Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007932.1 Hibiscus syriacus cultivar Beakdansim tig00110342_pilon, whole genome shotgun sequence
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: 1116633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:893603 original size:35 final size:35
Alignment explanation
Indices: 893557--893631 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
893547 CGTCACGAAC
*
893557 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
893592 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
893627 AGTAA
1 AGTAA
893632 TCTTCCTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:893736 original size:24 final size:24
Alignment explanation
Indices: 893709--893799 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
893699 CATAATTCAA
* *
893709 GTCAAGTATTATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
893733 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
893757 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
893780 GTCAGGTATCATGA-CAGAAT
1 GTCAAGTATCA-GATCAGAAT
893800 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 21 0.36
24 35 0.60
25 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:893769 original size:23 final size:24
Alignment explanation
Indices: 893721--893783 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 24
893711 CAAGTATTAT
*
893721 ATCAGAATCCAGGTCATGTATCAG
1 ATCAGAATCCAGGTCATATATCAG
*
893745 ATCAGAATCCATGTCA-ATATCAG
1 ATCAGAATCCAGGTCATATATCAG
893768 ATCAGAATCCAGGTCA
1 ATCAGAATCCAGGTCA
893784 GGTATCATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAGAATCCAGGTCATATATCAG
Found at i:896288 original size:15 final size:15
Alignment explanation
Indices: 896268--896309 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
896258 TGGTCAACGC
896268 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
*
896283 CGGTCAACGGGTCGA
1 CGGTCAACGGGTCAA
896298 --GTCAACGGGTCA
1 CGGTCAACGGGTCA
896310 GGTCGGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
15 14 0.56
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:896319 original size:18 final size:18
Alignment explanation
Indices: 896292--896326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
896282 ACGGTCAACG
896292 GGTCGAGTCAACGGGTCA
1 GGTCGAGTCAACGGGTCA
* *
896310 GGTCGGGTCAATGGGTC
1 GGTCGAGTCAACGGGTC
896327 GGGTAAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (18 bp):
GGTCGAGTCAACGGGTCA
Found at i:896326 original size:13 final size:13
Alignment explanation
Indices: 896269--896345 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 13
896259 GGTCAACGCC
*
896269 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
896284 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
896297 AGTCAACGGGTCAGGTCG
1 GGTCAAC--G---GGTCG
*
896315 GGTCAATGGGTCG
1 GGTCAACGGGTCG
*
896328 GGTAAACGGGTCG
1 GGTCAACGGGTCG
896341 GGTCA
1 GGTCA
896346 GGTTGGGTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
13 26 0.52
15 13 0.26
16 1 0.02
18 10 0.20
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:896326 original size:31 final size:31
Alignment explanation
Indices: 896284--896344 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
896274 ACGGGTCAAC
*
896284 GGTCAACGGGTCGAGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCAGGTCG
* * *
896315 GGTCAATGGGTCGGGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGAGTAAACGGGTCAGGTC
896345 AGGTTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTAAACGGGTCAGGTCG
Found at i:896760 original size:33 final size:34
Alignment explanation
Indices: 896712--896779 Score: 129
Period size: 33 Copynumber: 2.0 Consensus size: 34
896702 AACTAAATGA
896712 GTTATTACCGACGATACTTCCGACTGAAATTCAC
1 GTTATTACCGACGATACTTCCGACTGAAATTCAC
896746 GTTATTA-CGACGATACTTCCGACTGAAATTCAC
1 GTTATTACCGACGATACTTCCGACTGAAATTCAC
896779 G
1 G
896780 ACGAACGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (34 bp):
GTTATTACCGACGATACTTCCGACTGAAATTCAC
Found at i:897880 original size:24 final size:23
Alignment explanation
Indices: 897843--897892 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
897833 ATCCTCGTGA
*
897843 CACATTTTTCTCTGCTTTTGTGG
1 CACATTTTTCTCTGCTCTTGTGG
*
897866 CACATTTTTTTTCTGCTCTTGTGG
1 CACA-TTTTTCTCTGCTCTTGTGG
897890 CAC
1 CAC
897893 GTTCCTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.10, C:0.24, G:0.16, T:0.50
Consensus pattern (23 bp):
CACATTTTTCTCTGCTCTTGTGG
Found at i:900678 original size:22 final size:21
Alignment explanation
Indices: 900641--900682 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
900631 AAACAACCGA
*
900641 AAAACATGTCAAAAAGTATAAG
1 AAAACATGCCAAAAAG-ATAAG
*
900663 AAAACATGCCATAAAGATAA
1 AAAACATGCCAAAAAGATAA
900683 ATTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAACATGCCAAAAAGATAAG
Found at i:906289 original size:2 final size:2
Alignment explanation
Indices: 906282--906311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
906272 TCAAATTGGA
906282 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
906312 TTCTTGTCTT
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:910024 original size:37 final size:37
Alignment explanation
Indices: 909951--910024 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
909941 ATATATTTTA
*
909951 AATTTTGTAAAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
* * *
909988 AATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
910025 GTAATATTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
Found at i:913832 original size:16 final size:17
Alignment explanation
Indices: 913811--913842 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
913801 TGAGAAGAAA
913811 AATGAG-AGAAAATGAG
1 AATGAGAAGAAAATGAG
913827 AATGAGAAGAAAATGA
1 AATGAGAAGAAAATGA
913843 AAGAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (17 bp):
AATGAGAAGAAAATGAG
Found at i:919317 original size:21 final size:21
Alignment explanation
Indices: 919291--919338 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
919281 GTTTCCAGAT
919291 TCGCAACACGAACATT-GACTA
1 TCGCAACACGAAC-TTCGACTA
*
919312 TCGCAACGCGAACTTCGACTA
1 TCGCAACACGAACTTCGACTA
*
919333 TTGCAA
1 TCGCAA
919339 TGCGTTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
TCGCAACACGAACTTCGACTA
Found at i:919455 original size:42 final size:42
Alignment explanation
Indices: 919394--919698 Score: 497
Period size: 42 Copynumber: 7.3 Consensus size: 42
919384 TTATTTCAAA
*
919394 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
919434 TTCGCATTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
919476 TTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * * *
919518 TTCACGTTGCGATTTATTCCAATTTCATTGCGATAGTGGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
919560 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
919602 TTCGCGTTGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
919644 TTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
919686 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
919699 AGTTGAAGTA
Statistics
Matches: 243, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 10 0.04
42 233 0.96
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:919848 original size:6 final size:6
Alignment explanation
Indices: 919837--919863 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
919827 GACACGTATT
919837 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
919864 CGAGACGAGA
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:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:920641 original size:19 final size:19
Alignment explanation
Indices: 920617--920700 Score: 98
Period size: 19 Copynumber: 4.2 Consensus size: 19
920607 TCGTTGCGAT
920617 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
920636 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
920659 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
920678 CTTT-GACTATCGCAACGAA
1 -TTTGGACTATCGCAACGAA
920697 TTTG
1 TTTG
920701 TAATAAATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 26 0.47
20 2 0.04
21 14 0.25
23 10 0.18
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:920651 original size:21 final size:19
Alignment explanation
Indices: 920617--920715 Score: 83
Period size: 19 Copynumber: 4.9 Consensus size: 19
920607 TCGTTGCGAT
*
920617 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
920636 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* *
920659 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
920678 CTTT-GACTATCGCAACGAA
1 -TTTGGAATATCGCAACGAA
*
920697 TTTGTAATAAATCGCAACG
1 TTTGGAAT--ATCGCAACG
920716 CGAACTTCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
18 3 0.05
19 28 0.42
20 2 0.03
21 23 0.35
23 10 0.15
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:920731 original size:21 final size:21
Alignment explanation
Indices: 920646--920802 Score: 114
Period size: 21 Copynumber: 7.6 Consensus size: 21
920636 TTTGGAATAA
*
920646 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
920667 ATCGCAA--CGAACTTTGACT
1 ATCGCAACGCGAACTTCGACT
* *
920686 ATCGCAA--CGAA-TTTGTAAT
1 ATCGCAACGCGAACTTCG-ACT
920705 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
** **
920728 ATCGCAAATC-AGTTTCCAGA-T
1 ATCGCAACGCGAACTT-C-GACT
*
920749 -TCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
920769 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
920790 ATCGCAATGCGAA
1 ATCGCAACGCGAA
920803 TATATAAATC
Statistics
Matches: 110, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.04
19 26 0.24
20 12 0.11
21 57 0.52
22 2 0.02
23 6 0.05
24 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:928480 original size:69 final size:71
Alignment explanation
Indices: 928345--928485 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
928335 GTGACACATG
*
928345 TCATGTTCTGGCAATTTTAAAAAAATTATTTAAAATAAAAATAAAATTATATATATATAAATAAA
1 TCATGTTCTGGCAATTTTAAAAAAATTATTTAAAATAAAAATAAAATTATATATATAAAAATAAA
928410 TAAAAC
66 TAAAAC
*
928416 TCATGTTCTGGCAATTTTAAAAAAATTATTTAAAATAAAAAT-ATA-TATATATATAAAAATAAA
1 TCATGTTCTGGCAATTTTAAAAAAATTATTTAAAATAAAAATAAAATTATATATATAAAAATAAA
928479 TAAAAC
66 TAAAAC
928485 T
1 T
928486 TTAAAAAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 24 0.35
70 2 0.03
71 42 0.62
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (71 bp):
TCATGTTCTGGCAATTTTAAAAAAATTATTTAAAATAAAAATAAAATTATATATATAAAAATAAA
TAAAAC
Found at i:928492 original size:19 final size:21
Alignment explanation
Indices: 928470--928514 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
928460 ATATATATAT
928470 AAAAATAA-AT-AAAACTTTA
1 AAAAATAACATCAAAACTTTA
*
928489 AAAAA-AACCTCAAAACTTTA
1 AAAAATAACATCAAAACTTTA
928509 AAAAAT
1 AAAAAT
928515 TCAATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAATAACATCAAAACTTTA
Found at i:934680 original size:2 final size:2
Alignment explanation
Indices: 934675--934717 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
934665 TATGTGTGTT
* *
934675 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
934717 T
1 T
934718 GTATGTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:935274 original size:13 final size:12
Alignment explanation
Indices: 935252--935324 Score: 53
Period size: 13 Copynumber: 5.9 Consensus size: 12
935242 ACGTAAAATT
935252 TAAATGAATATAA
1 TAAAT-AATATAA
935265 TAAATAAATATAA
1 TAAAT-AATATAA
935278 T-AATAAT-TAA
1 TAAATAATATAA
*
935288 TAATATTAAT-TAT
1 TAA-A-TAATATAA
*
935301 TAAATATTATAA
1 TAAATAATATAA
*
935313 TATATAAATATA
1 TAAAT-AATATA
935325 GTAATTACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
10 4 0.08
11 7 0.14
12 11 0.22
13 27 0.55
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (12 bp):
TAAATAATATAA
Found at i:935282 original size:16 final size:16
Alignment explanation
Indices: 935261--935329 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
935251 TTAAATGAAT
935261 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
935277 ATAAT-AATTAATAATA
1 ATAATAAATAAAT-ATA
* * * *
935293 TTAATTATTAAATATT
1 ATAATAAATAAATATA
*
935309 ATAATATATAAATATA
1 ATAATAAATAAATATA
*
935325 GTAAT
1 ATAAT
935330 TACAATAGAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
15 6 0.15
16 29 0.73
17 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:935305 original size:32 final size:32
Alignment explanation
Indices: 935269--935331 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
935259 ATATAATAAA
* *
935269 TAAATATAATAATA-ATTAATAATATTAATTAT
1 TAAATATAATAATATATAAAT-ATAGTAATTAT
*
935301 TAAATATTATAATATATAAATATAGTAATTA
1 TAAATATAATAATATATAAATATAGTAATTA
935332 CAATAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (32 bp):
TAAATATAATAATATATAAATATAGTAATTAT
Found at i:935625 original size:12 final size:12
Alignment explanation
Indices: 935608--935633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
935598 AATCTCTTTC
935608 ATATATTCAACG
1 ATATATTCAACG
935620 ATATATTCAACG
1 ATATATTCAACG
935632 AT
1 AT
935634 TTCATATCAT
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATATTCAACG
Found at i:938094 original size:35 final size:35
Alignment explanation
Indices: 938050--938123 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
938040 CAACCCATCA
* *
938050 GACCTGACTCAGCAGCTCA-CAAAGAGAATCCAACC
1 GACCCGACTCAACAGCTCACCAAA-AGAATCCAACC
*
938085 GACCCGACTCAACAGCTCACCAAAAGAATCCAGCC
1 GACCCGACTCAACAGCTCACCAAAAGAATCCAACC
938120 GACC
1 GACC
938124 GAATTGGAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.36, C:0.38, G:0.16, T:0.09
Consensus pattern (35 bp):
GACCCGACTCAACAGCTCACCAAAAGAATCCAACC
Found at i:939203 original size:22 final size:23
Alignment explanation
Indices: 939155--939204 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
939145 AGTATTTATG
939155 TTTTAGTCTTGTTATTATGTATTA
1 TTTTAGTCTTGTTA-TATGTATTA
*
939179 TTTTATTCTTGTTA-ATGT-TTGA
1 TTTTAGTCTTGTTATATGTATT-A
939201 TTTT
1 TTTT
939205 GGTAATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
24 13 0.54
ACGTcount: A:0.18, C:0.04, G:0.12, T:0.66
Consensus pattern (23 bp):
TTTTAGTCTTGTTATATGTATTA
Found at i:940106 original size:25 final size:25
Alignment explanation
Indices: 940064--940123 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
940054 GTCTACAAAA
940064 ATATT-TTATTATATATATATTTATT
1 ATATTATTATTATATATATATTT-TT
940089 -TATTATTATTACTA-ATATATTTTT
1 ATATTATTATTA-TATATATATTTTT
*
940113 ATTTTATTATT
1 ATATTATTATT
940124 TTTACAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 6 0.19
25 23 0.74
26 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATATTATTATTATATATATATTTTT
Found at i:941413 original size:22 final size:22
Alignment explanation
Indices: 941383--941424 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
941373 GCATTACACT
*
941383 TTATGTGAT-ATGCATTTATGTG
1 TTATATGATAATG-ATTTATGTG
941405 TTATATGATAATGATTTATG
1 TTATATGATAATGATTTATG
941425 AAACAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (22 bp):
TTATATGATAATGATTTATGTG
Found at i:942603 original size:18 final size:18
Alignment explanation
Indices: 942580--942614 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
942570 AGGGATTATC
942580 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
942598 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
942615 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:944739 original size:20 final size:19
Alignment explanation
Indices: 944710--944749 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
944700 TGATTTATGT
*
944710 ATAAGGAATAAATAAATGA
1 ATAAGGAATAAAGAAATGA
944729 ATAATGGAATAAAGAAATGA
1 ATAA-GGAATAAAGAAATGA
944749 A
1 A
944750 AGGGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (19 bp):
ATAAGGAATAAAGAAATGA
Found at i:944775 original size:13 final size:13
Alignment explanation
Indices: 944759--944784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
944749 AAGGGATTGA
944759 GTTAAAGGATCAG
1 GTTAAAGGATCAG
944772 GTTAAAGGATCAG
1 GTTAAAGGATCAG
944785 ATACGATAAA
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:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
GTTAAAGGATCAG
Found at i:946067 original size:18 final size:20
Alignment explanation
Indices: 946044--946086 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
946034 AATAAATGAA
946044 CATCGAATGCA-A-GGAGTG
1 CATCGAATGCATAGGGAGTG
946062 CATCG-ATGCATAGGGAGTG
1 CATCGAATGCATAGGGAGTG
946081 CATCGA
1 CATCGA
946087 TACACCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (20 bp):
CATCGAATGCATAGGGAGTG
Found at i:947789 original size:18 final size:19
Alignment explanation
Indices: 947740--947798 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 19
947730 TCGAGGGATT
*
947740 ATCAGTGGTCCTTCAGGAC
1 ATCAGTGGTCCTTCGGGAC
*
947759 ATATCATTGGTCCTTCGGGAC
1 --ATCAGTGGTCCTTCGGGAC
947780 AT-AGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
947798 A
1 A
947799 AATATTCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.46
19 2 0.06
21 17 0.49
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:948679 original size:33 final size:33
Alignment explanation
Indices: 948642--948704 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
948632 ATAAATCAAC
948642 GTATTTGAATCCTATTAAAACACTAAAACCAAG
1 GTATTTGAATCCTATTAAAACACTAAAACCAAG
* * *
948675 GTATTTGAGTCCTATTGAAATACTAAAACC
1 GTATTTGAATCCTATTAAAACACTAAAACC
948705 GAAGCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (33 bp):
GTATTTGAATCCTATTAAAACACTAAAACCAAG
Found at i:949017 original size:17 final size:17
Alignment explanation
Indices: 948995--949040 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
948985 ACTTATTCTT
*
948995 TTTATTTCATTTATTTA
1 TTTATTTCATTTATATA
949012 TTTATTT-ACTTTATATA
1 TTTATTTCA-TTTATATA
949029 TATT-TTTCATTT
1 T-TTATTTCATTT
949041 TCTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 21 0.84
18 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTCATTTATATA
Found at i:949068 original size:26 final size:29
Alignment explanation
Indices: 949016--949089 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
949006 TATTTATTTA
949016 TTTACTTTATATATATTTTTCATTTTCTC
1 TTTACTTTATATATATTTTTCATTTTCTC
* * *
949045 TTTATTTTA-ATAT-TTTTTTA-TTTCTT
1 TTTACTTTATATATATTTTTCATTTTCTC
949071 TTTACATTGTTATATATAT
1 TTTAC--T-TTATATATAT
949090 ATATATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
26 9 0.25
27 6 0.17
28 5 0.14
29 11 0.31
30 4 0.11
31 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTACTTTATATATATTTTTCATTTTCTC
Found at i:949129 original size:14 final size:14
Alignment explanation
Indices: 949104--949149 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
949094 ATATTTTTTC
*
949104 TTTTTTTATTAATA
1 TTTTATTATTAATA
949118 TTATTA-TATTAATA
1 TT-TTATTATTAATA
*
949132 TTTTATTATTATTA
1 TTTTATTATTAATA
949146 TTTT
1 TTTT
949150 CTCATGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATTATTAATA
Found at i:952430 original size:25 final size:25
Alignment explanation
Indices: 952396--952448 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
952386 AACATTTGTC
952396 AAAGAGCTGTAACTCTAAAAGCATT
1 AAAGAGCTGTAACTCTAAAAGCATT
* *
952421 AAAGAGCTGTAACTCTGAAAGTATT
1 AAAGAGCTGTAACTCTAAAAGCATT
952446 AAA
1 AAA
952449 AGAGTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAGAGCTGTAACTCTAAAAGCATT
Found at i:953043 original size:110 final size:110
Alignment explanation
Indices: 952847--953389 Score: 830
Period size: 110 Copynumber: 5.0 Consensus size: 110
952837 GATGGTGGTT
* * * *
952847 GCTCAACTTCACAGCGAAGGGGCGACTGACGGTCAATAAATAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
952912 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
952957 GCTCAACTTCACAGCGAAGGGGCGGCTTACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
953022 AATTTTAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
953067 GCTCAACTTCACAGCGAAGGGGCGACTGAATGT---CAAACAACATTTCAGTTTCATTCAGAATC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
953129 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
953174 GCTCAACTTCACAGCGAATGGGTGACTGACTGTCAGCAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
953239 AATTTCAACTTCACAGTGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
953284 GCTCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTCCAG-TT--TT-AGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * *
953345 AATTTCAACTTCACGGCGAAGGATATTGGCCTTGAAACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
953390 ATATTTGGAT
Statistics
Matches: 395, Mismatches: 35, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
106 45 0.11
107 102 0.26
109 2 0.01
110 246 0.62
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:953225 original size:217 final size:217
Alignment explanation
Indices: 952847--953389 Score: 817
Period size: 217 Copynumber: 2.5 Consensus size: 217
952837 GATGGTGGTT
* * * *
952847 GCTCAACTTCACAGCGAAGGGGCGACTGACGGTCAATAAATAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTC---AAACAACATTTCAGTTTCATTCAGAGTC
952912 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
63 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGG
* * *
952977 GGCGGCTTACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAGTGAA
128 GGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAA
*
953042 GGATATTGGACTCGAGACAACACAA
193 GGATATTAGACTCGAGACAACACAA
* *
953067 GCTCAACTTCACAGCGAAGGGGCGACTGAATGTCAAACAACATTTCAGTTTCATTCAGAATCAAT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAAACAACATTTCAGTTTCATTCAGAGTCAAT
* *
953132 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAATGGGT
66 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGC
* *
953197 GACTGACTGTCAGCAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGA
131 GACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGA
953262 TATTAGACTCGAGACAACACAA
196 TATTAGACTCGAGACAACACAA
*
953284 GCTCAACTTCACAGCGAAGGGGCGACTGGCTGTC-AACAAACAACTTTCCAG-TT--TT-AGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAAAC-AAC-A-TTT-CAGTTTCATTCAGAGT
* * * *
953344 CAATTTCAACTTCACGGCGAAGGATATTGGCCTTGAAACAACACAA
62 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
953390 ATATTTGGAT
Statistics
Matches: 298, Mismatches: 21, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
216 49 0.16
217 208 0.70
218 1 0.00
219 5 0.02
220 35 0.12
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (217 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAAACAACATTTCAGTTTCATTCAGAGTCAAT
TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGC
GACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGA
TATTAGACTCGAGACAACACAA
Found at i:953622 original size:84 final size:82
Alignment explanation
Indices: 953498--954094 Score: 558
Period size: 84 Copynumber: 7.2 Consensus size: 82
953488 TCGTGCCCAC
* * * * **
953498 CAAAGGCCTTCAAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCG
953563 AGAAGGGTTATCTTCTAA
66 AGAAGGGTTATCTTC-AA
* * * *
953581 CTAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTC
* * * *
953646 AAGAAGAGCTATCTGC--
65 GAGAAGGGTTATCTTCAA
* * * * * * * * *
953662 CAAAGACCATCGAATTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTC
* * *
953727 TAGAAGGGTTATCTGTGAC
65 GAGAAGGGTTATCT-TCAA
* * *
953746 CAAAAGACGTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTC
*
953811 GAGAAGGGTTATCTGCCAA
65 GAGAAGGGTTATCT-TCAA
* * *
953830 CCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 -CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTC
* *
953895 GAGAAGGGCTATCTGC--
65 GAGAAGGGTTATCTTCAA
* * * * * * * * * *
953911 CAAAGACCCTCGAGATCGATTACACTCAGCTTCGAGGGCACATCATATACGGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTC
*
953976 TAGAAGGGTTATCTGTCAA
65 GAGAAGGGTTATCT-TCAA
* * * * * * *
953995 CAAAGACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTTCAGCATAGCTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTACAGCATAACTTAAGTC
* * *
954060 AAGAAGGGCTATC-T-AC
65 GAGAAGGGTTATCTTCAA
954076 CAAAGACCTTCGAGTTCGA
1 CAAAGACCTTCGAGTTCGA
954095 TTCCATTCAG
Statistics
Matches: 422, Mismatches: 80, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
80 50 0.12
81 96 0.23
82 2 0.00
83 9 0.02
84 241 0.57
85 24 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (82 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCG
AGAAGGGTTATCTTCAA
Found at i:953810 original size:165 final size:162
Alignment explanation
Indices: 953496--954094 Score: 558
Period size: 165 Copynumber: 3.6 Consensus size: 162
953486 TATCGTGCCC
* * * * * * ** * * *
953496 ACCAAAGGCCTTCAAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGG
* * * * *
953561 CGAGAAGGGTTATCTTCTAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCA
66 CAAGAAGGGCTA---TCTGACCAAAGACCTTCGAGTTCGACTACGATCAGCTCAAAGGCATATCA
* * * *
953626 TTTGCAGCATAGCTTAAGTCAAGAAGAGCTATCTG
128 TTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG
* * * * * * *
953661 -CCAAAGACCATCGAATTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTACAGCATAGCTCAAG
* * * *
953725 GCTAGAAGGGTTATCTGTGACCAAAAGACGTTCGAGTTCGACTACGATCAGCTCCAAGGCATATC
65 GCAAGAAGGGCTATC--TGACC-AAAGACCTTCGAGTTCGACTACGATCAGCTCAAAGGCATATC
*
953790 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
127 ATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG
* * * * *
953826 CCAACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
1 ---ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCA
* * * * * * * *
953891 AGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGATCGATTAC-ACTCAGCTTCGAGGGCACAT
63 AGGCAAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACGA-TCAGC-TCAAAGGCATAT
* * * * *
953954 CATATACGGCATAACTCAAGGCTAGAAGGGTTATCTG
126 CATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG
* * *
953991 TCAACAAAGACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTTCAGCATAGCTCA
1 --ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTACAGCATAGCTCA
954056 AGGCAAGAAGGGCTATCT-ACCAAAGACCTTCGAGTTCGA
63 AGGCAAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGA
954095 TTCCATTCAG
Statistics
Matches: 357, Mismatches: 65, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
162 2 0.01
163 1 0.00
164 86 0.24
165 202 0.57
166 2 0.01
168 38 0.11
169 26 0.07
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (162 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGG
CAAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACGATCAGCTCAAAGGCATATCATTT
ACAGCATAACTTAAGTCAAGAAGGGTTATCTG
Found at i:953877 original size:249 final size:246
Alignment explanation
Indices: 953498--954094 Score: 842
Period size: 249 Copynumber: 2.4 Consensus size: 246
953488 TCGTGCCCAC
* * * * **
953498 CAAAGGCCTTCAAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCG
* *
953563 AGAAGGGTTATCTTCTAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATT
66 AGAAGGGTTATC-TC-AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
953628 TGCAGCATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGACCATCGA-ATTCGATTACACTCAGC
129 TGCAGCATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGACCATCGAGA-TCGATTACACTCAGC
* * *
953692 TTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGAC
193 TTCGAGGGCACATCATATACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAA
*
953746 CAAAAGACGTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTC
* *
953811 GAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
65 GAGAAGGGTTATCT--CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
* * *
953876 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGATCGATTACACTCAGC
128 TTGCAGCATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGACCATCGAGATCGATTACACTCAGC
**
953941 TTCGAGGGCACATCATATACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA
193 TTCGAGGGCACATCATATACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAA
* * * * * * *
953995 CAAAGACCTTCGAGTTCGACT-CCACTCAGCTCAAAGGCACCATCATTTTCAGCATAGCTCAAGG
1 CAAAGACCTTCGAGTTCGACTACGA-TCAGCTCCAAGGCA-TATCATTTACAGCATAACTTAAGT
* *
954059 CAAGAAGGGCTATCT--ACCAAAGACCTTCGAGTTCGA
64 CGAGAAGGGTTATCTCAACCAAAGACCTTCGAGTTCGA
954095 TTCCATTCAG
Statistics
Matches: 313, Mismatches: 30, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
245 20 0.06
247 2 0.01
248 34 0.11
249 255 0.81
250 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (246 bp):
CAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCG
AGAAGGGTTATCTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTG
CAGCATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGACCATCGAGATCGATTACACTCAGCTTC
GAGGGCACATCATATACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAA
Found at i:954468 original size:3 final size:3
Alignment explanation
Indices: 954436--954504 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
954426 TCTACAAAAA
954436 TAT T-T TAT TA- TAT TAT ATATT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TA-T TA-T TAT TAT TAT TAT TAT TAT TAT
*
954482 TAT TA- TAT TTT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
954505 TTTGTAGGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 8 0.14
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:954596 original size:33 final size:33
Alignment explanation
Indices: 954554--954624 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
954544 TTCAAAAAAT
*
954554 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAATCCTATTGAAACACTA
954587 AAACCAACGTATTTGAATCCTATTGAAACACTA
1 AAACCAACGTATTTGAATCCTATTGAAACACTA
954620 AAACC
1 AAACC
954625 GAAGCATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (33 bp):
AAACCAACGTATTTGAATCCTATTGAAACACTA
Found at i:954933 original size:17 final size:19
Alignment explanation
Indices: 954911--954957 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
954901 TTTGACTTTT
954911 TTTATTTCATTTAT-T-TA
1 TTTATTTCATTTATATATA
954928 TTTATTT-ACTTTATATATA
1 TTTATTTCA-TTTATATATA
954947 TTT-TTTCATTT
1 TTTATTTCATTT
954958 TCTCCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 7 0.27
19 6 0.23
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTCATTTATATATA
Found at i:955038 original size:14 final size:14
Alignment explanation
Indices: 955021--955068 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
955011 TAATTATTTT
955021 TCTTTTTTTATTAA
1 TCTTTTTTTATTAA
* *
955035 TCTTATTATATTAA
1 TCTTTTTTTATTAA
* *
955049 TATTTTTTTATTAT
1 TCTTTTTTTATTAA
955063 TCTTTT
1 TCTTTT
955069 CTCATGTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TCTTTTTTTATTAA
Found at i:957308 original size:18 final size:19
Alignment explanation
Indices: 957279--957317 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
957269 ATAGAGTAAG
*
957279 TTTCTCTTCTTTCTTTTTC
1 TTTCTCTTCTTTCTGTTTC
957298 TTTCT-TTCTTTCTGTTTC
1 TTTCTCTTCTTTCTGTTTC
957316 TT
1 TT
957318 GCTGTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTCTCTTCTTTCTGTTTC
Found at i:957315 original size:14 final size:14
Alignment explanation
Indices: 957279--957317 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
957269 ATAGAGTAAG
957279 TTTCTC-TTCTTTC
1 TTTCTCTTTCTTTC
*
957292 TTTTTCTTTCTTTC
1 TTTCTCTTTCTTTC
*
957306 TTTCTGTTTCTT
1 TTTCTCTTTCTT
957318 GCTGTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTCTCTTTCTTTC
Found at i:957814 original size:3 final size:3
Alignment explanation
Indices: 957780--957859 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
957770 GCTCGGTTTG
* * * * *
957780 TAA TAT TAA TAAA TAAA TAA TTA TAT TAA TAA TAA TAA TTA -AA TTA
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
957826 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
957860 TAAATAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 3 0.05
3 54 0.84
4 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:957816 original size:26 final size:23
Alignment explanation
Indices: 957780--957871 Score: 91
Period size: 23 Copynumber: 3.9 Consensus size: 23
957770 GCTCGGTTTG
*
957780 TAATATTAATAAATAAATAATTATA
1 TAATAATAAT-AAT-AATAATTATA
*
957805 TTAATAATAATAATTA-AATTATAA
1 -TAATAATAATAATAATAATTAT-A
*
957829 TAATAATAATAATAATAATAATA
1 TAATAATAATAATAATAATTATA
957852 TAATAAT-ATAAATAA-AATTA
1 TAATAATAAT-AATAATAATTA
957872 AAATGAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.10
23 33 0.57
24 7 0.12
25 3 0.05
26 9 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATAATAATAATAATAATTATA
Found at i:958127 original size:17 final size:17
Alignment explanation
Indices: 958105--958160 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
958095 TGGAATAAGC
958105 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
* *
958122 TCTTCTTCTCCTGATG-AGT
1 TCTTCTTAT--T-ATGAACT
*
958141 TCTTCTCATTATGAACT
1 TCTTCTTATTATGAACT
958158 TCT
1 TCT
958161 CTGGGAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
19 10 0.33
20 3 0.10
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:958301 original size:93 final size:92
Alignment explanation
Indices: 958121--958311 Score: 271
Period size: 93 Copynumber: 2.1 Consensus size: 92
958111 TATTATGAAC
* *
958121 TTCTTC-TTCTCCTGATGAGTTCTTCTCATTATGAACTTCTCTGGGAAAACTGACCCATCAAGTG
1 TTCTTCTTTCTCCAGATGAGTTCTTCTCATTATGAACTTCTCTGAGAAAACTGACCCATCAAGTG
*
958185 ATGGATTTGAGTAAAAATCTGAACAAA
66 ATGGATTTGAGCAAAAATCTGAACAAA
* * * *
958212 TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCT-AGAAAAGTTGATCCATCAAG
1 TTCTTCTTTCTCCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGAGAAAA-CTGACCCATCAAG
958276 TGATGGATTTGAGCAAAAAGT-TGAACAAA
64 TGATGGATTTGAGCAAAAA-TCTGAACAAA
958305 TTCTTCT
1 TTCTTCT
958312 CATTATGAAC
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
91 6 0.07
92 33 0.37
93 49 0.55
94 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (92 bp):
TTCTTCTTTCTCCAGATGAGTTCTTCTCATTATGAACTTCTCTGAGAAAACTGACCCATCAAGTG
ATGGATTTGAGCAAAAATCTGAACAAA
Found at i:958339 original size:113 final size:113
Alignment explanation
Indices: 958219--958852 Score: 1027
Period size: 113 Copynumber: 5.6 Consensus size: 113
958209 AAATTCTTCT
**** * * * *
958219 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAGAAAAGTTGATCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
*
958284 TTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
* *
958332 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
* *
958397 TTGAGGAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCATCC
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
* *
958445 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGACAAGATAATCTATCAAGTGATAGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
958510 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
958558 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
* * *
958623 TTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAATTTCTTCTTCC
66 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
* * *
958671 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATC-AGATGATGGA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG-TGATAGA
* * *
958735 TTTGAGCAAAAGGTTCAACAAATTCTTCTCATTATGAATTTCTTCTTCC
65 TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
*
958784 TTCTTCAGATGAGTTCTTCTAATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
958849 TTGA
66 TTGA
958853 ATTTTTGCTA
Statistics
Matches: 489, Mismatches: 30, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
112 2 0.00
113 485 0.99
114 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (113 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGAT
TTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
Found at i:959791 original size:84 final size:84
Alignment explanation
Indices: 959643--960245 Score: 1070
Period size: 83 Copynumber: 7.2 Consensus size: 84
959633 ATTTCTACTA
* * * *
959643 TGAGCAAATTCATCTTTTAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
959708 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
* * *
959727 TGGGCACATTCATCTTTCAGATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
959792 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
*
959811 T-AGCACATTCATTTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
*
959875 CACTTCCAGAATATGCTA-
66 CACTTCCAGAAGATGCTAT
959893 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
*
959958 CACTTCTAGAAGATGCTA-
66 CACTTCCAGAAGATGCTAT
959976 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
960041 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
*
960060 TGGGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
960125 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
*
960144 TGGGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
1 TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
960209 CACTTCCAGAAGATGCTA-
66 CACTTCCAGAAGATGCTAT
960227 TGAGCACATTCATCTTTCA
1 TGAGCACATTCATCTTTCA
960246 GCTAATGTTT
Statistics
Matches: 501, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
82 1 0.00
83 254 0.51
84 246 0.49
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (84 bp):
TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCCAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTAT
Found at i:973567 original size:14 final size:14
Alignment explanation
Indices: 973542--973582 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
973532 ACAGAGTAAG
973542 TTTCTCTTCTTTCTT
1 TTTCT-TTCTTTCTT
973557 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
*
973571 TTCTATTTCTTT
1 TT-TCTTTCTTT
973583 GCTGTGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:973573 original size:19 final size:19
Alignment explanation
Indices: 973542--973582 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
973532 ACAGAGTAAG
*
973542 TTTCTCTTCTTTCTTTTTC
1 TTTCTCTTCTTTCTATTTC
973561 TTTCT-TTCTTTTCTATTTC
1 TTTCTCTTC-TTTCTATTTC
973580 TTT
1 TTT
973583 GCTGTGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTCTTCTTTCTATTTC
Found at i:973574 original size:13 final size:15
Alignment explanation
Indices: 973542--973572 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
973532 ACAGAGTAAG
973542 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
973557 TTTCT-TTCTTTCTT
1 TTTCTCTTCTTTCTT
973571 TT
1 TT
973573 CTATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:974089 original size:3 final size:3
Alignment explanation
Indices: 974060--974130 Score: 97
Period size: 3 Copynumber: 22.7 Consensus size: 3
974050 CCGGGTTTTG
* *
974060 TAA TAT TAA TAAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
974108 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
974131 TAAATAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
3 52 0.84
4 10 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:978773 original size:22 final size:22
Alignment explanation
Indices: 978742--978802 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
978732 AGAAAAAACG
* *
978742 AAAAATGTGCCACAAAGGTAGA
1 AAAAACGTGCCACAAAGGCAGA
* *
978764 GAAAACGTGCCACAAAGGCATA
1 AAAAACGTGCCACAAAGGCAGA
978786 AATAAACGTGCCACAAA
1 AA-AAACGTGCCACAAA
978803 TGCATAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAACGTGCCACAAAGGCAGA
Found at i:978796 original size:23 final size:22
Alignment explanation
Indices: 978742--978809 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
978732 AGAAAAAACG
* * *
978742 AAAAATGTGCCACAAAGGTAGA
1 AAAAACGTGCCACAAAGGCATA
*
978764 GAAAACGTGCCACAAAGGCATA
1 AAAAACGTGCCACAAAGGCATA
*
978786 AATAAACGTGCCACAAATGCATA
1 AA-AAACGTGCCACAAAGGCATA
978809 A
1 A
978810 TTATTCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (22 bp):
AAAAACGTGCCACAAAGGCATA
Found at i:980588 original size:28 final size:28
Alignment explanation
Indices: 980548--980663 Score: 205
Period size: 28 Copynumber: 4.1 Consensus size: 28
980538 CGAGAGCATC
* *
980548 CGAGGCAATCCGAACGAGGGCATCCGAG
1 CGAGGCCATCCGAACGAGGGCAACCGAG
980576 CGAGGCCATCCGAACGAGGGCAACCGAG
1 CGAGGCCATCCGAACGAGGGCAACCGAG
980604 CGAGGCCATCCGAACGAGGGCAACCGAG
1 CGAGGCCATCCGAACGAGGGCAACCGAG
*
980632 CGAGGCCATCCGAACGAGGGTAACCGAG
1 CGAGGCCATCCGAACGAGGGCAACCGAG
980660 CGAG
1 CGAG
980664 CTATGCGAGG
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 85 1.00
ACGTcount: A:0.28, C:0.30, G:0.36, T:0.05
Consensus pattern (28 bp):
CGAGGCCATCCGAACGAGGGCAACCGAG
Found at i:980663 original size:14 final size:14
Alignment explanation
Indices: 980555--980651 Score: 122
Period size: 14 Copynumber: 6.9 Consensus size: 14
980545 ATCCGAGGCA
980555 ATCCGAACGAGGGC
1 ATCCGAACGAGGGC
* *
980569 ATCCGAGCGAGGCC
1 ATCCGAACGAGGGC
980583 ATCCGAACGAGGGC
1 ATCCGAACGAGGGC
* * *
980597 AACCGAGCGAGGCC
1 ATCCGAACGAGGGC
980611 ATCCGAACGAGGGC
1 ATCCGAACGAGGGC
* * *
980625 AACCGAGCGAGGCC
1 ATCCGAACGAGGGC
980639 ATCCGAACGAGGG
1 ATCCGAACGAGGG
980652 TAACCGAGCG
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.36, T:0.05
Consensus pattern (14 bp):
ATCCGAACGAGGGC
Found at i:981339 original size:30 final size:30
Alignment explanation
Indices: 981272--981405 Score: 198
Period size: 30 Copynumber: 4.4 Consensus size: 30
981262 TTTAGTTAAT
* * *
981272 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGTTG-AAGTTAT-ATTAAAGAA
* *
981303 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
981333 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
981363 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
981393 TAGTTTATTAGTT
1 TAGTTTATTAGTT
981406 ATTTAAGGGA
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.06
30 79 0.83
31 10 0.11
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:981341 original size:15 final size:16
Alignment explanation
Indices: 981318--981402 Score: 67
Period size: 15 Copynumber: 5.6 Consensus size: 16
981308 TATTAGTTTA
981318 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
981334 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
981348 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
981364 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
981378 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
981394 AGTT-TATTA
1 AGTTATATTA
981403 GTTATTTAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
14 10 0.19
15 29 0.55
16 14 0.26
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:981487 original size:15 final size:16
Alignment explanation
Indices: 981459--981492 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
981449 GTTTGTTACG
981459 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
981475 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
981490 TTA
1 TTA
981493 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:982754 original size:23 final size:21
Alignment explanation
Indices: 982706--982764 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
982696 GTATAATATG
*
982706 TTATTATTATTTAAATTAACT
1 TTATTATTATTTAAATCAACT
* *
982727 ATATTATTTGATTTAAATCAATT
1 TTATTA-TT-ATTTAAATCAACT
*
982750 TTATTGTTAATTTAA
1 TTATTATT-ATTTAA
982765 TTGTACAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.17
22 10 0.33
23 15 0.50
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATTATTATTTAAATCAACT
Found at i:983852 original size:26 final size:26
Alignment explanation
Indices: 983819--983939 Score: 86
Period size: 26 Copynumber: 5.0 Consensus size: 26
983809 GTATCAAATA
983819 ATTA-AAT-ATTAATAATAAATCATT
1 ATTATAATGATTAATAATAAATCATT
* *
983843 ATTAATAAT-A--ATTACTAAATCATT
1 ATT-ATAATGATTAATAATAAATCATT
*
983867 ATTA-AATCATT-AT--T--ATCATT
1 ATTATAATGATTAATAATAAATCATT
* *
983887 ATTATAATGATTATTACTAAATCATT
1 ATTATAATGATTAATAATAAATCATT
*
983913 ATTATAATGATT-ATTATCAAATCATT
1 ATTATAATGATTAATAAT-AAATCATT
983939 A
1 A
983940 CTAAATCATC
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
20 10 0.13
21 6 0.08
22 5 0.06
23 2 0.03
24 20 0.26
25 3 0.04
26 31 0.40
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATAATGATTAATAATAAATCATT
Found at i:983873 original size:35 final size:35
Alignment explanation
Indices: 983834--983988 Score: 142
Period size: 35 Copynumber: 4.4 Consensus size: 35
983824 ATATTAATAA
*
983834 TAAATCATTATTAATAATA-ATTACTAAATCATTAT
1 TAAATCATTATTAATAATATATTA-TAAATCATTAC
* *
983869 TAAATCATTATT-ATCAT-TATTATAATGATTATTAC
1 TAAATCATTATTAATAATATATTATAA--ATCATTAC
983904 TAAATCATTATT-ATAATGATTATTATCAAATCATTAC
1 TAAATCATTATTAATAAT-A-TATTAT-AAATCATTAC
* * *
983941 TAAATCATCAGTACATTAA-ATATTA-AAATCATTAT
1 TAAATCATTATTA-A-TAATATATTATAAATCATTAC
983976 TAAATCATTATTA
1 TAAATCATTATTA
983989 TCAAATCATT
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
33 3 0.03
34 8 0.08
35 54 0.54
37 22 0.22
38 7 0.07
39 3 0.03
40 3 0.03
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (35 bp):
TAAATCATTATTAATAATATATTATAAATCATTAC
Found at i:983899 original size:12 final size:12
Alignment explanation
Indices: 983884--983929 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
983874 CATTATTATC
983884 ATTATTATAATG
1 ATTATTATAATG
*
983896 ATTATTACTAAATC
1 ATTATTA-T-AATG
983910 ATTATTATAATG
1 ATTATTATAATG
983922 ATTATTAT
1 ATTATTAT
983930 CAAATCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 18 0.60
13 2 0.07
14 10 0.33
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (12 bp):
ATTATTATAATG
Found at i:984526 original size:49 final size:49
Alignment explanation
Indices: 984438--984770 Score: 479
Period size: 49 Copynumber: 6.6 Consensus size: 49
984428 AATAATTATT
* *
984438 ATAATTTCATGATTACTAAATTATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACT-AATCATTACTATCAAATCATTAAATATTAATA
984488 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
984537 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
* * * *
984586 ATAATTTCCTTATTACTATTCAATATTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
*
984635 ATAATTTCATTATTATTAATCATTACTAAATAATTACTATCAAATCATTAAATATTAATA
1 ATAATTTC------A-T--T-ATTACT-AATCATTACTATCAAATCATTAAATATTAATA
984695 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
*
984744 ATAATTTTATTATTA-TAATCATTACTA
1 ATAATTTCATTATTACTAATCATTACTA
984771 AATCATTACT
Statistics
Matches: 259, Mismatches: 13, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
48 12 0.05
49 178 0.69
50 22 0.08
51 1 0.00
53 1 0.00
54 1 0.00
56 1 0.00
58 1 0.00
59 6 0.02
60 36 0.14
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (49 bp):
ATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATATTAATA
Found at i:984671 original size:109 final size:108
Alignment explanation
Indices: 984548--984798 Score: 432
Period size: 109 Copynumber: 2.3 Consensus size: 108
984538 TAATTTCATT
* * *
984548 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCCTTATTACTATTCAATAT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCAATAC
984612 TATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATC
66 TATCAAATCATTAAATATTAATAATAATTTCATTATTA-TAATC
* *
984656 ATTACTAAATAATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCAATAC
*
984721 TATCAAATCATTAAATATTAATAATAATTTTATTATTATAATC
66 TATCAAATCATTAAATATTAATAATAATTTCATTATTATAATC
984764 ATTACTAAATCATTACTATCAAATCATTAAATATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATT
984799 GGTTGACTTA
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
108 45 0.33
109 90 0.67
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (108 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCAATAC
TATCAAATCATTAAATATTAATAATAATTTCATTATTATAATC
Found at i:989720 original size:5 final size:5
Alignment explanation
Indices: 989712--989740 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
989702 GATTAAGTTG
989712 CCATC CCATC CCATC CCATC CCATC CCAT
1 CCATC CCATC CCATC CCATC CCATC CCAT
989741 ACCACTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
CCATC
Found at i:990378 original size:14 final size:15
Alignment explanation
Indices: 990359--990397 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
990349 CGTTATTATT
*
990359 TATATTGTTATT-TA
1 TATATTATTATTGTA
990373 TATATTATTATTGTA
1 TATATTATTATTGTA
990388 T-TATTATTAT
1 TATATTATTAT
990398 AAATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
TATATTATTATTGTA
Found at i:990403 original size:26 final size:26
Alignment explanation
Indices: 990351--990408 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
990341 TTTCTTCCCG
* *
990351 TTATTATTTATATTGTTATTTATATA
1 TTATTATTTATATTATTATTTAAATA
*
990377 TTATTA-TTGTATTATTATTATAAATA
1 TTATTATTTATATTATTATT-TAAATA
990403 TTATTA
1 TTATTA
990409 ATAAATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TTATTATTTATATTATTATTTAAATA
Found at i:992676 original size:12 final size:12
Alignment explanation
Indices: 992659--992683 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
992649 TCAATTCATT
992659 TTTTATTTTTTA
1 TTTTATTTTTTA
992671 TTTTATTTTTTA
1 TTTTATTTTTTA
992683 T
1 T
992684 ATCCTTATAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:993748 original size:22 final size:22
Alignment explanation
Indices: 993702--993757 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
993692 GCATATATGC
*
993702 ATTTGCATTTTATTTGTGTTAT
1 ATTTGCATTTTATTTGTATTAT
993724 ATTTGCATTATTATATT-TATT-T
1 ATTTGCATT-TTAT-TTGTATTAT
993746 ATTTAGCATTTT
1 ATTT-GCATTTT
993758 TTTTTGCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 16 0.53
23 12 0.40
24 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.62
Consensus pattern (22 bp):
ATTTGCATTTTATTTGTATTAT
Found at i:1001980 original size:137 final size:137
Alignment explanation
Indices: 1001717--1002256 Score: 830
Period size: 137 Copynumber: 3.9 Consensus size: 137
1001707 TTGATATTTG
* * *
1001717 AGCAACATCATCCCTAGATAACCATATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCT
1 AGCAACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
* *
1001782 TTAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATTAGAACTCCTCATC
66 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
1001847 ACGAAGA
131 ACGAAGA
* * **
1001854 AGCAACATCATCATTAGATAACCAGATGTCCTCATCATGAAGGAAATGTGTTATCTCAAATATCT
1 AGCAACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
* * ** * *
1001919 TTAAAGATGGCCA-ACCGTCCTTATCACGAAGGAACAATGTCATCAATTGATCAAAATTCCTCAT
66 TTAAAGATGGCCAGA-CGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCAT
1001983 CACGAAGA
130 CACGAAGA
*
1001991 AGCATCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
1 AGCAACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
*
1002056 TTAAAGATGGCCAGACGTCCTCATCATGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
66 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
1002121 ACGAAGA
131 ACGAAGA
* * * *
1002128 AGTATCATCATCCTTAGATAACCAGATATCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
1 AGCAACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
* * ** *
1002193 TTAAAGATGGCTAGACGTCCTCATCATGAAGGAACAATGTCATCCATTGATCAGAATTCCTCAT
66 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCAT
1002257 TATAAAGGAA
Statistics
Matches: 367, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
136 1 0.00
137 365 0.99
138 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (137 bp):
AGCAACATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
ACGAAGA
Found at i:1003941 original size:2 final size:2
Alignment explanation
Indices: 1003934--1003979 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1003924 ACACATTAAG
1003934 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
1003976 AT AT
1 AT AT
1003980 GAAAATTGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1005013 original size:135 final size:135
Alignment explanation
Indices: 1004869--1005115 Score: 485
Period size: 135 Copynumber: 1.8 Consensus size: 135
1004859 ATGATTACAA
*
1004869 AAATAAATATATAATAATAATTTTTAATCTTTACATTATTTTATGTAGTAATTTTTCATCTTTTC
1 AAATAAATATATAATAATAATTTTTAATCATTACATTATTTTATGTAGTAATTTTTCATCTTTTC
1004934 AATTTCTTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAGCACAAAAATGAGAGAGAT
66 AATTTCTTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAGCACAAAAATGAGAGAGAT
1004999 GGGGG
131 GGGGG
1005004 AAATAAATATATAATAATAATTTTTAATCATTACATTATTTTATGTAGTAATTTTTCATCTTTTC
1 AAATAAATATATAATAATAATTTTTAATCATTACATTATTTTATGTAGTAATTTTTCATCTTTTC
1005069 AATTTCTTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAG
66 AATTTCTTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAG
1005116 GGCTGGCAAT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 111 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (135 bp):
AAATAAATATATAATAATAATTTTTAATCATTACATTATTTTATGTAGTAATTTTTCATCTTTTC
AATTTCTTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAGCACAAAAATGAGAGAGAT
GGGGG
Found at i:1005481 original size:16 final size:16
Alignment explanation
Indices: 1005451--1005481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1005441 TGAAACTCGA
*
1005451 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
1005467 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
1005482 AATCAAGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:1006667 original size:15 final size:15
Alignment explanation
Indices: 1006644--1006676 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1006634 AGATTACCCC
*
1006644 AAAATATTAAATGAG
1 AAAAGATTAAATGAG
1006659 AAAAGATTAAATGAG
1 AAAAGATTAAATGAG
1006674 AAA
1 AAA
1006677 CTTTGGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (15 bp):
AAAAGATTAAATGAG
Found at i:1007279 original size:22 final size:24
Alignment explanation
Indices: 1007254--1007311 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 24
1007244 AATAAAGCTT
* *
1007254 TCATCTTTGAAAATAGA-A-TCTA
1 TCATCTTTGAAAAGAGATAGGCTA
1007276 TCATCTTT--AAAGAGATAGGCTA
1 TCATCTTTGAAAAGAGATAGGCTA
1007298 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
1007312 TGTAGATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.20
21 1 0.03
22 19 0.63
24 4 0.13
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (24 bp):
TCATCTTTGAAAAGAGATAGGCTA
Found at i:1011799 original size:1 final size:1
Alignment explanation
Indices: 1011793--1011855 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
1011783 TTTTCCTTCC
* * * * * * *
1011793 TTTTTTTTCTTTTTTTCTTTTTGTTTTTTTTTTGTTTTTTGTTTTTGTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1011856 CTTCTTCTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.05, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:1011830 original size:24 final size:23
Alignment explanation
Indices: 1011793--1011858 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 23
1011783 TTTTCCTTCC
1011793 TTTTTTTTCTTTTTTTCTTTTTG
1 TTTTTTTTCTTTTTTTCTTTTTG
* *
1011816 TTTTTTTTTTGTTTTTTGTTTTTG
1 TTTTTTTTCT-TTTTTTCTTTTTG
1011840 TTTTTTTTCTTTTTTTCTT
1 TTTTTTTTCTTTTTTTCTT
1011859 CTTCTTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (23 bp):
TTTTTTTTCTTTTTTTCTTTTTG
Found at i:1016701 original size:21 final size:22
Alignment explanation
Indices: 1016675--1016715 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1016665 TTAATACCTG
1016675 AATAAAATAA-AAAAAAATATT
1 AATAAAATAATAAAAAAATATT
*
1016696 AATAAAATAATATAAAAATA
1 AATAAAATAATAAAAAAATA
1016716 ATAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AATAAAATAATAAAAAAATATT
Found at i:1018860 original size:3 final size:3
Alignment explanation
Indices: 1018852--1018896 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1018842 ATTTTTTATT
* *
1018852 TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1018897 AAAACGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1025167 original size:21 final size:21
Alignment explanation
Indices: 1025138--1025182 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1025128 GGGCATGTTA
1025138 GTTTCTGGTGGTATGCAATAT
1 GTTTCTGGTGGTATGCAATAT
*
1025159 GTTTTTGGTGGTATGCAATAT
1 GTTTCTGGTGGTATGCAATAT
1025180 GTT
1 GTT
1025183 CCTGCTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.07, G:0.29, T:0.47
Consensus pattern (21 bp):
GTTTCTGGTGGTATGCAATAT
Found at i:1035730 original size:28 final size:28
Alignment explanation
Indices: 1035697--1035752 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1035687 AACAAATGGC
*
1035697 TCCTGGACTCCAAACCAATAGCACACAA
1 TCCTGGACTCCAAACCAATAACACACAA
1035725 TCCTGGACTCCAAACCAATAACACACAA
1 TCCTGGACTCCAAACCAATAACACACAA
1035753 AACACAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (28 bp):
TCCTGGACTCCAAACCAATAACACACAA
Found at i:1040318 original size:18 final size:18
Alignment explanation
Indices: 1040297--1040349 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1040287 TAAATTAAAA
*
1040297 CAATTAAAATTAAAGAAT
1 CAATTAAAATTAAAGAAG
* *
1040315 CAA-TAAGATTTCAAGAAG
1 CAATTAA-AATTAAAGAAG
*
1040333 GAATTAAAATTAAAGAA
1 CAATTAAAATTAAAGAA
1040350 ACAAAATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (18 bp):
CAATTAAAATTAAAGAAG
Found at i:1045242 original size:20 final size:19
Alignment explanation
Indices: 1045217--1045256 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1045207 GTGTATAAGA
*
1045217 AATAAATAAAGGAAGAATGG
1 AATAAAGAAAGGAA-AATGG
*
1045237 AATAAAGAAATGAAAATGG
1 AATAAAGAAAGGAAAATGG
1045256 A
1 A
1045257 TTGAAGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (19 bp):
AATAAAGAAAGGAAAATGG
Found at i:1054330 original size:65 final size:64
Alignment explanation
Indices: 1054167--1054335 Score: 212
Period size: 65 Copynumber: 2.6 Consensus size: 64
1054157 TAAAAAGGTA
* *
1054167 TCAAATGGCATGTCTTTAGAAGTTAGGTTTGGCCATGAAATAAGTCCGGCCATTAAAGGTACAT
1 TCAAATGGTATGTCCTTAGAAGTTAGGTTTGGCCATGAAATAAGTCCGGCCATTAAAGGTACAT
* * ** * * * *
1054231 TCCGAATGGTATGTCCTTAGAAGGTAGGCCTGGCCATTAGATAAGTTCGGCCATTAAAGGTATAT
1 T-CAAATGGTATGTCCTTAGAAGTTAGGTTTGGCCATGAAATAAGTCCGGCCATTAAAGGTACAT
* *
1054296 CTCAAATGGTATGTCCCTAGAAGTTAGATTTGGCCATGAA
1 -TCAAATGGTATGTCCTTAGAAGTTAGGTTTGGCCATGAA
1054336 TTTGGTATAG
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
64 1 0.01
65 83 0.98
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (64 bp):
TCAAATGGTATGTCCTTAGAAGTTAGGTTTGGCCATGAAATAAGTCCGGCCATTAAAGGTACAT
Found at i:1065555 original size:177 final size:178
Alignment explanation
Indices: 1065258--1065613 Score: 705
Period size: 177 Copynumber: 2.0 Consensus size: 178
1065248 GTGTTAAAAT
1065258 ATGGGAAATTAAAAGTGATAGATGAATTTATTTATGGCACATAAAAGAGGAGTGGATAAGCATGC
1 ATGGGAAATTAAAAGTGATAGATGAATTTATTTATGGCACATAAAAGAGGAGTGGATAAGCATGC
1065323 TCTATCTTTACACATTTAAAGCCCTTCAAAATTGCCATTCACTCATGTCGCAGCCGTCTCTCGGT
66 TCTATCTTTACACATTTAAAGCCCTTCAAAATTGCCATTCACTCATGTCGCAGCCGTCTCTCGGT
1065388 TGAGCCCCGAATTGGGTTTCGACTTGAATGAATTGGGTTGGAGTCGCC
131 TGAGCCCCGAATTGGGTTTCGACTTGAATGAATTGGGTTGGAGTCGCC
1065436 ATGGGAAATTAAAAGTGATAGATGAATTTATTTATGGCACATAAAAGA-GAGTGGATAAGCATGC
1 ATGGGAAATTAAAAGTGATAGATGAATTTATTTATGGCACATAAAAGAGGAGTGGATAAGCATGC
1065500 TCTATCTTTACACATTTAAAGCCCTTCAAAATTGCCATTCACTCATGTCGCAGCCGTCTCTCGGT
66 TCTATCTTTACACATTTAAAGCCCTTCAAAATTGCCATTCACTCATGTCGCAGCCGTCTCTCGGT
1065565 TGAGCCCCGAATTGGGTTTCGACTTGAATGAATTGGGTTGGAGTCGCC
131 TGAGCCCCGAATTGGGTTTCGACTTGAATGAATTGGGTTGGAGTCGCC
1065613 A
1 A
1065614 CCGATCATTT
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
177 130 0.73
178 48 0.27
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (178 bp):
ATGGGAAATTAAAAGTGATAGATGAATTTATTTATGGCACATAAAAGAGGAGTGGATAAGCATGC
TCTATCTTTACACATTTAAAGCCCTTCAAAATTGCCATTCACTCATGTCGCAGCCGTCTCTCGGT
TGAGCCCCGAATTGGGTTTCGACTTGAATGAATTGGGTTGGAGTCGCC
Found at i:1065892 original size:14 final size:13
Alignment explanation
Indices: 1065873--1065904 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1065863 ATAGACATGT
1065873 TAAAAAATAATAAA
1 TAAAAAATAAT-AA
1065887 TAAAAAATAATAA
1 TAAAAAATAATAA
1065900 TAAAA
1 TAAAA
1065905 CTATCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:1065962 original size:17 final size:20
Alignment explanation
Indices: 1065932--1065971 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
1065922 TCAAATGAGG
1065932 AAAAATGTGAATAAAAG-GA
1 AAAAATGTGAATAAAAGAGA
1065951 AAAAATG-G-ATAAAAGAGA
1 AAAAATGTGAATAAAAGAGA
1065969 AAA
1 AAA
1065972 TATATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
AAAAATGTGAATAAAAGAGA
Found at i:1067333 original size:37 final size:36
Alignment explanation
Indices: 1067279--1067592 Score: 305
Period size: 36 Copynumber: 8.5 Consensus size: 36
1067269 ATTTTTTTTT
* * *
1067279 AAACTATATAATATATATGTTTAAAAAATAATTTTCA
1 AAACTATATAATATATATGTTTCAAAAAT-GTTTTAA
*
1067316 AAACTATATAATTTATAT-TTTCAAAAATTGTTTTAA
1 AAACTATATAATATATATGTTTCAAAAA-TGTTTTAA
*
1067352 AAACTTATATATTATATATAT-TTTCAAAAACGTTTTAA
1 AAAC-TATATA--ATATATATGTTTCAAAAATGTTTTAA
* **
1067390 AAATTATATAATATATATATGTTTTTTAAAATGTTTTAA
1 AAACTATAT-A-ATATATATG-TTTCAAAAATGTTTTAA
*
1067429 AAACTATATAATATATGTGTTTTC-AAAATGTTTTAA
1 AAACTATATAATATATATG-TTTCAAAAATGTTTTAA
1067465 AAACTATATACTATATATATGTTTTCAAAAATGTTTTAA
1 AAACTATATA--ATATATATG-TTTCAAAAATGTTTTAA
** * * **
1067504 AATTTATATATTATATATATTTTTAAAATGTTTTAA
1 AAACTATATAATATATATGTTTCAAAAATGTTTTAA
* *
1067540 AAACTATATATTATACATAT-TTTC-AAAATGTTTTCA
1 AAACTATATA--ATATATATGTTTCAAAAATGTTTTAA
*
1067576 AAATTATATAATATATA
1 AAACTATATAATATATA
1067593 CATATATATT
Statistics
Matches: 237, Mismatches: 28, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
34 6 0.03
36 82 0.35
37 60 0.25
38 31 0.13
39 58 0.24
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
AAACTATATAATATATATGTTTCAAAAATGTTTTAA
Found at i:1068829 original size:164 final size:162
Alignment explanation
Indices: 1068237--1069501 Score: 1343
Period size: 165 Copynumber: 7.7 Consensus size: 162
1068227 TTTGCCTCTA
* * * * * *
1068237 AGCTGAGTGTAATCGAACTCGAAGGTC-TTTAGTAGATAACCCTTCTCGACTTAAGCTATGCTGC
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGC
* * * * * * *
1068301 AAATGATGGTGGCTTTG-AGTTGAGTGTAGTAGAACTCGAAGGTCTTTGGTGACAGATAACCATT
66 AAATGAT-GTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTT
* * * * * * *
1068365 CT-ATCCTTGAGTTATGCTGTAAATGGTGTGCCCTCGA
127 CTCA-ACTTAAGCTATGCTGCAAATGATGTG-CCTTGG
* * * * * * *
1068402 AGCTAAGTGTAATCGAACTCGAAGATC-TTTGGCAGATAGCCCTTCTTGACTTAAGTTATACTGC
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGC
* * * * * **
1068466 AAATGATGTGCCTTAG-AGATGAGCGTAGTTTAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
66 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTT
* * * * * * *
1068530 CTCGACTTAAGTTATACTGAAAATGATATGCTTTAG
127 CTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* *
1068566 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTT-G-G-CAGATAACCCTTCTAGCCTTAAGTTATGC
* * * * *
1068631 CGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
63 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTC
**
1068696 TTGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
128 TCAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* * * *
1068731 AGCCGAGCGTAATCGAACTCAAAGGTCTTTGTTGGTAGATAACCCTTTTAGCCTTAAGTTATGCT
1 AGCTGAGCGTAATCGAACTCGAAGGTC-TT-TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCT
* *
1068796 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCT
64 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCT
* *
1068861 CGACTTAAGCTATGCTGCAAATGATATGCCTTGG
129 CAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* * * * *
1068895 AGCTGAGCTTAGTCAAACTCAAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGCCTTAAGTTATGC
* * * * * * * *
1068960 TGTAAGTGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGAAAATATCCCTTC
63 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTC
*
1069025 TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
128 TCAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* *
1069060 AGCCGAGCGTAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCT
1 AGCTGAGCGTAATCGAACTCGAAGGTC-TT-TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCT
* * * *
1069125 GCAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAAATAGCCCTTCT
64 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCT
* * *
1069190 CAACTTAAGTTATGTTGCAAATGATGTACCTTGG
129 CAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* * * * * *
1069224 AGCTGAGCATAGTCAAACTCGAAGATCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGT
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGCCTTAAGTTATGC
* * * * * *
1069289 TGTAAATTATGTGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGGCAGTTAGCCCTTC
63 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTC
* ** *
1069354 TCAACTTAAGCTATGTTGCAAATGATGCACCTTAG
128 TCAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* * * *
1069389 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTGAGTTATGCT
1 AGCTGAGCGTAATCGAACTCGAAGGTC-TT-TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCT
* *
1069454 GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTT
64 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
1069502 AAAAAATGGC
Statistics
Matches: 947, Mismatches: 131, Indels: 45
0.84 0.12 0.04
Matches are distributed among these distances:
162 8 0.01
163 4 0.00
164 404 0.43
165 447 0.47
166 10 0.01
167 12 0.01
168 41 0.04
169 21 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (162 bp):
AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGC
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCA
ACTTAAGCTATGCTGCAAATGATGTGCCTTGG
Found at i:1068885 original size:329 final size:329
Alignment explanation
Indices: 1068237--1069501 Score: 1578
Period size: 329 Copynumber: 3.8 Consensus size: 329
1068227 TTTGCCTCTA
* * * * * * * *
1068237 AGCTGAGTGTAATCGAACTCGAAGGTC-TTTAG-T--AGATAACCCTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
* * * * * * * *
1068298 TGCAAATGATGGTGGCTTTG-AGTTGAGTGTAGTAGAACTCGAAGGTCTTTGGTGACAGATAACC
66 TGTAAATGAT-GTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTT-G-G-CAGATAACC
* * * * * * * * ** * *
1068362 ATTC-TATCCTTGAGTTATGCTGTAAATGGTGTGCCCTCGAAGCTAAGTGTAATCGAACTCGAAG
127 CTTCTTA-ACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCCGAGCGTAATCGAACTCAAAG
* * * * * * *
1068426 ATC--T-TTGGCAGATAGCCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTAG-AGATG
190 GTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTG
* * ** * * *
1068487 AGCGTAGTTTAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGAAA
255 AGTGTAATCGAACTCGAAGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGTTATGCTGCAA
* *
1068552 ATGATATGCTTTAG
316 ATGATATGCCTTGG
* *
1068566 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
*
1068631 CGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
66 TGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
*
1068696 TTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
131 TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
* * *
1068761 GTTGGTAGATAACCCTTTTAGCCTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
196 GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
*
1068826 ATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCC
261 ATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1068891 TTGG
326 TTGG
* *
1068895 AGCTGAGCTTAGTCAAACTCAAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
* * * *
1068960 TGTAAGTGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGAAAATATCCCTTC
66 TGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
1069025 TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
131 TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
* *
1069090 GTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGTA
196 GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
* * * * * * *
1069155 ATCGAACTCAAAGGTCTTTGGCAAATAGCCCTTCTCAACTTAAGTTATGTTGCAAATGATGTACC
261 ATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1069220 TTGG
326 TTGG
* * *
1069224 AGCTGAGCATAGTCAAACTCGAAGATCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGT
1 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
* * * * * *
1069289 TGTAAATTATGTGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGGCAGTTAGCCCTTC
66 TGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
* * ** * * * *
1069354 TCAACTTAAGCTATGTTGCAAATGATGCACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
131 TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
* * *
1069419 GTTGGCAGATAACCCTTCTCGACTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTA
196 GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
*
1069484 ATCGAACTCGAGGGTCTT
261 ATCGAACTCGAAGGTCTT
1069502 AAAAAATGGC
Statistics
Matches: 827, Mismatches: 99, Indels: 20
0.87 0.10 0.02
Matches are distributed among these distances:
329 650 0.79
330 37 0.04
331 3 0.00
332 52 0.06
333 85 0.10
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (329 bp):
AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCCTTGGCAGATAACCCTTC
TTAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCCGAGCGTAATCGAACTCAAAGGTCTTT
GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
ATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
TTGG
Found at i:1072948 original size:7 final size:7
Alignment explanation
Indices: 1072938--1072970 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1072928 TGTCTAAATG
1072938 CATGATA
1 CATGATA
*
1072945 CATGATG
1 CATGATA
1072952 CATGATA
1 CATGATA
1072959 CATGATA
1 CATGATA
1072966 CATGA
1 CATGA
1072971 AATGTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (7 bp):
CATGATA
Found at i:1072954 original size:14 final size:14
Alignment explanation
Indices: 1072935--1072970 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1072925 AAATGTCTAA
1072935 ATGCATGATACATG
1 ATGCATGATACATG
1072949 ATGCATGATACATG
1 ATGCATGATACATG
*
1072963 ATACATGA
1 ATGCATGA
1072971 AATGTTCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (14 bp):
ATGCATGATACATG
Found at i:1073874 original size:68 final size:69
Alignment explanation
Indices: 1073764--1073901 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 69
1073754 AAGAAGGAAA
1073764 TGAAATCAAAACAGCCTAGGGTTTGCAATGAGGTTTTGGGGTGGGCTCTAATTCCATGTACTCTC
1 TGAAATCAAAACAGCCTAGGGTTTGCAATGAGGTTTTGGGGTGGGCTCTAATTCCATGTACTCTC
1073829 CCGG
66 CCGG
1073833 TGAAATC-AAACAGCCTAGGGTTTGCAATGAGGTTTTGGGGTGGGCTCTAATTCCATGTACTCTC
1 TGAAATCAAAACAGCCTAGGGTTTGCAATGAGGTTTTGGGGTGGGCTCTAATTCCATGTACTCTC
1073897 CCGG
66 CCGG
1073901 T
1 T
1073902 TTAGGTTCTA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 62 0.90
69 7 0.10
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (69 bp):
TGAAATCAAAACAGCCTAGGGTTTGCAATGAGGTTTTGGGGTGGGCTCTAATTCCATGTACTCTC
CCGG
Found at i:1075588 original size:16 final size:15
Alignment explanation
Indices: 1075563--1075592 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1075553 TTGTGATGTC
1075563 GGTCGTCCCGGGATG
1 GGTCGTCCCGGGATG
1075578 GGTCAGTCCCGGGAT
1 GGTC-GTCCCGGGAT
1075593 TATCGGTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.27, G:0.43, T:0.20
Consensus pattern (15 bp):
GGTCGTCCCGGGATG
Found at i:1075773 original size:3 final size:3
Alignment explanation
Indices: 1075757--1075850 Score: 111
Period size: 3 Copynumber: 30.7 Consensus size: 3
1075747 AAAGGAAAAA
*
1075757 AAT AAGT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1075803 AAT AAT AAA AAG AAGGT AAAT AAT AAT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AA--T -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1075849 AA
1 AA
1075851 ATTTTTTTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
2 4 0.05
3 70 0.88
4 4 0.05
6 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1075872 original size:24 final size:24
Alignment explanation
Indices: 1075842--1075887 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1075832 TAATAATATA
* *
1075842 ATATAATAAATTTTTTTAAAAACT
1 ATATAATAAATATGTTTAAAAACT
*
1075866 ATATAATATATATGTTTAAAAA
1 ATATAATAAATATGTTTAAAAA
1075888 ATAATTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATAATAAATATGTTTAAAAACT
Found at i:1075972 original size:112 final size:112
Alignment explanation
Indices: 1075855--1076149 Score: 343
Period size: 112 Copynumber: 2.6 Consensus size: 112
1075845 TAATAAATTT
*
1075855 TTTTAAAAACTATATAATATATATG-TTTAAAAAATAATTTTCAA-AACTATATAAT-T-TATAT
1 TTTTAAAAATTATATAATATATATGATTTAAAAAAT-ATTTT-AAGAACTATATAATATATATAT
* *
1075916 TTTCAAAAATTGTTTTAAAAACTTATATATTATATATAT-TTTTCAAAAACG
64 TTTC-AAAA-TGTTTTAAAAAC-TATATAATATATATATGGTTTCAAAAACG
* ** * *
1075967 TTTTAAAAATTATATGATATATATGATTTTTAAAATGTTTTAAGAACTATATAATATATATGTTT
1 TTTTAAAAATTATATAATATATATGATTTAAAAAATATTTTAAGAACTATATAATATATATATTT
*
1076032 TCAAAATGTTTTAAAAACTATATAATATATATATGGTTTCAAAAATG
66 TCAAAATGTTTTAAAAACTATATAATATATATATGGTTTCAAAAACG
* ** * * * *
1076079 TTTTAAAAATTATATATTATATAT-ATTTTCAAAATGTTTTGAA-AACTAGATATTATACATATT
1 TTTTAAAAATTATATAATATATATGATTTAAAAAATATTTT-AAGAACTATATAATATATATATT
1076142 TTCAAAAT
65 TTCAAAAT
1076150 TATACATATT
Statistics
Matches: 161, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
111 56 0.35
112 84 0.52
113 13 0.08
114 8 0.05
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (112 bp):
TTTTAAAAATTATATAATATATATGATTTAAAAAATATTTTAAGAACTATATAATATATATATTT
TCAAAATGTTTTAAAAACTATATAATATATATATGGTTTCAAAAACG
Found at i:1076025 original size:75 final size:76
Alignment explanation
Indices: 1075855--1076148 Score: 290
Period size: 75 Copynumber: 4.0 Consensus size: 76
1075845 TAATAAATTT
* ** *
1075855 TTTTAAAAACTATATA--ATATATATGTTTAAAAAATAATTTTCAAAACTATATAAT-T-TATAT
1 TTTTAAAAACTATATATTATATATAT-TTTCAAAAA-CGTTTTAAAAACTATATAATATATATAT
1075916 --TTTCAAAAATTG
64 GATTTCAAAAA-TG
1075928 TTTTAAAAACTTATATATTATATATATTTTTCAAAAACGTTTTAAAAA-T-TAT-ATGATATATA
1 TTTTAAAAAC-TATATATTATATATA-TTTTCAAAAACGTTTTAAAAACTATATAAT-ATATATA
**
1075990 TGATTTTTAAAATG
63 TGATTTCAAAAATG
* * * * *
1076004 TTTTAAGAACTATATAATATATATGTTTTC-AAAATGTTTTAAAAACTATATAATATATATATGG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAACGTTTTAAAAACTATATAATATATATATGA
1076068 TTTCAAAAATG
66 TTTCAAAAATG
* * * * * *
1076079 TTTTAAAAATTATATATTATATATATTTTC-AAAATGTTTTGAAAACTAGATATTATACATAT--
1 TTTTAAAAACTATATATTATATATATTTTCAAAAACGTTTTAAAAACTATATAATATATATATGA
1076141 TTTCAAAA
66 TTTCAAAA
1076149 TTATACATAT
Statistics
Matches: 188, Mismatches: 21, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
72 2 0.01
73 35 0.19
74 14 0.07
75 101 0.54
76 28 0.15
77 8 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (76 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAACGTTTTAAAAACTATATAATATATATATGA
TTTCAAAAATG
Found at i:1076149 original size:36 final size:36
Alignment explanation
Indices: 1075855--1076149 Score: 308
Period size: 36 Copynumber: 8.0 Consensus size: 36
1075845 TAATAAATTT
* * ** *
1075855 TTTTAAAAACTATATAATATATATGTTTAAAAAATAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAAT-G
* *
1075892 TTTTCAAAACTATATA--ATTTATATTTTCAAAAATTG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAA-TG
*
1075928 TTTTAAAAACTTATATATTATATATATTTTTCAAAAACG
1 TTTTAAAAAC-TATATATTATATATA-TTTTC-AAAATG
* *
1075967 TTTTAAAAATTATATGA-TATATATGATTTTTAAAATG
1 TTTTAAAAACTATAT-ATTATATAT-ATTTTCAAAATG
* * *
1076004 TTTTAAGAACTATATAATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
*
1076040 TTTTAAAAACTATATAATATATATATGGTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATAT--TTTC-AAAATG
*
1076079 TTTTAAAAATTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
* * *
1076115 TTTTGAAAACTAGATATTATACATATTTTCAAAAT
1 TTTTAAAAACTATATATTATATATATTTTCAAAAT
1076150 TATACATATT
Statistics
Matches: 222, Mismatches: 24, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
35 8 0.04
36 85 0.38
37 51 0.23
38 20 0.09
39 48 0.22
40 10 0.05
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATG
Found at i:1076153 original size:18 final size:18
Alignment explanation
Indices: 1076130--1076167 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1076120 AAAACTAGAT
1076130 ATTATACATATTTTCAAA
1 ATTATACATATTTTCAAA
*
1076148 ATTATACATATTTTTAAA
1 ATTATACATATTTTCAAA
1076166 AT
1 AT
1076168 GTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATACATATTTTCAAA
Found at i:1076195 original size:54 final size:54
Alignment explanation
Indices: 1076094--1076203 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
1076084 AAAATTATAT
* * *
1076094 ATTATATATATTTTCAAAATGTTTTGAAAACTAGATATTATACATATTTTCAAA
1 ATTATACATATTTTCAAAATGTTTTAAAAACTAGATATCATACATATTTTCAAA
* * * *
1076148 ATTATACATATTTTTAAAATGTTTTAAAAATTATATATCATATATATTTTCAAA
1 ATTATACATATTTTCAAAATGTTTTAAAAACTAGATATCATACATATTTTCAAA
1076202 AT
1 AT
1076204 ATTTTCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (54 bp):
ATTATACATATTTTCAAAATGTTTTAAAAACTAGATATCATACATATTTTCAAA
Found at i:1076197 original size:36 final size:34
Alignment explanation
Indices: 1076155--1076227 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 34
1076145 AAAATTATAC
* *
1076155 ATATTTTTAAAATGTTTTAAAAATTATATATCATAT
1 ATATTTTCAAAATATTTTAAAAATTATATA--ATAT
*
1076191 ATATTTTCAAAATATTTTCAAAATTATATAATAT
1 ATATTTTCAAAATATTTTAAAAATTATATAATAT
1076225 ATA
1 ATA
1076228 CATATATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 7 0.21
36 27 0.79
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (34 bp):
ATATTTTCAAAATATTTTAAAAATTATATAATAT
Found at i:1077147 original size:19 final size:19
Alignment explanation
Indices: 1077098--1077149 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1077088 GCACTCAAAA
*
1077098 AATATTATTTT-ATTTTTT
1 AATATTATTTTAATATTTT
**
1077116 AATATTAAATTAATATTTT
1 AATATTATTTTAATATTTT
*
1077135 AATATCATTTTAATA
1 AATATTATTTTAATA
1077150 AAAATATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTAATATTTT
Found at i:1077172 original size:24 final size:25
Alignment explanation
Indices: 1077127--1077173 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1077117 ATATTAAATT
* * *
1077127 AATATTTTAATATCATTTTAATAAA
1 AATATTTTAATATAAATATAATAAA
1077152 AATA-TTTAATATAAATATAATA
1 AATATTTTAATATAAATATAATA
1077174 TAATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AATATTTTAATATAAATATAATAAA
Found at i:1077183 original size:11 final size:11
Alignment explanation
Indices: 1077130--1077184 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1077120 TTAAATTAAT
*
1077130 ATTTTAATATC
1 ATTTTAATATA
*
1077141 ATTTTAATAAAA
1 ATTTTAAT-ATA
1077153 ATATTTAATATA
1 AT-TTTAATATA
* *
1077165 AATATAATATA
1 ATTTTAATATA
1077176 ATTTTAATA
1 ATTTTAATA
1077185 ATACTATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 23 0.66
12 6 0.17
13 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAATATA
Found at i:1077685 original size:29 final size:30
Alignment explanation
Indices: 1077642--1077719 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
1077632 CCCATAAAAT
* *
1077642 ATAATTTATTTTACGTAAAACAGTTTT-AG
1 ATAATTCATTTTACGTAAAACAATTTTCAG
* *
1077671 GTAATTCATTTTACGTAAAATAATTTTCAG
1 ATAATTCATTTTACGTAAAACAATTTTCAG
1077701 ATAATTCATTTTACGTAAA
1 ATAATTCATTTTACGTAAA
1077720 TTATTTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
ATAATTCATTTTACGTAAAACAATTTTCAG
Found at i:1077721 original size:15 final size:15
Alignment explanation
Indices: 1077644--1077725 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 15
1077634 CATAAAATAT
*
1077644 AATTTATTTTACGTA
1 AATTCATTTTACGTA
* *
1077659 AA-ACAGTTTTAGGT-
1 AATTCA-TTTTACGTA
1077673 AATTCATTTTACGTA
1 AATTCATTTTACGTA
* *
1077688 AAATAATTTT-CAG-A
1 AATTCATTTTAC-GTA
1077702 TAATTCATTTTACGTA
1 -AATTCATTTTACGTA
1077718 AATT-ATTT
1 AATTCATTT
1077726 ATTTAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
14 16 0.31
15 33 0.65
16 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (15 bp):
AATTCATTTTACGTA
Found at i:1081464 original size:60 final size:59
Alignment explanation
Indices: 1081358--1081472 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
1081348 ATTTGACACG
* * ** * * *
1081358 ATGCCTTCAAGTTCCAGGGGAGGTATTCAACTGCGAGCTTATTCGACCTCAATGTCGAT
1 ATGCCTGCAAGTTCAAGGGGAGACATTCAACTACCAGCTTATTCGACCTAAATGTCGAT
*
1081417 ATGCCTGCAAGTTCAAGGGGAAGACATTCAACTACCAGCTTGTTCGACCTAAATGT
1 ATGCCTGCAAGTTCAAGGGG-AGACATTCAACTACCAGCTTATTCGACCTAAATGT
1081473 AGGCATCGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 18 0.38
60 29 0.62
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (59 bp):
ATGCCTGCAAGTTCAAGGGGAGACATTCAACTACCAGCTTATTCGACCTAAATGTCGAT
Found at i:1087580 original size:20 final size:20
Alignment explanation
Indices: 1087535--1087580 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1087525 GACCAACAAA
*
1087535 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
1087555 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
1087574 ATCGCAA
1 ATCGCAA
1087581 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:1087683 original size:20 final size:21
Alignment explanation
Indices: 1087658--1087709 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1087648 TTTTCTCAAT
*
1087658 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1087678 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1087699 TCGCAATGCGA
1 TCGCAATGCGA
1087710 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Done.