Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 137 of 190
Found at i:40414156 original size:32 final size:32
Alignment explanation
Indices: 40414120--40414185 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40414110 TCATTTTATG
40414120 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
40414152 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
40414184 TT
1 TT
40414186 CGTTTCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (32 bp):
TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
Found at i:40417281 original size:24 final size:23
Alignment explanation
Indices: 40417254--40417329 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
40417244 AGATATTTAT
*
40417254 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
40417278 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
40417302 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
40417325 ATTAA
1 ATTAA
40417330 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:40417297 original size:12 final size:11
Alignment explanation
Indices: 40417268--40417311 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
40417258 TTTATTTATA
40417268 TAATATATAAAT
1 TAAT-TATAAAT
*
40417280 TAATTATAAAG
1 TAATTATAAAT
40417291 TATATTATTAAAT
1 TA-ATTA-TAAAT
40417304 TAATTATA
1 TAATTATA
40417312 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:40417323 original size:14 final size:17
Alignment explanation
Indices: 40417291--40417328 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
40417281 AATTATAAAG
40417291 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
40417308 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
40417322 TATATTA
1 TATATTA
40417329 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:40418360 original size:3 final size:3
Alignment explanation
Indices: 40418334--40418409 Score: 82
Period size: 3 Copynumber: 24.7 Consensus size: 3
40418324 GTGAGGTAAG
* * * *
40418334 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT ATAT ATAT ATAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT
40418381 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40418410 AGATGAGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 50 0.79
4 11 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:40418597 original size:24 final size:27
Alignment explanation
Indices: 40418560--40418623 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40418550 AATTGCGGAT
*
40418560 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
40418584 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
40418610 TTGTGATTGAATTG
1 TAATGATTGAATTG
40418624 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:40422099 original size:20 final size:20
Alignment explanation
Indices: 40422074--40422121 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40422064 TAAATCGAGC
*
40422074 CTTTGATGCCCTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
40422094 CTTTGAGGCCTTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
40422114 TTTTGAGG
1 CTTTGAGG
40422122 TAATTCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
CTTTGAGGCCCTAAAAATAG
Found at i:40424957 original size:11 final size:11
Alignment explanation
Indices: 40424943--40424968 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40424933 TTAGATTAAA
40424943 ATATTATTATT
1 ATATTATTATT
40424954 ATATTATTATT
1 ATATTATTATT
40424965 ATAT
1 ATAT
40424969 ATATAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTATTATT
Found at i:40425001 original size:16 final size:17
Alignment explanation
Indices: 40424980--40425011 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40424970 TATAAAACAA
40424980 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
40424996 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
40425012 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:40425963 original size:25 final size:25
Alignment explanation
Indices: 40425912--40425967 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40425902 ACTTTAGCGC
* ****
40425912 GCTCTCTGATTATTAGCACTTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
40425937 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
40425962 GCTCTC
1 GCTCTC
40425968 CGTTTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:40430048 original size:42 final size:42
Alignment explanation
Indices: 40429999--40430084 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
40429989 TGATAAAAGA
40429999 TTCATTATGACAGGAAGTAACAACGTTGTTTCTGCTTTTTGT
1 TTCATTATGACAGGAAGTAACAACGTTGTTTCTGCTTTTTGT
40430041 TTCATTATGACAGGAAGTAACAACGTTGTTTCTGCTTTTTGT
1 TTCATTATGACAGGAAGTAACAACGTTGTTTCTGCTTTTTGT
40430083 TT
1 TT
40430085 TTTTTTTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCATTATGACAGGAAGTAACAACGTTGTTTCTGCTTTTTGT
Found at i:40433790 original size:25 final size:25
Alignment explanation
Indices: 40433756--40433806 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40433746 TATGACTGAG
40433756 TGAATCTAGGTTATCTCTATAAAAC
1 TGAATCTAGGTTATCTCTATAAAAC
40433781 TGAATCTAGGTTATCTCTATAAAAC
1 TGAATCTAGGTTATCTCTATAAAAC
40433806 T
1 T
40433807 AAGGTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (25 bp):
TGAATCTAGGTTATCTCTATAAAAC
Found at i:40448105 original size:15 final size:15
Alignment explanation
Indices: 40448085--40448115 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40448075 ATTACATAAT
40448085 ATATAAAATAATATA
1 ATATAAAATAATATA
*
40448100 ATATAAAATATTATA
1 ATATAAAATAATATA
40448115 A
1 A
40448116 ACTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:40448990 original size:27 final size:27
Alignment explanation
Indices: 40448932--40448993 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
40448922 CCTATCAGGT
*
40448932 AGGCACCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
40448959 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
40448986 AGGCGCCA
1 AGGCGCCA
40448994 TTACTAGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:40449179 original size:21 final size:21
Alignment explanation
Indices: 40449155--40449198 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40449145 AATAAACACC
40449155 AAAAAAT-TTTTAAAAATAAA
1 AAAAAATATTTTAAAAATAAA
* *
40449175 AAAAAGTATTTTACAAATAAA
1 AAAAAATATTTTAAAAATAAA
40449196 AAA
1 AAA
40449199 TAAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAAATATTTTAAAAATAAA
Found at i:40449382 original size:19 final size:19
Alignment explanation
Indices: 40449360--40449397 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40449350 AATTTAATTT
*
40449360 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
40449379 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
40449398 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:40449640 original size:22 final size:22
Alignment explanation
Indices: 40449615--40449750 Score: 164
Period size: 22 Copynumber: 5.7 Consensus size: 22
40449605 TCTATATTTA
40449615 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
40449637 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
40449659 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
*
40449686 GTATGAATATTGCAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
40449708 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
*
40449735 GTATGAATACTGTAAT
1 GTATGAATATTGTAAT
40449751 GTCGGTATAT
Statistics
Matches: 101, Mismatches: 3, Indels: 17
0.83 0.02 0.14
Matches are distributed among these distances:
22 51 0.50
23 2 0.02
24 7 0.07
25 7 0.07
26 2 0.02
27 32 0.32
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:40449692 original size:71 final size:71
Alignment explanation
Indices: 40449607--40449803 Score: 233
Period size: 71 Copynumber: 2.7 Consensus size: 71
40449597 ATAAATTATC
* *
40449607 TATATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 TATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTTGTATGAATACTGT
40449672 AATAT-
66 AATATG
*
40449677 TATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
1 TAT-ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAA
*
40449742 TACTGTAATGTCGG
60 TACTGTAATAT--G
* *
40449756 TATATATTG--T-AATATTGTAA-TTTTTTGTATGAATATTGTAATTATTTT
1 TATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTT
40449804 ATAATTAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
69 4 0.04
70 3 0.03
71 38 0.34
72 4 0.04
73 4 0.04
74 20 0.18
75 9 0.08
76 21 0.19
78 5 0.05
79 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (71 bp):
TATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTTGTATGAATACTGT
AATATG
Found at i:40449697 original size:49 final size:49
Alignment explanation
Indices: 40449615--40449803 Score: 234
Period size: 49 Copynumber: 4.0 Consensus size: 49
40449605 TCTATATTTA
40449615 GTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTT
*
40449659 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTT
1 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTT
* * **
40449708 GTATGAATATTGTAATATTATAATTTTGTATGAATACTGTAA--TGTCG
1 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTT
* *
40449755 GTAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTT
1 GTATGAATATTGTAATATTATAA--TTTTGTATGAATATTGTAATTTTTTT
40449804 ATAATTAATT
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
44 13 0.10
45 17 0.14
46 3 0.02
47 25 0.20
49 66 0.53
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (49 bp):
GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTT
Found at i:40449868 original size:19 final size:19
Alignment explanation
Indices: 40449846--40449883 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40449836 TATAAATTTA
*
40449846 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
40449865 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
40449884 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:40450140 original size:27 final size:28
Alignment explanation
Indices: 40450102--40450178 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
40450092 CCGGCCCGGC
*
40450102 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
40450129 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
40450156 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
40450179 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:40450706 original size:24 final size:23
Alignment explanation
Indices: 40450674--40450719 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
40450664 AATACTCATA
40450674 TTTATATTATTAAAATATTTATAT
1 TTTATATTA-TAAAATATTTATAT
40450698 TTTATATTATAAAATATTTATA
1 TTTATATTATAAAATATTTATA
40450720 AATTGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATATTATAAAATATTTATAT
Found at i:40450731 original size:23 final size:23
Alignment explanation
Indices: 40450675--40450731 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
40450665 ATACTCATAT
* **
40450675 TTATATTATTAAAATATTTATATT
1 TTATAATA-TAAAATATTTATAAA
*
40450699 TTATATTATAAAATATTTATAAA
1 TTATAATATAAAATATTTATAAA
*
40450722 TTGTAATATA
1 TTATAATATA
40450732 TATTTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATAATATAAAATATTTATAAA
Found at i:40451132 original size:3 final size:3
Alignment explanation
Indices: 40451124--40451160 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40451114 TAGAAACAAT
40451124 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40451161 GAACAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40452649 original size:16 final size:16
Alignment explanation
Indices: 40452628--40452663 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40452618 TTTGGTTCGC
40452628 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40452644 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40452660 TGTA
1 TGTA
40452664 ATAGCAGATC
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:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40462067 original size:22 final size:22
Alignment explanation
Indices: 40462041--40462086 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40462031 ATATGTTTCG
40462041 ATATATGCTAT-ATTAGATTGAA
1 ATATATGC-ATGATTAGATTGAA
*
40462063 ATATATGCATGATTATATTGAA
1 ATATATGCATGATTAGATTGAA
40462085 AT
1 AT
40462087 TTTAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATATGCATGATTAGATTGAA
Found at i:40464516 original size:17 final size:17
Alignment explanation
Indices: 40464494--40464530 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
40464484 ATCGTAACGC
40464494 TTAGTCTCTTAATTGGG
1 TTAGTCTCTTAATTGGG
40464511 TTAGTCTCTTAATTGGG
1 TTAGTCTCTTAATTGGG
40464528 TTA
1 TTA
40464531 TAAAATGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.49
Consensus pattern (17 bp):
TTAGTCTCTTAATTGGG
Found at i:40465406 original size:21 final size:21
Alignment explanation
Indices: 40465380--40465435 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
40465370 AACAGCGGTG
*
40465380 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
40465401 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
40465422 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
40465436 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:40466363 original size:11 final size:12
Alignment explanation
Indices: 40466334--40466366 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40466324 TTCAGCTTGG
*
40466334 ATGCTGGTCTGC
1 ATGCTGGTTTGC
40466346 ATGCTGGTTTGC
1 ATGCTGGTTTGC
40466358 -TGCTGGTTT
1 ATGCTGGTTT
40466367 CCTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:40468881 original size:12 final size:13
Alignment explanation
Indices: 40468862--40468887 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40468852 GATTGAGTAC
40468862 CAAAAAAATTAAG
1 CAAAAAAATTAAG
40468875 CAAAAAAATTAAG
1 CAAAAAAATTAAG
40468888 GGTTCATTGA
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:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
CAAAAAAATTAAG
Found at i:40470074 original size:24 final size:24
Alignment explanation
Indices: 40470023--40470075 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40470013 ATCCCCATAT
* *
40470023 TTTTTTCGTTTTAAGTAATTTAAT
1 TTTTTTCCTTTTAAGTAATTTAAA
* **
40470047 TTTTTTCCTTTTATGTTCTTTAAA
1 TTTTTTCCTTTTAAGTAATTTAAA
40470071 TTTTT
1 TTTTT
40470076 CTCTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.68
Consensus pattern (24 bp):
TTTTTTCCTTTTAAGTAATTTAAA
Found at i:40476119 original size:95 final size:95
Alignment explanation
Indices: 40475956--40476146 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
40475946 AATCTCCTTA
40475956 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
40476021 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
*
40476051 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTGCATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
40476116 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
40476146 G
1 G
40476147 CTATTCCTTT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (95 bp):
GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
TCTCATGATGGCTTGCACCCCAATTGTTTT
Found at i:40491958 original size:31 final size:29
Alignment explanation
Indices: 40491888--40491961 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
40491878 GGCTCAGGTT
* *
40491888 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
40491917 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
40491948 ACATTTTAGTCACT
1 ACATTTTAGTCACT
40491962 GAGCCATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:40492586 original size:31 final size:29
Alignment explanation
Indices: 40492522--40492590 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40492512 ACGATAATGT
* *
40492522 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
40492551 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
40492582 AAGTGACTA
1 AAGTGACTA
40492591 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:40494352 original size:12 final size:13
Alignment explanation
Indices: 40494323--40494355 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40494313 TTTTTAACTA
*
40494323 ATAATTGTAAATT
1 ATAATTATAAATT
40494336 ATAATTATAAA-T
1 ATAATTATAAATT
40494348 ATAATTAT
1 ATAATTAT
40494356 CACAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:40494727 original size:19 final size:22
Alignment explanation
Indices: 40494699--40494744 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
40494689 AGATCATACC
40494699 TTTT-AAATAAT-TTT-TAAT-
1 TTTTAAAATAATCTTTATAATA
40494717 TTTTAAAATAATCTTTATAATA
1 TTTTAAAATAATCTTTATAATA
40494739 TTTTAA
1 TTTTAA
40494745 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 3 0.12
21 4 0.17
22 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATAATCTTTATAATA
Found at i:40505039 original size:19 final size:21
Alignment explanation
Indices: 40505004--40505058 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
40504994 TTATTTTTAT
40505004 ATTTTTATACTTTTT-AAATA
1 ATTTTTATACTTTTTAAAATA
40505024 ATTTTTA-A-TTTCTTAAAATA
1 ATTTTTATACTTT-TTAAAATA
*
40505044 ATTTTTATAATTTTT
1 ATTTTTATACTTTTT
40505059 TTTGGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 19 0.61
21 3 0.10
22 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATACTTTTTAAAATA
Found at i:40505749 original size:7 final size:7
Alignment explanation
Indices: 40505737--40505767 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40505727 TATAATAATA
40505737 AAAATTT
1 AAAATTT
40505744 AAAATTT
1 AAAATTT
40505751 AAAATTT
1 AAAATTT
40505758 AAAATTT
1 AAAATTT
40505765 AAA
1 AAA
40505768 GATATCTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:40509150 original size:3 final size:3
Alignment explanation
Indices: 40509142--40509173 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40509132 GGTTGGGGAT
40509142 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
40509174 GATGATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40511431 original size:504 final size:504
Alignment explanation
Indices: 40510484--40511494 Score: 2022
Period size: 504 Copynumber: 2.0 Consensus size: 504
40510474 TCCATAAATT
40510484 ACAGAGGGTTTGCGAGCCAACTTAATTATCACAAAATACCAAAGAGTTTGGAGTCAAGGGCGAAG
1 ACAGAGGGTTTGCGAGCCAACTTAATTATCACAAAATACCAAAGAGTTTGGAGTCAAGGGCGAAG
40510549 CCAGAAAAATTTTTTAGGGGCAAATGAAATTTTAATTTTTAATAGTCTATATATTTATAATTTTT
66 CCAGAAAAATTTTTTAGGGGCAAATGAAATTTTAATTTTTAATAGTCTATATATTTATAATTTTT
40510614 AAAGGATTAAATCAAATTTTTATAATATTAGGGGGGCTGGGGCCCCTGCCACCCCCCTAGATTCG
131 AAAGGATTAAATCAAATTTTTATAATATTAGGGGGGCTGGGGCCCCTGCCACCCCCCTAGATTCG
40510679 CTTCTGTTTGGAGTCTAAAGAACAACATGCAACTGTATTCAAGATTTAAGTGCTAAGATCCAAAC
196 CTTCTGTTTGGAGTCTAAAGAACAACATGCAACTGTATTCAAGATTTAAGTGCTAAGATCCAAAC
40510744 AGTTCTTACAGAACCGAATTTTGAAACAAGTTACCTACCTGTCCTGTAGCCAAACCACCCTTGCC
261 AGTTCTTACAGAACCGAATTTTGAAACAAGTTACCTACCTGTCCTGTAGCCAAACCACCCTTGCC
40510809 TCTACCACACTTCCCCTTCAGAGGCCCAAGTGCCTTTGTCAACCATTCTGATACCTCCAATCGCT
326 TCTACCACACTTCCCCTTCAGAGGCCCAAGTGCCTTTGTCAACCATTCTGATACCTCCAATCGCT
40510874 TGATAGATTCAGATTTCTCTGGTACACCAGCATAAACAACAGCCTTGTTTGTAGTTTCATCGATA
391 TGATAGATTCAGATTTCTCTGGTACACCAGCATAAACAACAGCCTTGTTTGTAGTTTCATCGATA
40510939 CTGAAAACCATAACTGGCATTTCCTGTTTACTAATTGGCAACATTTAGC
456 CTGAAAACCATAACTGGCATTTCCTGTTTACTAATTGGCAACATTTAGC
40510988 ACAGAGGGTTTGCGAGCCAACTTAATTATCACAAAATACCAAAGAGTTTGGAGTCAAGGGCGAAG
1 ACAGAGGGTTTGCGAGCCAACTTAATTATCACAAAATACCAAAGAGTTTGGAGTCAAGGGCGAAG
40511053 CCAGAAAAATTTTTTAGGGGCAAATGAAATTTTAATTTTTAATAGTCTATATATTTATAATTTTT
66 CCAGAAAAATTTTTTAGGGGCAAATGAAATTTTAATTTTTAATAGTCTATATATTTATAATTTTT
40511118 AAAGGATTAAATCAAATTTTTATAATATTAGGGGGGCTGGGGCCCCTGCCACCCCCCTAGATTCG
131 AAAGGATTAAATCAAATTTTTATAATATTAGGGGGGCTGGGGCCCCTGCCACCCCCCTAGATTCG
40511183 CTTCTGTTTGGAGTCTAAAGAACAACATGCAACTGTATTCAAGATTTAAGTGCTAAGATCCAAAC
196 CTTCTGTTTGGAGTCTAAAGAACAACATGCAACTGTATTCAAGATTTAAGTGCTAAGATCCAAAC
40511248 AGTTCTTACAGAACCGAATTTTGAAACAAGTTACCTACCTGTCCTGTAGCCAAACCACCCTTGCC
261 AGTTCTTACAGAACCGAATTTTGAAACAAGTTACCTACCTGTCCTGTAGCCAAACCACCCTTGCC
40511313 TCTACCACACTTCCCCTTCAGAGGCCCAAGTGCCTTTGTCAACCATTCTGATACCTCCAATCGCT
326 TCTACCACACTTCCCCTTCAGAGGCCCAAGTGCCTTTGTCAACCATTCTGATACCTCCAATCGCT
40511378 TGATAGATTCAGATTTCTCTGGTACACCAGCATAAACAACAGCCTTGTTTGTAGTTTCATCGATA
391 TGATAGATTCAGATTTCTCTGGTACACCAGCATAAACAACAGCCTTGTTTGTAGTTTCATCGATA
40511443 CTGAAAACCATAACTGGCATTTCCTGTTTACTAATTGGCAACATTTAGC
456 CTGAAAACCATAACTGGCATTTCCTGTTTACTAATTGGCAACATTTAGC
40511492 ACA
1 ACA
40511495 AACGTGCAAA
Statistics
Matches: 507, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
504 507 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (504 bp):
ACAGAGGGTTTGCGAGCCAACTTAATTATCACAAAATACCAAAGAGTTTGGAGTCAAGGGCGAAG
CCAGAAAAATTTTTTAGGGGCAAATGAAATTTTAATTTTTAATAGTCTATATATTTATAATTTTT
AAAGGATTAAATCAAATTTTTATAATATTAGGGGGGCTGGGGCCCCTGCCACCCCCCTAGATTCG
CTTCTGTTTGGAGTCTAAAGAACAACATGCAACTGTATTCAAGATTTAAGTGCTAAGATCCAAAC
AGTTCTTACAGAACCGAATTTTGAAACAAGTTACCTACCTGTCCTGTAGCCAAACCACCCTTGCC
TCTACCACACTTCCCCTTCAGAGGCCCAAGTGCCTTTGTCAACCATTCTGATACCTCCAATCGCT
TGATAGATTCAGATTTCTCTGGTACACCAGCATAAACAACAGCCTTGTTTGTAGTTTCATCGATA
CTGAAAACCATAACTGGCATTTCCTGTTTACTAATTGGCAACATTTAGC
Found at i:40514491 original size:29 final size:29
Alignment explanation
Indices: 40514436--40514492 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
40514426 ATGTTTACAG
** *
40514436 TTCAAAATAGGTTATTTACATACATAATT
1 TTCAAAATAAATTATTTACATAAATAATT
* *
40514465 TTCAAAATAAATTATTTTCGTAAATAAT
1 TTCAAAATAAATTATTTACATAAATAAT
40514493 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (29 bp):
TTCAAAATAAATTATTTACATAAATAATT
Found at i:40517180 original size:10 final size:10
Alignment explanation
Indices: 40517165--40517194 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
40517155 GTAAGACATA
40517165 TTATAAATAT
1 TTATAAATAT
40517175 TTATAAATA-
1 TTATAAATAT
40517184 TTATAAATAT
1 TTATAAATAT
40517194 T
1 T
40517195 AAGCAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTATAAATAT
Found at i:40517187 original size:9 final size:9
Alignment explanation
Indices: 40517162--40517195 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
40517152 TTGGTAAGAC
40517162 ATATTATAA
1 ATATTATAA
40517171 ATATTTATAA
1 ATA-TTATAA
40517181 ATATTATAA
1 ATATTATAA
40517190 ATATTA
1 ATATTA
40517196 AGCAATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATTATAA
Found at i:40524155 original size:29 final size:30
Alignment explanation
Indices: 40524088--40524158 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
40524078 ATTTGATCTT
* *
40524088 ATTTAATTCTTTTTAATAATACAATGACTA
1 ATTTAATTCTATTTAATAATACAAGGACTA
* * *
40524118 AATTGATTC-ATTTAATAATA-GAGGAACTA
1 ATTTAATTCTATTTAATAATACAAGG-ACTA
40524147 ATTTAATTCTAT
1 ATTTAATTCTAT
40524159 CCCTATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
28 2 0.06
29 21 0.66
30 9 0.28
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTAATTCTATTTAATAATACAAGGACTA
Found at i:40526262 original size:19 final size:16
Alignment explanation
Indices: 40526222--40526266 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
40526212 TTGAAAATTC
40526222 AAAA-TTAAAAATAAA
1 AAAATTTAAAAATAAA
40526237 AAAATTTAACAAATAAA
1 AAAATTTAA-AAATAAA
40526254 AAATTATTTAAAA
1 AAA--ATTTAAAA
40526267 GTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 10 0.38
18 2 0.08
19 6 0.23
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTTAAAAATAAA
Found at i:40526405 original size:2 final size:2
Alignment explanation
Indices: 40526398--40526429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40526388 TACAAATAGA
40526398 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
40526430 TAAAATCCCA
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:40526942 original size:20 final size:20
Alignment explanation
Indices: 40526917--40526965 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
40526907 TTTTCTTTAA
40526917 ATTATTTTATTTATA-AGACT
1 ATTATTTTATTTATAGA-ACT
*
40526937 ATTATTTTATTTATAGAATT
1 ATTATTTTATTTATAGAACT
40526957 ATTATTTTA
1 ATTATTTTA
40526966 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTATTTTATTTATAGAACT
Found at i:40527042 original size:22 final size:24
Alignment explanation
Indices: 40526998--40527052 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
40526988 AATGAGAAAA
* *
40526998 ATATTTATTTATAATTTTATAT-G
1 ATATTTATTTATAAATCTATATGG
40527021 -TATTTATTTATAAAATCT-TATGG
1 ATATTTATTTAT-AAATCTATATGG
40527044 ATATTTATT
1 ATATTTATT
40527053 GAAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 14 0.52
23 5 0.19
24 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (24 bp):
ATATTTATTTATAAATCTATATGG
Found at i:40533448 original size:37 final size:38
Alignment explanation
Indices: 40533393--40533481 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 38
40533383 ATGCAATTTT
*
40533393 AAAAATATATTAAAAAAATACGAACTGATAAATTTTGA
1 AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
* *
40533431 AAAAATAT-TTAAGAAAATACGATCTGATAAATTTTCA
1 AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
40533468 AAAAA-A-ATTAAAAA
1 AAAAATATATTAAAAA
40533482 TAAAATGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 7 0.15
37 31 0.67
38 8 0.17
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.28
Consensus pattern (38 bp):
AAAAATATATTAAAAAAATACGAACTGATAAATTTTCA
Found at i:40534508 original size:37 final size:37
Alignment explanation
Indices: 40534467--40534543 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
40534457 ATTCCAAAAA
*
40534467 TAATA-TTATTTTAATA-TATTTAATATTAAATTTAAT-T
1 TAATACTTAGTTTAATAGTATTT--TATTAAA-TTAATAT
40534504 TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
1 TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
40534541 TAA
1 TAA
40534544 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 5 0.14
37 16 0.44
38 10 0.28
39 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (37 bp):
TAATACTTAGTTTAATAGTATTTTATTAAATTAATAT
Found at i:40536716 original size:27 final size:27
Alignment explanation
Indices: 40536678--40536744 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40536668 TCATGCCCCA
* *
40536678 TGTTTAATGTCCTAGCG-AATTTCCTCG
1 TGTTTACTGTCCTAACGTAATTTCC-CG
* *
40536705 TGTTTACTGTCCCAACGTACTTTCCCG
1 TGTTTACTGTCCTAACGTAATTTCCCG
*
40536732 CGTTTACTGTCCT
1 TGTTTACTGTCCT
40536745 GACGGACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.40
Consensus pattern (27 bp):
TGTTTACTGTCCTAACGTAATTTCCCG
Found at i:40546745 original size:22 final size:22
Alignment explanation
Indices: 40546719--40546760 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40546709 ATAAATACTG
*
40546719 TAACATG-GTAATTTTTTTATAA
1 TAACATGAG-AATTGTTTTATAA
40546741 TAACATGAGAATTGTTTTAT
1 TAACATGAGAATTGTTTTAT
40546761 GTAAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (22 bp):
TAACATGAGAATTGTTTTATAA
Found at i:40548709 original size:13 final size:13
Alignment explanation
Indices: 40548693--40548725 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40548683 GAGTTGTAGA
40548693 AAATAAACAAAAT
1 AAATAAACAAAAT
*
40548706 AAATAAATAAAAT
1 AAATAAACAAAAT
40548719 AAATAAA
1 AAATAAA
40548726 ATAGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAACAAAAT
Found at i:40548727 original size:9 final size:9
Alignment explanation
Indices: 40548693--40548745 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
40548683 GAGTTGTAGA
40548693 AAATAAACA-
1 AAATAAA-AT
40548702 AAAT-AAAT
1 AAATAAAAT
40548710 AAATAAAAT
1 AAATAAAAT
40548719 AAATAAAAT
1 AAATAAAAT
* *
40548728 AGAAGAAAGT
1 A-AATAAAAT
40548738 AAATAAAA
1 AAATAAAA
40548746 AACGCAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 1 0.03
8 6 0.16
9 23 0.62
10 7 0.19
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:40549596 original size:44 final size:44
Alignment explanation
Indices: 40549548--40550312 Score: 441
Period size: 44 Copynumber: 17.8 Consensus size: 44
40549538 CTGTGGTTTT
* * *
40549548 AATCTGCTCCGCTGCAA-CTTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
*
40549592 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* *
40549636 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * *
40549680 GATCTGCTCAGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTA-TCTTC
** * * *
40549726 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TAC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* ** ** * *
40549767 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * * * *
40549806 AATCCGCTCCACTATAATCTCAAGGAGATAGGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * *
40549850 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTA-TCTTC
** * * *
40549896 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TAC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* ** ** * *
40549937 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * * *
40549976 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* *
40550020 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-GTAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACT-A-TCTTC
** * * *
40550066 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGGCTTGA-TA-CGATC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAA-GATT-ACTATC-TTC
* * * *
40550111 CA-CT-CT--ACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * *
40550146 AATCTGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * **
40550190 GATCTGCTTCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* *
40550234 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-TATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** * *
40550280 GGTCTACTCCACTGTAATCTCAGGGAGATAAGA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
40550313 CCTGTATACT
Statistics
Matches: 575, Mismatches: 98, Indels: 94
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.00
36 3 0.01
37 2 0.00
39 70 0.12
40 10 0.02
41 79 0.14
43 4 0.01
44 252 0.44
45 13 0.02
46 137 0.24
47 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
Found at i:40549843 original size:170 final size:170
Alignment explanation
Indices: 40549647--40550273 Score: 1098
Period size: 170 Copynumber: 3.7 Consensus size: 170
40549637 ATCTGCTCTG
* * *
40549647 CTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCAGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
40549712 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
40549777 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
*
40549817 CTATAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
40549882 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
40549947 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
40549987 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* * *
40550052 ATCTGTAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGGCTTGATACGATCCACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
*
40550117 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCTGCTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
*
40550157 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTTCGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* ** * *
40550222 ATCT-C--TGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGATA
66 ATCTGCAAT-TCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATA
40550274 TTCTTCGGTC
Statistics
Matches: 438, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
167 1 0.00
168 38 0.09
170 399 0.91
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (170 bp):
CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
Found at i:40561446 original size:2 final size:2
Alignment explanation
Indices: 40561383--40561427 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40561373 AATTATCATA
40561383 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
40561425 AT A
1 AT A
40561428 AGTAAGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40561471 original size:44 final size:43
Alignment explanation
Indices: 40561431--40561517 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
40561421 ATATATAAGT
* *
40561431 AAGCATATACATATA-TACGTATATAACTATCATAAAATATAA
1 AAGCATATACATATAGTACATATATAACAATCATAAAATATAA
* * **
40561473 AAGTATATATATATAGGTACATATATAGGAATCATAAAATATAA
1 AAGCATATACATATA-GTACATATATAACAATCATAAAATATAA
40561517 A
1 A
40561518 GAATATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 13 0.35
44 24 0.65
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (43 bp):
AAGCATATACATATAGTACATATATAACAATCATAAAATATAA
Found at i:40565560 original size:15 final size:17
Alignment explanation
Indices: 40565525--40565562 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
40565515 GAATGAAAAG
*
40565525 AAAATTGAAAGAGTAGA
1 AAAATAGAAAGAGTAGA
40565542 AAAATAGAAAGA-T-GA
1 AAAATAGAAAGAGTAGA
40565557 AAAATA
1 AAAATA
40565563 TAATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (17 bp):
AAAATAGAAAGAGTAGA
Found at i:40571497 original size:11 final size:11
Alignment explanation
Indices: 40571481--40571577 Score: 57
Period size: 11 Copynumber: 9.4 Consensus size: 11
40571471 ATTTTTTTAA
40571481 TTTTAAAATAC
1 TTTTAAAATAC
40571492 TTTTAAAATAC
1 TTTTAAAATAC
*
40571503 TTTTTTTAAAT--
1 --TTTTAAAATAC
*
40571514 TTTT-TAA-A-
1 TTTTAAAATAC
**
40571522 TTTTAAAATTT
1 TTTTAAAATAC
40571533 TTTTAAAATAC
1 TTTTAAAATAC
* *
40571544 TTTT---TTAA
1 TTTTAAAATAC
*
40571552 TTTTAAAATAT
1 TTTTAAAATAC
40571563 TTTTAAAATAC
1 TTTTAAAATAC
40571574 TTTT
1 TTTT
40571578 TTTAATTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
8 12 0.18
9 6 0.09
11 40 0.61
13 8 0.12
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40571525 original size:41 final size:39
Alignment explanation
Indices: 40571465--40571577 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 39
40571455 ATTTTTATTA
*
40571465 TTTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAATTTTTTAAATTTTAAAATACTTTTAAAATAC
**
40571503 TTTTTTTAAATTTTTTAAATTTTAAAATTTTTTTAAAATAC
1 -TTTTTT-AATTTTTTAAATTTTAAAATACTTTTAAAATAC
**
40571544 TTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTTTTAATTTTTTAA-A-TTTTAAAATACTTTT
40571578 TTTAATTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 14 0.22
40 7 0.11
41 42 0.67
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTTTTAATTTTTTAAATTTTAAAATACTTTTAAAATAC
Found at i:40571579 original size:30 final size:30
Alignment explanation
Indices: 40571492--40571586 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
40571482 TTTAAAATAC
* *
40571492 TTTTAAAATACTTTTTTTAAAT--TTTTTAAA
1 TTTTAAAATA--TTTTTAAAATACTTTTTTAA
*
40571522 TTTTAAAATTTTTTTAAAATACTTTTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTTAA
40571552 TTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TTTTAAAATATTTTTAAAATAC-TTTTTTAA
40571583 TTTT
1 TTTT
40571587 TGTTTTAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
28 9 0.16
30 37 0.64
31 12 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:40574518 original size:19 final size:19
Alignment explanation
Indices: 40574494--40574532 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40574484 ATTTATCGTT
40574494 TTATAGCAAAGTCATCACA
1 TTATAGCAAAGTCATCACA
40574513 TTATAGCAAAGTCATCACA
1 TTATAGCAAAGTCATCACA
40574532 T
1 T
40574533 AGCTTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (19 bp):
TTATAGCAAAGTCATCACA
Found at i:40575337 original size:43 final size:42
Alignment explanation
Indices: 40575290--40575429 Score: 138
Period size: 42 Copynumber: 3.3 Consensus size: 42
40575280 TCCCAGACCT
* * *
40575290 GGTCTTACATGTAATCAAATAACGATGCCACTATCTCATACAA
1 GGTCTTACACGTAATCAAAT-ACGATGCCAATATCTCAGACAA
* * * *
40575333 GGTCTTACACGAAATCATATACGATGCCAATGTCTCAGACAT
1 GGTCTTACACGTAATCAAATACGATGCCAATATCTCAGACAA
* * **
40575375 GGTCTTACACGTAAATCTCAAAT-CGATGCCAACATCCCAGACGT
1 GGTCTTACACGT-AA--TCAAATACGATGCCAATATCTCAGACAA
40575419 GGTCTTACACG
1 GGTCTTACACG
40575430 ATATCACATA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.36
43 19 0.23
44 28 0.35
45 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATACGATGCCAATATCTCAGACAA
Found at i:40576437 original size:13 final size:13
Alignment explanation
Indices: 40576419--40576445 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40576409 CACAAACGAT
40576419 AAAATTTTCACAC
1 AAAATTTTCACAC
40576432 AAAATTTTCACAC
1 AAAATTTTCACAC
40576445 A
1 A
40576446 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:40586778 original size:16 final size:17
Alignment explanation
Indices: 40586757--40586794 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
40586747 TAAAATTTAA
40586757 TTTTATTGCTATA-TTT
1 TTTTATTGCTATACTTT
**
40586773 TTTTATTTTTATACTTT
1 TTTTATTGCTATACTTT
40586790 TTTTA
1 TTTTA
40586795 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTGCTATACTTT
Found at i:40590217 original size:16 final size:17
Alignment explanation
Indices: 40590190--40590227 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
40590180 AATAAAAAAC
40590190 ATATAT-TTTAT-ATTA
1 ATATATGTTTATAATTA
40590205 ATATATGTTTATAATTA
1 ATATATGTTTATAATTA
40590222 A-ATATG
1 ATATATG
40590228 AATATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 10 0.48
17 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
ATATATGTTTATAATTA
Found at i:40591966 original size:4 final size:4
Alignment explanation
Indices: 40591957--40592016 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
40591947 TATATATCAT
40591957 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
40592005 TACA TACA TACA
1 TACA TACA TACA
40592017 ATAATGTACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:40592339 original size:30 final size:30
Alignment explanation
Indices: 40592305--40592362 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
40592295 GTCTACGCCA
40592305 CCATCGGCATCTCCTTCTCCTTCCTCTCCG
1 CCATCGGCATCTCCTTCTCCTTCCTCTCCG
*
40592335 CCATCTGCATCTCCTTCTCCTTCCTCTC
1 CCATCGGCATCTCCTTCTCCTTCCTCTC
40592363 TGGCTGCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.36
Consensus pattern (30 bp):
CCATCGGCATCTCCTTCTCCTTCCTCTCCG
Found at i:40593947 original size:19 final size:19
Alignment explanation
Indices: 40593925--40593962 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40593915 CCATTGTCAC
*
40593925 CCACCGTAATAAAATTTGT
1 CCACAGTAATAAAATTTGT
*
40593944 CCACAGTAATTAAATTTGT
1 CCACAGTAATAAAATTTGT
40593963 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
CCACAGTAATAAAATTTGT
Found at i:40595494 original size:16 final size:16
Alignment explanation
Indices: 40595470--40595518 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
40595460 ATGTACGTGT
* *
40595470 ATAAACAAATATATAA
1 ATAAACAAACAAATAA
*
40595486 ATAAGCAAACAAATAA
1 ATAAACAAACAAATAA
**
40595502 ATAAATGAACAAATAA
1 ATAAACAAACAAATAA
40595518 A
1 A
40595519 GGATTAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.18
Consensus pattern (16 bp):
ATAAACAAACAAATAA
Found at i:40597588 original size:16 final size:17
Alignment explanation
Indices: 40597567--40597598 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40597557 AAATATGCAA
40597567 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
40597583 TCACATAACTTCATAT
1 TCACATAACTTCATAT
40597599 CATCAATTCA
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:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:40597825 original size:43 final size:43
Alignment explanation
Indices: 40597759--40597929 Score: 210
Period size: 43 Copynumber: 4.0 Consensus size: 43
40597749 GACTCGTACA
*
40597759 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
40597802 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* * *
40597843 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-TCG
*
40597886 ATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATATCG
40597929 A
1 A
40597930 AAATCCTATG
Statistics
Matches: 110, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 28 0.25
42 16 0.15
43 61 0.55
44 5 0.05
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:40597900 original size:84 final size:84
Alignment explanation
Indices: 40597759--40597916 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
40597749 GACTCGTACA
* * *
40597759 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGAC-GTGG
40597823 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
*
40597843 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ACTGTCCCAGACGTG
40597906 GTCTTACACGA
64 GTCTTACACGA
40597917 TAACATATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:40599867 original size:13 final size:13
Alignment explanation
Indices: 40599851--40599883 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40599841 GGGTTTGTAA
40599851 AAAATAAATAAAT
1 AAAATAAATAAAT
*
40599864 AAAATAAGTAAAT
1 AAAATAAATAAAT
40599877 -AAATAAA
1 AAAATAAA
40599884 AACAGGAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:40600708 original size:30 final size:31
Alignment explanation
Indices: 40600652--40600710 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
40600642 GGAGGTGGGA
* *
40600652 TGGGAGGGGTGTAAAAGTTTTAGGGGAAAAG
1 TGGGAGGGGAGTAAAAATTTTAGGGGAAAAG
*
40600683 TGGGA-GGGAGTAAAAATTTTCGGGGAAA
1 TGGGAGGGGAGTAAAAATTTTAGGGGAAA
40600711 GTAAATGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.42, T:0.22
Consensus pattern (31 bp):
TGGGAGGGGAGTAAAAATTTTAGGGGAAAAG
Found at i:40600920 original size:9 final size:9
Alignment explanation
Indices: 40600906--40600939 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
40600896 TATAGTTTGA
*
40600906 TATTCGGGT
1 TATTCGAGT
*
40600915 TATTCGAAT
1 TATTCGAGT
40600924 TATTCGAGT
1 TATTCGAGT
40600933 TATTCGA
1 TATTCGA
40600940 ATTCAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.44
Consensus pattern (9 bp):
TATTCGAGT
Found at i:40600929 original size:18 final size:18
Alignment explanation
Indices: 40600906--40600942 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40600896 TATAGTTTGA
*
40600906 TATTCGGGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
40600924 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
40600942 T
1 T
40600943 CAAAACTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:40605016 original size:82 final size:80
Alignment explanation
Indices: 40604917--40605080 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 80
40604907 TTAGGATGTT
* *
40604917 TGCCAATTAACACCCACACAATAAAAACACTTTAGCTGGTAAAACACAACGAATTGCTCACAAGT
1 TGCCAATTAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAGT
40604982 GCTTGTAGGAAAAAGA
66 GCTTGTAGG-AAAAGA
40604998 TGCCAATTAAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAG
1 TGCCAATT-AACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAG
40605063 TGCTTGTAGGAAAAGA
65 TGCTTGTAGGAAAAGA
40605079 TG
1 TG
40605081 AAGAATTGAA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
81 16 0.20
82 64 0.80
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (80 bp):
TGCCAATTAACACCCACACAATAAAAACACTTAAGCTAGTAAAACACAACGAATTGCTCACAAGT
GCTTGTAGGAAAAGA
Found at i:40605925 original size:17 final size:18
Alignment explanation
Indices: 40605893--40605927 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40605883 TGAAATTTAT
*
40605893 CAAGTTTTATTTCAAAAA
1 CAAGCTTTATTTCAAAAA
40605911 CAAGCTTTA-TTCAAAAA
1 CAAGCTTTATTTCAAAAA
40605928 TATTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
CAAGCTTTATTTCAAAAA
Found at i:40610676 original size:22 final size:23
Alignment explanation
Indices: 40610634--40610677 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40610624 CATAATGTAT
*
40610634 TTTTAAAAAAAGATATTTAAAAG
1 TTTTAAAAAAAGATATATAAAAG
*
40610657 TTTTAAAGAAA-ATATATAAAA
1 TTTTAAAAAAAGATATATAAAA
40610678 ATTATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
TTTTAAAAAAAGATATATAAAAG
Found at i:40613685 original size:28 final size:28
Alignment explanation
Indices: 40613654--40613716 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
40613644 ATTCTCAATC
**
40613654 TTCAATCTCCCGTTTTTAA-TTTTATATT
1 TTCAATCTCCAATTTTTAATTTTTA-ATT
* *
40613682 TTCAATATTCAATTTTTAATTTTTAATT
1 TTCAATCTCCAATTTTTAATTTTTAATT
40613710 TTCAATC
1 TTCAATC
40613717 CTCAATTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (28 bp):
TTCAATCTCCAATTTTTAATTTTTAATT
Found at i:40613697 original size:21 final size:21
Alignment explanation
Indices: 40613673--40613715 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40613663 CCGTTTTTAA
40613673 TTTTATATTTTCAATATTCAAT
1 TTTTA-ATTTTCAATATTCAAT
* *
40613695 TTTTAATTTTTAATTTTCAAT
1 TTTTAATTTTCAATATTCAAT
40613716 CCTCAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATTTTCAATATTCAAT
Found at i:40613721 original size:28 final size:28
Alignment explanation
Indices: 40613666--40613723 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
40613656 CAATCTCCCG
*
40613666 TTTTTAATTTTATATTTTCAATATTCAA
1 TTTTTAATTTTATATTTTCAATACTCAA
*
40613694 TTTTTAATTTT-TAATTTTCAATCCTCAA
1 TTTTTAATTTTAT-ATTTTCAATACTCAA
40613722 TT
1 TT
40613724 CTCAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAATTTTATATTTTCAATACTCAA
Found at i:40615170 original size:7 final size:7
Alignment explanation
Indices: 40615154--40615199 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
40615144 ATAAATATAT
40615154 ATTTTT-
1 ATTTTTA
40615160 ATTTTTA
1 ATTTTTA
40615167 ATTTTTA
1 ATTTTTA
40615174 ATTTTTA
1 ATTTTTA
40615181 ATTTTTA
1 ATTTTTA
40615188 ATTTTTA
1 ATTTTTA
40615195 ATTTT
1 ATTTT
40615200 AAAATACTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:40616268 original size:4 final size:4
Alignment explanation
Indices: 40616261--40616317 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
40616251 TTTACTTTTC
* *
40616261 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
40616309 CATG TATG T
1 TATG TATG T
40616318 GTTGTGTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:40619499 original size:8 final size:9
Alignment explanation
Indices: 40619472--40619497 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40619462 CACGTTCACC
40619472 GGGTAAAAA
1 GGGTAAAAA
40619481 GGGTAAAAA
1 GGGTAAAAA
40619490 GGGTAAAA
1 GGGTAAAA
40619498 GGAAGAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
GGGTAAAAA
Found at i:40619832 original size:6 final size:6
Alignment explanation
Indices: 40619821--40619847 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40619811 TGCAAGATCC
40619821 CTGCTT CTGCTT CTGCTT CTGCTT CTG
1 CTGCTT CTGCTT CTGCTT CTGCTT CTG
40619848 ATACTAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.19, T:0.48
Consensus pattern (6 bp):
CTGCTT
Found at i:40619964 original size:15 final size:15
Alignment explanation
Indices: 40619955--40619989 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40619945 ACCAGCTCCT
40619955 CCTCCTCCAGCACCA
1 CCTCCTCCAGCACCA
* *
40619970 CCTCCTGCGGCACCA
1 CCTCCTCCAGCACCA
40619985 CCTCC
1 CCTCC
40619990 CAAAGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.60, G:0.11, T:0.14
Consensus pattern (15 bp):
CCTCCTCCAGCACCA
Found at i:40623955 original size:19 final size:18
Alignment explanation
Indices: 40623933--40623972 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
40623923 ATATAATAAA
* *
40623933 ATAATAAATATGTAATTAT
1 ATAATAAAAATAT-ATTAT
40623952 ATAATAAAAATATATTAT
1 ATAATAAAAATATATTAT
40623970 ATA
1 ATA
40623973 CATTATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAATAAAAATATATTAT
Found at i:40624193 original size:24 final size:23
Alignment explanation
Indices: 40624126--40624193 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
40624116 AATTTATTTG
40624126 ATATATTTTTC-TTTATA-TATA
1 ATATATTTTTCTTTTATAGTATA
* **
40624147 ATATTTATTTTTGTAGTATTAGTATA
1 ATA--TATTTTTCTTTTA-TAGTATA
40624173 ATATATTTTTCTTTCTATAGT
1 ATATATTTTTCTTT-TATAGT
40624194 TGCTACTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
21 3 0.09
23 7 0.20
24 14 0.40
25 4 0.11
26 7 0.20
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
ATATATTTTTCTTTTATAGTATA
Found at i:40624875 original size:35 final size:35
Alignment explanation
Indices: 40624836--40624904 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
40624826 TAATTTGAAT
* *
40624836 ATTTTATATTTATC-TCAAATAATATTAATGTTATA
1 ATTTTAGAATTATCTTCAAATAAT-TTAATGTTATA
* *
40624871 ATTTTAGAATTATCTTCAATTTATTTAATGTTAT
1 ATTTTAGAATTATCTTCAAATAATTTAATGTTAT
40624905 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (35 bp):
ATTTTAGAATTATCTTCAAATAATTTAATGTTATA
Found at i:40625653 original size:19 final size:19
Alignment explanation
Indices: 40625616--40625657 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
40625606 ATGTTATAAT
40625616 TATAGGAAATCTAAAATTA
1 TATAGGAAATCTAAAATTA
*
40625635 CTATAGTAAATCT-AAATTA
1 -TATAGGAAATCTAAAATTA
40625654 TATA
1 TATA
40625658 ATTTAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (19 bp):
TATAGGAAATCTAAAATTA
Found at i:40629316 original size:12 final size:12
Alignment explanation
Indices: 40629295--40629329 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40629285 AATAAGAACA
40629295 TACATAAAAATG
1 TACATAAAAATG
* *
40629307 TCCATCAAAATG
1 TACATAAAAATG
40629319 TACATAAAAAT
1 TACATAAAAAT
40629330 ACATATGGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (12 bp):
TACATAAAAATG
Found at i:40629593 original size:17 final size:18
Alignment explanation
Indices: 40629560--40629593 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40629550 ATTTATTTTG
40629560 TAAATCAACAATTATAAA
1 TAAATCAACAATTATAAA
*
40629578 TAAATC-ACACTTATAA
1 TAAATCAACAATTATAA
40629594 TGTACATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATCAACAATTATAAA
Found at i:40646389 original size:42 final size:42
Alignment explanation
Indices: 40646343--40646454 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
40646333 AGCTGAACGG
* *
40646343 AAACCCATAAGGGTTAATCTGAAGCTCAGAAGAGCTAAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
* *
40646385 AAACCCATTAGGGTTAAACTGAAGCTCAAAAGAGCTGAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
* *
40646427 AAACCCATAAAGGTTAAACTGAAACTCA
1 AAACCCATAAGGGTTAAACTGAAGCTCA
40646455 TATGAGTTAC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.19
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTA
Found at i:40646446 original size:21 final size:21
Alignment explanation
Indices: 40646378--40646456 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
40646368 TCAGAAGAGC
* *
40646378 TAAACTAAAACCCATTAGGGT
1 TAAACTAAAACCCATAAAGGT
* * * *
40646399 TAAACTGAAGCTCA-AAAGAGC
1 TAAACTAAAACCCATAAAG-GT
*
40646420 TGAACTAAAACCCATAAAGGT
1 TAAACTAAAACCCATAAAGGT
* *
40646441 TAAACTGAAACTCATA
1 TAAACTAAAACCCATA
40646457 TGAGTTACTG
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 2 0.05
21 36 0.86
22 4 0.10
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (21 bp):
TAAACTAAAACCCATAAAGGT
Found at i:40647711 original size:26 final size:28
Alignment explanation
Indices: 40647656--40647713 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
40647646 AATTTTAAAA
* *
40647656 TATTTTTAAAATATATATTTTTATTTTT
1 TATTTTTAAAATATATATTTTTAGTGTT
*
40647684 TATTTTTAAAATA-A-ATTTTTGGTGTT
1 TATTTTTAAAATATATATTTTTAGTGTT
40647710 TATT
1 TATT
40647714 AAAAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 13 0.48
27 1 0.04
28 13 0.48
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
TATTTTTAAAATATATATTTTTAGTGTT
Found at i:40671141 original size:12 final size:12
Alignment explanation
Indices: 40671124--40671149 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40671114 CAAAACAGGC
40671124 TTTTAGTGGCGT
1 TTTTAGTGGCGT
40671136 TTTTAGTGGCGT
1 TTTTAGTGGCGT
40671148 TT
1 TT
40671150 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.31, T:0.54
Consensus pattern (12 bp):
TTTTAGTGGCGT
Found at i:40671198 original size:40 final size:40
Alignment explanation
Indices: 40671154--40671290 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
40671144 GCGTTTGGAT
*
40671154 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGCTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
** * *
40671194 AAAAAACATCGCTAAAGATCCAGTATTAGCGGCGTTTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCG-TTTTAG
* * * * **
40671235 -GAAAACGCAGCTAAAAA-CTAGCATTAGCGGCGTTTTCC
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
* *
40671273 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
40671291 CCTAAGCACA
Statistics
Matches: 77, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
38 4 0.05
39 26 0.34
40 42 0.55
41 5 0.06
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTAG
Found at i:40671677 original size:41 final size:41
Alignment explanation
Indices: 40671329--40671670 Score: 544
Period size: 41 Copynumber: 8.3 Consensus size: 41
40671319 TTTCGGGGCG
40671329 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* *
40671370 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
*
40671411 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
40671452 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* * * * *
40671493 TTAGAGGCGTTTTTTAGGAAGCGCCGCTAATGCTCCGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
* *
40671534 TTAGCGGCGTTTTTGAAGAAACGCCACTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
40671575 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GAGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTG-GTCT
* *
40671616 TTAGCGGCGTTTTTTGAA-AAGCGCTGCTAATGCTCGGGTCT
1 TTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
40671657 TTAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
40671671 AAAAAAGTGC
Statistics
Matches: 277, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
40 6 0.02
41 262 0.95
42 9 0.03
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
Found at i:40672143 original size:15 final size:15
Alignment explanation
Indices: 40672113--40672158 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
40672103 TGATTTGCGA
*
40672113 TTTAAGAGTT-GGGG
1 TTTAAGATTTAGGGG
40672127 TTTAA-AGTTTAGGGG
1 TTTAAGA-TTTAGGGG
40672142 TTTAAGATTTAGGGG
1 TTTAAGATTTAGGGG
40672157 TT
1 TT
40672159 AAGGGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 7 0.25
15 19 0.68
16 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (15 bp):
TTTAAGATTTAGGGG
Found at i:40672167 original size:15 final size:15
Alignment explanation
Indices: 40672123--40672167 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
40672113 TTTAAGAGTT
*
40672123 GGGGTTTAAAGTTTA
1 GGGGTTTAAGGTTTA
*
40672138 GGGGTTTAAGATTTA
1 GGGGTTTAAGGTTTA
40672153 GGGG-TTAAGGGTTTA
1 GGGGTTTAA-GGTTTA
40672168 TGTTTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (15 bp):
GGGGTTTAAGGTTTA
Found at i:40672629 original size:21 final size:22
Alignment explanation
Indices: 40672605--40672646 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40672595 GCCTTTTTTT
40672605 CCCTAA-ATTCCCCCCTAAAAC
1 CCCTAATATTCCCCCCTAAAAC
* *
40672626 CCCTAATTTTTCCCCCTAAAA
1 CCCTAATATTCCCCCCTAAAA
40672647 TTTGTATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.31, C:0.43, G:0.00, T:0.26
Consensus pattern (22 bp):
CCCTAATATTCCCCCCTAAAAC
Found at i:40675747 original size:42 final size:43
Alignment explanation
Indices: 40675686--40675780 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
40675676 AGATATGTTT
* ** *
40675686 TAGCGGTGTTTGTGTGAAAAG-CGTCGCTAAAGGCCTATTCTA
1 TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
* * * *
40675728 TAGCGGCGTTTGTACGAAAAGTCGTTGCTAAATATCTGTTCTA
1 TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
40675771 TAGCGGCGTT
1 TAGCGGCGTT
40675781 CTTTAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 18 0.41
43 26 0.59
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
TAGCGGCGTTTGTACGAAAAGTCGTCGCTAAAGACCTATTCTA
Found at i:40681620 original size:18 final size:17
Alignment explanation
Indices: 40681578--40681620 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
40681568 TTTTTAAGTT
*
40681578 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
40681595 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
40681613 TATAATTT
1 TATAATTT
40681621 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:40682811 original size:183 final size:183
Alignment explanation
Indices: 40682503--40682872 Score: 686
Period size: 183 Copynumber: 2.0 Consensus size: 183
40682493 CATAGAGACT
** *
40682503 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTTGGTATCGAGTTTAGGGACTAAATTGAATAAA
1 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCAGTATAGAGTTTAGGGACTAAATTGAATAAA
*
40682568 TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
66 ATAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
*
40682633 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
131 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTAAAATGA
40682686 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCAGTATAGAGTTTAGGGACTAAATTGAATAAA
1 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCAGTATAGAGTTTAGGGACTAAATTGAATAAA
40682751 ATAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
66 ATAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
*
40682816 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTAAAATTA
131 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTAAAATGA
40682869 TATT
1 TATT
40682873 TTTATTAATA
Statistics
Matches: 181, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 181 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (183 bp):
TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCAGTATAGAGTTTAGGGACTAAATTGAATAAA
ATAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTAAAATGA
Found at i:40684200 original size:3 final size:3
Alignment explanation
Indices: 40684192--40684223 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40684182 TAAAGTGAAG
40684192 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40684224 GAGATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40684338 original size:8 final size:9
Alignment explanation
Indices: 40684312--40684337 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40684302 AAATAGAAGA
40684312 AGAAGGGGG
1 AGAAGGGGG
40684321 AGAAGGGGG
1 AGAAGGGGG
40684330 AGAAGGGG
1 AGAAGGGG
40684338 ATGTTCAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (9 bp):
AGAAGGGGG
Found at i:40685474 original size:75 final size:75
Alignment explanation
Indices: 40685372--40685515 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
40685362 TGGGCACACA
* * *
40685372 ATCGTCAGTTAATCCGACTAGCGCTGGGCGCAAACACCGTTGGTTCATCCAACTAGAGCTGGGCT
1 ATCGTCAGTTAACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
40685437 CACAACTATT
66 CACAACTATT
* * ** *
40685447 ATCGTCAG-TATACCCGACTAGCACTGGGTGCAAATAGTGTTAGTTTATCCAACTAGAGCTGGGC
1 ATCGTCAGTTA-ACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGC
40685511 TCACA
65 TCACA
40685516 TTCAATACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.03
75 58 0.97
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (75 bp):
ATCGTCAGTTAACCCGACTAGCACTGGGCGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
CACAACTATT
Found at i:40685540 original size:75 final size:75
Alignment explanation
Indices: 40685372--40685554 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 75
40685362 TGGGCACACA
* * * *
40685372 ATCGTCAGTTAATCCGACTAGCGCTGGGCGCAAACACCGTTGGTTCATCCAACTAGAGCTGGGCT
1 ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
*
40685437 CACAACTATT
66 CACAACTAAT
* * * ** *
40685447 ATCGTCAGTATACCCGACTAGCACTGGGTGCAAATAGTGTTAGTTTATCCAACTAGAGCTGGGCT
1 ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
*
40685512 CAC-ATTCAAT
66 CACAACT-AAT
* **
40685522 A-CTGTCGGTAAATTCGACTAGCGCTGGGTGCAA
1 ATC-GTCAGTAAACCCGACTAGCGCTGGGTGCAA
40685555 TCTTCTTTGC
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 3 0.03
75 86 0.97
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (75 bp):
ATCGTCAGTAAACCCGACTAGCGCTGGGTGCAAACACCGTTAGTTCATCCAACTAGAGCTGGGCT
CACAACTAAT
Found at i:40695357 original size:17 final size:17
Alignment explanation
Indices: 40695335--40695432 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
40695325 AATTCAAGAC
40695335 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
40695352 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
40695371 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* **
40695389 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTTTTA-A
*
40695408 TTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
40695426 TTATGTA
1 TTATGTA
40695433 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 24 0.41
18 9 0.16
19 8 0.14
20 17 0.29
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:40695414 original size:20 final size:18
Alignment explanation
Indices: 40695350--40695441 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 18
40695340 TAATGTTTTT
*
40695350 AATTATGTAGTGATTCAA
1 AATTATGTAGTGATTTAA
* **
40695368 AGACTTATGTAAT-ATTTTT
1 A-A-TTATGTAGTGATTTAA
40695387 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
40695405 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
40695424 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
40695442 TTCGGGTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
17 20 0.36
18 8 0.15
19 7 0.13
20 20 0.36
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:40695439 original size:37 final size:37
Alignment explanation
Indices: 40695330--40695441 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
40695320 GTGTTAATTC
*
40695330 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
*
40695367 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
40695404 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
40695441 A
1 A
40695442 TTCGGGTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:40695457 original size:9 final size:10
Alignment explanation
Indices: 40695442--40695540 Score: 120
Period size: 9 Copynumber: 10.2 Consensus size: 10
40695432 AGTGATTTAA
40695442 TTCGGGTAAT
1 TTCGGGTAAT
40695452 TT-GGGTAATT
1 TTCGGGTAA-T
40695462 TTCGGGTAAT
1 TTCGGGTAAT
40695472 TT-GGGTAATT
1 TTCGGGTAA-T
40695482 TTCGGGTAA-
1 TTCGGGTAAT
40695491 TTCGGGTAATT
1 TTCGGGTAA-T
40695502 TTCGGGTAA-
1 TTCGGGTAAT
40695511 TTCGGGT-AT
1 TTCGGGTAAT
*
40695520 TTCGGGT-TT
1 TTCGGGTAAT
40695529 TTCGGGTAAT
1 TTCGGGTAAT
40695539 TT
1 TT
40695541 TTAACCAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 16
0.81 0.02 0.16
Matches are distributed among these distances:
8 1 0.01
9 43 0.54
10 14 0.18
11 21 0.27
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.44
Consensus pattern (10 bp):
TTCGGGTAAT
Found at i:40695467 original size:20 final size:20
Alignment explanation
Indices: 40695442--40695541 Score: 143
Period size: 20 Copynumber: 5.1 Consensus size: 20
40695432 AGTGATTTAA
40695442 TTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTTGGGTAATT
40695462 TTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTTGGGTAATT
*
40695482 TTCGGGTAATTCGGGTAATT
1 TTCGGGTAATTTGGGTAATT
*
40695502 TTCGGGTAATTCGGGT-A-T
1 TTCGGGTAATTTGGGTAATT
*
40695520 TTCGGGT-TTTTCGGGTAATT
1 TTCGGGTAATTT-GGGTAATT
40695540 TT
1 TT
40695542 TAACCAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.03
18 12 0.16
19 2 0.03
20 58 0.78
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.45
Consensus pattern (20 bp):
TTCGGGTAATTTGGGTAATT
Found at i:40695481 original size:29 final size:29
Alignment explanation
Indices: 40695442--40695540 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
40695432 AGTGATTTAA
40695442 TTCGGGTAATTTGGGTAATTTTCGGGTAAT
1 TTCGGGTAATTTGGGTAA-TTTCGGGTAAT
40695472 TT-GGGTAATTTTCGGGTAA-TTCGGGTAATT
1 TTCGGGTAA-TTT-GGGTAATTTCGGGTAA-T
* *
40695502 TTCGGGTAATTCGGGT-ATTTCGGGT-TT
1 TTCGGGTAATTTGGGTAATTTCGGGTAAT
40695529 TTCGGGTAATTT
1 TTCGGGTAATTT
40695541 TTAACCAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
27 12 0.20
28 1 0.02
29 26 0.43
30 10 0.16
31 12 0.20
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.44
Consensus pattern (29 bp):
TTCGGGTAATTTGGGTAATTTCGGGTAAT
Found at i:40695663 original size:29 final size:29
Alignment explanation
Indices: 40695602--40695663 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
40695592 TTATTAACCG
* * **
40695602 AAAAAAATTTCGGTTCGGTTAATTATTTT
1 AAAAAAAATTCGGTTCGGTTAATCATTAA
40695631 AAAAAAAATTCGGTTCGGTTAA-CAGTTAA
1 AAAAAAAATTCGGTTCGGTTAATCA-TTAA
40695660 AAAA
1 AAAA
40695664 TTTGGGAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAAAAAATTCGGTTCGGTTAATCATTAA
Found at i:40695859 original size:39 final size:39
Alignment explanation
Indices: 40695780--40695869 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
40695770 TAAAAAATAT
* *
40695780 TTATATTAAAAAACATTACCAAAAATATAATAAATGTTTTA
1 TTATATTAAAAAAC--TACAAAAAATATAATAAATATTTTA
40695821 TTATATTAAAAAAC-ACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACTACAAA-AAATATAATAAATATTTTA
*
40695860 TTGTATTAAA
1 TTATATTAAA
40695870 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 4 0.09
39 27 0.60
41 14 0.31
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (39 bp):
TTATATTAAAAAACTACAAAAAATATAATAAATATTTTA
Found at i:40705078 original size:25 final size:25
Alignment explanation
Indices: 40705050--40705119 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
40705040 CATATAATAA
40705050 ATTATATTAATT-ATATTCATAATTT
1 ATTATATTAATTAATATTCAT-ATTT
*
40705075 ATTATA-TAATTAATATTTATATTT
1 ATTATATTAATTAATATTCATATTT
40705099 AATTATTAATATAATTAATAT
1 -ATTA-T-AT-TAATTAATAT
40705120 AATTATTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 9 0.24
25 17 0.45
26 1 0.03
27 1 0.03
29 10 0.26
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTATATTAATTAATATTCATATTT
Done.