Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 4 of 19
Found at i:405986 original size:33 final size:37
Alignment explanation
Indices: 405948--406041 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 37
405938 ATGCACATTC
405948 ATAAATTATATAAATTCATGA-AT-TTAAATAT-TT-
1 ATAAATTATATAAATTCATGAGATATTAAATATATTA
*
405981 ATAAATTATA-AATATACATGAATGATATTAAATATATTA
1 ATAAATTATATAA-ATTCATG-A-GATATTAAATATATTA
* *
406020 ATAAATTATATACATTTATGAG
1 ATAAATTATATAAATTCATGAG
406042 TCTTAACAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
32 2 0.04
33 16 0.33
34 1 0.02
36 2 0.04
37 9 0.18
38 3 0.06
39 15 0.31
40 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (37 bp):
ATAAATTATATAAATTCATGAGATATTAAATATATTA
Found at i:406469 original size:13 final size:13
Alignment explanation
Indices: 406451--406489 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
406441 CGATAAATTT
406451 TTTATTTTTTAAA
1 TTTATTTTTTAAA
406464 TTTATTTTTTATAA
1 TTTATTTTTTA-AA
**
406478 TAAATTTTTTAA
1 TTTATTTTTTAA
406490 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTTTTTAAA
Found at i:410790 original size:17 final size:17
Alignment explanation
Indices: 410750--410791 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
410740 TTTATTTTTT
*
410750 AATAAAATTATAAATAT
1 AATAAAATTATAAATAC
*
410767 AAAAAAATTA-AAACTAC
1 AATAAAATTATAAA-TAC
410784 AATAAAAT
1 AATAAAAT
410792 AGTTAGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAATTATAAATAC
Found at i:411819 original size:20 final size:19
Alignment explanation
Indices: 411794--411846 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
411784 TATTTATAAT
411794 TAATTATAAATAAATTTAAA
1 TAATTATAAATAAA-TTAAA
411814 TAATTATATAA-AAA-TAAA
1 TAATTATA-AATAAATTAAA
* *
411832 AAATTATAATTAAAT
1 TAATTATAAATAAAT
411847 ATATGATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.04
18 14 0.50
20 11 0.39
21 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATTATAAATAAATTAAA
Found at i:411921 original size:25 final size:28
Alignment explanation
Indices: 411893--411951 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 28
411883 TATTTTTGAG
411893 TAAATAAAATTT-TAAAAGT-AT-CAAA-
1 TAAATAAAATTTAT-AAAGTAATACAAAT
*
411918 TAAATTAAATTTATAAAGTAATACAAAT
1 TAAATAAAATTTATAAAGTAATACAAAT
411946 TAAATA
1 TAAATA
411952 TTATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 16 0.57
26 3 0.11
27 4 0.14
28 5 0.18
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
TAAATAAAATTTATAAAGTAATACAAAT
Found at i:412199 original size:21 final size:21
Alignment explanation
Indices: 412123--412203 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
412113 ATTGTTGTAG
* *
412123 TAAGATTAGTTATTGTAATGT-
1 TAAGATTAGATATTATAAT-TA
* * *
412144 TGAGATT-GAATACTATAATGA
1 TAAGATTAG-ATATTATAATTA
412165 TAAGATTA-AGTATTATAATTA
1 TAAGATTAGA-TATTATAATTA
412186 TAAGATTAGATATT-TAAT
1 TAAGATTAGATATTATAAT
412204 GGTAAAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
20 6 0.13
21 40 0.85
22 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAGATTAGATATTATAATTA
Found at i:412367 original size:23 final size:24
Alignment explanation
Indices: 412341--412400 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
412331 TATATTTATT
* *
412341 TTCAAAATAATTATTAAA-ATATA
1 TTCAAAATAATAATAAAATATATA
* *
412364 TTCATATTATATAATAAAATATATA
1 TTCAAAATA-ATAATAAAATATATA
*
412389 TTAAAAATAATA
1 TTCAAAATAATA
412401 TTCATAATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 7 0.25
24 10 0.36
25 11 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
TTCAAAATAATAATAAAATATATA
Found at i:412372 original size:19 final size:19
Alignment explanation
Indices: 412350--412415 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
412340 TTTCAAAATA
412350 ATTATTAAAATATATTCAT
1 ATTATTAAAATATATTCAT
*
412369 ATTATATAATAAAATA-T-AT
1 ATTAT-TAA-AATATATTCAT
412388 ATTA--AAAATAATATTCAT
1 ATTATTAAAAT-ATATTCAT
412406 A--ATTAAAATA
1 ATTATTAAAATA
412416 AATTAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
15 2 0.05
16 6 0.16
17 2 0.05
18 8 0.21
19 11 0.29
20 4 0.11
21 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTATTAAAATATATTCAT
Found at i:412383 original size:35 final size:36
Alignment explanation
Indices: 412344--412424 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
412334 ATTTATTTTC
412344 AAAATAATTATT-AAAAT-ATATTCAT-ATTATATAAT
1 AAAATAATTATTAAAAATAATATTCATAATTA-A-AAT
412379 AAAAT-ATATATTAAAAATAATATTCATAATTAAAAT
1 AAAATAAT-TATTAAAAATAATATTCATAATTAAAAT
*
412415 AAATTAATTA
1 AAAATAATTA
412425 AATAAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
34 2 0.05
35 9 0.22
36 14 0.35
37 11 0.28
38 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAATAATTATTAAAAATAATATTCATAATTAAAAT
Found at i:412413 original size:18 final size:18
Alignment explanation
Indices: 412353--412416 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
412343 CAAAATAATT
412353 ATTAAAAT-ATATTCAT-
1 ATTAAAATAATATTCATA
*
412369 ATTATATAATAA-AAT-ATA
1 ATTA-A-AATAATATTCATA
412387 TATTAAAAATAATATTCATA
1 -ATT-AAAATAATATTCATA
412407 ATTAAAATAA
1 ATTAAAATAA
412417 ATTAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
16 4 0.11
17 3 0.08
18 17 0.45
19 10 0.26
20 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAAAATAATATTCATA
Found at i:412916 original size:15 final size:15
Alignment explanation
Indices: 412896--412932 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
412886 AATCTTCATT
* *
412896 AATTTAAGTTAAATC
1 AATTTAAATTAAATA
412911 AATTTAAATTAAATA
1 AATTTAAATTAAATA
412926 AATTTAA
1 AATTTAA
412933 TTCGACCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTTAAATTAAATA
Found at i:413391 original size:19 final size:19
Alignment explanation
Indices: 413367--413413 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
413357 TAACTTAAAA
*
413367 ATATTTAATTTTTAA-ATAT
1 ATATTTAA-ATTTAATATAT
*
413386 ATATTTAAATTTAATATTT
1 ATATTTAAATTTAATATAT
413405 ATATTTAAA
1 ATATTTAAA
413414 ATTCAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTAAATTTAATATAT
Found at i:413404 original size:13 final size:13
Alignment explanation
Indices: 413369--413412 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
413359 ACTTAAAAAT
*
413369 ATTTAATTTTTAA
1 ATTTAATATTTAA
*
413382 ATAT-ATATTTAA
1 ATTTAATATTTAA
*
413394 ATTTAATATTTAT
1 ATTTAATATTTAA
413407 ATTTAA
1 ATTTAA
413413 AATTCAAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAATATTTAA
Found at i:418448 original size:27 final size:26
Alignment explanation
Indices: 418410--418464 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
418400 CTTAAAATTT
*
418410 ATTAATATAAAT-TATTAATATATTGAA
1 ATTAATATAAATATA-AAATATATT-AA
418437 ATTAATATAAATATAAAATATATTAA
1 ATTAATATAAATATAAAATATATTAA
418463 AT
1 AT
418465 ACGATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 20 0.77
28 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTAATATAAATATAAAATATATTAA
Found at i:424452 original size:16 final size:16
Alignment explanation
Indices: 424431--424476 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
424421 ATACAGAATT
*
424431 AAATTATTTTTTAAAA
1 AAATTATATTTTAAAA
424447 AAATTA-ATTTTAAAA
1 AAATTATATTTTAAAA
*
424462 AATTTATAATTTTAA
1 AAATTAT-ATTTTAA
424477 TGATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
16 6 0.23
17 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTATATTTTAAAA
Found at i:424977 original size:18 final size:18
Alignment explanation
Indices: 424954--425028 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
424944 TAGCTATATT
424954 ATATTTATGTTATTTTTA
1 ATATTTATGTTATTTTTA
* *
424972 ATATTT-TAATTATTTTAA
1 ATATTTAT-GTTATTTTTA
*
424990 AAATATTATG-TATTTATATA
1 ATAT-TTATGTTATTT-T-TA
425010 A-ATTTTAT-TTATTTTTA
1 ATA-TTTATGTTATTTTTA
425027 AT
1 AT
425029 TTTTTTTATG
Statistics
Matches: 44, Mismatches: 5, Indels: 16
0.68 0.08 0.25
Matches are distributed among these distances:
17 4 0.09
18 23 0.52
19 13 0.30
20 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATATTTATGTTATTTTTA
Found at i:425535 original size:25 final size:23
Alignment explanation
Indices: 425483--425536 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
425473 ATTATAATAA
425483 TATTA-TTTTTCATATTATATTT
1 TATTATTTTTTCATATTATATTT
*
425505 TAATTATTTTTCTCTTATTATATTT
1 T-ATTATTTTT-TCATATTATATTT
425530 GTATTAT
1 -TATTAT
425537 ATCTAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 4 0.15
24 4 0.15
25 17 0.63
26 1 0.04
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTTTTTCATATTATATTT
Found at i:427828 original size:2 final size:2
Alignment explanation
Indices: 427821--427859 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
427811 ACTTGTTGCA
427821 AT AT AT 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 AT AT AT A
427860 ACACTTTTCT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:428329 original size:25 final size:25
Alignment explanation
Indices: 428301--428350 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
428291 TATCAACATG
428301 ATATAGATAAGATAATATAAATTTA
1 ATATAGATAAGATAATATAAATTTA
428326 ATATAGATAAGATAATATAAATTTA
1 ATATAGATAAGATAATATAAATTTA
428351 GAGTTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (25 bp):
ATATAGATAAGATAATATAAATTTA
Found at i:429189 original size:135 final size:135
Alignment explanation
Indices: 429050--429303 Score: 291
Period size: 135 Copynumber: 1.9 Consensus size: 135
429040 TTAGTTTACG
* * *
429050 TAATTAATTAAAATTT-AGTGAATGGATTCATAAAACT-CAAAATTTAATTCATTTAATTCAT-A
1 TAATTAATTAAAATTTAAG-GAATGAATTCATAAAA-TACAAAATTTAATCCAATTAATTCATGA
** * *
429112 TAACATAGAGTTTAGATCAAGAGATTAACTCAATTAGTATA-CAAAGTTCAGAGTTTAGTTCAAT
64 -AACATAGAACTTAGATAAAGAGATTAACTCAATTAGTATATCAAA-TTCAAAGTTTAGTTCAAT
429176 TAATTCATA
127 TAATTCATA
* * * * * *
429185 TAATTAGTTAACATTTAAGGGATTAATTCATAAAATACAAAGTTTAGTCCAATTAATTCATGAAA
1 TAATTAATTAAAATTTAAGGAATGAATTCATAAAATACAAAATTTAATCCAATTAATTCATGAAA
* ** *
429250 CCTAGAACTTATCTAAAGAGATTAACTTAATTAGTATATCAAATTCAAAGTTTA
66 CATAGAACTTAGATAAAGAGATTAACTCAATTAGTATATCAAATTCAAAGTTTA
429304 ATTGATTCAT
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
134 1 0.01
135 90 0.92
136 7 0.07
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (135 bp):
TAATTAATTAAAATTTAAGGAATGAATTCATAAAATACAAAATTTAATCCAATTAATTCATGAAA
CATAGAACTTAGATAAAGAGATTAACTCAATTAGTATATCAAATTCAAAGTTTAGTTCAATTAAT
TCATA
Found at i:429496 original size:18 final size:19
Alignment explanation
Indices: 429464--429506 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
429454 TAATATTTAT
*
429464 AATATTTTTTATATTCTCA
1 AATATATTTTATATTCTCA
429483 AATATATTTT-TATTCTCA
1 AATATATTTTATATTCTCA
429501 AATATA
1 AATATA
429507 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATATTTTATATTCTCA
Found at i:430798 original size:30 final size:29
Alignment explanation
Indices: 430764--430856 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 29
430754 ATGTTACATA
430764 AATTTTAATATATTTATATATTTAAATTAT
1 AATTTTAATATATTTATATATTT-AATTAT
* *
430794 AATTTTATTATTTTTTAATATATTTTAATTAT
1 AATTTTAATA-TATTT-ATATA-TTTAATTAT
* * *
430826 -TTTTTATATCATATTCATATATATAATTAT
1 AATTTTA-AT-ATATTTATATATTTAATTAT
430856 A
1 A
430857 TTGCATCACA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
30 17 0.34
31 14 0.28
32 15 0.30
33 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
AATTTTAATATATTTATATATTTAATTAT
Found at i:430815 original size:21 final size:20
Alignment explanation
Indices: 430766--430831 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
430756 GTTACATAAA
*
430766 TTTTAATATA-TTTA-TATA
1 TTTTAATATATTTTATTATT
*
430784 TTTAAATTATAATTTTATTATT
1 TTTTAA-TAT-ATTTTATTATT
430806 TTTTAATATATTTTAATTATT
1 TTTTAATATATTTT-ATTATT
430827 TTTTA
1 TTTTA
430832 TATCATATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.12
19 3 0.08
20 6 0.15
21 18 0.45
22 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATATATTTTATTATT
Found at i:430826 original size:9 final size:10
Alignment explanation
Indices: 430765--430828 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
430755 TGTTACATAA
430765 ATTTTAATAT
1 ATTTTAATAT
430775 A-TTT-ATAT
1 ATTTTAATAT
*
430783 ATTTAAATTAT
1 ATTTTAA-TAT
*
430794 AATTTTATTAT
1 -ATTTTAATAT
*
430805 TTTTTAATAT
1 ATTTTAATAT
430815 ATTTTAAT-T
1 ATTTTAATAT
430824 ATTTT
1 ATTTT
430829 TTATATCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 5 0.11
9 11 0.25
10 17 0.39
11 6 0.14
12 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:432666 original size:2 final size:2
Alignment explanation
Indices: 432659--432694 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
432649 ACTCCTAATC
432659 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
432695 ATCTACCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:433729 original size:13 final size:13
Alignment explanation
Indices: 433711--433760 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
433701 ACTATTAAAT
433711 TTAAAATAAATTA
1 TTAAAATAAATTA
433724 TTAAAATAATATTA
1 TTAAAATAA-ATTA
*
433738 TTTTAAAATAATTTA
1 --TTAAAATAAATTA
433753 TTAAAATA
1 TTAAAATA
433761 TTGATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 17 0.52
14 4 0.12
15 3 0.09
16 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAATAAATTA
Found at i:438558 original size:15 final size:15
Alignment explanation
Indices: 438538--438583 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
438528 GATCATGTCC
*
438538 ATCCACCACTTGTTT
1 ATCCACCACCTGTTT
* *
438553 ATCCACTACCTGTTC
1 ATCCACCACCTGTTT
438568 ATCCACCACCTGTTT
1 ATCCACCACCTGTTT
438583 A
1 A
438584 CGCAGCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.35
Consensus pattern (15 bp):
ATCCACCACCTGTTT
Found at i:439220 original size:18 final size:18
Alignment explanation
Indices: 439179--439223 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
439169 AAAGCATTAT
*
439179 AAATTAAT-AAGAATACA
1 AAATTAATAAAAAATACA
* *
439196 AATTTAATAAAAAATATA
1 AAATTAATAAAAAATACA
439214 AAATTAATAA
1 AAATTAATAA
439224 GCATATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATTAATAAAAAATACA
Found at i:439564 original size:16 final size:16
Alignment explanation
Indices: 439543--439577 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
439533 TACTTAATAT
*
439543 TTATTAGTATAATTAA
1 TTATTAATATAATTAA
439559 TTATTAATATAATTAA
1 TTATTAATATAATTAA
439575 TTA
1 TTA
439578 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAATATAATTAA
Found at i:444719 original size:94 final size:90
Alignment explanation
Indices: 444233--444936 Score: 636
Period size: 94 Copynumber: 7.8 Consensus size: 90
444223 GATTCAATAG
* *
444233 CATTTCAAAGTCCACACAAGTCGGTGGCAACCCATTTCAAAGCTCACAAGTCAGTGGCATCATTT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCATTT
* * *
444298 CAAAGCGCACAAGTTGGTGACAACT
66 CAAAGCCCACAAGTCGGTGGCAACT
* * ** *
444323 CATTTCAAAG-TC-CACAAGTCAGTGGC-A-TTATTTCAAAGTCCACAAGTCAGTGGCATCATTT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCATTT
*
444384 CAAAGCGCACAAGTCGGTGGCAACT
66 CAAAGCCCACAAGTCGGTGGCAACT
* * * *
444409 CATTTCAAAGCCCACACAAGTCGATGGCAACTCATTTTCAAAGTCCACAAGTCAGTGGCATCCTT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCA-TTTCAAAGCCCACAAGTCAGTGGCATCATT
* ** *
444474 TTAAAGCCCACAAGTTAGTGACAACT
65 TCAAAGCCCACAAGTCGGTGGCAACT
* * * * ** *
444500 CATTTAAAAGCCCACACAAGTCGATGGCAACTCATTTGAAAGCCTACACAAGTTGGTGGCAACCC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCC--CACAAGTCAGTGGC-A-TC
444565 ATTTCAAAGCCCACAAGTCGGTGGCAACT
62 ATTTCAAAGCCCACAAGTCGGTGGCAACT
*
444594 CATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGT-AGGTGGCAACTCA
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCA-GTGGC-A-TCA
* * *
444658 TTTAAAAGCCTACACAAGTCGATGGTAACT
63 TTTCAAAGCC--CACAAGTCGGTGGCAACT
* * * * * *
444688 CATTTGAAAGCCCACATAAGTTGGTGGCAACCCTTTTCAAAGCCCACAAGACAGTGGCA-CTTTT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATC-ATT
* *
444752 TCAAAGCCCACAAGTCAGTGAC-AC-
65 TCAAAGCCCACAAGTCGGTGGCAACT
* * * * * *
444776 CTTTTCAAAG-CC-CACAAGAT-AGT-G-AGA-TCTTTTCAAAGCCCACAAGTCAGTGACATCCT
1 CATTTCAAAGCCCACACAAG-TCGGTGGCA-ACCCATTTCAAAGCCCACAAGTCAGTGGCATCAT
* ** *
444835 TTCAAAACCCACAAGTCATTGGCATC-
64 TTCAAAGCCCACAAGTCGGTGGCAACT
* * * **
444861 CTTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCACACAAGTTGGTGGCAACTC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A-TC
*
444922 TTTTCAAAGCCCACA
62 ATTTCAAAGCCCACA
444937 TAAGTTAGTG
Statistics
Matches: 522, Mismatches: 66, Indels: 53
0.81 0.10 0.08
Matches are distributed among these distances:
84 48 0.09
85 34 0.07
86 74 0.14
87 16 0.03
88 34 0.07
89 19 0.04
90 30 0.06
91 84 0.16
92 47 0.09
93 2 0.00
94 133 0.25
95 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (90 bp):
CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCATTT
CAAAGCCCACAAGTCGGTGGCAACT
Found at i:444873 original size:57 final size:56
Alignment explanation
Indices: 444235--444954 Score: 351
Period size: 62 Copynumber: 12.1 Consensus size: 56
444225 TTCAATAGCA
* * * * * *
444235 TTTCAAAGTCCACACAAGTCGGTGGCAACCCATTTCAAAGCTCACAAGTCAGTGGCATCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ATCCTTTTCAAAGCCCACAAGTCAGTGACA-CC
* ** * * * * * **
444295 TTTCAAAGCGCACAAGTTGGTGACAACTCATTTCAAAGTCCACAAGTCAGTGGCATTA
1 TTTCAAAGCCCACAAGTCAGTGGCATC-CTTTTCAAAGCCCACAAGTCAGTGACA-CC
* * * * *
444353 TTTCAAAGTCCACAAGTCAGTGGCAT-CATTTCAAAGCGCACAAGTCGGTGGCAACTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGAC-AC-C
* * *
444410 ATTTCAAAGCCCACACAAGTC-GATGGCAACTCATTTTCAAAGTCCACAAGTCAGTGGCATCC
1 -TTTCAAAG-CC-CACAAGTCAG-TGGC-A-TCCTTTTCAAAGCCCACAAGTCAGTGACA-CC
* * * * * * *
444472 TTTTAAAGCCCACAAGTTAGTGACAACTCATTTAAAAGCCCACACAAGTC-GATGGCAACTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-CTTTTCAAAG-CC-CACAAGTCAG-TGAC-AC-C
* ** * * * *
444533 ATTTGAAAGCCTACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGCAACTC
1 -TTTCAAAGCC--CACAAGTCAGTGGC-ATCCTTTTCAAAGCCCACAAGTCAGTGAC-AC-C
* * * * *
444595 ATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGT-AGGTGGCAACTC
1 -TTTCAAAG-CC-CACAAGTCAGTGGC-ATCCTTTTCAAAGCCCACAAGTCA-GTGAC-AC-C
* * * * * ** *
444657 ATTTAAAAGCCTACACAAGTC-GATGGTAACTCATTTGAAAGCCCACATAAGTTGGTGGCAACCC
1 -TTTCAAAGCC--CACAAGTCAG-TGGCATC-CTTTTCAAAGCCCAC--AAGTCAGTGAC-A-CC
* *
444721 TTTTCAAAGCCCACAAGACAGTGGCA-CTTTTTCAAAGCCCACAAGTCAGTGACACC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGACACC
444777 TTTTCAAAGCCCACAAGAT-AGTGAG-AT-CTTTTCAAAGCCCACAAGTCAGTGACATCC
1 -TTTCAAAGCCCACAAG-TCAGTG-GCATCCTTTTCAAAGCCCACAAGTCAGTGACA-CC
* * *
444834 TTTCAAAACCCACAAGTCATTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGACA-CC
** * *
444891 TTTCAAAGCCCACACAAGTTGGTGGCAACTCTTTTCAAAGCCCACATAAGTTAGTGACACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATC-CTTTTCAAAGCCCAC--AAGTCAGTGACACC
444952 TTT
1 TTT
444955 TTTTTAAAAG
Statistics
Matches: 549, Mismatches: 66, Indels: 89
0.78 0.09 0.13
Matches are distributed among these distances:
55 2 0.00
56 93 0.17
57 44 0.08
58 85 0.15
59 28 0.05
60 63 0.11
61 21 0.04
62 140 0.26
63 28 0.05
64 42 0.08
65 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGACACC
Found at i:444942 original size:32 final size:30
Alignment explanation
Indices: 444233--444936 Score: 595
Period size: 28 Copynumber: 23.5 Consensus size: 30
444223 GATTCAATAG
*
444233 CATTTCAAAGTCCACACAAGTCGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAACT
* *
444265 CATTTCAAAGCTCACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* * *
444293 CATTTCAAAGCGCACAAGTTGGTGACAACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444323 CATTTCAAAGTCCACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* * *
444351 TATTTCAAAGTCCACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
*
444379 CATTTCAAAGCGCACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
*
444409 CATTTCAAAGCCCACACAAGTCGATGGCAACT
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAACT
* *
444441 CATTTTCAAAGTCCACAAGTCAGTGGC-A-T
1 CA-TTTCAAAGCCCACAAGTCGGTGGCAACT
* * ** *
444470 CCTTTTAAAGCCCACAAGTTAGTGACAACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444500 CATTTAAAAGCCCACACAAGTCGATGGCAACT
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAACT
* * *
444532 CATTTGAAAGCCTACACAAGTTGGTGGCAACC
1 CATTTCAAAGCC--CACAAGTCGGTGGCAACT
444564 CATTTCAAAGCCCACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444594 CATTTGAAAGCCCACACAAGTCGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAACT
*
444626 CATTTCAAAGCCCACAAGTAGGTGGCAACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* * *
444656 CATTTAAAAGCCTACACAAGTCGATGGTAACT
1 CATTTCAAAGCC--CACAAGTCGGTGGCAACT
* * *
444688 CATTTGAAAGCCCACATAAGTTGGTGGCAACC
1 CATTTCAAAGCCCAC--AAGTCGGTGGCAACT
* * *
444720 CTTTTCAAAGCCCACAAGACAGTGGC-ACT
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* * *
444749 -TTTTCAAAGCCCACAAGTCAGTGAC-AC-
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444776 CTTTTCAAAGCCCACAAGAT-AGT-G-AGA-T
1 CATTTCAAAGCCCACAAG-TCGGTGGCA-ACT
* * *
444804 CTTTTCAAAGCCCACAAGTCAGTGAC-A-T
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* * ** *
444832 CCTTTCAAAACCCACAAGTCATTGGCATC-
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444861 CTTTTCAAAGCCCACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACAAGTCGGTGGCAACT
* *
444889 CCTTTCAAAGCCCACACAAGTTGGTGGCAACT
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAACT
*
444921 CTTTTCAAAGCCCACA
1 CATTTCAAAGCCCACA
444937 TAAGTTAGTG
Statistics
Matches: 562, Mismatches: 77, Indels: 68
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.00
28 192 0.34
29 35 0.06
30 135 0.24
31 25 0.04
32 166 0.30
33 8 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (30 bp):
CATTTCAAAGCCCACAAGTCGGTGGCAACT
Found at i:445955 original size:20 final size:20
Alignment explanation
Indices: 445878--445955 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
445868 TTTTTACCCA
* * *
445878 AATGTATCAATATATTTTTC
1 AATGTATCGATACATTCTTC
* * *
445898 AATATATCGATACATAT-ATG
1 AATGTATCGATACAT-TCTTC
445918 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
445938 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
445956 ATCTTTTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:449241 original size:17 final size:15
Alignment explanation
Indices: 449210--449245 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
449200 TTTATAATAT
449210 ATTTTTTAATTTTAA
1 ATTTTTTAATTTTAA
449225 ATTTTTATAACTTTTAA
1 ATTTTT-TAA-TTTTAA
449242 ATTT
1 ATTT
449246 AGAATGGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTTTAATTTTAA
Found at i:451674 original size:55 final size:55
Alignment explanation
Indices: 451622--451724 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
451612 TCCTCATTTT
* *
451622 TTAACTTATA-TTCAAAGAACCCTAACTTGCTTTTATCATTGCTAATTTTCATTA
1 TTAACTTAGAGTTCAAAGAACCATAACTTGCTTTTATCATTGCTAATTTTCATTA
* *
451676 TTAGCTTAGAGTTCAAAGAACCATACCTTGCTTTTATCATTGCTAATTT
1 TTAACTTAGAGTTCAAAGAACCATAACTTGCTTTTATCATTGCTAATTT
451725 GACAATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 8 0.18
55 36 0.82
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (55 bp):
TTAACTTAGAGTTCAAAGAACCATAACTTGCTTTTATCATTGCTAATTTTCATTA
Found at i:451971 original size:21 final size:21
Alignment explanation
Indices: 451947--451987 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
451937 ATATTTTATT
451947 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
451968 TAAATATTAATATAAAATAT
1 TAAATATTAATATAAAATAT
451988 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:452764 original size:25 final size:27
Alignment explanation
Indices: 452736--452793 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 27
452726 GTTATGCTAT
*
452736 AATTTTTTTATTT-TTTATAAAAT-TA
1 AATTTTTTTATTTATATATAAAATATA
*
452761 AA-TTTTTTATTTATATATTAAATATA
1 AATTTTTTTATTTATATATAAAATATA
452787 AATTTTT
1 AATTTTT
452794 AAAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.36
25 10 0.36
26 4 0.14
27 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTTTTTTATTTATATATAAAATATA
Found at i:457127 original size:2 final size:2
Alignment explanation
Indices: 457120--457170 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
457110 CTCTTCAACA
457120 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
457162 TC TC TC TC T
1 TC TC TC TC T
457171 TTTGGTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:457312 original size:11 final size:11
Alignment explanation
Indices: 457283--457314 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
457273 TGGATTATTT
*
457283 AATTAAAAATA
1 AATTAAATATA
457294 AATTAAATATA
1 AATTAAATATA
457305 AATTAAATAT
1 AATTAAATAT
457315 TTGATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTAAATATA
Found at i:461458 original size:11 final size:11
Alignment explanation
Indices: 461442--461483 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
461432 TAAAAATTAT
461442 ATTAAATTTAA
1 ATTAAATTTAA
* *
461453 ATTAAAAATTAT
1 ATT-AAATTTAA
461465 A-TAAATTTAA
1 ATTAAATTTAA
461475 ATTAAATTT
1 ATTAAATTT
461484 TATCAGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 7 0.28
11 11 0.44
12 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:461486 original size:22 final size:23
Alignment explanation
Indices: 461431--461480 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
461421 TTTTGATTTT
461431 TTAAAAATTATATTAAATTTAAA
1 TTAAAAATTATATTAAATTTAAA
461454 TTAAAAATTATA-TAAATTTAAA
1 TTAAAAATTATATTAAATTTAAA
461476 TTAAA
1 TTAAA
461481 TTTTATCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAAATTATATTAAATTTAAA
Found at i:462186 original size:35 final size:35
Alignment explanation
Indices: 462111--462187 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
462101 AATAAAAATT
* * ** * *
462111 ATTATTTAAAAAATAATTAAAATTTATGTTTGATAT
1 ATTA-TTAAAAAATAAATAAAATATATAATTAATAA
*
462147 ATTATTAAAAAATAAATAATATATATAATTAATAA
1 ATTATTAAAAAATAAATAAAATATATAATTAATAA
462182 ATTATT
1 ATTATT
462188 CTATTAGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTATTAAAAAATAAATAAAATATATAATTAATAA
Found at i:462678 original size:30 final size:30
Alignment explanation
Indices: 462644--462751 Score: 139
Period size: 30 Copynumber: 3.6 Consensus size: 30
462634 TTTTTATCAT
* *
462644 ATTATTTTTTTAATATAAATAAAATTTTTA
1 ATTATTTATTTAATATAAATATAATTTTTA
* *
462674 ATTA-TTATTCAATATAAATATAATTTATTT
1 ATTATTTATTTAATATAAATATAATTT-TTA
462704 ATT-TTTATTTAATATAAATATAATTTTTA
1 ATTATTTATTTAATATAAATATAATTTTTA
462733 ATTATTTATTATACATATA
1 ATTATTTATT-TA-ATATA
462752 TAAATATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
29 24 0.36
30 36 0.54
31 2 0.03
32 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTATTTATTTAATATAAATATAATTTTTA
Found at i:462737 original size:26 final size:26
Alignment explanation
Indices: 462652--462751 Score: 101
Period size: 26 Copynumber: 3.6 Consensus size: 26
462642 ATATTATTTT
*
462652 TTTAATATAAATAAAATTTTTAATTA
1 TTTAATATAAATATAATTTTTAATTA
*
462678 TTATTCAATATAAATATAATTTATTTATTTTTA
1 -T-TT-AATATAAATATAA-TT-TTTA--ATTA
462711 TTTAATATAAATATAATTTTTAATTA
1 TTTAATATAAATATAATTTTTAATTA
* *
462737 TTTATTATACATATA
1 TTTAATATAAATATA
462752 TAAATATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
26 16 0.26
27 1 0.02
28 6 0.10
29 14 0.23
30 15 0.24
31 6 0.10
32 1 0.02
33 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAATATAAATATAATTTTTAATTA
Found at i:463633 original size:19 final size:21
Alignment explanation
Indices: 463594--463639 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
463584 AAAATTTTTC
463594 TAAAAAATACATCATTAAAAA
1 TAAAAAATACATCATTAAAAA
*
463615 TAAAAAATA-ATTATT-AAAA
1 TAAAAAATACATCATTAAAAA
463634 TAAAAA
1 TAAAAA
463640 TCTTCCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.42
20 5 0.21
21 9 0.38
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAAATACATCATTAAAAA
Found at i:464967 original size:21 final size:21
Alignment explanation
Indices: 464913--464970 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
464903 CTCTAATCTG
* *
464913 AATTTATATAAAAAATGATAA
1 AATTAATATAAAAAATAATAA
* * *
464934 AATTAACAAAAAAAATAATAT
1 AATTAATATAAAAAATAATAA
*
464955 AATTATTATAAAAAAT
1 AATTAATATAAAAAAT
464971 TCAAAAATAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTAATATAAAAAATAATAA
Found at i:470830 original size:20 final size:21
Alignment explanation
Indices: 470797--470843 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
470787 TTTTTTCAAT
470797 TTTTTATTAATTATTAATTAG
1 TTTTTATTAATTATTAATTAG
*
470818 TTTTTA-TATTTATTAATTTA-
1 TTTTTATTAATTATTAA-TTAG
470838 TTTTTA
1 TTTTTA
470844 ATAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTATTAATTATTAATTAG
Found at i:470858 original size:28 final size:29
Alignment explanation
Indices: 470822--470901 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
470812 AATTAGTTTT
* *
470822 TATATTTATTAATTTATTTTTAATA-AAA
1 TATAATTATTAATTTATATTTAATACAAA
* *
470850 TTTAATTATT-ATTTATCATTTAATACAAG
1 TATAATTATTAATTTAT-ATTTAATACAAA
* *
470879 TATAATT-TTAATTAATGTTTAAT
1 TATAATTATTAATTTATATTTAAT
470902 TATTTAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 6 0.14
28 23 0.55
29 13 0.31
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
TATAATTATTAATTTATATTTAATACAAA
Found at i:489588 original size:13 final size:13
Alignment explanation
Indices: 489566--489595 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
489556 GCAGTCTAGT
489566 AAGAAAAAAAAGAG
1 AAGAAAAAAAA-AG
489580 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
489593 AAG
1 AAG
489596 GCAACAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAG
Found at i:494744 original size:31 final size:31
Alignment explanation
Indices: 494706--494771 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
494696 TTAATTTTAT
494706 TTTTAAAATATTTACGATAAAAAACTACTCA
1 TTTTAAAATATTTACGATAAAAAACTACTCA
*
494737 TTTTAAAATATTTACGATAAAAAACTACTTA
1 TTTTAAAATATTTACGATAAAAAACTACTCA
494768 TTTT
1 TTTT
494772 CTTAATTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (31 bp):
TTTTAAAATATTTACGATAAAAAACTACTCA
Found at i:496595 original size:20 final size:20
Alignment explanation
Indices: 496566--496605 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
496556 CAAATTAATT
*
496566 TAATATAAATTATTATTTAA
1 TAATAAAAATTATTATTTAA
*
496586 TAATAAAAATTTTTATTTAA
1 TAATAAAAATTATTATTTAA
496606 ATTTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAAAATTATTATTTAA
Found at i:501602 original size:21 final size:21
Alignment explanation
Indices: 501556--501595 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
501546 TTTAATAAAT
501556 AAAAAATTA-TTAATAGTATTA
1 AAAAAATTATTTAATA-TATTA
501577 AAAAAATTATTTAAT-TATT
1 AAAAAATTATTTAATATATT
501596 GATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAAAATTATTTAATATATTA
Found at i:501602 original size:22 final size:22
Alignment explanation
Indices: 501554--501612 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
501544 ATTTTAATAA
501554 ATAAAAAATTA-TTAATAGTATT
1 ATAAAAAATTATTTAATA-TATT
501576 A-AAAAAATTATTTAAT-TATT
1 ATAAAAAATTATTTAATATATT
*
501596 GATAAAATATTAATTTA
1 -ATAAAAAATT-ATTTA
501613 TAATCTAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.12
21 10 0.31
22 13 0.41
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAAAAAATTATTTAATATATT
Found at i:501801 original size:14 final size:14
Alignment explanation
Indices: 501775--501826 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
501765 GCTTATAATT
501775 TTAAAATTACAAAAA
1 TTAAAA-TACAAAAA
*
501790 TTAAAATACAAAAT
1 TTAAAATACAAAAA
* *
501804 TTAATAATATAAAGA
1 TTAA-AATACAAAAA
501819 TTAAAATA
1 TTAAAATA
501827 TCTTTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 15 0.47
15 17 0.53
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (14 bp):
TTAAAATACAAAAA
Found at i:501945 original size:16 final size:17
Alignment explanation
Indices: 501909--501946 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
501899 GGTAGGTTCA
*
501909 AGTTCGGGTTCATTCTG
1 AGTTCGGGCTCATTCTG
501926 -GTTCGGGCTCATTC-G
1 AGTTCGGGCTCATTCTG
501941 AGTTCG
1 AGTTCG
501947 AATTTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.37
Consensus pattern (17 bp):
AGTTCGGGCTCATTCTG
Found at i:502419 original size:12 final size:12
Alignment explanation
Indices: 502402--502437 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
502392 AAAAATGTAA
502402 AATATATTTAAT
1 AATATATTTAAT
*
502414 AATATATTTAAA
1 AATATATTTAAT
*
502426 AATCTATTTAAT
1 AATATATTTAAT
502438 CTTAACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATATTTAAT
Found at i:505417 original size:12 final size:12
Alignment explanation
Indices: 505400--505424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
505390 ACTGCTTGAG
505400 TGGGGCAAATTA
1 TGGGGCAAATTA
505412 TGGGGCAAATTA
1 TGGGGCAAATTA
505424 T
1 T
505425 ATTGTCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (12 bp):
TGGGGCAAATTA
Found at i:505836 original size:21 final size:21
Alignment explanation
Indices: 505806--505846 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
505796 AATGATACAT
*
505806 ATTTTTAAAA-TATATTAAAAA
1 ATTTTAAAAACTA-ATTAAAAA
505827 ATTTTAAAAACTAATTAAAA
1 ATTTTAAAAACTAATTAAAA
505847 GAAAACATGA
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:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTTAAAAACTAATTAAAAA
Found at i:506957 original size:3 final size:3
Alignment explanation
Indices: 506949--506985 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
506939 ACAAACAAGG
506949 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
506986 TGAAGGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:507680 original size:27 final size:27
Alignment explanation
Indices: 507628--507680 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
507618 TATAATTATA
*
507628 TTTTAATTTTATTATTTTTTATTAAAT
1 TTTTAATTTTATTATTTTTTAATAAAT
* *
507655 TTTTTATTTT-TTTTTTTTTAGATAAA
1 TTTTAATTTTATTATTTTTTA-ATAAA
507681 AATAACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTAATTTTATTATTTTTTAATAAAT
Found at i:507864 original size:19 final size:19
Alignment explanation
Indices: 507842--507887 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
507832 ATTATAAATA
507842 TTAATATAAAAATATTATT
1 TTAATATAAAAATATTATT
***
507861 TTAATATTTTAATATTATT
1 TTAATATAAAAATATTATT
507880 TTAA-ATAA
1 TTAATATAA
507888 TAACACAGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAAAATATTATT
Found at i:509070 original size:27 final size:27
Alignment explanation
Indices: 509032--509091 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
509022 AAAATTTTAA
509032 AAAAATTTAAAATATAA-TA-TAATAT
1 AAAAATTTAAAATATAATTATTAATAT
*
509057 AAAAATTATGAAAATATAATTATTTATAT
1 AAAAATT-T-AAAATATAATTATTAATAT
509086 AAAAAT
1 AAAAAT
509092 AAATAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 7 0.23
26 1 0.03
27 9 0.30
28 2 0.07
29 11 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAAATTTAAAATATAATTATTAATAT
Found at i:509528 original size:26 final size:25
Alignment explanation
Indices: 509499--509590 Score: 76
Period size: 26 Copynumber: 3.6 Consensus size: 25
509489 TAAATAATAT
*
509499 AAATTAATTTTTTAAAAAAATTTAAA
1 AAATTAA-TTTTTAAATAAATTTAAA
* ** *
509525 AAATTTAATATTTATTTAATTTTAAA
1 AAA-TTAATTTTTAAATAAATTTAAA
* * *
509551 AAATTAATTATTAAATATATTAAAA
1 AAATTAATTTTTAAATAAATTTAAA
*
509576 AAATAATATTTTTAA
1 AAATTA-ATTTTTAA
509591 TCGATATAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
25 20 0.40
26 26 0.52
27 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTAATTTTTAAATAAATTTAAA
Found at i:510856 original size:31 final size:32
Alignment explanation
Indices: 510804--510865 Score: 74
Period size: 31 Copynumber: 1.9 Consensus size: 32
510794 AATGAATACG
* *
510804 ATTTTTAATTAACATTATTT-AAGATAATTGA
1 ATTTTTAAATAACATAATTTAAAGATAATTGA
510835 ATTTTTAAAT-ACATAATTTTAAAAGATAATT
1 ATTTTTAAATAACATAA-TTT-AAAGATAATT
510866 ATTACGGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 5 0.19
31 12 0.46
33 9 0.35
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (32 bp):
ATTTTTAAATAACATAATTTAAAGATAATTGA
Found at i:511659 original size:3 final size:3
Alignment explanation
Indices: 511651--511702 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
511641 TTCCAAACTT
511651 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
511699 TTA T
1 TTA T
511703 CGGTTGCTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:512779 original size:24 final size:24
Alignment explanation
Indices: 512722--512779 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 24
512712 AATTATATAT
*
512722 ATATTATTATTATTTAATATTTTAA
1 ATATTATTA-TAATTAATATTTTAA
* *
512747 AAAAT-TTATAATTAAGTA-TTTAA
1 ATATTATTATAATTAA-TATTTTAA
512770 ATATTATTAT
1 ATATTATTAT
512780 CATTTACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
23 14 0.54
24 9 0.35
25 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATTATTATAATTAATATTTTAA
Found at i:513058 original size:29 final size:28
Alignment explanation
Indices: 513016--513093 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
513006 AAAATATTGC
* * *
513016 TTTATTCAACTATTAAACCATAGATTAA
1 TTTATTTAAATATTAAATCATAGATTAA
* **
513044 TGTTATTTAAATATTTAATTTTAGATTAA
1 T-TTATTTAAATATTAAATCATAGATTAA
*
513073 TTT-TTTAAATATCAAATCATA
1 TTTATTTAAATATTAAATCATA
513094 AAAAATAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
27 14 0.36
28 3 0.08
29 22 0.56
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (28 bp):
TTTATTTAAATATTAAATCATAGATTAA
Found at i:519718 original size:769 final size:770
Alignment explanation
Indices: 518240--519780 Score: 2604
Period size: 769 Copynumber: 2.0 Consensus size: 770
518230 TATTTTACAA
* * * *
518240 CCTCATGAGTACAATAAACTTGAACCATGAGCATGATTATGTATTAGAGCCTTAACTCAACTTTT
1 CCTCATGAGTACAATAAACTTGAACCACGAGCATGATTATGTATTAAAGCCTCAACTCAACTCTT
* *
518305 TTCTCATCGTTGTACTAGAGTAAGTCATCCCTCTGTCCTTCTTAAAGATGTCCATGTCTATTCCA
66 TCCTCATCGTTGTACTAGAGTAAGTCATCCCTCTGTCATTCTTAAAGATGTCCATGTCTATTCCA
* *
518370 CTATTGTCTCTCTATATGAACCTCGCACCTATTGTGAGGTTAAAACTGGCCCTTTTATGGTAAAA
131 CTATTGTCTCTCTATATGAACCTCGCACCTATTGTGAGGCTAAAACTGGCCCTTTTATGGCAAAA
518435 AACAATGGCAGAAGAACTAAAGGCTCTTAGCAATACCAATACTTGGGACTTGGTTGATTTACCTC
196 AACAATGGCAGAAGAACTAAAGGCTCTTAGCAATACCAATACTTGGGACTTGGTTGATTTACCTC
* *
518500 CACATAAATCTATTGTTGGTTGTAAATGGGTCTATAAAATAAAGACTCGAGCTGATAGATCAGTT
261 CACATAAATCTATTGTTGGTTATAAATGGGTCTATAAAATAAAGACTCGAGCTGATAGATCAATT
518565 GAAAGAAATAAAGCATGCCTTATTGCTAAAGGATTTACTCAAGAATATGGCATTGACTATGAGAA
326 GAAAGAAATAAAGCATGCCTTATTGCTAAAGGATTTACTCAAGAATATGGCATTGACTATGAGAA
* * * * *
518630 GACCTTTGTTCTCGTAGCTTGCTTGACCTTATTTTGTAGCCTTATTGCAATTGTAGCTAGCAAAC
391 GACCTTTGTTCTCGTAGCTTGCTTGACCTTAATTCGTAGCCTTATTGCAACTGTAGCCAACAAAC
* * * *
518695 GTTGGTAACTATTTCAAATGGATGTCAAGAATGCCTTTTTTAATGGTGATCTCATAAAAGAAGTG
456 ATTGGCAACTATTTCAAATGGATGTCAAGAATGCCTTTCTTAATGGTGATCTCATAAAAGAAGCG
* **
518760 TACATGCAACCTTTAGTTGAGTATGATCATCCATCTAATAAGGTTTGCTGTCTTCGCAAAGTCTT
521 TACATGCAACCTTTACTTGAGTATGATCATCCATCTAATAAGGTTTGCCATCTTCGCAAAGTCTT
* * *
518825 ATATGGACTTAAGCAAGCTCCTCGAGTATGGTTTGCTAAATTTAGTTCCACTATCAGCCACCCTG
586 ATATGGACTTAAGCAAGCTCCCCGAGCATGGTTTGCTAAATTTAGTTCCACTATCAACCACCCTG
* *
518890 GTTTTTAGTCTAGCTCTTATGACCATGCCTTGTTTCTTCACAAGACTAATCAAGGATGTACTCCT
651 ATTTCTAGTCTAGCTCTTATGACCATGCCTTGTTTCTTCACAAGACTAATCAAGGATGTACTCCT
* *
518955 CTTCTTCTGTATGTTGATGACATGATCATAACTATTGATGCCATTTAGGGTATCT
716 CTTCTTCTATATGTTGATGACATGATCATAACTAGTGATGCCATTTAGGGTATCT
*
519010 CCTCATGAGTATAATAAACTTGAACCACGAGCATGATTATGTATTAAAGCCTCAACTCAACTCTT
1 CCTCATGAGTACAATAAACTTGAACCACGAGCATGATTATGTATTAAAGCCTCAACTCAACTCTT
* * *
519075 TCCTTATTGTTGTACTAGAGTAAGTCATCCCTCTGTCATTCTTAAAGATTTCCATGTCTATTCCA
66 TCCTCATCGTTGTACTAGAGTAAGTCATCCCTCTGTCATTCTTAAAGATGTCCATGTCTATTCCA
* * *
519140 TTATTGTCTCTCTATATGAACCTCGCACCTATTGTGAGGCTAGATCTGGCCC-TTTATGGCAAAA
131 CTATTGTCTCTCTATATGAACCTCGCACCTATTGTGAGGCTAAAACTGGCCCTTTTATGGCAAAA
* *
519204 AGCAATGGCAGAAGAACTAGAGGCTCTTAGCAATACCAATACTTGGGACTTGGTTGATTTACCTC
196 AACAATGGCAGAAGAACTAAAGGCTCTTAGCAATACCAATACTTGGGACTTGGTTGATTTACCTC
*
519269 CACATAAATTTATCT-TTGGTTATAAATGGGTCTATAAAATAAAGACTCGAGCTGATAGATCAAT
261 CACATAAATCTAT-TGTTGGTTATAAATGGGTCTATAAAATAAAGACTCGAGCTGATAGATCAAT
* *
519333 TGAAAGATATAAAGCATGCCTTATTGCT-ATGAGATTTACTCAAGAATATGGCATTGACTATGAG
325 TGAAAGAAATAAAGCATGCCTTATTGCTAAAG-GATTTACTCAAGAATATGGCATTGACTATGAG
*
519397 AAGACCTTTTTTCTCGTAGCTTGCTTGACCTTAATTCGTAGCCTTATTGCAACTGTAGCCAACAA
389 AAGACCTTTGTTCTCGTAGCTTGCTTGACCTTAATTCGTAGCCTTATTGCAACTGTAGCCAACAA
*
519462 ACATTGGCAACTATTTCAAATGGATGTCAAGAATGCCTTTCTTAATGGTGATCTCATAGAAGAAG
454 ACATTGGCAACTATTTCAAATGGATGTCAAGAATGCCTTTCTTAATGGTGATCTCATAAAAGAAG
519527 CGTACATGCAA-CTTCTACTTGAGTATGATCATCCATCTAATAAGGTTTGCCATCTTCGCAAAGT
519 CGTACATGCAACCTT-TACTTGAGTATGATCATCCATCTAATAAGGTTTGCCATCTTCGCAAAGT
*
519591 CTTATATGGACTTAAGCAAGCTCCCCGAGCATGGTTTGGTAAATTTAGTTCCACTATCAACCACC
583 CTTATATGGACTTAAGCAAGCTCCCCGAGCATGGTTTGCTAAATTTAGTTCCACTATCAACCACC
519656 CTGATTTCTAGTCTAGCTCTTATGACCATGCCTTGTTTCTTCACAAGACTAATCAAGGATGTACT
648 CTGATTTCTAGTCTAGCTCTTATGACCATGCCTTGTTTCTTCACAAGACTAATCAAGGATGTACT
* * *
519721 CCTCTTTTTTTATATGTTGATGACATGATCATAACTGGTGATGCCATTTAGGGTATCT
713 CCTCTTCTTCTATATGTTGATGACATGATCATAACTAGTGATGCCATTTAGGGTATCT
519779 CC
1 CC
519781 ACTCTCAAAT
Statistics
Matches: 721, Mismatches: 47, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
768 5 0.01
769 547 0.76
770 169 0.23
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (770 bp):
CCTCATGAGTACAATAAACTTGAACCACGAGCATGATTATGTATTAAAGCCTCAACTCAACTCTT
TCCTCATCGTTGTACTAGAGTAAGTCATCCCTCTGTCATTCTTAAAGATGTCCATGTCTATTCCA
CTATTGTCTCTCTATATGAACCTCGCACCTATTGTGAGGCTAAAACTGGCCCTTTTATGGCAAAA
AACAATGGCAGAAGAACTAAAGGCTCTTAGCAATACCAATACTTGGGACTTGGTTGATTTACCTC
CACATAAATCTATTGTTGGTTATAAATGGGTCTATAAAATAAAGACTCGAGCTGATAGATCAATT
GAAAGAAATAAAGCATGCCTTATTGCTAAAGGATTTACTCAAGAATATGGCATTGACTATGAGAA
GACCTTTGTTCTCGTAGCTTGCTTGACCTTAATTCGTAGCCTTATTGCAACTGTAGCCAACAAAC
ATTGGCAACTATTTCAAATGGATGTCAAGAATGCCTTTCTTAATGGTGATCTCATAAAAGAAGCG
TACATGCAACCTTTACTTGAGTATGATCATCCATCTAATAAGGTTTGCCATCTTCGCAAAGTCTT
ATATGGACTTAAGCAAGCTCCCCGAGCATGGTTTGCTAAATTTAGTTCCACTATCAACCACCCTG
ATTTCTAGTCTAGCTCTTATGACCATGCCTTGTTTCTTCACAAGACTAATCAAGGATGTACTCCT
CTTCTTCTATATGTTGATGACATGATCATAACTAGTGATGCCATTTAGGGTATCT
Found at i:521205 original size:33 final size:33
Alignment explanation
Indices: 521155--521226 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
521145 CTTTTTTTTT
* *
521155 TATTATTAAGTAGAATTTCAATTGCATAAAAATC
1 TATT-TTAAGTAAAATTTCAATTGCATAAAAATA
**
521189 TATTTTAAGTAAAATTTCAATTTTATAAAAATA
1 TATTTTAAGTAAAATTTCAATTGCATAAAAATA
521222 TATTT
1 TATTT
521227 CTAATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
TATTTTAAGTAAAATTTCAATTGCATAAAAATA
Found at i:522251 original size:29 final size:28
Alignment explanation
Indices: 522183--522251 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
522173 AATTTTATAT
*
522183 TAAT-ATTTATATATTTTTATAATTAAA
1 TAATAATTTAAATATTTTTATAATTAAA
* **
522210 T-TTAAATAAAAATATTTTTATCAATTAAA
1 TAAT-AATTTAAATATTTTTAT-AATTAAA
522239 TAATAATTTAAAT
1 TAATAATTTAAAT
522252 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 13 0.42
29 15 0.48
30 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TAATAATTTAAATATTTTTATAATTAAA
Found at i:525101 original size:11 final size:11
Alignment explanation
Indices: 525087--525148 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
525077 TTTATTTTAC
525087 ATTTATATTTT
1 ATTTATATTTT
525098 ATTTATATTATT
1 ATTTATATT-TT
*
525110 TTTTAT-TTTT
1 ATTTATATTTT
525120 ATATTATATATTT
1 AT-TTATAT-TTT
*
525133 ATAATTATATTAT
1 AT--TTATATTTT
525146 ATT
1 ATT
525149 AAAATTTATC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 3 0.07
11 16 0.37
12 8 0.19
13 9 0.21
14 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTATATTTT
Found at i:525126 original size:23 final size:22
Alignment explanation
Indices: 525088--525132 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
525078 TTATTTTACA
525088 TTTATATTTTATTTATATTATTT
1 TTTATATTTTATTTATA-TATTT
525111 TTTAT-TTTTATATTATATATTT
1 TTTATATTTTAT-TTATATATTT
525133 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATATTTTATTTATATATTT
Found at i:525141 original size:14 final size:13
Alignment explanation
Indices: 525087--525147 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 13
525077 TTTATTTTAC
525087 ATTTATATT-T-T
1 ATTTATATTATAT
525098 ATTTATATTAT-T
1 ATTTATATTATAT
* *
525110 TTTTAT-TTTTAT
1 ATTTATATTATAT
525122 ATTATATATT-TAT
1 ATT-TATATTATAT
*
525135 AATTATATTATAT
1 ATTTATATTATAT
525148 TAAAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 12 0.29
12 16 0.39
13 11 0.27
14 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATATTATAT
Found at i:525141 original size:37 final size:37
Alignment explanation
Indices: 525064--525145 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
525054 TACAATTATG
* *
525064 TATATTATGTTTTTTTATTTTACATTTATATTTTATT
1 TATATTATGTTTTTATATTTTACATTTATATTTTAAT
*
525101 TATATTAT-TTTTTAT-TTTTATATTATATATTTATAAT
1 TATATTATGTTTTTATATTTTACATT-TATATTT-TAAT
525138 TATATTAT
1 TATATTAT
525146 ATTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 8 0.20
36 13 0.32
37 19 0.47
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (37 bp):
TATATTATGTTTTTATATTTTACATTTATATTTTAAT
Found at i:525533 original size:17 final size:17
Alignment explanation
Indices: 525511--525551 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
525501 ATAGGATAGG
525511 ATATAAATAAATAAATA
1 ATATAAATAAATAAATA
*
525528 ATATAAATATATAAATA
1 ATATAAATAAATAAATA
*
525545 ATTTAAA
1 ATATAAA
525552 ATTAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAATAAATAAATA
Found at i:525578 original size:25 final size:28
Alignment explanation
Indices: 525522--525578 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 28
525512 TATAAATAAA
525522 TAAA-TAATATAAATATATAAATAATTT
1 TAAATTAATATAAATATATAAATAATTT
* *
525549 AAAATTAATAT-AATA-A-AAATTATTT
1 TAAATTAATATAAATATATAAATAATTT
525574 TAAAT
1 TAAAT
525579 ATATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 1 0.04
27 7 0.27
28 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAATTAATATAAATATATAAATAATTT
Found at i:526135 original size:30 final size:29
Alignment explanation
Indices: 526063--526135 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
526053 TTTAAGTTAG
526063 ATAAATTTTTATATTTTTCTTATATTTAAAA
1 ATAAATTTTTA-ATTTTTCTTATATTT-AAA
** *
526094 ATAAAAATTTAATTTTTAATTTATATTT-AA
1 ATAAATTTTTAATTTTT--CTTATATTTAAA
526124 ATAAATTTTTAA
1 ATAAATTTTTAA
526136 CATTTATACT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 18 0.51
31 9 0.26
32 8 0.23
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
ATAAATTTTTAATTTTTCTTATATTTAAA
Found at i:526363 original size:21 final size:22
Alignment explanation
Indices: 526319--526379 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
526309 GTAAAAAATA
* *
526319 AAAATATATTTATAATAATATTT
1 AAAA-ATATTTATAATTATTTTT
*
526342 -ATAATATTTATAATTATTTTT
1 AAAAATATTTATAATTATTTTT
526363 AAAAATATTT-T-ATTATT
1 AAAAATATTTATAATTATT
526380 AAATAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 17 0.52
22 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAAAATATTTATAATTATTTTT
Found at i:526386 original size:31 final size:32
Alignment explanation
Indices: 526317--526391 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 32
526307 TAGTAAAAAA
*
526317 TAAA-AATATATTTATAATAATATTTATAATAT
1 TAAATAAT-TATTTATAAAAATATTTATAATAT
* * *
526349 T-TATAATTATTTTTAAAAATATTT-TATTAT
1 TAAATAATTATTTATAAAAATATTTATAATAT
*
526379 TAAATAATAATTT
1 TAAATAATTATTT
526392 GAGTAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
30 6 0.17
31 25 0.71
32 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TAAATAATTATTTATAAAAATATTTATAATAT
Found at i:526596 original size:2 final size:2
Alignment explanation
Indices: 526589--526615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
526579 CTCTTTTAAC
526589 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 A
526616 ATTCTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527110 original size:25 final size:28
Alignment explanation
Indices: 527082--527146 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
527072 ATTTTTATAA
527082 AATAAATATAAATAAT-TTTTA-TT-TT
1 AATAAATATAAATAATATTTTATTTATT
* *
527107 AATAAA-AT-GATATTATTTTATTTATT
1 AATAAATATAAATAATATTTTATTTATT
527133 AATAATATATAAAT
1 AATAA-ATATAAAT
527147 TTATACATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 4 0.13
24 7 0.23
25 8 0.26
26 7 0.23
27 1 0.03
28 2 0.06
29 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
AATAAATATAAATAATATTTTATTTATT
Found at i:527410 original size:25 final size:26
Alignment explanation
Indices: 527364--527419 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
527354 AACTTGGATA
* *
527364 AGAATTTTTATTTAAAATAATTGTGG
1 AGAATTTTTATTCAAAATAATTATGG
* * *
527390 AGAATTTTTCTTCAATA-AATTATGT
1 AGAATTTTTATTCAAAATAATTATGG
527415 AGAAT
1 AGAAT
527420 ATTTGGGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (26 bp):
AGAATTTTTATTCAAAATAATTATGG
Found at i:527933 original size:32 final size:30
Alignment explanation
Indices: 527897--527980 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 30
527887 GAAAATAATA
* *
527897 AAATTTAGAATATTTTAATTAAAAATGATTAT
1 AAATTTA-AATATTTAAATTAAAAATGATT-C
* *
527929 AAATTTTAAATAATTCAAATTTAAAATGATTC
1 AAA-TTTAAAT-ATTTAAATTAAAAATGATTC
527961 AAATTTAAAATATTTAAATT
1 AAATTT-AAATATTTAAATT
527981 TATAACGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 11 0.25
32 13 0.30
33 20 0.45
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTTAAATATTTAAATTAAAAATGATTC
Found at i:527950 original size:16 final size:15
Alignment explanation
Indices: 527897--527982 Score: 73
Period size: 16 Copynumber: 5.5 Consensus size: 15
527887 GAAAATAATA
* *
527897 AAATTTAGAATATTT
1 AAATTTAAAATATTC
* * *
527912 TAATTAAAAATGATTAT
1 AAATTTAAAAT-ATT-C
*
527929 AAATTTTAAATAATTC
1 AAATTTAAAAT-ATTC
527945 AAATTTAAAATGATTC
1 AAATTTAAAAT-ATTC
*
527961 AAATTTAAAATATTT
1 AAATTTAAAATATTC
527976 AAATTTA
1 AAATTTA
527983 TAACGGTTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
15 18 0.31
16 28 0.48
17 12 0.21
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (15 bp):
AAATTTAAAATATTC
Found at i:527953 original size:15 final size:15
Alignment explanation
Indices: 527933--527982 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
527923 GATTATAAAT
527933 TTTAAATAATTCAAA
1 TTTAAATAATTCAAA
*
527948 TTTAAAATGATTCAAA
1 TTT-AAATAATTCAAA
*
527964 TTTAAA-ATATTTAAA
1 TTTAAATA-ATTCAAA
527979 TTTA
1 TTTA
527983 TAACGGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
TTTAAATAATTCAAA
Found at i:528162 original size:31 final size:31
Alignment explanation
Indices: 528116--528175 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
528106 AAACTCAAAA
*
528116 ATAAATTAAAATTAAAATTATTTAAATAATT
1 ATAAATTAAAATTAAAATAATTTAAATAATT
* *
528147 ATAATTTAAATTTAAAATAATTTAAATAA
1 ATAAATTAAAATTAAAATAATTTAAATAA
528176 AAAAACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAAATTAAAATTAAAATAATTTAAATAATT
Found at i:528173 original size:16 final size:16
Alignment explanation
Indices: 528113--528173 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
528103 ATTAAACTCA
* *
528113 AAAATAAATTAAAATT
1 AAAATAATTTAAATTT
*
528129 AAAATTATTTAAA--T
1 AAAATAATTTAAATTT
*
528143 AATTATAATTTAAATTT
1 AA-AATAATTTAAATTT
528160 AAAATAATTTAAAT
1 AAAATAATTTAAAT
528174 AAAAAAACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
14 3 0.08
15 9 0.24
16 22 0.59
17 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:528179 original size:16 final size:15
Alignment explanation
Indices: 528112--528178 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
528102 GATTAAACTC
*
528112 AAAAATAAATTAAAAT
1 AAAAAT-AATTTAAAT
* *
528128 TAAAATTATTTAAAT
1 AAAAATAATTTAAAT
**
528143 AATTATAATTTAAATT
1 AAAAATAATTTAAA-T
*
528159 TAAAATAATTTAAAT
1 AAAAATAATTTAAAT
528174 AAAAA
1 AAAAA
528179 AACTTATAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
15 22 0.56
16 17 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATAATTTAAAT
Found at i:528830 original size:27 final size:27
Alignment explanation
Indices: 528799--528859 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
528789 TTATGCTCTT
528799 TTTATAGTAAATTTAATAATTTATATA
1 TTTATAGTAAATTTAATAATTTATATA
** * *
528826 TTTATTTTAAATTTAATTATTTTTATA
1 TTTATAGTAAATTTAATAATTTATATA
528853 TATTATA
1 T-TTATA
528860 ATTATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTATAGTAAATTTAATAATTTATATA
Found at i:528862 original size:24 final size:25
Alignment explanation
Indices: 528799--528885 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 25
528789 TTATGCTCTT
528799 TTTATAGTAAATTTAATAATTTATA-TA
1 TTTATA-TAAA-TT-ATAATTTATATTA
528826 TTTAT-T---TTA-AATTTA-ATTA
1 TTTATATAAATTATAATTTATATTA
* *
528845 TTTTTATATATTATAA-TTATATTA
1 TTTATATAAATTATAATTTATATTA
*
528869 TTTATATAAATTTTAAT
1 TTTATATAAATTATAAT
528886 ACATTAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
18 1 0.02
19 12 0.25
20 2 0.04
21 2 0.04
23 6 0.12
24 19 0.40
25 1 0.02
27 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTATATAAATTATAATTTATATTA
Found at i:528882 original size:34 final size:34
Alignment explanation
Indices: 528844--528909 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
528834 AAATTTAATT
* * * *
528844 ATTTTTATATATT-ATAATTATATTATTTATATAA
1 ATTTTAATACATTAATAA-TATATGATATATATAA
528878 ATTTTAATACATTAATAATATATGATATATAT
1 ATTTTAATACATTAATAATATATGATATATAT
528910 TTTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
ATTTTAATACATTAATAATATATGATATATATAA
Found at i:529432 original size:22 final size:24
Alignment explanation
Indices: 529379--529432 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
529369 ATAAAATTAT
529379 TATATATTTTTATTTTATTTTTAAA
1 TATAT-TTTTTATTTTATTTTTAAA
529404 T-TAATTTTTTA-TTT-TTTTTAAA
1 TAT-ATTTTTTATTTTATTTTTAAA
529426 TATATTT
1 TATATTT
529433 AAAGAGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 13 0.48
23 4 0.15
24 7 0.26
25 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TATATTTTTTATTTTATTTTTAAA
Found at i:533829 original size:23 final size:23
Alignment explanation
Indices: 533803--533851 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
533793 TGGACATGTT
533803 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
533826 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
533849 AAA
1 AAA
533852 TGCATGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:533851 original size:21 final size:22
Alignment explanation
Indices: 533803--533857 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
533793 TGGACATGTT
533803 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAAT-AA
533826 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
533847 AAAAATGCATG
1 AAAAATGCATG
533858 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 12 0.38
23 20 0.62
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:534818 original size:20 final size:20
Alignment explanation
Indices: 534771--534845 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
534761 AAAAAGACAT
*
534771 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
534790 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
534811 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
534831 AATGTATCGATACAT
1 AATGTATCGATACAT
534846 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:534839 original size:40 final size:39
Alignment explanation
Indices: 534768--534845 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
534758 GGTAAAAAGA
* *
534768 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
534807 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
534846 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:535695 original size:23 final size:23
Alignment explanation
Indices: 535661--535704 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
535651 ACTTGTGGGC
*
535661 TTTGAAAGAGTGCCACTGACTCG
1 TTTGAAAAAGTGCCACTGACTCG
535684 TTTGAAAAAGTGCCACTGACT
1 TTTGAAAAAGTGCCACTGACT
535705 TGCGTGGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (23 bp):
TTTGAAAAAGTGCCACTGACTCG
Found at i:535891 original size:145 final size:144
Alignment explanation
Indices: 535455--536881 Score: 1287
Period size: 145 Copynumber: 10.1 Consensus size: 144
535445 CACTGACACA
* ** * * *
535455 TGTGGGCTTTGAAAAGAGTGTTACTAACTTGCGTGGGCTTTAAAAAG-GTGCCACTGACTTGCGT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGAGTGCCACTGACTT--GT
* * *
535519 GGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTT
61 GGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTT
* *
535581 TGAAA-GGTGCCATTGACT
126 TAAAAGGGTGCCACTGACT
* * * *
535599 CGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGC-TTGAAAGG-GTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
* ** *
535662 TTG-AAAGAGTGCCACTGAC---T-CG-TTTGAAAAAGTGCCACTGACTTGCGTGGGCTTTGAAA
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAAA
535721 GGAGTGCCACTGACTT
131 GG-GTGCCACTGAC-T
* *
535737 GTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 -TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * **
535801 TTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGATCTTTAAA
65 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAA
* *
535865 AGGAGTGTCACTGATTT
130 AGG-GTGCCACTGA-CT
* * *
535882 GTGTGGGCTTTAAAAGTGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAATTGTGGGC
1 -TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * * * *
535946 TTCGCAATG-GTGCCATTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGC--GGGCTCTAAA
65 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAA
*
536008 AGGGTGCCACTAACT
130 AGGGTGCCACTGACT
* *
536023 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
*
536088 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAA
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGCGTGGGCTTTAAA
536151 AGGAGTGCCACTGACTT
130 AGG-GTGCCACTGAC-T
* *
536168 GTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAATTGTGGGC
1 -TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
536232 TTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAA
65 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTT-AA
536296 AAGGGTGCCACTGACT
129 AAGGGTGCCACTGACT
* * *
536312 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
* *
536377 TTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAA
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGCGTGGGCTTTAAA
536442 AGGGTGCCACTGACT
130 AGGGTGCCACTGACT
* * * * * * *
536457 TGTGGGCTTTGAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGG-GTGCCACGGAGTTGTGGAC-
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
* * * * * * * * * *
536519 -TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGTGCCACAGAGTT--GTGGAC-TTAAAA
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAAA
* * * *
536580 GAGATGTCACGGAGT
131 G-GGTGCCACTGACT
* * * * * * * * * * *
536595 TATGGAC-TTAAAAGGGTGCCACGGAGTTATGGAC-TTAAAAGG-GTGCCACGGAGTTGTGGTC-
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
* * * * * * * *
536656 TT-AAAAGGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTT--GTGGAC-TTAAA
66 TTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAA
** * *
536716 AGAATGCCACGGAGT
130 AGGGTGCCACTGACT
* * * * * * * * *
536731 TGTGGACTTTAAAAGGATGCCAC-GAAGTTGTGGAC-TT-AAAGGGGATGCCACGGAGTTGTGGA
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACTTGTGGGCTTTGAAAGGAG-TGCCACTGACTTGTGGG
* * * * * * * *
536793 C-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTT--GTGGAC-TTAA
64 CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAA
* *
536852 AAGGGTGCCACGGAGT
129 AAGGGTGCCACTGACT
536868 TGTGGGCTTT-AAAG
1 TGTGGGCTTTGAAAG
536882 AGGTCACACT
Statistics
Matches: 1131, Mismatches: 114, Indels: 84
0.85 0.09 0.06
Matches are distributed among these distances:
133 21 0.02
134 1 0.00
135 14 0.01
136 28 0.02
137 208 0.18
138 85 0.08
139 31 0.03
140 116 0.10
141 61 0.05
142 34 0.03
143 114 0.10
144 82 0.07
145 264 0.23
146 72 0.06
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (144 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCT
TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTAAAA
GGGTGCCACTGACT
Found at i:536558 original size:110 final size:111
Alignment explanation
Indices: 535487--536885 Score: 878
Period size: 110 Copynumber: 12.4 Consensus size: 111
535477 ACTAACTTGC
* * * * * *
535487 GTGGGCTTTAAAAAGGTGCCACTGACTTGCGTGGGCTTT-GAAAGGATGCCACTGACTCGTGGGC
1 GTGGACTTTAAAAGGGTGCCACGGAGTT--GTGGGCTTTAAAAAGG-TGCCACTGACTTGTGGGC
* * * * * ** * *
535551 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCATTGACTC
63 TTTAAAAGGGTGCCACAGACTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
* * * * * * *
535600 GTGGGCTTTGAAAA-GGTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACTTGTGGGCTT
1 GTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTT
* * * * * * *
535663 TGAAAGAGTGCCACTGACTCGT----TTGAAAA-AGTGCCACTGACTT
65 TAAAAGGGTGCCACAGACTTGTGGACTT-AAAAGGGTGCCACGGAGTT
* * * * * * * *
535706 GCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGG
1 --GTGGACTTTAAAAGG-GTGCCACGGA-GT-TGTGGGCTTTAAAAAGGTGCCACTGACTTGTGG
* * * * * * * * *
535771 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTC
61 GCTTTAAAAGGGTGCCACAGACTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
* * * * ** * * *
535823 GTGGGCTTTGAAAA-GGTACCACTGACTTGCGTGATCTTTAAAAGGAGTGTCACTGATTTGTGTG
1 GTGGACTTT-AAAAGGGTGCCACGGAGTT--GTGGGCTTTAAAAAG-GTGCCACTGA-CT-TGTG
* * * * * * *
535887 GGCTTTAAAAGTGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAATT
60 GGCTTTAAAAGGGTGCCACAGACTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
* *** * ** * ** * * *
535940 GTGGGCTTCGCAATGGTGCCATTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGGGCTCT
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTT
* * * *
536005 AAAAGGGTGCCACTA-ACTTGTGGGCTTTGAAAGGGTGCCACTGACTT
66 AAAAGGGTGCCAC-AGACTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
* * * * *
536052 GTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
1 GTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAG-GTGCCACTGACTTGTGGGCT
* * * * * *
536117 TTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGT
64 TTAAAAGG-GTGCCACAGACTTGTGGAC-TTAAAAGG-GTGCCACGGA-GT-T
* * * * *
536170 GTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTGAATTGTGGGCTT
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAG-GTGCCACTGACTTGTGGGCTT
*** * * * * * *
536234 CGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTT
65 TAAAAGGGTGCCACAGACTTGTGGACTT-AAAAGGGTGCCACGGAGTT
* * * * * *
536282 GCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 --GTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGC
* * ** * *
536347 TTTGAAAAGAGTGCCACTA-ACTTGTGGGCTTTGAAAAGAATGCCACTGACTT
63 TTT-AAAAGGGTGCCAC-AGACTTGTGGAC-TT-AAAAGGGTGCCACGGAGTT
* * * * *
536399 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC
1 GTGGACTTTAAAAGG-GTGCCACGGA-GT-TGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGC
* *
536464 TTTGAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
63 TTTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGTGCCACGGAGTT
* * * * *
536513 GTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGTGCCACAGAGTTGTGGAC-TT
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTT
* * * * *
536576 AAAAGAGATGTCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTT
66 AAAAG-GGTGCCACAGACTTGTGGACTTAAAAGGGTGCCACGGAGTT
* * * * * *
536623 ATGGAC-TTAAAAGGGTGCCACGGAGTTGTGGTC-TTAAAAGGGATGCCACGGAGTTGTGGAC-T
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGG-TGCCACTGACTTGTGGGCTT
* * **
536685 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACGGAGTT
65 TAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGTGCCACGGAGTT
* * * ** * * *
536732 GTGGACTTTAAAAGGATGCCACGAAGTTGTGGAC-TTAAAGGGGATGCCACGGAGTTGTGGAC-T
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGG-TGCCACTGACTTGTGGGCTT
* *
536795 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
65 TAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGTGCCACGGAGTT
*
536842 GTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGAGGT
1 GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGT
536886 CACACTACTA
Statistics
Matches: 1102, Mismatches: 137, Indels: 98
0.82 0.10 0.07
Matches are distributed among these distances:
105 2 0.00
106 14 0.01
107 3 0.00
108 10 0.01
109 89 0.08
110 275 0.25
111 17 0.02
112 115 0.10
113 56 0.05
114 105 0.10
115 149 0.14
116 90 0.08
117 167 0.15
118 10 0.01
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (111 bp):
GTGGACTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTT
AAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGTGCCACGGAGTT
Found at i:536881 original size:27 final size:28
Alignment explanation
Indices: 535455--536881 Score: 1278
Period size: 28 Copynumber: 50.5 Consensus size: 28
535445 CACTGACACA
* ** *
535455 TGTGGGCTTTGAAAAGAGTGTTACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
535484 TGCGTGGGCTTTAAAAAGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
*
535514 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
535544 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
535572 TGTGGGCTTTGAAA-GGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
535599 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
535627 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
535654 TGTGGGCTTTGAAAGAGTGCCACTGAC-
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
535681 --T-CG-TTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
535705 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
535737 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
535766 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
535794 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
535822 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * *
535850 TGCGTGATCTTTAAAAGGAGTGTCACTGATTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGA-CT
* *
535882 GTGTGGGCTTTAAAAGTGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
535911 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
535939 TGTGGGCTTCGCAATGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
535967 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
535995 TGCGGGCTCTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
536023 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
536051 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
536080 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
536109 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACT
536138 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
536168 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
536197 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
536225 TGTGGGCTTCGCAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
536253 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
536281 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGGTGCCACTGACT
*
536312 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
536340 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
**
536369 TGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
536398 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
536428 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
536457 TGTGGGCTTTGAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
536485 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * *
536512 TGTGGAC-TAAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
536539 TGTGGACTTTAAAAAGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
536567 TGTGGAC-TTAAAAGAGATGTCACGGAGT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* * * * *
536595 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
536622 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
536649 TGTGGTC-TTAAAAGGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGG-TGCCACTGACT
* * * *
536677 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** * *
536704 TGTGGAC-TTAAAAGAATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
536731 TGTGGACTTTAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * *
536759 TGTGGAC-TT-AAAGGGGATGCCACGGAGT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGACT
* * * *
536787 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
536814 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
536841 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
536868 TGTGGGCTTT-AAAG
1 TGTGGGCTTTGAAAG
536882 AGGTCACACT
Statistics
Matches: 1238, Mismatches: 120, Indels: 82
0.86 0.08 0.06
Matches are distributed among these distances:
23 19 0.02
24 1 0.00
25 1 0.00
26 3 0.00
27 280 0.23
28 540 0.44
29 178 0.14
30 109 0.09
31 103 0.08
32 2 0.00
33 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:537911 original size:11 final size:10
Alignment explanation
Indices: 537894--537923 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
537884 GGGTGAAAAG
537894 GTTTTTTTTT
1 GTTTTTTTTT
537904 GTTTTTTTTT
1 GTTTTTTTTT
537914 GTTTTTTTTT
1 GTTTTTTTTT
537924 AGGTTTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:538225 original size:23 final size:24
Alignment explanation
Indices: 538199--538250 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
538189 TTTTATTTTG
*
538199 TTTTTGCACTTTTTCTTTTCA-TT
1 TTTTTGCACTTTTGCTTTTCAGTT
** *
538222 TTTTTGTGCTTTTGCTTTTGAGTT
1 TTTTTGCACTTTTGCTTTTCAGTT
538246 TTTTT
1 TTTTT
538251 TTGTTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTTTGCACTTTTGCTTTTCAGTT
Found at i:544400 original size:21 final size:24
Alignment explanation
Indices: 544358--544407 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
544348 TGGACATGTT
544358 AAAAATGCATGAAACATAATAAAA
1 AAAAATGCATGAAACATAATAAAA
*
544382 AAAAATGCATAAAACATAATAAAA
1 AAAAATGCATGAAACATAATAAAA
544406 AA
1 AA
544408 TGCATGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.70, C:0.08, G:0.06, T:0.16
Consensus pattern (24 bp):
AAAAATGCATGAAACATAATAAAA
Found at i:545372 original size:20 final size:20
Alignment explanation
Indices: 545325--545399 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
545315 AAAAAGACAT
*
545325 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
545344 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
545365 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
545385 AATGTATCGATACAT
1 AATGTATCGATACAT
545400 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:545393 original size:40 final size:39
Alignment explanation
Indices: 545322--545399 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
545312 GGTAAAAAGA
* *
545322 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
545361 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
545400 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:548783 original size:1 final size:1
Alignment explanation
Indices: 548777--548888 Score: 71
Period size: 1 Copynumber: 112.0 Consensus size: 1
548767 GGCGTCCTCC
* ** * ** ** * *
548777 AAAAAAAAAAAAACAAAAAAAATGAAAAAACAAAAAAAAATGAATGAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
548842 AAAAGAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
548889 GGGGGTCCGG
Statistics
Matches: 80, Mismatches: 31, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.04
Consensus pattern (1 bp):
A
Found at i:548811 original size:23 final size:23
Alignment explanation
Indices: 548778--548882 Score: 98
Period size: 23 Copynumber: 4.8 Consensus size: 23
548768 GCGTCCTCCA
548778 AAAAAAAAAAAACAAAAAAAATG
1 AAAAAAAAAAAACAAAAAAAATG
* **
548801 AAAAAACAAAAA-AAAATGAATG
1 AAAAAAAAAAAACAAAAAAAATG
548823 --AAAAAAAAAACAAAAAAACA--
1 AAAAAAAAAAAACAAAAAAA-ATG
*
548843 AAAGAAAAAAAAACAAAAACAAT-
1 AAA-AAAAAAAAACAAAAAAAATG
*
548866 -AAAAAAACAAACAAAAA
1 AAAAAAAAAAAACAAAAA
548883 CAAAAAGGGG
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
20 9 0.13
21 19 0.28
22 13 0.19
23 27 0.40
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAAAAAATG
Found at i:548827 original size:44 final size:42
Alignment explanation
Indices: 548779--548887 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 42
548769 CGTCCTCCAA
* *
548779 AAAAAAAAAAACAAAAA-AAATGAAAAAACAAAAAAAAATGAAT
1 AAAAAAAAAAACAAAAACAAAAGAAAAAA-AAAAAAAAA-CAAT
* *
548822 GAAAAAAAAAACAAAAAAACAAAAGAAAAAAAAACAAAAACAAT
1 -AAAAAAAAAA-ACAAAAACAAAAGAAAAAAAAAAAAAAACAAT
*
548866 AAAAAAACAAACAAAAACAAAA
1 AAAAAAAAAAACAAAAACAAAA
548888 AGGGGGTCCG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
42 11 0.19
43 9 0.16
44 13 0.23
45 14 0.25
46 10 0.18
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (42 bp):
AAAAAAAAAAACAAAAACAAAAGAAAAAAAAAAAAAAACAAT
Found at i:548883 original size:21 final size:21
Alignment explanation
Indices: 548779--548885 Score: 110
Period size: 21 Copynumber: 5.0 Consensus size: 21
548769 CGTCCTCCAA
*
548779 AAAAAAAAAAACAAAAAAAAT
1 AAAAAAAAAAACAAAAACAAT
**
548800 GAAAAAACAAAAA-AAAATGAAT
1 -AAAAAA-AAAAACAAAAACAAT
*
548822 GAAAAAAAAAACAAAAAAACAA-
1 -AAAAAAAAAA-ACAAAAACAAT
548844 AAGAAAAAAAAACAAAAACAAT
1 AA-AAAAAAAAACAAAAACAAT
*
548866 AAAAAAACAAACAAAAACAA
1 AAAAAAAAAAACAAAAACAA
548886 AAAGGGGGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
21 32 0.43
22 31 0.42
23 11 0.15
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAACAAT
Found at i:548889 original size:43 final size:44
Alignment explanation
Indices: 548780--548889 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 44
548770 GTCCTCCAAA
* *
548780 AAAAAAAAAAC-AAAAAAAATGAAAAAACAAAAAAAAATGAATG
1 AAAAAAAAAACAAAAAAAAAAGAAAAAACAAAAAAAAATCAATG
*
548823 AAAAAAAAAACAAAAAAACAAAAGAAAAAA-AAACAAAAA-CAAT-
1 AAAAAAAAAAC-AAAAAA-AAAAGAAAAAACAAAAAAAAATCAATG
548866 AAAAAAACAAACAAAAACAAAAAG
1 AAAAAAA-AAACAAAAA-AAAAAG
548890 GGGGTCCGGA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
43 28 0.47
44 8 0.14
45 13 0.22
46 10 0.17
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.04
Consensus pattern (44 bp):
AAAAAAAAAACAAAAAAAAAAGAAAAAACAAAAAAAAATCAATG
Found at i:550385 original size:30 final size:29
Alignment explanation
Indices: 550330--550779 Score: 328
Period size: 30 Copynumber: 15.3 Consensus size: 29
550320 TCACCCTTCA
* *
550330 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
550359 AAAGCCCACAAGTCGGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
550388 GAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
550416 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
550446 GAAGCCCACAAGTCGGCGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
550475 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
550505 TTTTGTAAGCTCACAACTCTA-TAGCA-CTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCATCT-TTTTC
* * *
550539 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
550566 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
550596 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
550625 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
550654 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
550684 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
550713 AAAGCCCACAAGTCAGTGGCAATC---TTC
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
* * *
550740 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
*
550770 CAAGCCCACA
1 AAAGCCCACA
550780 CAAGTCGGTG
Statistics
Matches: 338, Mismatches: 59, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
26 2 0.01
27 60 0.18
28 46 0.14
29 60 0.18
30 148 0.44
33 2 0.01
34 5 0.01
35 15 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:550431 original size:27 final size:27
Alignment explanation
Indices: 550389--550441 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
550379 ATTTTTTTCG
*
550389 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
550416 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
550442 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:550644 original size:88 final size:88
Alignment explanation
Indices: 550539--550760 Score: 378
Period size: 88 Copynumber: 2.6 Consensus size: 88
550529 CACTCTTTTC
*
550539 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
550604 ACAAGTCAGTGGCAACCTTTAAA
66 ACAAGTCAGTGGCAACCTTTAAA
*
550627 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
550692 ACAAGTCAGTGGCAACCTTTAAA
66 ACAAGTCAGTGGCAACCTTTAAA
* * *
550715 AGCCCACAAGTCAGTGGCA--ATCTTC-AAAGCCCACAAATCAGTGGCA
1 AGCCCACAAGTTAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCA
550761 CCCTTTTCCC
Statistics
Matches: 129, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
85 20 0.16
86 4 0.03
88 105 0.81
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (88 bp):
AGCCCACAAGTTAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
ACAAGTCAGTGGCAACCTTTAAA
Found at i:550655 original size:58 final size:59
Alignment explanation
Indices: 550326--550795 Score: 331
Period size: 58 Copynumber: 8.0 Consensus size: 59
550316 TTCATCACCC
* *** * ***
550326 TTCAAAAGTCCACAAGTCAGTGGCATTTTTTTC-AAAGCCCACAAGTCGGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* * * *
550385 TTCGAAAGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * * * * * *
550442 TTCCGAAGCCCACAAGTCGGCGGCA-TCTTTTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * * * * *
550502 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTC---AGCCCACAAGTTAGTGGCACCCTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
***
550563 TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * **
550622 TT-AAAAGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* *
550681 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCAATC-
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* ** *
550737 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCCAAGCCCACACAAGTCGGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAG-CC-CACAAGTCAGTGGCAACC
550796 CTTCTAAGCC
Statistics
Matches: 330, Mismatches: 58, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
55 22 0.07
56 8 0.02
57 69 0.21
58 75 0.23
59 66 0.20
60 48 0.15
61 5 0.02
62 15 0.05
63 1 0.00
64 14 0.04
65 7 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:550862 original size:49 final size:49
Alignment explanation
Indices: 550800--551094 Score: 325
Period size: 49 Copynumber: 6.0 Consensus size: 49
550790 GCAACCCTTC
* *
550800 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
550849 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
550898 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
550941 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * *
550993 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * *
551048 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
551095 ACTTTTCTCA
Statistics
Matches: 213, Mismatches: 19, Indels: 28
0.82 0.07 0.11
Matches are distributed among these distances:
43 41 0.19
44 1 0.00
48 1 0.00
49 86 0.40
50 1 0.00
51 2 0.01
52 38 0.18
53 2 0.01
54 2 0.01
55 38 0.18
56 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:550953 original size:43 final size:43
Alignment explanation
Indices: 550892--550984 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
550882 TTGGCACCTT
550892 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
550935 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
550978 CACCTTT
1 CACCTTT
550985 TCCATCTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
Found at i:550962 original size:22 final size:22
Alignment explanation
Indices: 550894--550962 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
550884 GGCACCTTCA
550894 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
550916 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
550937 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
550959 CCTT
1 CCTT
550963 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:550973 original size:92 final size:95
Alignment explanation
Indices: 550846--551037 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 95
550836 GCACCTTTAT
550846 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-CACCTTTAAGTCCAATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTTAAGTCCAATA
*
550909 TAGCTGGCCTTGAATCAGCACATTGGCA-C
66 TAGCTGGCCTTGAATCAGCACATTGACATC
* *
550938 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTTCCACCTTTAAGTCCAAT
*
551003 GTAGCTGGCCTTGAATCAGCACATTGACATC
65 ATAGCTGGCCTTGAATCAGCACATTGACATC
551034 CTTT
1 CTTT
551038 TTCTCATCTT
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
92 44 0.48
94 2 0.02
95 41 0.45
96 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (95 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCACATTGACATC
Found at i:551016 original size:52 final size:53
Alignment explanation
Indices: 550938--551091 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 53
550928 ACATTGGCAC
550938 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
550990 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
551045 CTTTAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
551092 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 7 0.08
55 35 0.41
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:551938 original size:33 final size:33
Alignment explanation
Indices: 551901--551967 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
551891 TTCAACGATT
551901 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
551934 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
551967 T
1 T
551968 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Done.