Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold321
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: 1060354
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 6
Found at i:436069 original size:34 final size:33
Alignment explanation
Indices: 435991--436075 Score: 86
Period size: 37 Copynumber: 2.5 Consensus size: 33
435981 TGAATTTTAA
*
435991 ATATTTAA-ATAT-TTATTTTATATTAAAAATT
1 ATATTTAATATATATTTTTTTATATTAAAAATT
436022 ATATTATTAAATATATATTTTTATTA-ATTAAAAAATT
1 ATA-T-TT-AATATATATTTTT-TTATATT-AAAAATT
*
436059 ATATTTAATATTTATTT
1 ATATTTAATATATATTT
436076 AATATTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 3 0.07
32 1 0.02
33 2 0.04
34 12 0.27
35 6 0.13
36 8 0.18
37 13 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTAATATATATTTTTTTATATTAAAAATT
Found at i:436076 original size:11 final size:11
Alignment explanation
Indices: 436060--436095 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
436050 TAAAAAATTA
436060 TATTTAATATT
1 TATTTAATATT
436071 TATTTAATATT
1 TATTTAATATT
*
436082 AAATTTAATATT
1 -TATTTAATATT
436094 TA
1 TA
436096 AATATCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTAATATT
Found at i:436089 original size:12 final size:12
Alignment explanation
Indices: 436056--436098 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
436046 TAATTAAAAA
*
436056 ATTATATTTAAT
1 ATTAAATTTAAT
*
436068 ATT-TATTTAAT
1 ATTAAATTTAAT
436079 ATTAAATTTAAT
1 ATTAAATTTAAT
436091 ATTTAAAT
1 A-TTAAAT
436099 ATCTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.39
12 11 0.39
13 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:437905 original size:20 final size:19
Alignment explanation
Indices: 437880--437917 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
437870 ATATTTTTAA
*
437880 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
437900 TATATTTATATATAAAAT
1 TATATTTATATATAAAAT
437918 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:439065 original size:16 final size:15
Alignment explanation
Indices: 439049--439098 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
439039 GTTCGGGTTA
439049 TTTTT-AGTTTAGGT
1 TTTTTGAGTTTAGGT
* *
439063 TATTTTGATTTTGGGT
1 T-TTTTGAGTTTAGGT
*
439079 TTTTCGAGTTTAGGT
1 TTTTTGAGTTTAGGT
439094 TTTTT
1 TTTTT
439099 ACTTTTTGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 1 0.04
15 19 0.68
16 8 0.29
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.64
Consensus pattern (15 bp):
TTTTTGAGTTTAGGT
Found at i:439158 original size:14 final size:14
Alignment explanation
Indices: 439139--439186 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
439129 TTCATATTTA
*
439139 AATTTTTTCAGATG
1 AATTTTTTCATATG
** *
439153 AATTTTTAAATTTG
1 AATTTTTTCATATG
439167 AATTTTTTCATATG
1 AATTTTTTCATATG
439181 -ATTTTT
1 AATTTTT
439187 AAATTCAAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.58
Consensus pattern (14 bp):
AATTTTTTCATATG
Found at i:439184 original size:27 final size:28
Alignment explanation
Indices: 439134--439191 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
439124 TTAGATTCAT
439134 ATTTAAATTTTTTCAGATGAATTTTTAA
1 ATTTAAATTTTTTCAGATGAATTTTTAA
* *
439162 ATTTGAATTTTTTCATATG-ATTTTTAA
1 ATTTAAATTTTTTCAGATGAATTTTTAA
439189 ATT
1 ATT
439192 CAAGTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (28 bp):
ATTTAAATTTTTTCAGATGAATTTTTAA
Found at i:442630 original size:17 final size:17
Alignment explanation
Indices: 442610--442673 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
442600 TATGAAAATT
442610 TAATATTAATATTTATA
1 TAATATTAATATTTATA
*
442627 TAATATGAAT-TGTTA-A
1 TAATATTAATAT-TTATA
442643 TAA-ATTTAA-ATTTATA
1 TAATA-TTAATATTTATA
442659 TAATATGTAATATTT
1 TAATAT-TAATATTT
442674 TAAATATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
15 4 0.11
16 14 0.37
17 16 0.42
18 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TAATATTAATATTTATA
Found at i:442719 original size:21 final size:22
Alignment explanation
Indices: 442685--442725 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
442675 AAATATAATT
442685 ATAATATAAAAAATATACATAA
1 ATAATATAAAAAATATACATAA
442707 ATAATAT-AAAAATATACAT
1 ATAATATAAAAAATATACAT
442726 TACAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAATATAAAAAATATACATAA
Found at i:442733 original size:21 final size:21
Alignment explanation
Indices: 442675--442733 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
442665 GTAATATTTT
*
442675 AAATATA-ATTATAATATAAA
1 AAATATACATTAAAATATAAA
*
442695 AAATATACATAAATAATAT-AA
1 AAATATACATTAA-AATATAAA
442716 AAATATACATTACAAATA
1 AAATATACATTA-AAATA
442734 AACAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATACATTAAAATATAAA
Found at i:442740 original size:21 final size:20
Alignment explanation
Indices: 442675--442740 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
442665 GTAATATTTT
*
442675 AAATATA-ATTATAATATAAA
1 AAATATACATTA-AAAATAAA
442695 AAATATACA-TAAATAATATAA
1 AAATATACATTAAA-AATA-AA
*
442716 AAATATACATTACAAATAAA
1 AAATATACATTAAAAATAAA
442736 CAAAT
1 -AAAT
442741 TATAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.05
20 14 0.36
21 20 0.51
22 3 0.08
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATACATTAAAAATAAA
Found at i:442938 original size:4 final size:4
Alignment explanation
Indices: 442939--443049 Score: 123
Period size: 4 Copynumber: 27.8 Consensus size: 4
442929 ACATACATAC
* * * * *
442939 ATAT ATAT ATAT ATAC ATAC ATAT ATAT ATAC ATAC ATAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
442987 ATAT ACAT ATAT ATAC ATAC ATAT ATAT ATAT ACAT ATAT ATAT ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
443035 ATAC ATAT ATAT ATA
1 ATAT ATAT ATAT ATA
443050 GTAGGTAAGG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:442956 original size:16 final size:16
Alignment explanation
Indices: 442935--443049 Score: 149
Period size: 16 Copynumber: 6.9 Consensus size: 16
442925 TTACACATAC
442935 ATACATATATATATAT
1 ATACATATATATATAT
*
442951 ATACATACATATATAT
1 ATACATATATATATAT
* *
442967 ATACATACATATATAC
1 ATACATATATATATAT
* *
442983 ATATATATACATATAT
1 ATACATATATATATAT
442999 ATACATACATATATATAT
1 ATACAT--ATATATATAT
443017 ATACATATATATATAT
1 ATACATATATATATAT
443033 ACATACATATATATATA
1 --ATACATATATATATA
443050 GTAGGTAAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
16 57 0.66
18 30 0.34
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
ATACATATATATATAT
Found at i:442956 original size:20 final size:20
Alignment explanation
Indices: 442931--443049 Score: 143
Period size: 20 Copynumber: 6.0 Consensus size: 20
442921 TTTATTACAC
442931 ATACATACATATATATATAT
1 ATACATACATATATATATAT
*
442951 ATACATACATATATATATAC
1 ATACATACATATATATATAT
*
442971 ATACAT--ATATACATATAT
1 ATACATACATATATATATAT
* *
442989 ATACATATATATACATACATAT
1 ATACATACATAT--ATATATAT
* * *
443011 ATATATATACATATATATAT
1 ATACATACATATATATATAT
443031 ATACATACATATATATATA
1 ATACATACATATATATATA
443050 GTAGGTAAGG
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
18 16 0.19
20 52 0.62
22 16 0.19
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
ATACATACATATATATATAT
Found at i:442964 original size:14 final size:14
Alignment explanation
Indices: 442945--443047 Score: 133
Period size: 14 Copynumber: 7.6 Consensus size: 14
442935 ATACATATAT
442945 ATATATATACATAC
1 ATATATATACATAC
442959 ATATATAT--ATAC
1 ATATATATACATAC
*
442971 ATACATAT--ATAC
1 ATATATATACATAC
*
442983 ATATATATACATAT
1 ATATATATACATAC
* *
442997 ATATACATACATAT
1 ATATATATACATAC
*
443011 ATATATATACATAT
1 ATATATATACATAC
443025 ATATATATACATAC
1 ATATATATACATAC
443039 ATATATATA
1 ATATATATA
443048 TAGTAGGTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
12 22 0.27
14 59 0.73
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:442971 original size:32 final size:32
Alignment explanation
Indices: 442935--443049 Score: 144
Period size: 34 Copynumber: 3.6 Consensus size: 32
442925 TTACACATAC
442935 ATACATATATATATATATACATACATATATAT
1 ATACATATATATATATATACATACATATATAT
* *
442967 ATACATACATATATACATATATATACATATATAT
1 ATACAT--ATATATATATATACATACATATATAT
* * *
443001 ACATACATATATATATATACAT--ATATATAT
1 ATACATATATATATATATACATACATATATAT
*
443031 ATACATACATATATATATA
1 ATACATATATATATATATA
443050 GTAGGTAAGG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
30 23 0.33
32 20 0.29
34 27 0.39
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.39
Consensus pattern (32 bp):
ATACATATATATATATATACATACATATATAT
Found at i:443718 original size:2 final size:2
Alignment explanation
Indices: 443705--443738 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
443695 TCAGTTTTAC
*
443705 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
443739 TGACACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:446769 original size:24 final size:21
Alignment explanation
Indices: 446717--446791 Score: 57
Period size: 24 Copynumber: 3.4 Consensus size: 21
446707 ATATAATTTT
446717 TAATATAATATAAT-TAAAAAA
1 TAATA-AATATAATATAAAAAA
*
446738 -CATAAATATAATATAAAAAA
1 TAATAAATATAATATAAAAAA
*
446758 TTAATTATAATA-AGATATAAAATA
1 -TAA-TA-AATATA-ATATAAAAAA
446782 TAATTAAATA
1 TAA-TAAATA
446792 AAGGACTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.18
20 10 0.22
22 5 0.11
23 9 0.20
24 13 0.29
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
TAATAAATATAATATAAAAAA
Found at i:446770 original size:22 final size:22
Alignment explanation
Indices: 446745--446792 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
446735 AAACATAAAT
*
446745 ATAATATAAAAAAT-TAATTATA
1 ATAAGATAAAAAATATAATTA-A
*
446767 ATAAGATATAAAATATAATTAA
1 ATAAGATAAAAAATATAATTAA
446789 ATAA
1 ATAA
446793 AGGACTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAGATAAAAAATATAATTAA
Found at i:447583 original size:22 final size:21
Alignment explanation
Indices: 447538--447583 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
447528 ATAAATTATT
*
447538 AAAATATTAATATTTATATAA
1 AAAATATTAATATTTAAATAA
447559 AAAATATATAATATATTAAATAA
1 AAAATAT-TAATAT-TTAAATAA
447582 AA
1 AA
447584 TTACGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 6 0.27
23 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATTAATATTTAAATAA
Found at i:447915 original size:15 final size:16
Alignment explanation
Indices: 447878--447918 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
447868 GATTAATTTT
447878 TTTTTTAA-ATATATA
1 TTTTTTAATATATATA
*
447893 TATATTTAATATAT-TA
1 T-TTTTTAATATATATA
447909 TTTTTTAATA
1 TTTTTTAATA
447919 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 9 0.41
17 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTAATATATATA
Found at i:449037 original size:6 final size:6
Alignment explanation
Indices: 449026--449054 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
449016 GTTGTGGACC
449026 ATGGCT ATGGCT ATGGCT ATGGCT ATGGC
1 ATGGCT ATGGCT ATGGCT ATGGCT ATGGC
449055 CAAGGGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
ATGGCT
Found at i:457467 original size:3 final size:3
Alignment explanation
Indices: 457452--457492 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
457442 GATAGATTCT
* *
457452 TGA TGA CGA TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
457493 GAAAATTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:462069 original size:15 final size:15
Alignment explanation
Indices: 462039--462077 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
462029 AATTATTTTT
*
462039 TATATTTATATTTAAA
1 TATATTTA-ATATAAA
462055 TATATTTAATATAAA
1 TATATTTAATATAAA
462070 TAT-TTTAA
1 TATATTTAA
462078 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTAATATAAA
Found at i:466910 original size:20 final size:21
Alignment explanation
Indices: 466875--466917 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
466865 TAAAATTTAA
* *
466875 ATAATTAAAAATTTATTATTT
1 ATAAATAAAAATTTATGATTT
466896 ATAAATAAAAA-TTATGATTT
1 ATAAATAAAAATTTATGATTT
466916 AT
1 AT
466918 TTTTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAAATAAAAATTTATGATTT
Found at i:467572 original size:18 final size:17
Alignment explanation
Indices: 467549--467590 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
467539 TAAAATTGTT
467549 AATTTATATAATTTTTAA
1 AATTTATATAATTTTT-A
*
467567 AATTTAT-TTATTATTTA
1 AATTTATATAATT-TTTA
467584 AATTTAT
1 AATTTAT
467591 TAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTATATAATTTTTA
Found at i:467597 original size:18 final size:19
Alignment explanation
Indices: 467549--467605 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
467539 TAAAATTGTT
467549 AATTTA-TATAATT-TTTAA
1 AATTTATTA-AATTATTTAA
*
467567 AATTTATT-TATTATTT-A
1 AATTTATTAAATTATTTAA
467584 AATTTATTAAATTATTTTAA
1 AATTTATTAAATTA-TTTAA
467604 AA
1 AA
467606 AATAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 12 0.38
18 13 0.41
19 4 0.12
20 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTATTAAATTATTTAA
Found at i:477666 original size:4 final size:4
Alignment explanation
Indices: 477659--477692 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
477649 TATATGTGTG
*
477659 TGTA TGTA TGTA TGTA TGTA TGTA TGTC TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
477693 GGTATCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:484497 original size:2 final size:2
Alignment explanation
Indices: 484490--484521 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
484480 GAATCCTACA
484490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
484522 GATGGAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486173 original size:19 final size:21
Alignment explanation
Indices: 486130--486177 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
486120 TATTATATTT
486130 ATTTTTATATATTGATAATATA
1 ATTTTT-TATATTGATAATATA
*
486152 ATTTTTTA-ATTTATAA-ATA
1 ATTTTTTATATTGATAATATA
486171 ATTTTTT
1 ATTTTTT
486178 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 2 0.08
22 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTTTATATTGATAATATA
Found at i:486176 original size:20 final size:22
Alignment explanation
Indices: 486130--486178 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
486120 TATTATATTT
*
486130 ATTTTTATATATTGATAATATA
1 ATTTTTTTATATTGATAATATA
*
486152 A-TTTTTTA-ATTTATAA-ATA
1 ATTTTTTTATATTGATAATATA
486171 ATTTTTTT
1 ATTTTTTT
486179 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 6 0.25
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTTATATTGATAATATA
Found at i:491524 original size:17 final size:18
Alignment explanation
Indices: 491490--491529 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
491480 TTGTTTCATC
491490 TTTTATTCATTTGATATT
1 TTTTATTCATTTGATATT
* *
491508 TTTTATTTATTT-TTATT
1 TTTTATTCATTTGATATT
491525 TTTTA
1 TTTTA
491530 ATTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTATTCATTTGATATT
Found at i:491596 original size:3 final size:3
Alignment explanation
Indices: 491588--491618 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
491578 AATATAATTA
491588 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
491619 AAAAGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:497832 original size:27 final size:28
Alignment explanation
Indices: 497780--497846 Score: 127
Period size: 27 Copynumber: 2.4 Consensus size: 28
497770 TGGTTGTAGC
497780 TGCTGCTGCTGCCTGCATCAGTGGTTGT
1 TGCTGCTGCTGCCTGCATCAGTGGTTGT
497808 TGCTGCTGCTGCC-GCATCAGTGGTTGT
1 TGCTGCTGCTGCCTGCATCAGTGGTTGT
497835 TGCTGCTGCTGC
1 TGCTGCTGCTGC
497847 TGCTGAGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 26 0.67
28 13 0.33
ACGTcount: A:0.06, C:0.27, G:0.33, T:0.34
Consensus pattern (28 bp):
TGCTGCTGCTGCCTGCATCAGTGGTTGT
Found at i:499354 original size:18 final size:18
Alignment explanation
Indices: 499312--499363 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
499302 CCCACCCAAG
499312 AAAAATTAAGCAAAAAAAAC
1 AAAAATTAAG--AAAAAAAC
* *
499332 TAAAATTAAGAAAAAGAC
1 AAAAATTAAGAAAAAAAC
*
499350 AAAAAATAAGAAAA
1 AAAAATTAAGAAAA
499364 TGAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 19 0.68
20 9 0.32
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.12
Consensus pattern (18 bp):
AAAAATTAAGAAAAAAAC
Found at i:499371 original size:18 final size:18
Alignment explanation
Indices: 499333--499373 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
499323 AAAAAAAACT
* *
499333 AAAATTAAGAAAAAGACA
1 AAAAATAAGAAAAAGAAA
*
499351 AAAAATAAGAAAATGAAA
1 AAAAATAAGAAAAAGAAA
499369 AAAAA
1 AAAAA
499374 AAACAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAATAAGAAAAAGAAA
Found at i:499977 original size:4 final size:4
Alignment explanation
Indices: 499968--500015 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
499958 TTAAAATATG
* *
499968 TATT TATT TATT TA-T TA-T TAAT TATT TATT TATT TAGTT TAAT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT
500015 T
1 T
500016 TAAATATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
3 6 0.15
4 29 0.74
5 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:499994 original size:18 final size:20
Alignment explanation
Indices: 499971--500015 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
499961 AAATATGTAT
499971 TTATTTATTTA-TTA-TTAA
1 TTATTTATTTATTTAGTTAA
499989 TTATTTATTTATTTAGTTTAA
1 TTATTTATTTATTTAG-TTAA
500010 TTATTT
1 TTATTT
500016 TAAATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
21 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATTTATTTATTTAGTTAA
Found at i:500017 original size:22 final size:22
Alignment explanation
Indices: 499968--500015 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
499958 TTAAAATATG
*
499968 TATTTATTTATTTATTATTAAT
1 TATTTATTTATTTAGTATTAAT
499990 TATTTATTTATTTAGT-TTAAT
1 TATTTATTTATTTAGTATTAAT
500011 TATTT
1 TATTT
500016 TAAATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTATTTATTTAGTATTAAT
Found at i:500584 original size:17 final size:16
Alignment explanation
Indices: 500547--500585 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
500537 TAATTTTTAC
500547 AAAAAATAATAATAAT
1 AAAAAATAATAATAAT
* *
500563 TAAAAATAGATAATTAT
1 AAAAAATA-ATAATAAT
500580 AAAAAA
1 AAAAAA
500586 AAACAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAATAATAATAAT
Found at i:500587 original size:35 final size:34
Alignment explanation
Indices: 500547--500614 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
500537 TAATTTTTAC
* *
500547 AAAAAATAATAATAATTAAAAATAGATAATTATAAA
1 AAAAAACAA-AATAAATAAAAATAGA-AATTATAAA
*
500583 AAAAAACAAAATAAATAACAATAGAAATTATA
1 AAAAAACAAAATAAATAAAAATAGAAATTATA
500615 GCTAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.24
35 14 0.48
36 8 0.28
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (34 bp):
AAAAAACAAAATAAATAAAAATAGAAATTATAAA
Found at i:503184 original size:14 final size:14
Alignment explanation
Indices: 503165--503192 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
503155 TCAACCAAAT
503165 TAAAAATATAATGA
1 TAAAAATATAATGA
503179 TAAAAATATAATGA
1 TAAAAATATAATGA
503193 AGTTGAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
TAAAAATATAATGA
Found at i:503328 original size:2 final size:2
Alignment explanation
Indices: 503321--503350 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
503311 AAAATAATAA
503321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
503351 TAGGAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513205 original size:39 final size:40
Alignment explanation
Indices: 513149--513225 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
513139 TTCGTCTAGA
* *
513149 TTGAAGGGTATCGAAGCATGGAGGATTGTATTCTGAATAT
1 TTGAAGGGTATCGAAGCATGGAGGATTGGATTCCGAATAT
*
513189 TTGAA-GGTATCGAAGCATGGATGATTGGATTCCGAAT
1 TTGAAGGGTATCGAAGCATGGAGGATTGGATTCCGAAT
513226 GTCAGCATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.31
Consensus pattern (40 bp):
TTGAAGGGTATCGAAGCATGGAGGATTGGATTCCGAATAT
Found at i:515623 original size:23 final size:24
Alignment explanation
Indices: 515593--515646 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
515583 AATATTAAAG
515593 TAAT-TTAAAA-ATTAATTT-TAT
1 TAATATTAAAATATTAATTTATAT
*
515614 TAATTATTAAAATATTATTTTATAT
1 TAA-TATTAAAATATTAATTTATAT
515639 TAATATTA
1 TAATATTA
515647 TATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 1 0.04
23 6 0.21
24 12 0.43
25 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATATTAAAATATTAATTTATAT
Found at i:515639 original size:18 final size:20
Alignment explanation
Indices: 515618--515663 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
515608 TTTTATTAAT
515618 TATTAA-AATAT-TATTTTA
1 TATTAATAATATATATTTTA
*
515636 TATTAATATTATATATTTTA
1 TATTAATAATATATATTTTA
515656 TAATTAAT
1 T-ATTAAT
515664 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 8 0.33
21 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTAATAATATATATTTTA
Found at i:515714 original size:18 final size:17
Alignment explanation
Indices: 515655--515720 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
515645 TATATATTTT
*
515655 ATAATTAATTTAAATAAAA
1 ATAA-TAATTTAAAT-TAA
* *
515674 ATATTATTTTATAATTAA
1 ATAATAATTTA-AATTAA
515692 ATAATAATTTAAATTAA
1 ATAATAATTTAAATTAA
515709 AT--TAATTTAAAT
1 ATAATAATTTAAAT
515721 ACATAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 10 0.24
17 8 0.20
18 17 0.41
19 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATAATTTAAATTAA
Found at i:515727 original size:18 final size:17
Alignment explanation
Indices: 515657--515729 Score: 55
Period size: 15 Copynumber: 4.2 Consensus size: 17
515647 TATATTTTAT
515657 AATTAATTTAAATAA-A
1 AATTAATTTAAATAATA
* *
515673 AATATTATTT-TATAATTA
1 AAT-TAATTTAAATAA-TA
515691 AATAATAATTTAAAT--TA
1 AAT--TAATTTAAATAATA
515708 AATTAATTTAAATACATA
1 AATTAATTTAAATA-ATA
515726 AATT
1 AATT
515730 TTTATGCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
15 10 0.22
16 7 0.16
17 10 0.22
18 10 0.22
19 6 0.13
20 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATTTAAATAATA
Found at i:520590 original size:16 final size:16
Alignment explanation
Indices: 520569--520604 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
520559 AATTTACATG
520569 ATATTCAGATATATAT
1 ATATTCAGATATATAT
520585 ATATTCAGATATATAT
1 ATATTCAGATATATAT
520601 ATAT
1 ATAT
520605 ATATATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
ATATTCAGATATATAT
Found at i:521889 original size:29 final size:27
Alignment explanation
Indices: 521855--521914 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
521845 TTTTAAAAAA
521855 TTAATATTTAATAAATTTTAATTTTAATT
1 TTAATATTT-ATAAATTTTAA-TTTAATT
* * *
521884 TTAATATTTATAATTTTTTATTTATTT
1 TTAATATTTATAAATTTTAATTTAATT
521911 TTAA
1 TTAA
521915 ATTATGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 9 0.32
29 9 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTAATATTTATAAATTTTAATTTAATT
Found at i:522476 original size:25 final size:28
Alignment explanation
Indices: 522448--522502 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
522438 AATACAAAAG
522448 TAAAATA-AT-TAT-TAAAAAATTAAAT
1 TAAAATATATATATATAAAAAATTAAAT
*
522473 TAAAATATATATATAATAAATAATTAAAT
1 TAAAATATATATAT-ATAAAAAATTAAAT
522502 T
1 T
522503 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 2 0.08
27 3 0.12
29 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATATATATATATAAAAAATTAAAT
Found at i:524299 original size:16 final size:16
Alignment explanation
Indices: 524231--524323 Score: 61
Period size: 16 Copynumber: 6.0 Consensus size: 16
524221 TTTATATAAA
*
524231 TTTTAATATATTAATAAT
1 TTTTATTATATT-AT-AT
* *
524249 TTTTATTATA-AAAAT
1 TTTTATTATATTATAT
*
524264 TTTTA--ATA-TAAAT
1 TTTTATTATATTATAT
*
524277 TTATATTATATTATAT
1 TTTTATTATATTATAT
*
524293 TTTTATTATTTTATAT
1 TTTTATTATATTATAT
* *
524309 ATTTAATAT-TTATAT
1 TTTTATTATATTATAT
524324 AATTATTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
13 11 0.18
15 16 0.26
16 26 0.42
18 9 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTATATTATAT
Found at i:524314 original size:45 final size:45
Alignment explanation
Indices: 524217--524317 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
524207 TTAAAATATT
524217 TATATTT-ATATAAATTTTAATATATTAATAATTTTTATTATAAA
1 TATATTTAATATAAATTTTAATATATTAATAATTTTTATTATAAA
* * * **
524261 AATTTTTAATATAAATTTATATTATATT-AT-ATTTTTATTATTTTA
1 TATATTTAATATAAATTT-TAATATATTAATAATTTTTATTA-TAAA
524306 TATATTTAATAT
1 TATATTTAATAT
524318 TTATATAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 15 0.32
45 24 0.51
46 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (45 bp):
TATATTTAATATAAATTTTAATATATTAATAATTTTTATTATAAA
Found at i:524319 original size:7 final size:8
Alignment explanation
Indices: 524270--524329 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
524260 AAATTTTTAA
*
524270 TATAAATT
1 TATATATT
524278 TATATTATAT
1 TATA-TAT-T
*
524288 TATATTTT
1 TATATATT
524296 TAT-TATTT
1 TATATA-TT
524304 TATATATT
1 TATATATT
524312 TA-ATATT
1 TATATATT
*
524319 TATATAAT
1 TATATATT
524327 TAT
1 TAT
524330 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 8 0.19
8 24 0.56
9 6 0.14
10 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:524733 original size:13 final size:13
Alignment explanation
Indices: 524716--524749 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
524706 AATTAATTAA
524716 AATAAATATCAAT
1 AATAAATATCAAT
* *
524729 CATAAATATTAAT
1 AATAAATATCAAT
524742 AATAAATA
1 AATAAATA
524750 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATATCAAT
Found at i:524754 original size:16 final size:15
Alignment explanation
Indices: 524733--524781 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
524723 ATCAATCATA
524733 AATATTAATAATAAAT
1 AATATTAATAAT-AAT
524749 AATATTAA-AATAAT
1 AATATTAATAATAAT
* *
524763 AA-AATAATAATCAT
1 AATATTAATAATAAT
524777 AATAT
1 AATAT
524782 CATATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 4 0.14
16 8 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATTAATAATAAT
Found at i:526743 original size:14 final size:14
Alignment explanation
Indices: 526724--526758 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
526714 AAGAATATTT
526724 TAATTTATATTAAA
1 TAATTTATATTAAA
526738 TAATTTATATTAAA
1 TAATTTATATTAAA
526752 T-ATTTAT
1 TAATTTAT
526759 TATAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATTTATATTAAA
Found at i:526758 original size:13 final size:13
Alignment explanation
Indices: 526726--526771 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
526716 GAATATTTTA
526726 ATTTATATTAAAT
1 ATTTATATTAAAT
526739 AATTTATATTAAAT
1 -ATTTATATTAAAT
*
526753 ATTTAT-TATAATT
1 ATTTATAT-TAAAT
526766 ATTTAT
1 ATTTAT
526772 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 1 0.03
13 16 0.53
14 13 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTATATTAAAT
Found at i:527149 original size:18 final size:19
Alignment explanation
Indices: 527107--527165 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
527097 ATTTTTTAAT
*
527107 ATTTTAATTATATAATTAA
1 ATTTTAATTATATAAATAA
527126 ATTTTAATTA-ATAAATATA
1 ATTTTAATTATATAAATA-A
*
527145 ATTTAAATTATA-AAA-AA
1 ATTTTAATTATATAAATAA
527162 ATTT
1 ATTT
527166 ATTTCAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 5 0.14
18 7 0.19
19 23 0.64
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTAATTATATAAATAA
Found at i:528099 original size:42 final size:41
Alignment explanation
Indices: 528020--528148 Score: 125
Period size: 42 Copynumber: 3.0 Consensus size: 41
528010 AAAATATATT
* * * *
528020 TAAAAAATAATAAATAAATAAAATATTTAATATATTTTTAATA
1 TAAAAAAT-ATAAATTAAT-AAATATTTATTAAATTTTTAAAA
**
528063 TATTAAATATAAATTAATAAATATTTATTAAAATTTTTAAAA
1 TAAAAAATATAAATTAATAAATATTTATT-AAATTTTTAAAA
*
528105 TAAAAAATATATAATTATTATAATATATT-TTAAATTTTATAAAA
1 TAAAAAATATA-AATTAATA-AATAT-TTATTAAATTTT-TAAAA
528149 ATAATTAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
41 10 0.14
42 28 0.39
43 20 0.28
44 12 0.17
45 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (41 bp):
TAAAAAATATAAATTAATAAATATTTATTAAATTTTTAAAA
Found at i:528103 original size:20 final size:20
Alignment explanation
Indices: 528040--528103 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
528030 TAAATAAATA
*
528040 AAATATTTAAT-ATATTTTT
1 AAATATTTAATAAAATTTTT
* **
528059 AATATATTAAATATAAATTAAT
1 AA-ATATTTAATA-AAATTTTT
*
528081 AAATATTTATTAAAATTTTT
1 AAATATTTAATAAAATTTTT
528101 AAA
1 AAA
528104 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 8 0.24
22 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATATTTAATAAAATTTTT
Found at i:528103 original size:34 final size:36
Alignment explanation
Indices: 528060--528185 Score: 100
Period size: 39 Copynumber: 3.5 Consensus size: 36
528050 TATATTTTTA
* * *
528060 ATATATTAAATATAAATTAATAAATATTTATTA-AA-
1 ATATTTTAAATATAAA-AAATAAATAATTATTATAAT
*
528095 AT-TTTTAAA-ATAAAAAATATATAATTATTATAAT
1 ATATTTTAAATATAAAAAATAAATAATTATTATAAT
* * * *
528129 ATATTTTAAATTTTATAAAAATAATTAATTAAATATAAA
1 ATATTTTAAA-TATA-AAAAATAAATAATT-ATTATAAT
*
528168 ATTTTTTAAA-ATAAAAAA
1 ATATTTTAAATATAAAAAA
528186 ATTAGACCCT
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
32 13 0.18
33 7 0.10
34 8 0.11
35 9 0.12
36 5 0.07
37 4 0.05
38 12 0.16
39 15 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
ATATTTTAAATATAAAAAATAAATAATTATTATAAT
Found at i:528113 original size:78 final size:74
Alignment explanation
Indices: 528023--528185 Score: 179
Period size: 78 Copynumber: 2.1 Consensus size: 74
528013 ATATATTTAA
* * *
528023 AAAATAATAAATAAATAAAATATT-TAATATATTTTTAA-TATATTAAATATAAATTAA-TAAAT
1 AAAATAAAAAATAAAT-AAATATTATAATATATTTTAAATTATA-TAAAAAT-AATTAATTAAAT
528085 ATTTATTAAAATTTTT
63 A--TA--AAAATTTTT
* * *
528101 AAAATAAAAAATATATAATTATTATAATATATTTTAAATTTTATAAAAATAATTAATTAAATATA
1 AAAATAAAAAATAAATAAATATTATAATATATTTTAAATTATATAAAAATAATTAATTAAATATA
*
528166 AAATTTTTT
66 AAAATTTTT
528175 AAAATAAAAAA
1 AAAATAAAAAA
528186 ATTAGACCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
74 19 0.25
76 2 0.03
77 12 0.16
78 39 0.52
79 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (74 bp):
AAAATAAAAAATAAATAAATATTATAATATATTTTAAATTATATAAAAATAATTAATTAAATATA
AAAATTTTT
Found at i:531876 original size:16 final size:16
Alignment explanation
Indices: 531855--531902 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
531845 TTTTATATAA
531855 ATTTTAATATATTAAT
1 ATTTTAATATATTAAT
531871 ATTTT-ATATTATATAAT
1 ATTTTAATA-TAT-TAAT
531888 A-TTTAATATACTTAA
1 ATTTTAATATA-TTAA
531903 AAATCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.11
16 16 0.57
17 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTAATATATTAAT
Found at i:531889 original size:17 final size:17
Alignment explanation
Indices: 531847--531896 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
531837 ATAATATATT
531847 TTATATAA-ATTTTA-A
1 TTATATAATATTTTATA
531862 -TATATTAATATTTTATA
1 TTATA-TAATATTTTATA
*
531879 TTATATAATATTTAATA
1 TTATATAATATTTTATA
531896 T
1 T
531897 ACTTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.13
15 3 0.10
16 6 0.20
17 13 0.43
18 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATAATATTTTATA
Found at i:533077 original size:24 final size:24
Alignment explanation
Indices: 533031--533077 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
533021 AAAAAAATTA
* *
533031 AAAAATATTAAATATATTTATATC
1 AAAAATATAAAATATATTAATATC
533055 AAAAATATAATAATAT-TTAATAT
1 AAAAATATAA-AATATATTAATAT
533078 TTATCCCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATATAAAATATATTAATATC
Found at i:538694 original size:29 final size:28
Alignment explanation
Indices: 538652--538710 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
538642 TTTTATAAAT
* *
538652 AAATTTACAGTTTAAAAATATAAATATTA
1 AAATTTAAAATTTAAAAATAT-AATATTA
* *
538681 AAATTTAAAATTTAAATATATTATATTA
1 AAATTTAAAATTTAAAAATATAATATTA
538709 AA
1 AA
538711 TATAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
AAATTTAAAATTTAAAAATATAATATTA
Found at i:538709 original size:21 final size:19
Alignment explanation
Indices: 538666--538737 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
538656 TTACAGTTTA
* *
538666 AAAATATAAATATTAAAATTT
1 AAAATATAAAAATT-ATA-TT
*
538687 AAAATTTAAATATATTATATT
1 AAAATATAAA-A-ATTATATT
*
538708 -AAATATAAAAATTATTTT
1 AAAATATAAAAATTATATT
538726 AAAATAATAAAA
1 AAAAT-ATAAAA
538738 TAAATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 7 0.17
19 5 0.12
20 14 0.33
21 11 0.26
22 2 0.05
23 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATAAAAATTATATT
Found at i:547033 original size:5 final size:5
Alignment explanation
Indices: 547025--547057 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
547015 CTTGGCTTTA
*
547025 GTCTG GTCTG GTCTG GTCTG GTCTG GTTTG GTC
1 GTCTG GTCTG GTCTG GTCTG GTCTG GTCTG GTC
547058 CTCTCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.42
Consensus pattern (5 bp):
GTCTG
Found at i:547774 original size:17 final size:18
Alignment explanation
Indices: 547740--547778 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
547730 TCATTTTCAT
**
547740 AATAATATAAATTTTAAA
1 AATAATATAAATAATAAA
547758 AATAAT-TAAATAATAAA
1 AATAATATAAATAATAAA
547775 AATA
1 AATA
547779 TTTTTCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATATAAATAATAAA
Found at i:548206 original size:22 final size:20
Alignment explanation
Indices: 548175--548223 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
548165 TGAAACAAAT
548175 AAATGAAATTGAAAAGTATACAA
1 AAATGAAATT-AAAA-TATA-AA
548198 AAAT-AAATTAAAATATAAA
1 AAATGAAATTAAAATATAAA
548217 AAA-GAAA
1 AAATGAAA
548224 AGAGAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 4 0.16
22 5 0.20
23 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.20
Consensus pattern (20 bp):
AAATGAAATTAAAATATAAA
Found at i:551006 original size:9 final size:9
Alignment explanation
Indices: 550992--551019 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
550982 ACGAACTCGT
550992 TCGCTTCAC
1 TCGCTTCAC
551001 TCGCTTCAC
1 TCGCTTCAC
551010 TCGCTTCAC
1 TCGCTTCAC
551019 T
1 T
551020 GTTGATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.43, G:0.11, T:0.36
Consensus pattern (9 bp):
TCGCTTCAC
Found at i:551308 original size:21 final size:20
Alignment explanation
Indices: 551284--551335 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
551274 TGTATCTAAA
551284 ATTTTAAATTTTTATAATAAT
1 ATTTTAAATTTTTATAAT-AT
* * *
551305 ATTTTAAAATTTTTTTAGTCT
1 ATTTT-AAATTTTTATAATAT
551326 ATTTTAAATT
1 ATTTTAAATT
551336 GAGTTTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 11 0.41
22 11 0.41
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTAAATTTTTATAATAT
Found at i:559069 original size:3 final size:3
Alignment explanation
Indices: 559061--559094 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
559051 TATCGCCTAC
559061 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
559095 GAACGACGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:567571 original size:14 final size:13
Alignment explanation
Indices: 567549--567586 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
567539 TTGCTTTTCA
567549 AAAAATTTTAAAT
1 AAAAATTTTAAAT
*
567562 AAATAATTTTAATT
1 AAA-AATTTTAAAT
567576 AAAAATTTTAA
1 AAAAATTTTAA
567587 TATATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAAATTTTAAAT
Found at i:567584 original size:13 final size:13
Alignment explanation
Indices: 567549--567587 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
567539 TTGCTTTTCA
*
567549 AAAAATTTTAAAT
1 AAAAATTTTAATT
567562 AAATAATTTTAATT
1 AAA-AATTTTAATT
567576 AAAAATTTTAAT
1 AAAAATTTTAAT
567588 ATATTTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAATTTTAATT
Found at i:574523 original size:19 final size:19
Alignment explanation
Indices: 574501--574594 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
574491 TGATTACATT
574501 TAAATATTATATATTTATA
1 TAAATATTATATATTTATA
* *
574520 TAAATATTAATTTATTAATAA
1 TAAATATT-ATATATTTAT-A
** * *
574541 TTCATACTTTATAAATTTTTA
1 TAAATA--TTATATATTTATA
574562 TAAA-ATTAATATATTTATA
1 TAAATATT-ATATATTTATA
574581 T-AATATTATATATT
1 TAAATATTATATATT
574595 AATTATTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
18 11 0.19
19 21 0.37
20 9 0.16
21 8 0.14
22 6 0.11
23 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATATTATATATTTATA
Found at i:574592 original size:29 final size:28
Alignment explanation
Indices: 574548--574615 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
574538 TAATTCATAC
*
574548 TTTATA-AATTTTTATA-AAATTAATATA
1 TTTATATAATTTATATATAAATT-ATATA
* *
574575 TTTATATAATATTATATATTAATTATTTA
1 TTTATATAAT-TTATATATAAATTATATA
*
574604 TTTATATTATTT
1 TTTATATAATTT
574616 CATCGGACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 6 0.18
28 5 0.15
29 19 0.56
30 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTATATAATTTATATATAAATTATATA
Found at i:574941 original size:16 final size:17
Alignment explanation
Indices: 574912--574943 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
574902 TTAAAATTAA
574912 TTAAATTAAATTAAATT
1 TTAAATTAAATTAAATT
574929 TTAAATT-AATTAAAT
1 TTAAATTAAATTAAAT
574944 CAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTAAATTAAATT
Found at i:575013 original size:37 final size:32
Alignment explanation
Indices: 574929--575013 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 32
574919 AAATTAAATT
* * *
574929 TTAAATTAATTAAATCAAATAAAAATATATTT
1 TTAAATTAATTTAATCAAATAAAAAAATATTA
**
574961 TTAAATTAAACTAATCAAATTAAATTTAAAATATTGA
1 TTAAATTAATTTAATCAAA-TAAA---AAAATATT-A
574998 TTAAATTAATTTAATC
1 TTAAATTAATTTAATC
575014 TGTTTCAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
32 16 0.39
33 4 0.10
36 7 0.17
37 14 0.34
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (32 bp):
TTAAATTAATTTAATCAAATAAAAAAATATTA
Found at i:575127 original size:38 final size:39
Alignment explanation
Indices: 575076--575151 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
575066 ATATAAATGA
* * *
575076 AATTTTATATTATATATTTTTAAATTATAA-TAAAAATAT
1 AATTTTATATTATAT-TATATAAAATATAATTAAAAATAT
575115 AATTTTAT-TTATATTATATAAAATATAATTAAAAATA
1 AATTTTATATTATATTATATAAAATATAATTAAAAATA
575152 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 11 0.33
38 14 0.42
39 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
AATTTTATATTATATTATATAAAATATAATTAAAAATAT
Found at i:575203 original size:13 final size:13
Alignment explanation
Indices: 575187--575244 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
575177 TATTTAACTG
575187 TTAATTTTAAAAA
1 TTAATTTTAAAAA
*
575200 TTAATATTTAACTTAA
1 TTAAT-TTTAA--AAA
*
575216 TTAA-TTAAAAAA
1 TTAATTTTAAAAA
575228 TTAATTTTAAAAA
1 TTAATTTTAAAAA
575241 TTAA
1 TTAA
575245 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 6 0.16
13 16 0.43
14 9 0.24
16 6 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAATTTTAAAAA
Found at i:575210 original size:27 final size:27
Alignment explanation
Indices: 575177--575237 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
575167 TTATTAAGCT
575177 TATTTAACTGTTAATT-TT-AAAAATTAA
1 TATTTAAC--TTAATTATTAAAAAATTAA
575204 TATTTAACTTAATTAATTAAAAAATTAA
1 TATTTAACTTAATT-ATTAAAAAATTAA
575232 T-TTTAA
1 TATTTAA
575238 AAATTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 6 0.19
27 15 0.48
28 10 0.32
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTAACTTAATTATTAAAAAATTAA
Found at i:575237 original size:41 final size:44
Alignment explanation
Indices: 575187--575269 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 44
575177 TATTTAACTG
* *
575187 TTAATTTTAAAAATT-AAT-ATTTAACTTA-ATTAATTAAAAAA
1 TTAATTTTAAAAATTAAATAAATTAAATTATATTAATTAAAAAA
575228 TTAATTTTAAAAATTAAATAAATTAAATTATATTAATTAAAA
1 TTAATTTTAAAAATTAAATAAATTAAATTATATTAATTAAAA
575270 TTAATCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 15 0.41
42 3 0.08
43 8 0.22
44 11 0.30
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (44 bp):
TTAATTTTAAAAATTAAATAAATTAAATTATATTAATTAAAAAA
Found at i:575678 original size:21 final size:21
Alignment explanation
Indices: 575654--575702 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 21
575644 TATTTTAAAT
*
575654 AATTATAAATAAATATGTAAC
1 AATTATAAATAAAAATGTAAC
* *
575675 AATT-TTAATAAAAATTTAAC
1 AATTATAAATAAAAATGTAAC
575695 -A-TATAAAT
1 AATTATAAAT
575703 TCATATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 13 0.57
21 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTATAAATAAAAATGTAAC
Found at i:575998 original size:2 final size:2
Alignment explanation
Indices: 575987--576027 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
575977 TTTACCTCAA
575987 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576028 GTGGGAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:582825 original size:80 final size:81
Alignment explanation
Indices: 582732--582973 Score: 391
Period size: 80 Copynumber: 3.0 Consensus size: 81
582722 ACCATTGTTC
*
582732 TTACTTTGTTGCTTTTGACTCATAGGTTTTAGCTTTTTTAAC-TCTTTTAGTTTGCACATTGTTT
1 TTACTTTGTTGCTTTTGACTCATAGCTTTTAGCTTTTTTAACGTCTTTTAGTTTGCACATTGTTT
*
582796 TGTTTTTGTAGCGCAA
66 TGTTTTTGTAGCACAA
* *
582812 TTACTTTGTTGCTTTTGACTCATAGCCTTTAGC-TTTTTGACGTCTTTTAGTTTGCACATTGTTT
1 TTACTTTGTTGCTTTTGACTCATAGCTTTTAGCTTTTTTAACGTCTTTTAGTTTGCACATTGTTT
582876 TGTTTTTGTAGCACAA
66 TGTTTTTGTAGCACAA
* * * *
582892 TTACTTTGTTGCTTTTGACTTATAGCTTTT-GGTTTTTTTACGTCTTTTACTTTGCACATTGTTT
1 TTACTTTGTTGCTTTTGACTCATAGCTTTTAGCTTTTTTAACGTCTTTTAGTTTGCACATTGTTT
582956 TGTTTTTGTAGCACAA
66 TGTTTTTGTAGCACAA
582972 TT
1 TT
582974 TTGGTTATTT
Statistics
Matches: 151, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
79 8 0.05
80 143 0.95
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (81 bp):
TTACTTTGTTGCTTTTGACTCATAGCTTTTAGCTTTTTTAACGTCTTTTAGTTTGCACATTGTTT
TGTTTTTGTAGCACAA
Found at i:590361 original size:8 final size:9
Alignment explanation
Indices: 590333--590369 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
590323 CTTTGCTCTC
590333 ACATCACAT
1 ACATCACAT
590342 GACATCACAT
1 -ACATCACAT
590352 ACAT-ACAT
1 ACATCACAT
590360 ACAT-ACAT
1 ACATCACAT
590368 AC
1 AC
590370 GTTCCTATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 14 0.52
9 4 0.15
10 9 0.33
ACGTcount: A:0.46, C:0.30, G:0.03, T:0.22
Consensus pattern (9 bp):
ACATCACAT
Found at i:590365 original size:12 final size:13
Alignment explanation
Indices: 590331--590369 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
590321 CACTTTGCTC
590331 TCACATCACATGACA
1 TCACAT-ACAT-ACA
590346 TCACATACATACA
1 TCACATACATACA
590359 T-ACATACATAC
1 TCACATACATAC
590370 GTTCCTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 4 0.17
15 6 0.25
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.23
Consensus pattern (13 bp):
TCACATACATACA
Found at i:591328 original size:15 final size:15
Alignment explanation
Indices: 591308--591343 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
591298 AAAAATAATT
591308 TATAATACATTTAAA
1 TATAATACATTTAAA
*
591323 TATAATACGTTTAAA
1 TATAATACATTTAAA
591338 TATAAT
1 TATAAT
591344 TATATTCGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATAATACATTTAAA
Found at i:596672 original size:2 final size:2
Alignment explanation
Indices: 596665--596690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
596655 TCATTCTTAG
596665 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
596691 AGATACGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:596848 original size:2 final size:2
Alignment explanation
Indices: 596841--596876 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
596831 GATTTACTTT
596841 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
596877 GTAAGGGGGT
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:602284 original size:2 final size:2
Alignment explanation
Indices: 602267--602304 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
602257 ACTCAGAAAC
* *
602267 AT AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
602305 GAGTACAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:606437 original size:19 final size:19
Alignment explanation
Indices: 606415--606454 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
606405 TAAATTTACT
606415 TATAAAATATAA-ATATTAA
1 TATAAAA-ATAATATATTAA
*
606434 TATAAAAATAATATTTTAA
1 TATAAAAATAATATATTAA
606453 TA
1 TA
606455 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAAAAATAATATATTAA
Found at i:606630 original size:16 final size:17
Alignment explanation
Indices: 606604--606635 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
606594 AATTAATAAA
606604 TATATTATAAATTTTAT
1 TATATTATAAATTTTAT
606621 TATA-TATAAATTTTA
1 TATATTATAAATTTTA
606636 ATTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAAATTTTAT
Found at i:608838 original size:18 final size:18
Alignment explanation
Indices: 608815--608863 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
608805 TTTAATTTTA
*
608815 AAATTTTTAAAATTAAAT
1 AAATTTTTAAAATAAAAT
* *
608833 AAATTTATAATATAAAAT
1 AAATTTTTAAAATAAAAT
608851 AAATTTATTAAAA
1 AAATTT-TTAAAA
608864 AATTATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTTTAAAATAAAAT
Found at i:608942 original size:21 final size:24
Alignment explanation
Indices: 608918--608974 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
608908 TAATTTATTT
608918 AATTATTT-TAAAATT-T-TAAAA
1 AATTATTTATAAAATTATATAAAA
*
608939 AATTATTTATAATATTATATAAAA
1 AATTATTTATAAAATTATATAAAA
*
608963 AATAATTATATA
1 AATTATT-TATA
608975 TTAATATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.27
22 6 0.20
23 1 0.03
24 11 0.37
25 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTATTTATAAAATTATATAAAA
Found at i:609255 original size:15 final size:17
Alignment explanation
Indices: 609235--609266 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
609225 CGGTGACAGG
609235 ATAATTT-T-TTTTAAT
1 ATAATTTATATTTTAAT
609250 ATAATTTATATTTTAAT
1 ATAATTTATATTTTAAT
609267 CCAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTATATTTTAAT
Found at i:609539 original size:2 final size:2
Alignment explanation
Indices: 609532--609571 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
609522 CTCTGTGAGT
609532 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
609572 AACCCGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:612586 original size:2 final size:2
Alignment explanation
Indices: 612579--612615 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
612569 GAGGTTTCCA
612579 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
612616 TACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:615682 original size:2 final size:2
Alignment explanation
Indices: 615675--615723 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
615665 ATCAGGTTGT
615675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
615717 TA GA TA T
1 TA TA TA T
615724 CAAGATGCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:619945 original size:20 final size:20
Alignment explanation
Indices: 619920--619962 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
619910 GTATTGGTTG
619920 AATGAAAAAATATAATTTTT
1 AATGAAAAAATATAATTTTT
*
619940 AATGAAAAATTATAATTTTT
1 AATGAAAAAATATAATTTTT
619960 AAT
1 AAT
619963 AACAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AATGAAAAAATATAATTTTT
Found at i:619975 original size:23 final size:20
Alignment explanation
Indices: 619924--619969 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
619914 TGGTTGAATG
619924 AAAAAA-TATAATTTTTAAT
1 AAAAAATTATAATTTTTAAT
*
619943 GAAAAATTATAATTTTTAAT
1 AAAAAATTATAATTTTTAAT
619963 AACAAAA
1 AA-AAAA
619970 AATTATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAAATTATAATTTTTAAT
Found at i:623358 original size:2 final size:2
Alignment explanation
Indices: 623351--623384 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
623341 TTGGACAAGG
623351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
623385 TAATGTCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:624319 original size:11 final size:12
Alignment explanation
Indices: 624273--624341 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
624263 TAAAACATAC
624273 AATATAAAAGTA-
1 AATATAAAA-TAT
*
624285 AATATTAAATAT
1 AATATAAAATAT
*
624297 -AT-T-TAATA-
1 AATATAAAATAT
624305 AATATAAAAT-T
1 AATATAAAATAT
624316 AATATGATAAATAT
1 AATAT-A-AAATAT
624330 AATATAAAATAT
1 AATATAAAATAT
624342 TTAAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
9 6 0.13
10 2 0.04
11 12 0.26
12 15 0.33
13 5 0.11
14 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:625208 original size:20 final size:20
Alignment explanation
Indices: 625185--625241 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
625175 GAATTATATT
625185 TAAAATATTATATATTTATA
1 TAAAATATTATATATTTATA
*
625205 T-AAATTTTA-ATATATTA-A
1 TAAAATATTATATAT-TTATA
*
625223 TAAATTATT-T-TATTTATA
1 TAAAATATTATATATTTATA
625241 T
1 T
625242 TTTTATGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 15 0.50
20 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:625252 original size:16 final size:16
Alignment explanation
Indices: 625233--625269 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
625223 TAAATTATTT
625233 TATTTATAT-TTTTATG
1 TATTTATATATTTT-TG
625249 TATTTATATATTTTTG
1 TATTTATATATTTTTG
625265 TATTT
1 TATTT
625270 GTATCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TATTTATATATTTTTG
Found at i:629889 original size:6 final size:6
Alignment explanation
Indices: 629878--629906 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
629868 TCATTGATCT
629878 GAGCTA GAGCTA GAGCTA GAGCTA GAGCT
1 GAGCTA GAGCTA GAGCTA GAGCTA GAGCT
629907 GCAGATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.34, T:0.17
Consensus pattern (6 bp):
GAGCTA
Found at i:630969 original size:14 final size:15
Alignment explanation
Indices: 630952--630982 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
630942 TTCAAAAAGT
630952 AAAAAAGAAAAA-AA
1 AAAAAAGAAAAACAA
630966 AAAAAAGAAAAACAA
1 AAAAAAGAAAAACAA
630981 AA
1 AA
630983 TGAAAGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAACAA
Found at i:633104 original size:118 final size:118
Alignment explanation
Indices: 632896--633133 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
632886 AAACCTATAG
632896 CATCAGAATTGTAAAAGCCTGACTTTGGATCATAATATAAACCAATACTTTGATTGTAGTAATAG
1 CATCAGAATTGTAAAAGCCTGACTTTGGATCATAATATAAACCAATACTTTGATTGTAGTAATAG
632961 ACTGAACTCCTGTCGTACCCAGTCTGTATCAAGCTGTATCAGTTACAATAGTA
66 ACTGAACTCCTGTCGTACCCAGTCTGTATCAAGCTGTATCAGTTACAATAGTA
633014 CATCAGAATTGTAAAAGCCTGACTTTGGATCATAATATAAACCAATACTTTGATTGTAGTAATAG
1 CATCAGAATTGTAAAAGCCTGACTTTGGATCATAATATAAACCAATACTTTGATTGTAGTAATAG
633079 ACTGAACTCCTGTCGTACCCAGTCTGTATCAAGCTGTATCAGTTACAATAGTA
66 ACTGAACTCCTGTCGTACCCAGTCTGTATCAAGCTGTATCAGTTACAATAGTA
633132 CA
1 CA
633134 CTTAGTTATT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (118 bp):
CATCAGAATTGTAAAAGCCTGACTTTGGATCATAATATAAACCAATACTTTGATTGTAGTAATAG
ACTGAACTCCTGTCGTACCCAGTCTGTATCAAGCTGTATCAGTTACAATAGTA
Found at i:634423 original size:18 final size:18
Alignment explanation
Indices: 634374--634423 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
634364 TTCCCTCCTT
*
634374 TCCCCTGCCTCTTCTTCC
1 TCCCCTGCCCCTTCTTCC
* *
634392 TCTCCT--CCC-ACTTCC
1 TCCCCTGCCCCTTCTTCC
634407 TCCCCTGCCCCTTCTTC
1 TCCCCTGCCCCTTCTTC
634424 TCCTTCCTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 3 0.12
18 9 0.38
ACGTcount: A:0.02, C:0.58, G:0.04, T:0.36
Consensus pattern (18 bp):
TCCCCTGCCCCTTCTTCC
Found at i:634465 original size:22 final size:22
Alignment explanation
Indices: 634426--634490 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
634416 CCTTCTTCTC
* *
634426 CTTCCTCTG-TCCTTTCCTCCT
1 CTTCCCCTGCTCCTCTCCTCCT
*
634447 CTTCCCCTGCTCCTCTCCTCTT
1 CTTCCCCTGCTCCTCTCCTCCT
634469 CTTCACCCTCGCTTCC-CTCCTC
1 CTTC-CCCT-GC-TCCTCTCCTC
634491 TCCTTCCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.22
22 14 0.38
23 4 0.11
24 8 0.22
25 3 0.08
ACGTcount: A:0.02, C:0.54, G:0.05, T:0.40
Consensus pattern (22 bp):
CTTCCCCTGCTCCTCTCCTCCT
Found at i:634489 original size:24 final size:22
Alignment explanation
Indices: 634381--634497 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 22
634371 CTTTCCCCTG
634381 CCTCTTCTT--CCT-CTCCTC-
1 CCTCTTCTTCCCCTGCTCCTCT
* * *
634399 CCACTTCCTCCCCTGCCCCT-T
1 CCTCTTCTTCCCCTGCTCCTCT
* * * *
634420 CTTCTCCTTCCTCTG-TCCTTT
1 CCTCTTCTTCCCCTGCTCCTCT
*
634441 CCTCCTCTTCCCCTGCTCCTCT
1 CCTCTTCTTCCCCTGCTCCTCT
634463 CCTCTTCTTCACCCTCGCTTCC-CT
1 CCTCTTCTTC-CCCT-GC-TCCTCT
*
634487 CCTCTCCTTCC
1 CCTCTTCTTCC
634498 TTGCCACCTC
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
18 7 0.09
20 6 0.08
21 26 0.35
22 14 0.19
23 5 0.07
24 13 0.18
25 3 0.04
ACGTcount: A:0.02, C:0.56, G:0.03, T:0.39
Consensus pattern (22 bp):
CCTCTTCTTCCCCTGCTCCTCT
Found at i:637227 original size:29 final size:30
Alignment explanation
Indices: 637184--637251 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 30
637174 AACCTTTGAG
637184 ATAATTTTGTTAACCTTTAATATAAGTAAT
1 ATAATTTTGTTAACCTTTAATATAAGTAAT
637214 -TAATTTTGTTAACCTTTAATATAAGTAAT
1 ATAATTTTGTTAACCTTTAATATAAGTAAT
*
637243 ATAAGTTTG
1 ATAATTTTG
637252 GCAACTCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (30 bp):
ATAATTTTGTTAACCTTTAATATAAGTAAT
Found at i:637320 original size:32 final size:31
Alignment explanation
Indices: 637266--637343 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
637256 CTCTTAATTT
* *
637266 ACTTTTGATATTATTTGAAATAATTTTTATA
1 ACTTTTGATATAATTTGAAATAATTTTGATA
* * *
637297 TCTTTTTATATAATTTTATAATAATTTTGATA
1 ACTTTTGATATAATTTGA-AATAATTTTGATA
637329 ACTTTTGATA-AATTT
1 ACTTTTGATATAATTT
637344 CAATAACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 19 0.49
32 20 0.51
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (31 bp):
ACTTTTGATATAATTTGAAATAATTTTGATA
Found at i:643173 original size:23 final size:20
Alignment explanation
Indices: 643127--643175 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
643117 TTTAAAAATA
*
643127 ATATATTAATTAATACATAT
1 ATATTTTAATTAATACATAT
643147 -TATTTTAATTAATATCATTAT
1 ATATTTTAATTAATA-CA-TAT
643168 CATATTTT
1 -ATATTTT
643176 TCAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 3 0.12
23 6 0.25
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTTAATTAATACATAT
Found at i:643405 original size:14 final size:15
Alignment explanation
Indices: 643386--643414 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
643376 ATAGTTTGAA
643386 TTTTAAA-TTAAATT
1 TTTTAAATTTAAATT
643400 TTTTAAATTTAAATT
1 TTTTAAATTTAAATT
643415 AAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTAAATTTAAATT
Found at i:643429 original size:20 final size:19
Alignment explanation
Indices: 643387--643435 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
643377 TAGTTTGAAT
643387 TTTAAATTAAATTTTTTAAA
1 TTTAAATTAAATTTTTT-AA
643407 TTTAAATTAAATTAATTTT-A
1 TTTAAATTAAATT--TTTTAA
643427 TTTAAATTA
1 TTTAAATTA
643436 CTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 23 0.85
22 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAATTAAATTTTTTAA
Found at i:643853 original size:13 final size:13
Alignment explanation
Indices: 643835--643860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
643825 AGCCAAAAGC
643835 AAGGTAAAAATTA
1 AAGGTAAAAATTA
643848 AAGGTAAAAATTA
1 AAGGTAAAAATTA
643861 TTCATCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AAGGTAAAAATTA
Found at i:644021 original size:26 final size:25
Alignment explanation
Indices: 643973--644046 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
643963 ACACAAAAAT
643973 AATATAA-TATATATGATAAATTTA
1 AATATAATTATATATGATAAATTTA
643997 AATATAATTAATATAT-ATAATATTTA
1 AATATAATT-ATATATGATAA-ATTTA
* * *
644023 TATTTAATT-T-TTTGATAAATTTA
1 AATATAATTATATATGATAAATTTA
644046 A
1 A
644047 TAATTTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 7 0.17
24 12 0.29
25 5 0.12
26 18 0.43
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
AATATAATTATATATGATAAATTTA
Done.