Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 7 of 47
Found at i:854313 original size:19 final size:18
Alignment explanation
Indices: 854254--854314 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
854244 TAAATATAAA
*
854254 ATATAATTTTTTAAATAT
1 ATATATTTTTTTAAATAT
*
854272 ATA-ATTTTTTTAAAAAAATT
1 ATATATTTTTTT--AAATA-T
854292 ATATATTTTTATTAAATAT
1 ATATATTTTT-TTAAATAT
854311 ATAT
1 ATAT
854315 TTCTATGTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 7 0.20
18 3 0.09
19 9 0.26
20 8 0.23
21 6 0.17
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATTTTTTTAAATAT
Found at i:854599 original size:23 final size:21
Alignment explanation
Indices: 854573--854637 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
854563 TTTTTATTTT
*
854573 TTAAAAAATTTTATTTTATAATA
1 TTAAAATATTTTATTTT-TAA-A
*
854596 TTAAAATTTTTTATTAATTTAAA
1 TTAAAATATTTTATT--TTTAAA
*
854619 ATAAAATATTTTATTTTTA
1 TTAAAATATTTTATTTTTA
854638 TTACTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.11
23 27 0.75
24 3 0.08
25 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATATTTTATTTTTAAA
Found at i:854609 original size:18 final size:18
Alignment explanation
Indices: 854586--854620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
854576 AAAAATTTTA
854586 TTTTA-TAATATTAAAATT
1 TTTTATTAAT-TTAAAATT
854604 TTTTATTAATTTAAAAT
1 TTTTATTAATTTAAAAT
854621 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATTAATTTAAAATT
Found at i:854948 original size:4 final size:4
Alignment explanation
Indices: 854939--854985 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
854929 GGATATGAGA
* *
854939 TTAT TTAT TTAT TTAT TTA- TTATT TTAAT TAAT TAAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT-AT TTAT TTAT TTAT TTAT TT
854986 TTGCTAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 30 0.79
5 4 0.11
6 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:855960 original size:32 final size:33
Alignment explanation
Indices: 855922--855993 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
855912 ATATTAAATA
* *
855922 TTTATATAAATTTTGA-TATGTTAA-TAATTTAT
1 TTTATATAAATTTTAATTA-ATTAATTAATTTAT
855954 TTTATATAAATTTTAATTAATTAATTAATTTAT
1 TTTATATAAATTTTAATTAATTAATTAATTTAT
*
855987 ATTATAT
1 TTTATAT
855994 TTTTATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (33 bp):
TTTATATAAATTTTAATTAATTAATTAATTTAT
Found at i:855985 original size:28 final size:31
Alignment explanation
Indices: 855921--855988 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
855911 AATATTAAAT
855921 ATTTATATAAATTTTGATATGTTAATAATTTA
1 ATTTATATAAATTTTGATA-GTTAATAATTTA
*
855953 TTTTATATAAATTTT-A-A-TTAATTAA-TTA
1 ATTTATATAAATTTTGATAGTTAA-TAATTTA
855981 ATTTATAT
1 ATTTATAT
855989 TATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 14 0.42
29 3 0.09
30 1 0.03
31 1 0.03
32 14 0.42
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
ATTTATATAAATTTTGATAGTTAATAATTTA
Found at i:857229 original size:3 final size:3
Alignment explanation
Indices: 857221--857246 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
857211 GTTACAAGTC
857221 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
857247 GTGTGGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:859632 original size:20 final size:20
Alignment explanation
Indices: 859608--859645 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
859598 TGGTTGAATA
*
859608 AAAAAATGT-ATTTTTTATG
1 AAAAAATATAATTTTTTATG
859627 AAAAAATATAATTTTTTAT
1 AAAAAATATAATTTTTTAT
859646 AGCCAAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAAAATATAATTTTTTATG
Found at i:867808 original size:2 final size:2
Alignment explanation
Indices: 867801--867829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
867791 GAAAATGTTG
867801 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 A
867830 GTTATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:873935 original size:2 final size:2
Alignment explanation
Indices: 873928--873966 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
873918 CTTTTATGTG
873928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
873967 CACACACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:874441 original size:19 final size:19
Alignment explanation
Indices: 874397--874444 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
874387 TAATAAAAAA
874397 TTTGAA-TT-AAACTTTAG
1 TTTGAATTTAAAACTTTAG
* *
874414 TTTAAAATTTAAAAGTTTAG
1 TTT-GAATTTAAAACTTTAG
874434 TTTGAATTTAA
1 TTTGAATTTAA
874445 TAAATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 2 0.08
19 9 0.36
20 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTGAATTTAAAACTTTAG
Found at i:886098 original size:18 final size:18
Alignment explanation
Indices: 886075--886131 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
886065 ATATTGTTCC
886075 TATTATAGTTTCTGGTTG
1 TATTATAGTTTCTGGTTG
*
886093 TATTATA---T-T-GTTCC
1 TATTATAGTTTCTGGTT-G
886107 TATTATAGTTTCTGGTTG
1 TATTATAGTTTCTGGTTG
886125 TATTATA
1 TATTATA
886132 TTGTTCCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.10
14 8 0.26
15 1 0.03
17 1 0.03
18 15 0.48
19 3 0.10
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (18 bp):
TATTATAGTTTCTGGTTG
Found at i:886103 original size:32 final size:32
Alignment explanation
Indices: 886062--886154 Score: 186
Period size: 32 Copynumber: 2.9 Consensus size: 32
886052 ACTTAAGAGC
886062 ATTATATTGTTCCTATTATAGTTTCTGGTTGT
1 ATTATATTGTTCCTATTATAGTTTCTGGTTGT
886094 ATTATATTGTTCCTATTATAGTTTCTGGTTGT
1 ATTATATTGTTCCTATTATAGTTTCTGGTTGT
886126 ATTATATTGTTCCTATTATAGTTTCTGGT
1 ATTATATTGTTCCTATTATAGTTTCTGGT
886155 AGTTCTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (32 bp):
ATTATATTGTTCCTATTATAGTTTCTGGTTGT
Found at i:891958 original size:27 final size:27
Alignment explanation
Indices: 891928--891980 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
891918 GTCATCATCT
891928 TATATTTTGATAATTAAATATTTCAAG
1 TATATTTTGATAATTAAATATTTCAAG
*
891955 TATATTTTGATATTTAAATATTTCAA
1 TATATTTTGATAATTAAATATTTCAA
891981 AATAAGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (27 bp):
TATATTTTGATAATTAAATATTTCAAG
Found at i:899038 original size:21 final size:22
Alignment explanation
Indices: 899014--899062 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
899004 TAATTTTAAA
899014 AAATAAAAATTTTTTAA-ATAT
1 AAATAAAAATTTTTTAACATAT
** *
899035 AAATATGATTTTTTTAACATAT
1 AAATAAAAATTTTTTAACATAT
*
899057 TAATAA
1 AAATAA
899063 TGCTACATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATAAAAATTTTTTAACATAT
Found at i:899180 original size:26 final size:27
Alignment explanation
Indices: 899137--899194 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
899127 AACGTGTATA
*
899137 ATAAAAGTAAAATTTAAATATCAAATT
1 ATAAAAGTAAAATTTAAATACCAAATT
* *
899164 GTAAAAG-AAATTTTAAATACCAAATT
1 ATAAAAGTAAAATTTAAATACCAAATT
899190 ATAAA
1 ATAAA
899195 TTAAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (27 bp):
ATAAAAGTAAAATTTAAATACCAAATT
Found at i:899200 original size:26 final size:26
Alignment explanation
Indices: 899137--899201 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
899127 AACGTGTATA
* *
899137 ATAAAAGTAAAATTTAAATATCAAATT
1 ATAAAA-TAAATTTTAAATACCAAATT
* *
899164 GTAAAAGAAATTTTAAATACCAAATT
1 ATAAAATAAATTTTAAATACCAAATT
*
899190 ATAAATTAAATT
1 ATAAAATAAATT
899202 ATAATATAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (26 bp):
ATAAAATAAATTTTAAATACCAAATT
Found at i:899598 original size:16 final size:17
Alignment explanation
Indices: 899577--899608 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
899567 TTTTAAAATC
899577 AATTTTTATTT-TTTTA
1 AATTTTTATTTATTTTA
899593 AATTTTTATTTATTTT
1 AATTTTTATTTATTTT
899609 TACCTGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
AATTTTTATTTATTTTA
Found at i:900051 original size:22 final size:22
Alignment explanation
Indices: 900012--900069 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
900002 TTTTGACTAT
900012 TTTAA-ATTTAAATAAATCGAG
1 TTTAATATTTAAATAAATCGAG
* *
900033 TTTAATATTTAGATTAATCGAG
1 TTTAATATTTAAATAAATCGAG
*
900055 TTTGATTATTTAAAT
1 TTT-AATATTTAAAT
900070 CACTTAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 5 0.16
22 17 0.55
23 9 0.29
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (22 bp):
TTTAATATTTAAATAAATCGAG
Found at i:900163 original size:15 final size:16
Alignment explanation
Indices: 900130--900163 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
900120 TTTATTAATT
900130 TTAAACTCAAATCAAA
1 TTAAACTCAAATCAAA
*
900146 TTAAACTTAAAT-AAA
1 TTAAACTCAAATCAAA
900161 TTA
1 TTA
900164 TTTGATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAACTCAAATCAAA
Found at i:901507 original size:25 final size:27
Alignment explanation
Indices: 901467--901518 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
901457 GTAAGATTAT
901467 TTTATTATTTTAAATT-A-TTAAAATA
1 TTTATTATTTTAAATTAATTTAAAATA
901492 TTTA-TATTTTATAATTAATTTAAAATA
1 TTTATTATTTTA-AATTAATTTAAAATA
901519 AAAATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 1 0.04
27 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTATTTTAAATTAATTTAAAATA
Found at i:901539 original size:20 final size:23
Alignment explanation
Indices: 901509--901562 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
901499 TTTATAATTA
*
901509 ATTTAAAATAAA-AATACTTTT-T
1 ATTT-AAATAAATAATAATTTTAT
901531 A-TTAAATAAATAATAATTTTAT
1 ATTTAAATAAATAATAATTTTAT
901553 ATTTAAATAA
1 ATTTAAATAA
901563 CCTTCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.25
21 10 0.36
22 3 0.11
23 8 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAATAAATAATAATTTTAT
Found at i:904529 original size:2 final size:2
Alignment explanation
Indices: 904522--904549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
904512 AATGAGCTGT
904522 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
904550 AATAACTATA
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):
TA
Found at i:904775 original size:20 final size:20
Alignment explanation
Indices: 904738--904775 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
904728 TATATAATTA
*
904738 TATATTATAAAAATATTATT
1 TATATTATAAAAAAATTATT
904758 TATATTA-AAACAAAATTA
1 TATATTATAAA-AAAATTA
904776 AATCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATTATAAAAAAATTATT
Found at i:909639 original size:23 final size:24
Alignment explanation
Indices: 909605--909653 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
909595 TAAAATTTTA
*
909605 TAAATATAAATATATTAAATAAAT
1 TAAATATAAATATAATAAATAAAT
*
909629 TAAATAT-AATATAATATATAAAT
1 TAAATATAAATATAATAAATAAAT
909652 TA
1 TA
909654 TGATATCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATAAATATAATAAATAAAT
Found at i:909650 original size:18 final size:18
Alignment explanation
Indices: 909603--909651 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
909593 ATTAAAATTT
*
909603 TATAA-ATATAAATATAT
1 TATAATATATAAATATAA
*
909620 TA-AATAAATTAAATATAA
1 TATAATATA-TAAATATAA
909638 TATAATATATAAAT
1 TATAATATATAAAT
909652 TATGATATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 4 0.15
18 15 0.58
19 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAATATATAAATATAA
Found at i:909659 original size:19 final size:18
Alignment explanation
Indices: 909603--909659 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
909593 ATTAAAATTT
909603 TATAAATATAAATATATTAA
1 TATAAATATAAAT-TA-TAA
909623 -ATAAAT-TAAA-TATAA
1 TATAAATATAAATTATAA
*
909638 TATAATATATAAATTATGA
1 TATAA-ATATAAATTATAA
909657 TAT
1 TAT
909660 CGAATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 3 0.09
16 6 0.19
17 2 0.06
18 8 0.25
19 13 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TATAAATATAAATTATAA
Found at i:910718 original size:21 final size:22
Alignment explanation
Indices: 910694--910739 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
910684 ATATTTTTTA
*
910694 TTAT-AAAATAATAATTT-AAAT
1 TTATAAAAAAAAT-ATTTAAAAT
910715 TTATAAAAAAAATATTTAAAAT
1 TTATAAAAAAAATATTTAAAAT
910737 TTA
1 TTA
910740 AATTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATAAAAAAAATATTTAAAAT
Found at i:917664 original size:3 final size:3
Alignment explanation
Indices: 917656--917680 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
917646 TTTGGCTATC
917656 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
917681 GACTTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:922365 original size:2 final size:2
Alignment explanation
Indices: 922358--922385 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
922348 CTTTAATTTA
922358 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
922386 TTATGGTGCT
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:925286 original size:30 final size:30
Alignment explanation
Indices: 925236--925295 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
925226 ACATAAGTTT
*
925236 ATATTTTTTATTATATTATAAATATATTTAAA
1 ATATTTTATATTATATTATAAAT-T-TTTAAA
925268 ATATTTTATATT-TA-TATAAATTTTTAAA
1 ATATTTTATATTATATTATAAATTTTTAAA
925296 CATTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 6 0.22
29 1 0.04
30 7 0.26
31 2 0.07
32 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTTATATTATATTATAAATTTTTAAA
Found at i:926750 original size:33 final size:34
Alignment explanation
Indices: 926713--926779 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
926703 AATAGATTTT
* * *
926713 ATTT-AATATCATTAAAA-AAATTATTTACTTTAA
1 ATTTAAATAT-ATAAAAATAAAATATTTAATTTAA
926746 ATTTAAATATATAAAAATAAAATATTTAATTTAA
1 ATTTAAATATATAAAAATAAAATATTTAATTTAA
926780 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (34 bp):
ATTTAAATATATAAAAATAAAATATTTAATTTAA
Found at i:926792 original size:28 final size:28
Alignment explanation
Indices: 926745--926798 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
926735 ATTTACTTTA
926745 AATTTAAATATATAAAAATAAAATATTT
1 AATTTAAATATATAAAAATAAAATATTT
926773 AATTT-AATA-ATAAAATAATAAAATAT
1 AATTTAAATATAT-AAA-AATAAAATAT
926799 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.08
27 7 0.29
28 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTTAAATATATAAAAATAAAATATTT
Found at i:926913 original size:20 final size:22
Alignment explanation
Indices: 926890--926929 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
926880 AACTTTTTTT
926890 ATATT-ATTATT-TTTTATAAA
1 ATATTAATTATTATTTTATAAA
*
926910 ATATTAATTTTTATTTTATA
1 ATATTAATTATTATTTTATA
926930 TATATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTAATTATTATTTTATAAA
Found at i:927389 original size:19 final size:19
Alignment explanation
Indices: 927365--927456 Score: 101
Period size: 19 Copynumber: 5.3 Consensus size: 19
927355 GTAATATTAT
927365 AAATAAAATTATAATATAA
1 AAATAAAATTATAATATAA
*
927384 AAATAAGATTATAATATAA
1 AAATAAAATTATAATATAA
*
927403 AAATAAAA-AATAATAT--
1 AAATAAAATTATAATATAA
*
927419 AAATACAA-TATAA-AT-A
1 AAATAAAATTATAATATAA
927435 AAATAAAATTAT-AT-TAA
1 AAATAAAATTATAATATAA
927452 AAATA
1 AAATA
927457 TGAACTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
15 2 0.03
16 20 0.32
17 9 0.14
18 7 0.11
19 25 0.40
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (19 bp):
AAATAAAATTATAATATAA
Found at i:927433 original size:11 final size:11
Alignment explanation
Indices: 927362--927443 Score: 57
Period size: 11 Copynumber: 7.6 Consensus size: 11
927352 TATGTAATAT
927362 TATAAATAAAA
1 TATAAATAAAA
*
927373 T-T--ATAATA
1 TATAAATAAAA
* *
927381 TAAAAATAAGAT
1 TATAAATAA-AA
927393 TATAATATAAAA
1 TATAA-ATAAAA
*
927405 -ATAAAAAATAA
1 TATAAATAA-AA
*
927416 TATAAATACAA
1 TATAAATAAAA
927427 TATAAATAAAA
1 TATAAATAAAA
927438 TA-AAAT
1 TATAAAT
927444 TATATTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
8 6 0.11
10 8 0.15
11 25 0.46
12 11 0.20
13 4 0.07
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (11 bp):
TATAAATAAAA
Found at i:927749 original size:28 final size:26
Alignment explanation
Indices: 927717--927790 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 26
927707 TATTTTAAAT
*
927717 AAATTAAAATTTATTTTTATTTAATTTA
1 AAATTAAAATTTATTTTTA--TAATGTA
* *
927745 TAATTAAATTTTATTTTTATAATGTA
1 AAATTAAAATTTATTTTTATAATGTA
*
927771 AAAATAAATATTTATTTTTA
1 AAATTAAA-ATTTATTTTTA
927791 AATTAATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 12 0.31
27 10 0.26
28 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
AAATTAAAATTTATTTTTATAATGTA
Found at i:928034 original size:22 final size:21
Alignment explanation
Indices: 927996--928055 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
927986 ATTTTTAATT
927996 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
928017 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
* * *
928037 -AATTTTAATAATATAATAT
1 TAAATTTAATTATAAAATAT
928056 TTTTAAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 5 0.15
21 12 0.36
22 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:931464 original size:22 final size:23
Alignment explanation
Indices: 931436--931493 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
931426 AGACAAATTT
931436 ATTATTTTAAAAATCATAAG-TA-
1 ATTATTTTAAAAAT-ATAAGTTAG
931458 ATTA-TTTAAAAATATAAGTTAG
1 ATTATTTTAAAAATATAAGTTAG
931480 TATTATTTTAAAAA
1 -ATTATTTTAAAAA
931494 AATGACACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 4 0.12
23 4 0.12
24 8 0.25
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
ATTATTTTAAAAATATAAGTTAG
Found at i:931492 original size:23 final size:22
Alignment explanation
Indices: 931435--931492 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
931425 AAGACAAATT
931435 TATTATTTTAAAAATCATAAGTA
1 TATTATTTT-AAAATCATAAGTA
*
931458 -ATTATTTAAAAAT-ATAAGTTA
1 TATTATTTTAAAATCATAAG-TA
931479 GTATTATTTTAAAA
1 -TATTATTTTAAAA
931493 AAATGACACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.17
21 7 0.23
22 7 0.23
23 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TATTATTTTAAAATCATAAGTA
Found at i:936654 original size:19 final size:19
Alignment explanation
Indices: 936630--936667 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
936620 AAGGATTAAA
936630 AAGAAA-AAAGAGAAGGAAG
1 AAGAAACAAAGA-AAGGAAG
936649 AAGAAACAAAGAAAGGAAG
1 AAGAAACAAAGAAAGGAAG
936668 GAAGGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (19 bp):
AAGAAACAAAGAAAGGAAG
Found at i:939182 original size:17 final size:16
Alignment explanation
Indices: 939160--939204 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
939150 AATATAATAA
939160 TTATATTTAAAATATTT
1 TTATATTTAAAA-ATTT
*
939177 TTATATTTTATAAATTT
1 TTATA-TTTAAAAATTT
939194 TTATATATTAA
1 TTATAT-TTAA
939205 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 17 0.71
18 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTAAAAATTT
Found at i:939252 original size:21 final size:21
Alignment explanation
Indices: 939219--939259 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
939209 AAAAATATAT
939219 TTTTTTAAATATTT-ATATTA
1 TTTTTTAAATATTTAATATTA
*
939239 TTTTTTACATTATTTAATATT
1 TTTTTTA-AATATTTAATATT
939260 TAAATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTTAAATATTTAATATTA
Found at i:939816 original size:14 final size:13
Alignment explanation
Indices: 939787--939817 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
939777 AGATTATCTT
939787 AAAATAATTTTTA
1 AAAATAATTTTTA
*
939800 AAAATAATTTTTC
1 AAAATAATTTTTA
939813 AAAAT
1 AAAAT
939818 TATATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATAATTTTTA
Found at i:941607 original size:9 final size:9
Alignment explanation
Indices: 941582--941617 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
941572 TTTCCTCAAA
941582 TTTCTTTCC
1 TTTCTTTCC
941591 TTTTTCTTTCC
1 --TTTCTTTCC
941602 TTTCTTTCC
1 TTTCTTTCC
941611 TTTCTTT
1 TTTCTTT
941618 TTTTTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTCTTTCC
Found at i:942848 original size:3 final size:3
Alignment explanation
Indices: 942840--942868 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
942830 TCACATCTAT
942840 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
942869 TCTTTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:944491 original size:2 final size:2
Alignment explanation
Indices: 944484--944512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
944474 TGTTTTTGTT
944484 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
944513 ATTGCGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:947341 original size:30 final size:30
Alignment explanation
Indices: 947307--947367 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
947297 TGCTTGCTTT
947307 ATTGAAGGCTCTTTC-ACTAAAAGTTGTTTC
1 ATTGAAGGCTCTTTCTACT-AAAGTTGTTTC
* * * *
947337 ATTGAGGGGTTTTTCTCCTAAAGTTGTTTC
1 ATTGAAGGCTCTTTCTACTAAAGTTGTTTC
947367 A
1 A
947368 CCAAATGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (30 bp):
ATTGAAGGCTCTTTCTACTAAAGTTGTTTC
Found at i:950858 original size:14 final size:15
Alignment explanation
Indices: 950839--950873 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
950829 GAAATGATTC
950839 ATTATAATTTT-TTT
1 ATTATAATTTTCTTT
950853 ATTATAATTTTCTTT
1 ATTATAATTTTCTTT
950868 -TTATAA
1 ATTATAA
950874 ACTAACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTATAATTTTCTTT
Found at i:952070 original size:3 final size:3
Alignment explanation
Indices: 952062--952088 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
952052 ATTCGTGAGC
952062 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
952089 CTAAGCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:952350 original size:10 final size:10
Alignment explanation
Indices: 952331--952375 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
952321 AATACGATGT
*
952331 TAAAATAATA
1 TAAAAAAATA
952341 TAAAAAAATA
1 TAAAAAAATA
952351 -AAATAAAATA
1 TAAA-AAAATA
952361 T-AAAAAATA
1 TAAAAAAATA
952370 TAAAAA
1 TAAAAA
952376 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 10 0.32
10 21 0.68
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:952354 original size:18 final size:20
Alignment explanation
Indices: 952331--952374 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
952321 AATACGATGT
952331 TAAAAT-AATATAAAAAA-A
1 TAAAATAAATATAAAAAATA
952349 TAAAATAAAATATAAAAAATA
1 TAAAAT-AAATATAAAAAATA
952370 TAAAA
1 TAAAA
952375 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAATAAATATAAAAAATA
Found at i:952417 original size:43 final size:44
Alignment explanation
Indices: 952355--952469 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 44
952345 AAAATAAAAT
*
952355 AAAATATAAA-AAATATAAAAATTTATTAAAAT-TTAT-ATAAT-A
1 AAAATATAAATATA-ATAAAAATTTATTAAAATATTATGAT-ATCA
* *
952397 TAAATTATTAATATAAT-AAAATTT-TTAAAATAATTATGATATCA
1 -AAAATATAAATATAATAAAAATTTATTAAAAT-ATTATGATATCA
952441 AAAATATAAATATAATAAAAA--TATTAAAA
1 AAAATATAAATATAATAAAAATTTATTAAAA
952470 AAATACTGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
41 7 0.12
42 8 0.13
43 36 0.60
44 9 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (44 bp):
AAAATATAAATATAATAAAAATTTATTAAAATATTATGATATCA
Found at i:952424 original size:17 final size:18
Alignment explanation
Indices: 952389--952430 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
952379 ATTAAAATTT
952389 ATATAATATAAATTATTA
1 ATATAATATAAATTATTA
*
952407 ATATAATA-AAATTTTTA
1 ATATAATATAAATTATTA
*
952424 AAATAAT
1 ATATAAT
952431 TATGATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATATAAATTATTA
Found at i:953230 original size:20 final size:20
Alignment explanation
Indices: 953192--953229 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
953182 AATAATTAAT
*
953192 ATATTTAAATTTAAATTTTA
1 ATATTTAAATGTAAATTTTA
*
953212 ATATTTACATGT-AATTTT
1 ATATTTAAATGTAAATTTT
953230 TTTATTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATTTAAATGTAAATTTTA
Found at i:955113 original size:2 final size:2
Alignment explanation
Indices: 955106--955139 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
955096 CAATCACCAC
955106 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
955140 AAAGGCCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:955661 original size:22 final size:21
Alignment explanation
Indices: 955636--955677 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
955626 AAATAAAAAA
955636 ATAATTT-TATATTAATATTTAC
1 ATAATTTATA-ATTAA-ATTTAC
955658 ATAATTTATAATTAAATTTA
1 ATAATTTATAATTAAATTTA
955678 AATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATTTATAATTAAATTTAC
Found at i:955667 original size:21 final size:22
Alignment explanation
Indices: 955636--955677 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
955626 AAATAAAAAA
955636 ATAATTTTAT-ATTAATATTTAC
1 ATAATTTTATAATTAA-ATTTAC
955658 ATAA-TTTATAATTAAATTTA
1 ATAATTTTATAATTAAATTTA
955678 AATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTTTATAATTAAATTTAC
Found at i:956601 original size:30 final size:30
Alignment explanation
Indices: 956567--956628 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
956557 TATTTGTTAA
* *
956567 TTTTAGATTTAAATATATAACTCCTATTAT
1 TTTTAGAGTTAAATATATAAATCCTATTAT
* *
956597 TTTTAGGGTTAAATATATAAATTCTATTAT
1 TTTTAGAGTTAAATATATAAATCCTATTAT
956627 TT
1 TT
956629 CAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTTAGAGTTAAATATATAAATCCTATTAT
Found at i:961388 original size:14 final size:14
Alignment explanation
Indices: 961369--961409 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
961359 TAAAATCAAA
961369 TTAATTTTATTAAT
1 TTAATTTTATTAAT
**
961383 TTAATTAAATTAAT
1 TTAATTTTATTAAT
961397 TTAAATTTTATTA
1 TT-AATTTTATTA
961410 TAATTATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTTTATTAAT
Found at i:962012 original size:17 final size:17
Alignment explanation
Indices: 961986--962028 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
961976 GCATTTTTTC
* *
961986 TTATTTTTTTTCTAATA
1 TTATTATTTTTATAATA
*
962003 TTATTATTTTTATATTA
1 TTATTATTTTTATAATA
*
962020 TAATTATTT
1 TTATTATTT
962029 ATTTTATCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATTTTTATAATA
Found at i:962117 original size:14 final size:14
Alignment explanation
Indices: 962098--962124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
962088 TTCATTTCTA
962098 ATATTATTATTTTG
1 ATATTATTATTTTG
962112 ATATTATTATTTT
1 ATATTATTATTTT
962125 TATACCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
ATATTATTATTTTG
Found at i:963017 original size:2 final size:2
Alignment explanation
Indices: 963010--963048 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
963000 TAGGGAGTGT
963010 TA TA 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 TA TA T
963049 GTCTATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:967379 original size:15 final size:16
Alignment explanation
Indices: 967347--967383 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
967337 TTTTATAAAA
967347 TAATATTTAATAAATT
1 TAATATTTAATAAATT
*
967363 TAATATTTAA-AATTT
1 TAATATTTAATAAATT
967378 TAATAT
1 TAATAT
967384 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTAATAAATT
Found at i:974992 original size:2 final size:2
Alignment explanation
Indices: 974985--975016 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
974975 CTGGTTCAAT
974985 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
975017 TACAAGTTCT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:976691 original size:17 final size:17
Alignment explanation
Indices: 976669--976701 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
976659 TCTTAACTGG
976669 ATCAAACAAAAGCTAAC
1 ATCAAACAAAAGCTAAC
976686 ATCAAACAAAAGCTAA
1 ATCAAACAAAAGCTAA
976702 AATATAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (17 bp):
ATCAAACAAAAGCTAAC
Found at i:977215 original size:2 final size:2
Alignment explanation
Indices: 977208--977244 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
977198 TACATGAAAC
977208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
977245 TCTGGTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:978632 original size:12 final size:11
Alignment explanation
Indices: 978615--978648 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
978605 AATATATTAA
978615 TAAAATAATGAT
1 TAAAATAAT-AT
978627 TAAAATAATAT
1 TAAAATAATAT
978638 TAAAAATAATA
1 T-AAAATAATA
978649 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.14
12 18 0.86
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:978980 original size:17 final size:18
Alignment explanation
Indices: 978946--979012 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
978936 ATTTTGATAA
**
978946 ATATTTATTTTTTTAATT
1 ATATTTATTTTTAAAATT
978964 -TATTTATTTTTAAAATT
1 ATATTTATTTTTAAAATT
*
978981 ATAATATTATTTTTAAAAAT
1 AT-AT-TTATTTTTAAAATT
979001 AT-TTTATATTTT
1 ATATTTAT-TTTT
979013 TTTAGTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 19 0.45
18 6 0.14
19 2 0.05
20 15 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTATTTTTAAAATT
Found at i:980863 original size:16 final size:16
Alignment explanation
Indices: 980842--980879 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
980832 AAAATATCAT
980842 ATTATTTAATTAAATA
1 ATTATTTAATTAAATA
* *
980858 ATTATTTTATTAAATG
1 ATTATTTAATTAAATA
980874 ATTATT
1 ATTATT
980880 ATATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTATTTAATTAAATA
Found at i:980884 original size:16 final size:16
Alignment explanation
Indices: 980850--980884 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
980840 ATATTATTTA
*
980850 ATTAAATAATTATTTT
1 ATTAAATAATTATTAT
*
980866 ATTAAATGATTATTAT
1 ATTAAATAATTATTAT
980882 ATT
1 ATT
980885 TATTATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTAAATAATTATTAT
Found at i:984258 original size:89 final size:88
Alignment explanation
Indices: 984159--984336 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 88
984149 TTATAATTTT
984159 TTTATTATATTAGCAGTGTATTAAGATAATTATCTTTATATATATTAATTTTAAAGTCGACCTAT
1 TTTATTATATTAGCAGTGTATTAAGATAATTATCTTTATATATATTAATTTTAAAGTCGACCTAT
984224 TCAAATAAACAATCATGCTTGATC
66 TCAAATAAACAATC-TGCTTGATC
984248 TTTATTATATTAGCAGTGTATTAAGATAATTATCTTTATATATATTAATTTTAAAGTCGACCTAT
1 TTTATTATATTAGCAGTGTATTAAGATAATTATCTTTATATATATTAATTTTAAAGTCGACCTAT
984313 TCAAATAAACAATCTGCTTGATC
66 TCAAATAAACAATCTGCTTGATC
984336 T
1 T
984337 GATCGGTTTA
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 10 0.11
89 79 0.89
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (88 bp):
TTTATTATATTAGCAGTGTATTAAGATAATTATCTTTATATATATTAATTTTAAAGTCGACCTAT
TCAAATAAACAATCTGCTTGATC
Found at i:986062 original size:34 final size:33
Alignment explanation
Indices: 986014--986234 Score: 230
Period size: 34 Copynumber: 6.5 Consensus size: 33
986004 TGGTAAAAAC
*
986014 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
986047 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
986081 CACCCATTTAATCAATAATGATAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
986115 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * * *
986149 CTCCCATTTAGTTAACAATGGCAAACC-ATCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
986183 CACTCATTTAATCAACAATGGTAAACTACAAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
986217 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
986235 TCTCCCACTT
Statistics
Matches: 155, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
33 23 0.15
34 126 0.81
35 6 0.04
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:986130 original size:68 final size:68
Alignment explanation
Indices: 986016--986234 Score: 271
Period size: 68 Copynumber: 3.2 Consensus size: 68
986006 GTAAAAACCA
* * *
986016 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
986080 TCAC
65 TCAC
* ** * *
986084 CCATTTAATCAATAATGATAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
986149 CTC
66 CAC
* * * * * * *
986152 CCATTTAGTTAACAATGGCAAACCATCAAATCACTCATTTAATCAACAATGGTAAACTACAAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
986217 CA-
66 CAC
986219 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
986235 TCTCCCACTT
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
67 16 0.13
68 111 0.87
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:986193 original size:102 final size:101
Alignment explanation
Indices: 986009--986234 Score: 308
Period size: 102 Copynumber: 2.2 Consensus size: 101
985999 AGGTTTGGTA
* * *
986009 AAAACCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCC
1 AAAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACC
* *
986074 ACCAAATCACCCATTTAATCAATAATGATAAGCTAC
66 ACCAAATCACCCATTTAATCAACAATGATAAACTAC
* ** * * * *
986110 CAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGCAAAC
1 AAAATCAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAAC
* * *
986175 CATCAAATCACTCATTTAATCAACAATGGTAAACTAC
65 CACCAAATCACCCATTTAATCAACAATGATAAACTAC
986212 AAAATCACCATTTAATCAACAAT
1 AAAATCACCATTTAATCAACAAT
986235 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 19 0.18
102 87 0.82
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
AAAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACC
ACCAAATCACCCATTTAATCAACAATGATAAACTAC
Found at i:990688 original size:34 final size:34
Alignment explanation
Indices: 990641--990858 Score: 232
Period size: 34 Copynumber: 6.4 Consensus size: 34
990631 GGTAAAAACC
**
990641 ACCATTTAATCAACAATGACAACCTACCAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
* * *
990675 ATCATTTAGTCAACAATAGTAAGCC-ACCAAAT-T
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* *
990708 ACACATTTAATCAATAATGGTAAGCTACCAAAT-T
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* *
990742 TCTCATTTAATCAACAATGGTAAGCTACCAAATCT
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* * *
990777 CCCATTTAGTCAACAATGGCAAACC-ACCAAATC-
1 ACCATTTAATCAACAATGG-TAACCTACCAAATCT
*
990810 ACCCATTTAATCAACAATGGTAAACTACCAAATC-
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
990844 ACCATTTAATCAACA
1 ACCATTTAATCAACA
990859 TAATTATCCA
Statistics
Matches: 156, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
33 20 0.13
34 129 0.83
35 7 0.04
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:990756 original size:68 final size:67
Alignment explanation
Indices: 990641--990858 Score: 265
Period size: 68 Copynumber: 3.2 Consensus size: 67
990631 GGTAAAAACC
* * * * * *
990641 ACCATTTAATCAACAATGACAACCTACCAAATCTATCATTTAGTCAACAATAGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAA
990706 TT
66 TT
* * * *
990708 ACACATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAA
1 AC-CATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAA
990773 ATCT
65 AT-T
* * * * * *
990777 CCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAA
1 ACCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAA
*
990842 TC
66 TT
990844 ACCATTTAATCAACA
1 ACCATTTAATCAACA
990859 TAATTATCCA
Statistics
Matches: 127, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 15 0.12
68 110 0.87
69 2 0.02
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (67 bp):
ACCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAAA
TT
Found at i:990785 original size:102 final size:101
Alignment explanation
Indices: 990640--990858 Score: 303
Period size: 102 Copynumber: 2.2 Consensus size: 101
990630 TGGTAAAAAC
* * *
990640 CACCATTTAATCAACAATGACAACCTACCAAATCTATCATTTAGTCAACAATAGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
* * *
990705 ATTACACATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACACATTTAATCAACAATGGTAAACTACCAAAT
** ** * * *
990741 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCA
*
990806 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACACATTTAATCAACAATGGTAAACTACCAAAT
990843 CACCATTTAATCAACA
1 CACCATTTAATCAACA
990859 TAATTATCCA
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 14 0.14
102 87 0.86
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
ATCACACATTTAATCAACAATGGTAAACTACCAAAT
Found at i:994218 original size:23 final size:23
Alignment explanation
Indices: 994192--994235 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
994182 ACATATTACT
*
994192 TTTAAAAATTAATATTCAATAAA
1 TTTAAAAATTAAAATTCAATAAA
* *
994215 TTTAAAATTTAAAATTTAATA
1 TTTAAAAATTAAAATTCAATA
994236 TGTATAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAATTAAAATTCAATAAA
Found at i:994486 original size:13 final size:14
Alignment explanation
Indices: 994465--994493 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
994455 AATAGTATAC
994465 ATAT-TTTTTTCTA
1 ATATGTTTTTTCTA
994478 ATATGTTTTTTCTA
1 ATATGTTTTTTCTA
994492 AT
1 AT
994494 TTAATCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (14 bp):
ATATGTTTTTTCTA
Found at i:996344 original size:23 final size:22
Alignment explanation
Indices: 996310--996360 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
996300 ATTATTTTTA
996310 TTAATAAGTTATATTTTAAATT
1 TTAATAAGTTATATTTTAAATT
*
996332 TTAATTAAGTTATATTTTTAATT
1 TTAA-TAAGTTATATTTTAAATT
*
996355 TAAATA
1 TTAATA
996361 CTTGATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTAATAAGTTATATTTTAAATT
Found at i:996635 original size:18 final size:17
Alignment explanation
Indices: 996596--996639 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
996586 TGTTATTTAT
**
996596 TTTTCTTATTTTTATCCT
1 TTTT-TTATTTTTATCAA
996614 TTTTTTATTTTTAATCAA
1 TTTTTTATTTTT-ATCAA
996632 TTTTTTAT
1 TTTTTTAT
996640 CTCTAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTATTTTTATCAA
Found at i:1000916 original size:10 final size:10
Alignment explanation
Indices: 1000901--1000931 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1000891 TTATTTAATT
1000901 TATTTAAAAA
1 TATTTAAAAA
1000911 TATTTAAAAA
1 TATTTAAAAA
1000921 TATTTAAAAA
1 TATTTAAAAA
1000931 T
1 T
1000932 TAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:1001028 original size:16 final size:17
Alignment explanation
Indices: 1000994--1001031 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1000984 AGAAAAAAAA
1000994 GAAAGAAAAGGAAGGAG
1 GAAAGAAAAGGAAGGAG
*
1001011 GAAAGAAAA-GAGGGAG
1 GAAAGAAAAGGAAGGAG
1001027 GAAAG
1 GAAAG
1001032 TGGAGCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAGGAAGGAG
Found at i:1001294 original size:18 final size:17
Alignment explanation
Indices: 1001268--1001311 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1001258 AAATTGGTTG
*
1001268 TCTTCCCCTTTCCCTCTC
1 TCTTTCCCTTTCCCT-TC
* *
1001286 TCTTTCCCTTTCTCTTT
1 TCTTTCCCTTTCCCTTC
1001303 TCTTTCCCT
1 TCTTTCCCT
1001312 CGATTCATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
TCTTTCCCTTTCCCTTC
Found at i:1001448 original size:28 final size:28
Alignment explanation
Indices: 1001383--1001448 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1001373 GACTAACCGA
1001383 CCTTCCTGC-CTCTTTTTTCTCTCTCTTC
1 CCTT-CTGCTCTCTTTTTTCTCTCTCTTC
* *
1001411 CATTC-CCTCTCTCTTTTTCTCTC-CTTC
1 CCTTCTGCTCTCT-TTTTTCTCTCTCTTC
1001438 CCTTCTGCTCT
1 CCTTCTGCTCT
1001449 TCCTTTCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 1 0.03
27 13 0.42
28 17 0.55
ACGTcount: A:0.02, C:0.44, G:0.03, T:0.52
Consensus pattern (28 bp):
CCTTCTGCTCTCTTTTTTCTCTCTCTTC
Found at i:1001621 original size:8 final size:8
Alignment explanation
Indices: 1001608--1001671 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
1001598 TTTTAAATGC
1001608 TTTTTAGT
1 TTTTTAGT
*
1001616 TTTTTAAT
1 TTTTTAGT
*
1001624 TTTATAGT
1 TTTTTAGT
1001632 TTTTATCA-T
1 TTTT-T-AGT
*
1001641 TTTTTAAATT
1 TTTTT--AGT
1001651 TTTTTAGT
1 TTTTTAGT
1001659 TTTTTA-T
1 TTTTTAGT
1001666 TTTTTA
1 TTTTTA
1001672 AAAATTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 7 0.15
8 25 0.54
9 7 0.15
10 7 0.15
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (8 bp):
TTTTTAGT
Found at i:1001643 original size:25 final size:24
Alignment explanation
Indices: 1001608--1001672 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 24
1001598 TTTTAAATGC
1001608 TTTTTAGTTTTTTAA-TTTTATAGT
1 TTTTTA-TTTTTTAATTTTTATAGT
*
1001632 TTTTATCATTTTTTAAATTTTTTTAGT
1 TTTT-T-ATTTTTT-AATTTTTATAGT
1001659 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
1001673 AAATTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 6 0.17
25 14 0.39
26 4 0.11
27 12 0.33
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTTATTTTTTAATTTTTATAGT
Found at i:1001676 original size:27 final size:27
Alignment explanation
Indices: 1001623--1001731 Score: 77
Period size: 29 Copynumber: 3.9 Consensus size: 27
1001613 AGTTTTTTAA
*
1001623 TTTTATAGTTTTTATCATTTTTT-AAAT
1 TTTTTTAGTTTTTAT-ATTTTTTAAAAT
1001650 TTTTTTAGTTTTT-TATTTTTTAAAAATT
1 TTTTTTAGTTTTTATATTTTTT-AAAA-T
1001678 TATTTTTA-TTTTTGA-ATTTTTTTATAAA-
1 T-TTTTTAGTTTTT-ATA-TTTTTTA-AAAT
1001706 -TTTTTAGATATTTTCATATTTTTTAA
1 TTTTTTAG-T-TTTT-ATATTTTTTAA
1001732 TTTTTTAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
25 7 0.10
26 7 0.10
27 15 0.22
28 9 0.13
29 20 0.29
30 10 0.15
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (27 bp):
TTTTTTAGTTTTTATATTTTTTAAAAT
Found at i:1001680 original size:43 final size:44
Alignment explanation
Indices: 1001597--1001680 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 44
1001587 GTTTCTTGCA
***
1001597 TTTTTAAATGCTTTTTAGTTTTTTAATTTTATAGTTTTTATCAT
1 TTTTTAAATGCTTTTTAGTTTTTTAATTTTATAAAATTTATCAT
* *
1001641 TTTTTAAAT-TTTTTTAGTTTTTT-ATTTTTTAAAAATTTAT
1 TTTTTAAATGCTTTTTAGTTTTTTAATTTTAT-AAAATTTAT
1001681 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 6 0.18
43 19 0.56
44 9 0.26
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (44 bp):
TTTTTAAATGCTTTTTAGTTTTTTAATTTTATAAAATTTATCAT
Found at i:1001736 original size:9 final size:9
Alignment explanation
Indices: 1001639--1001743 Score: 54
Period size: 9 Copynumber: 11.4 Consensus size: 9
1001629 AGTTTTTATC
1001639 ATTTTTTAA
1 ATTTTTTAA
*
1001648 ATTTTTTTA
1 ATTTTTTAA
*
1001657 GTTTTTT--
1 ATTTTTTAA
1001664 ATTTTTTAAAA
1 ATTTTTT--AA
**
1001675 ATTTATTTTT
1 ATTT-TTTAA
*
1001685 ATTTTTGAA
1 ATTTTTTAA
*
1001694 TTTTTTTATA
1 ATTTTTTA-A
* *
1001704 AATTTTTAG
1 ATTTTTTAA
* *
1001713 ATATTTTCAT
1 AT-TTTTTAA
1001723 ATTTTTT-A
1 ATTTTTTAA
1001731 ATTTTTTAA
1 ATTTTTTAA
1001740 ATTT
1 ATTT
1001744 AAAAAAATTA
Statistics
Matches: 70, Mismatches: 18, Indels: 16
0.67 0.17 0.15
Matches are distributed among these distances:
7 6 0.09
8 7 0.10
9 32 0.46
10 18 0.26
11 4 0.06
12 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.69
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:1006729 original size:2 final size:2
Alignment explanation
Indices: 1006724--1006753 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1006714 AAAAAAGGTG
1006724 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
1006754 GAAAAATAAA
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:1006914 original size:12 final size:12
Alignment explanation
Indices: 1006897--1006921 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1006887 AGGTGGTAGA
1006897 GTGATTAGCAAG
1 GTGATTAGCAAG
1006909 GTGATTAGCAAG
1 GTGATTAGCAAG
1006921 G
1 G
1006922 AGCATGGCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GTGATTAGCAAG
Found at i:1007051 original size:2 final size:2
Alignment explanation
Indices: 1007044--1007088 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1007034 ATGGGAATTA
1007044 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
1007086 AT A
1 AT A
1007089 AATGTTCGAT
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:1009522 original size:15 final size:15
Alignment explanation
Indices: 1009502--1009531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1009492 ATGTCTTACT
*
1009502 TATATTTTTTATATA
1 TATATTTTTAATATA
1009517 TATATTTTTAATATA
1 TATATTTTTAATATA
1009532 AGTATGAAAG
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTTTTAATATA
Found at i:1012126 original size:9 final size:9
Alignment explanation
Indices: 1012112--1012217 Score: 53
Period size: 9 Copynumber: 11.2 Consensus size: 9
1012102 GAGATCAACA
1012112 TAATATATT
1 TAATATATT
*
1012121 TAATATA-A
1 TAATATATT
1012129 T-ATAT-TT
1 TAATATATT
1012136 TAAATATGATT
1 T-AATAT-ATT
1012147 AATAAATATATT
1 --T-AATATATT
1012159 TAATATATAT
1 TAATATAT-T
1012169 TATATTTATATT
1 TA-A--TATATT
1012181 TAA-A-ATT
1 TAATATATT
*
1012188 TAATTTATT
1 TAATATATT
1012197 TAATA-ATT
1 TAATATATT
1012205 TATATTATATT
1 TA-A-TATATT
1012216 TA
1 TA
1012218 TATTTATATA
Statistics
Matches: 77, Mismatches: 4, Indels: 30
0.69 0.04 0.27
Matches are distributed among these distances:
7 11 0.14
8 7 0.09
9 26 0.34
10 6 0.08
11 9 0.12
12 6 0.08
13 12 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
TAATATATT
Found at i:1012141 original size:16 final size:14
Alignment explanation
Indices: 1012111--1012176 Score: 70
Period size: 13 Copynumber: 4.9 Consensus size: 14
1012101 TGAGATCAAC
1012111 ATAATATATTTAAT
1 ATAATATATTTAAT
1012125 ATAATATATTT--T
1 ATAATATATTTAAT
1012137 A-AATATGA-TTAAT
1 ATAATAT-ATTTAAT
1012150 A-AATATATTTAAT
1 ATAATATATTTAAT
1012163 ATATATTATATTTA
1 ATA-A-TATATTTA
1012177 TATTTAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.16
12 4 0.09
13 13 0.29
14 12 0.27
15 1 0.02
16 8 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATAATATATTTAAT
Found at i:1012141 original size:41 final size:40
Alignment explanation
Indices: 1012089--1012175 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 40
1012079 AAAAGTCATA
1012089 ATATTTTAAATATGAGATCAACATAATATATTTAATATA-A-T
1 ATATTTTAAATAT--GATCAACA-AATATATTTAATATATATT
* *
1012130 ATATTTTAAATATGATTAATAAATATATTTAATATATATT
1 ATATTTTAAATATGATCAACAAATATATTTAATATATATT
1012170 ATATTT
1 ATATTT
1012176 ATATTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
38 15 0.36
39 7 0.17
40 7 0.17
41 13 0.31
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (40 bp):
ATATTTTAAATATGATCAACAAATATATTTAATATATATT
Found at i:1012179 original size:6 final size:6
Alignment explanation
Indices: 1012153--1012226 Score: 68
Period size: 6 Copynumber: 12.8 Consensus size: 6
1012143 GATTAATAAA
* *
1012153 TATATT TA-ATA TATA-T TATATT TATATT TAAAATT TA-ATT TAT-TT
1 TATATT TATATT TATATT TATATT TATATT T-ATATT TATATT TATATT
*
1012198 AATAATT TATA-T TATATT TATATT TATAT
1 TAT-ATT TATATT TATATT TATATT TATAT
1012227 AATTTTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
5 22 0.39
6 25 0.45
7 9 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:1012229 original size:29 final size:28
Alignment explanation
Indices: 1012153--1012229 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
1012143 GATTAATAAA
* *
1012153 TATATTTAATATATATTATATTTATATT
1 TATATTTAATTTATATAATATTTATATT
* *
1012181 TAAAATTTAATTTATTTAATAATTTATA-T
1 T-ATATTTAATTTATATAAT-ATTTATATT
1012210 TATATTTATATTTATATAAT
1 TATATTTA-ATTTATATAAT
1012230 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.17
29 26 0.65
30 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTTAATTTATATAATATTTATATT
Found at i:1015858 original size:16 final size:16
Alignment explanation
Indices: 1015837--1015869 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1015827 ATAATGGAGG
*
1015837 ACTTCTGTTGGTCACC
1 ACTTCTGTCGGTCACC
1015853 ACTTCTGTCGGTCACC
1 ACTTCTGTCGGTCACC
1015869 A
1 A
1015870 TTAACAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.33, G:0.18, T:0.33
Consensus pattern (16 bp):
ACTTCTGTCGGTCACC
Found at i:1024079 original size:22 final size:24
Alignment explanation
Indices: 1024054--1024101 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1024044 TTTAAAATTA
1024054 TTTAAA-TTATTT-TTATT-TAAAT
1 TTTAAATTTATTTATT-TTATAAAT
1024076 TTTAAATTTATTTATTTTATAAAT
1 TTTAAATTTATTTATTTTATAAAT
1024100 TT
1 TT
1024102 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 8 0.35
24 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTAAATTTATTTATTTTATAAAT
Found at i:1024087 original size:17 final size:17
Alignment explanation
Indices: 1024044--1024105 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1024034 CATAATATTA
*
1024044 TTTAAAATTATTTAAAT
1 TTTAAATTTATTTAAAT
1024061 TATT---TTTATTTAAAT
1 T-TTAAATTTATTTAAAT
*
1024076 TTTAAATTTATTT-ATT
1 TTTAAATTTATTTAAAT
1024092 TTATAAATTTATTT
1 TT-TAAATTTATTT
1024106 TATTATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 4 0.11
17 19 0.50
18 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAAATTTATTTAAAT
Found at i:1024102 original size:23 final size:21
Alignment explanation
Indices: 1024053--1024102 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 21
1024043 ATTTAAAATT
1024053 ATTTAAATTATTTTTATTTAA
1 ATTTAAATTATTTTTATTTAA
1024074 ATTTTAAATTTATTTATT-TTATAA
1 A-TTTAAA-TTATTT-TTATT-TAA
1024098 ATTTA
1 ATTTA
1024103 TTTTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.04
22 6 0.24
23 12 0.48
24 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAAATTATTTTTATTTAA
Found at i:1024115 original size:17 final size:16
Alignment explanation
Indices: 1024077--1024115 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1024067 TATTTAAATT
*
1024077 TTAAATTTATTTATTT
1 TTAAATTTATTTATTA
1024093 TATAAATTTATTTTATTA
1 T-TAAATTTA-TTTATTA
1024111 TTAAA
1 TTAAA
1024116 ATATAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAAATTTATTTATTA
Found at i:1024640 original size:21 final size:20
Alignment explanation
Indices: 1024598--1024642 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1024588 ATACCCATCA
**
1024598 TTTTATTTAAAAATTCTTAT
1 TTTTATTTAAAAATTCCAAT
*
1024618 TTTTATTTGAAAATTACCAAT
1 TTTTATTTAAAAATT-CCAAT
1024639 TTTT
1 TTTT
1024643 TAATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATTTAAAAATTCCAAT
Found at i:1025619 original size:15 final size:15
Alignment explanation
Indices: 1025601--1025636 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1025591 TAAAAAATTA
* *
1025601 TTTTATATTAATATT
1 TTTTATATTAAAAAT
1025616 TTTTATATTAAAAAT
1 TTTTATATTAAAAAT
1025631 TTTTAT
1 TTTTAT
1025637 GTGTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATATTAAAAAT
Found at i:1025820 original size:34 final size:34
Alignment explanation
Indices: 1025768--1025838 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1025758 AATTATATTC
* * * *
1025768 ATATTTAAAAAATTATTAAATCATTAATACTTAA
1 ATATCTAAAAAATCATTAAACCATTAATAATTAA
*
1025802 ATATCTAAAGAATCATTAAACCATTAATAATTAA
1 ATATCTAAAAAATCATTAAACCATTAATAATTAA
1025836 ATA
1 ATA
1025839 AAGTAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (34 bp):
ATATCTAAAAAATCATTAAACCATTAATAATTAA
Found at i:1026834 original size:3 final size:3
Alignment explanation
Indices: 1026826--1026860 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1026816 AAAGCAAAAC
*
1026826 AAT AAT AAT AAT CAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1026861 AATTTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1031571 original size:22 final size:21
Alignment explanation
Indices: 1031523--1031571 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1031513 TAAAATATCA
*
1031523 AAAAATTTAAATTAATAAATT
1 AAAAATTAAAATTAATAAATT
*
1031544 ATAAATTAAATATTAATATAA-T
1 AAAAATTAAA-ATTAATA-AATT
1031566 AAAAAT
1 AAAAAT
1031572 ATTTGTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.35
22 13 0.57
23 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATTAAAATTAATAAATT
Found at i:1032055 original size:34 final size:34
Alignment explanation
Indices: 1032017--1032115 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 34
1032007 GTTAAGTATA
*
1032017 TTAGGTAAATATATTATGTGTGTTAGGTACTGTG
1 TTAGGTAAATATATTAAGTGTGTTAGGTACTGTG
* **
1032051 TTAGGTGAACAATATATTAAGTGTGTTAAGTGGTGTG
1 TTAGGT--A-AATATATTAAGTGTGTTAGGTACTGTG
* * *
1032088 TTAGGTAAACATATTAGGTGCGTTAGGT
1 TTAGGTAAATATATTAAGTGTGTTAGGT
1032116 GAATATATCT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
34 23 0.43
35 1 0.02
36 1 0.02
37 29 0.54
ACGTcount: A:0.28, C:0.04, G:0.28, T:0.39
Consensus pattern (34 bp):
TTAGGTAAATATATTAAGTGTGTTAGGTACTGTG
Found at i:1037045 original size:79 final size:79
Alignment explanation
Indices: 1036927--1037112 Score: 191
Period size: 79 Copynumber: 2.4 Consensus size: 79
1036917 TAATATTTTA
* * * * *
1036927 AAAATAAAAAC-AGAGTTGGAGTATCTCCTGGGAAATAACAGGGTTGGACTA-TCTCTGATTGT-
1 AAAATAAAATCGAG-GTTGGAGTATCCCCTGCGAAATAACAGGGTTAGACTATTC-CCGATTGTG
* *
1036989 AGAAAATCGGTGTTCTG
64 A-AAAATCGATATTCTG
* * * * *
1037006 GAAATAAGATTGGGGTTGGAGTATCCCCT-CGAAAGTAACAGGGTTAGAGTATTCCCGATTGTGA
1 AAAATAAAATCGAGGTTGGAGTATCCCCTGCGAAA-TAACAGGGTTAGACTATTCCCGATTGTGA
1037070 AAAATCGATATTCTG
65 AAAATCGATATTCTG
*
1037085 AAAATAAAATCGAGGTTAGAGTATCCCC
1 AAAATAAAATCGAGGTTGGAGTATCCCC
1037113 GATGGTCAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
78 4 0.05
79 78 0.91
80 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
AAAATAAAATCGAGGTTGGAGTATCCCCTGCGAAATAACAGGGTTAGACTATTCCCGATTGTGAA
AAATCGATATTCTG
Found at i:1037107 original size:51 final size:51
Alignment explanation
Indices: 1037044--1037163 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
1037034 TCGAAAGTAA
* * *
1037044 CAGGGTTAGAGTATTCCCGATTGTGAAAAATCGATATTCTGA-AAATAAAAT
1 CAGGGTTAGAGTATCCCCGATGGTCAAAAATCGATATT-TGAGAAATAAAAT
* *
1037095 C-GAGGTTAGAGTATCCCCGATGGTCAAAAATCGATGTTTTAGAAATAAAAT
1 CAG-GGTTAGAGTATCCCCGATGGTCAAAAATCGATATTTGAGAAATAAAAT
1037146 CAGGGTTAGAGTATCCCC
1 CAGGGTTAGAGTATCCCC
1037164 TTAAAAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 3 0.05
51 57 0.93
52 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
CAGGGTTAGAGTATCCCCGATGGTCAAAAATCGATATTTGAGAAATAAAAT
Found at i:1037237 original size:130 final size:130
Alignment explanation
Indices: 1036991--1037502 Score: 580
Period size: 130 Copynumber: 3.9 Consensus size: 130
1036981 CTGATTGTAG
* * * * * * * *
1036991 AAAATCGGTGTTCTGGAAATAAGATTGGGGTTGGAGTATCCCCTCGAAAGTAACAGGG-TTAGAG
1 AAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAAC-GGGATTGGAG
* * * * * *
1037055 TATTCCCGATTGTGAAAAATCGATATTCTGAAAATAAAATCGAGGTTAGAGTATCCCCGATGGTC
65 TATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATGGTG
1037120 A
130 A
* ** *
1037121 AAAATCGATGTTTTAGAAATAAAATCAGGGTTAGAGTATCCCCTTAAAAATAACGGGGTTGGAGT
1 AAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGATTGGAGT
* * * * * * * ** *
1037186 ATCCCCAATTATGAAAATTTGGTGTTCTGAAAATAAAACCGGGGTTGGAGTATCATCGATGGTGG
66 ATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATGGTGA
* *
1037251 AAAATTGATGTTTT-GAAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTGGAG
1 AAAATCGATGTTTTAG-AAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGATTGGAG
* * * *
1037315 TATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCAAGGTTAAAGTATCTCCGATGATG
65 TATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATGGTG
1037380 A
130 A
* * * * *
1037381 AAACTCGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGATTGGAGT
1 AAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGATTGGAGT
* ** * *
1037446 ATCCACGATTGTGAAAAATTTGTGCTT-TAAAAATAAAATCGAGGTTTGAGTATCCCC
66 ATCCCCGATTGTGAAAAATCGGTG-TTCTAAAAATAAAACCGAGGTTAGAGTATCCCC
1037503 TCAAAAATAA
Statistics
Matches: 319, Mismatches: 59, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
129 4 0.01
130 313 0.98
131 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (130 bp):
AAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGATTGGAGT
ATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCGAGGTTAGAGTATCCCCGATGGTGA
Found at i:1037419 original size:51 final size:51
Alignment explanation
Indices: 1037309--1037423 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
1037299 AATAACGAGA
*
1037309 TTGGAGTATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAACCAAGG
1 TTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAAAAATAAAACCAAGG
** * * * **
1037360 TTAAAGTATCTCCGA-TGATGAAAACTCGATGTTTTAAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATTG-TGAAAAATCGATGTTCTAAAAATAAAACCAAGG
1037411 TTGGAGTATCCCC
1 TTGGAGTATCCCC
1037424 TCGGAAATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 2 0.04
51 50 0.96
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAAAAATAAAACCAAGG
Found at i:1037434 original size:260 final size:260
Alignment explanation
Indices: 1036967--1037499 Score: 651
Period size: 260 Copynumber: 2.0 Consensus size: 260
1036957 GGAAATAACA
* * * * * * *
1036967 GGGTTGGACTATCTCTGATTGTAGAAAATCGGTGTTCTGGAAATAAGATTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCTCTGATGGTAGAAAATCGATGTTCTGAAAATAAAATCGGGGTTAGAGTATCC
* * * * * *
1037032 CCTCGAAAGTAACAGGGTTAGAGTATTCCCGATTGTGAAAAATCGATATTCTGAAAATAAAATCG
66 CCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTGAAAAATCGATATTCTAAAAATAAAACCA
* * * *
1037097 AGGTTAGAGTATCCCCGATGGTCAAAAATCGATGTTTTAGAAATAAAATCAGGGTTAGAGTATCC
131 AGGTTAAAGTATCCCCGATGATCAAAAATCGATGTTTTAAAAATAAAACCAGGGTTAGAGTATCC
* * * *
1037162 CCTTAAAAATAACGGGGTTGGAGTATCCCCAATTATG-AAAATTTGGTG-TTCTGAAAATAAAAC
196 CCTCAAAAATAACGGGATTGGAGTATCCACAATTATGAAAAATTT-GTGCTT-TAAAAATAAAAC
1037225 CG
259 CG
* * *
1037227 GGGTTGGAGTATCATC-GATGGTGGAAAATTGATGTTTTGAAAATAAAATCGGGGTTAGAGTATC
1 GGGTTGGAGTATC-TCTGATGGTAGAAAATCGATGTTCTGAAAATAAAATCGGGGTTAGAGTATC
* * *
1037291 CCCTCGAAAATAAC-GAGATTGGAGTATCCCCGATTGTGAAAAATCGGTGTTCTAAAAATAAAAC
65 CCCTCGAAAATAACAG-GATTAGAGTATCCCCGATTGTGAAAAATCGATATTCTAAAAATAAAAC
* * * * *
1037355 CAAGGTTAAAGTATCTCCGATGATGAAAACTCGATGTTTTAAAAATAAAACCGGGGTTGGAGTAT
129 CAAGGTTAAAGTATCCCCGATGATCAAAAATCGATGTTTTAAAAATAAAACCAGGGTTAGAGTAT
** * * *
1037420 CCCCTCGGAAATAACGGGATTGGAGTATCCACGATTGTGAAAAATTTGTGCTTTAAAAATAAAAT
194 CCCCTCAAAAATAACGGGATTGGAGTATCCACAATTATGAAAAATTTGTGCTTTAAAAATAAAAC
1037485 CG
259 CG
* *
1037487 AGGTTTGAGTATC
1 GGGTTGGAGTATC
1037500 CCCTCAAAAA
Statistics
Matches: 230, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
259 1 0.00
260 218 0.95
261 11 0.05
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (260 bp):
GGGTTGGAGTATCTCTGATGGTAGAAAATCGATGTTCTGAAAATAAAATCGGGGTTAGAGTATCC
CCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTGAAAAATCGATATTCTAAAAATAAAACCA
AGGTTAAAGTATCCCCGATGATCAAAAATCGATGTTTTAAAAATAAAACCAGGGTTAGAGTATCC
CCTCAAAAATAACGGGATTGGAGTATCCACAATTATGAAAAATTTGTGCTTTAAAAATAAAACCG
Found at i:1037497 original size:79 final size:80
Alignment explanation
Indices: 1037392--1037641 Score: 254
Period size: 79 Copynumber: 3.2 Consensus size: 80
1037382 AACTCGATGT
* * * *
1037392 TTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGATTGGAGTATCCACGATTG
1 TTTAAAAATAAAACCGAGGTTAGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATTG
* *
1037457 TGAAAAATTTG-TGC
66 TGAAAAATTCGATAC
* * ** * * * *
1037471 TTTAAAAATAAAATCGAGGTTTGAGTATCCCCTCAAAAATAATAGGATTAGAGTATCCCCAATGG
1 TTTAAAAATAAAACCGAGGTTAGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATTG
*
1037536 TGAAATA-TCGATAC
66 TGAAAAATTCGATAC
* * * * * * *
1037550 TTTGAAAATAAAACCGAGATTAGAGTATCCCATTGGAAATAGTGGGGTTGGAGTATCCCCGAGTG
1 TTTAAAAATAAAACCGAGGTTAGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATTG
* *
1037615 TGAAAAA-TCGGTAT
66 TGAAAAATTCGATAC
*
1037629 TTTAGAAATAAAA
1 TTTAAAAATAAAA
1037642 ACATGAATAA
Statistics
Matches: 136, Mismatches: 34, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
78 2 0.01
79 134 0.99
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (80 bp):
TTTAAAAATAAAACCGAGGTTAGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATTG
TGAAAAATTCGATAC
Found at i:1042431 original size:51 final size:51
Alignment explanation
Indices: 1042296--1042438 Score: 198
Period size: 51 Copynumber: 2.8 Consensus size: 51
1042286 CTATGAAAAG
* *
1042296 TTGCTTGCATGTATCGATACATTTAAAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGCAAAT
* *
1042347 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTTATAGTGTATCGATACATCTGGGCAAAT
***
1042398 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTTAT-AGTGTATCGATACA
1042439 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.02
51 54 0.66
52 26 0.32
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGCAAAT
Found at i:1042445 original size:13 final size:13
Alignment explanation
Indices: 1042427--1042451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042417 CAAAGATCAG
1042427 TGTATCGATACAA
1 TGTATCGATACAA
1042440 TGTATCGATACA
1 TGTATCGATACA
1042452 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1042533 original size:13 final size:13
Alignment explanation
Indices: 1042515--1042539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042505 CAAAAAAATA
1042515 TGTATCGATACAT
1 TGTATCGATACAT
1042528 TGTATCGATACA
1 TGTATCGATACA
1042540 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.