Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold416
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: 1156864
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 4 of 8
Found at i:426083 original size:19 final size:19
Alignment explanation
Indices: 426059--426095 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
426049 TAAAAAATAT
426059 AAATAAATAATTT-TATTAA
1 AAATAAAT-ATTTGTATTAA
426078 AAATAAATATTTGTATTA
1 AAATAAATATTTGTATTA
426096 TATTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
AAATAAATATTTGTATTAA
Found at i:426216 original size:25 final size:25
Alignment explanation
Indices: 426188--426237 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
426178 TATATTCACA
426188 TTTT-ATATTATTATATTTTA-ATTAT
1 TTTTAATA-TATTAT-TTTTATATTAT
426213 TTTTAATATATTATTTTTATATTAT
1 TTTTAATATATTATTTTTATATTAT
426238 ATAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 15 0.65
26 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTAATATATTATTTTTATATTAT
Found at i:426455 original size:16 final size:16
Alignment explanation
Indices: 426436--426520 Score: 66
Period size: 16 Copynumber: 5.0 Consensus size: 16
426426 TAAAAAATAA
426436 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
426452 AATTTAAATTTATAACGATTT
1 AATTTAAATTTA-AA--A--T
*
426473 AATTAAAATTTAAAA-
1 AATTTAAATTTAAAAT
426488 AATATTAAATTTTAAAA-
1 AAT-TTAAA-TTTAAAAT
* *
426505 AAATCAAATTTAAAAT
1 AATTTAAATTTAAAAT
426521 TGATTCGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
15 10 0.18
16 20 0.35
17 11 0.19
18 1 0.02
19 1 0.02
20 2 0.04
21 12 0.21
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:426496 original size:17 final size:16
Alignment explanation
Indices: 426473--426519 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
426463 ATAACGATTT
426473 AATTAAAATTTAAAAA
1 AATTAAAATTTAAAAA
*
426489 ATATTAAATTTTAAAAA
1 A-ATTAAAATTTAAAAA
*
426506 AA-TCAAATTTAAAA
1 AATTAAAATTTAAAA
426520 TTGATTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 15 0.56
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTAAAATTTAAAAA
Found at i:426673 original size:26 final size:26
Alignment explanation
Indices: 426566--426673 Score: 73
Period size: 25 Copynumber: 4.2 Consensus size: 26
426556 AATAAAAGTG
*
426566 ATTAAATTATAATTAAATAAT-TTTTT
1 ATTAAA-TATAATAAAATAATATTTTT
* **
426592 ATATAATTA-AAT-TTATAATATTTTT
1 AT-TAAATATAATAAAATAATATTTTT
* ** *
426617 ATTAATTTATTTTAAAATGA-A-TTTT
1 ATTAA-ATATAATAAAATAATATTTTT
*
426642 AATAAATATAATAAAATAATATTTTT
1 ATTAAATATAATAAAATAATATTTTT
426668 ATTAAA
1 ATTAAA
426674 AATATTTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
24 18 0.30
25 22 0.36
26 15 0.25
27 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
ATTAAATATAATAAAATAATATTTTT
Found at i:428257 original size:16 final size:16
Alignment explanation
Indices: 428238--428268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
428228 CCAAAAATAC
*
428238 TTAAATTTAAAAAGAA
1 TTAAATCTAAAAAGAA
428254 TTAAATCTAAAAAGA
1 TTAAATCTAAAAAGA
428269 CTCTTAACCA
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:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
TTAAATCTAAAAAGAA
Found at i:428598 original size:24 final size:23
Alignment explanation
Indices: 428549--428606 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
428539 CATAATTAAG
**
428549 AATTATTTATTTTATTAATTTTTTA
1 AATTA-TTA-TTTATTAATTGATTA
428574 AATTATTATTTATTAAGTTGATTA
1 AATTATTATTTATTAA-TTGATTA
*
428598 AATAATTAT
1 AATTATTAT
428607 AAAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.28
24 16 0.55
25 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
AATTATTATTTATTAATTGATTA
Found at i:429528 original size:13 final size:13
Alignment explanation
Indices: 429510--429539 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
429500 ATAATTCATC
429510 ATGTATCGATACA
1 ATGTATCGATACA
429523 ATGTATCGATACA
1 ATGTATCGATACA
429536 ATGT
1 ATGT
429540 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:429629 original size:19 final size:19
Alignment explanation
Indices: 429585--429640 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
429575 CTGCTAGTTT
**
429585 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
429605 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
429624 CATGTATCGATACAATG
1 CATGTATCGATACAATG
429641 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:429643 original size:13 final size:13
Alignment explanation
Indices: 429625--429651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
429615 TACAATGAAC
429625 ATGTATCGATACA
1 ATGTATCGATACA
429638 ATGTATCGATACA
1 ATGTATCGATACA
429651 A
1 A
429652 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:431273 original size:20 final size:20
Alignment explanation
Indices: 431248--431319 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
431238 TCACAATTTT
431248 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
*
431268 TATCGATACATGGTTCATTG
1 TATCGATACATTGTTCATTG
* * *
431288 TATCGATACATTTTTCAATA
1 TATCGATACATTGTTCATTG
431308 TATCGATACATT
1 TATCGATACATT
431320 CAAGCATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
TATCGATACATTGTTCATTG
Found at i:432547 original size:19 final size:18
Alignment explanation
Indices: 432522--432618 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
432512 ATTTCAACGA
432522 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
432540 TGTTGTATCGATAC-T-A-
1 T-TTGTATCGATACATAAG
432556 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
432572 TGTTGTATCGATAC-T-A-
1 T-TTGTATCGATACATAAG
432588 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
432604 TTTTGTATCGATACA
1 -TTTGTATCGATACA
432619 ATGTACAGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
15 2 0.03
17 2 0.03
18 3 0.05
19 35 0.53
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:432560 original size:32 final size:32
Alignment explanation
Indices: 432524--432623 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
432514 TTCAACGATT
432524 TGTATCGATACATAAGTGTTGTATCGATACTA
1 TGTATCGATACATAAGTGTTGTATCGATACTA
432556 TGTATCGATACATAAGTGTTGTATCGATACTA
1 TGTATCGATACATAAGTGTTGTATCGATACTA
* *
432588 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACTA
432620 TGTA
1 TGTA
432624 CAGTTACGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACTA
Found at i:432561 original size:13 final size:13
Alignment explanation
Indices: 432543--432598 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 13
432533 ACATAAGTGT
432543 TGTATCGATACTA
1 TGTATCGATACTA
432556 TGTATCGATACATAA
1 TGTATCGATAC-T-A
432571 GTGTTGTATCGATACTA
1 ----TGTATCGATACTA
432588 TGTATCGATAC
1 TGTATCGATAC
432599 ATAAGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.59
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.30
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (13 bp):
TGTATCGATACTA
Found at i:432746 original size:52 final size:52
Alignment explanation
Indices: 432706--432829 Score: 239
Period size: 52 Copynumber: 2.4 Consensus size: 52
432696 CTGATCTTTA
432706 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
*
432758 TATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
432810 TATCGATACATGCAGGCAAA
1 TATCGATACATGCAGGCAAA
432830 ATTTCATATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
Found at i:433890 original size:32 final size:33
Alignment explanation
Indices: 433849--433910 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
433839 TAGCCAAACT
*
433849 TGTATCGATACA-C-AAAGTATGTATCGATATAA
1 TGTATCGATACACCAAAAAT-TGTATCGATATAA
433881 TGTATCGATACACCAAAAATTGTATCGATA
1 TGTATCGATACACCAAAAATTGTATCGATA
433911 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 11 0.41
34 4 0.15
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATATAA
Found at i:433910 original size:33 final size:32
Alignment explanation
Indices: 433849--433910 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
433839 TAGCCAAACT
*
433849 TGTATCGATACACAAAGTATGTATCGATATAA
1 TGTATCGATACACAAAATATGTATCGATATAA
433881 TGTATCGATACACCAAAA-ATTGTATCGATA
1 TGTATCGATACA-CAAAATA-TGTATCGATA
433911 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATATAA
Found at i:433933 original size:10 final size:10
Alignment explanation
Indices: 433915--433949 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
433905 TCGATACATT
*
433915 GGCTTGTAAC
1 GGCTAGTAAC
433925 GGCTAGTAAC
1 GGCTAGTAAC
433935 GGCTAGTAAC
1 GGCTAGTAAC
433945 GGCTA
1 GGCTA
433950 TATTTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (10 bp):
GGCTAGTAAC
Found at i:440101 original size:13 final size:13
Alignment explanation
Indices: 440083--440121 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
440073 ACATTTTTCT
440083 TTGTATCGATACA
1 TTGTATCGATACA
440096 TTGTATCGATACA
1 TTGTATCGATACA
*
440109 CTGTATCGATACA
1 TTGTATCGATACA
440122 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:442674 original size:19 final size:20
Alignment explanation
Indices: 442649--442700 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
442639 GTAGCCAAAC
*
442649 TTGTATCGATACA-C-AAAG
1 TTGTATCGATACACCAAAAA
442667 TATGTATCGATACACCAAAAA
1 T-TGTATCGATACACCAAAAA
442688 TTGTATCGATACA
1 TTGTATCGATACA
442701 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 13 0.43
21 4 0.13
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:449421 original size:22 final size:22
Alignment explanation
Indices: 449375--449425 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
449365 TTTTGTTGAT
* *
449375 AATTTTG-A-TGAAAAATGAAG
1 AATTTTGAAGTGAAAAATAAAA
*
449395 TATTTTGAAGTGAAAAATAAAA
1 AATTTTGAAGTGAAAAATAAAA
449417 AA-TTTGAAG
1 AATTTTGAAG
449426 AAGATTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (22 bp):
AATTTTGAAGTGAAAAATAAAA
Found at i:455031 original size:13 final size:13
Alignment explanation
Indices: 455013--455037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
455003 CAAAGATCAG
455013 TGTATCGATACAA
1 TGTATCGATACAA
455026 TGTATCGATACA
1 TGTATCGATACA
455038 TTTGGGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:455122 original size:32 final size:32
Alignment explanation
Indices: 455081--455151 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
455071 AGCTTCGTAG
455081 CGATACATTGTATCGATACAACACTCGTGTAT
1 CGATACATTGTATCGATACAACACTCGTGTAT
* **
455113 CGATACATTGTATCGATACAACATTTTTGTAT
1 CGATACATTGTATCGATACAACACTCGTGTAT
455145 CGATACA
1 CGATACA
455152 AATCATTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTCGTGTAT
Found at i:455126 original size:13 final size:13
Alignment explanation
Indices: 455108--455132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
455098 ACAACACTCG
455108 TGTATCGATACAT
1 TGTATCGATACAT
455121 TGTATCGATACA
1 TGTATCGATACA
455133 ACATTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:459228 original size:13 final size:13
Alignment explanation
Indices: 459210--459234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459200 TAATTCATCA
459210 TGTATCGATACAT
1 TGTATCGATACAT
459223 TGTATCGATACA
1 TGTATCGATACA
459235 AACAGTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:459289 original size:20 final size:19
Alignment explanation
Indices: 459264--459316 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
459254 CTACCAGTTT
* *
459264 CATGTATCGATACAATTGTC
1 CATGTATCGATACAAAT-AC
459284 CATGTATCGATACAAATAC
1 CATGTATCGATACAAATAC
459303 CTATGTATCGATAC
1 C-ATGTATCGATAC
459317 TTTGAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAAATAC
Found at i:460626 original size:27 final size:27
Alignment explanation
Indices: 460588--460658 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
460578 GGTTGAAAAC
460588 GGGGTTGGAGTGTCCCCTC-AGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGA-AGGAAT
460615 GGGGTTGGAGTGTCCCCTCGAAGGAAT
1 GGGGTTGGAGTGTCCCCTCGAAGGAAT
*
460642 AGGGTTGGAGTGTCCCC
1 GGGGTTGGAGTGTCCCC
460659 GCCGAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 41 0.98
28 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.41, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGAAGGAAT
Found at i:462858 original size:33 final size:32
Alignment explanation
Indices: 462799--462910 Score: 118
Period size: 33 Copynumber: 3.3 Consensus size: 32
462789 ATTTACCTGC
*
462799 ATGTATCGATACATTGTGTATCGATACA-AAGATCA
1 ATGTATCGATACA--ATGTATCGATACATAAG-T-A
* * *
462834 ATGTATCGATATAATGTATTGATACATTTAGTA
1 ATGTATCGATACAATGTATCGATACA-TAAGTA
*
462867 ATGTATCGATACAATGTATCGATACATTTAGTA
1 ATGTATCGATACAATGTATCGATACA-TAAGTA
462900 ATGTATCGATA
1 ATGTATCGATA
462911 TATTTCCTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
33 54 0.78
34 1 0.01
35 14 0.20
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACAATGTATCGATACATAAGTA
Found at i:462884 original size:13 final size:13
Alignment explanation
Indices: 462866--462892 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
462856 TACATTTAGT
462866 AATGTATCGATAC
1 AATGTATCGATAC
462879 AATGTATCGATAC
1 AATGTATCGATAC
462892 A
1 A
462893 TTTAGTAATG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:462904 original size:20 final size:20
Alignment explanation
Indices: 462845--462915 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
462835 TGTATCGATA
*
462845 TAATGTATTGATACATTTAG
1 TAATGTATCGATACATTTAG
462865 TAATGTATCGATAC------
1 TAATGTATCGATACATTTAG
462879 -AATGTATCGATACATTTAG
1 TAATGTATCGATACATTTAG
*
462898 TAATGTATCGATATATTT
1 TAATGTATCGATACATTT
462916 CCTTGGCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
13 13 0.31
20 29 0.69
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (20 bp):
TAATGTATCGATACATTTAG
Found at i:462952 original size:13 final size:13
Alignment explanation
Indices: 462930--462987 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
462920 GGCAGTAGCT
*
462930 TTGTAGCGATACA
1 TTGTATCGATACA
462943 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
462959 CTTATGTATCGATACA
1 --T-TGTATCGATACA
462975 TTGTATCGATACA
1 TTGTATCGATACA
462988 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:462968 original size:19 final size:19
Alignment explanation
Indices: 462944--463006 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
462934 AGCGATACAT
462944 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
462963 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
462976 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
462995 TGTATCGATACA
1 TGTATCGATACA
463007 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:462977 original size:32 final size:32
Alignment explanation
Indices: 462931--463006 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
462921 GCAGTAGCTT
*
462931 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
462963 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
462995 TGTATCGATACA
1 TGTATCGATACA
463007 GTTACTGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:463869 original size:57 final size:58
Alignment explanation
Indices: 463797--463921 Score: 198
Period size: 57 Copynumber: 2.2 Consensus size: 58
463787 TAAACAGAGG
* * *
463797 TATTTATAGGTTGGATTGTAATCTAATTTTTTT-TTTAAATTCTTGCACAAGTAAAGT
1 TATTTATAGGCTGGATTGTAATCTAATTTTTTTCTTTAAATTCTTACACAAGTAAAGA
* *
463854 TGTTTATAGGCTGGATTGTAATCTAATTTTTTTCTTTAAATTCTTACACAAGTAGAGA
1 TATTTATAGGCTGGATTGTAATCTAATTTTTTTCTTTAAATTCTTACACAAGTAAAGA
463912 TATTTATAGG
1 TATTTATAGG
463922 TTGAATCATG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 31 0.51
58 30 0.49
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (58 bp):
TATTTATAGGCTGGATTGTAATCTAATTTTTTTCTTTAAATTCTTACACAAGTAAAGA
Found at i:465191 original size:14 final size:14
Alignment explanation
Indices: 465174--465200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
465164 AAAATTTTAA
465174 AATATTTTTATATC
1 AATATTTTTATATC
465188 AATATTTTTATAT
1 AATATTTTTATAT
465201 TTTTATAATT
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:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATTTTTATATC
Found at i:465441 original size:22 final size:22
Alignment explanation
Indices: 465402--465456 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
465392 AAATAAATTT
465402 TATTTAAATTTAATTATAAAAA
1 TATTTAAATTTAATTATAAAAA
*
465424 TATTTACATATTAA-TATAAAAA
1 TATTTAAAT-TTAATTATAAAAA
465446 -ATTTTAAATTT
1 TA-TTTAAATTT
465457 TTTATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.10
22 22 0.76
23 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTAAATTTAATTATAAAAA
Found at i:466350 original size:20 final size:20
Alignment explanation
Indices: 466325--466377 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
466315 CTAAGTGAAG
*
466325 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAGGA-AA
*
466345 TGTATCGATACATGATGAAA
1 TGTATCGATACATGAGGAAA
466365 TGTATCGATACAT
1 TGTATCGATACAT
466378 TATGCTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAGGAAA
Found at i:470361 original size:20 final size:20
Alignment explanation
Indices: 470346--470395 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
470336 CGATACAATT
470346 TATCGATACATTATACCATG
1 TATCGATACATTATACCATG
470366 TATCGATACATTATACCATG
1 TATCGATACATTATACCATG
470386 TATCGATACA
1 TATCGATACA
470396 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (20 bp):
TATCGATACATTATACCATG
Found at i:471069 original size:21 final size:22
Alignment explanation
Indices: 471015--471067 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
471005 AGTTTTCGTT
* *
471015 TTTCTGCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
* *
471037 TTTTTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
471059 TTTCTCCCC
1 TTTCTCCCC
471068 TTTTGTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.32, G:0.06, T:0.38
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:479100 original size:20 final size:20
Alignment explanation
Indices: 479075--479128 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
479065 GTTACAAGCA
479075 ATGTATCGATACAATTCAT-C
1 ATGTATCGATACAATT-ATAC
479095 ATGTATCGATAC-ATTATACC
1 ATGTATCGATACAATTATA-C
479115 ATGTATCGATACAA
1 ATGTATCGATACAA
479129 ACAATGGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.06
19 3 0.10
20 25 0.81
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTATAC
Found at i:479182 original size:20 final size:20
Alignment explanation
Indices: 479157--479211 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
479147 CTGCCAATTT
* **
479157 CATGTATCGCTACAATTGTC
1 CATGTATCGATACAATTGAA
479177 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
479196 CATGTATCGATACAAT
1 CATGTATCGATACAAT
479212 ATATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:480394 original size:28 final size:28
Alignment explanation
Indices: 480338--480414 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
480328 GGAATGAAGT
**
480338 CGGGGTTGGAGTATCCCCTCG--GAGGTAA
1 CGGGGTTGGAGTAT--CCTCGATGAAATAA
480366 CGGGGTTGGAGTATCCTCGATGAAATAA
1 CGGGGTTGGAGTATCCTCGATGAAATAA
*
480394 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCTCGAT
480415 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.11
28 39 0.89
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCGATGAAATAA
Found at i:480462 original size:52 final size:49
Alignment explanation
Indices: 480397--480578 Score: 220
Period size: 52 Copynumber: 3.6 Consensus size: 49
480387 GAAATAACGA
* * *
480397 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTT-GAAATAAAACCG
* * *
480448 GAGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGAA-ATAAAACCG
* *
480500 GGATTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGAAATAAAACCGG
1 GG-TTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAATAAAACC-G
*
480551 GGTTGGAGTATCCCCGATTATGAGAAAT
1 GGTTGGAGTATCCCCGATTATGAAAAAT
480579 CAATATTTCG
Statistics
Matches: 115, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
50 32 0.28
51 25 0.22
52 47 0.41
53 11 0.10
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAATAAAACCG
Found at i:483185 original size:21 final size:21
Alignment explanation
Indices: 483159--483200 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
483149 GTATCGATAC
483159 AATGTATCAATACATTTCCTT
1 AATGTATCAATACATTTCCTT
*
483180 AATGTATCGATACATTTCCTT
1 AATGTATCAATACATTTCCTT
483201 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (21 bp):
AATGTATCAATACATTTCCTT
Found at i:483236 original size:13 final size:13
Alignment explanation
Indices: 483218--483296 Score: 86
Period size: 13 Copynumber: 5.5 Consensus size: 13
483208 GCTTCGTAGT
483218 GATACATTGTATC
1 GATACATTGTATC
483231 GATACAACTCATGTATC
1 GATAC-A-T--TGTATC
483248 GATACATTGTATC
1 GATACATTGTATC
483261 GATACAACTCATGTATC
1 GATAC-A-T--TGTATC
483278 GATACATTGTATC
1 GATACATTGTATC
483291 GATACA
1 GATACA
483297 AAACTCTTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
13 28 0.48
14 2 0.03
15 4 0.07
16 2 0.03
17 22 0.38
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:483247 original size:17 final size:16
Alignment explanation
Indices: 483225--483315 Score: 95
Period size: 17 Copynumber: 5.8 Consensus size: 16
483215 AGTGATACAT
483225 TGTATCGATACAACTC
1 TGTATCGATACAACTC
483241 ATGTATCGATAC-A-T-
1 -TGTATCGATACAACTC
483255 TGTATCGATACAACTC
1 TGTATCGATACAACTC
483271 ATGTATCGATAC-A-T-
1 -TGTATCGATACAACTC
483285 TGTATCGATACAAAACTC
1 TGTATCGATAC--AACTC
483303 TTGTATCGATACA
1 -TGTATCGATACA
483316 TTTACTGAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.34
14 1 0.02
15 3 0.05
16 3 0.05
17 24 0.38
19 11 0.17
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (16 bp):
TGTATCGATACAACTC
Found at i:483252 original size:30 final size:30
Alignment explanation
Indices: 483218--483317 Score: 173
Period size: 30 Copynumber: 3.3 Consensus size: 30
483208 GCTTCGTAGT
483218 GATACATTGTATCGATACAACTCATGTATC
1 GATACATTGTATCGATACAACTCATGTATC
483248 GATACATTGTATCGATACAACTCATGTATC
1 GATACATTGTATCGATACAACTCATGTATC
*
483278 GATACATTGTATCGATACAAAACTCTTGTATC
1 GATACATTGTATCGATAC--AACTCATGTATC
483310 GATACATT
1 GATACATT
483318 TACTGAATGT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 48 0.72
32 19 0.28
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (30 bp):
GATACATTGTATCGATACAACTCATGTATC
Found at i:484186 original size:20 final size:19
Alignment explanation
Indices: 484137--484187 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
484127 TGTATTGATA
* **
484137 CATTATATCGATACATGCT
1 CATTATATTGATACATAAT
*
484156 CATTGTATTGATACATAAT
1 CATTATATTGATACATAAT
484175 CAATTATATTGAT
1 C-ATTATATTGAT
484188 GCATGAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (19 bp):
CATTATATTGATACATAAT
Found at i:487936 original size:20 final size:21
Alignment explanation
Indices: 487911--487950 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
487901 AATTTTCTAG
487911 AATGTATCGATACAT-TGAAT
1 AATGTATCGATACATCTGAAT
487931 AATGTATCGATACATCTGAA
1 AATGTATCGATACATCTGAA
487951 AAACCCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATCTGAAT
Found at i:489908 original size:19 final size:19
Alignment explanation
Indices: 489884--489944 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
489874 ACAGAAAATG
489884 TATCGATACATAAGTGTTT
1 TATCGATACATAAGTGTTT
489903 TATCGATAC--AA-TG---
1 TATCGATACATAAGTGTTT
489916 TATCGATACATAAGT-TTT
1 TATCGATACATAAGTGTTT
489934 GTATCGATACA
1 -TATCGATACA
489945 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
16 3 0.09
17 2 0.06
19 19 0.54
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATACATAAGTGTTT
Found at i:489921 original size:32 final size:32
Alignment explanation
Indices: 489880--489952 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
489870 ACAAACAGAA
489880 AATGTATCGATACATAAGTGTTT-TATCGATAC
1 AATGTATCGATACATAAGT-TTTGTATCGATAC
489912 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTATCGATAC
489944 AATGTATCG
1 AATGTATCG
489953 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 3 0.08
32 37 0.93
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTTTTGTATCGATAC
Found at i:489995 original size:21 final size:21
Alignment explanation
Indices: 489969--490010 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
489959 AGCTACTGCC
*
489969 AAGGAAATGTATCGATACATT
1 AAGGAAATGTACCGATACATT
*
489990 AAGGAATTGTACCGATACATT
1 AAGGAAATGTACCGATACATT
490011 GTATCGATAC
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:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTACCGATACATT
Found at i:492444 original size:52 final size:53
Alignment explanation
Indices: 492387--492751 Score: 163
Period size: 51 Copynumber: 6.9 Consensus size: 53
492377 CAATTGTTCA
* *
492387 TAATCGGGGATACT-CATA-TCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCA-ACT-CCGATTTTATTTCCAAAAACACCAATTTTCCTT
*
492439 TAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTT--TT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* * * ** * * ** *
492490 ACAATCGAGGATACTCTAA--CC--TTGTTATTTCGTCGGGGATACTCCAA--CCCCGT
1 -TAATCGGGGATACTCCAACTCCGATT-TTATTTC--C--AAAAACACCAATTTTCCTT
* * * * * *** *
492543 TACCTCTGAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATTGA-TTT-CTCA
1 TA-ATC---GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCT-T
* * * * *
492598 TAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACTAATTTTCC-A
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* * * * *
492649 TAATCGAGGATACTCTAACCCCGGTTTTATCTT-C-AAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACTCCGATTTTAT-TTCCAAAAACACCAATTTTCCTT
* *
492701 TAATTGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTTC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACC-AATTTTC
492752 ACAATCAAGG
Statistics
Matches: 237, Mismatches: 47, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
48 2 0.01
49 7 0.03
50 2 0.01
51 82 0.35
52 73 0.31
53 35 0.15
54 13 0.05
55 2 0.01
56 11 0.05
57 1 0.00
58 2 0.01
59 6 0.03
60 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCTT
Found at i:492610 original size:51 final size:51
Alignment explanation
Indices: 492552--492772 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
492542 TTACCTCTGA
** * * *
492552 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTC-CATAATC
492603 GGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACACTAATTTTCCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACTAATTTTCCATAATC
* * * * *
492654 GAGGATACTCTAACCCCGGTTTTATCTTCAAAACACTAATTTTCCTTTAATT
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCC-ATAATC
* * * * * *
492706 GGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTT-CACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACA-CTAATTTTCCATAATC
**
492758 AAGGATACTCCAACC
1 GGGGATACTCCAACC
492773 TCGTTATTTC
Statistics
Matches: 140, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
50 4 0.03
51 74 0.53
52 48 0.34
53 7 0.05
54 7 0.05
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCATAATC
Found at i:492792 original size:28 final size:28
Alignment explanation
Indices: 492760--492831 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
492750 TCACAATCAA
* ** *
492760 GGATACTCCAACCTCGTTATTTC-GTCGG
1 GGATACTCCAACCCCGTTACCTCTG-AGG
492788 GGATACTCCAACCCCGTTACCTCTGAGG
1 GGATACTCCAACCCCGTTACCTCTGAGG
492816 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
492832 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCTGAGG
Found at i:492850 original size:262 final size:262
Alignment explanation
Indices: 492385--492882 Score: 845
Period size: 262 Copynumber: 1.9 Consensus size: 262
492375 CTCAATTGTT
* * *
492385 CATAATCGGGGATACTCATATCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
1 CATAATCGAGGATACTCATACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGAT
* * * * *
492450 ACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTTACAATCGAGGATACTCTAACCTTGT
66 ACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTTCACAATCAAGGATACTCCAACCTCGT
**
492515 TATTTCGTCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCGACTTTATTTT
131 TATTTCGTCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCGACTTTATTCC
492580 CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTT
196 CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTT
492645 TC
261 TC
* *
492647 CATAATCGAGGATACTC-TAACCCCGGTTTTATCTTCAAAACACTAATTTTCCTTTAATTGGGGA
1 CATAATCGAGGATACTCAT-ACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGA
492711 TACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTTCACAATCAAGGATACTCCAACCTCG
65 TACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTTCACAATCAAGGATACTCCAACCTCG
*
492776 TTATTTCGTCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCGGCTTTATTC
130 TTATTTCGTCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCGACTTTATTC
* *
492841 CCAAAATATTGATTTCTCATAATTGGGGATACTCCAATCCCG
195 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
492883 TTATTTCCGA
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
261 1 0.00
262 219 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (262 bp):
CATAATCGAGGATACTCATACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGAT
ACTCCAACTCTGATTTTATTTCCAAAAACACCAAATTTTCACAATCAAGGATACTCCAACCTCGT
TATTTCGTCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCCGACTTTATTCC
CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTT
TC
Found at i:494414 original size:33 final size:33
Alignment explanation
Indices: 494357--494421 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
494347 TACCACTGTT
* *
494357 TGTATCGATACATGGCATAATGTATCAATACAA
1 TGTATCGATACATGGAAGAATGTATCAATACAA
*
494390 TGTATCGATACAT-GAAGAATTGTATCGATACA
1 TGTATCGATACATGGAAGAA-TGTATCAATACA
494422 TTGCCTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGGAAGAATGTATCAATACAA
Found at i:494488 original size:52 final size:52
Alignment explanation
Indices: 494410--494527 Score: 227
Period size: 52 Copynumber: 2.3 Consensus size: 52
494400 CATGAAGAAT
*
494410 TGTATCGATACATTGCCTTAAATGGCGATAAACGGCTATAATTTCAAATGCA
1 TGTATCGATACATTGCCTTAAATGGCGATAAACAGCTATAATTTCAAATGCA
494462 TGTATCGATACATTGCCTTAAATGGCGATAAACAGCTATAATTTCAAATGCA
1 TGTATCGATACATTGCCTTAAATGGCGATAAACAGCTATAATTTCAAATGCA
494514 TGTATCGATACATT
1 TGTATCGATACATT
494528 ATGAATTGTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATTGCCTTAAATGGCGATAAACAGCTATAATTTCAAATGCA
Found at i:496302 original size:13 final size:13
Alignment explanation
Indices: 496284--496309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
496274 CAATTTTTTG
496284 TGTATCGATACAT
1 TGTATCGATACAT
496297 TGTATCGATACAT
1 TGTATCGATACAT
496310 ACTTGCTGTA
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:504209 original size:32 final size:33
Alignment explanation
Indices: 504168--504247 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
504158 CACTTTTAGA
* ***
504168 TGTATCGATACATTGTATCGATATATG-TTCAT
1 TGTATCGATACATTGTATCGATACATGAAGAAT
504200 TGTATCGATACGATT-TATCGATACATGAAGAAT
1 TGTATCGATAC-ATTGTATCGATACATGAAGAAT
504233 TGTATCGATACATTG
1 TGTATCGATACATTG
504248 CCTCAAACGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACATGAAGAAT
Found at i:505110 original size:19 final size:19
Alignment explanation
Indices: 505086--505213 Score: 166
Period size: 19 Copynumber: 6.6 Consensus size: 19
505076 CGATACATTA
505086 TATCGATACATGCTTATTG
1 TATCGATACATGCTTATTG
*
505105 TATCGATACATGTTTATTG
1 TATCGATACATGCTTATTG
*
505124 TATTGATACATGCTTATTG
1 TATCGATACATGCTTATTG
*
505143 TATCGATACATGCTCATTG
1 TATCGATACATGCTTATTG
* *
505162 TATCGATACATACTCAATTG
1 TATCGATACATGCT-TATTG
* *
505182 TATCGATACATACTCAATTG
1 TATCGATACATGCT-TATTG
*
505202 TATCGACACATG
1 TATCGATACATG
505214 AAACTGGCAG
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 65 0.66
20 34 0.34
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (19 bp):
TATCGATACATGCTTATTG
Found at i:508439 original size:20 final size:19
Alignment explanation
Indices: 508385--508440 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
508375 AAAACCCTTA
*
508385 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
508405 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
508425 AATGTATCGATACATG
1 AAAGTATCGATACATG
508441 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:508538 original size:20 final size:20
Alignment explanation
Indices: 508491--508542 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
508481 GTAGCCAAAC
*
508491 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
*
508511 -TGTGTCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
508530 TTGTATCGATACA
1 TTGTATCGATACA
508543 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:512607 original size:15 final size:15
Alignment explanation
Indices: 512587--512617 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
512577 TAAAAATGTC
*
512587 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
512602 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
512617 C
1 C
512618 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:514865 original size:20 final size:20
Alignment explanation
Indices: 514822--514867 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
514812 AAATCTTTTG
514822 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
514843 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
514863 CAAAA
1 CAAAA
514868 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:517277 original size:20 final size:20
Alignment explanation
Indices: 517234--517285 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
517224 GTAGCCAAAC
*
517234 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
517254 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
517273 TTGTATCGATACA
1 TTGTATCGATACA
517286 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:523189 original size:27 final size:26
Alignment explanation
Indices: 523159--523210 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
523149 ATTTATATTA
*
523159 TAAAATATTAAGATATAAAAAATACTT
1 TAAAAGATTAA-ATATAAAAAATACTT
*
523186 TAAAAGATTAATTATAAAAAATACT
1 TAAAAGATTAAATATAAAAAATACT
523211 CTCAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAAAGATTAAATATAAAAAATACTT
Found at i:524566 original size:13 final size:13
Alignment explanation
Indices: 524548--524574 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
524538 ATATATTGCT
524548 TTGTATCGATACA
1 TTGTATCGATACA
524561 TTGTATCGATACA
1 TTGTATCGATACA
524574 T
1 T
524575 GTTTATTGTA
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:524566 original size:33 final size:32
Alignment explanation
Indices: 524529--524592 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
524519 CACACCCAGA
*
524529 TGTATCGATATATATTGCT-TTGTATCGATACAT
1 TGTATCGATACATATT--TATTGTATCGATACAT
*
524562 TGTATCGATACATGTTTATTGTATCGATACA
1 TGTATCGATACATATTTATTGTATCGATACA
524593 CCATGAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.04
32 13 0.46
33 14 0.50
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATATTTATTGTATCGATACAT
Found at i:525558 original size:10 final size:10
Alignment explanation
Indices: 525539--525569 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
525529 GTATCGATAC
525539 ATGAACAGTG
1 ATGAACAGTG
*
525549 ATGAATAGTG
1 ATGAACAGTG
525559 ATGAACAGTG
1 ATGAACAGTG
525569 A
1 A
525570 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:525629 original size:18 final size:19
Alignment explanation
Indices: 525593--525629 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
525583 CTACTACCAA
525593 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
525612 TGTATCGATACA-ATTTTG
1 TGTATCGATACATATTTTG
525630 GCTACTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:525657 original size:53 final size:53
Alignment explanation
Indices: 525593--525729 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
525583 CTACTACCAA
525593 TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
* *
525646 TGTATCGATACATATTGTGTGTATCGATACAATTTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
525699 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
525730 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
Found at i:525762 original size:20 final size:20
Alignment explanation
Indices: 525699--525769 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
525689 GCCAATGTCC
**
525699 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
525719 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
525739 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
*
525759 TGTATTGATAC
1 TGTATCGATAC
525770 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 37 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:525833 original size:21 final size:21
Alignment explanation
Indices: 525809--525849 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
525799 GTCAACCTTG
525809 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
525830 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
525850 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:528183 original size:20 final size:20
Alignment explanation
Indices: 528148--528199 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
528138 TATGTTGCGT
* *
528148 ATTGTATCGATACATTGTGA
1 ATTGTATTGATACATTGTCA
* *
528168 ATTGTATTGATGCATTTTCA
1 ATTGTATTGATACATTGTCA
*
528188 CTTGTATTGATA
1 ATTGTATTGATA
528200 AAAATGAAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTGTATTGATACATTGTCA
Found at i:529471 original size:11 final size:11
Alignment explanation
Indices: 529455--529480 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
529445 ACAAAAGCCT
529455 TATTTTGATAA
1 TATTTTGATAA
529466 TATTTTGATAA
1 TATTTTGATAA
529477 TATT
1 TATT
529481 ATATTCATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TATTTTGATAA
Found at i:533110 original size:20 final size:20
Alignment explanation
Indices: 533086--533139 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
533076 CACACCTAGA
*
533086 TGTATCGATACATATTG-CT
1 TGTATCGATACATATTGAAT
*
533105 TAGTATCGATACACATTGAAT
1 T-GTATCGATACATATTGAAT
533126 TGTATCGATACATA
1 TGTATCGATACATA
533140 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATATTGAAT
Found at i:533185 original size:13 final size:13
Alignment explanation
Indices: 533167--533191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
533157 AACTCACTCA
533167 GTATCGATACATT
1 GTATCGATACATT
533180 GTATCGATACAT
1 GTATCGATACAT
533192 GATGAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:533224 original size:20 final size:20
Alignment explanation
Indices: 533179--533224 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
533169 ATCGATACAT
* *
533179 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATAAAC
* *
533199 TATATCGATACATGGTAAAC
1 TGTATCGATACATGATAAAC
533219 TGTATC
1 TGTATC
533225 AATATATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATGATAAAC
Found at i:538393 original size:13 final size:13
Alignment explanation
Indices: 538375--538401 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
538365 ACATATTGCT
538375 TTGTATCGATACA
1 TTGTATCGATACA
538388 TTGTATCGATACA
1 TTGTATCGATACA
538401 T
1 T
538402 GTTCATAGTA
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:538400 original size:33 final size:32
Alignment explanation
Indices: 538356--538419 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
538346 CACACCCAGA
* *
538356 TGTATCAATACATATTGCTTTGTATCGATACAT
1 TGTATCAATACATATT-CATAGTATCGATACAT
* *
538389 TGTATCGATACATGTTCATAGTATCGATACA
1 TGTATCAATACATATTCATAGTATCGATACA
538420 CATTGAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (32 bp):
TGTATCAATACATATTCATAGTATCGATACAT
Found at i:538434 original size:20 final size:19
Alignment explanation
Indices: 538387--538439 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
538377 GTATCGATAC
** *
538387 ATTGTATCGATACATGTTC
1 ATTGTATCGATACACATTA
*
538406 ATAGTATCGATACACATTGA
1 ATTGTATCGATACACATT-A
538426 ATTGTATCGATACA
1 ATTGTATCGATACA
538440 TAAAACTAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACACATTA
Found at i:538606 original size:23 final size:23
Alignment explanation
Indices: 538579--538624 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
538569 TTATGAAAAG
*
538579 TATCGATATATACAAGTGTGAAT
1 TATCGATATATACAAGCGTGAAT
*
538602 TATCGATATATAGAAGCGTGAAT
1 TATCGATATATACAAGCGTGAAT
538625 GTGTGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (23 bp):
TATCGATATATACAAGCGTGAAT
Found at i:538762 original size:10 final size:9
Alignment explanation
Indices: 538733--538775 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
538723 CCAATAGGTG
538733 AAGAACAAC
1 AAGAACAAC
538742 AAGAACAAC
1 AAGAACAAC
538751 AAGAACCAAC
1 AAGAA-CAAC
*
538761 AAGAAACATC
1 AAG-AACAAC
538771 AAGAA
1 AAGAA
538776 ATCCAAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 16 0.52
10 13 0.42
11 2 0.06
ACGTcount: A:0.65, C:0.21, G:0.12, T:0.02
Consensus pattern (9 bp):
AAGAACAAC
Found at i:538776 original size:10 final size:10
Alignment explanation
Indices: 538736--538776 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
538726 ATAGGTGAAG
538736 AACAACAAG-
1 AACAACAAGA
538745 AACAACAAGA
1 AACAACAAGA
*
538755 ACCAACAAGA
1 AACAACAAGA
*
538765 AACATCAAGA
1 AACAACAAGA
538775 AA
1 AA
538777 TCCAAGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.66, C:0.22, G:0.10, T:0.02
Consensus pattern (10 bp):
AACAACAAGA
Found at i:540145 original size:3 final size:3
Alignment explanation
Indices: 540137--540170 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
540127 TCAACCATCA
*
540137 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
540171 AGTTGACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:541791 original size:51 final size:51
Alignment explanation
Indices: 541695--541814 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
541685 TAGAAAATAA
* * *
541695 CGGGGTTGGAGTATCCCCGATCGTGAAAAATCGATGATTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATCATGAAAAATCAATGATTTAGAAATAAAAC
* * * * *
541746 CGGGGTTGGAGAATCCCCGATTATGAGAAATTAAT-ATTTTAGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATCATGAAAAATCAATGA-TTTAGAAATAAAAC
*
541797 CGCGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
541815 TCGAAAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 57 0.98
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATCATGAAAAATCAATGATTTAGAAATAAAAC
Found at i:541830 original size:79 final size:78
Alignment explanation
Indices: 541746--542011 Score: 283
Period size: 79 Copynumber: 3.4 Consensus size: 78
541736 GAAATAAAAC
541746 CGGGGTTGGAGAATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGCGGTTGGAGTAT
1 CGGGGTTGGAGAATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCCG-GGTTGGAGTAT
541811 CCCCTCGAAAATAA
65 CCCCTCGAAAATAA
* * * * * * *
541825 TGGGGTTAGAGTATCCCCAATTATGAGAAATCAATATTTTAGGAATAAAGTCGGGGGTTGGAGTA
1 CGGGGTTGGAGAATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAG-C-CGGGTTGGAGTA
*
541890 TCCCCTTGAAAATAA
64 TCCCCTCGAAAATAA
* * * * * * *
541905 CGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTTAAAAATAAAACCAGGGTTGGAGTGT
1 CGGGGTTGGAGAATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCC-GGGTTGGAGTAT
541967 CCCCTC-AGAAATAA
65 CCCCTCGA-AAATAA
* *
541981 CGGGGTTGGA-ATATCCCTGATTGTGA-AAATT
1 CGGGGTTGGAGA-ATCCCCGATTATGAGAAATT
542012 CGGTGCTTTG
Statistics
Matches: 155, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
75 1 0.01
76 39 0.25
77 21 0.14
78 5 0.03
79 47 0.30
80 41 0.26
81 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (78 bp):
CGGGGTTGGAGAATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGGGTTGGAGTATC
CCCTCGAAAATAA
Found at i:542047 original size:51 final size:50
Alignment explanation
Indices: 541985--542149 Score: 197
Period size: 51 Copynumber: 3.2 Consensus size: 50
541975 AAATAACGGG
* * * *
541985 GTTGGAATATCCCTGATTGTGAAAATTCGGTGCTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAATT-GGTGTTTTGGAAATAAAATCGGA
* *
542036 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * *
542087 GTTGGAGTATCCCCGATTAAGAGAAATTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATGA-AAATTGGTGTTTTGGAAATAAAATCGGA
542137 GATTGGAGTATCC
1 G-TTGGAGTATCC
542150 TCGAGATGAA
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.03
51 90 0.91
52 6 0.06
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:542049 original size:79 final size:76
Alignment explanation
Indices: 541879--542049 Score: 193
Period size: 76 Copynumber: 2.2 Consensus size: 76
541869 ATAAAGTCGG
* * *
541879 GGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAA
1 GGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAATATCCCCGATGAAAAATTGATGCTTTAA
541944 AAATAAAACCA
66 AAATAAAACCA
* * * *
541955 GGGTTGGAGTGTCCCCTCAG-AAATAACGGGGTTGGAATATCCCTGATTGTGAAAATTCGGTGCT
1 GGGTTGGAGTATCCCCT-AGAAAATAACGGGGTTGGAATATCCCCGA-TG-AAAAATT-GATGCT
** *
542019 TTGGAAATAAAATC-
62 TTAAAAATAAAACCA
542033 GGAGTTGGAGTATCCCC
1 GG-GTTGGAGTATCCCC
542050 GATTATGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
76 40 0.51
77 3 0.04
78 8 0.10
79 28 0.35
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (76 bp):
GGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAATATCCCCGATGAAAAATTGATGCTTTAA
AAATAAAACCA
Found at i:544558 original size:21 final size:20
Alignment explanation
Indices: 544512--544590 Score: 95
Period size: 21 Copynumber: 3.9 Consensus size: 20
544502 AACTTCCTAG
*** *
544512 ATGTATCGATACATAGATTG
1 ATGTATCGATACATTTCTTA
544532 ATGTATCGATACATTTCTGTA
1 ATGTATCGATACATTTCT-TA
*
544553 ATGTATCTATACATTTCCTTA
1 ATGTATCGATACATTT-CTTA
544574 ATGTATCGATACATTTC
1 ATGTATCGATACATTTC
544591 CTTGGCAGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 16 0.31
21 33 0.65
22 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTA
Found at i:544591 original size:21 final size:21
Alignment explanation
Indices: 544532--544593 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
544522 ACATAGATTG
544532 ATGTATCGATACATTT-CTGTA
1 ATGTATCGATACATTTCCT-TA
*
544553 ATGTATCTATACATTTCCTTA
1 ATGTATCGATACATTTCCTTA
544574 ATGTATCGATACATTTCCTT
1 ATGTATCGATACATTTCCTT
544594 GGCAGTAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (21 bp):
ATGTATCGATACATTTCCTTA
Found at i:544653 original size:32 final size:32
Alignment explanation
Indices: 544612--544682 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
544602 CTTCGTAGCA
544612 ATACATTGTATCGATACAAA-ACTTATATATCG
1 ATACATTGTATCGATA-AAACACTTATATATCG
*
544644 ATACATTGTATCGATAAAACACTTATGTATCG
1 ATACATTGTATCGATAAAACACTTATATATCG
544676 ATACATT
1 ATACATT
544683 TTTTGTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATAAAACACTTATATATCG
Found at i:545581 original size:43 final size:42
Alignment explanation
Indices: 545458--545629 Score: 161
Period size: 42 Copynumber: 4.0 Consensus size: 42
545448 CTATTTTTCG
* *
545458 AGGAAAAAAGGAAAATGAAATGTGTCATGCTCTTTGAGGACTAGA
1 AGGAAAAAAGGAAAA-GAAATGCGTCCTGCTCTTTGAGGAC-A-A
545503 AGGGAAAAGAAGGAAATA-AAGA-GCGTCCTGCTCTTTGAGGACAA
1 A-GGAAAA-AAGGAAA-AGAA-ATGCGTCCTGCTCTTTGAGGACAA
*
545547 AGGAGAAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAA
1 AGGAAAAAAGGAAAA-GAAATGCGTCCTGCTCTTTGAGGACAA
* * * * **
545590 AAG-AAAGAGGAAAATAAAGTGAGTCCTATTCTTTGAGGAC
1 AGGAAAAAAGGAAAAGAAA-TGCGTCCTGCTCTTTGAGGAC
545630 TACAAAGTGC
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
41 4 0.04
42 35 0.32
43 31 0.28
44 2 0.02
45 2 0.02
46 26 0.24
47 8 0.07
48 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.19
Consensus pattern (42 bp):
AGGAAAAAAGGAAAAGAAATGCGTCCTGCTCTTTGAGGACAA
Found at i:545601 original size:42 final size:42
Alignment explanation
Indices: 545463--545629 Score: 151
Period size: 43 Copynumber: 3.9 Consensus size: 42
545453 TTTCGAGGAA
* * *
545463 AAAAGGAAAATGAAA-TGTGTCATGCTCTTTGAGGACTAGAAGGG
1 AAAAGGAAAA-GAAAGTGCGTCCTGCTCTTTGAGGAC-A-AAGAG
* * *
545507 AAAAGAAGGAAATAAAGAGCGTCCTGCTCTTTGAGGACAAAGGAG
1 AAAAG--GAAAAGAAAGTGCGTCCTGCTCTTTGAGGACAAA-GAG
545552 AAAAGGAAAACGAAA-TGCGTCCTGCTCTTTGAGGACAAA-AG
1 AAAAGGAAAA-GAAAGTGCGTCCTGCTCTTTGAGGACAAAGAG
* * **
545593 AAAGAGGAAAATAAAGTGAGTCCTATTCTTTGAGGAC
1 AAA-AGGAAAAGAAAGTGCGTCCTGCTCTTTGAGGAC
545630 TACAAAGTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
41 8 0.08
42 25 0.24
43 27 0.26
44 10 0.10
45 11 0.11
46 22 0.21
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.20
Consensus pattern (42 bp):
AAAAGGAAAAGAAAGTGCGTCCTGCTCTTTGAGGACAAAGAG
Found at i:545873 original size:155 final size:156
Alignment explanation
Indices: 545568--545910 Score: 494
Period size: 155 Copynumber: 2.2 Consensus size: 156
545558 AAAACGAAAT
* * * *
545568 GCGTCCTGCTCTTTGAGGACAAAAGAAAGAG-GAAAATAAAGTGAGTCCTATTCTTTGAGGACTA
1 GCGTCCTGCTCTTTGAGGAC---TGAAAG-GTGAAAAGAAAGAGAGTCCTACTCTTTGAGGACTA
*
545632 CAAAGTGCCACCAACTTGAGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTGGAA
62 CAAAGTGCCACCAACTTGAGTGGGCCTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTGGAA
*
545697 GGTGCTACCAACTCATGTGGGCTTTAAAAG
127 GGTGCCACCAACTCATGTGGGCTTTAAAAG
* *
545727 GCGTCCTGCTCTTTGAGGACTGAAAGGTGAAAAGAAAGAGCGTCCTGCTCTTTGAGGACTA-AAA
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGAAAAGAAAGAGAGTCCTACTCTTTGAGGACTACAAA
* * * * *
545791 GGTGCCACCAACTTGTGTGGGCCTT-AAAAGGAAAAGGCGTCCTATTCTTTGAGGACTGGAGGGT
66 -GTGCCACCAACTTGAGTGGGCCTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTGGAAGGT
545855 GCCACCAACTCATGTGGGCTTTAAAAG
130 GCCACCAACTCATGTGGGCTTTAAAAG
*
545882 GCGTCCTGCTCTTTGAGGACTGAAGGGTG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTG
545911 CCACCAACTT
Statistics
Matches: 168, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
155 93 0.55
156 55 0.33
159 20 0.12
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (156 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGAAAAGAAAGAGAGTCCTACTCTTTGAGGACTACAAA
GTGCCACCAACTTGAGTGGGCCTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTGGAAGGTG
CCACCAACTCATGTGGGCTTTAAAAG
Found at i:545909 original size:55 final size:55
Alignment explanation
Indices: 545761--545965 Score: 239
Period size: 55 Copynumber: 3.6 Consensus size: 55
545751 AGGTGAAAAG
* * *
545761 AAAGAGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCCTTAAAAGGA
1 AAAG-GCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGG-CTT-----TA
* ** **
545823 AAAGGCGTCCTATTCTTTGAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTTA
1 AAAGGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTA
* * *
545878 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTT
1 AAAGGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTA
*
545933 AAAGGCGTCCTACTCTTGGAGGACTAAAGGGTG
1 AAAGGCGTCCTACTCTTTGAGGACTAAAGGGTG
545966 AAAAGAGAGA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
55 80 0.63
60 3 0.02
61 39 0.31
62 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (55 bp):
AAAGGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTA
Found at i:545939 original size:210 final size:213
Alignment explanation
Indices: 545666--546185 Score: 692
Period size: 210 Copynumber: 2.4 Consensus size: 213
545656 CTTTGAAAAG
* * * **
545666 AAAAAGGCATCCTACTCTTTGAGGACTGGAA-GGTGCTACCAACTCATGTGGGCTTTAAAAGGCG
1 AAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
545730 TCCTGCTCTTTGAGGACTGAAA-GGTGAAAAGAAAGAGCGTCCTGCTCTTTGAGGACTAAAAGGT
66 TCCTGCTCTTTGAGGACTGAAAGGGTGAAAAGAAAGAGCGTCCTGCTCTTTGAGGACTAAAAGGT
* * *
545794 GCCACCAACTTGTGTGGGCCTTAAAAGGAAAAGGCGTCCTATTCTTTGAGGACTG-GAGGGTGCC
131 GCCACCAACTTGTGTGGGCCTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAGA-AGTGCC
545858 ACCAACTCATGTGGGCTTT
195 ACCAACTCATGTGGGCTTT
*
545877 -AAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGGTGCCACCAACTTGTGTGGGCTTTTAAAGGCG
1 AAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * * * *
545940 TCCTACTCTTGGAGGACT-AAAGGGTGAAAAGAGAGAGCGTCTTGCTCTTTGAGGACTAGAAGGT
66 TCCTGCTCTTTGAGGACTGAAAGGGTGAAAAGAAAGAGCGTCCTGCTCTTTGAGGACTAAAAGGT
* * *
546004 GCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACTGAGAAGTGCCA
131 GCCACCAACTTGTGTGGGCCTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAGAAGTGCCA
*
546069 CCAACTCGTGTGGGCTTT
196 CCAACTCATGTGGGCTTT
* *
546087 GAAAGGCAAAAGCGTCCTGCTCTTTGAGGACTGGAAGGTGCGCCACCAACTTGTGTGGGCTTTGC
1 --AA---AAAGGCGTCCTGCTCTTTGAGGACTGGAAGG-GTGCCACCAACTTGTGTGGGCTTT--
*
546152 AAAAAGAAAGCATCCTGCTCTTTGAGGACTGAAA
58 -AAAAG---GCGTCCTGCTCTTTGAGGACTGAAA
546186 AGTGCCACCA
Statistics
Matches: 267, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
209 6 0.02
210 181 0.68
211 2 0.01
213 1 0.00
216 24 0.09
217 5 0.02
218 23 0.09
221 4 0.01
224 18 0.07
225 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (213 bp):
AAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
TCCTGCTCTTTGAGGACTGAAAGGGTGAAAAGAAAGAGCGTCCTGCTCTTTGAGGACTAAAAGGT
GCCACCAACTTGTGTGGGCCTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAGAAGTGCCA
CCAACTCATGTGGGCTTT
Found at i:546074 original size:61 final size:61
Alignment explanation
Indices: 545982--546740 Score: 761
Period size: 61 Copynumber: 12.8 Consensus size: 61
545972 GAGAGCGTCT
*
545982 TGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCT
1 TGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
546043 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCAAAA-GCGTCC
1 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCATCC
*
546104 TGCTCTTTGAGGACTG-GAAGGTGCGCCACCAACTTGTGTGGGCTTTGCAAAAAG-AAA-GCATC
1 TGCTCTTTGAGGACTGAGAA-GT--GCCACCAACTTGTGTGGGCTTT--AAAAGGAAAAGGCATC
546166 C
61 C
* * *
546167 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGGCATCC
1 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * * * *
546228 TACTCTTTGAGGACTAAGAAGTGCCATCAACTCGTGTGGGCTTT-----G-AAAGGCATCT
1 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * * *
546283 TGCTCTTTGAGGACTG-GAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGTGAAAGTG--TCC
1 TGCTCTTTGAGGACTGAG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAG-GCATCC
* *
546344 TGCTCTTTGAGGACTG-GAAGGTGCCACCAACTTGTGTGGGCTTCGCAAAAAG-AAA-GCATCC
1 TGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTT--TAAAAGGAAAAGGCATCC
* * * * * * *
546405 TACTATTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAATGCGTTC
1 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
546466 TGCTTTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
1 TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
*
546520 TACTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT------AAAAGGCATCC
1 TGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
*
546575 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
1 TGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* *
546630 TACTCTTTGAGGACT-AGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCC
1 TGCTCTTTGAGGACTGA-GAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
546691 TGCTCTTTGAGGACT-AAAAGGTGCTACCAGCTTGTGTGGGCTTTAAAAGG
1 TGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGG
546741 CATCCTGCTC
Statistics
Matches: 602, Mismatches: 57, Indels: 78
0.82 0.08 0.11
Matches are distributed among these distances:
54 25 0.04
55 171 0.28
56 2 0.00
59 10 0.02
60 39 0.06
61 283 0.47
62 14 0.02
63 52 0.09
64 2 0.00
65 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (61 bp):
TGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
Found at i:546308 original size:116 final size:115
Alignment explanation
Indices: 545982--546755 Score: 861
Period size: 116 Copynumber: 6.6 Consensus size: 115
545972 GAGAGCGTCT
*
545982 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCT
1 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCT
* * * *
546047 CTTTGAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCAAAA-GCGTCC
60 CTTTGAGGACTGA-AAATGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCATCC
*
546104 TGCTCTTTGAGGACTGGAAGGTGCGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAGCATCCTG
1 TGCTCTTTGAGGACTAGAAGGT--GCCACCAACTTGTGTGGGCTTTG---AAAG---GCATCCTG
* *
546169 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGGCATCC
58 CTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * * *
546228 TACTCTTTGAGGACTAAGAA-GTGCCATCAACTCGTGTGGGCTTTGAAAGGCATCTTGCTCTTTG
1 TGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTG
* * *
546292 AGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGTGAAAGTG--TCC
65 AGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAG-GCATCC
* * *
546344 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTCGCAAAAAGAAAGCATCCTACT
1 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTG---AAAG---GCATCCTGCT
* * * * *
546409 ATTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAATGCGTTC
60 CTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
546466 TGCTTTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGA
1 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGA
*
546530 GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT------AAAAGGCATCC
66 GGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* *
546575 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTTTG
1 TGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTG
* * *
546639 AGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCC
65 AGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * * *
546691 TGCTCTTTGAGGACTAAAAGGTGCTACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGA
1 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGA
546756 AGACAAAAAG
Statistics
Matches: 569, Mismatches: 50, Indels: 72
0.82 0.07 0.10
Matches are distributed among these distances:
109 22 0.04
110 77 0.14
111 3 0.01
115 49 0.09
116 152 0.27
117 9 0.02
118 5 0.01
119 9 0.02
120 1 0.00
121 40 0.07
122 103 0.18
123 6 0.01
124 90 0.16
125 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (115 bp):
TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGA
GGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
Found at i:546984 original size:125 final size:121
Alignment explanation
Indices: 546779--547052 Score: 379
Period size: 125 Copynumber: 2.2 Consensus size: 121
546769 AAAGGAGGGA
* * * * *
546779 GCGTCCTACTCTTTGAGGACT-AAGAAGCGCCACCAACTTGTGTGGGCTTTAAAAGGAAGAGGTG
1 GCGTCCTGCTCTTTGAGGACTGAAG--GCGCCACCAACTTGGGTAGGCTTTAAAAGAAAAAGGTG
*
546843 TCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAT
64 TCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAG-AAAAAG
* * *
546902 GCGTCCTGCTTTTTTGAGGACTGAAGGTGCCACCAACTTGGGTAGGCTTTGAAAAGAAAAAATGT
1 GCGTCCTGC-TCTTTGAGGACTGAAGGCGCCACCAACTTGGGTAGGCTTT-AAAAG-AAAAAGGT
* *
546967 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAG
63 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAG
547026 GCGTCCTGCTCTTTGAGGACTGGAAGG
1 GCGTCCTGCTCTTTGAGGACT-GAAGG
547053 GCTAAAAGAG
Statistics
Matches: 134, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
123 40 0.30
124 34 0.25
125 60 0.45
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (121 bp):
GCGTCCTGCTCTTTGAGGACTGAAGGCGCCACCAACTTGGGTAGGCTTTAAAAGAAAAAGGTGTC
CTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAG
Found at i:546993 original size:62 final size:61
Alignment explanation
Indices: 546779--547046 Score: 331
Period size: 63 Copynumber: 4.3 Consensus size: 61
546769 AAAGGAGGGA
* * * * *
546779 GCGTCCTACTCTTTGAGGACTAAGAAGCGCCACCAACTTGTGTGGGCTTT-AAAAGGAAGAG
1 GCGTCCTACTCTTTGAGGACTAA-AGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAG
* * *
546840 GTGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAT
1 GCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAG-AAAAAG
* * * * * * *
546902 GCGTCCTGCTTTTTTGAGGACTGAAGGTGCCACCAACTTGGGTAGGCTTTGAAAAGAAAAAAT
1 GCGTCCTAC-TCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAG-AAAAAG
* *
546965 GTGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAG
1 GCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAG
*
547026 GCGTCCTGCTCTTTGAGGACT
1 GCGTCCTACTCTTTGAGGACT
547047 GGAAGGGCTA
Statistics
Matches: 178, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
60 23 0.13
61 50 0.28
62 51 0.29
63 54 0.30
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
GCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAG
Found at i:553276 original size:79 final size:78
Alignment explanation
Indices: 553193--553398 Score: 270
Period size: 79 Copynumber: 2.6 Consensus size: 78
553183 GAGATAGTAA
* * *
553193 CGGGGTTGGAGTATCCTTTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCC-CTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-A
*
553258 -TTTGGAAATAAAAT
64 TTTTAGAAATAAAAT
* * * *
553272 CGGGGTTGGAGTATCCCCTCAAAGATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCTTGAAA-ATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
*
553337 TTTAGAAATAAAGT
65 TTTAGAAATAAAAT
* *
553351 TGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTAT-CCCTTGAAAATAACGGGGTTGGAGTATCCCCGA
553399 CGATTAACGG
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.05
79 100 0.90
80 6 0.05
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
TTAGAAATAAAAT
Found at i:553414 original size:27 final size:26
Alignment explanation
Indices: 553352--553425 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 26
553342 AAATAAAGTT
553352 GGGGTTGGAGTATCCCCTCGAAAATAAC
1 GGGGTTGGAGTAT-CCC-CGAAAATAAC
* *
553380 GGGGTTGGAGTATCCCCGACGATTAAC
1 GGGGTTGGAGTATCCCCGA-AAATAAC
553407 GGGGTTGGAGTATCCCCGA
1 GGGGTTGGAGTATCCCCGA
553426 TGAAAAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 27 0.63
28 13 0.30
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
GGGGTTGGAGTATCCCCGAAAATAAC
Found at i:553461 original size:103 final size:104
Alignment explanation
Indices: 553272--553497 Score: 294
Period size: 103 Copynumber: 2.2 Consensus size: 104
553262 GAAATAAAAT
*
553272 CGGGGTTGGAGTATCCCCTCAAAGATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTAT-CCCTCAAAGATAACGGGGTTGGAGTATCCCCG--TATGAAAAATTAATAT
** * *
553337 TTTAGAAATAAAGTTGGGGTTGGAGTATCCCCTCGAAAATAA
63 TTTAGAAATAAAACTAGGGTTGGAGTATCCCCTCAAAAATAA
* * * *
553379 CGGGGTTGGAGTATCCC-CGACGATTAACGGGGTTGGAGTATCCCCG-ATGAAAAATTGATGTTT
1 CGGGGTTGGAGTATCCCTCAAAGA-TAACGGGGTTGGAGTATCCCCGTATGAAAAATTAATATTT
* *
553442 TAGAAATAAAACTAGGGTTGGAGTGTCCCTTCAAAAATAA
65 TAGAAATAAAACTAGGGTTGGAGTATCCCCTCAAAAATAA
*
553482 CGGGGTTGGAATATCC
1 CGGGGTTGGAGTATCC
553498 TTGATTGTGA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
103 63 0.59
105 4 0.04
106 25 0.24
107 14 0.13
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (104 bp):
CGGGGTTGGAGTATCCCTCAAAGATAACGGGGTTGGAGTATCCCCGTATGAAAAATTAATATTTT
AGAAATAAAACTAGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:553529 original size:182 final size:183
Alignment explanation
Indices: 553218--553550 Score: 436
Period size: 182 Copynumber: 1.8 Consensus size: 183
553208 CTTTTGAAAA
* *
553218 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTGGAAATAAAATCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGA-T-TGAAAAATCGATGATTTAGAAATAAAATCAGGGTTGGAG
* * * *
553283 TATCCCCTCAAAGATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAA
64 TATCCCCTCAAAAATAACGGGGTTGGAATATCCCCGATTATGAGAAATCAATACTTTAGAAATAA
* * *
553348 AGTTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGACGAT
129 AATCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGACGAT
* *
553403 TAACGGGGTTGGAGTATCCCCGA-TGAAAAATTGATGTTTTAGAAATAAAA-CTAGGGTTGGAGT
1 TAACGGGGTTGGAGTATCCCCGATTGAAAAATCGATGATTTAGAAATAAAATC-AGGGTTGGAGT
* * ** * * ** * *
553466 GTCCCTTCAAAAATAACGGGGTTGGAATATCCTTGATTGTGAGAAGTCGGTGCTTTGGAAATAAA
65 ATCCCCTCAAAAATAACGGGGTTGGAATATCCCCGATTATGAGAAATCAATACTTTAGAAATAAA
553531 ATCGGAGTTGGAGTATCCCC
130 ATCGGAGTTGGAGTATCCCC
553551 GATTATGGAA
Statistics
Matches: 126, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
181 1 0.01
182 102 0.81
185 23 0.18
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (183 bp):
TAACGGGGTTGGAGTATCCCCGATTGAAAAATCGATGATTTAGAAATAAAATCAGGGTTGGAGTA
TCCCCTCAAAAATAACGGGGTTGGAATATCCCCGATTATGAGAAATCAATACTTTAGAAATAAAA
TCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGACGAT
Found at i:553578 original size:51 final size:51
Alignment explanation
Indices: 553514--553650 Score: 161
Period size: 51 Copynumber: 2.7 Consensus size: 51
553504 GTGAGAAGTC
* *
553514 GGTGCTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATG-GAAAATG
1 GGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAG-AAATG
* * * *
553565 GGTGTTTTAGAAATAAAATCGAAGTTGCAGTATCCCCGATTAAGAGAAATT
1 GGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAGAAATG
* * *
553616 GATGTTTTGGAAATGAAACCGG-GATTGGAGTATCC
1 GGTGTTTTGGAAATAAAATCGGAG-TTGGAGTATCC
553651 TCGAGATGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.01
51 70 0.97
52 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAGAAATG
Found at i:558146 original size:27 final size:27
Alignment explanation
Indices: 558116--558185 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
558106 ATAGAGCCTA
* *
558116 GGCCATACAAGATGAAAATTGGATTAT
1 GGCCATGCAAGAGGAAAATTGGATTAT
558143 GGCCATGCAAGAGGAAAATTGGATTAT
1 GGCCATGCAAGAGGAAAATTGGATTAT
558170 GGCCATGCAAGAGGAA
1 GGCCATGCAAGAGGAA
558186 CTAAACCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.20
Consensus pattern (27 bp):
GGCCATGCAAGAGGAAAATTGGATTAT
Found at i:562481 original size:13 final size:13
Alignment explanation
Indices: 562463--562487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562453 ATATTGCTTA
562463 GTATCGATACATT
1 GTATCGATACATT
562476 GTATCGATACAT
1 GTATCGATACAT
562488 GTTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:562580 original size:20 final size:20
Alignment explanation
Indices: 562555--562603 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
562545 AACTCACTCA
*
562555 GTATCGATACATGATAAATT
1 GTATCGATACATGATAAAAT
*
562575 GTATCGATACATGGTAAAAT
1 GTATCGATACATGATAAAAT
562595 GTATCGATA
1 GTATCGATA
562604 TATTGTGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGATAAAAT
Found at i:564029 original size:16 final size:17
Alignment explanation
Indices: 564010--564046 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
564000 CTCGAACCTG
564010 AAATGATCTAAACCC-A
1 AAATGATCTAAACCCGA
564026 AAATGATCTAAACCCGA
1 AAATGATCTAAACCCGA
564043 AAAT
1 AAAT
564047 AACCTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (17 bp):
AAATGATCTAAACCCGA
Found at i:567093 original size:52 final size:51
Alignment explanation
Indices: 567034--567204 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 51
567024 AAATAATAAG
** *
567034 GTTGGAGTATCCTTGATTGTGAAAAATTGATGTTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTTAGAAATAAAA-CGGA
* ** * * *
567086 GTTGGAGTATCCCCAATTAAAGGAAAATTGGTGTTTTGA-AAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGGAAAATTGATGTTTTTAGAAATAAAA-CGGA
* *
567138 GTTGGAGTATCCCCGATTGTGGAAAATT-A-GCGTTTTAGAAATAAAACCGA
1 GTTGGAGTATCCCCGATTGTGGAAAATTGATG-TTTTTAGAAATAAAACGGA
567188 GGTTGGAGTATCCCCGA
1 -GTTGGAGTATCCCCGA
567205 ATATGAGAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 6 0.06
51 32 0.33
52 43 0.44
53 15 0.15
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTTAGAAATAAAACGGA
Found at i:567183 original size:51 final size:51
Alignment explanation
Indices: 567033--567253 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
567023 GAAATAATAA
** * * *
567033 GGTTGGAGTATCCTTGATTGTGAAAAATT-GATGTTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAG-TG-TTTTAGAAATAAAACCGG
* * * *
567085 AGTTGGAGTATCCCCAATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTAG-AAATAAAACCGG
* * *
567137 GGTTGGAGTATCCCCGATTGTGGAAAATTAGCGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * * *
567188 GGTTGGAGTATCCCCGAATAT-GAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAACCGG
567239 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
567254 TCGGAGGTAA
Statistics
Matches: 140, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
50 2 0.01
51 80 0.57
52 48 0.34
53 9 0.06
54 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:567276 original size:28 final size:27
Alignment explanation
Indices: 567236--567308 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
567226 GAAATAAAGC
**
567236 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGA-GTAA
* *
567264 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGAGGAGTAA
*
567291 CGGGATTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
567309 AATGAGAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.19, C:0.22, G:0.36, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGGAGTAA
Found at i:567344 original size:103 final size:105
Alignment explanation
Indices: 567190--567387 Score: 265
Period size: 103 Copynumber: 1.9 Consensus size: 105
567180 AAAACCGAGG
* *
567190 TTGGAGTATCCCCGAATATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCT
1 TTGGAGTATCCCC-AATATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCT
* ** *
567255 CGGAGGTAACGGGGTTGGAGTATCCCCGATGATTAACGGGA
65 CAGAAATAACGGGGTTGGAATATCCCCGATGATTAACGGGA
** * * *
567296 TTGGAGTATCCCC-A-ATGAGAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGTGTCCCCTC
1 TTGGAGTATCCCCAATATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTC
*
567359 AGAAATAACGGGGTTGGAATATCTCCGAT
66 AGAAATAACGGGGTTGGAATATCCCCGAT
567388 TGTGAAAAGT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
103 66 0.82
104 1 0.01
106 13 0.16
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (105 bp):
TTGGAGTATCCCCAATATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTC
AGAAATAACGGGGTTGGAATATCCCCGATGATTAACGGGA
Found at i:567438 original size:51 final size:51
Alignment explanation
Indices: 567371--567491 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
567361 AAATAACGGG
* * * * *
567371 GTTGGAATATCTCCGATTGTGAAAAGTCGGTGCTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTAGAAATAAAATCGGA
* *
567422 GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTAGAAATAAAATCGGA
567473 GTTGGAGTATCCCCGATTA
1 GTTGGAGTATCCCCGATTA
567492 AGAGAAATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTAGAAATAAAATCGGA
Found at i:567507 original size:51 final size:51
Alignment explanation
Indices: 567408--567536 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
567398 CGGTGCTTTG
* *
567408 GAAATAAAATCGGAGTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTA
1 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTA
* * *
567459 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAGAAATTGATGTTTTG
1 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTA
* * *
567510 GAAATGAAACCAGGA-TTAGAGTATCCC
1 GAAATAAAATC-GGAGTTGGAGTATCCC
567537 TTCGAAAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 66 0.96
52 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (51 bp):
GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTA
Found at i:567708 original size:51 final size:50
Alignment explanation
Indices: 567552--567724 Score: 179
Period size: 51 Copynumber: 3.4 Consensus size: 50
567542 AAATAACAGG
* * * *
567552 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTT-AAGAAT-AAAGCAGGG
1 GTTGGAGTATCCCCGATTATGA-AAATTAGTATTTTGAA-AATAAAATC-GGA
* * * *
567603 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATG-AAAATT--AGTATTTTGAAAATAAAATCGGA
*
567656 GTTGGAGTATCCCCAATTATAGAAAATTAGTATTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTAGTATTTTGAAAATAAAATCGGA
*
567707 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
567725 GCAGAGAATT
Statistics
Matches: 101, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
51 60 0.59
52 1 0.01
53 34 0.34
54 6 0.06
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATTAGTATTTTGAAAATAAAATCGGA
Found at i:570089 original size:13 final size:13
Alignment explanation
Indices: 570071--570096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
570061 AACTTCCTAG
570071 ATGTATCGATACA
1 ATGTATCGATACA
570084 ATGTATCGATACA
1 ATGTATCGATACA
570097 TTTCCTTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:570109 original size:21 final size:21
Alignment explanation
Indices: 570083--570124 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
570073 GTATCGATAC
570083 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
570104 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
570125 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Done.