Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:416641 original size:21 final size:21
Alignment explanation
Indices: 416617--416657 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
416607 ACATACCACC
416617 CCAAGCGTTGGACACACCTCT
1 CCAAGCGTTGGACACACCTCT
416638 CCAAGCGTTGGACACACCTC
1 CCAAGCGTTGGACACACCTC
416658 ATCCTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.39, G:0.20, T:0.17
Consensus pattern (21 bp):
CCAAGCGTTGGACACACCTCT
Found at i:424927 original size:76 final size:75
Alignment explanation
Indices: 424835--425046 Score: 234
Period size: 76 Copynumber: 2.8 Consensus size: 75
424825 TAGAAAACGA
* * *
424835 TTTTTAAAAACATATAATATATATTTTAAAAAATGGTTTTGAAAATATATATATAATATATGGTT
1 TTTTTAAAAACATATAATATATATTTTAAAAAAT-TTTTTGAAAATGTATATATAATATATAGTT
424900 TTGAAAACAT-G
65 TTGAAAA-ATCG
* * * *
424911 TTTTTCAAAACGTATAATATA-GTTTTAAAAACATTTTTTTG-AAA-GCATATATAATATATAGT
1 TTTTTAAAAACATATAATATATATTTTAAAAA-A-TTTTTTGAAAATGTATATATAATATATAGT
*
424973 TTTTAAAAATCGG
64 TTTGAAAAATC-G
** *
424986 TTTTGGAAAACATATAATATATAGTTTTTAAAATATTTTTTGAAAATGTATATATAATATA
1 TTTTTAAAAACATATAATATATA--TTTTAAAAAATTTTTTGAAAATGTATATATAATATA
425047 GTCTGTGAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
73 2 0.02
74 22 0.19
75 31 0.27
76 32 0.28
77 5 0.04
78 21 0.19
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (75 bp):
TTTTTAAAAACATATAATATATATTTTAAAAAATTTTTTGAAAATGTATATATAATATATAGTTT
TGAAAAATCG
Found at i:425083 original size:18 final size:16
Alignment explanation
Indices: 425060--425096 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
425050 TGTGAAAACG
425060 TTTTTTTTAACATATATT
1 TTTTTTTTAA-ATA-ATT
425078 TTTTTTTTAAATAATT
1 TTTTTTTTAAATAATT
425094 TTT
1 TTT
425097 CGGAAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 3 0.16
18 10 0.53
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTTTAAATAATT
Found at i:425202 original size:29 final size:29
Alignment explanation
Indices: 425142--425211 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
425132 AGTATATACA
* * *
425142 TATTATTATTTTATTTTATTTTTTGTTTT
1 TATTATTATTTTATTTTATTATTTATTCT
*
425171 TATTTTTATTTTA-TTTACTTATTTATTCT
1 TATTATTATTTTATTTTA-TTATTTATTCT
*
425200 TATTATCATTTT
1 TATTATTATTTT
425212 TTGGTTCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (29 bp):
TATTATTATTTTATTTTATTATTTATTCT
Found at i:426459 original size:15 final size:15
Alignment explanation
Indices: 426436--426473 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
426426 AATTTGATCC
*
426436 TTTAATTTTTATCTA
1 TTTATTTTTTATCTA
*
426451 TTTATTTTTTATTTA
1 TTTATTTTTTATCTA
426466 TTTATTTT
1 TTTATTTT
426474 ATTTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTTTATCTA
Found at i:426465 original size:4 final size:4
Alignment explanation
Indices: 426443--426481 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
426433 TCCTTTAATT
*
426443 TTTA TCTA TTTA TTT- TTTA TTTA TTTA TTTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT
426482 TCTGTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:426556 original size:24 final size:24
Alignment explanation
Indices: 426519--426615 Score: 63
Period size: 24 Copynumber: 4.0 Consensus size: 24
426509 AGTATTTTTA
* *
426519 TTAACATGTGTTTTCTTTTCTATT
1 TTAACATTTTTTTTCTTTTCTATT
* *
426543 TTAACATTTTTTTTATTTTAT-TT
1 TTAACATTTTTTTTCTTTTCTATT
** * * *
426566 TTTCCTATTTTTATT-TTTTCAAAAT
1 TTAAC-ATTTTTTTTCTTTTC-TATT
*
426591 TTAACATTTTTTATTCTATTCTATT
1 TTAACATTTTTT-TTCTTTTCTATT
426616 CTATTCGTTT
Statistics
Matches: 52, Mismatches: 16, Indels: 9
0.68 0.21 0.12
Matches are distributed among these distances:
23 9 0.17
24 31 0.60
25 8 0.15
26 4 0.08
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (24 bp):
TTAACATTTTTTTTCTTTTCTATT
Found at i:428620 original size:23 final size:21
Alignment explanation
Indices: 428568--428626 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 21
428558 TATTATAATT
*
428568 TTTATGTATATTATGATTAGAG
1 TTTAT-TATATTATAATTAGAG
428590 TTCT-TTATATTATCAATATAGAG
1 TT-TATTATATTAT-AAT-TAGAG
428613 TTTATTATAATTAT
1 TTTATTAT-ATTAT
428627 TGTATATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 8 0.26
22 6 0.19
23 12 0.39
24 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTATTATATTATAATTAGAG
Found at i:433105 original size:24 final size:23
Alignment explanation
Indices: 433073--433135 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
433063 CGATTCCCCT
433073 GGGGGGAATC-AGTTCCCCTTCAAA
1 GGGGGGAATCGA-TTCCCCTTC-AA
433097 GGGGGGAATCGATTCCCCTTCAA
1 GGGGGGAATCGATTCCCCTTCAA
*
433120 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
433136 TCTATCCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 15 0.41
23 2 0.05
24 19 0.51
25 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGATTCCCCTTCAA
Found at i:436782 original size:30 final size:30
Alignment explanation
Indices: 436713--436770 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
436703 AATTTAAGGA
436713 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
436743 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
436771 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:436867 original size:8 final size:8
Alignment explanation
Indices: 436854--436961 Score: 53
Period size: 8 Copynumber: 15.0 Consensus size: 8
436844 GGTGTCAAAG
436854 TGCATCCA
1 TGCATCCA
436862 TGCATCCA
1 TGCATCCA
*
436870 TGCATCCC
1 TGCATCCA
*
436878 TGCA---G
1 TGCATCCA
436883 TGCATCCA
1 TGCATCCA
*
436891 TGCATCCC
1 TGCATCCA
436899 TGCA---A
1 TGCATCCA
436904 TGCATCCA
1 TGCATCCA
*
436912 TACAT-C-
1 TGCATCCA
*
436918 TGCA-CTAA
1 TGCATC-CA
*
436926 TGCATCGA
1 TGCATCCA
436934 TGCAT-CA
1 TGCATCCA
*
436941 TG--T-AA
1 TGCATCCA
436946 TGCATCCA
1 TGCATCCA
436954 TGCATCCA
1 TGCATCCA
436962 AACATCGAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
5 12 0.16
6 3 0.04
7 5 0.07
8 54 0.72
9 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:436886 original size:21 final size:21
Alignment explanation
Indices: 436861--436960 Score: 107
Period size: 21 Copynumber: 4.8 Consensus size: 21
436851 AAGTGCATCC
436861 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
436882 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
436903 ATGCATCCATACAT--CTGCACTA
1 ATGCATCCATGCATCCCTG--C-A
* * *
436925 ATGCATCGATGCAT-CATGTA
1 ATGCATCCATGCATCCCTGCA
436945 ATGCATCCATGCATCC
1 ATGCATCCATGCATCC
436961 AAACATCGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
19 3 0.05
20 14 0.21
21 34 0.52
22 13 0.20
23 2 0.03
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (21 bp):
ATGCATCCATGCATCCCTGCA
Found at i:436948 original size:20 final size:19
Alignment explanation
Indices: 436923--437033 Score: 65
Period size: 20 Copynumber: 5.9 Consensus size: 19
436913 ACATCTGCAC
436923 TAATGCATCGATGCATCAT
1 TAATGCATCGATGCATCAT
*
436942 GTAATGCATCCATGCATCCA-
1 -TAATGCATCGATGCAT-CAT
*
436962 -AA--CATCGAATACA--AT
1 TAATGCATCG-ATGCATCAT
*
436977 TAGTGCATCGATGCATC-T
1 TAATGCATCGATGCATCAT
* *
436995 TGCTATGCATCGATGCATCCT
1 T--AATGCATCGATGCATCAT
*
437016 TGCATGCATCGATGCATC
1 T-AATGCATCGATGCATC
437034 CTGCGATGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
14 1 0.01
16 5 0.07
17 8 0.11
18 9 0.13
20 44 0.62
21 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (19 bp):
TAATGCATCGATGCATCAT
Found at i:437034 original size:20 final size:21
Alignment explanation
Indices: 436980--437053 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 21
436970 ATACAATTAG
*
436980 TGCATCGATGCAT-CTTGCTA
1 TGCATCGATGCATCCTTGCGA
437000 TGCATCGATGCATCCTTGC-A
1 TGCATCGATGCATCCTTGCGA
437020 TGCATCGATGCATCC-TGCGA
1 TGCATCGATGCATCCTTGCGA
*
437040 TGCATCCATGCATC
1 TGCATCGATGCATC
437054 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 3 0.06
20 43 0.84
21 5 0.10
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCGA
Found at i:438486 original size:14 final size:15
Alignment explanation
Indices: 438461--438489 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
438451 TAATGATAAA
438461 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
438476 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
438490 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:440346 original size:30 final size:30
Alignment explanation
Indices: 440275--440334 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
440265 ACAATTTAAG
440275 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
440305 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
440335 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:440451 original size:21 final size:21
Alignment explanation
Indices: 440425--440524 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
440415 AAGTGCATCC
440425 ATGCATCCATGAATCCGTGCA
1 ATGCATCCATGAATCCGTGCA
* *
440446 GTGCATCCATGAATCCTTGCA
1 ATGCATCCATGAATCCGTGCA
* * **
440467 ATGCATCCATGCATCTGCACTA
1 ATGCATCCATGAATCCGTGC-A
* * * *
440489 ATGCATCGATGCAT-CATGTA
1 ATGCATCCATGAATCCGTGCA
440509 ATGCATCCATGAATCC
1 ATGCATCCATGAATCC
440525 AAACATCGAA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 13 0.21
21 34 0.56
22 14 0.23
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (21 bp):
ATGCATCCATGAATCCGTGCA
Found at i:440494 original size:22 final size:20
Alignment explanation
Indices: 440447--440519 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
440437 ATCCGTGCAG
* * *
440447 TGCATCCATGAATCCTTGCAA
1 TGCATCCATGCAT-CATGTAA
440468 TGCATCCATGCATC-TGCACTAA
1 TGCATCCATGCATCATG---TAA
*
440490 TGCATCGATGCATCATGTAA
1 TGCATCCATGCATCATGTAA
440510 TGCATCCATG
1 TGCATCCATG
440520 AATCCAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 12 0.27
22 15 0.34
23 2 0.05
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TGCATCCATGCATCATGTAA
Found at i:440512 original size:20 final size:20
Alignment explanation
Indices: 440487--440618 Score: 77
Period size: 20 Copynumber: 6.8 Consensus size: 20
440477 GCATCTGCAC
440487 TAATGCATCGATGCATCATG
1 TAATGCATCGATGCATCATG
* *
440507 TAATGCATCCATGAATCCA--
1 TAATGCATCGATGCAT-CATG
440526 -AA--CATCGAATGCA--AT-
1 TAATGCATCG-ATGCATCATG
* *
440541 TAGTGCATCGATGCATCTTG
1 TAATGCATCGATGCATCATG
*
440561 CT-ATGCATCGATGCATCTTG
1 -TAATGCATCGATGCATCATG
*
440581 CT-ATGCATCGATGCATCCTTG
1 -TAATGCATCGATGCAT-CATG
**
440602 CCATGCATCGATGCATC
1 TAATGCATCGATGCATC
440619 CATGCATCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
14 1 0.01
16 5 0.05
17 9 0.10
18 7 0.08
19 1 0.01
20 48 0.52
21 21 0.23
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (20 bp):
TAATGCATCGATGCATCATG
Found at i:440568 original size:12 final size:12
Alignment explanation
Indices: 440551--440589 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
440541 TAGTGCATCG
440551 ATGCATCTTGCT
1 ATGCATCTTGCT
440563 ATGCATC--G--
1 ATGCATCTTGCT
440571 ATGCATCTTGCT
1 ATGCATCTTGCT
440583 ATGCATC
1 ATGCATC
440590 GATGCATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (12 bp):
ATGCATCTTGCT
Found at i:442059 original size:14 final size:15
Alignment explanation
Indices: 442034--442062 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
442024 TGATGGTAAA
442034 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
442049 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
442063 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:443896 original size:30 final size:30
Alignment explanation
Indices: 443825--443884 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
443815 ACAATTTAAG
443825 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
443855 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
443885 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:443981 original size:8 final size:8
Alignment explanation
Indices: 443968--444016 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
443958 GGTGTCAAAG
443968 TGCATCCA
1 TGCATCCA
443976 TGCATCCA
1 TGCATCCA
*
443984 TGCATCCC
1 TGCATCCA
443992 TGCA---A
1 TGCATCCA
443997 TGCATCCA
1 TGCATCCA
*
444005 TGCATCCC
1 TGCATCCA
444013 TGCA
1 TGCA
444017 ATGCACCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
5 4 0.11
8 31 0.89
ACGTcount: A:0.22, C:0.39, G:0.14, T:0.24
Consensus pattern (8 bp):
TGCATCCA
Found at i:443999 original size:21 final size:21
Alignment explanation
Indices: 443975--444031 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
443965 AAGTGCATCC
443975 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
443996 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
444017 ATGCACCCATGCATC
1 ATGCATCCATGCATC
444032 TGCACTAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (21 bp):
ATGCATCCATGCATCCCTGCA
Found at i:444475 original size:14 final size:15
Alignment explanation
Indices: 444450--444478 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
444440 TGATGGTAAA
444450 GGAAGATAAAGAAAG
1 GGAAGATAAAGAAAG
444465 GGAAGAT-AAGAAAG
1 GGAAGATAAAGAAAG
444479 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (15 bp):
GGAAGATAAAGAAAG
Found at i:446338 original size:30 final size:30
Alignment explanation
Indices: 446267--446326 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
446257 ACAATTTAAG
446267 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
446297 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
446327 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:446423 original size:8 final size:8
Alignment explanation
Indices: 446410--446458 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
446400 GGTGTCAAAG
446410 TGCATCCA
1 TGCATCCA
446418 TGCATCCA
1 TGCATCCA
446426 TGCATCC-
1 TGCATCCA
446433 --C-TCCA
1 TGCATCCA
446438 GTGCATCCA
1 -TGCATCCA
*
446447 TGCATCCC
1 TGCATCCA
446455 TGCA
1 TGCA
446459 ATGCACCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
4 3 0.09
5 1 0.03
8 27 0.77
9 4 0.11
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.24
Consensus pattern (8 bp):
TGCATCCA
Found at i:446442 original size:21 final size:20
Alignment explanation
Indices: 446414--446473 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
446404 TCAAAGTGCA
446414 TCCATGCATCCATGCATCCC
1 TCCATGCATCCATGCATCCC
446434 TCCAGTGCATCCATGCATCCC
1 TCCA-TGCATCCATGCATCCC
* *
446455 TGCAATGCACCCATGCATC
1 T-CCATGCATCCATGCATC
446474 TGCACTAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 4 0.11
21 30 0.83
22 2 0.06
ACGTcount: A:0.22, C:0.42, G:0.13, T:0.23
Consensus pattern (20 bp):
TCCATGCATCCATGCATCCC
Found at i:448779 original size:30 final size:30
Alignment explanation
Indices: 448708--448767 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
448698 ACAATTTAAG
448708 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
448738 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
448768 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:448864 original size:8 final size:8
Alignment explanation
Indices: 448851--448958 Score: 53
Period size: 8 Copynumber: 15.0 Consensus size: 8
448841 GGTGTCAAAG
448851 TGCATCCA
1 TGCATCCA
448859 TGCATCCA
1 TGCATCCA
*
448867 TGCATCCG
1 TGCATCCA
*
448875 TGCA---G
1 TGCATCCA
448880 TGCATCCA
1 TGCATCCA
* *
448888 TGAATCCT
1 TGCATCCA
448896 TGCA---A
1 TGCATCCA
448901 TGCATCCA
1 TGCATCCA
448909 TGCAT-C-
1 TGCATCCA
*
448915 TGCA-CTAA
1 TGCATC-CA
*
448923 TGCATCGA
1 TGCATCCA
448931 TGCAT-CA
1 TGCATCCA
*
448938 TG--T-AA
1 TGCATCCA
448943 TGCATCCA
1 TGCATCCA
448951 TGCATCCA
1 TGCATCCA
448959 AACATCGAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 26
0.67 0.10 0.23
Matches are distributed among these distances:
5 13 0.17
6 4 0.05
7 5 0.07
8 53 0.70
9 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (8 bp):
TGCATCCA
Found at i:448884 original size:21 final size:21
Alignment explanation
Indices: 448858--448957 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
448848 AAGTGCATCC
448858 ATGCATCCATGCATCCGTGCA
1 ATGCATCCATGCATCCGTGCA
* * *
448879 GTGCATCCATGAATCCTTGCA
1 ATGCATCCATGCATCCGTGCA
* **
448900 ATGCATCCATGCATCTGCACTA
1 ATGCATCCATGCATCCGTGC-A
* * *
448922 ATGCATCGATGCAT-CATGTA
1 ATGCATCCATGCATCCGTGCA
448942 ATGCATCCATGCATCC
1 ATGCATCCATGCATCC
448958 AAACATCGAA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 14 0.23
21 33 0.54
22 14 0.23
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (21 bp):
ATGCATCCATGCATCCGTGCA
Found at i:448945 original size:20 final size:20
Alignment explanation
Indices: 448920--449051 Score: 86
Period size: 20 Copynumber: 6.8 Consensus size: 20
448910 GCATCTGCAC
448920 TAATGCATCGATGCATCATG
1 TAATGCATCGATGCATCATG
*
448940 TAATGCATCCATGCATCCA--
1 TAATGCATCGATGCAT-CATG
448959 -AA--CATCGAATGCA--AT-
1 TAATGCATCG-ATGCATCATG
* *
448974 TAGTGCATCGATGCATCTTG
1 TAATGCATCGATGCATCATG
*
448994 CT-ATGCATCGATGCATCTTG
1 -TAATGCATCGATGCATCATG
*
449014 CT-ATGCATCGATGCATCCTTG
1 -TAATGCATCGATGCAT-CATG
**
449035 CCATGCATCGATGCATC
1 TAATGCATCGATGCATC
449052 CTACGATGCA
Statistics
Matches: 94, Mismatches: 6, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.01
16 5 0.05
17 10 0.11
18 7 0.07
19 1 0.01
20 49 0.52
21 21 0.22
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (20 bp):
TAATGCATCGATGCATCATG
Found at i:449001 original size:12 final size:12
Alignment explanation
Indices: 448984--449022 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
448974 TAGTGCATCG
448984 ATGCATCTTGCT
1 ATGCATCTTGCT
448996 ATGCATC--G--
1 ATGCATCTTGCT
449004 ATGCATCTTGCT
1 ATGCATCTTGCT
449016 ATGCATC
1 ATGCATC
449023 GATGCATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (12 bp):
ATGCATCTTGCT
Found at i:449045 original size:41 final size:41
Alignment explanation
Indices: 448977--449071 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
448967 ATGCAATTAG
* * * *
448977 TGCATCGATGCAT-CTTGCTATGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
449017 TGCATCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
1 TGCATCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
*
449058 TGCATCCATGCATC
1 TGCATCGATGCATC
449072 AAGGCTGCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (41 bp):
TGCATCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
Found at i:449062 original size:20 final size:20
Alignment explanation
Indices: 448977--449071 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
448967 ATGCAATTAG
*
448977 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCCTGCTA
*
448997 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCCTGCTA
*
449017 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCC-TGCTA
* *
449038 TGCATCGATGCATCCTACGA
1 TGCATCGATGCATCCTGCTA
*
449058 TGCATCCATGCATC
1 TGCATCGATGCATC
449072 AAGGCTGCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 50 0.72
21 19 0.28
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCTA
Found at i:450505 original size:14 final size:15
Alignment explanation
Indices: 450480--450508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
450470 TGATGGTAAA
450480 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
450495 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
450509 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:452365 original size:30 final size:30
Alignment explanation
Indices: 452294--452353 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
452284 ACAATTTAAG
452294 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
452324 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
452354 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:452470 original size:21 final size:20
Alignment explanation
Indices: 452444--452542 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 20
452434 AAGTGCATCT
452444 ATGCATCCATGCATCTGTGCA
1 ATGCATCCATGCATCTGT-CA
* *
452465 GTGCATCCATGAATCCT-TGCA
1 ATGCATCCATGCAT-CTGT-CA
*
452486 ATGCATCCATGCATCAGCTCTA
1 ATGCATCCATGCATCTG-TC-A
*
452508 ATGCATCGATGCATCATGT-A
1 ATGCATCCATGCATC-TGTCA
452528 ATGCATCCATGCATC
1 ATGCATCCATGCATC
452543 CAAACATCGA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 16 0.25
21 29 0.45
22 19 0.29
23 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
ATGCATCCATGCATCTGTCA
Found at i:452531 original size:20 final size:20
Alignment explanation
Indices: 452485--452637 Score: 83
Period size: 20 Copynumber: 7.8 Consensus size: 20
452475 GAATCCTTGC
* *
452485 AATGCATCCATGCATCAGCTCT
1 AATGCATCGATGCATCA--TGT
452507 AATGCATCGATGCATCATGT
1 AATGCATCGATGCATCATGT
*
452527 AATGCATCCATGCATCCA---
1 AATGCATCGATGCAT-CATGT
452545 AA--CATCGAATGCA--AT-T
1 AATGCATCG-ATGCATCATGT
* *
452561 AGTGCATCGATGCATCTTGCT
1 AATGCATCGATGCATCATG-T
*
452582 -ATGCATCGATGCATCTTGCT
1 AATGCATCGATGCATCATG-T
* * *
452602 -ATGCACCGATGCATCCTTGC
1 AATGCATCGATGCAT-CATGT
*
452622 CATGCATCGATGCATC
1 AATGCATCGATGCATC
452638 CTACGATGCA
Statistics
Matches: 109, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.01
16 5 0.05
17 10 0.09
18 7 0.06
19 1 0.01
20 49 0.45
21 20 0.18
22 16 0.15
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (20 bp):
AATGCATCGATGCATCATGT
Found at i:452647 original size:41 final size:41
Alignment explanation
Indices: 452563--452657 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
452553 ATGCAATTAG
* * * * *
452563 TGCATCGATGCAT-CTTGCTATGCATCGATGCATCTTGCTA
1 TGCACCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
452603 TGCACCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
1 TGCACCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
452644 TGCATCC-ATGCATC
1 TGCA-CCGATGCATC
452658 AAGGCTGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 12 0.25
41 34 0.71
42 2 0.04
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCACCGATGCATCCTTGCCATGCATCGATGCATCCTACGA
Found at i:452648 original size:20 final size:20
Alignment explanation
Indices: 452563--452657 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
452553 ATGCAATTAG
*
452563 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCCTGCTA
*
452583 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCCTGCTA
* *
452603 TGCACCGATGCATCCTTGCCA
1 TGCATCGATGCATCC-TGCTA
* *
452624 TGCATCGATGCATCCTACGA
1 TGCATCGATGCATCCTGCTA
*
452644 TGCATCCATGCATC
1 TGCATCGATGCATC
452658 AAGGCTGCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 49 0.73
21 18 0.27
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCTA
Found at i:459441 original size:2 final size:2
Alignment explanation
Indices: 459434--459468 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
459424 GTTATAGAGC
459434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
459469 ACTCGTCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:460850 original size:3 final size:3
Alignment explanation
Indices: 460842--460874 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
460832 AAAAAGTGAA
460842 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
460875 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:460879 original size:3 final size:3
Alignment explanation
Indices: 460873--460908 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
460863 AATAATAATA
460873 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
460909 GAAAATTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:464734 original size:3 final size:3
Alignment explanation
Indices: 464726--464756 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
464716 AAAATATTAT
464726 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
464757 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:464761 original size:3 final size:3
Alignment explanation
Indices: 464755--464829 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
464745 AATAATAATA
464755 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
464803 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
464830 TTACAAGTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:466163 original size:23 final size:23
Alignment explanation
Indices: 466114--466163 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
466104 TTTATGTTTA
* * *
466114 TTTTTTTATTTTATGTTTTACTG
1 TTTTTTTATTTGATATTTTAATG
466137 TTTTTTTATTTGATATTTTAAT-
1 TTTTTTTATTTGATATTTTAATG
466159 TTTTT
1 TTTTT
466164 AAATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (23 bp):
TTTTTTTATTTGATATTTTAATG
Found at i:473112 original size:21 final size:21
Alignment explanation
Indices: 473083--473157 Score: 98
Period size: 21 Copynumber: 3.5 Consensus size: 21
473073 CGTGGGGGGT
*
473083 ATCGATTCCCTCAAGGAAGGA
1 ATCGGTTCCCTCAAGGAAGGA
473104 ATCGGTTCCCTCAAGGAAGGA
1 ATCGGTTCCCTCAAGGAAGGA
*
473125 ATCGGTTCCCATTCAAAGG-GGGA
1 ATCGGTTCCC--TC-AAGGAAGGA
473148 ATCGGTTCCC
1 ATCGGTTCCC
473158 CTTCAAGGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 30 0.61
23 15 0.31
24 4 0.08
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (21 bp):
ATCGGTTCCCTCAAGGAAGGA
Found at i:473168 original size:22 final size:22
Alignment explanation
Indices: 473101--473179 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
473091 CCTCAAGGAA
*
473101 GGAATCGGTT-CCC-TCAAGGAA
1 GGAATCGGTTCCCCTTCAAGG-G
*
473122 GGAATCGGTTCCCATTCAAAGGG
1 GGAATCGGTTCCCCTTC-AAGGG
473145 GGAATCGGTTCCCCTTCAAGGG
1 GGAATCGGTTCCCCTTCAAGGG
* *
473167 GGTATCGATTCCC
1 GGAATCGGTTCCC
473180 TCTGCCCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.20
22 18 0.36
23 18 0.36
24 4 0.08
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (22 bp):
GGAATCGGTTCCCCTTCAAGGG
Found at i:473180 original size:21 final size:21
Alignment explanation
Indices: 473077--473180 Score: 95
Period size: 21 Copynumber: 4.8 Consensus size: 21
473067 AGAACCCGTG
* *
473077 GGGGGTATCGATTCCC-TCAA
1 GGGGGAATCGGTTCCCTTCAA
*
473097 GGAAGGAATCGGTTCCC-TCAA
1 GG-GGGAATCGGTTCCCTTCAA
*
473118 GGAAGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCC-TTC-AA
473142 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTT-CCCTTCAA
* *
473164 GGGGGTATCGATTCCCT
1 GGGGGAATCGGTTCCCT
473181 CTGCCCTATA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.03
21 36 0.49
22 13 0.18
23 15 0.21
24 7 0.10
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTTCAA
Found at i:478329 original size:11 final size:11
Alignment explanation
Indices: 478307--478342 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
478297 GTTTGATGCC
478307 TTCTCT-TTGA
1 TTCTCTCTTGA
478317 TTCTCTCTTGA
1 TTCTCTCTTGA
478328 TTCTCTCTTGA
1 TTCTCTCTTGA
478339 TTCT
1 TTCT
478343 AGTTGCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:481667 original size:11 final size:11
Alignment explanation
Indices: 481651--481680 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
481641 AAATACTTTG
481651 TAAAATTATTT
1 TAAAATTATTT
481662 TAAAATTATTT
1 TAAAATTATTT
*
481673 TAAGATTA
1 TAAAATTA
481681 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:482718 original size:37 final size:36
Alignment explanation
Indices: 482677--482781 Score: 115
Period size: 37 Copynumber: 2.9 Consensus size: 36
482667 TAAAGACAAT
482677 TTTTCTTAAAA-AAATTTTTGTCTCGCTTGAGAAAGTC
1 TTTTC-TAAAACAAA-TTTTGTCTCGCTTGAGAAAGTC
*
482714 TTTTCTAAAACTAAATTTTGTCTCGCTTGAGAAAAT-
1 TTTTCTAAAAC-AAATTTTGTCTCGCTTGAGAAAGTC
* * **
482750 TTCTCTCAAAACAAACTTCATCTCGCTTGAGA
1 TTTTCT-AAAACAAATTTTGTCTCGCTTGAGA
482782 CATTCTCCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 27 0.45
37 30 0.50
38 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTCTAAAACAAATTTTGTCTCGCTTGAGAAAGTC
Found at i:482781 original size:36 final size:37
Alignment explanation
Indices: 482697--482781 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
482687 AAAATTTTTG
* * * **
482697 TCTCGCTTGAGAAAGTCTTTTCTAAAACTAAATTTTG
1 TCTCGCTTGAGAAAATCTTCTCTAAAACTAAACTTCA
482734 TCTCGCTTGAGAAAAT-TTCTCTCAAAAC-AAACTTCA
1 TCTCGCTTGAGAAAATCTTCTCT-AAAACTAAACTTCA
482770 TCTCGCTTGAGA
1 TCTCGCTTGAGA
482782 CATTCTCCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 22 0.52
37 20 0.48
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (37 bp):
TCTCGCTTGAGAAAATCTTCTCTAAAACTAAACTTCA
Found at i:482964 original size:74 final size:70
Alignment explanation
Indices: 482808--482949 Score: 169
Period size: 72 Copynumber: 2.0 Consensus size: 70
482798 TAAAATATTT
* * * *
482808 AAAACAAAATTGATCTCACATGAGATTGTTTTCCTAAGAACAAATTTTGCCTCGATGGAGACAAT
1 AAAACAAAATTAATCGCACATGAGATTGTTTTCCTAAAAAAAAATTTTGCCTCGATGGAGACAAT
482873 TTTCC
66 TTTCC
* * *
482878 ATTAAACAAAATTAATCGCACTTGAGATTGTTTTCTCTAAAAAGAAAATTTTGTCTC-ACTTGAG
1 A--AAACAAAATTAATCGCACATGAGATTGTTTTC-CTAAAAA-AAAATTTTGCCTCGA-TGGAG
482942 ACAATTTT
61 ACAATTTT
482950 TACTCAAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
70 1 0.02
72 29 0.48
73 7 0.12
74 23 0.38
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (70 bp):
AAAACAAAATTAATCGCACATGAGATTGTTTTCCTAAAAAAAAATTTTGCCTCGATGGAGACAAT
TTTCC
Found at i:483318 original size:66 final size:65
Alignment explanation
Indices: 482956--483527 Score: 679
Period size: 66 Copynumber: 8.6 Consensus size: 65
482946 TTTTTACTCA
* * * * * *
482956 AAACAAATTTTTTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTTAAGTCTTTTTCACT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAA-TCTTTGAA-TCTGTTTCCCT
483021 TG
64 TG
* * * *
483023 AAATAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAAAGTCTTT-AAGTTTGTTTCCC
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAA-TCTTTGAA-TCTGTTTCCC
483087 TTG
63 TTG
* * * *
483090 AAATAGAGTTTTGTCTCTCTTGAGACAGTTTCT-TTCAAA-ACAAATGTCTTTGAGTCTGTTTCC
1 AAACA-AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-AA--TCTTTGAATCTGTTTCC
483153 CTTG
62 CTTG
* *
483157 AAACAAATTTTGTCTCCCTTGAGACAGTCTCTCGTT-AAACATC-ATCTTTGAGATC-GTTTCCC
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTC-TTGAAACA-CAATCTTTGA-ATCTGTTTCCC
483219 TTG
63 TTG
* * * *
483222 AAACGAATTTAGTCTCTCTTGAGACAAGTTTCTCATGAAACATCAATCTTTGAATCGGTTTCCCT
1 AAACAAATTTTGTCTCTCTTGAGAC-AGTTTCTCTTGAAACA-CAATCTTTGAATCTGTTTCCCT
483287 TG
64 TG
* * *
483289 AAACAAATTTTTTCTCTCTTGAAACAGTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-AATCTTTGAATCTGTTTCCCTT
483354 G
65 G
* * * *
483355 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGTATGTTTCCTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-AATCTTTGAATCTGTTTCCCTT
483420 G
65 G
* *
483421 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-AATCTTTGAATCTGTTTCCCTT
483486 G
65 G
*
483487 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
483528 AAACCCTTAG
Statistics
Matches: 454, Mismatches: 36, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
65 42 0.09
66 252 0.56
67 114 0.25
68 45 0.10
69 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAATCTTTGAATCTGTTTCCCTTG
Found at i:483319 original size:36 final size:35
Alignment explanation
Indices: 483279--483529 Score: 144
Period size: 36 Copynumber: 7.5 Consensus size: 35
483269 CTTTGAATCG
*
483279 GTTTCCCTTGAAACAAATTTTTTCTCTCTTGAAACA
1 GTTTCCCTTGAAACAAA-TTTTTCTCTCTTGAGACA
* * * *
483315 GTTTCTCTTGAAACACAA-----ATCT-TTGAGTCT
1 GTTTCCCTTGAAACA-AATTTTTCTCTCTTGAGACA
*
483345 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTT-TCTCTCTTGAGACA
* * *
483381 GTTTCTCTTGAAACACAA-----ATCT-TTGAGTA-T
1 GTTTCCCTTGAAACA-AATTTTTCTCTCTTGAG-ACA
* *
483411 GTTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTT-TCTCTCTTGAGACA
* * * *
483447 GTTTCTCTTGAAACACAA-----ATCT-TTGAGTCT
1 GTTTCCCTTGAAACA-AATTTTTCTCTCTTGAGACA
*
483477 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTT-TCTCTCTTGAGACA
*
483513 GTTTCTCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
483530 ACCCTTAGAC
Statistics
Matches: 158, Mismatches: 31, Indels: 52
0.66 0.13 0.22
Matches are distributed among these distances:
29 6 0.04
30 57 0.36
31 8 0.05
35 7 0.04
36 74 0.47
37 6 0.04
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (35 bp):
GTTTCCCTTGAAACAAATTTTTCTCTCTTGAGACA
Found at i:483349 original size:30 final size:30
Alignment explanation
Indices: 483315--483491 Score: 117
Period size: 30 Copynumber: 5.5 Consensus size: 30
483305 TCTTGAAACA
483315 GTTTCTCTTGAAACACAAATCTTTGAGTCT
1 GTTTCTCTTGAAACACAAATCTTTGAGTCT
* * * *
483345 GTTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACACAA----ATCT---TTGAGTCT
*
483381 GTTTCTCTTGAAACACAAATCTTTGAGTAT
1 GTTTCTCTTGAAACACAAATCTTTGAGTCT
* * *
483411 GTTTC-CTTTGAAACA-AATTTTGTCTCCCTTGAGACA
1 GTTTCTC-TTGAAACACAA----ATCT---TTGAGTCT
483447 GTTTCTCTTGAAACACAAATCTTTGAGTCT
1 GTTTCTCTTGAAACACAAATCTTTGAGTCT
*
483477 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
483492 AATTTTGTCT
Statistics
Matches: 112, Mismatches: 17, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
29 5 0.04
30 52 0.46
33 12 0.11
36 38 0.34
37 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (30 bp):
GTTTCTCTTGAAACACAAATCTTTGAGTCT
Found at i:484688 original size:59 final size:61
Alignment explanation
Indices: 484619--484738 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 61
484609 GTATTTTACC
484619 TTTTTATTTAACAAG-TACTTTTTAGGCTTAAATAAAATGAAAAATTGCTC-TAGATCCTT
1 TTTTTATTTAACAAGTTACTTTTTAGGCTTAAATAAAATGAAAAATTGCTCTTAGATCCTT
484678 TTTTTATTTAACAAGTTACTTTTTAGGCTTAAATAAAATGAAAAATTGCTCTTAGATCCTT
1 TTTTTATTTAACAAGTTACTTTTTAGGCTTAAATAAAATGAAAAATTGCTCTTAGATCCTT
484739 GTATATTACA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 15 0.25
60 35 0.59
61 9 0.15
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (61 bp):
TTTTTATTTAACAAGTTACTTTTTAGGCTTAAATAAAATGAAAAATTGCTCTTAGATCCTT
Found at i:484946 original size:22 final size:22
Alignment explanation
Indices: 484900--484946 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
484890 GACCCTCATA
* * *
484900 TTTTATGTTTATTTTTTTATGT
1 TTTTATGTTTATTATTTGATAT
484922 TTTTATGTTTATTATTTGATAT
1 TTTTATGTTTATTATTTGATAT
484944 TTT
1 TTT
484947 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTATGTTTATTATTTGATAT
Found at i:486680 original size:32 final size:33
Alignment explanation
Indices: 486639--486704 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
486629 ATTCGAAAAA
486639 TAAATAAAAGGTAGTATCTTTTTT-CTTTTGAT
1 TAAATAAAAGGTAGTATCTTTTTTACTTTTGAT
486671 TAAATAAAAGGTAGTATCTTTTTTACTTTTGAT
1 TAAATAAAAGGTAGTATCTTTTTTACTTTTGAT
486704 T
1 T
486705 TGGTCTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (33 bp):
TAAATAAAAGGTAGTATCTTTTTTACTTTTGAT
Found at i:486843 original size:23 final size:22
Alignment explanation
Indices: 486812--486873 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
486802 CTTTTCTTTT
486812 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
486835 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
486858 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
486874 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:486870 original size:24 final size:23
Alignment explanation
Indices: 486827--486872 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
486817 ATGTAATATT
*
486827 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
486850 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
486873 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:486912 original size:9 final size:9
Alignment explanation
Indices: 486898--487055 Score: 51
Period size: 8 Copynumber: 16.9 Consensus size: 9
486888 TATATAAATA
486898 TATTATTTT
1 TATTATTTT
486907 TATTATCAGTTT
1 TATTAT---TTT
* *
486919 TATTAATTA
1 TATTATTTT
* *
486928 TATATATATA
1 TAT-TATTTT
486938 TATTTACTTTT
1 TA-TTA-TTTT
486949 TATT-TTTT
1 TATTATTTT
*
486957 TATTTTATATATA
1 TA--TTAT-T-TT
486970 TATTATTTT
1 TATTATTTT
*
486979 TACT-TTTT
1 TATTATTTT
486987 TATTA-TTT
1 TATTATTTT
486995 TATTTATTTGT
1 TA-TTATTT-T
*
487006 T-TTATTTC
1 TATTATTTT
487014 TA-TATTTT
1 TATTATTTT
* *
487022 TCTTCTTTT
1 TATTATTTT
*
487031 TCTT-TTTT
1 TATTATTTT
*
487039 TCTTTATTTT
1 T-ATTATTTT
487049 TA-TATTT
1 TATTATTT
487056 ATTTTACTTA
Statistics
Matches: 114, Mismatches: 16, Indels: 39
0.67 0.09 0.23
Matches are distributed among these distances:
8 35 0.31
9 35 0.31
10 20 0.18
11 12 0.11
12 9 0.08
13 3 0.03
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (9 bp):
TATTATTTT
Found at i:486956 original size:8 final size:8
Alignment explanation
Indices: 486945--487061 Score: 58
Period size: 9 Copynumber: 13.8 Consensus size: 8
486935 ATATATTTAC
486945 TTTTTATT
1 TTTTTATT
486953 TTTTTA-T
1 TTTTTATT
*
486960 TTTATATAT
1 TTTTTAT-T
* *
486969 ATATTATT
1 TTTTTATT
486977 TTTACTT-TT
1 TTT--TTATT
*
486986 TTATTATT
1 TTTTTATT
486994 TTATTTATT
1 TT-TTTATT
487003 TGTTTTATT
1 T-TTTTATT
* *
487012 TCTATATT
1 TTTTTATT
*
487020 TTTCTTCTT
1 TTT-TTATT
*
487029 TTTCTTTTT
1 TTT-TTATT
487038 TTCTTTATT
1 TT-TTTATT
*
487047 TTTATATT
1 TTTTTATT
487055 TATTTTA
1 T-TTTTA
487062 CTTACTATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 19
0.69 0.14 0.16
Matches are distributed among these distances:
7 8 0.10
8 25 0.30
9 45 0.55
10 4 0.05
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTATT
Found at i:486966 original size:26 final size:25
Alignment explanation
Indices: 486936--487051 Score: 73
Period size: 26 Copynumber: 4.6 Consensus size: 25
486926 TATATATATA
486936 TATATTTACTTTTTATTTTTTTATTT
1 TATATTTA-TTTTTATTTTTTTATTT
* *
486962 TATATATA-TATTATTTTTACTT-TTT
1 TATATTTATTTTTATTTTT--TTATTT
*
486987 TATTATTT-TATTTATTTGTTTTATTT
1 TA-TATTTATTTTTATTT-TTTTATTT
* *
487013 CTATATTT-TTCTTCTTTTTCTT-TTT
1 -TATATTTATTTTTATTTTT-TTATTT
*
487038 T-TCTTTATTTTTAT
1 TATATTTATTTTTAT
487052 ATTTATTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
23 4 0.06
24 15 0.21
25 12 0.17
26 35 0.50
27 4 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (25 bp):
TATATTTATTTTTATTTTTTTATTT
Found at i:486971 original size:32 final size:30
Alignment explanation
Indices: 486930--486990 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
486920 ATTAATTATA
*
486930 TATATATATATTTACTTTTTATTTTTTTATTT
1 TATATATATA-TTA-TTTTTACTTTTTTATTT
486962 TATATATATATTATTTTTACTTTTTTATT
1 TATATATATATTATTTTTACTTTTTTATT
486991 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 15 0.54
31 3 0.11
32 10 0.36
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (30 bp):
TATATATATATTATTTTTACTTTTTTATTT
Found at i:486996 original size:38 final size:36
Alignment explanation
Indices: 486869--486999 Score: 122
Period size: 38 Copynumber: 3.5 Consensus size: 36
486859 TTAGTATATA
* ** *
486869 TTTTTATTTTTTTAGATTATATATAAATATA-TTA-
1 TTTTTATTATTTTATTTTATATATATATATATTTAC
486903 TTTTTATTATCAGTTTTATTAATTATATATATATATATTTAC
1 TTTTTA-T-T-A-TTTTATT--TTATATATATATATATTTAC
* *
486945 TTTTTATTTTTTTATTTTATATATATATTATTTTTAC
1 TTTTTATTATTTTATTTTATATATATA-TATATTTAC
486982 TTTTTTATTATTTTATTT
1 -TTTTTATTATTTTATTT
487000 ATTTGTTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 16
0.78 0.07 0.16
Matches are distributed among these distances:
34 6 0.08
35 1 0.01
36 12 0.15
37 8 0.10
38 28 0.35
40 15 0.19
41 4 0.05
42 6 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (36 bp):
TTTTTATTATTTTATTTTATATATATATATATTTAC
Found at i:486997 original size:22 final size:22
Alignment explanation
Indices: 486949--486999 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
486939 ATTTACTTTT
486949 TATT-TTTTTATTTTATATATA
1 TATTATTTTTATTTTATATATA
*
486970 TATTATTTTTACTTTTTTAT-TA
1 TATTATTTTTA-TTTTATATATA
*
486992 TTTTATTT
1 TATTATTT
487000 ATTTGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTATTTTTATTTTATATATA
Found at i:490141 original size:16 final size:16
Alignment explanation
Indices: 490122--490182 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
490112 GGGCAAAAAG
*
490122 AAAAAAAGAAGAAGCA
1 AAAAAAAAAAGAAGCA
490138 AAAAAAAACAA-AAGCA
1 AAAAAAAA-AAGAAGCA
490154 AAAAAAAAAAGAA-CA
1 AAAAAAAAAAGAAGCA
490169 AAAAGAAAAAAGAA
1 AAAA-AAAAAAGAA
490183 AAAGGGACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
15 8 0.20
16 31 0.76
17 2 0.05
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAGCA
Found at i:490156 original size:13 final size:13
Alignment explanation
Indices: 490116--490185 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 13
490106 TAAAAAGGGC
490116 AAAAAG-AAAAAA
1 AAAAAGCAAAAAA
490128 AGAAGAAGCAAAAAAAA
1 A-AA-AAGC--AAAAAA
490145 ACAAAAGCAAAAAA
1 A-AAAAGCAAAAAA
490159 AAAAAGAACAAAAAGA
1 AAAAAG--CAAAAA-A
490175 AAAAAG-AAAAA
1 AAAAAGCAAAAA
490186 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
12 1 0.02
13 12 0.24
14 10 0.20
15 6 0.12
16 11 0.22
17 9 0.18
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAGCAAAAAA
Found at i:490157 original size:7 final size:7
Alignment explanation
Indices: 490116--490185 Score: 54
Period size: 7 Copynumber: 9.6 Consensus size: 7
490106 TAAAAAGGGC
490116 AAAAAGA
1 AAAAAGA
490123 AAAAA-A
1 AAAAAGA
*
490129 GAAGAAGCA
1 -AAAAAG-A
*
490138 AAAAAAA
1 AAAAAGA
*
490145 ACAAAAGC
1 A-AAAAGA
490153 AAAAA-A
1 AAAAAGA
490159 AAAAAGAA
1 AAAAAG-A
490167 CAAAAAGA
1 -AAAAAGA
490175 AAAAAGA
1 AAAAAGA
490182 AAAA
1 AAAA
490186 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 6 0.12
7 26 0.52
8 11 0.22
9 7 0.14
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:490172 original size:22 final size:21
Alignment explanation
Indices: 490116--490196 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 21
490106 TAAAAAGGGC
490116 AAAAAGAA-AAAAAGAAGAAGCAA
1 AAAAAGAACAAAAAGAA-AA--AA
490139 AAAAA-AAC-AAAAGCAAAAAA
1 AAAAAGAACAAAAAG-AAAAAA
490159 AAAAAGAACAAAAAGAAAAAA
1 AAAAAGAACAAAAAGAAAAAA
*
490180 GAAAAAGGGACAAAAAG
1 -AAAAA-GAACAAAAAG
490197 CACATGCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
20 7 0.14
21 9 0.18
22 19 0.37
23 16 0.31
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAGAACAAAAAGAAAAAA
Found at i:490186 original size:35 final size:35
Alignment explanation
Indices: 490117--490186 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
490107 AAAAAGGGCA
* *
490117 AAAAGAAAAAAAGAAGAAGCAAAAAAAAACAAAAGC
1 AAAAGAAAAAAAGAACAA-CAAAAAAAAAAAAAAGC
490153 AAAA-AAAAAAAGAACAA-AAAGAAAAAAGAAAAAG
1 AAAAGAAAAAAAGAACAACAAA-AAAAAA-AAAAAG
490187 GGACAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.10
34 6 0.20
35 17 0.57
36 4 0.13
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (35 bp):
AAAAGAAAAAAAGAACAACAAAAAAAAAAAAAAGC
Found at i:490804 original size:21 final size:21
Alignment explanation
Indices: 490778--490817 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
490768 AGCTAACCCA
490778 TCAAACC-TTTGAGCATCAATG
1 TCAAACCATTT-AGCATCAATG
490799 TCAAACCATTTAGCATCAA
1 TCAAACCATTTAGCATCAA
490818 ATGAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (21 bp):
TCAAACCATTTAGCATCAATG
Found at i:491283 original size:18 final size:18
Alignment explanation
Indices: 491246--491283 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
491236 TCAACATCAA
**
491246 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATTTGGGG
491264 ATATTGGGGCATTTGGGG
1 ATATTGGGGCATTTGGGG
491282 AT
1 AT
491284 TCAACATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.37, T:0.39
Consensus pattern (18 bp):
ATATTGGGGCATTTGGGG
Found at i:491943 original size:36 final size:36
Alignment explanation
Indices: 491835--491956 Score: 181
Period size: 37 Copynumber: 3.3 Consensus size: 36
491825 ATTGAAAACA
*
491835 TTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAA-TTTCGTCTCTCTTGAGACAG
* *
491872 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTCGTCTCTCTTGAGACAG
* *
491909 TTTCCCTTGAAATAAATTTCGTCTATCTTAAGACAG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
491945 TTTCCCTTGAAA
1 TTTCCCTTGAAA
491957 CAAAATCTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 32 0.42
37 42 0.55
38 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
Found at i:491969 original size:139 final size:133
Alignment explanation
Indices: 491753--492021 Score: 324
Period size: 139 Copynumber: 2.0 Consensus size: 133
491743 ACTAGAAGAG
* * * *
491753 TTTTGTCTTTCTTGAGACAGTTCCCTTGAAACAAATTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 TTTTGTCTCTCTTGAGACAGTTCCCTTGAAACAAATTGTCTACCTTAAGACAGTTTCCCTTGAAA
* * * * *
491818 CATAAACATTGAAAACATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAGTTTCCCTTGAA
66 CATAAACATTGAAAACATTTCCCCTAAAACAAATTTT-GTC-C-CTTGAGACAGTTACCCTTGAA
491883 ACAAAA
128 ACAAAA
* *
491889 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTCGTCTATCTTAAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAG-TTCCCTTGAAACAAA-TT-GTCTACCTTAAGACAGTTTCCCTTG
* *** *
491954 AAACA-AAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCCCTTGAGACAGTTACTCTTGA
63 AAACATAAA-CATTGAAAACATTTCCCCTAAAACAAATTTTGTCCCTTGAGACAGTTACCCTTGA
492018 AACA
127 AACA
492022 CAAAATCTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
136 40 0.35
137 15 0.13
138 8 0.07
139 50 0.44
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (133 bp):
TTTTGTCTCTCTTGAGACAGTTCCCTTGAAACAAATTGTCTACCTTAAGACAGTTTCCCTTGAAA
CATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCCCTTGAGACAGTTACCCTTGAAACA
AAA
Found at i:492025 original size:65 final size:66
Alignment explanation
Indices: 491939--492100 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 66
491929 GTCTATCTTA
*
491939 AGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAACA-AATTTTG-TCCCT
1 AGACAGTTTCTCTTGAAACACAAAATCTTTGAATTTATTT-CCCTAAAACATAATTTTGTTCCCT
492000 TG
65 TG
* * *
492002 AGACAGTTACTCTTGAAACACAAAATC-TTAAATTTATTTCCTTAAAACATAATTTTGTTTCCCT
1 AGACAGTTTCTCTTGAAACACAAAATCTTTGAATTTATTTCCCTAAAACATAATTTTG-TTCCCT
492066 TG
65 TG
* *
492068 AGAC-GTTTCTCATGAAACAACAGATATCTTTGA
1 AGACAGTTTCTCTTGAAAC-ACA-AAATCTTTGA
492101 GATCGTTTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
63 22 0.27
64 20 0.24
65 20 0.24
66 14 0.17
67 4 0.05
68 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (66 bp):
AGACAGTTTCTCTTGAAACACAAAATCTTTGAATTTATTTCCCTAAAACATAATTTTGTTCCCTT
G
Found at i:492628 original size:105 final size:103
Alignment explanation
Indices: 492439--493403 Score: 881
Period size: 105 Copynumber: 9.4 Consensus size: 103
492429 GGTTTTAGCT
* *
492439 AGAGTCAATTTCGACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
492504 CGAAGGGACGGCT-AGTTGTCAACAATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGA-TTGTCAACAA-AATTT-CCAGTTTC
* * * * * * * *
492544 AGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACCCAAGGCAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * * *
492609 TGAAGGGGCGGCTGATTGTCGAC-AAA----CAATTTT
66 CGAAGGGACGGCTGATTGTCAACAAAATTTCCAGTTTC
* * *
492642 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
492707 CGAAGGGACGACTG-TATGTCAACAATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGAT-TGTCAACAA-AATTT-CCAGTTTC
* * * * ** * *
492747 AGGGCCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAGGACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
492812 CGAA-GG--GGCTGACTGTCGAC--AA---GCAATTTC
66 CGAAGGGACGGCTGATTGTCAACAAAATTTCCAGTTTC
* *
492842 GGAGCCAATCTCAACTTCACAGCGAAGGATA-TGGACTCGAGACAACACAAGTTCAACTTCAC-A
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
492905 -GAA-GGACGGCTGGTTGTCAACAAATAATTTCCCAATTCC
66 CGAAGGGACGGCTGATTGTCAAC-AA-AATTT-CCAGTTTC
* * * * *
492944 AGAGCCGATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTC
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTC
* *
493008 ACAACGAAGGAACGGCTGGTTGTCAACGAACAACTTT-CAGTTTC
62 ACAACGAAGGGACGGCTGATTGTCAAC-AA-AA-TTTCCAGTTTC
** * * * *
493052 A-TCCGCGATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTT
1 AGAGC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTT
* * * * *
493115 CACAACGAATGGACGGTTGGTTGTCAACAAACATTTTACAAATTTC
61 CACAACGAAGGGACGGCTGATTGTCAACAAA-A-TTT-CCAGTTTC
*
493161 AGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAG--AACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
493224 CGAAGGGACGGCTGATTGTCAACAAGATTT-C-G-TTC
66 CGAAGGGACGGCTGATTGTCAACAAAATTTCCAGTTTC
* * * * *
493259 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
493324 CGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCC
66 CGAAGGGACGGCTGATTGTCAAC-AA-AATTT-CCAGTTTC
* *
493365 AGAACCAA-TTCAACTTCACAGCGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
493404 GAACAATATT
Statistics
Matches: 705, Mismatches: 112, Indels: 86
0.78 0.12 0.10
Matches are distributed among these distances:
92 5 0.01
94 37 0.05
95 33 0.05
97 1 0.00
98 120 0.17
99 3 0.00
100 41 0.06
101 3 0.00
102 47 0.07
103 3 0.00
104 47 0.07
105 168 0.24
106 44 0.06
107 10 0.01
108 90 0.13
109 48 0.07
110 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (103 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGATTGTCAACAAAATTTCCAGTTTC
Found at i:492801 original size:203 final size:204
Alignment explanation
Indices: 492452--493400 Score: 998
Period size: 203 Copynumber: 4.6 Consensus size: 204
492442 GTCAATTTCG
*
492452 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * *
492517 AGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACC
66 GGTTGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* ** * *
492582 CAAGGCAGCACAAGCTCAACTTCACAGTGAAGGGGCGGCTGATTGTCGACAAACAATT-TTGGAG
131 CAAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTCTTGGAG
492646 CCAATCTCA
196 CCAATCTCA
*
492655 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* *
492720 -GTATGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 GGT-TGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * *
492784 CCAAGACAGGACAAGCTCAACTTCACAGCGAA-GG--GGCTGACTGTCGACAAGCAATT-TCGGA
130 CCAAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTCTTGGA
492845 GCCAATCTCA
195 GCCAATCTCA
*
492855 ACTTCACAGCGAAGGATA-TGGACTCGAGACAACACAAGTTCAACTTCAC-A-GAA-GGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * * * *
492916 GGTTGTCAACAAATAATTTCCCAATTCCAGAGCCGATTTCAACTCCAC-GACGGAGGATATCGTG
66 GGTTGTCAAC-AATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG
* * * * * * *
492980 CTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACGAACAACTTT
127 -GACCCAAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAA--TT
** * * *
493045 CAGTTTCATCCGCGATTTCA
189 C--TTGGA-GC-CAATCTCA
* * * *
493065 ACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAATGGAC
1 ACTTCACAG-CGAAGGATAT--TG-AACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * * * *
493129 GGTTGGTTGTCAACAA-ACATTTTACAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATAT
62 GGCTGGTTGTCAACAATA-A-TTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* * * * *
493193 TGGACTCGAGA-A-CACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGATTTC
125 TGGACCCAAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTC
* * *
493255 GTTCAGAGTCAATTTCA
190 -TT-GGAGCCAATCTCA
* * * *
493272 ACTTCACAGCGAAGGATATT-AGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGC
1 ACTTCACAGCGAAGGATATTGA-ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
** * * * * *
493336 TGACTGTCAACAAACAATTTCCCGGTTCCAGAACCAA-TTCAACTTCACAGCGGAGGATATTGGA
65 TGGTTGTCAAC-AATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
493400 C
129 C
493401 TCGGAACAAT
Statistics
Matches: 635, Mismatches: 78, Indels: 66
0.82 0.10 0.08
Matches are distributed among these distances:
196 14 0.02
197 46 0.07
198 1 0.00
199 32 0.05
200 81 0.13
201 1 0.00
202 4 0.01
203 192 0.30
204 59 0.09
205 6 0.01
206 1 0.00
207 22 0.03
208 6 0.01
209 6 0.01
210 20 0.03
211 3 0.00
212 40 0.06
213 3 0.00
214 35 0.06
215 4 0.01
216 6 0.01
217 52 0.08
218 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (204 bp):
ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
GGTTGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
CAAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTCTTGGAG
CCAATCTCA
Found at i:493076 original size:108 final size:107
Alignment explanation
Indices: 492876--493357 Score: 466
Period size: 108 Copynumber: 4.6 Consensus size: 107
492866 AAGGATATGG
*
492876 ACTCGAGACAACACAAGTTCAACTTCAC-A-GAAGGACGGCTGGTTGTCAACAAATAATTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGACGGCTGGTTGTCAACAAACAATTT-CCA
* *
492939 ATTCCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCT
65 ATTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCC
* *
492982 ACCCGAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACGAACAACTTT-C
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGG-ACGGCTGGTTGTCAACAAACAA-TTTCC
* **
493046 AGTTTCA-TCCGCGATTTCAACTCCACGACGGAGGATATCGTGCC
64 AATTTCAGAGC-CGATTTCAACTCCACGACGGAGGATATCGTGCC
* * *
493090 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGTTGGTTGTCAACAAACATTTTACA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAA-GGACGGCTGGTTGTCAACAAACAATTT-CC
* * *
493155 AATTTCAGAGCCAATTTCAACTTCGCA-G-CGAAGGATAT--TG-G
64 AATTTCAGAGCCGATTTCAAC-TC-CACGACGGAGGATATCGTGCC
* *
493196 ACTCGAG--AACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-GATTT-C-
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAA-GGACGGCTGGTTGTCAACAAACAATTTCCA
* * * * *
493255 -GTTCAGAGTCAATTTCAACTTCAC-AGCGAAGGATAT--TAG--
65 ATTTCAGAGCCGATTTCAACTCCACGA-CGGAGGATATCGT-GCC
* * * * **
493294 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAA-GGACGGCTGGTTGTCAACAAACAATTTCC
493358 CGGTTCCAGA
Statistics
Matches: 322, Mismatches: 34, Indels: 43
0.81 0.09 0.11
Matches are distributed among these distances:
96 2 0.01
97 1 0.00
98 35 0.11
99 1 0.00
100 39 0.12
101 2 0.01
102 7 0.02
103 3 0.01
104 41 0.13
106 34 0.11
107 7 0.02
108 95 0.30
109 46 0.14
110 7 0.02
111 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (107 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGACGGCTGGTTGTCAACAAACAATTTCCAA
TTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCC
Found at i:493871 original size:34 final size:35
Alignment explanation
Indices: 493813--493906 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 35
493803 GTCAAAATAG
493813 GATTCAAACT-CTCAAAATAGGATAGAATTCTGCTAT
1 GATTC-AACTCCT-AAAATAGGATAGAATTCTGCTAT
*
493849 GATTCAACTCCTAAAA-AGGATAGAATTTTGCTAT
1 GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
* *
493883 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTCAACTCCTAAA-ATAGGAT
493907 CCACAAGCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
34 18 0.35
35 20 0.39
36 8 0.16
37 5 0.10
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
Found at i:494200 original size:23 final size:24
Alignment explanation
Indices: 494169--494214 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
494159 TTTTCTTTTT
494169 TTTTCATGTAATATT-TTTTTTACA
1 TTTTCATGT-ATATTCTTTTTTACA
*
494193 TTTT-ATGTATTTTCTTTTTTAC
1 TTTTCATGTATATTCTTTTTTAC
494215 TTAGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTCATGTATATTCTTTTTTACA
Found at i:494246 original size:24 final size:22
Alignment explanation
Indices: 494184--494248 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
494174 ATGTAATATT
* * *
494184 TTTTTTACATTTTATGTATTTTC
1 TTTTTTA-ATTATATATATTTTA
*
494207 TTTTTTACTTAGTATATATTTTTA
1 TTTTTTAATTA-TATATA-TTTTA
494231 TTTTTTAGATTATATATA
1 TTTTTTA-ATTATATATA
494249 AAATATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 17 0.50
25 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTTAATTATATATATTTTA
Found at i:494310 original size:6 final size:6
Alignment explanation
Indices: 494301--494410 Score: 57
Period size: 6 Copynumber: 17.7 Consensus size: 6
494291 TATTTACTTT
* *
494301 TTTTTA TTTTTA TTTATATA TATATTA TTTTTA CTTTTTA TTATTA -TTTTA
1 TTTTTA TTTTTA TTT-T-TA T-TTTTA TTTTTA -TTTTTA TTTTTA TTTTTA
* * * *
494352 TTTATT- TGTTTTA TTTCTATA TTTTT- TTCTTC TTTTTC TTTAT- TTTTTA
1 TTT-TTA T-TTTTA TTT-T-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
494401 TATTTA TTTT
1 TTTTTA TTTT
494411 ACTTACTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
5 12 0.15
6 43 0.52
7 17 0.21
8 9 0.11
9 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:494318 original size:28 final size:27
Alignment explanation
Indices: 494278--494375 Score: 80
Period size: 28 Copynumber: 3.7 Consensus size: 27
494268 AGTTTTATTA
* * *
494278 ATTTATATATATATATTTACTTTTTTTT
1 ATTTTTATTTATATATTTA-TTATTTTT
*
494306 ATTTTTATTTATATATATATTATTTTT
1 ATTTTTATTTATATATTTATTATTTTT
494333 ACTTTTTA-TTAT-TA-TT-TTATTTATT
1 A-TTTTTATTTATATATTTATTATTT-TT
*
494358 -TGTTTTATTTCTATATTT
1 AT-TTTTATTTATATATTT
494376 TTTTCTTCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
23 1 0.02
24 11 0.19
25 6 0.10
26 4 0.07
27 14 0.24
28 22 0.38
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (27 bp):
ATTTTTATTTATATATTTATTATTTTT
Found at i:494321 original size:34 final size:38
Alignment explanation
Indices: 494257--494356 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
494247 TAAAATATAT
* * *
494257 TTTTTATTATCAGTTTTATTAATTTATATATATATATTTAC
1 TTTTTATTATTA-TTTTATTTATATATATAT-TAT-TTTAC
*
494298 TTTTTTTTA-T-TTTTATTTATATATATATTATTTTTAC
1 TTTTTATTATTATTTTATTTATATATATATTA-TTTTAC
494335 TTTTTATTATTATTTTATTTAT
1 TTTTTATTATTATTTTATTTAT
494357 TTGTTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 15 0.29
38 18 0.35
39 10 0.20
41 8 0.16
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (38 bp):
TTTTTATTATTATTTTATTTATATATATATTATTTTAC
Found at i:494374 original size:21 final size:20
Alignment explanation
Indices: 494335--494409 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
494325 TTATTTTTAC
494335 TTTTTATTATTATTT-TAT-T
1 TTTTTATT-TTATTTCTATAT
* *
494354 TATTTGTTTTATTTCTATAT
1 TTTTTATTTTATTTCTATAT
* *
494374 TTTTT-TCTTCTTTTTCTTTAT
1 TTTTTAT-TT-TATTTCTATAT
494395 TTTTTATATTTATTT
1 TTTTTAT-TTTATTT
494410 TACTTACTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 7 0.16
21 18 0.41
22 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTATTTCTATAT
Found at i:494410 original size:22 final size:22
Alignment explanation
Indices: 494348--494438 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
494338 TTATTATTAT
*
494348 TTTATTTATTTGT-TTTA-TTTC
1 TTTATTT-TTTATCTTTATTTTC
*
494369 TATATTTTTT-TCTTCT-TTTTC
1 TTTATTTTTTATCTT-TATTTTC
*
494390 TTTATTTTTTATATTTATTTTAC
1 TTTATTTTTTATCTTTATTTT-C
* * *
494413 -TTACTATTTATCTTTGTTTTC
1 TTTATTTTTTATCTTTATTTTC
494434 TTTAT
1 TTTAT
494439 CTTATCTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.02
20 5 0.09
21 22 0.40
22 26 0.47
23 1 0.02
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTATTTTTTATCTTTATTTTC
Found at i:494515 original size:15 final size:15
Alignment explanation
Indices: 494497--494526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
494487 TATTTATTTC
*
494497 TTACCTTTTTATCTA
1 TTACATTTTTATCTA
494512 TTACATTTTTATCTA
1 TTACATTTTTATCTA
494527 ACATGGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACATTTTTATCTA
Found at i:494908 original size:2 final size:2
Alignment explanation
Indices: 494901--494926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
494891 AAGGTTTACC
494901 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
494927 GTAAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:497802 original size:12 final size:12
Alignment explanation
Indices: 497777--497883 Score: 85
Period size: 12 Copynumber: 8.9 Consensus size: 12
497767 ACGGAGATAT
* *
497777 CAGAAATCAAAA
1 CAGAATTCAGAA
497789 CAGAATTCAGAA
1 CAGAATTCAGAA
*
497801 CA-AATATCATAA
1 CAGAAT-TCAGAA
*
497813 CAGAATCCA-AA
1 CAGAATTCAGAA
*
497824 TCAGAAATCAGAA
1 -CAGAATTCAGAA
*
497837 CAGAATTCAGAT
1 CAGAATTCAGAA
* *
497849 CATAATTCATAA
1 CAGAATTCAGAA
497861 CAGAATTCA-AA
1 CAGAATTCAGAA
*
497872 TCAGAAATCAGA
1 -CAGAATTCAGA
497884 TAAAACATTC
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
11 7 0.09
12 63 0.83
13 6 0.08
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:497809 original size:24 final size:25
Alignment explanation
Indices: 497777--497881 Score: 98
Period size: 24 Copynumber: 4.4 Consensus size: 25
497767 ACGGAGATAT
*
497777 CAGAA-ATCAAAACAGAATTCAGAA
1 CAGAATATCATAACAGAATTCAGAA
*
497801 CA-AATATCATAACAGAATCCA-AA
1 CAGAATATCATAACAGAATTCAGAA
* *
497824 TCAGAA-ATCAGAACAGAATTCAGAT
1 -CAGAATATCATAACAGAATTCAGAA
*
497849 CATAAT-TCATAACAGAATTCA-AA
1 CAGAATATCATAACAGAATTCAGAA
497872 TCAGAA-ATCA
1 -CAGAATATCA
497882 GATAAAACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
23 5 0.08
24 57 0.88
25 3 0.05
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (25 bp):
CAGAATATCATAACAGAATTCAGAA
Found at i:497846 original size:48 final size:48
Alignment explanation
Indices: 497775--497883 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
497765 AAACGGAGAT
*
497775 ATCAGAAATCAAAACAGAATTCAGAACA-AATATCATAACAGAATCCAA
1 ATCAGAAATCAGAACAGAATTCAGAACATAAT-TCATAACAGAATCCAA
* *
497823 ATCAGAAATCAGAACAGAATTCAGATCATAATTCATAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGAACATAATTCATAACAGAATCCAA
497871 ATCAGAAATCAGA
1 ATCAGAAATCAGA
497884 TAAAACATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 54 0.95
49 3 0.05
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACATAATTCATAACAGAATCCAA
Found at i:516507 original size:12 final size:13
Alignment explanation
Indices: 516490--516573 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 13
516480 TAAAAAACAC
*
516490 AAAAAAGAGAGAA
1 AAAAAAGAAAGAA
516503 AAAAAAGAAAG-A
1 AAAAAAGAAAGAA
*
516515 ATAAAAGATATAGCAA
1 AAAAAAGA-A-AG-AA
* *
516531 AAAAAAGCACACAA
1 AAAAAAG-AAAGAA
516545 AAAGAAAGAAAGAA
1 AAA-AAAGAAAGAA
* *
516559 GAGAAAG-AAGAA
1 AAAAAAGAAAGAA
516571 AAA
1 AAA
516574 GAGAAAAAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
12 14 0.26
13 15 0.28
14 12 0.22
15 5 0.09
16 7 0.13
17 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.04
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:516558 original size:8 final size:9
Alignment explanation
Indices: 516545--516599 Score: 59
Period size: 8 Copynumber: 6.7 Consensus size: 9
516535 AAGCACACAA
516545 AAAGAA-AG
1 AAAGAAGAG
516553 AAAGAAGAG
1 AAAGAAGAG
516562 AAAG-A-AG
1 AAAGAAGAG
516569 AAA-AAGAG
1 AAAGAAGAG
516577 AAA-AAGAG
1 AAAGAAGAG
516585 AAATGAA-AG
1 AAA-GAAGAG
516594 AAAGAA
1 AAAGAA
516600 TAAAGAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.14
8 23 0.55
9 11 0.26
10 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (9 bp):
AAAGAAGAG
Found at i:516606 original size:28 final size:26
Alignment explanation
Indices: 516543--516608 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
516533 AAAAGCACAC
516543 AAAAAGAAAGAAAGAAGAGAAAGAAGA
1 AAAAAGAAA-AAAGAAGAGAAAGAAGA
516570 AAAAGAGAAAAAGAGAA-ATGAAAGAAAGA
1 AAAA-AGAAAAA-AGAAGA-GAAAG-AAGA
*
516599 ATAAAGAAAA
1 AAAAAGAAAA
516609 CAGATCCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.21
28 20 0.59
29 7 0.21
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAAAAGAAGAGAAAGAAGA
Found at i:518756 original size:23 final size:23
Alignment explanation
Indices: 518710--518756 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
518700 CATTGGTTTC
*
518710 TATTTTGCAAAAAGTTAAATCTA
1 TATTTTGCAAAAAGTAAAATCTA
*
518733 TATTTTGTAAAAAG-AAAATGCTA
1 TATTTTGCAAAAAGTAAAAT-CTA
518756 T
1 T
518757 TTTCATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (23 bp):
TATTTTGCAAAAAGTAAAATCTA
Found at i:521698 original size:15 final size:17
Alignment explanation
Indices: 521671--521703 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
521661 GCCTTTTTCT
521671 TAGCTCTAGTATC-TTC
1 TAGCTCTAGTATCATTC
521687 TAGCTC-AGTATCATTC
1 TAGCTCTAGTATCATTC
521703 T
1 T
521704 CACACTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (17 bp):
TAGCTCTAGTATCATTC
Found at i:522986 original size:12 final size:11
Alignment explanation
Indices: 522960--522989 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
522950 AAGTAGAAAG
*
522960 AAAAGCAACAT
1 AAAAACAACAT
522971 AAAAACAACAT
1 AAAAACAACAT
522982 AAAAACAA
1 AAAAACAA
522990 GTTAGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.17, G:0.03, T:0.07
Consensus pattern (11 bp):
AAAAACAACAT
Found at i:526641 original size:3 final size:3
Alignment explanation
Indices: 526621--526669 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
526611 GTCTGTAAAA
* *
526621 AAT AAT AA- AAA AATT AAT AAT AAT AAT AAT AAT AA- AAT ATT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
526665 AAT AA
1 AAT AA
526670 CCCGGGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:528351 original size:15 final size:16
Alignment explanation
Indices: 528320--528352 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
528310 TTGTAATTAC
528320 TAATAATAACGATGAG
1 TAATAATAACGATGAG
*
528336 TAATACTAAC-ATGAG
1 TAATAATAACGATGAG
528351 TA
1 TA
528353 TCATTACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (16 bp):
TAATAATAACGATGAG
Found at i:530857 original size:590 final size:591
Alignment explanation
Indices: 529691--530870 Score: 2116
Period size: 590 Copynumber: 2.0 Consensus size: 591
529681 ATTCAACATT
529691 CAATCTCCTAAAATAAATCATAACCATTTAAAAAATTAACCCATAAAATTATCTATTATTATTCA
1 CAATCTCCTAAAATAAATCATAACCATTTAAAAAATTAACCCATAAAATTATCTATTATTATTCA
529756 CTCACCAAAAACAACATATTAAACTTTAAAACTAAAACAAACCCAACAAAAAAACTCATAACATT
66 CTCACCAAAAACAACATATTAAACTTTAAAACTAAAACAAACCCAACAAAAAAACTCATAACATT
529821 GTAACACAAATCTTATTAATTTATTGGGGTTTCTTTTGGTTCAAACCCAAGACATTAAAAGTAAA
131 GTAACACAAATCTTATTAATTTATTGGGGTTTCTTTTGGTTCAAACCCAAGACATTAAAAGTAAA
*
529886 AAATATTTAAAATTTAAAACATAAATAAAATAAAAATTATTAAATCTTTAAGCCTCTTCTTTTCA
196 AAATATTTAAAATCTAAAACATAAATAAAATAAAAATTATTAAATCTTTAAGCCTCTTCTTTTCA
* *
529951 TCAAAATCAGAAAAATTTAGACTCCCATGTTTGTTTTATGTTTGTGTTTTTCATAATAAAAAAAT
261 TCAAAATCAGAAAAATTTAGACTCCCATGTTTGTTTTATGTCTGTGTTTTTCATAATAAAAAAAC
530016 TTCATTTCTTTTCTTGTAGTTGTATTGTTGAAAGCTTCCCTGTCTTTCTTTGTTGAAAAATCATC
326 TTCATTTCTTTTCTTGTAGTTGTATTGTTGAAAGCTTCCCTGTCTTTCTTTGTTGAAAAATCATC
* * *
530081 AATTGGAACATCGGGTCTCATATTTTCCTCGCTTTCTTATCCAAAAAACAGGTATAGGGCTGGTT
391 AATTGGAAAATCGAGTCTCATATTTTCCTCGCTTTCTTATCCAAAAAACAGGTATAGGGCCGGTT
* *
530146 CTTCCACCAAAGGAGACGCCAGAGGCAGAGACGGAGAAGATCAAACTCCTTCTTCACTTTCTTAA
456 CTGCCACCAAAGGAGACGCCAGAGGCAGAGACAGAGAAGATCAAACTCCTTCTTCACTTTCTTAA
* *
530211 AGGGTTGAAAAATAACACAGCTGGTAAGTGTCTGGCTGTGAATCTGGTCCTTTCCTTCTTTTTT-
521 AGGGTTGAAAAATAACACAGCCGGTAAATGTCTGGCTGTGAATCTGGTCCTTTCCTT-TTTTTTC
530275 TTTCTTC
585 TTTCTTC
*
530282 CAATCTCCTAAAATAAATCATAACCATTTAAAACATTAACCCATAAAATTATCTATTATTATTCA
1 CAATCTCCTAAAATAAATCATAACCATTTAAAAAATTAACCCATAAAATTATCTATTATTATTCA
*
530347 CTCACCAAAAACAACATATTAAACTTTAAAACTAAAACAAACCCAAC-AAAAAACTCGTAACATT
66 CTCACCAAAAACAACATATTAAACTTTAAAACTAAAACAAACCCAACAAAAAAACTCATAACATT
* *
530411 GTAACCCAAATCTTATTAATTTATTGGGGTTTCTTTTGGTTCAAACCTAAGACATTAAAAGTAAA
131 GTAACACAAATCTTATTAATTTATTGGGGTTTCTTTTGGTTCAAACCCAAGACATTAAAAGTAAA
530476 AAATATTTAAAATCTAAAACATAAATAAAATAAAAATTATTAAATCTTTAAGCCTCTTCTTTTCA
196 AAATATTTAAAATCTAAAACATAAATAAAATAAAAATTATTAAATCTTTAAGCCTCTTCTTTTCA
*
530541 TCAAAATCAGAAAAATTTGGACTCCCATGTTTGTTTTATGTCTGTGTTTTTCAT-A-AAAAAAAC
261 TCAAAATCAGAAAAATTTAGACTCCCATGTTTGTTTTATGTCTGTGTTTTTCATAATAAAAAAAC
*
530604 TTCTTTTCTTTTCTTGTAGTTGTATTGTTGAAAGCTTCCCTGGTCTTTCTTTGTTGAAAAATCAT
326 TTCATTTCTTTTCTTGTAGTTGTATTGTTGAAAGCTTCCCT-GTCTTTCTTTGTTGAAAAATCAT
* * * *
530669 CAATTGGAAAATCGAGTCTCATATTTTCCTCTCTTTCTTGTCCAAAAAATAGGTATAGGTCCGGT
390 CAATTGGAAAATCGAGTCTCATATTTTCCTCGCTTTCTTATCCAAAAAACAGGTATAGGGCCGGT
530734 TCTGCCACCAAAGGAGACGCCAGAGGCAGAGACAGAGAAGATCAAACTCCTTCTTCACTTTCTTA
455 TCTGCCACCAAAGGAGACGCCAGAGGCAGAGACAGAGAAGATCAAACTCCTTCTTCACTTTCTTA
*
530799 AAGGGTTGAAAAATAACATAGCCGGTAAATGTCTGGCTGTGAATCTGGTCCTTTTCCTTTTTTTT
520 AAGGGTTGAAAAATAACACAGCCGGTAAATGTCTGGCTGTGAATCTGGTCC-TTTCCTTTTTTTT
530864 CTTTCTT
584 CTTTCTT
530871 TCAAGCTTTA
Statistics
Matches: 565, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
588 47 0.08
589 199 0.35
590 208 0.37
591 111 0.20
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (591 bp):
CAATCTCCTAAAATAAATCATAACCATTTAAAAAATTAACCCATAAAATTATCTATTATTATTCA
CTCACCAAAAACAACATATTAAACTTTAAAACTAAAACAAACCCAACAAAAAAACTCATAACATT
GTAACACAAATCTTATTAATTTATTGGGGTTTCTTTTGGTTCAAACCCAAGACATTAAAAGTAAA
AAATATTTAAAATCTAAAACATAAATAAAATAAAAATTATTAAATCTTTAAGCCTCTTCTTTTCA
TCAAAATCAGAAAAATTTAGACTCCCATGTTTGTTTTATGTCTGTGTTTTTCATAATAAAAAAAC
TTCATTTCTTTTCTTGTAGTTGTATTGTTGAAAGCTTCCCTGTCTTTCTTTGTTGAAAAATCATC
AATTGGAAAATCGAGTCTCATATTTTCCTCGCTTTCTTATCCAAAAAACAGGTATAGGGCCGGTT
CTGCCACCAAAGGAGACGCCAGAGGCAGAGACAGAGAAGATCAAACTCCTTCTTCACTTTCTTAA
AGGGTTGAAAAATAACACAGCCGGTAAATGTCTGGCTGTGAATCTGGTCCTTTCCTTTTTTTTCT
TTCTTC
Found at i:535350 original size:22 final size:22
Alignment explanation
Indices: 535301--535352 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
535291 TTCAATGGCC
*
535301 GGTCAACGCCGGTCAAAGTTCT
1 GGTCAACGCCGATCAAAGTTCT
** *
535323 AATCAACGCCGATCAAATTTCT
1 GGTCAACGCCGATCAAAGTTCT
535345 GGTCAACG
1 GGTCAACG
535353 GTGGTCAACG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (22 bp):
GGTCAACGCCGATCAAAGTTCT
Found at i:547197 original size:65 final size:63
Alignment explanation
Indices: 546999--547208 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
546989 TGCACTAAGA
* * * *
546999 GTGCATCCATGCATCAAGTGCATTCGATGTTTC--AAAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATA-TC--AGTGCATCGATGCATGGTT
547062 G
63 G
*
547063 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATACTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATA-TCAGTGCATCGATGCATGGT-T
547128 -
63 G
** **
547128 GTGCATCGATGCATGTAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATATCA--GTGCATCGATGCATGG-T
547191 TG
62 TG
*
547193 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
547209 CTCTGACAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.39
65 61 0.50
66 1 0.01
67 7 0.06
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATATCAGTGCATCGATGCATGGTTG
Found at i:553327 original size:22 final size:21
Alignment explanation
Indices: 553285--553324 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
553275 GAGTTTATTT
*
553285 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
553306 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
553325 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:555295 original size:18 final size:17
Alignment explanation
Indices: 555241--555289 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
555231 TTGGACCCTT
* *
555241 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
555259 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
555277 AGTGCATTCGATG
1 AGTGCA-TCGATG
555290 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:555347 original size:28 final size:28
Alignment explanation
Indices: 555314--555375 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
555304 GAGTGCATCG
*
555314 ATGCATGGCTGGTGCATCGATGCATCAA
1 ATGCATGGCTGGTGAATCGATGCATCAA
555342 ATGCATGGCTGGTGAATCGATGCATCAA
1 ATGCATGGCTGGTGAATCGATGCATCAA
555370 ATGCAT
1 ATGCAT
555376 TCGATGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (28 bp):
ATGCATGGCTGGTGAATCGATGCATCAA
Found at i:555423 original size:93 final size:92
Alignment explanation
Indices: 555265--555440 Score: 248
Period size: 93 Copynumber: 1.9 Consensus size: 92
555255 CTAAGAGTGC
* *
555265 ATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCA
1 ATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCA
555330 TCGATGCATCAAATGCATGGCTGGTGA
66 TCGATGCATCAAATGCATGGCTGGTGA
* * * *
555357 ATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATGT
1 ATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GGT
*
555420 GCATCGATGCATGAAATGCAT
63 GCATCGATGCATCAAATGCAT
555441 TCGATGTTCC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
92 25 0.34
93 46 0.62
94 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (92 bp):
ATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCA
TCGATGCATCAAATGCATGGCTGGTGA
Found at i:555487 original size:65 final size:64
Alignment explanation
Indices: 555342--555498 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 64
555332 GATGCATCAA
* * *
555342 ATGCATGGCTGGTGAATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCG
1 ATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCCATAAAAT-CTCAGTGCATCG
* * **
555407 GTGCATGGTAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCCATTTAAT-TCATGGTGCAT
1 ATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTCCATAAAATCTCA--GTGCAT
555469 CG
63 CG
*
555471 ATGCATGGATTGGTGCATCGGTGCATCA
1 ATGCATGG-TTGGTGCATCGATGCATCA
555499 CTCTGACAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
62 3 0.04
64 24 0.31
65 49 0.64
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
ATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCCATAAAATCTCAGTGCATCG
Found at i:561811 original size:35 final size:35
Alignment explanation
Indices: 561772--561846 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
561762 GTTAGTCGAA
*
561772 ATATCCGAACAACGAGAATATATTCTATTATTGTG
1 ATATCCAAACAACGAGAATATATTCTATTATTGTG
* * *
561807 ATATCCAAACAATGAGAATATATTGTATTCTTGTG
1 ATATCCAAACAACGAGAATATATTCTATTATTGTG
561842 ATATC
1 ATATC
561847 GAATGTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (35 bp):
ATATCCAAACAACGAGAATATATTCTATTATTGTG
Found at i:562277 original size:59 final size:58
Alignment explanation
Indices: 562156--562290 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 58
562146 TTCTTTCGAC
* * ** *
562156 TATTAAAAGTTACAAAATAATCATCGATAATAGGGTGTTGCTTTGTTGAGTCACCGAC
1 TATTAAAAGTTACAAAATAATCACCGATAACAGGGTGTTGCTTTGAGGAGTCACCGAA
* * *
562214 TATTAAAATGTTTCAAAATAATCCCCGATAACAGTGTGTTGCTTTGAGGAGT-ACCCGAA
1 TATTAAAA-GTTACAAAATAATCACCGATAACAGGGTGTTGCTTTGAGGAGTCA-CCGAA
*
562273 TATTAAAAATTACAAAAT
1 TATTAAAAGTTACAAAAT
562291 TGTCTCGCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 17 0.26
59 48 0.74
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (58 bp):
TATTAAAAGTTACAAAATAATCACCGATAACAGGGTGTTGCTTTGAGGAGTCACCGAA
Found at i:563284 original size:20 final size:20
Alignment explanation
Indices: 563255--563307 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
563245 CGATTCAAGT
*
563255 GGTATTGATACCAAGAGG-G
1 GGTATCGATACCAAGAGGAG
* * *
563274 GAGTATCGATACTATGAGGAT
1 G-GTATCGATACCAAGAGGAG
563295 GGTATCGATACCA
1 GGTATCGATACCA
563308 TTGTTAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAAGAGGAG
Found at i:563376 original size:22 final size:19
Alignment explanation
Indices: 563330--563370 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
563320 TGCAGAAATG
*
563330 GTATCAGTACCATAATAGA
1 GTATCGGTACCATAATAGA
*
563349 GTATCGGTACCATAATATA
1 GTATCGGTACCATAATAGA
563368 GTA
1 GTA
563371 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (19 bp):
GTATCGGTACCATAATAGA
Found at i:563381 original size:22 final size:19
Alignment explanation
Indices: 563337--563383 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
563327 ATGGTATCAG
*
563337 TACCATAATAGAGTATCGG
1 TACCATAATAGAGTATCGA
563356 TACCATAATATAGTAGTATCGA
1 TACCAT-A-ATAG-AGTATCGA
563378 TACCAT
1 TACCAT
563384 GGTAGGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 4 0.17
22 13 0.54
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (19 bp):
TACCATAATAGAGTATCGA
Found at i:563802 original size:55 final size:55
Alignment explanation
Indices: 563763--564325 Score: 885
Period size: 55 Copynumber: 10.3 Consensus size: 55
563753 TAATTTGTTT
* *
563763 ATGAATTTCCGTATAGGCACTTTATGTGTAAACATAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
563818 ATGAATTTCCGTATAGGCACTTTATGTGTAAACATAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * *
563873 ATGAATTTCCATATGGACACTTTATGTGTAAACTTAATAAATTCATACTAAGTTG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
563928 ATGAATTTCCGTATGGGCATTTTTTGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
563983 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
564038 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
564093 ATGAATTTCAGAATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
564148 ATGAATTTTCGTATGGGCAATTTATGTGTAAATTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * * *
564203 ATGAATTTTCGTATGGACACTTTATTTGTAGACTTAAAAAATTCATACTAAGAGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * *
564258 ATGAATTTCTGTATGGGCACTTTATGTGTAAAC-TAGGAAATTCATAATAAGTGT
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
564312 ATAAATTTCCGTAT
1 ATGAATTTCCGTAT
564326 TGGTAGTGGG
Statistics
Matches: 468, Mismatches: 40, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
54 28 0.06
55 440 0.94
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:564788 original size:27 final size:27
Alignment explanation
Indices: 564758--564811 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
564748 CAAATCCAAT
*
564758 GGTTTATATTATTTTCCATCATTTTAA
1 GGTTTATACTATTTTCCATCATTTTAA
*
564785 GGTTTATACTATTTTCTATCATTTTAA
1 GGTTTATACTATTTTCCATCATTTTAA
564812 AATATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (27 bp):
GGTTTATACTATTTTCCATCATTTTAA
Found at i:569239 original size:54 final size:54
Alignment explanation
Indices: 569173--569398 Score: 353
Period size: 54 Copynumber: 4.2 Consensus size: 54
569163 CAGTATCAAT
*
569173 ACCGTTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATA
1 ACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATA
* * *
569227 ATCGTTTTGGCACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATA
1 ACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATA
** * *
569281 ACCGTTTCAGAACTAAGTGTGCATTTCACAGAATTCATCCTAGGTGGATGAATA
1 ACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATA
* *
569335 ACCGTTTCGGCACTAAGTATGCATTTCACAGAATTCATCCTATGTGGATGAATA
1 ACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATA
*
569389 ACCATTTTGG
1 ACCGTTTTGG
569399 TATTATGTAT
Statistics
Matches: 157, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 157 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
ACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATA
Found at i:569670 original size:17 final size:17
Alignment explanation
Indices: 569643--569682 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
569633 AATTTACAAT
569643 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
569659 TAATTATAAATAATATC
1 TAATTATAAATAATATC
569676 TAATTAT
1 TAATTAT
569683 TCAAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTATAAATAATATC
Done.