTATTAATTTATTAATAATAATATAAAA
*
587337 TTTTAA-ATAAA
1 TATTAATATAAA
587348 TTTTTACGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
48 3 0.06
49 21 0.40
50 23 0.43
51 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (50 bp):
TATTAATATAAAAATAAATTTTTTATTAATTTATTAATAATAATATAAAA
Found at i:587505 original size:33 final size:33
Alignment explanation
Indices: 587467--587545 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
587457 AAAATTTTAG
* *
587467 ATATAATATAATCAAATAATTTA-AAAT-AATAAA
1 ATATAATAT-AT-AAATAAATAATAAATAAATAAA
*
587500 ATATAAAATATAAATAAATAATAAATAAATAAA
1 ATATAATATATAAATAAATAATAAATAAATAAA
587533 ATATAATTATATA
1 ATATAA-TATATA
587546 TTATTAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 8 0.21
32 6 0.15
33 20 0.51
34 5 0.13
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (33 bp):
ATATAATATATAAATAAATAATAAATAAATAAA
Found at i:587508 original size:15 final size:15
Alignment explanation
Indices: 587488--587538 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
587478 TCAAATAATT
587488 TAAAATAATAAAATA
1 TAAAATAATAAAATA
*
587503 TAAAAT-ATAAATAAA
1 TAAAATAATAAA-ATA
587518 TAATAAATAAATAAAATA
1 T-A-AAAT-AATAAAATA
587536 TAA
1 TAA
587539 TTATATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 5 0.17
15 9 0.31
16 2 0.07
17 5 0.17
18 3 0.10
19 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAATAATAAAATA
Found at i:587538 original size:11 final size:11
Alignment explanation
Indices: 587494--587600 Score: 53
Period size: 11 Copynumber: 9.8 Consensus size: 11
587484 AATTTAAAAT
587494 AATAAAATATAA
1 AATAAAATAT-A
*
587506 AATATAA-ATA
1 AATAAAATATA
587516 AATAATAA-ATA
1 AATAA-AATATA
587527 AATAAAATAT-
1 AATAAAATATA
* * *
587537 AATTATATATT
1 AATAAAATATA
*
587548 ATTAAAATAT-
1 AATAAAATATA
* *
587558 -TTTAAATATA
1 AATAAAATATA
* *
587568 ATTATAATATA
1 AATAAAATATA
*
587579 CGAATAAAACATA
1 --AATAAAATATA
587592 AATAAAATA
1 AATAAAATA
587601 ATTATCAGCT
Statistics
Matches: 74, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
9 8 0.11
10 15 0.20
11 37 0.50
12 6 0.08
13 8 0.11
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.34
Consensus pattern (11 bp):
AATAAAATATA
Found at i:587551 original size:10 final size:10
Alignment explanation
Indices: 587471--587578 Score: 56
Period size: 10 Copynumber: 11.6 Consensus size: 10
587461 TTTTAGATAT
*
587471 AATATAATCA
1 AATATAATTA
*
587481 AATA-ATTTA
1 AATATAATTA
587490 AA-ATAA-TA
1 AATATAATTA
*
587498 AA-AT-ATAA
1 AATATAATTA
*
587506 AATATAAAT-
1 AATATAATTA
587515 AA-ATAA-TA
1 AATATAATTA
*
587523 AATA-AATAA
1 AATATAATTA
587532 AATATAATTA
1 AATATAATTA
* *
587542 TATATTATTA
1 AATATAATTA
*
587552 AA-ATATTTTA
1 AATATA-ATTA
587562 AATATAATTA
1 AATATAATTA
587572 TAATATA
1 -AATATA
587579 CGAATAAAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
7 2 0.03
8 18 0.25
9 18 0.25
10 26 0.36
11 9 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
AATATAATTA
Found at i:591574 original size:15 final size:16
Alignment explanation
Indices: 591554--591584 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
591544 CAACTAATTT
591554 TCTTGATT-TATTTTC
1 TCTTGATTCTATTTTC
591569 TCTTGATTCTATTTTC
1 TCTTGATTCTATTTTC
591585 GACAGGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.13, C:0.16, G:0.06, T:0.65
Consensus pattern (16 bp):
TCTTGATTCTATTTTC
Found at i:596559 original size:8 final size:8
Alignment explanation
Indices: 596546--596627 Score: 51
Period size: 8 Copynumber: 9.9 Consensus size: 8
596536 ATAAATTTTA
596546 ATATATTT
1 ATATATTT
596554 ATATA-TT
1 ATATATTT
*
596561 ATTTATATT
1 ATATAT-TT
596570 ATAT-TTGT
1 ATATATT-T
*
596578 ATTATATAT
1 A-TATATTT
* *
596587 AAATTTTTT
1 ATA-TATTT
*
596596 AATAGATTT
1 -ATATATTT
596605 ATATATTT
1 ATATATTT
*
596613 ATACATTT
1 ATATATTT
596621 ATATATT
1 ATATATT
596628 GTACTTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
7 7 0.13
8 29 0.53
9 16 0.29
10 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (8 bp):
ATATATTT
Found at i:596574 original size:11 final size:11
Alignment explanation
Indices: 596547--596584 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
596537 TAAATTTTAA
596547 TATATTTATA-
1 TATATTTATAT
596557 TATTATTTATAT
1 TA-TATTTATAT
*
596569 TATATTTGTAT
1 TATATTTATAT
596580 TATAT
1 TATAT
596585 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:596622 original size:16 final size:16
Alignment explanation
Indices: 596601--596651 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
596591 TTTTTAATAG
596601 ATTTATATATTTATAC
1 ATTTATATATTTATAC
*
596617 ATTTATATA-TTGTAC
1 ATTTATATATTTATAC
*
596632 -TTT-T-TATTTATTC
1 ATTTATATATTTATAC
596645 ATTTATA
1 ATTTATA
596652 CAATTAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
12 2 0.07
13 5 0.18
14 6 0.21
15 6 0.21
16 9 0.32
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTATATATTTATAC
Found at i:596623 original size:51 final size:50
Alignment explanation
Indices: 596533--596630 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 50
596523 TAATTAATTT
* **
596533 TATATAAATTTTAATATATTTATATATTATTTATATTATAT-TTGTATTA
1 TATATAAATTTTAATAGATTTATATATTATACATATTATATATTGTATTA
596582 TATATAAATTTTTTAATAGATTTATATATTTATACAT-TTATATATTGTA
1 TATATAAA--TTTTAATAGATTTATATA-TTATACATATTATATATTGTA
596631 CTTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 8 0.19
51 23 0.55
52 11 0.26
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (50 bp):
TATATAAATTTTAATAGATTTATATATTATACATATTATATATTGTATTA
Found at i:597888 original size:10 final size:10
Alignment explanation
Indices: 597873--597936 Score: 58
Period size: 10 Copynumber: 6.0 Consensus size: 10
597863 AATTCGTATA
597873 TTAATATATT
1 TTAATATATT
597883 TTAATATATT
1 TTAATATATT
597893 TTAATA-ATAT
1 TTAATATAT-T
* *
597903 TTAAAATTTT
1 TTAATATATT
597913 TTATTATATAAATT
1 TTA--ATAT--ATT
597927 TTAATATATT
1 TTAATATATT
597937 AATAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.05
10 29 0.66
11 1 0.02
12 7 0.16
14 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTAATATATT
Found at i:597927 original size:16 final size:16
Alignment explanation
Indices: 597906--597959 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
597896 ATAATATTTA
597906 AAATTTTTTATTATAT
1 AAATTTTTTATTATAT
597922 AAATTTTAATATATTA-AT
1 AAATTTT--T-TATTATAT
*
597940 -AA-TTTATATTATAT
1 AAATTTTTTATTATAT
597954 AAATTT
1 AAATTT
597960 AAATATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 2 0.06
16 12 0.39
17 2 0.06
18 3 0.10
19 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTTTTTATTATAT
Found at i:597928 original size:14 final size:14
Alignment explanation
Indices: 597911--597959 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
597901 ATTTAAAATT
597911 TTTTATTATATAAA
1 TTTTATTATATAAA
*
597925 TTTTAATATATTAATAA
1 TTTTATTATA-T-A-AA
597942 TTTATATTATATAAA
1 TTT-TATTATATAAA
597957 TTT
1 TTT
597960 AAATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 2 0.07
17 6 0.21
18 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTATTATATAAA
Found at i:597950 original size:32 final size:32
Alignment explanation
Indices: 597890--597970 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
597880 ATTTTAATAT
*
597890 ATTTTAATAATATTTAAAATTTTTTATTATATAA
1 ATTTTAAT-ATA-TTAAAATTTTATATTATATAA
597924 ATTTTAATATATTAATAA-TTTATATTATATAA
1 ATTTTAATATATTAA-AATTTTATATTATATAA
*
597956 ATTTAAATAT-TTAAA
1 ATTTTAATATATTAAA
597971 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 1 0.02
31 4 0.09
32 26 0.59
33 5 0.11
34 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTTAATATATTAAAATTTTATATTATATAA
Found at i:597958 original size:15 final size:15
Alignment explanation
Indices: 597914--597960 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
597904 TAAAATTTTT
597914 TATTATATAAATTT-
1 TATTATATAAATTTA
*
597928 TAATATATTAATAATTTA
1 TATTATA-T-A-AATTTA
597946 TATTATATAAATTTA
1 TATTATATAAATTTA
597961 AATATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 2 0.07
17 6 0.22
18 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATATAAATTTA
Found at i:597984 original size:32 final size:31
Alignment explanation
Indices: 597898--597985 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 31
597888 ATATTTTAAT
*
597898 AATATTTAAA-ATTTTTTATTATATAAATTTT
1 AATATTTAAATATTTTTT-TTATATAAATTTA
* *
597929 AATATATT-AATAATTTATATTATATAAATTTA
1 AATAT-TTAAAT-ATTTTTTTTATATAAATTTA
597961 AATATTTAAATTATTTTTTTTATAT
1 AATATTTAAA-TATTTTTTTTATAT
597986 TTTACATCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.19
32 32 0.68
33 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
AATATTTAAATATTTTTTTTATATAAATTTA
Found at i:600754 original size:332 final size:321
Alignment explanation
Indices: 600159--600816 Score: 1147
Period size: 332 Copynumber: 2.0 Consensus size: 321
600149 ATTAATTTAC
* *
600159 TTGCAAAGTTAAAAATTTTTTGCTAGTATAAATATGAACTATTCTCTTTTGAACGTGATAAAACA
1 TTGCAAAGTTAAAAATTTTTTGCTAGTATAAATATGAACTATTCTCTCTTCAACGTGATAAAACA
*
600224 TTCATATGGTAAAATTTTACTCATACTTATAAAATGTATATCGAATATAAATACCAATTTTAAAA
66 TTCATAGGGTAAAATTTTACTCATACTTATAAAATGTATATCGAATATAAATACCAATTTTAAAA
*
600289 TAATTGGAAAGTGGTAGCAGCATAGTGAGGAACTTCTTTATGAATATTTTGAAGCATTCAGAAGC
131 TAATTGGAAAGTGGTAGCAGCATAATGAGGAACTTCTTTATGAATATTTTGAAGCATTCAGAAGC
600354 ACATCATTCCAAACTTCTGGTTTAGTAATTAAATCAATCCATTTATGATTAGCAATCACATGAGA
196 ACATCATTCCAAACTTCTGGTTTAGTAATTAAATCAATCCATTTATGATTAGCAATCACATGAGA
600419 ACCCAAACTGATGATTAGCATCACCTTGGAAGAACCACACGCTTTTCGTTTTTGTTGCCTG
261 ACCCAAACTGATGATTAGCATCACCTTGGAAGAACCACACGCTTTTCGTTTTTGTTGCCTG
600480 TTGCAAAGTTAAAAATTTTTTGCTAGTATAAATATGAACTATTCTCTCTTCAACGTGATAAAACA
1 TTGCAAAGTTAAAAATTTTTTGCTAGTATAAATATGAACTATTCTCTCTTCAACGTGATAAAACA
* *
600545 TTCATAGGGTAAAATTTTATTCATACTTATAAGATGTATATCGAATATAAATACCATAAACGTAA
66 TTCATAGGGTAAAATTTTACTCATACTTATAAAATGTATATCGAATATAAATA-C-----C----
600610 GAATTTTAAAATAATTGGAAAGTGGTAGCAGCATAATGAGGAACTTCTTTATGAATATTTTGAAG
121 -AATTTTAAAATAATTGGAAAGTGGTAGCAGCATAATGAGGAACTTCTTTATGAATATTTTGAAG
*
600675 CATTCAGAAGCACATCATTGCAAACTTCTGGTTTAGTAATTAAATCAATCCATTTATGATTAGCA
185 CATTCAGAAGCACATCATTCCAAACTTCTGGTTTAGTAATTAAATCAATCCATTTATGATTAGCA
600740 ATCACATGAGAACCCAAACTGATGATTAGCATCACCTTGGAAGAACCACACGCTTTTCGTTTTTG
250 ATCACATGAGAACCCAAACTGATGATTAGCATCACCTTGGAAGAACCACACGCTTTTCGTTTTTG
600805 TTGCCTG
315 TTGCCTG
600812 -TGCAA
1 TTGCAA
600817 CAAAGGAATT
Statistics
Matches: 319, Mismatches: 7, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
321 113 0.35
322 1 0.00
327 1 0.00
331 5 0.02
332 199 0.62
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (321 bp):
TTGCAAAGTTAAAAATTTTTTGCTAGTATAAATATGAACTATTCTCTCTTCAACGTGATAAAACA
TTCATAGGGTAAAATTTTACTCATACTTATAAAATGTATATCGAATATAAATACCAATTTTAAAA
TAATTGGAAAGTGGTAGCAGCATAATGAGGAACTTCTTTATGAATATTTTGAAGCATTCAGAAGC
ACATCATTCCAAACTTCTGGTTTAGTAATTAAATCAATCCATTTATGATTAGCAATCACATGAGA
ACCCAAACTGATGATTAGCATCACCTTGGAAGAACCACACGCTTTTCGTTTTTGTTGCCTG
Found at i:601777 original size:2 final size:2
Alignment explanation
Indices: 601770--601802 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
601760 ACCAAATTTA
601770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
601803 AAGAGTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:607997 original size:16 final size:16
Alignment explanation
Indices: 607976--608018 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
607966 TTTTTGTTTT
607976 AATTATTTTAAATTTA
1 AATTATTTTAAATTTA
*
607992 AATTATTTTAATTTTA
1 AATTATTTTAAATTTA
*
608008 AATAATTTTAA
1 AATTATTTTAA
608019 GTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:609930 original size:26 final size:26
Alignment explanation
Indices: 609888--609938 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
609878 GTTCGGAAAG
*
609888 GATGAAAGAGAAATATCCAT-ATCATA
1 GATGAAACAGAAATAT-CATGATCATA
609914 GATGAAACA-AAATTATCATGATCAT
1 GATGAAACAGAAA-TATCATGATCAT
609939 GTCATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (26 bp):
GATGAAACAGAAATATCATGATCATA
Found at i:636630 original size:2 final size:2
Alignment explanation
Indices: 636623--636654 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
636613 NNNNNACTGA
636623 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
636655 AGAGAGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:636659 original size:2 final size:2
Alignment explanation
Indices: 636654--636683 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
636644 GTGTGTGTGT
636654 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
636684 ATGATTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:642862 original size:6 final size:6
Alignment explanation
Indices: 642852--642887 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
642842 CCTTTGGCTC
* *
642852 TCCTCC TCCTCT TTCTCT TCCTCT TCCTCT TCCTCT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
642888 ATTGTCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCTCT
Found at i:643881 original size:7 final size:7
Alignment explanation
Indices: 643869--643920 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
643859 TTTTTATTTA
643869 TTTTAAT
1 TTTTAAT
643876 TTTTAAT
1 TTTTAAT
*
643883 TTTTACT
1 TTTTAAT
*
643890 TTTTACT
1 TTTTAAT
*
643897 TTTTACTT
1 TTTTA-AT
643905 TTTATAAT
1 TTT-TAAT
643913 TTTTAAT
1 TTTTAAT
643920 T
1 T
643921 AATTTTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
7 30 0.75
8 8 0.20
9 2 0.05
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:644269 original size:19 final size:20
Alignment explanation
Indices: 644237--644276 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
644227 ATTTTATGAT
644237 AATAAAATAGAATTAGAATAA
1 AATAAAATA-AATTAGAATAA
*
644258 AATAAAAT-AATTATAATAA
1 AATAAAATAAATTAGAATAA
644277 TAGTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAAAATAAATTAGAATAA
Found at i:646035 original size:34 final size:35
Alignment explanation
Indices: 645997--646063 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
645987 GTAATATTTT
*
645997 GATAA-ATATTATTTTTAAAATTTTTTA-GAATTAA
1 GATAATATATTATGTTT-AAATTTTTTATGAATTAA
* *
646031 GATAATTTTTTATGTTTAAATTTTTTATGAATT
1 GATAATATATTATGTTTAAATTTTTTATGAATT
646064 TTTTTTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.55
Consensus pattern (35 bp):
GATAATATATTATGTTTAAATTTTTTATGAATTAA
Found at i:646136 original size:15 final size:15
Alignment explanation
Indices: 646118--646167 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
646108 TTAAATTTTA
646118 ATAATAATTATTATT
1 ATAATAATTATTATT
646133 ATAATAA-TATTTATT
1 ATAATAATTA-TTATT
*
646148 ATAAT--TTATAATT
1 ATAATAATTATTATT
646161 ATAATAA
1 ATAATAA
646168 ATATAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 9 0.30
14 4 0.13
15 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATAATTATTATT
Found at i:646174 original size:15 final size:15
Alignment explanation
Indices: 646118--646179 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
646108 TTAAATTTTA
* *
646118 ATAATAATTATTATT
1 ATAATAAATATAATT
646133 ATAAT-AATAT--TT
1 ATAATAAATATAATT
* *
646145 ATTATAATTTATAATT
1 ATAATAA-ATATAATT
646161 ATAATAAATATAA-T
1 ATAATAAATATAATT
646175 ATAAT
1 ATAAT
646180 CGAAAATACT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.16
13 1 0.03
14 13 0.34
15 10 0.26
16 8 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:648859 original size:2 final size:2
Alignment explanation
Indices: 648854--648886 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
648844 CTCTCTTTGA
648854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
648887 ATAAAACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:649322 original size:2 final size:2
Alignment explanation
Indices: 649315--649343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
649305 TTATCAAAAT
649315 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 T
649344 TACATTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:649962 original size:21 final size:20
Alignment explanation
Indices: 649921--649971 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
649911 AATATATAGA
649921 ATTTTATAAATAAATAAATTT
1 ATTTTATAAATAAAT-AATTT
*
649942 ATTTTCATAATATAAATATTTT
1 ATTTT-ATAA-ATAAATAATTT
*
649964 ATATTATA
1 ATTTTATA
649972 TTATAAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTATAAATAAATAATTT
Found at i:651512 original size:2 final size:2
Alignment explanation
Indices: 651507--651537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
651497 CAGCTGAGGT
651507 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
651538 TCAAGAGTAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:655731 original size:20 final size:20
Alignment explanation
Indices: 655706--655743 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
655696 GTAAAAACAC
655706 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
655726 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
655744 TGGGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:660654 original size:20 final size:21
Alignment explanation
Indices: 660613--660656 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
660603 TTGTTTATCT
660613 TAAAAAATTTTAAATATAAAA
1 TAAAAAATTTTAAATATAAAA
* *
660634 TAAATAATTTT-AATATTAAA
1 TAAAAAATTTTAAATATAAAA
660654 TAA
1 TAA
660657 GTATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAAATTTTAAATATAAAA
Found at i:661339 original size:24 final size:23
Alignment explanation
Indices: 661312--661401 Score: 74
Period size: 26 Copynumber: 3.7 Consensus size: 23
661302 TATTATATTT
661312 ATTATAATTATAAAAATAATAAAA
1 ATTATAATTATAAAAATAA-AAAA
* *
661336 ATTATTAAATTAATTATAATAAAAATTA
1 ATTA-T-AATT-ATAAAAATAAAAA--A
*
661364 ATTATAAATATTAAAAAT-AAAAA
1 ATTATAATTA-TAAAAATAAAAAA
*
661387 ATTATTATTATAAAA
1 ATTATAATTATAAAA
661402 TAATAATGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
22 5 0.09
23 9 0.17
24 4 0.08
25 6 0.11
26 15 0.28
27 9 0.17
28 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTATAATTATAAAAATAAAAAA
Found at i:661356 original size:27 final size:24
Alignment explanation
Indices: 661325--661407 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 24
661315 ATAATTATAA
661325 AAATAATAAAAATTATT-AA-ATT
1 AAATAATAAAAATTATTAAATATT
661347 AATTATAATAAAAATTAATTATAAATATT
1 AA--ATAATAAAAATT-A-T-TAAATATT
* *
661376 AAA-AATAAAAAATTATT-ATTATA
1 AAATAAT-AAAAATTATTAAATATT
661399 AAATAATAA
1 AAATAATAA
661408 TGATAGTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
22 2 0.04
23 9 0.18
24 16 0.32
25 2 0.04
26 5 0.10
27 9 0.18
28 2 0.04
29 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATAAAAATTATTAAATATT
Found at i:661475 original size:22 final size:22
Alignment explanation
Indices: 661450--661491 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
661440 TATTAAAATT
*
661450 TATTTT-TATATTAATATTTATA
1 TATTTTATAAATTAA-ATTTATA
661472 TATTTTATAAATTAAATTTA
1 TATTTTATAAATTAAATTTA
661492 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTATAAATTAAATTTATA
Found at i:663016 original size:129 final size:129
Alignment explanation
Indices: 662756--663020 Score: 335
Period size: 129 Copynumber: 2.1 Consensus size: 129
662746 ATTTATTGAC
* * * *
662756 TAAATAAATTAGTGTAAAATTTATTTTTGTCTTTGGGTTTTGATTCATGTGATACTCAATCTATT
1 TAAATAAATTAGGGTAAAATTTATTTTTATCTTTAGATTTTGATTCATGTGATACTCAATCTATT
* * * *
662821 CTTATATATTTTTTTCTAACATCACATGTGTTTTGACTATTATTAATGTGATATAATAATATAA
66 CTTATATATTTATTTCTAACATCAAATGTGATTTAACTATTATTAATGTGATATAATAATATAA
* *
662885 TAAATAAATTAGGGTAAAATTTATTTTTATCTTTATATTTTCG-TTTATGTGATACTCAATCTAT
1 TAAATAAATTAGGGTAAAATTTATTTTTATCTTTAGATTTT-GATTCATGTGATACTCAATCTAT
* * ***
662949 T-TT-TAT-TTTATTT-TAACATCAAATGTGATTTAA-TCGTTGTTAATGTGGCGTAATAATATA
65 TCTTATATATTTATTTCTAACATCAAATGTGATTTAACT-ATTATTAATGTGATATAATAATATA
663009 A
129 A
663010 TAAATAAATTA
1 TAAATAAATTA
663021 TGATATACTC
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
124 1 0.01
125 49 0.41
126 6 0.05
127 3 0.03
128 2 0.02
129 57 0.48
130 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.48
Consensus pattern (129 bp):
TAAATAAATTAGGGTAAAATTTATTTTTATCTTTAGATTTTGATTCATGTGATACTCAATCTATT
CTTATATATTTATTTCTAACATCAAATGTGATTTAACTATTATTAATGTGATATAATAATATAA
Found at i:663195 original size:80 final size:82
Alignment explanation
Indices: 663111--663272 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 82
663101 ACAAAAGCAT
*
663111 AAAGTTAAAAATTAAC-TTTTTTT-ACTTTA-AAAATGTGATATTATATCTTTATAAAAAATAAA
1 AAAGTTAAAAATTAACTTTTTTTTAAC-TTAGAAAATGTGATATTATAACTTTATAAAAAATAAA
663173 ATAAAAGGCTAAAGATAC
65 ATAAAAGGCTAAAGATAC
* *
663191 AAAGTTAAAAATTAACTTTTTTTTTAACTTAGAAAATGTGATATTATAACTTTATGAAAAATAGA
1 AAAGTTAAAAATTAAC-TTTTTTTTAACTTAGAAAATGTGATATTATAACTTTATAAAAAATAAA
* *
663256 ATAAAATGTTAAAGATA
65 ATAAAAGGCTAAAGATA
663273 TAAGTGTGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
80 16 0.22
82 10 0.14
83 47 0.64
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (82 bp):
AAAGTTAAAAATTAACTTTTTTTTAACTTAGAAAATGTGATATTATAACTTTATAAAAAATAAAA
TAAAAGGCTAAAGATAC
Found at i:663686 original size:2 final size:2
Alignment explanation
Indices: 663679--663720 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
663669 GCAATTTCCC
663679 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
663721 CATACACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:664164 original size:13 final size:13
Alignment explanation
Indices: 664139--664189 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
664129 TTTTATAATT
664139 TTAATATTTTATTA
1 TTAATA-TTTATTA
664153 TTAATATTTATTA
1 TTAATATTTATTA
* *
664166 TAAATAATTA-TA
1 TTAATATTTATTA
*
664178 ATAATATTTATT
1 TTAATATTTATT
664190 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 9 0.29
13 16 0.52
14 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAATATTTATTA
Found at i:664473 original size:13 final size:14
Alignment explanation
Indices: 664447--664480 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
664437 ATCTAAAATT
664447 TTTTAAAGATATAA
1 TTTTAAAGATATAA
664461 TTTTAAA-ATATAA
1 TTTTAAAGATATAA
664474 TTATTAA
1 TT-TTAA
664481 GAATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTAAAGATATAA
Found at i:664697 original size:2 final size:2
Alignment explanation
Indices: 664690--664737 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
664680 AAATCAATTA
664690 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
664732 AT AT AT
1 AT AT AT
664738 TAAGAGAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:666098 original size:23 final size:21
Alignment explanation
Indices: 666064--666105 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
666054 ATGTTATTTT
666064 TTAAATATAATTATATAAATTAA
1 TTAAATATAATT-T-TAAATTAA
666087 TTAAAT-TAAATTTTAAATT
1 TTAAATAT-AATTTTAAATT
666106 TTAATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATATAATTTTAAATTAA
Found at i:666711 original size:16 final size:17
Alignment explanation
Indices: 666658--666721 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 17
666648 GAACTTAATA
* *
666658 TAAATAT-TTTAAATTT
1 TAAATATATATAAAATT
* *
666674 TATATA-ATATAAATTT
1 TAAATATATATAAAATT
*
666690 TTAATATAT-TAAAATT
1 TAAATATATATAAAATT
*
666706 TAAATAAATATAAAAT
1 TAAATATATATAAAAT
666722 ATATTAAACG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 30 0.79
17 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATATATATAAAATT
Found at i:668722 original size:14 final size:13
Alignment explanation
Indices: 668696--668735 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
668686 ATAATTAATA
*
668696 TAATATAAATTAT
1 TAATATAACTTAT
668709 TAATATAATCTTAT
1 TAATATAA-CTTAT
*
668723 TAAGATAACTTAT
1 TAATATAACTTAT
668736 GATAATCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (13 bp):
TAATATAACTTAT
Found at i:669336 original size:20 final size:21
Alignment explanation
Indices: 669304--669344 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
669294 AATCGAAGAT
*
669304 AATAAATAATTATTTTTAAAA
1 AATAAATAATTATTCTTAAAA
669325 AATAAA-AATTATTCTTAAAA
1 AATAAATAATTATTCTTAAAA
669345 GATTTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAAATAATTATTCTTAAAA
Found at i:671367 original size:2 final size:2
Alignment explanation
Indices: 671360--671398 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
671350 GCAAATATTT
671360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
671399 GTGAAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:671896 original size:20 final size:20
Alignment explanation
Indices: 671873--671939 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
671863 ATATATAATT
671873 TATATAAATAAAATATAAAA
1 TATATAAATAAAATATAAAA
*
671893 TATA-ATGATAAAAT-TAAATA
1 TATATA-AATAAAATATAAA-A
* *
671913 AATATAAATAATATA-AAAA
1 TATATAAATAAAATATAAAA
*
671932 TTTATAAA
1 TATATAAA
671940 ATCATCTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 12 0.32
20 24 0.65
21 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (20 bp):
TATATAAATAAAATATAAAA
Done.