Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold88
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: 1260485
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 5 of 8
Found at i:551463 original size:2 final size:2
Alignment explanation
Indices: 551458--551499 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
551448 TCAGCCTTCC
*
551458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
551500 TCGTATTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:562745 original size:17 final size:19
Alignment explanation
Indices: 562713--562750 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
562703 TTTGACATGA
*
562713 ATATGTATCAGATATAGGT
1 ATATGTATCAGATATAAGT
562732 ATATGT-TC-GATATAAGT
1 ATATGTATCAGATATAAGT
562749 AT
1 AT
562751 GTTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (19 bp):
ATATGTATCAGATATAAGT
Found at i:563857 original size:59 final size:60
Alignment explanation
Indices: 563764--563882 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 60
563754 GTAAATGGTC
* *
563764 TGGTGTGACTCAAAAGCCAGCAATGAAGGAGCATTAGAATTACCATTATCAGAGGGCCAA
1 TGGTGTGACTCAAAAGCCAGCAAAGAAGGAGCATTAGAATCACCATTATCAGAGGGCCAA
563824 TGGTGTGACTCAAAA-CCAGCAAAGAAGGAGCATTAGAATCACCATTATCAGAGGGCCAA
1 TGGTGTGACTCAAAAGCCAGCAAAGAAGGAGCATTAGAATCACCATTATCAGAGGGCCAA
563883 ATTCAAGTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 42 0.74
60 15 0.26
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (60 bp):
TGGTGTGACTCAAAAGCCAGCAAAGAAGGAGCATTAGAATCACCATTATCAGAGGGCCAA
Found at i:564800 original size:2 final size:2
Alignment explanation
Indices: 564793--564826 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
564783 ATTAATAATT
*
564793 TC TC TC TC TC TC TC TC CC 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
564827 CATGATGTGC
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:564963 original size:2 final size:2
Alignment explanation
Indices: 564958--564982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
564948 TATGTGTGTG
564958 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
564983 TTATTTCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:570475 original size:3 final size:3
Alignment explanation
Indices: 570467--570504 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
570457 ACGAAGAAAC
* *
570467 AAT AAT AAT AAT AAC AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
570505 ATCTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:570484 original size:15 final size:15
Alignment explanation
Indices: 570464--570504 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
570454 AAAACGAAGA
570464 AACAATAATAATAAT
1 AACAATAATAATAAT
*
570479 AACAATAATAATGAT
1 AACAATAATAATAAT
*
570494 AATAATAATAA
1 AACAATAATAA
570505 ATCTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (15 bp):
AACAATAATAATAAT
Found at i:587702 original size:2 final size:2
Alignment explanation
Indices: 587697--587731 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
587687 GAGAAAGAAA
587697 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 A
587732 GATGAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:588135 original size:16 final size:16
Alignment explanation
Indices: 588114--588147 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
588104 TTGCTGTCTC
*
588114 TCCATTGCTTTTCAGA
1 TCCATTCCTTTTCAGA
588130 TCCATTCCTTTTCAGA
1 TCCATTCCTTTTCAGA
588146 TC
1 TC
588148 AGAACTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (16 bp):
TCCATTCCTTTTCAGA
Found at i:591109 original size:17 final size:18
Alignment explanation
Indices: 591074--591111 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
591064 ATATTTTAAA
*
591074 AAATTTAAATAAAATATT
1 AAATTTAAATAAAAAATT
591092 AAATTTAAA-AAAAAATT
1 AAATTTAAATAAAAAATT
591109 AAA
1 AAA
591112 CAAAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTTAAATAAAAAATT
Found at i:593224 original size:11 final size:12
Alignment explanation
Indices: 593200--593272 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 12
593190 TCAACTAAAC
*
593200 TTATATTTTGTA
1 TTATATTTTATA
593212 TTAT-TTTTATA
1 TTATATTTTATA
*
593223 TTATA-ATTATA
1 TTATATTTTATA
**
593234 TT-TA--AAATA
1 TTATATTTTATA
593243 TTATATATTTATA
1 TTATAT-TTTATA
*
593256 -TAAATTTTATA
1 TTATATTTTATA
593267 TTATAT
1 TTATAT
593273 ATATATTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 5 0.11
10 4 0.09
11 23 0.49
12 12 0.26
13 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:593245 original size:20 final size:19
Alignment explanation
Indices: 593220--593275 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
593210 TATTATTTTT
*
593220 ATATTATAATTATATTTAAA
1 ATATTATAATTATATAT-AA
593240 ATATTATATATT-TATATAA
1 ATATTATA-ATTATATATAA
*
593259 ATTTTAT-ATTATATATA
1 ATATTATAATTATATATA
593276 TATTTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 6 0.19
19 8 0.25
20 12 0.38
21 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATAATTATATATAA
Found at i:593262 original size:10 final size:10
Alignment explanation
Indices: 593244--593355 Score: 76
Period size: 10 Copynumber: 11.6 Consensus size: 10
593234 TTTAAAATAT
593244 TATATATTTA
1 TATATATTTA
*
593254 TATAAATTT-
1 TATATATTTA
*
593263 TATAT-TATA
1 TATATATTTA
*
593272 TATATATTTT
1 TATATATTTA
593282 TATCA-ATTT-
1 TAT-ATATTTA
*
593291 TA-ACACCTTTA
1 TATATA--TTTA
593302 TATA-ATTT-
1 TATATATTTA
*
593310 TATATATATA
1 TATATATTTA
*
593320 TATATATATA
1 TATATATTTA
*
593330 TATATATATA
1 TATATATTTA
*
593340 TATATATATA
1 TATATATTTA
593350 TATATA
1 TATATA
593356 CACGCATCCA
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
7 1 0.01
8 7 0.08
9 17 0.20
10 56 0.65
11 4 0.05
12 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (10 bp):
TATATATTTA
Found at i:593270 original size:16 final size:17
Alignment explanation
Indices: 593229--593280 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
593219 TATATTATAA
593229 TTATATT-TA-AAATAT
1 TTATATTATATAAATAT
593244 TATATATTTATATAAAT-T
1 T-TATA-TTATATAAATAT
*
593262 TTATATTATATATATAT
1 TTATATTATATAAATAT
593279 TT
1 TT
593281 TTATCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
17 9 0.29
18 4 0.13
19 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATATAAATAT
Found at i:593271 original size:22 final size:22
Alignment explanation
Indices: 593216--593278 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
593206 TTTGTATTAT
*
593216 TTTTATATTATAATTATATTTAAA
1 TTTTATATTAT-ATT-TATATAAA
* *
593240 ATAT-TA-TATATTTATATAAA
1 TTTTATATTATATTTATATAAA
*
593260 TTTTATATTATATATATAT
1 TTTTATATTATATTTATAT
593279 TTTTATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 9 0.29
21 5 0.16
22 13 0.42
23 2 0.06
24 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATATTATATTTATATAAA
Found at i:593315 original size:2 final size:2
Alignment explanation
Indices: 593310--593355 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
593300 TATATAATTT
593310 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
593352 TA TA
1 TA TA
593356 CACGCATCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:598873 original size:25 final size:25
Alignment explanation
Indices: 598835--598885 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
598825 CATCCTGGTA
*
598835 ATGCAAGAAGTAAA-AAAGTATTCTT
1 ATGCAAGAACTAAATAAA-TATTCTT
598860 ATGCAAGAACTAAATAAATATTCTT
1 ATGCAAGAACTAAATAAATATTCTT
598885 A
1 A
598886 CTTCTAGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (25 bp):
ATGCAAGAACTAAATAAATATTCTT
Found at i:598935 original size:2 final size:2
Alignment explanation
Indices: 598930--598954 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
598920 ATATATATAT
598930 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
598955 TCATCAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:599795 original size:2 final size:2
Alignment explanation
Indices: 599788--599813 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
599778 CCCTCTATTG
599788 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
599814 GTGTTTTCTT
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:600282 original size:28 final size:29
Alignment explanation
Indices: 600240--600321 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
600230 ATGAGTTCTG
*
600240 AATTTATATAAATTTTTATATTTTTATTGT
1 AATTTAAATAAATTTTTATATTTTTATT-T
*
600270 -ATTTAAA-AAATTTTAATATTTATT-TTT
1 AATTTAAATAAATTTTTATATTT-TTATTT
600297 AATTTAAATAAATTTTTAT-TTTTTA
1 AATTTAAATAAATTTTTATATTTTTA
600322 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 3 0.07
28 25 0.56
29 17 0.38
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
AATTTAAATAAATTTTTATATTTTTATTT
Found at i:607527 original size:50 final size:50
Alignment explanation
Indices: 607470--607571 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
607460 AGGTAGTTAG
607470 TTATGCCAACCTCAAATGTATTTGTAGTATTAACACATATTGTCAACAAA
1 TTATGCCAACCTCAAATGTATTTGTAGTATTAACACATATTGTCAACAAA
607520 TTATGCCAACCTCAAATGTATTTGTAGTATTAACACATATTGTCAACAAA
1 TTATGCCAACCTCAAATGTATTTGTAGTATTAACACATATTGTCAACAAA
607570 TT
1 TT
607572 TGTTGCTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (50 bp):
TTATGCCAACCTCAAATGTATTTGTAGTATTAACACATATTGTCAACAAA
Found at i:613051 original size:6 final size:6
Alignment explanation
Indices: 613037--613075 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
613027 AAGAAGTTCA
613037 CCTCCC CC-CCC CC-CCC CCTTCCC CCTCCC CCTCCC CCTC
1 CCTCCC CCTCCC CCTCCC CC-TCCC CCTCCC CCTCCC CCTC
613076 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.32
6 16 0.52
7 5 0.16
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTCCC
Found at i:614100 original size:5 final size:5
Alignment explanation
Indices: 614090--614155 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
614080 AAATAATTAA
* * * * *
614090 AATAT AATAT AAAATAT AATTT AATAT ATAAAT AATTT AATAA AAAAT
1 AATAT AATAT --AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT
614138 AATAT AAATAT AATAT AA
1 AATAT -AATAT AATAT AA
614156 ATTATTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
5 33 0.70
6 9 0.19
7 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:614104 original size:12 final size:12
Alignment explanation
Indices: 614074--614156 Score: 83
Period size: 12 Copynumber: 7.6 Consensus size: 12
614064 ATATGATACG
614074 ATATAAAA-ATA
1 ATATAAAATATA
614085 AT-TAAAATATA
1 ATATAAAATATA
614096 ATATAAAATATA
1 ATATAAAATATA
* *
614108 ATTTAATATATA
1 ATATAAAATATA
*
614120 A-AT--AATTTA
1 ATATAAAATATA
614129 ATA-AAAA-ATA
1 ATATAAAATATA
614139 ATAT-AAATATA
1 ATATAAAATATA
614150 ATATAAA
1 ATATAAA
614157 TTATTAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
9 5 0.09
10 14 0.24
11 17 0.29
12 22 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:615072 original size:14 final size:15
Alignment explanation
Indices: 615055--615139 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
615045 TTTTATCAAA
*
615055 AAAATTAA-TAACTT
1 AAAATTAATTAACAT
615069 AAAATTAATTAACAT
1 AAAATTAATTAACAT
615084 AAAA-TAATTTAA-ATTT
1 AAAATTAA-TTAACA--T
*
615100 AAAATAAATTAA-ATTT
1 AAAATTAATTAACA--T
*
615116 AAAA-TAATTAAAAT
1 AAAATTAATTAACAT
*
615130 AAAAATAATT
1 AAAATTAATT
615140 TAAATCTAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 17 0.28
15 24 0.39
16 18 0.30
17 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTAATTAACAT
Found at i:615081 original size:15 final size:15
Alignment explanation
Indices: 615055--615126 Score: 60
Period size: 16 Copynumber: 4.8 Consensus size: 15
615045 TTTTATCAAA
615055 AAAATTAA-TAACTT
1 AAAATTAATTAACTT
*
615069 AAAATTAATTAACAT
1 AAAATTAATTAACTT
*
615084 AAAA-TAATTTAAATTT
1 AAAATTAA-TT-AACTT
* *
615100 AAAATAAATTAAATTT
1 AAAATTAATT-AACTT
615116 AAAA-TAATTAA
1 AAAATTAATTAA
615127 AATAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 13 0.27
15 15 0.31
16 19 0.39
17 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTAATTAACTT
Found at i:615103 original size:31 final size:31
Alignment explanation
Indices: 615052--615185 Score: 96
Period size: 31 Copynumber: 4.3 Consensus size: 31
615042 TAATTTTATC
* * *
615052 AAAAAAATTAATAACTTAAAATTAATTAACA-T
1 AAAATAATTAA-AATTTAAAATAAATTAA-ATT
*
615084 AAAATAATTTAAATTTAAAATAAATTAAATTT
1 AAAATAATTAAAATTTAAAATAAATTAAA-TT
* *
615116 AAAATAATTAAAA-TAAAAATAATTTAAATCT
1 AAAATAATTAAAATTTAAAATAAATTAAAT-T
* * *
615147 AAAA-AATTTAAAAAATT-AAATAAAATAACTT
1 AAAATAA-TT-AAAATTTAAAATAAATTAAATT
*
615178 AAATTAAT
1 AAAATAAT
615186 CTATCCTAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
30 4 0.05
31 40 0.48
32 38 0.46
33 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATAATTAAAATTTAAAATAAATTAAATT
Found at i:615155 original size:15 final size:16
Alignment explanation
Indices: 615083--615158 Score: 102
Period size: 16 Copynumber: 4.9 Consensus size: 16
615073 TTAATTAACA
615083 TAAAATAATTTAAATT
1 TAAAATAATTTAAATT
*
615099 TAAAATAAATTAAATT
1 TAAAATAATTTAAATT
*
615115 TAAAATAA-TTAAAAT
1 TAAAATAATTTAAATT
* *
615130 AAAAATAATTTAAATC
1 TAAAATAATTTAAATT
615146 TAAAA-AATTTAAA
1 TAAAATAATTTAAA
615159 AAATTAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
15 21 0.40
16 32 0.60
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:618872 original size:6 final size:6
Alignment explanation
Indices: 618861--618901 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
618851 TTTCCCTTGC
* *
618861 TCTCAT TCTCAT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
618902 CTTGTGCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (6 bp):
TCTCTT
Found at i:621318 original size:125 final size:121
Alignment explanation
Indices: 621100--621348 Score: 435
Period size: 125 Copynumber: 2.0 Consensus size: 121
621090 TTCATTTGAT
*
621100 ACTATACTGCCTTATACACCATCGAAGACGGTCTCCAGGACACCATAACACCCACCACCAGTCAA
1 ACTATACTGCCATATACACCATCGAAGACGGTCTCCAGGACACCATAACACCCACCACCAGTCAA
*
621165 GCACTCCACTCTGACTTTTTAATATGTCCAATCTTTTCCTAGCCTTTCACAGCCTA
66 GCACTCCACTCTGACTTTTTAATATGTCCAAACTTTTCCTAGCCTTTCACAGCCTA
*
621221 ACTATACTGCCATATACACCATCGAAGACGGTCTCCAGGATACCATAACAAACACCCACCACCAG
1 ACTATACTGCCATATACACCATCGAAGACGGTCTCCAGGACACCAT----AACACCCACCACCAG
621286 TCAAGCACTCCACTCTGACTTTTTAATATGTCCAAACTTTTCCTAGCCTTTCACAGCCTA
62 TCAAGCACTCCACTCTGACTTTTTAATATGTCCAAACTTTTCCTAGCCTTTCACAGCCTA
621346 ACT
1 ACT
621349 CACCAAAGAG
Statistics
Matches: 121, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
121 44 0.36
125 77 0.64
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (121 bp):
ACTATACTGCCATATACACCATCGAAGACGGTCTCCAGGACACCATAACACCCACCACCAGTCAA
GCACTCCACTCTGACTTTTTAATATGTCCAAACTTTTCCTAGCCTTTCACAGCCTA
Found at i:625229 original size:21 final size:21
Alignment explanation
Indices: 625194--625237 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
625184 TTTTAAAACG
*
625194 TTAATAATTTATATTATAAATT
1 TTAATAATATATATT-TAAATT
*
625216 TTAA-AATATATATTTATATT
1 TTAATAATATATATTTAAATT
625236 TT
1 TT
625238 TAATTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATAATATATATTTAAATT
Found at i:630901 original size:24 final size:24
Alignment explanation
Indices: 630860--630910 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
630850 TATTTTAGTA
* *
630860 AAAAAAATTTGTAGATTTAAATTT
1 AAAAAAATTTATAAATTTAAATTT
*
630884 AAAAAATTTTATAAATTTAAATTT
1 AAAAAAATTTATAAATTTAAATTT
630908 AAA
1 AAA
630911 TTTAAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AAAAAAATTTATAAATTTAAATTT
Found at i:631065 original size:11 final size:11
Alignment explanation
Indices: 631046--631122 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 11
631036 TTTAAATTTG
*
631046 TATATTATAAT
1 TATAATATAAT
631057 TATAATATAAT
1 TATAATATAAT
*
631068 TAAAATAT-AT
1 TATAATATAAT
*
631078 TATATTATATAAAA
1 TATA--ATAT-AAT
* *
631092 AATAATATAAA
1 TATAATATAAT
*
631103 TATAATAAAAT
1 TATAATATAAT
631114 T-T-ATATAAT
1 TATAATATAAT
631123 ATTATTTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.11
10 6 0.11
11 29 0.55
12 8 0.15
14 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATAATATAAT
Found at i:631100 original size:19 final size:18
Alignment explanation
Indices: 631058--631113 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
631048 TATTATAATT
*
631058 ATAATAT-AAT-TAAAAT
1 ATAATATAAATATAAAAA
* *
631074 ATATTATATTATATAAAAA
1 ATAATATA-AATATAAAAA
631093 ATAATATAAATATAATAAA
1 ATAATATAAATATAA-AAA
631112 AT
1 AT
631114 TTATATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.19
18 8 0.26
19 17 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATATAAATATAAAAA
Found at i:634061 original size:12 final size:12
Alignment explanation
Indices: 634044--634068 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
634034 TGTGATTGAT
634044 ATTATTATTATA
1 ATTATTATTATA
634056 ATTATTATTATA
1 ATTATTATTATA
634068 A
1 A
634069 CCTTGTTGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:635483 original size:39 final size:39
Alignment explanation
Indices: 635429--635512 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
635419 CAAGAATCAT
* *
635429 AAAAAGTACGAGAAATTCGACGAAGAAATTGAAACAAAG
1 AAAAAGAACGAGAAATTCAACGAAGAAATTGAAACAAAG
* * * *
635468 AAAAAGAAGGAGAAATTCAACTAAGAAATTGAAATAAAT
1 AAAAAGAACGAGAAATTCAACGAAGAAATTGAAACAAAG
635507 AAAAAG
1 AAAAAG
635513 CATTTCCGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (39 bp):
AAAAAGAACGAGAAATTCAACGAAGAAATTGAAACAAAG
Found at i:636847 original size:21 final size:22
Alignment explanation
Indices: 636786--636848 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
636776 AAAAAATCTT
* * *
636786 TAATAAAATT-AAAATTTATTC
1 TAATAATATTAAAAATTTACTA
*
636807 TATTAATATTAAAATGATTTACTA
1 TAATAATATTAAAA--ATTTACTA
636831 TAATAAT-TTAAAAATTTA
1 TAATAATATTAAAAATTTA
636849 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.38
22 3 0.09
23 6 0.18
24 12 0.35
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATAATATTAAAAATTTACTA
Found at i:637986 original size:29 final size:29
Alignment explanation
Indices: 637929--637995 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
637919 AAAATTTAAA
* *
637929 ATTTTTA-ATTTATTTAATTTTATATTTAT
1 ATTTTTATA-TTATATAATTTTATAATTAT
637958 ATTTTTATATTATATAATATTT-TAATTAT
1 ATTTTTATATTATATAAT-TTTATAATTAT
*
637987 -TTTTAATAT
1 ATTTTTATAT
637996 ATCAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 21 0.64
30 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
ATTTTTATATTATATAATTTTATAATTAT
Found at i:637987 original size:19 final size:20
Alignment explanation
Indices: 637941--637995 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
637931 TTTTAATTTA
*
637941 TTTAATT-TTATATTTATAT
1 TTTAATTATTATATTAATAT
*
637960 TTTTA-TATTATA-TAATAT
1 TTTAATTATTATATTAATAT
637978 TTTAATTATT-T-TTAATAT
1 TTTAATTATTATATTAATAT
637996 ATCAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAATTATTATATTAATAT
Found at i:639022 original size:2 final size:2
Alignment explanation
Indices: 639015--639040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
639005 TATGGTAGGT
639015 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
639041 GTTTAATTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:640087 original size:2 final size:2
Alignment explanation
Indices: 640080--640142 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
640070 AACATTTAAA
* * * * *
640080 AT AT AT AT AT AT AT AT GT GT GT AT GT GT 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
640122 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
640143 AAATATAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:643828 original size:14 final size:14
Alignment explanation
Indices: 643809--643836 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
643799 TTTAAGTTTG
643809 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
643823 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
643837 TTGAATTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAAAATTTAAT
Found at i:643877 original size:21 final size:22
Alignment explanation
Indices: 643853--643906 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
643843 TTTATGAAAT
* *
643853 TTTATTTTTAA-AAAATTTAAA
1 TTTATTTTAAATAAAAATTAAA
643874 TTTAATTTTAAATAAAAATTAAA
1 TTT-ATTTTAAATAAAAATTAAA
643897 -TTA-TTTAAAT
1 TTTATTTTAAAT
643907 TTATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 9 0.31
23 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATTTTAAATAAAAATTAAA
Found at i:643896 original size:32 final size:33
Alignment explanation
Indices: 643860--643924 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
643850 AATTTTATTT
643860 TTAAAAAATTTAAATTTAATT-TTAAATAAAAA
1 TTAAAAAATTTAAATTTAATTATTAAATAAAAA
** * *
643892 TTAAATTATTTAAATTTATTTATTTAATAAAAA
1 TTAAAAAATTTAAATTTAATTATTAAATAAAAA
643925 ATTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAAAAAATTTAAATTTAATTATTAAATAAAAA
Found at i:643937 original size:33 final size:32
Alignment explanation
Indices: 643867--643950 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
643857 TTTTTAAAAA
643867 ATTTAAATTTAATTTTAAATAAAAATTAAATT
1 ATTTAAATTTAATTTTAAATAAAAATTAAATT
* *
643899 ATTTAAATTTATTTATTTAATAAAAAATT--ATT
1 ATTTAAATTTAATT-TTAAAT-AAAAATTAAATT
* * *
643931 TTTTTAATTTAAATTTAAAT
1 ATTTAAATTTAATTTTAAAT
643951 TATTTATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
31 5 0.12
32 26 0.60
33 5 0.12
34 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTAAATTTAATTTTAAATAAAAATTAAATT
Found at i:643947 original size:6 final size:6
Alignment explanation
Indices: 643936--643984 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
643926 TTATTTTTTT
* *
643936 AATTTA AATTTA AA-TT- -ATTTA TATTTA AATTTA AATTCA AA-TTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
643980 AATTT
1 AATTT
643985 TTTATTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
3 1 0.03
4 2 0.06
5 6 0.17
6 27 0.75
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:643955 original size:15 final size:15
Alignment explanation
Indices: 643937--643966 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
643927 TATTTTTTTA
643937 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
*
643952 ATTTATATTTAAATT
1 ATTTAAATTTAAATT
643967 TAAATTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:643961 original size:21 final size:20
Alignment explanation
Indices: 643933--643972 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
643923 AAATTATTTT
643933 TTTAATTTAAATTTAAATTA
1 TTTAATTTAAATTTAAATTA
643953 TTTATATTTAAATTTAAATT
1 TTTA-ATTTAAATTTAAATT
643973 CAAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATTTAAATTTAAATTA
Found at i:643966 original size:27 final size:24
Alignment explanation
Indices: 643923--643988 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 24
643913 ATTTAATAAA
*
643923 AAATTATTTTTTTAATTTAAATTT
1 AAATTATTTTTTTAATTTAAATTC
643947 AAATTATTTATATTTAAATTTAAATTC
1 AAATTATTT-T-TTT-AATTTAAATTC
*
643974 AAATTAAATTTTTTA
1 AAATT-ATTTTTTTA
643989 TTATTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 9 0.25
25 2 0.06
26 6 0.17
27 16 0.44
28 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATTATTTTTTTAATTTAAATTC
Found at i:644038 original size:20 final size:22
Alignment explanation
Indices: 643991--644040 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
643981 ATTTTTTATT
*
643991 ATTAATTAAAAATAAAATATAC
1 ATTAATTAAAAATAAAATATAA
644013 A-T-ATTAAAAATAAAA-A-AA
1 ATTAATTAAAAATAAAATATAA
644031 ATTAATTAAA
1 ATTAATTAAA
644041 TTCACAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 19 0.76
21 1 0.04
22 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
ATTAATTAAAAATAAAATATAA
Found at i:644759 original size:201 final size:199
Alignment explanation
Indices: 644412--645006 Score: 838
Period size: 201 Copynumber: 3.0 Consensus size: 199
644402 GTTATGGCTC
* * * *
644412 TGAGCCTTCCGCAGCGGCTGATGATGATCGGTCATCCATGGCTTTGAATCTTTAGCCATCAAGGC
1 TGAGCCTTCAGCAGCGGCTGCTGATGATCAGTCATCAATGGCTTTG-ATCTTTAGCCATCAA-GC
* *
644477 TCTCCATTCATGAATATCAGACACTGGGTTTAACAGAGGGTTGGAACCCTTTTCCAGCAAAGGTT
64 TCTCCATTCATGAATATCAGACACTGGGTTCAACAGAGGGTTGGAACCCTTTTCCAGAAAAGGTT
* * * *
644542 CAAACGACCAAGTTTCAACATCTTCCTTGCCATTATCTTCTTCAGCTTTCAAAGCAGTCCATTGA
129 GATACGACCCAGTTTCAACATCTTCCTTGCCATTATCTTCTTCGGCTTTCAAAGCAGTCCATTGA
644607 TAGCTA
194 TAGCTA
* * * * *
644613 TGAGCCTGCAGCAACGGCTGCTGATGATCAGTCATCAATAGCTTTGATTCTTTGGTCATCGAAGC
1 TGAGCCTTCAGCAGCGGCTGCTGATGATCAGTCATCAATGGCTTTGA-TCTTTAGCCATC-AAGC
* * * * *
644678 TCGCCATTCATGAATATCGGATACTGGGTTCAACAGAGGGTCGGAACCCTTTTCCAGAAAAGGTG
64 TCTCCATTCATGAATATCAGACACTGGGTTCAACAGAGGGTTGGAACCCTTTTCCAGAAAAGGTT
* *
644743 GATACGACCCAGTTTCAATATCTTCCTTGCCATTATCTTCTTCGGCTTTCAAAGCAGTCCGTTGA
129 GATACGACCCAGTTTCAACATCTTCCTTGCCATTATCTTCTTCGGCTTTCAAAGCAGTCCATTGA
644808 TAGCTA
194 TAGCTA
* * * *
644814 TGAGCCTTCGGCAGCGGCTGCTGATGAT-AGTTCATCAATGGCTTCGCATCTTTAACCTTCAAAG
1 TGAGCCTTCAGCAGCGGCTGCTGATGATCAG-TCATCAATGGCTTTG-ATCTTTAGCCATC-AAG
*
644878 CTCTCCATTCATGAATATCAGACACTGGGTTCAACAGAGGGTTGCAACCCTTTTCCAGAAAAGGT
63 CTCTCCATTCATGAATATCAGACACTGGGTTCAACAGAGGGTTGGAACCCTTTTCCAGAAAAGGT
* *
644943 TGATACGACCCAGTTTCAACACCTTCCTTGTCATTA-C--CTTCGGCTTTCAAAGCAGTCCATTG
128 TGATACGACCCAGTTTCAACATCTTCCTTGCCATTATCTTCTTCGGCTTTCAAAGCAGTCCATTG
645005 AT
193 AT
645007 GGAGGCTGGA
Statistics
Matches: 348, Mismatches: 42, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
198 26 0.07
200 4 0.01
201 315 0.91
202 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (199 bp):
TGAGCCTTCAGCAGCGGCTGCTGATGATCAGTCATCAATGGCTTTGATCTTTAGCCATCAAGCTC
TCCATTCATGAATATCAGACACTGGGTTCAACAGAGGGTTGGAACCCTTTTCCAGAAAAGGTTGA
TACGACCCAGTTTCAACATCTTCCTTGCCATTATCTTCTTCGGCTTTCAAAGCAGTCCATTGATA
GCTA
Found at i:647538 original size:2 final size:2
Alignment explanation
Indices: 647531--647560 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
647521 AATTAAGATA
647531 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
647561 GAAAGACATT
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:647899 original size:25 final size:25
Alignment explanation
Indices: 647849--647903 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
647839 TATATAATAT
* *
647849 AAATTATATAATATATATAAATAAA
1 AAATAATATAATATACATAAATAAA
* *
647874 AAATAATATAAT-TACATAATTGAA
1 AAATAATATAATATACATAAATAAA
647898 AAATAA
1 AAATAA
647904 ATTAAACTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAATATAATATACATAAATAAA
Found at i:648891 original size:31 final size:33
Alignment explanation
Indices: 648845--648944 Score: 87
Period size: 36 Copynumber: 2.9 Consensus size: 33
648835 ATATTTTATT
*
648845 TTTTATTAATTTTTAAA-TATA-AATAATATATA
1 TTTT-TTAATATTTAAACTATATAATAATATATA
* * *
648877 TTTTTTAATATTTAAACTATATTATTATATATGT
1 TTTTTTAATATTTAAACTATATAATAATATAT-A
* *
648911 TTTTTTATATGATATAAATTATATAATACATATA
1 TTTTTTA-AT-ATTTAAACTATATAATA-ATATA
648945 AATATAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
31 11 0.20
32 8 0.15
33 8 0.15
34 7 0.13
35 2 0.04
36 13 0.24
37 5 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (33 bp):
TTTTTTAATATTTAAACTATATAATAATATATA
Found at i:649923 original size:9 final size:9
Alignment explanation
Indices: 649909--649956 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
649899 AATTATCGAG
649909 AGAAAAAAA
1 AGAAAAAAA
649918 AGAAAAAAA
1 AGAAAAAAA
*
649927 GGAAAAAAA
1 AGAAAAAAA
649936 A-AAAGTGAAAA
1 AGAAA---AAAA
649947 AGAAAAAAA
1 AGAAAAAAA
649956 A
1 A
649957 TTATGTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 3 0.09
9 22 0.67
11 5 0.15
12 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:649937 original size:21 final size:20
Alignment explanation
Indices: 649911--649956 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
649901 TTATCGAGAG
649911 AAAAAAAAGAAAAAAAGGAAA
1 AAAAAAAAGAAAAAAA-GAAA
**
649932 AAAAAAAAGTGAAAAAGAAA
1 AAAAAAAAGAAAAAAAGAAA
649952 AAAAA
1 AAAAA
649957 TTATGTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAGAAA
Found at i:650523 original size:19 final size:20
Alignment explanation
Indices: 650499--650543 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
650489 TTATATATAT
650499 TTATTTAAAATAAA-AAATA
1 TTATTTAAAATAAATAAATA
*
650518 TTATTT-AAATAAATAATTA
1 TTATTTAAAATAAATAAATA
650537 TTATTTA
1 TTATTTA
650544 TTATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTTAAAATAAATAAATA
Found at i:652192 original size:21 final size:21
Alignment explanation
Indices: 652166--652208 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
652156 ACTGTCGTGG
652166 ATTCTTTTTAAATTTGGAAAT
1 ATTCTTTTTAAATTTGGAAAT
652187 ATTCTTTTTAAATTTGGAAAT
1 ATTCTTTTTAAATTTGGAAAT
652208 A
1 A
652209 AATTTTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (21 bp):
ATTCTTTTTAAATTTGGAAAT
Found at i:652216 original size:20 final size:21
Alignment explanation
Indices: 652170--652216 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
652160 TCGTGGATTC
**
652170 TTTTTAAATTTGGAAATATTC
1 TTTTTAAATTTGGAAATATAA
652191 TTTTTAAATTTGGAAATA-AA
1 TTTTTAAATTTGGAAATATAA
652211 TTTTTA
1 TTTTTA
652217 GGCTCACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTTTAAATTTGGAAATATAA
Found at i:652948 original size:22 final size:23
Alignment explanation
Indices: 652907--652954 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
652897 CTTACTCTTT
652907 TTTTAATTATATAAAATATATTA
1 TTTTAATTATATAAAATATATTA
* *
652930 TTTTAA-TATATATATTATATTA
1 TTTTAATTATATAAAATATATTA
652952 TTT
1 TTT
652955 ATATCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAATTATATAAAATATATTA
Found at i:655822 original size:17 final size:17
Alignment explanation
Indices: 655800--655834 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
655790 CCGTGGTGAA
655800 AGCCTGGGTTGCGGATC
1 AGCCTGGGTTGCGGATC
*
655817 AGCCTGGGTTGCGTATC
1 AGCCTGGGTTGCGGATC
655834 A
1 A
655835 AAGTGCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.37, T:0.26
Consensus pattern (17 bp):
AGCCTGGGTTGCGGATC
Found at i:656586 original size:26 final size:26
Alignment explanation
Indices: 656550--656600 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
656540 GATGAGGGTG
*
656550 GAGAATAGGCTATAATTTGGAACTTA
1 GAGAAGAGGCTATAATTTGGAACTTA
656576 GAGAAGAGGCTATAATTTGGAACTT
1 GAGAAGAGGCTATAATTTGGAACTT
656601 TCTACTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (26 bp):
GAGAAGAGGCTATAATTTGGAACTTA
Found at i:656629 original size:2 final size:2
Alignment explanation
Indices: 656622--656654 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
656612 AATAACCCAC
656622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
656655 CATACGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:659448 original size:2 final size:2
Alignment explanation
Indices: 659441--659472 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
659431 GTTTTAGAAG
659441 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
659473 CTCCGTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:659594 original size:176 final size:176
Alignment explanation
Indices: 659293--659648 Score: 497
Period size: 176 Copynumber: 2.0 Consensus size: 176
659283 GGTTTCAGAT
* * * *
659293 TCTCCTCTATAATCCTTCCTCTTTCTCTCCTCTCAATAACCCTCAAGTGCAATCATTGTTTTTAC
1 TCTCCTCCATAATCCTTCCTCTTTATCTCATCTCAATAACCCTCAAATGCAATCATTGTTTTTAC
* *
659358 ACAATCATGAGGGATTTCATGCAATTCTCCAACTTTTGATTATGTCTTTTGTCTCATAAAAACCA
66 AAAATCATGAGGGATTTCATGCAATTCTCCAACTTTTGATTATGTCTTTTGTCCCATAAAAACCA
*
659423 TCTGCGTGGTTTTAGAAGTCTCTCTCTCTCTCTCTCTCTCTCTCTC
131 TCTGCATGGTTTTAGAAGTCTCTCTCTCTCTCTCTCTCTCTCTCTC
* *
659469 TCTCCTCCGTAATCCTTCCTCTTTATCTCATCTCAATAA-CCTCAAAT-CTGAT-ACTTGTTTTT
1 TCTCCTCCATAATCCTTCCTCTTTATCTCATCTCAATAACCCTCAAATGC-AATCA-TTGTTTTT
* * * * *
659531 GCATAAAATCTTGAGGGGTTTCATGCTATTCTCCAAC-TTTGCTCT-TGTCTTTTGTCCCATAAA
64 --ACAAAATCATGAGGGATTTCATGCAATTCTCCAACTTTTGAT-TATGTCTTTTGTCCCATAAA
*
659594 AACCATCTGCATGTTTTTAGAAGTCTCTCTCTCTCTCTCTCTCTCTCTCTC
126 AACCATCTGCATGGTTTTAGAAGTCTCTCTCTCTCTCTCTCTCTCTCTCTC
659645 TCTC
1 TCTC
659649 TCTCTCTCAC
Statistics
Matches: 160, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
174 2 0.01
175 17 0.11
176 110 0.69
177 31 0.19
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.42
Consensus pattern (176 bp):
TCTCCTCCATAATCCTTCCTCTTTATCTCATCTCAATAACCCTCAAATGCAATCATTGTTTTTAC
AAAATCATGAGGGATTTCATGCAATTCTCCAACTTTTGATTATGTCTTTTGTCCCATAAAAACCA
TCTGCATGGTTTTAGAAGTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Found at i:659624 original size:2 final size:2
Alignment explanation
Indices: 659617--659656 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
659607 TTTTTAGAAG
659617 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
659657 ACCTCCATTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:659964 original size:2 final size:2
Alignment explanation
Indices: 659957--659992 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
659947 TTTTCAATGA
*
659957 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
659993 GGTTGATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:661467 original size:2 final size:2
Alignment explanation
Indices: 661460--661504 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
661450 ATAACCCATT
*
661460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
661502 TA T
1 TA T
661505 TCATTTTGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:662599 original size:20 final size:20
Alignment explanation
Indices: 662571--662613 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
662561 TACCAAATGC
* *
662571 ATATTTTTATTAATAATTTA
1 ATATATTTAATAATAATTTA
* *
662591 ATATATTTAATATTTATTTA
1 ATATATTTAATAATAATTTA
662611 ATA
1 ATA
662614 ATACATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTTAATAATAATTTA
Found at i:666850 original size:2 final size:2
Alignment explanation
Indices: 666843--666888 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
666833 CAGATCTTTA
666843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
666885 AT AT
1 AT AT
666889 GATTTTCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:667065 original size:2 final size:2
Alignment explanation
Indices: 667058--667085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
667048 TGCTCAAAAC
667058 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
667086 GACTGCTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:667887 original size:15 final size:14
Alignment explanation
Indices: 667863--667905 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
667853 AATTTTAATA
*
667863 TAAATTTTTTTATT
1 TAAATATTTTTATT
*
667877 TAAATAATTTTAATT
1 TAAAT-ATTTTTATT
667892 TAAATATTTTTATT
1 TAAATATTTTTATT
667906 AATAAATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAAATATTTTTATT
Found at i:669782 original size:19 final size:19
Alignment explanation
Indices: 669758--669794 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
669748 GTATTAGCGA
669758 TTTTCTGGCAACACTGGTC
1 TTTTCTGGCAACACTGGTC
*
669777 TTTTCTGGCAACGCTGGT
1 TTTTCTGGCAACACTGGT
669795 TCTTCCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (19 bp):
TTTTCTGGCAACACTGGTC
Found at i:672770 original size:18 final size:18
Alignment explanation
Indices: 672744--672778 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
672734 AATTTAGTTT
* *
672744 AAATCTTAACAAATATTA
1 AAATATTAAAAAATATTA
672762 AAATATTAAAAAATATT
1 AAATATTAAAAAATATT
672779 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATTAAAAAATATTA
Found at i:672786 original size:18 final size:19
Alignment explanation
Indices: 672765--672803 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
672755 AATATTAAAA
672765 TATTAA-AAAATATTTT-TT
1 TATTAATAAAAT-TTTTATT
672783 TATTAATAAAATTTTTATT
1 TATTAATAAAATTTTTATT
672802 TA
1 TA
672804 AATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTAATAAAATTTTTATT
Found at i:673785 original size:16 final size:16
Alignment explanation
Indices: 673766--673828 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
673756 TCAATATGAT
673766 TTAAAATTAAAATAAC
1 TTAAAATTAAAATAAC
673782 TT-AAATTAAAAATAAC
1 TTAAAATT-AAAATAAC
* * *
673798 TCAAACTCAAAAATAAC
1 TTAAAAT-TAAAATAAC
673815 TCTAAAATTTAAAA
1 T-TAAAA-TTAAAA
673829 ATTCAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
15 5 0.14
16 11 0.31
17 12 0.33
18 7 0.19
19 1 0.03
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAATTAAAATAAC
Found at i:673789 original size:15 final size:16
Alignment explanation
Indices: 673769--673830 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 16
673759 ATATGATTTA
673769 AAATT-AAAATAACTT
1 AAATTAAAAATAACTT
*
673784 AAATTAAAAATAACTC
1 AAATTAAAAATAACTT
*
673800 AAACTCAAAAATAACTCT
1 AAA-TTAAAAATAACT-T
673818 AAAATTTAAAAAT
1 -AAA-TTAAAAAT
673831 TCAAATTAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
15 5 0.13
16 12 0.32
17 11 0.29
19 10 0.26
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTAAAAATAACTT
Found at i:680884 original size:5 final size:5
Alignment explanation
Indices: 680876--680900 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
680866 AAAAGAAAAA
680876 GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG
680901 CAGGGGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:691821 original size:19 final size:21
Alignment explanation
Indices: 691799--691850 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
691789 ATTAAAATAT
691799 TTAAATTTAAA-GTTTTAT-A
1 TTAAATTTAAATGTTTTATAA
*
691818 TT-AATATTAATATTTTTTATAA
1 TTAAAT-TTAA-ATGTTTTATAA
691840 TTAAATTTAAA
1 TTAAATTTAAA
691851 AAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.11
19 6 0.22
20 1 0.04
21 7 0.26
22 7 0.26
23 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAAATTTAAATGTTTTATAA
Found at i:692035 original size:19 final size:21
Alignment explanation
Indices: 691994--692036 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
691984 ATATATATAT
*
691994 ATATATATATTTAAATTATTA
1 ATATATATATTTAAATGATTA
*
692015 ATATATA-ATTTGAATGA-TA
1 ATATATATATTTAAATGATTA
692034 ATA
1 ATA
692037 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATATATATTTAAATGATTA
Found at i:693479 original size:14 final size:14
Alignment explanation
Indices: 693462--693501 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
693452 TATATTTAAA
693462 ATTAAATATAATTT
1 ATTAAATATAATTT
693476 ATTAAATATAA-TT
1 ATTAAATATAATTT
*
693489 ATAAAAATATAAT
1 AT-TAAATATAAT
693502 AAAATTATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAAATATAATTT
Found at i:693507 original size:19 final size:19
Alignment explanation
Indices: 693480--693516 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
693470 TAATTTATTA
*
693480 AATATAATTATAAAAATAT
1 AATAAAATTATAAAAATAT
*
693499 AATAAAATTATAGAAATA
1 AATAAAATTATAAAAATA
693517 CATAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAAAATTATAAAAATAT
Found at i:694090 original size:22 final size:25
Alignment explanation
Indices: 694060--694105 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
694050 AATAATAAAT
694060 AAATATTTAATTAAA-AT-AATTTA
1 AAATATTTAATTAAATATCAATTTA
*
694083 AAAT-TTTACTTAAATATCAATTT
1 AAATATTTAATTAAATATCAATTT
694106 TTTTTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATTTAATTAAATATCAATTTA
Found at i:694863 original size:22 final size:22
Alignment explanation
Indices: 694835--694876 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
694825 TTGATTTAAT
*
694835 TTAAAAATTATTATAAAATATA
1 TTAAAAATAATTATAAAATATA
*
694857 TTAAAAATAATTTTAAAATA
1 TTAAAAATAATTATAAAATA
694877 AAAATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAATAATTATAAAATATA
Found at i:699362 original size:32 final size:32
Alignment explanation
Indices: 699319--699385 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
699309 CATGAACGCT
* **
699319 TTAAAAATTAT-ATAATATGAATTATAAATAAA
1 TTAAAAATTATAATAA-ATAAAAAATAAATAAA
*
699351 TTAAAATTTATAATAAATAAAAAATAAATAAA
1 TTAAAAATTATAATAAATAAAAAATAAATAAA
699383 TTA
1 TTA
699386 TTCGATCTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (32 bp):
TTAAAAATTATAATAAATAAAAAATAAATAAA
Found at i:699531 original size:19 final size:21
Alignment explanation
Indices: 699487--699535 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
699477 GACTTGAATA
699487 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
*
699509 TTTAATATAAAATA-AT-TAT
1 TTTAATATAAAATATATAAAT
699528 TTTAATAT
1 TTTAATAT
699536 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 2 0.08
21 9 0.35
22 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:700012 original size:33 final size:35
Alignment explanation
Indices: 699947--700012 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 35
699937 ACAGCATGAA
*
699947 TTTGTCTATTTAAATGTTTTTAGCCAATAAATCTT
1 TTTGTCTATTTAAATGTTTTTAGCAAATAAATCTT
*
699982 TTTGTCT-TTTTAAT-TTTTTA-CAAATGAAATC
1 TTTGTCTATTTAAATGTTTTTAGCAAAT-AAATC
700013 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.14
33 11 0.39
34 6 0.21
35 7 0.25
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (35 bp):
TTTGTCTATTTAAATGTTTTTAGCAAATAAATCTT
Found at i:703075 original size:16 final size:16
Alignment explanation
Indices: 703054--703096 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
703044 TATTTTGAAT
703054 TTAATAATATTAAAAC
1 TTAATAATATTAAAAC
* ** *
703070 TTAATATTATTTTAAT
1 TTAATAATATTAAAAC
703086 TTAATAATATT
1 TTAATAATATT
703097 CGAGATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATAATATTAAAAC
Found at i:703108 original size:32 final size:32
Alignment explanation
Indices: 703044--703116 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
703034 TTGTTTCCTC
*
703044 TATTTTGAATTTAATAATATTAAAACTTAATAT
1 TATTTT-AATTTAATAATATTAAAACTAAATAT
* *
703077 TATTTTAATTTAATAATATTCGAGA-TAAATAT
1 TATTTTAATTTAATAATATT-AAAACTAAATAT
703109 TATTTTAA
1 TATTTTAA
703117 AAATTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 28 0.78
33 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (32 bp):
TATTTTAATTTAATAATATTAAAACTAAATAT
Found at i:703117 original size:12 final size:12
Alignment explanation
Indices: 703102--703141 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
703092 ATATTCGAGA
*
703102 TAAATATTATTT
1 TAAAAATTATTT
703114 TAAAAATT-TTT
1 TAAAAATTATTT
*
703125 TAAAAATAATTT
1 TAAAAATTATTT
703137 TAAAA
1 TAAAA
703142 GATGACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAAAATTATTT
Found at i:703165 original size:12 final size:12
Alignment explanation
Indices: 703110--703165 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
703100 GATAAATATT
703110 ATTTTAAAAAT-
1 ATTTTAAAAATA
*
703121 TTTTTAAAAATA
1 ATTTTAAAAATA
703133 ATTTTAAAAGATGA
1 ATTTTAAAA-AT-A
* * *
703147 CTATTAAGAATA
1 ATTTTAAAAATA
703159 ATTTTAA
1 ATTTTAA
703166 CAGTTATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 10 0.29
12 14 0.40
13 4 0.11
14 7 0.20
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (12 bp):
ATTTTAAAAATA
Found at i:703212 original size:20 final size:22
Alignment explanation
Indices: 703173--703212 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
703163 TAACAGTTAT
*
703173 AAATTATATATTTTTTAATATA
1 AAATTATATATTTTTAAATATA
703195 AAATTAT-T-TTTTTAAATA
1 AAATTATATATTTTTAAATA
703213 ATTATTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTATATATTTTTAAATATA
Found at i:703469 original size:12 final size:11
Alignment explanation
Indices: 703446--703475 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
703436 ATCATTTGTA
703446 AATATAATTTT
1 AATATAATTTT
703457 AATATATATTTT
1 AATATA-ATTTT
703469 AATATAA
1 AATATAA
703476 ATATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATATAATTTT
Found at i:703480 original size:29 final size:27
Alignment explanation
Indices: 703444--703508 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 27
703434 ATATCATTTG
703444 TAAATATAATTTTAA-TATATATTTTAATA
1 TAAATATAATTTTAATTAT-TA-TTT-ATA
703473 TAAATATAATTTTAATTATTATTTATA
1 TAAATATAATTTTAATTATTATTTATA
703500 TAAATATAA
1 TAAATATAA
703509 ATATACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.34
28 3 0.09
29 17 0.49
30 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAATATAATTTTAATTATTATTTATA
Found at i:706086 original size:22 final size:20
Alignment explanation
Indices: 706060--706110 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
706050 ATAATATCAA
706060 ATTAAAAAATATAATTAATAAT
1 ATTAAAAAAT-TAATTAA-AAT
*
706082 ATT-AAAAATTATTTAAAAT
1 ATTAAAAAATTAATTAAAAT
706101 ATTAATAAAA
1 ATTAA-AAAA
706111 AATTTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 7 0.27
21 10 0.38
22 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAAAAAATTAATTAAAAT
Found at i:706103 original size:19 final size:21
Alignment explanation
Indices: 706064--706105 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
706054 TATCAAATTA
706064 AAAAATATAATTAATAATATT
1 AAAAATATAATTAATAATATT
*
706085 AAAAAT-TATTTAA-AATATT
1 AAAAATATAATTAATAATATT
706104 AA
1 AA
706106 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATATAATTAATAATATT
Found at i:707163 original size:2 final size:2
Alignment explanation
Indices: 707156--707190 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
707146 GTCAGATTGT
707156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
707191 TCAAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:712993 original size:16 final size:17
Alignment explanation
Indices: 712972--713006 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
712962 ATGTAAAACT
712972 AAATTT-AAAATAATAA
1 AAATTTAAAAATAATAA
712988 AAATTTAAAAATAATAA
1 AAATTTAAAAATAATAA
713005 AA
1 AA
713007 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTTAAAAATAATAA
Found at i:714874 original size:10 final size:10
Alignment explanation
Indices: 714859--714888 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
714849 TAATATGATA
*
714859 AATTTAATTT
1 AATTTAAATT
714869 AATTTAAATT
1 AATTTAAATT
714879 AATTTAAATT
1 AATTTAAATT
714889 TTTTATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTTAAATT
Found at i:714967 original size:24 final size:25
Alignment explanation
Indices: 714910--714972 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
714900 ATGGATTTTG
714910 TTTAATT-TAAAATATTATTTTAAA
1 TTTAATTATAAAATATTATTTTAAA
* * *
714934 ATTAA-AATAATATATT-TTTTAAA
1 TTTAATTATAAAATATTATTTTAAA
714957 TTTAATTATAAAATAT
1 TTTAATTATAAAATAT
714973 ATAAATATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAATTATAAAATATTATTTTAAA
Found at i:716997 original size:32 final size:33
Alignment explanation
Indices: 716944--717005 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
716934 TATTATTACC
*
716944 AAATTACTATATTTAAAATTTATTTAAATATCA
1 AAATTACTATATTTAAAATTTAATTAAATATCA
* *
716977 AAATTA-TATGTTTAATATTTAATTAAATA
1 AAATTACTATATTTAAAATTTAATTAAATA
717006 ATTTATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (33 bp):
AAATTACTATATTTAAAATTTAATTAAATATCA
Found at i:717477 original size:16 final size:19
Alignment explanation
Indices: 717437--717478 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
717427 TGATCGTAGT
717437 AATAATAATATATATTATA
1 AATAATAATATATATTATA
*
717456 ATTAATAAT-TAT-TTA-A
1 AATAATAATATATATTATA
717472 AATAATA
1 AATAATA
717479 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 3 0.14
19 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATAATATATATTATA
Found at i:717536 original size:20 final size:20
Alignment explanation
Indices: 717498--717536 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
717488 ATAAATAATA
**
717498 ATTTTAAATTATATTATATT
1 ATTTTAAATTATAAAATATT
717518 ATTTTAAATTATAAAATAT
1 ATTTTAAATTATAAAATAT
717537 CTTAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTAAATTATAAAATATT
Found at i:719106 original size:19 final size:19
Alignment explanation
Indices: 719079--719115 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
719069 TAATGCTATA
*
719079 AATAGATTAAAAATATAAT
1 AATAAATTAAAAATATAAT
719098 AATAAATTAAAAATATAA
1 AATAAATTAAAAATATAA
719116 AAAATAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAAATTAAAAATATAAT
Found at i:719121 original size:23 final size:23
Alignment explanation
Indices: 719095--719139 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
719085 TTAAAAATAT
719095 AATA-ATAAATTAAAAATATAAAA
1 AATAGATAAATTAAAAA-ATAAAA
**
719118 AATAGATTTATTAAAAAATAAA
1 AATAGATAAATTAAAAAATAAA
719140 TCAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAGATAAATTAAAAAATAAAA
Found at i:719150 original size:16 final size:16
Alignment explanation
Indices: 719132--719170 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
719122 GATTTATTAA
719132 AAAATAAA-TCAAATT
1 AAAATAAACTCAAATT
719147 AAAATAAACTCAAATT
1 AAAATAAACTCAAATT
*
719163 TAAATAAA
1 AAAATAAA
719171 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAACTCAAATT
Found at i:719590 original size:16 final size:16
Alignment explanation
Indices: 719545--719600 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
719535 TCAAAATAAA
719545 ATAATTTTATTATTTT
1 ATAATTTTATTATTTT
*
719561 ATTATTTT-TATATTTT
1 ATAATTTTAT-TATTTT
*
719577 -TAATCTTTATTATTTA
1 ATAAT-TTTATTATTTT
719593 ATAATTTT
1 ATAATTTT
719601 TGGGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.12
16 24 0.73
17 5 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATAATTTTATTATTTT
Found at i:723238 original size:24 final size:24
Alignment explanation
Indices: 723185--723238 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
723175 AGAAATATTT
*
723185 TTATTATTTAAAAATATTAAAATA
1 TTATTTTTTAAAAATATTAAAATA
* * * *
723209 TAATTTTTTATAAATATTTATATA
1 TTATTTTTTAAAAATATTAAAATA
723233 TTATTT
1 TTATTT
723239 AATTATTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTTTTTAAAAATATTAAAATA
Found at i:723258 original size:21 final size:22
Alignment explanation
Indices: 723234--723285 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
723224 ATTTATATAT
723234 TATTTAATTATTTAAA-AATAA
1 TATTTAATTATTTAAATAATAA
723255 TATTTAATTA-TTAAATAATAA
1 TATTTAATTATTTAAATAATAA
*
723276 T-TTAAATTAT
1 TATTTAATTAT
723286 ATTATATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTAATTATTTAAATAATAA
Found at i:723267 original size:32 final size:32
Alignment explanation
Indices: 723221--723281 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
723211 ATTTTTTATA
** *
723221 AATATTTATATATTATTTAATTATTTAAAAAT
1 AATATTTATATATTAAATAATAATTTAAAAAT
723253 AATATTTA-ATTATTAAATAATAATTTAAA
1 AATATTTATA-TATTAAATAATAATTTAAA
723282 TTATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AATATTTATATATTAAATAATAATTTAAAAAT
Found at i:723299 original size:20 final size:17
Alignment explanation
Indices: 723276--723317 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
723266 TAAATAATAA
723276 TTTAAATTATATTATATTAT
1 TTTAAATTATA--A-ATTAT
723296 TTTAAATTATAAATTAT
1 TTTAAATTATAAATTAT
723313 TTTAA
1 TTTAA
723318 TTAAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 1 0.05
20 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTATAAATTAT
Found at i:723327 original size:17 final size:17
Alignment explanation
Indices: 723264--723327 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
723254 ATATTTAATT
* *
723264 ATTAAATAATAATTTAA
1 ATTAAATAATTATTTTA
*
723281 ATTATATTATATTATTTTAA
1 ATTA-AATA-ATTATTTT-A
*
723301 ATTATA-AATTATTTTA
1 ATTAAATAATTATTTTA
723317 ATTAAATAATT
1 ATTAAATAATT
723328 CAATTCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 6 0.16
17 16 0.43
18 4 0.11
19 6 0.16
20 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAAATAATTATTTTA
Found at i:724365 original size:18 final size:17
Alignment explanation
Indices: 724342--724381 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
724332 AATGTTATTG
*
724342 ATAAATTTATAGAAGATT
1 ATAAATTTA-AAAAGATT
724360 ATAAATTTAAAAAGATT
1 ATAAATTTAAAAAGATT
724377 -TAAAT
1 ATAAAT
724382 ACATAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
ATAAATTTAAAAAGATT
Found at i:724469 original size:16 final size:15
Alignment explanation
Indices: 724450--724489 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
724440 AAAAATATAA
*
724450 AAAATAATAAATTTTT
1 AAAA-AATAAATTTAT
724466 AAAAAATTAAATTTAT
1 AAAAAA-TAAATTTAT
724482 AAAAAATA
1 AAAAAATA
724490 TTAACTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATAAATTTAT
Found at i:724492 original size:18 final size:18
Alignment explanation
Indices: 724445--724493 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
724435 AGATTAAAAA
*
724445 TATAAAAAATAATAAATT
1 TATAAAAAATATTAAATT
*
724463 T-TTAAAAA-ATTAAATT
1 TATAAAAAATATTAAATT
724479 TATAAAAAATATTAA
1 TATAAAAAATATTAA
724494 CTATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.31
17 12 0.46
18 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAAAATATTAAATT
Found at i:724498 original size:16 final size:16
Alignment explanation
Indices: 724479--724520 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
724469 AAATTAAATT
*
724479 TATAAA-AAATATTAAC
1 TATAAATAAAT-TTAAA
724495 TATAAATAAATTTAAA
1 TATAAATAAATTTAAA
724511 TATAAATAAA
1 TATAAATAAA
724521 AAATTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAATAAATTTAAA
Found at i:727765 original size:1 final size:1
Alignment explanation
Indices: 727759--727848 Score: 63
Period size: 1 Copynumber: 90.0 Consensus size: 1
727749 AAATCTTCAC
* * ** * * * * **
727759 TTTTTTTTTTTTGTTTTTTTTTTTTCTTTTTCCTTTGTTTTGTTTTGTTTTTTTCTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
727824 TTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
727849 CCAATTGCCA
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.00, C:0.08, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:727812 original size:30 final size:30
Alignment explanation
Indices: 727762--727850 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
727752 TCTTCACTTT
* *
727762 TTTTTTTTTGTTTTTTTTTTTTCTTTTTCC
1 TTTTGTTTTGTTTTGTTTTTTTCTTTTTCC
727792 -TTTGTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTGTTTTGTTTTGTTTTTTTCTTTTTCC
*
727821 TTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTGTTTTGTTTTGTTTTTTTCTTTTTCC
727851 AATTGCCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 27 0.49
30 28 0.51
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (30 bp):
TTTTGTTTTGTTTTGTTTTTTTCTTTTTCC
Found at i:736733 original size:27 final size:28
Alignment explanation
Indices: 736703--736755 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
736693 TTATGGTCTC
*
736703 GATTAAATTCAAAA-TTTTTTTTATTTA
1 GATTAAATTCAAAAGTTTATTTTATTTA
*
736730 GATTAAATTTAAAAGTTTATTTTATT
1 GATTAAATTCAAAAGTTTATTTTATT
736756 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (28 bp):
GATTAAATTCAAAAGTTTATTTTATTTA
Found at i:738972 original size:57 final size:57
Alignment explanation
Indices: 738884--738999 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
738874 AGCGTAGCAT
738884 TTAGCTATCAATCTTGCCTTATAGCGAACATCTTTTTTACCAGAAAGACCTTCATTC
1 TTAGCTATCAATCTTGCCTTATAGCGAACATCTTTTTTACCAGAAAGACCTTCATTC
* *
738941 TTAGCTATTAATCTTGCCTTGTAGCGAACATCTTTTTTACCAGAAAGACCTTCATTC
1 TTAGCTATCAATCTTGCCTTATAGCGAACATCTTTTTTACCAGAAAGACCTTCATTC
738998 TT
1 TT
739000 TGCAAATACC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (57 bp):
TTAGCTATCAATCTTGCCTTATAGCGAACATCTTTTTTACCAGAAAGACCTTCATTC
Done.