Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 108 of 113
Found at i:21208023 original size:3 final size:3
Alignment explanation
Indices: 21208015--21208102 Score: 62
Period size: 3 Copynumber: 30.3 Consensus size: 3
21208005 TAGTCTGGTA
*
21208015 TAT TAT TA- TAT TAT GGTAT AAT TAT TA- TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
21208058 TA- TGT TAT GTAT TGT TAT CA- TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21208102 T
1 T
21208103 TTTTTTTCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
2 10 0.15
3 50 0.76
4 3 0.05
5 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:21208026 original size:8 final size:8
Alignment explanation
Indices: 21208013--21208095 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
21208003 TATAGTCTGG
21208013 TATATTAT
1 TATATTAT
21208021 TATATTAT
1 TATATTAT
** *
21208029 GGTATAAT
1 TATATTAT
21208037 TAT-TATAT
1 TATAT-TAT
21208045 TATATTAT
1 TATATTAT
21208053 TATATTAT
1 TATATTAT
21208061 GT-TATGTA-
1 -TATAT-TAT
*
21208069 T-TGTTAT
1 TATATTAT
*
21208076 CATATTAT
1 TATATTAT
21208084 TATTATTAT
1 TA-TATTAT
21208093 TAT
1 TAT
21208096 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
6 2 0.03
7 4 0.07
8 40 0.69
9 12 0.21
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:21208040 original size:19 final size:18
Alignment explanation
Indices: 21207997--21208047 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
21207987 TATTTTAGTC
* *
21207997 ATATTA-TATAGTCTGGT
1 ATATTATTATATTATGGT
21208014 ATATTATTATATTATGGT
1 ATATTATTATATTATGGT
21208032 ATAATTATTATATTAT
1 AT-ATTATTATATTAT
21208048 ATTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.20
18 11 0.37
19 13 0.43
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (18 bp):
ATATTATTATATTATGGT
Found at i:21208934 original size:6 final size:5
Alignment explanation
Indices: 21208889--21208927 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
21208879 TTTTTTTTTG
*
21208889 TTATT TTATT TTATT TTATT TTCTT TTGATT TTGATT TT
1 TTATT TTATT TTATT TTATT TTATT TT-ATT TT-ATT TT
21208928 TGATTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:21210012 original size:2 final size:2
Alignment explanation
Indices: 21210005--21210032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21209995 AACTCAAATT
21210005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21210033 AAAGGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21211368 original size:44 final size:44
Alignment explanation
Indices: 21211298--21211389 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
21211288 AATCCAACAC
* *
21211298 ACTTCTAGCTTTCAAAATATCGTATTCTTTGTTAATTTTCTCAT
1 ACTTCTAGCTTTCAAAATATCATATTCTTCGTTAATTTTCTCAT
* *
21211342 ACTTCTAGCTTTCAAAATGTCATATTCTTCGTTAATTTTCTCGT
1 ACTTCTAGCTTTCAAAATATCATATTCTTCGTTAATTTTCTCAT
21211386 ACTT
1 ACTT
21211390 TTCATCATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.49
Consensus pattern (44 bp):
ACTTCTAGCTTTCAAAATATCATATTCTTCGTTAATTTTCTCAT
Found at i:21212343 original size:33 final size:33
Alignment explanation
Indices: 21212280--21212343 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
21212270 AAAATGATAT
*
21212280 TATGAATAGATTAGATTAAATAATGGTATCCCA
1 TATGAATAGATTAGATTAAATAACGGTATCCCA
*
21212313 TATGAATAGATTAGATTAAATAACGTTATCC
1 TATGAATAGATTAGATTAAATAACGGTATCC
21212344 TATCTTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (33 bp):
TATGAATAGATTAGATTAAATAACGGTATCCCA
Found at i:21227260 original size:23 final size:23
Alignment explanation
Indices: 21227232--21227277 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21227222 TTTAATATAA
*
21227232 AATATAATATTATTTA-AAATTTT
1 AATATAA-ATTATATACAAATTTT
21227255 AATATAAATTATATACAAATTTT
1 AATATAAATTATATACAAATTTT
21227278 TGTGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATAAATTATATACAAATTTT
Found at i:21228723 original size:12 final size:12
Alignment explanation
Indices: 21228708--21228745 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
21228698 ATTTAATCAT
21228708 ATATTATATATA
1 ATATTATATATA
21228720 ATATTATATTATA
1 ATATTATA-TATA
21228733 ATA-TATATGATA
1 ATATTATAT-ATA
21228745 A
1 A
21228746 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 16 0.67
13 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
ATATTATATATA
Found at i:21228758 original size:22 final size:23
Alignment explanation
Indices: 21228693--21228758 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
21228683 TTTATAAAAG
*
21228693 ATAATATT-TAATCATATATTATAT
1 ATAATATTAT-ATTATATA-TATAT
21228717 ATAATATTATATTATAATATATAT
1 ATAATATTATATTAT-ATATATAT
*
21228741 GATAA-ATTTTATT-TATAT
1 -ATAATATTATATTATATAT
21228759 GAATATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 24 0.65
25 8 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATAATATTATATTATATATATAT
Found at i:21230535 original size:14 final size:15
Alignment explanation
Indices: 21230511--21230543 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
21230501 CCCTATTTAC
21230511 TTTGAAAAAATAATT
1 TTTGAAAAAATAATT
21230526 TTTG-AAAAATAATT
1 TTTGAAAAAATAATT
21230540 TTTG
1 TTTG
21230544 TATTTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTGAAAAAATAATT
Found at i:21231001 original size:25 final size:24
Alignment explanation
Indices: 21230973--21231032 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 24
21230963 TAAATATTTT
21230973 TATTTTATATATTATT-AAACATAAA
1 TATTTTATATATT-TTCAAA-ATAAA
*
21230998 TATTTT-TAATATTTTCATAATAAA
1 TATTTTAT-ATATTTTCAAAATAAA
21231022 TAATTTTATAT
1 T-ATTTTATAT
21231033 TTTACTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 9 0.30
25 20 0.67
26 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTATATATTTTCAAAATAAA
Found at i:21231151 original size:17 final size:16
Alignment explanation
Indices: 21231128--21231170 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
21231118 TCAATATAAA
*
21231128 ATATAAATATTTTATT
1 ATATAAATATTTTAAT
21231144 AGTATAAATATTTTAAT
1 A-TATAAATATTTTAAT
21231161 A-ATAAATATT
1 ATATAAATATT
21231171 ACTATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATAAATATTTTAAT
Found at i:21231248 original size:43 final size:42
Alignment explanation
Indices: 21231170--21231250 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
21231160 TAATAAATAT
* *
21231170 TACTATTTTAATATTAATAAAATAATATTTTAAGAATAGTGA
1 TACTATTTTAATATTAATAAAATAATATATAAAGAATAGTGA
* *
21231212 TACTATTTTAAATATT-TTAAAATATTAATATAAAGAATA
1 TACTATTTT-AATATTAATAAAATAAT-ATATAAAGAATA
21231251 ATAAATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 17 0.52
43 16 0.48
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (42 bp):
TACTATTTTAATATTAATAAAATAATATATAAAGAATAGTGA
Found at i:21231347 original size:16 final size:16
Alignment explanation
Indices: 21231328--21231369 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
21231318 GTAATTATTC
21231328 TTAAATATTAATAATT
1 TTAAATATTAATAATT
*
21231344 TT-AATAATAAATAATT
1 TTAAAT-ATTAATAATT
21231360 TTAATATATT
1 TTAA-ATATT
21231370 TTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 3 0.14
16 13 0.62
17 3 0.14
18 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATTAATAATT
Found at i:21231370 original size:10 final size:9
Alignment explanation
Indices: 21231335--21231400 Score: 61
Period size: 9 Copynumber: 7.7 Consensus size: 9
21231325 TTCTTAAATA
21231335 TTAATAATT
1 TTAATAATT
21231344 TTAATAA--
1 TTAATAATT
*
21231351 TAAATAATT
1 TTAATAATT
21231360 TTAATATATT
1 TTAATA-ATT
21231370 TTAATAA--
1 TTAATAATT
*
21231377 TAAATAATTT
1 TTAATAA-TT
21231387 TTAAT-ATT
1 TTAATAATT
21231395 TTAATA
1 TTAATA
21231401 GTTATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
7 12 0.26
8 7 0.15
9 14 0.30
10 13 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAATAATT
Found at i:21231370 original size:26 final size:26
Alignment explanation
Indices: 21231335--21231400 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
21231325 TTCTTAAATA
21231335 TTAATA-ATTTTAATAATAAATAATT
1 TTAATATATTTTAATAATAAATAATT
21231360 TTAATATATTTTAATAATAAATAATT
1 TTAATATATTTTAATAATAAATAATT
*
21231386 TTTA-ATATTTTAATA
1 TTAATATATTTTAATA
21231401 GTTATATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 17 0.44
26 22 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATATATTTTAATAATAAATAATT
Found at i:21231386 original size:16 final size:16
Alignment explanation
Indices: 21231247--21231392 Score: 62
Period size: 17 Copynumber: 9.2 Consensus size: 16
21231237 TAATATAAAG
21231247 AATAATAAATAATTTT
1 AATAATAAATAATTTT
* * *
21231263 -AT-TTAAGTATTTTT
1 AATAATAAATAATTTT
21231277 ATATTAATAAA-ATATTTT
1 A-A-TAATAAATA-ATTTT
*
21231295 AATATTAAAT-ATTTT
1 AATAATAAATAATTTT
* * *
21231310 ATTAAAATGTAATTATTCTT
1 A--ATAAT-AAATAATT-TT
*
21231330 AA-ATATTAATAATTTT
1 AATA-ATAAATAATTTT
21231346 AATAATAAATAA-TTT
1 AATAATAAATAATTTT
21231361 --TAAT--AT-ATTTT
1 AATAATAAATAATTTT
21231372 AATAATAAATAATTTTT
1 AATAATAAATAA-TTTT
21231389 AATA
1 AATA
21231393 TTTTAATAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 39
0.66 0.08 0.26
Matches are distributed among these distances:
10 1 0.01
11 5 0.05
13 8 0.08
14 9 0.09
15 13 0.13
16 19 0.19
17 23 0.23
18 14 0.14
19 3 0.03
20 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (16 bp):
AATAATAAATAATTTT
Found at i:21231548 original size:13 final size:14
Alignment explanation
Indices: 21231518--21231547 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21231508 TTTAAAATAT
21231518 AAATATTTTTCAAA
1 AAATATTTTTCAAA
*
21231532 AAATATTTTTTAAA
1 AAATATTTTTCAAA
21231546 AA
1 AA
21231548 TTAATTTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTTTTCAAA
Found at i:21236392 original size:12 final size:11
Alignment explanation
Indices: 21236375--21236426 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
21236365 TTTTTAAATT
21236375 TATTATTTTATA
1 TATTATTTTA-A
21236387 TATTATTTTAA
1 TATTATTTTAA
*
21236398 TATAATTTTTAA
1 TATTA-TTTTAA
*
21236410 TA-TATTTAAA
1 TATTATTTTAA
21236420 TA-TATTT
1 TATTATTT
21236427 AAGTATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 12 0.33
11 6 0.17
12 18 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:21236421 original size:22 final size:24
Alignment explanation
Indices: 21236380--21236423 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
21236370 AAATTTATTA
*
21236380 TTTTATATATTATTTTAATATAAT
1 TTTTATATATTATTTAAATATAAT
21236404 TTTTA-ATA-TATTTAAATATA
1 TTTTATATATTATTTAAATATA
21236424 TTTAAGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 3 0.16
24 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTATATATTATTTAAATATAAT
Found at i:21239745 original size:6 final size:6
Alignment explanation
Indices: 21239736--21239769 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
21239726 CCTTCCTTAA
* *
21239736 ATATAT ATATAT ATATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
21239770 TTGCAAGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (6 bp):
ATATAG
Found at i:21241828 original size:17 final size:18
Alignment explanation
Indices: 21241788--21241828 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21241778 ATGATAAAAT
21241788 AATTTATTTATTGATCAA
1 AATTTATTTATTGATCAA
**
21241806 AA-TTATTT-TTTCTCAA
1 AATTTATTTATTGATCAA
21241822 AATTTAT
1 AATTTAT
21241829 ACAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTATTTATTGATCAA
Found at i:21242654 original size:16 final size:16
Alignment explanation
Indices: 21242633--21242668 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21242623 TTATTAGATT
* *
21242633 TTTTTTTTGTTTTTCC
1 TTTTTTTTCTTTTTCA
21242649 TTTTTTTTCTTTTTCA
1 TTTTTTTTCTTTTTCA
21242665 TTTT
1 TTTT
21242669 ACTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCTTTTTCA
Found at i:21243441 original size:29 final size:29
Alignment explanation
Indices: 21243407--21243515 Score: 80
Period size: 30 Copynumber: 3.7 Consensus size: 29
21243397 CCTATATTTT
21243407 TTATTTTTAAAAATTTAATCTCTATAATA
1 TTATTTTTAAAAATTTAATCTCTATAATA
* ** *
21243436 TTA-TTTAAAAAATTTTGGTCAT-TGTAATA
1 TTATTTTTAAAAA-TTTAATC-TCTATAATA
* * *
21243465 TTATTTTTAAGAAATTTAGTC-CAAATAGTA
1 TTATTTTTAA-AAATTTAATCTC-TATAATA
21243495 TTATTTCTTAAAGAATTTAAT
1 TTATTT-TTAAA-AATTTAAT
21243516 TCTTGTGCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
28 8 0.13
29 17 0.27
30 23 0.37
31 14 0.23
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (29 bp):
TTATTTTTAAAAATTTAATCTCTATAATA
Found at i:21244085 original size:2 final size:2
Alignment explanation
Indices: 21244078--21244102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21244068 AATTAAATTC
21244078 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 A
21244103 GATACGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21250037 original size:103 final size:103
Alignment explanation
Indices: 21249858--21250063 Score: 358
Period size: 103 Copynumber: 2.0 Consensus size: 103
21249848 CAAAGTTGGC
* * * *
21249858 TCTGGGGGTACTAGCGATATGCCACCGAGGATGACGGGCCTCTGTTAGAGTGGGAGAGGATGTCA
1 TCTGGAGGTACTAGCGATATGCCACCGAGGACGACGAGCCTCTGTTAGAGTGGGAGAGGAAGTCA
21249923 TGGTCCTAGAGAGTCCTTACTTCAACAAATGAAGCACA
66 TGGTCCTAGAGAGTCCTTACTTCAACAAATGAAGCACA
* *
21249961 TCTGGAGGTACTAGCGATATGCCACCGAGGACGATGAGCCTCTGTTAGAGTGGGAGAGTAAGTCA
1 TCTGGAGGTACTAGCGATATGCCACCGAGGACGACGAGCCTCTGTTAGAGTGGGAGAGGAAGTCA
21250026 TGGTCCTAGAGAGTCCTTACTTCAACAAATGAAGCACA
66 TGGTCCTAGAGAGTCCTTACTTCAACAAATGAAGCACA
21250064 AACCTCTTCG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (103 bp):
TCTGGAGGTACTAGCGATATGCCACCGAGGACGACGAGCCTCTGTTAGAGTGGGAGAGGAAGTCA
TGGTCCTAGAGAGTCCTTACTTCAACAAATGAAGCACA
Found at i:21252986 original size:2 final size:2
Alignment explanation
Indices: 21252979--21253013 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21252969 CCTTCCTTAA
21252979 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
21253014 GATAGATAGA
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:21254223 original size:14 final size:15
Alignment explanation
Indices: 21254191--21254233 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
21254181 TGATTTTAGA
21254191 GTTTGGAGATTTTAG-G
1 GTTTGG-GATTTT-GTG
21254207 GTTTGGG-TTTTGTG
1 GTTTGGGATTTTGTG
21254221 GTTTGGGATTTTG
1 GTTTGGGATTTTG
21254234 ATTTAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 6 0.24
16 6 0.24
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (15 bp):
GTTTGGGATTTTGTG
Found at i:21254224 original size:44 final size:45
Alignment explanation
Indices: 21254176--21254446 Score: 156
Period size: 45 Copynumber: 5.8 Consensus size: 45
21254166 GAAGGTTTAG
* * * *
21254176 GGTTTTGATTTTA-GAGTTTGGAGATTTT-AGGGTTTGGGTTTTGT
1 GGTTTGGATTTTATGAGTTTTG-GATTTTAAGGGTTTGGATTTTGA
*
21254220 GGTTTGGGATTTTGATTTAAGGTTTTGGATTTT-AGGGATTTTGGATTTTGA
1 GGTTT-GGATTTT-A--TGA-GTTTTGGATTTTAAGGG--TTTGGATTTTGA
* * * * *
21254271 GGTTTGGATTTTA-GGGTTTCGGATTTTAAGGATTTGGATTCTGG
1 GGTTTGGATTTTATGAGTTTTGGATTTTAAGGGTTTGGATTTTGA
* * * *
21254315 GGTTTGGATTTTAGGGGTTTTGAATTTTAAGGGTTTGGATTTAGA
1 GGTTTGGATTTTATGAGTTTTGGATTTTAAGGGTTTGGATTTTGA
* * * ** * * *
21254360 GGATATTAGATTTTAGGGGTTTCAGATTTT-AGGATTTTGCATTTTAAGG
1 GG-T-TTGGATTTTATGAGTTTTGGATTTTAAGG-GTTTGGATTTT--GA
* *
21254409 GGATTTTGGATTTTAGGGGTTTTGGATTTTAAGGGTTT
1 GG--TTTGGATTTTATGAGTTTTGGATTTTAAGGGTTT
21254447 TAGAAACCTA
Statistics
Matches: 180, Mismatches: 30, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
44 28 0.16
45 44 0.24
46 8 0.04
47 29 0.16
49 40 0.22
50 16 0.09
51 15 0.08
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.48
Consensus pattern (45 bp):
GGTTTGGATTTTATGAGTTTTGGATTTTAAGGGTTTGGATTTTGA
Found at i:21254233 original size:51 final size:50
Alignment explanation
Indices: 21254168--21254326 Score: 138
Period size: 51 Copynumber: 3.3 Consensus size: 50
21254158 AGGATATGGA
* *
21254168 AGGTTTAGGG-TTTTGATTTTAGAGTTTGGAGATTTTAGGG-TTTGGGTTTTG
1 AGGTTT-GGGATTTTGATTTAAG-GTTTGG-GATTTTAGGGATTTGGATTTTG
* *
21254219 TGGTTTGGGATTTTGATTTAAGGTTTTGGATTTTAGGGATTTTGGATTTTG
1 AGGTTTGGGATTTTGATTTAAGGTTTGGGATTTTAGGGA-TTTGGATTTTG
* * * *
21254270 AGGTTT-GGA---T--TTTAGGGTTTCGGATTTTAAGGATTTGGATTCTG
1 AGGTTTGGGATTTTGATTTAAGGTTTGGGATTTTAGGGATTTGGATTTTG
*
21254314 GGGTTT-GGATTTT
1 AGGTTTGGGATTTT
21254327 AGGGGTTTTG
Statistics
Matches: 92, Mismatches: 10, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
44 18 0.20
45 20 0.22
47 2 0.02
49 10 0.11
50 11 0.12
51 31 0.34
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (50 bp):
AGGTTTGGGATTTTGATTTAAGGTTTGGGATTTTAGGGATTTGGATTTTG
Found at i:21254247 original size:35 final size:36
Alignment explanation
Indices: 21254198--21254270 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
21254188 AGAGTTTGGA
* *
21254198 GATTTTAGGGTTTGGGTTTT-GTGG-TTTGGGATTTT
1 GATTTAAGGGTTTGGATTTTAG-GGATTTGGGATTTT
* *
21254233 GATTTAAGGTTTTGGATTTTAGGGATTTTGGATTTT
1 GATTTAAGGGTTTGGATTTTAGGGATTTGGGATTTT
21254269 GA
1 GA
21254271 GGTTTGGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (36 bp):
GATTTAAGGGTTTGGATTTTAGGGATTTGGGATTTT
Found at i:21254253 original size:65 final size:64
Alignment explanation
Indices: 21254171--21254297 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 64
21254161 ATATGGAAGG
* * *
21254171 TTTAGGGTTTTGATTTTAGAG-TTTGGAGATTTT-AGGGTTTGGGTTTT-GTGGTTTGGGATTTT
1 TTTAAGGTTTTGATTTTAGAGATTTGG-GATTTTGA-GGTTTGGATTTTAG-GGTTTCGGATTTT
21254233 GA
63 GA
* *
21254235 TTTAAGGTTTTGGATTTTAGGGATTTTGGATTTTGAGGTTTGGATTTTAGGGTTTCGGATTTT
1 TTTAAGGTTTT-GATTTTAGAGATTTGGGATTTTGAGGTTTGGATTTTAGGGTTTCGGATTTT
21254298 AAGGATTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
64 10 0.19
65 38 0.70
66 6 0.11
ACGTcount: A:0.15, C:0.01, G:0.32, T:0.52
Consensus pattern (64 bp):
TTTAAGGTTTTGATTTTAGAGATTTGGGATTTTGAGGTTTGGATTTTAGGGTTTCGGATTTTGA
Found at i:21254278 original size:14 final size:14
Alignment explanation
Indices: 21254259--21254361 Score: 82
Period size: 15 Copynumber: 7.0 Consensus size: 14
21254249 TTTTAGGGAT
21254259 TTTGGATTTTGAGG
1 TTTGGATTTTGAGG
21254273 TTTGGATTTT-AGGG
1 TTTGGATTTTGA-GG
*
21254287 TTTCGGATTTTAAGG
1 TTT-GGATTTTGAGG
* *
21254302 ATTTGGATTCTGGGG
1 -TTTGGATTTTGAGG
*
21254317 TTTGGATTTTAGGGG
1 TTTGGATTTT-GAGG
* *
21254332 TTTTGAATTTTAAGGG
1 -TTTGGATTTTGA-GG
*
21254348 TTTGGATTTAGAGG
1 TTTGGATTTTGAGG
21254362 ATATTAGATT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
13 1 0.01
14 26 0.36
15 30 0.42
16 15 0.21
ACGTcount: A:0.17, C:0.02, G:0.34, T:0.47
Consensus pattern (14 bp):
TTTGGATTTTGAGG
Found at i:21254296 original size:15 final size:15
Alignment explanation
Indices: 21254171--21254447 Score: 174
Period size: 16 Copynumber: 17.7 Consensus size: 15
21254161 ATATGGAAGG
21254171 TTTAGGGTTTT-GAT
1 TTTAGGGTTTTGGAT
* *
21254185 TTTAGAGTTTGGAGAT
1 TTTAGGGTTTTG-GAT
*
21254201 TTTAGGG-TTTGGGT
1 TTTAGGGTTTTGGAT
*
21254215 TTT-GTGGTTTGGGATTTT
1 TTTAG-GGTTTTGGA---T
*
21254233 GATTTAAGGTTTTGGAT
1 --TTTAGGGTTTTGGAT
21254250 TTTAGGGATTTTGGAT
1 TTTAGGG-TTTTGGAT
21254266 TTT-GAGG-TTTGGAT
1 TTTAG-GGTTTTGGAT
*
21254280 TTTAGGGTTTCGGAT
1 TTTAGGGTTTTGGAT
* *
21254295 TTTAAGGATTTGGAT
1 TTTAGGGTTTTGGAT
* *
21254310 TCT-GGGGTTTGGAT
1 TTTAGGGTTTTGGAT
*
21254324 TTTAGGGGTTTTGAAT
1 TTTA-GGGTTTTGGAT
21254340 TTTAAGGG-TTTGGA-
1 TTT-AGGGTTTTGGAT
* *
21254354 TTTAGAGGATATTAGAT
1 TTTAG-GG-TTTTGGAT
**
21254371 TTTAGGGGTTTCAGAT
1 TTTA-GGGTTTTGGAT
* *
21254387 TTTAGGATTTTGCAT
1 TTTAGGGTTTTGGAT
21254402 TTTAAGGGGATTTTGGAT
1 TTT-A-GGG-TTTTGGAT
21254420 TTTAGGGGTTTTGGAT
1 TTTA-GGGTTTTGGAT
21254436 TTTAAGGGTTTT
1 TTT-AGGGTTTT
21254448 AGAAACCTAA
Statistics
Matches: 206, Mismatches: 31, Indels: 50
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.01
14 44 0.21
15 50 0.24
16 70 0.34
17 16 0.08
18 12 0.06
20 11 0.05
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (15 bp):
TTTAGGGTTTTGGAT
Found at i:21254867 original size:20 final size:20
Alignment explanation
Indices: 21254826--21254872 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
21254816 ATCATGTAAG
*
21254826 AATAAATAAAACAAACTCAA
1 AATAAATAAAACAAACTAAA
*
21254846 AATAACATAAAA-AAATTAAA
1 AATAA-ATAAAACAAACTAAA
*
21254866 AAAAAAT
1 AATAAAT
21254873 TTTTTTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (20 bp):
AATAAATAAAACAAACTAAA
Found at i:21255562 original size:15 final size:14
Alignment explanation
Indices: 21255521--21255554 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21255511 TGTGTGTGTC
21255521 TTTTTGTTTC-TATT
1 TTTTTG-TTCGTATT
21255535 TTTTTGTTCGTATT
1 TTTTTGTTCGTATT
21255549 TTTTTG
1 TTTTTG
21255555 GTTGGTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (14 bp):
TTTTTGTTCGTATT
Found at i:21255719 original size:24 final size:23
Alignment explanation
Indices: 21255688--21255743 Score: 103
Period size: 24 Copynumber: 2.4 Consensus size: 23
21255678 GGAAAGAAAA
21255688 GGTCCGAGAGTTGTTTTGAGAGG
1 GGTCCGAGAGTTGTTTTGAGAGG
21255711 TGGTCCGAGAGTTGTTTTGAGAGG
1 -GGTCCGAGAGTTGTTTTGAGAGG
21255735 GGTCCGAGA
1 GGTCCGAGA
21255744 TTTTAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.18, C:0.11, G:0.43, T:0.29
Consensus pattern (23 bp):
GGTCCGAGAGTTGTTTTGAGAGG
Found at i:21256432 original size:110 final size:110
Alignment explanation
Indices: 21256126--21256410 Score: 345
Period size: 110 Copynumber: 2.6 Consensus size: 110
21256116 GATGATACCG
* * * *
21256126 CAAGTCAAAAAATAATGAATTGATCGAGATAACATCGCGAATTGAATTTATGCCTGGAGGTCTTA
1 CAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGCGAATCGAATTTATGCCTGGAGGTCTTA
* * * *
21256191 CAAATCATGCTCGGAGGTCTTAAAGAATCGACTGGGATAACATCG
66 CAAATCATGCTCGAAGGTCTTAAAGAATCGACTGAGATAACACCA
* * * * * * * *
21256236 TAAGTTAAAAAATATAGAATCGATCGAGATAATACTGCGAATCAAAATTATGCCCGGAGGTCTTA
1 CAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGCGAATCGAATTTATGCCTGGAGGTCTTA
* * * *
21256301 GAAATCATGTTCGAAGGTCTTACAGAATTGACTGAGATAACACCA
66 CAAATCATGCTCGAAGGTCTTAAAGAATCGACTGAGATAACACCA
* * * * *
21256346 CAAGTCAAAAGATAAAGAATCGATCGGGATAACCCCGCGAATCGAATTTATGCTTGGAAGTCTTA
1 CAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGCGAATCGAATTTATGCCTGGAGGTCTTA
21256411 AAAGTTGTGC
Statistics
Matches: 142, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
110 142 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (110 bp):
CAAGTCAAAAAATAAAGAATCGATCGAGATAACACCGCGAATCGAATTTATGCCTGGAGGTCTTA
CAAATCATGCTCGAAGGTCTTAAAGAATCGACTGAGATAACACCA
Found at i:21256572 original size:23 final size:23
Alignment explanation
Indices: 21256546--21256594 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
21256536 GGTTTTAGAC
* *
21256546 ATCATGTTCGAAGGTCTTACAGA
1 ATCATGTCCGAAGGTCTTACAAA
*
21256569 ATCATGTCCGGAGGTCTTACAAA
1 ATCATGTCCGAAGGTCTTACAAA
21256592 ATC
1 ATC
21256595 GACTAGGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (23 bp):
ATCATGTCCGAAGGTCTTACAAA
Found at i:21256841 original size:23 final size:23
Alignment explanation
Indices: 21256800--21256860 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
21256790 TTTATGCGCA
* *
21256800 GAGGTCTTAGA-AATCATGCTCG
1 GAGGTCTTACAGAATCATGCCCG
21256822 GAGGTCTTACAGAATCATGCCCG
1 GAGGTCTTACAGAATCATGCCCG
21256845 GAGGTCTTACAGAATC
1 GAGGTCTTACAGAATC
21256861 GACTGGGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (23 bp):
GAGGTCTTACAGAATCATGCCCG
Found at i:21256957 original size:133 final size:131
Alignment explanation
Indices: 21256280--21256963 Score: 647
Period size: 133 Copynumber: 5.2 Consensus size: 131
21256270 CTGCGAATCA
* * * * * *
21256280 AAATTATGCCCGGAGGTCTTAGAAATCATGTTCGAAGGTCTTACAGAATTGACTGAGATAACACC
1 AAATTATGCCCGAAGGTCTTACAAATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACACC
** * * **
21256345 ACAAGTCAAAAGATAAAGAATCGATCGGGATAACCCCGCGAATCGAATTTATGCTTGGAA-GTCT
66 ACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGC--CCAAGGTCT
21256409 TA-
129 TAG
* * * ** * * *
21256411 AAAGTTGTGCCCGAAGATCTTAGAAATCATACCCGAAAGTCTTACAAAATCGACTGGGATAACAC
1 AAA-TTATGCCCGAAGGTCTTACAAATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACAC
** * ** * *** * * *
21256476 CGTAAGTTGAAAAATAAAGAATCGATCAAGATGACATTACGAATCAAATTTATACCCGGAGGTTT
65 CACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCC-AAGGTCT
21256541 TAG
129 TAG
* * ** * * *
21256544 ACATCATGTTCGAAGGTCTTACAGAATCATGTCCGGAGGTCTTACAAAATCGACTAGGATAATAC
1 AAATTATGCCCGAAGGTCTTACA-AATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACAC
* * * * * *
21256609 CACAA-TTCAAAAGATAAAAAATCGATTGGGATAACATCGCGAATAAAAATTATGCCCAGAGGTC
65 CACAAGTT-GAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCCA-AGGTC
21256673 TTAG
128 TTAG
* * * * * * *
21256677 AAATTTGTGCTCGAAGGTCTTAAAAATCATGTTCGGAGATCTTATAGAATCAACTGGGATAACAC
1 AAA-TTATGCCCGAAGGTCTTACAAATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACAC
* * * * *
21256742 CACAAGTCGAAAGATAAAGAATTGATCGGGATAACATCGCGAATCGAATTTATGCGCAGAGGTCT
65 CACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCCA-AGGTCT
21256807 TAG
129 TAG
* * * *
21256810 AAATCATGCTCGGAGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGACTGGGATAACAC
1 AAATTATGCCCGAAGGTCTTACA-AATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACAC
**
21256875 CACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGTAAATCAAATTTATGTCCCAAGGTCT
65 CACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATG-CCCAAGGTCT
21256940 T-G
129 TAG
* *
21256942 AAAGTTATACCCGGAGGTCTTA
1 AAA-TTATGCCCGAAGGTCTTA
21256964 GAGATTATGC
Statistics
Matches: 444, Mismatches: 97, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
131 4 0.01
132 133 0.30
133 287 0.65
134 20 0.05
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (131 bp):
AAATTATGCCCGAAGGTCTTACAAATCATGTCCGGAGGTCTTACAGAATCGACTGGGATAACACC
ACAAGTTGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCCAAGGTCTTA
G
Found at i:21256959 original size:22 final size:22
Alignment explanation
Indices: 21256933--21257029 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
21256923 TTTATGTCCC
21256933 AAGGTCTTGAAAG-TTATACCCG
1 AAGGTCTT-AAAGATTATACCCG
* * * *
21256955 GAGGTCTTAGAGATTATGCTCG
1 AAGGTCTTAAAGATTATACCCG
* *
21256977 AAGATCTTAAA-AGTTGTACCCG
1 AAGGTCTTAAAGA-TTATACCCG
*
21256999 AAGGTCTTAAAGATTATGCCCG
1 AAGGTCTTAAAGATTATACCCG
*
21257021 GAGGTCTTA
1 AAGGTCTTA
21257030 CAAATCTTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
21 4 0.07
22 53 0.91
23 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (22 bp):
AAGGTCTTAAAGATTATACCCG
Found at i:21257029 original size:44 final size:44
Alignment explanation
Indices: 21256924--21257029 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 44
21256914 TAAATCAAAT
* * *
21256924 TTATGTCCC-AAGGTCTTGAAAGTTATACCCGGAGGTCTTAGAGA
1 TTATG-CCCGAAGGTCTTAAAAGTTATACCCGAAGGTCTTAAAGA
* * *
21256968 TTATGCTCGAAGATCTTAAAAGTTGTACCCGAAGGTCTTAAAGA
1 TTATGCCCGAAGGTCTTAAAAGTTATACCCGAAGGTCTTAAAGA
*
21257012 TTATGCCCGGAGGTCTTA
1 TTATGCCCGAAGGTCTTA
21257030 CAAATCTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
TTATGCCCGAAGGTCTTAAAAGTTATACCCGAAGGTCTTAAAGA
Found at i:21257367 original size:41 final size:40
Alignment explanation
Indices: 21257281--21257385 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 40
21257271 TTCTGATAAA
* *
21257281 GGTTCCATCTAAACAGAGGCTTTGAAATCTTGATTAAAATT
1 GGTTCC-TCTAAACAGAGACTTTGAAATCTTGATTAAAATC
*
21257322 GGTTCCTCTTAAACAGAGACTTTGAAATCTTGATTGAGAA-C
1 GGTTCCTC-TAAACAGAGACTTTGAAATCTTGATT-AAAATC
*
21257363 GGTTCTTCCTAAACAGAGACTTT
1 GGTTCCT-CTAAACAGAGACTTT
21257386 AAAACTTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
40 2 0.04
41 51 0.89
42 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (40 bp):
GGTTCCTCTAAACAGAGACTTTGAAATCTTGATTAAAATC
Found at i:21263974 original size:19 final size:19
Alignment explanation
Indices: 21263942--21263982 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21263932 GATTGACCTA
*
21263942 AAATAAATACCACATATTC
1 AAATAAATACCACATAATC
21263961 AAATATAATA-CACATAATC
1 AAATA-AATACCACATAATC
21263980 AAA
1 AAA
21263983 GAAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAATACCACATAATC
Found at i:21265547 original size:16 final size:16
Alignment explanation
Indices: 21265526--21265709 Score: 109
Period size: 16 Copynumber: 11.8 Consensus size: 16
21265516 TGATTTAAGG
21265526 TTTTGGATTTTAGGGA
1 TTTTGGATTTTAGGGA
21265542 TTTTGGATTTT-GAGG-
1 TTTTGGATTTTAG-GGA
*
21265557 -TTTGGATTTTAGGGG
1 TTTTGGATTTTAGGGA
* * *
21265572 TTTCGAATTTTTTGGGA
1 TTTTGGA-TTTTAGGGA
*
21265589 -TTTGAATTTT-GGG-
1 TTTTGGATTTTAGGGA
*
21265602 GTTTGGATTTTA-GGA
1 TTTTGGATTTTAGGGA
* * *
21265617 GTTTCGAAATTTAGGG-
1 -TTTTGGATTTTAGGGA
*
21265633 GTTTGGA-TTTAGAGGA
1 TTTTGGATTTTAG-GGA
* *
21265649 TTTTAGATTTTAGGGG
1 TTTTGGATTTTAGGGA
* * *
21265665 TTTCGAATTTTA-TGA
1 TTTTGGATTTTAGGGA
21265680 TTTTGGATTTTAAAGGGA
1 TTTTGGATTTT--AGGGA
21265698 TTTTGGATTTTA
1 TTTTGGATTTTA
21265710 AGGGTTTTAG
Statistics
Matches: 128, Mismatches: 24, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
14 31 0.24
15 22 0.17
16 47 0.37
17 15 0.12
18 13 0.10
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (16 bp):
TTTTGGATTTTAGGGA
Found at i:21265558 original size:31 final size:30
Alignment explanation
Indices: 21265510--21265717 Score: 106
Period size: 31 Copynumber: 6.7 Consensus size: 30
21265500 TTGTGGTTTG
*
21265510 GGGTTTT-GA-TTTAAGGTTTTGGATTTTA
1 GGGTTTTGGATTTTGAGGTTTTGGATTTTA
21265538 GGGATTTTGGATTTTGAGG-TTTGGATTTTA
1 GGG-TTTTGGATTTTGAGGTTTTGGATTTTA
* * * *
21265568 GGGGTTTCGAATTTTTTG-GGATTTGAATTTT-
1 -GGGTTTTGGA--TTTTGAGGTTTTGGATTTTA
* * * *
21265599 GGGGTTTGGATTTT-AGGAGTTTCGAAATTTA
1 GGGTTTTGGATTTTGA-G-GTTTTGGATTTTA
* * *
21265630 GGGGTTTGGATTTAGAGGATTTTAGATTTTA
1 GGGTTTTGGATTTTGAGG-TTTTGGATTTTA
* * *
21265661 GGGGTTTCGAATTTT-ATGATTTTGGATTTTAAA
1 -GGGTTTTGGATTTTGA-GGTTTTGGATTTT--A
*
21265694 GGGATTTTGGATTTTAAGGGTTTT
1 GGG-TTTTGGATTTTGA-GGTTTT
21265718 AGAAACCTAG
Statistics
Matches: 136, Mismatches: 25, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
28 7 0.05
29 5 0.04
30 35 0.26
31 44 0.32
32 29 0.21
33 10 0.07
34 6 0.04
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (30 bp):
GGGTTTTGGATTTTGAGGTTTTGGATTTTA
Found at i:21265562 original size:14 final size:14
Alignment explanation
Indices: 21265506--21265642 Score: 85
Period size: 14 Copynumber: 9.1 Consensus size: 14
21265496 AGTTTTGTGG
*
21265506 TTTGGGGTTTTGAT
1 TTTGGGGTTTGGAT
** *
21265520 TTAAGGTTTTGGAT
1 TTTGGGGTTTGGAT
*
21265534 TTTAGGGATTTTGGAT
1 TTT-GGG-GTTTGGAT
*
21265550 TTTGAGGTTTGGAT
1 TTTGGGGTTTGGAT
*
21265564 TTTAGGGGTTTCGAATTT
1 TTT-GGGGTTT-GGA--T
* *
21265582 TTTGGGATTTGAAT
1 TTTGGGGTTTGGAT
21265596 TTTGGGGTTTGGAT
1 TTTGGGGTTTGGAT
* *
21265610 TTTAGGAGTTTCGAAAT
1 TTT-GGGGTTT-G-GAT
*
21265627 TTAGGGGTTTGGAT
1 TTTGGGGTTTGGAT
21265641 TT
1 TT
21265643 AGAGGATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
14 42 0.44
15 17 0.18
16 23 0.24
17 10 0.10
18 4 0.04
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.50
Consensus pattern (14 bp):
TTTGGGGTTTGGAT
Found at i:21265598 original size:46 final size:46
Alignment explanation
Indices: 21265533--21265675 Score: 180
Period size: 46 Copynumber: 3.1 Consensus size: 46
21265523 AGGTTTTGGA
21265533 TTTTAGGGATTTTGGATTTTGAGGTTTGGATTTTAGGGGTTTCGAAT
1 TTTTAGGGA-TTTGGATTTTGAGGTTTGGATTTTAGGGGTTTCGAAT
* * * *
21265580 TTTTTGGGATTTGAATTTTGGGGTTTGGATTTTAGGAGTTTCGAA-
1 TTTTAGGGATTTGGATTTTGAGGTTTGGATTTTAGGGGTTTCGAAT
* * * *
21265625 ATTTAGGGGTTTGGATTTAGAGGATTTTAGATTTTAGGGGTTTCGAAT
1 TTTTAGGGATTTGGATTTTGAGG--TTTGGATTTTAGGGGTTTCGAAT
21265673 TTT
1 TTT
21265676 ATGATTTTGG
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
45 17 0.21
46 33 0.41
47 28 0.35
48 2 0.03
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (46 bp):
TTTTAGGGATTTGGATTTTGAGGTTTGGATTTTAGGGGTTTCGAAT
Found at i:21267147 original size:8 final size:8
Alignment explanation
Indices: 21267130--21267174 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
21267120 ATTACCCTAC
*
21267130 TTTTTGTT
1 TTTTTATT
21267138 TTTTTATT
1 TTTTTATT
21267146 TTTTTATTT
1 TTTTTA-TT
*
21267155 TTTTTGTT
1 TTTTTATT
21267163 TTTTTATT
1 TTTTTATT
21267171 TTTT
1 TTTT
21267175 ATATAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.07, C:0.00, G:0.04, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:21267156 original size:17 final size:17
Alignment explanation
Indices: 21267136--21267174 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
21267126 CTACTTTTTG
21267136 TTTTTTTATTTTTTTAT
1 TTTTTTTATTTTTTTAT
*
21267153 TTTTTTTGTTTTTTTAT
1 TTTTTTTATTTTTTTAT
21267170 TTTTT
1 TTTTT
21267175 ATATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.90
Consensus pattern (17 bp):
TTTTTTTATTTTTTTAT
Found at i:21269534 original size:15 final size:14
Alignment explanation
Indices: 21269514--21269548 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
21269504 ACCATTTGTT
*
21269514 TTTTTTTCTTTTATA
1 TTTTTTTATTTTA-A
21269529 TTTTTTTATTTTAA
1 TTTTTTTATTTTAA
21269543 TTTTTT
1 TTTTTT
21269549 AATTAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTATTTTAA
Found at i:21269858 original size:5 final size:6
Alignment explanation
Indices: 21269843--21269882 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
21269833 TATTATTAGA
* *
21269843 TTTTTG TTTTTG TTTTTG TTTTT- CTATTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
21269883 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 3 0.10
6 26 0.90
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:21269872 original size:17 final size:17
Alignment explanation
Indices: 21269852--21269892 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
21269842 ATTTTTGTTT
*
21269852 TTGTTTTTGTTTTTCTA
1 TTGTTTTTGTTTTTATA
21269869 TTGTTTTTGTTTTTATA
1 TTGTTTTTGTTTTTATA
21269886 TT-TTTTT
1 TTGTTTTT
21269893 AGATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.07, C:0.02, G:0.10, T:0.80
Consensus pattern (17 bp):
TTGTTTTTGTTTTTATA
Found at i:21270218 original size:2 final size:2
Alignment explanation
Indices: 21270211--21270243 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21270201 AATTAAATTC
*
21270211 AT AT AT AT AT AT AA 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 A
21270244 CACGTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21271060 original size:2 final size:2
Alignment explanation
Indices: 21271053--21271078 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21271043 AATACTTCAA
21271053 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
21271079 GTATTCGAAG
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):
AT
Found at i:21274818 original size:59 final size:59
Alignment explanation
Indices: 21274726--21274843 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
21274716 ATGAAGATGT
21274726 TTCATTGGGATCTTGGTTTATCAGTTTAGATGTGGAGCATGTGGATGATAGGCTTAAGC
1 TTCATTGGGATCTTGGTTTATCAGTTTAGATGTGGAGCATGTGGATGATAGGCTTAAGC
**
21274785 TTCATTGGGATCTTGGTTTATTGGTTTAGATGTGGAGCATGTGGATGATAGGCTTAAGC
1 TTCATTGGGATCTTGGTTTATCAGTTTAGATGTGGAGCATGTGGATGATAGGCTTAAGC
21274844 AAGTTGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.21, C:0.09, G:0.31, T:0.38
Consensus pattern (59 bp):
TTCATTGGGATCTTGGTTTATCAGTTTAGATGTGGAGCATGTGGATGATAGGCTTAAGC
Found at i:21277567 original size:20 final size:21
Alignment explanation
Indices: 21277542--21277580 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
21277532 AAAATAAATT
21277542 AAAAAATTA-AAATAAAATGA
1 AAAAAATTATAAATAAAATGA
21277562 AAAAAATTATAAATAAAAT
1 AAAAAATTATAAATAAAAT
21277581 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAAAATTATAAATAAAATGA
Found at i:21277600 original size:21 final size:21
Alignment explanation
Indices: 21277531--21277602 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
21277521 ATAATTATTT
*
21277531 AAAAATAAATTAAAA-AATTA
1 AAAAATATATTAAAATAATTA
* ** * *
21277551 AAATAAAATGAAAAAAATTATAA
1 AAA-AATAT-ATTAAAATAATTA
21277574 ATAAAATATATTAAAATAATTA
1 A-AAAATATATTAAAATAATTA
21277596 AAAAATA
1 AAAAATA
21277603 AATATTACTG
Statistics
Matches: 37, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
20 3 0.08
21 9 0.24
22 15 0.41
23 8 0.22
24 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (21 bp):
AAAAATATATTAAAATAATTA
Found at i:21277607 original size:23 final size:21
Alignment explanation
Indices: 21277531--21277609 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 21
21277521 ATAATTATTT
21277531 AAAAAT-AAATTAAAAAATT-
1 AAAAATAAAATTAAAAAATTA
*
21277550 -AAAATAAAATGAAAAAAATTA
1 AAAAATAAAAT-TAAAAAATTA
21277571 TAAATAA-AATATATTAAAATAATTA
1 -AAA-AATAA-A-ATTAAAA-AATTA
21277596 AAAAATAAATATTA
1 AAAAATAAA-ATTA
21277610 CTGATGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 8 0.17
23 12 0.25
24 12 0.25
25 7 0.15
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (21 bp):
AAAAATAAAATTAAAAAATTA
Found at i:21281486 original size:21 final size:21
Alignment explanation
Indices: 21281456--21281497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21281446 GGGAAATTTT
21281456 TAAGAAAACCAA-AAAGAATC
1 TAAGAAAACCAACAAAGAATC
*
21281476 TAAGACAAACCAACTAAGAATC
1 TAAGA-AAACCAACAAAGAATC
21281498 AAAGGGGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.12
Consensus pattern (21 bp):
TAAGAAAACCAACAAAGAATC
Found at i:21282758 original size:34 final size:34
Alignment explanation
Indices: 21282715--21282783 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
21282705 GAAAACTTAG
21282715 AAATCTCACAATAAATTTCATATTAAATACCAAT
1 AAATCTCACAATAAATTTCATATTAAATACCAAT
*
21282749 AAATCTCACAATAAATTTCATATTAAATATCAAT
1 AAATCTCACAATAAATTTCATATTAAATACCAAT
21282783 A
1 A
21282784 TATTTACCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (34 bp):
AAATCTCACAATAAATTTCATATTAAATACCAAT
Found at i:21282763 original size:22 final size:22
Alignment explanation
Indices: 21282723--21282764 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21282713 AGAAATCTCA
* * *
21282723 CAATAAATTTCATATTAAATAC
1 CAATAAATCTCACAATAAATAC
21282745 CAATAAATCTCACAATAAAT
1 CAATAAATCTCACAATAAAT
21282765 TTCATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
CAATAAATCTCACAATAAATAC
Found at i:21284560 original size:18 final size:18
Alignment explanation
Indices: 21284517--21284561 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
21284507 TTAGTTTATA
21284517 AAAATTTAA-AAAAATAT
1 AAAATTTAATAAAAATAT
*
21284534 AAAAATTAATAAAAATAT
1 AAAATTTAATAAAAATAT
*
21284552 ATAATTTAAT
1 AAAATTTAAT
21284562 TTGACTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTAATAAAAATAT
Found at i:21284861 original size:22 final size:22
Alignment explanation
Indices: 21284818--21284862 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
21284808 AAATATATAT
*
21284818 TTTTTATTAAATTTATATATTA
1 TTTTTATTAAATTTATAAATTA
21284840 TTTTTATTAAAATTT-TAAATTA
1 TTTTTATT-AAATTTATAAATTA
21284862 T
1 T
21284863 ATTATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTATTAAATTTATAAATTA
Found at i:21284872 original size:23 final size:22
Alignment explanation
Indices: 21284808--21284889 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 22
21284798 TTAAATATAA
21284808 AAATATATATTTTTTATTAAATTTAT
1 AAAT-TATATTTTTTA--AAATTT-T
*
21284834 ATATTAT-TTTTATTAAAATTTT
1 AAATTATATTTT-TTAAAATTTT
*
21284856 AAATTATATTATTTTAATATTTT
1 AAATTATATT-TTTTAAAATTTT
21284879 ---TTATATTTTTT
1 AAATTATATTTTTT
21284890 TCAAAGCATC
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
22 7 0.14
23 17 0.34
24 6 0.12
25 6 0.12
26 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AAATTATATTTTTTAAAATTTT
Found at i:21285651 original size:14 final size:14
Alignment explanation
Indices: 21285632--21285671 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21285622 AATAAAAATT
21285632 AAAATAAAATTTTA
1 AAAATAAAATTTTA
*
21285646 AAAATAAAA-TATA
1 AAAATAAAATTTTA
21285659 AAAATATAAATTT
1 AAAATA-AAATTT
21285672 ACATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 12 0.55
15 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAAATTTTA
Found at i:21285672 original size:27 final size:26
Alignment explanation
Indices: 21285613--21285672 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
21285603 AATTAAATCT
* *
21285613 AATTTATATAATAAAAATTAAAATAA
1 AATTTATAAAATAAAAATAAAAATAA
21285639 AATTT-TAAAAATAAAATATAAAAATATA
1 AATTTAT-AAAATAAAA-ATAAAAATA-A
21285667 AATTTA
1 AATTTA
21285673 CATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 13 0.46
27 8 0.29
28 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATTTATAAAATAAAAATAAAAATAA
Found at i:21292821 original size:19 final size:18
Alignment explanation
Indices: 21292797--21292832 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
21292787 TTCATTTTTA
21292797 AAAAAAAGAAAAAAATTTC
1 AAAAAAA-AAAAAAATTTC
21292816 AAAAAAAAAAAAAATTT
1 AAAAAAAAAAAAAATTT
21292833 GCGGGCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAAAAAAAAATTTC
Found at i:21298720 original size:23 final size:26
Alignment explanation
Indices: 21298670--21298758 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 26
21298660 ATAAAAAATA
*
21298670 TATAAAAATATATATAATAATTTGAAATTT
1 TATAAAAA-AT-TATAAT-ATAT-AAATTT
21298700 TATAAAAAATTA-AATA-A-AAATTT
1 TATAAAAAATTATAATATATAAATTT
*
21298723 TA-ATAAAAATTATAATATATAATTTT
1 TATA-AAAAATTATAATATATAAATTT
*
21298749 TATATAAAAT
1 TATAAAAAAT
21298759 ACGATAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
22 1 0.02
23 16 0.31
24 4 0.08
25 1 0.02
26 13 0.25
27 4 0.08
28 2 0.04
29 2 0.04
30 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
TATAAAAAATTATAATATATAAATTT
Found at i:21298732 original size:12 final size:12
Alignment explanation
Indices: 21298694--21298758 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
21298684 TAATAATTTG
21298694 AAATTTT-ATAA
1 AAATTTTAATAA
* *
21298705 AAAATTAAATAA
1 AAATTTTAATAA
21298717 AAATTTTAATAA
1 AAATTTTAATAA
*
21298729 AAATTATAATATA
1 AAATTTTAATA-A
* *
21298742 TAATTTTTATATA
1 AAATTTTAATA-A
21298755 AAAT
1 AAAT
21298759 ACGATAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
11 5 0.12
12 24 0.56
13 14 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTTTAATAA
Found at i:21298757 original size:26 final size:23
Alignment explanation
Indices: 21298697--21298758 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 23
21298687 TAATTTGAAA
21298697 TTTTATAAAAAATTAAATAAAAAT
1 TTTTAT-AAAAATTAAATAAAAAT
* *
21298721 TTTAATAAAAATTATAATATATAAT
1 TTTTATAAAAATTA-AATA-AAAAT
21298746 TTTTATATAAAAT
1 TTTTATA-AAAAT
21298759 ACGATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.25
24 9 0.28
25 10 0.31
26 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTATAAAAATTAAATAAAAAT
Found at i:21300970 original size:14 final size:14
Alignment explanation
Indices: 21300938--21300971 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21300928 AATCAATTGA
21300938 TTATATATTTTATT
1 TTATATATTTTATT
* *
21300952 ATATATATTTTCTT
1 TTATATATTTTATT
21300966 TTATAT
1 TTATAT
21300972 GATTATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATATTTTATT
Found at i:21302570 original size:23 final size:24
Alignment explanation
Indices: 21302540--21302589 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
21302530 TATATACTTG
*
21302540 TGTCATTATTGAA-CTTTATT-TTA
1 TGTCATTATTAAAGC-TTATTATTA
21302563 TGTCATTATTAAAGCTTATTATTA
1 TGTCATTATTAAAGCTTATTATTA
21302587 TGT
1 TGT
21302590 TTCTTTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (24 bp):
TGTCATTATTAAAGCTTATTATTA
Found at i:21306446 original size:34 final size:35
Alignment explanation
Indices: 21306386--21306459 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
21306376 ATTATTTTAA
* *
21306386 TTAATTAAATTTAATATGGTAATATTATATTTCTT
1 TTAATTAAATTTAATATGCTAATATTATATTTATT
*
21306421 TTAATTAAATTT-ATATGCTATTATTATATTTATT
1 TTAATTAAATTTAATATGCTAATATTATATTTATT
21306455 TTAAT
1 TTAAT
21306460 ATGAAATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 24 0.67
35 12 0.33
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (35 bp):
TTAATTAAATTTAATATGCTAATATTATATTTATT
Found at i:21306940 original size:13 final size:12
Alignment explanation
Indices: 21306906--21306941 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
21306896 TGTTGATATG
21306906 AACATATATTTT
1 AACATATATTTT
21306918 AACATATATTTT
1 AACATATATTTT
*
21306930 AAGATTATATTT
1 AACA-TATATTT
21306942 GAGGCTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (12 bp):
AACATATATTTT
Found at i:21312181 original size:23 final size:24
Alignment explanation
Indices: 21312138--21312187 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
21312128 TCATAAAGAA
*
21312138 ACATAATAATAAGCTTTAATAATG
1 ACATAATAATAAGCTTCAATAATG
21312162 ACATAA-AATAAAG-TTCAATAATG
1 ACATAATAAT-AAGCTTCAATAATG
21312185 ACA
1 ACA
21312188 CAAGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (24 bp):
ACATAATAATAAGCTTCAATAATG
Found at i:21315220 original size:12 final size:12
Alignment explanation
Indices: 21315193--21315227 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
21315183 ATCTAACCTC
*
21315193 AAATATAATCTTA
1 AAATAT-ATGTTA
21315206 AAATATATGTTA
1 AAATATATGTTA
21315218 AAATATATGT
1 AAATATATGT
21315228 ACATATCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (12 bp):
AAATATATGTTA
Found at i:21316020 original size:13 final size:13
Alignment explanation
Indices: 21316002--21316026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21315992 TTCATTTCAT
21316002 TTCCAAAAGTTAG
1 TTCCAAAAGTTAG
21316015 TTCCAAAAGTTA
1 TTCCAAAAGTTA
21316027 CGTAGTAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
TTCCAAAAGTTAG
Found at i:21322284 original size:16 final size:16
Alignment explanation
Indices: 21322259--21322290 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21322249 TGAAATTGAA
21322259 ATGACCCAAACCAAAG
1 ATGACCCAAACCAAAG
*
21322275 ATGACTCAAACCAAAG
1 ATGACCCAAACCAAAG
21322291 CAATTGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.12, T:0.09
Consensus pattern (16 bp):
ATGACCCAAACCAAAG
Found at i:21322860 original size:4 final size:4
Alignment explanation
Indices: 21322853--21322890 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
21322843 ATGTGAAAAA
* *
21322853 AAAG AAAG GAAG AAAG AAAG AAAG AAAG AAAG GAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
21322891 GAGACAATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:21322870 original size:12 final size:12
Alignment explanation
Indices: 21322853--21322890 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
21322843 ATGTGAAAAA
21322853 AAAGAAAGGAAG
1 AAAGAAAGGAAG
*
21322865 AAAGAAAGAAAG
1 AAAGAAAGGAAG
21322877 AAAGAAAGGAAG
1 AAAGAAAGGAAG
21322889 AA
1 AA
21322891 GAGACAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAAGAAAGGAAG
Found at i:21328825 original size:28 final size:28
Alignment explanation
Indices: 21328791--21328854 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
21328781 TTTTTTAAAT
*
21328791 TAAAATAT-TAAATAATAATTTATTAATA
1 TAAAATATGTAAA-AATAATTTAATAATA
*
21328819 TAAAATATGTAAAATTAATTTAATAATA
1 TAAAATATGTAAAAATAATTTAATAATA
21328847 -AAATATAT
1 TAAA-ATAT
21328855 ACTTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.09
28 25 0.78
29 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAAATATGTAAAAATAATTTAATAATA
Found at i:21329276 original size:13 final size:12
Alignment explanation
Indices: 21329253--21329328 Score: 64
Period size: 12 Copynumber: 6.1 Consensus size: 12
21329243 ATTAAATATG
*
21329253 AAGAGAAAAAAA
1 AAGAAAAAAAAA
*
21329265 AAGAACAAAAAAT
1 AAGAA-AAAAAAA
21329278 AAGAAAAAAAATA
1 AAGAAAAAAAA-A
* **
21329291 AA-AAGAAATGA
1 AAGAAAAAAAAA
21329302 AAGTTAAAAAAAAA
1 AAG--AAAAAAAAA
21329316 AAGAAAAAAAAA
1 AAGAAAAAAAAA
21329328 A
1 A
21329329 GAATGAGTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
11 3 0.06
12 25 0.50
13 13 0.26
14 9 0.18
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.07
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:21330502 original size:15 final size:16
Alignment explanation
Indices: 21330467--21330504 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21330457 AGAAAATTTT
*
21330467 TTAAATACAAAAAATA
1 TTAAATACAAAAAAGA
*
21330483 TTAAATATAAAAAAGA
1 TTAAATACAAAAAAGA
21330499 -TAAATA
1 TTAAATA
21330505 AAGAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
TTAAATACAAAAAAGA
Found at i:21330513 original size:19 final size:18
Alignment explanation
Indices: 21330491--21330542 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
21330481 TATTAAATAT
21330491 AAAAAAGATAAATAAAG-A
1 AAAAAAGATAAA-AAAGAA
21330509 AAAAAAG--AAAAAAGAA
1 AAAAAAGATAAAAAAGAA
*
21330525 AAAAACAAATAAAAAAGA
1 AAAAA-AGATAAAAAAGA
21330543 GGGTTGACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 1 0.03
18 7 0.24
19 8 0.28
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.06
Consensus pattern (18 bp):
AAAAAAGATAAAAAAGAA
Found at i:21330517 original size:8 final size:8
Alignment explanation
Indices: 21330491--21330529 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
21330481 TATTAAATAT
21330491 AAAAAAGA
1 AAAAAAGA
21330499 TAAATAAAGA
1 -AAA-AAAGA
21330509 AAAAAAG-
1 AAAAAAGA
21330516 AAAAAAGA
1 AAAAAAGA
21330524 AAAAAA
1 AAAAAA
21330530 CAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.25
8 10 0.36
9 6 0.21
10 5 0.18
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (8 bp):
AAAAAAGA
Found at i:21333366 original size:21 final size:19
Alignment explanation
Indices: 21333327--21333366 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
21333317 TTAAAAAGTC
*
21333327 ATATTTTAAATTAATTTAA
1 ATATTTTAAATTAAATTAA
21333346 ATATGTTTAAACTTAAATTAA
1 ATAT-TTTAAA-TTAAATTAA
21333367 GTCAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
ATATTTTAAATTAAATTAA
Found at i:21335501 original size:110 final size:110
Alignment explanation
Indices: 21335304--21335524 Score: 361
Period size: 110 Copynumber: 2.0 Consensus size: 110
21335294 GATAATGCAC
* *
21335304 TTTCAACTTGAAGTTGCATGCAAAGGACTAGCATATTATAAAGGAGAAGTCACTTTGATAATAAG
1 TTTCAACTTGAAGTTGCATGCAAAGGACTAACATATTATAAAGGAGAAATCACTTTGATAATAAG
** * *
21335369 TATCGATATGCTTTGAGGTGTTCTGCATATTCCTTAATCTTTTTG
66 TATCGATATGCTTTGAAATGTTCTACATATTCCGTAATCTTTTTG
* *
21335414 TTTCAACTTGGAGTTGCATGCAAAGGACTAACATATTATAAAGGAGAAATCATTTTGATAATAAG
1 TTTCAACTTGAAGTTGCATGCAAAGGACTAACATATTATAAAGGAGAAATCACTTTGATAATAAG
*
21335479 TGTCGATATGCTTTGAAATGTTCTACATATTCCGTAATCTTTTTG
66 TATCGATATGCTTTGAAATGTTCTACATATTCCGTAATCTTTTTG
21335524 T
1 T
21335525 CATTGAGTTC
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (110 bp):
TTTCAACTTGAAGTTGCATGCAAAGGACTAACATATTATAAAGGAGAAATCACTTTGATAATAAG
TATCGATATGCTTTGAAATGTTCTACATATTCCGTAATCTTTTTG
Found at i:21338686 original size:2 final size:2
Alignment explanation
Indices: 21338679--21338710 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21338669 AGTTAAAACC
21338679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21338711 ATTCCTCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21339923 original size:10 final size:10
Alignment explanation
Indices: 21339908--21339937 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21339898 ATCGAGCTTT
21339908 TATATTTTAA
1 TATATTTTAA
21339918 TATATTTTAA
1 TATATTTTAA
21339928 T-TATTTTAA
1 TATATTTTAA
21339937 T
1 T
21339938 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:21340726 original size:3 final size:3
Alignment explanation
Indices: 21340718--21340764 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
21340708 ATTTTTTAAG
**
21340718 AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT AA- AA- AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21340763 AA
1 AA
21340765 AAAAAAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:21340852 original size:22 final size:23
Alignment explanation
Indices: 21340821--21340863 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
21340811 GTTGCCGCTC
21340821 GACCAACCCCTA-TCCAGCCCTT
1 GACCAACCCCTAGTCCAGCCCTT
* *
21340843 GACCAGCCCCTAGTTCAGCCC
1 GACCAACCCCTAGTCCAGCCC
21340864 AACTACAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.21, C:0.49, G:0.14, T:0.16
Consensus pattern (23 bp):
GACCAACCCCTAGTCCAGCCCTT
Found at i:21342272 original size:15 final size:15
Alignment explanation
Indices: 21342233--21342325 Score: 78
Period size: 16 Copynumber: 5.9 Consensus size: 15
21342223 TTCTAAAACC
*
21342233 CCTAAAATCCAAAACC
1 CCTAAAATCCAAAA-T
21342249 CCATAAAATCCAAAAT
1 CC-TAAAATCCAAAAT
*
21342265 CCTAAAATTCAAAAT
1 CCTAAAATCCAAAAT
* **
21342280 CCTAAAATTCGAAACC
1 CCTAAAA-TCCAAAAT
*
21342296 CCTAAAAATTCAAAAT
1 CCT-AAAATCCAAAAT
*
21342312 CCCTTAAATCCAAA
1 -CCTAAAATCCAAA
21342326 CCCTTAAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
15 19 0.31
16 23 0.38
17 19 0.31
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (15 bp):
CCTAAAATCCAAAAT
Found at i:21342278 original size:32 final size:30
Alignment explanation
Indices: 21342227--21342344 Score: 94
Period size: 32 Copynumber: 3.7 Consensus size: 30
21342217 TTAGGTTTCT
*
21342227 AAAACCCCTAAAATCCAAAACCCCATAAAATCC
1 AAAA-CCCTAAAATTCAAAA-CCC-TAAAATCC
* * *
21342260 AAAATCCTAAAATTCAAAATCCTAAAATTCG
1 AAAACCCTAAAATTCAAAACCCTAAAA-TCC
* *
21342291 AAACCCCTAAAAATTCAAAATCCCTTAAATCC
1 AAAACCCT-AAAATTCAAAA-CCCTAAAATCC
* *
21342323 -AAACCCTTAAAATCCGAAACCC
1 AAAACCC-TAAAATTCAAAACCC
21342345 CCAAAAATCT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
30 8 0.12
31 24 0.35
32 27 0.39
33 10 0.14
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.19
Consensus pattern (30 bp):
AAAACCCTAAAATTCAAAACCCTAAAATCC
Found at i:21342286 original size:8 final size:8
Alignment explanation
Indices: 21342233--21342287 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 8
21342223 TTCTAAAACC
21342233 CCTAAAAT
1 CCTAAAAT
*
21342241 CC-AAAACC
1 CCTAAAA-T
21342249 CCATAAAAT
1 CC-TAAAAT
21342258 CC-AAAAT
1 CCTAAAAT
21342265 CCTAAAAT
1 CCTAAAAT
*
21342273 TC-AAAAT
1 CCTAAAAT
21342280 CCTAAAAT
1 CCTAAAAT
21342288 TCGAAACCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
7 17 0.45
8 15 0.39
9 2 0.05
10 4 0.11
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (8 bp):
CCTAAAAT
Found at i:21342331 original size:14 final size:16
Alignment explanation
Indices: 21342228--21342344 Score: 71
Period size: 15 Copynumber: 7.4 Consensus size: 16
21342218 TAGGTTTCTA
* *
21342228 AAACCCCTAAAATCCA
1 AAACCCTTAAAATCCG
* *
21342244 AAACCCCATAAAATCCA
1 AAA-CCCTTAAAATCCG
* * *
21342261 AAATCC-TAAAATTCA
1 AAACCCTTAAAATCCG
* *
21342276 AAATCC-TAAAATTCG
1 AAACCCTTAAAATCCG
* * *
21342291 AAACCCCTAAAAATTCA
1 AAA-CCCTTAAAATCCG
21342308 AAATCCCTT-AAATCC-
1 AAA-CCCTTAAAATCCG
21342323 AAACCCTTAAAATCCG
1 AAACCCTTAAAATCCG
21342339 AAACCC
1 AAACCC
21342345 CCAAAAATCT
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
14 5 0.06
15 34 0.40
16 18 0.21
17 29 0.34
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.19
Consensus pattern (16 bp):
AAACCCTTAAAATCCG
Found at i:21342344 original size:48 final size:46
Alignment explanation
Indices: 21342227--21342353 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 46
21342217 TTAGGTTTCT
*
21342227 AAAACCCCTAAAATCCAAAACCCCATAAAATCCAAAATCCTAAAATTC
1 AAAA-CCCTAAAATCCGAAACCCCA-AAAATCCAAAATCCTAAAATTC
* * * *
21342275 AAAATCCTAAAATTCGAAACCCCTAAAAATTCAAAATCCCTTAAA-TC
1 AAAACCCTAAAATCCGAAACCCC-AAAAATCCAAAAT-CCTAAAATTC
*
21342322 CAAACCCTTAAAATCCGAAACCCCCAAAAATC
1 AAAACCC-TAAAATCCGAAA-CCCCAAAAATC
21342354 TGAAATTCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
47 34 0.52
48 28 0.42
49 4 0.06
ACGTcount: A:0.50, C:0.31, G:0.02, T:0.18
Consensus pattern (46 bp):
AAAACCCTAAAATCCGAAACCCCAAAAATCCAAAATCCTAAAATTC
Found at i:21343639 original size:21 final size:21
Alignment explanation
Indices: 21343614--21343655 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21343604 CAATGGTTGG
21343614 ATTTAATTGATTTTATTTTAT
1 ATTTAATTGATTTTATTTTAT
**
21343635 ATTTAATTTCTTTTATTTTAT
1 ATTTAATTGATTTTATTTTAT
21343656 TTTTCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTAATTGATTTTATTTTAT
Found at i:21347814 original size:14 final size:13
Alignment explanation
Indices: 21347795--21347825 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
21347785 ATAAAAAAAC
21347795 AAAAAAAGAGTAAA
1 AAAAAAAGAG-AAA
21347809 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
21347822 AAAA
1 AAAA
21347826 CAAACAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:21349838 original size:22 final size:22
Alignment explanation
Indices: 21349812--21349854 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21349802 TGAGATTCTA
*
21349812 TAAGACCTTCGGGCATGATTTC
1 TAAGACCTTCGGGCATAATTTC
21349834 TAAGACCTTCGGGCATAATTT
1 TAAGACCTTCGGGCATAATTT
21349855 TGATTTGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
TAAGACCTTCGGGCATAATTTC
Found at i:21350310 original size:22 final size:22
Alignment explanation
Indices: 21350284--21350326 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21350274 TGAGATTCTA
*
21350284 TAAGACCTTCGAGCATGATTTC
1 TAAGACCTTCGAGCATAATTTC
*
21350306 TAAGACCTTCGGGCATAATTT
1 TAAGACCTTCGAGCATAATTT
21350327 TGATTCGCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
TAAGACCTTCGAGCATAATTTC
Found at i:21350513 original size:472 final size:472
Alignment explanation
Indices: 21349629--21350574 Score: 1651
Period size: 472 Copynumber: 2.0 Consensus size: 472
21349619 TTTTTAAAAT
* * * * *
21349629 TTTAAAGTTTCATTGCCTCTGATTAGGAGGAACATTCAAAGATTTTGAGATTTGTAAGATTTTCG
1 TTTAAAGTTTCATTACCTCTGATTAGGAGAAACATTCAAAGATTTTAAGATTTGTAAGATCTCCG
*
21349694 AGCATAATCTCTAAGATCTTCAGGCACAACTTTCAAGACCTCCGAGTAAAAGATTTTAAAATTTT
66 AGCATAATCTCTAAGATCTTCAGGCACAACTTTCAAGACCTCCGAGCAAAAGATTTTAAAATTTT
*
21349759 TAAAGTTTCATTACCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTCTATAAGACCTTCGG
131 TAAAGTTTCATTACCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTCTATAAGACCTTCGA
* *
21349824 GCATGATTTCTAAGACCTTCGGGCATAATTTTGATTTGCGATGTTATCTCGATCAATCTTTATTT
196 GCATGATTTCTAAGACCTTCGGGCATAATTTTGATTCGCGATGTTATCCCGATCAATCTTTATTT
21349889 TTTGACTTACAGTGTTATCCCAGTCGATTCGTTAAGACCTCCGAACATAGTTTTGAATTACGATG
261 TTTGACTTACAGTGTTATCCCAGTCGATTCGTTAAGACCTCCGAACATAGTTTTGAATTACGATG
*
21349954 TTATCCCGATCGATTCTTTATTTCTCGACTTGTGATGTTGTCTCAATCGATTCTGTAAGACTTTC
326 TTATCCCGATCGATTCTTTATTTCTCGACTTGTGATGTTGTCTCAATCGATTCTGCAAGACTTTC
* *
21350019 GAGCATGATTTTTAAGACCTCCGGACATAATTTTGATTTACGGTATTATCCTAATCGATTCTTTA
391 GAGCATGATTTTTAAGACCTCCGGACATAATTTCGATTTACGGTATTATCCCAATCGATTCTTTA
21350084 TCTTTCAACTTGCGATG
456 TCTTTCAACTTGCGATG
21350101 TTTAAAGTTTCATTACCTCTGATTAGGAGAAACATTCAAAGATTTTAAGATTTGTAAGATCTCCG
1 TTTAAAGTTTCATTACCTCTGATTAGGAGAAACATTCAAAGATTTTAAGATTTGTAAGATCTCCG
* * *
21350166 GGCATAATCTCTAAGATCTTC-GAGCACAACTTTCAAGACCTTCGAGCAAAAGATTTTTAAATTT
66 AGCATAATCTCTAAGATCTTCAG-GCACAACTTTCAAGACCTCCGAGCAAAAGATTTTAAAATTT
*
21350230 TTAAAGTTTTATTACCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTCTATAAGACCTTCG
130 TTAAAGTTTCATTACCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTCTATAAGACCTTCG
* *
21350295 AGCATGATTTCTAAGACCTTCGGGCATAATTTTGATTCGCGGTGTTGTCCCGATCAATCTTTATT
195 AGCATGATTTCTAAGACCTTCGGGCATAATTTTGATTCGCGATGTTATCCCGATCAATCTTTATT
* *
21350360 TTTTGACTTACAGTGTTATCCCAGTCGATTTGTTAAGACCTCCGAACATAGTTTTGAATTACGGT
260 TTTTGACTTACAGTGTTATCCCAGTCGATTCGTTAAGACCTCCGAACATAGTTTTGAATTACGAT
* *
21350425 GTTATTCCGATCGATTCTTTATTTCTTGACTTGTGATGTTGTCTCAATCGATTCTGCAAGACTTT
325 GTTATCCCGATCGATTCTTTATTTCTCGACTTGTGATGTTGTCTCAATCGATTCTGCAAGACTTT
* *
21350490 CGAGCATGATTTTTAAGACCTCCGGATATAATTTCGATTTGCGGTATTATCCCAATCGATTCTTT
390 CGAGCATGATTTTTAAGACCTCCGGACATAATTTCGATTTACGGTATTATCCCAATCGATTCTTT
*
21350555 ATCTTTCAGCTTGCGATG
455 ATCTTTCAACTTGCGATG
21350573 TT
1 TT
21350575 ATCCCAATCG
Statistics
Matches: 448, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
471 1 0.00
472 447 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (472 bp):
TTTAAAGTTTCATTACCTCTGATTAGGAGAAACATTCAAAGATTTTAAGATTTGTAAGATCTCCG
AGCATAATCTCTAAGATCTTCAGGCACAACTTTCAAGACCTCCGAGCAAAAGATTTTAAAATTTT
TAAAGTTTCATTACCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTCTATAAGACCTTCGA
GCATGATTTCTAAGACCTTCGGGCATAATTTTGATTCGCGATGTTATCCCGATCAATCTTTATTT
TTTGACTTACAGTGTTATCCCAGTCGATTCGTTAAGACCTCCGAACATAGTTTTGAATTACGATG
TTATCCCGATCGATTCTTTATTTCTCGACTTGTGATGTTGTCTCAATCGATTCTGCAAGACTTTC
GAGCATGATTTTTAAGACCTCCGGACATAATTTCGATTTACGGTATTATCCCAATCGATTCTTTA
TCTTTCAACTTGCGATG
Found at i:21350585 original size:110 final size:109
Alignment explanation
Indices: 21350386--21350677 Score: 307
Period size: 110 Copynumber: 2.7 Consensus size: 109
21350376 TATCCCAGTC
* * * * * *
21350386 GATTTGTTAAGACCTCCGAACATAGTTTTGAATTACGGTGTTATTCCGATCGATTCTTTATTTCT
1 GATTT-TTAAGACCTCCGGACATAATTTTGATTTGCGGTGTTATCCCGATCGATTCTTTATCTCT
* * * * * *
21350451 TGACTTGTGATGTTGTCTCAATCGATTCTGCAAGACTTTCGAGCAT
65 TCACTTGCGATGTTATCCCAATCGATTCTGCAAGACCTCCG-GCAT
* * * *
21350497 GATTTTTAAGACCTCCGGATATAATTTCGATTTGCGGTATTATCCCAATCGATTCTTTATCT-TT
1 GATTTTTAAGACCTCCGGACATAATTTTGATTTGCGGTGTTATCCCGATCGATTCTTTATCTCTT
* *
21350561 CAGCTTGCGATGTTATCCCAATCGATTCTGTAAGACCTCCGGGAT
66 CA-CTTGCGATGTTATCCCAATCGATTCTGCAAGACCTCCGGCAT
* * * * ** * *
21350606 GATTTCTAAAACCTCTGGGCATAATTTTGATTTGTAGTGTTTTCCCGATCGATTCTTTATTTCTT
1 GATTTTTAAGACCTCCGGACATAATTTTGATTTGCGGTGTTATCCCGATCGATTCTTTATCTCTT
*
21350671 GACTTGC
66 CACTTGC
21350678 AGTGTTGTCT
Statistics
Matches: 148, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
109 61 0.41
110 82 0.55
111 5 0.03
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (109 bp):
GATTTTTAAGACCTCCGGACATAATTTTGATTTGCGGTGTTATCCCGATCGATTCTTTATCTCTT
CACTTGCGATGTTATCCCAATCGATTCTGCAAGACCTCCGGCAT
Found at i:21350704 original size:109 final size:110
Alignment explanation
Indices: 21350423--21350715 Score: 308
Period size: 109 Copynumber: 2.7 Consensus size: 110
21350413 TTGAATTACG
* *
21350423 GTGTTATT-CCGATCGATTCTTTATTTCTTGACTTGTGATGTTGTCTCAATCGATTCTGCAAGAC
1 GTGTT-TTCCCGATCGATTCTTTATTTCTTGACTTGCGATGTTGTCTCAATCGATTCTGTAAGAC
* * * * * *
21350487 TTTCGAGCATGATTTTTAAGACCTCCGGATATAATTTCGATTTGCG
65 CTCCGAGCATGATTTCTAAAACCTCCGGACATAATTTCGATTTGCA
* * * * * * *
21350533 GTATTATCCCAATCGATTCTTTATCT-TTCAGCTTGCGATGTTATCCCAATCGATTCTGTAAGAC
1 GTGTTTTCCCGATCGATTCTTTATTTCTTGA-CTTGCGATGTTGTCTCAATCGATTCTGTAAGAC
* * * * *
21350597 CTCCG-GGATGATTTCTAAAACCTCTGGGCATAATTTTGATTTGTA
65 CTCCGAGCATGATTTCTAAAACCTCCGGACATAATTTCGATTTGCA
* *
21350642 GTGTTTTCCCGATCGATTCTTTATTTCTTGACTTGC-AGTGTTGTCTCAGTCGACTT-TATAAGA
1 GTGTTTTCCCGATCGATTCTTTATTTCTTGACTTGCGA-TGTTGTCTCAATCGA-TTCTGTAAGA
*
21350705 CCTTCGAGCAT
64 CCTCCGAGCAT
21350716 AAATTCGATT
Statistics
Matches: 146, Mismatches: 31, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
108 1 0.01
109 85 0.58
110 60 0.41
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (110 bp):
GTGTTTTCCCGATCGATTCTTTATTTCTTGACTTGCGATGTTGTCTCAATCGATTCTGTAAGACC
TCCGAGCATGATTTCTAAAACCTCCGGACATAATTTCGATTTGCA
Found at i:21350781 original size:88 final size:87
Alignment explanation
Indices: 21350624--21350874 Score: 285
Period size: 88 Copynumber: 2.9 Consensus size: 87
21350614 AAACCTCTGG
* * * * *
21350624 GCATAATTTTGATTTGTAGTGTT-TTCCCGATCGATTCTTTATTTCTTGACTTGCAGTGTTGTCT
1 GCATAAATTCGATTCGTAGTGTTATT-CCGATCGATTCTTTATTTTTTGAC-TGCAGTGTTATCT
21350688 CAGTCGACTT-TATAAGACCTTCGA
64 CAGTCGA-TTCTATAAGACCTTCGA
* *
21350712 GCATAAATTCGATTCGTGGTGTTATTCCGATCGATTCTTTATTTTTTGACTGACGGTGTTATC-C
1 GCATAAATTCGATTCGTAGTGTTATTCCGATCGATTCTTTATTTTTTGACTG-CAGTGTTATCTC
21350776 TAGTCGATTCTATAAGACCTTCGA
65 -AGTCGATTCTATAAGACCTTCGA
* * * ** *
21350800 GCATAAATTCGATTCGCAGTGTTATCCCGATTGATT-TCTTATTTTTTGACTTGTGGTGTTATCG
1 GCATAAATTCGATTCGTAGTGTTATTCCGATCGATTCT-TTATTTTTTGAC-TGCAGTGTTATCT
*
21350864 CAATCGATTCT
64 CAGTCGATTCT
21350875 GTATGTCCTC
Statistics
Matches: 143, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
87 6 0.04
88 132 0.92
89 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (87 bp):
GCATAAATTCGATTCGTAGTGTTATTCCGATCGATTCTTTATTTTTTGACTGCAGTGTTATCTCA
GTCGATTCTATAAGACCTTCGA
Found at i:21351408 original size:179 final size:179
Alignment explanation
Indices: 21351194--21351520 Score: 478
Period size: 179 Copynumber: 1.8 Consensus size: 179
21351184 AATCCTGATT
* * *
21351194 TCTTTAATTCAAAATCACAATTTAATCTCGATTGTTGTTATTTTTTGACTCATGGTTTAA-TCTT
1 TCTTTAATTCAAAATCACAATTTAATCTCGATTGTTGTTATTTTCTGACTCACGATTTAATTC-T
*
21351258 GATCTCTTTATTC-TCTAATTTATAGTTCAATCCCGATCTCTTTAATTCAAAATCACAGTTTAAT
65 GATCTCTTTATTCTTC-AATTTACAGTTCAATCCCGATCTCTTTAATTCAAAATCACAGTTTAAT
21351322 CTCGATTGTTGTTATTTTTTAACTTCTTCAATTCACAATTTAATCTCAATA
129 CTCGATTGTTGTTATTTTTTAACTTCTTCAATTCACAATTTAATCTCAATA
** * * * *
21351373 TCTTTAATTCAAAATCGTAGTTTAATTTTGATTGTTGTTATTTTCTGACTCGCGATTTAATTCTG
1 TCTTTAATTCAAAATCACAATTTAATCTCGATTGTTGTTATTTTCTGACTCACGATTTAATTCTG
* * * **
21351438 ATCTCTTTATTCTTCGATTTACGGTTCAATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCT
66 ATCTCTTTATTCTTCAATTTACAGTTCAATCCCGATCTCTTTAATTCAAAATCACAGTTTAATCT
*
21351503 TGATTGTTGTTATTTTTT
131 CGATTGTTGTTATTTTTT
21351521 GACTCGTGAT
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
179 126 0.97
180 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.49
Consensus pattern (179 bp):
TCTTTAATTCAAAATCACAATTTAATCTCGATTGTTGTTATTTTCTGACTCACGATTTAATTCTG
ATCTCTTTATTCTTCAATTTACAGTTCAATCCCGATCTCTTTAATTCAAAATCACAGTTTAATCT
CGATTGTTGTTATTTTTTAACTTCTTCAATTCACAATTTAATCTCAATA
Found at i:21351479 original size:102 final size:102
Alignment explanation
Indices: 21351363--21351635 Score: 390
Period size: 102 Copynumber: 2.7 Consensus size: 102
21351353 TTCACAATTT
* * * *
21351363 AATCTCAATATCTTTAATTCAAAATCGTAGTTTAATTTTGATTGTTGTTATTTTCTGACTCGCGA
1 AATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATTTTCTGACTCGTGA
*
21351428 TTTAATTCTGATCTCTTTATTCT-TCGATTTACG-G-TTC
66 TTTAATTCTGATCTCTTTATTCTCT-GA-TT-CGTGATTA
*
21351465 AATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATTTTTTGACTCGTGA
1 AATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATTTTCTGACTCGTGA
*
21351530 TTTAATTCTGGTCTCTTTATTCTCTGATTCGTGATTA
66 TTTAATTCTGATCTCTTTATTCTCTGATTCGTGATTA
* * * * *
21351567 AACCTCGATCTCTTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTAATCTCTGACTCGTGA
1 AATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATTTTCTGACTCGTGA
21351632 TTTA
66 TTTA
21351636 TTCCCTGTCA
Statistics
Matches: 155, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
100 2 0.01
101 3 0.02
102 149 0.96
103 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (102 bp):
AATCTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATTTTCTGACTCGTGA
TTTAATTCTGATCTCTTTATTCTCTGATTCGTGATTA
Found at i:21352282 original size:57 final size:55
Alignment explanation
Indices: 21352118--21352443 Score: 278
Period size: 57 Copynumber: 5.5 Consensus size: 55
21352108 TTGTATAGAA
* ** * * *
21352118 AAAATTGATACTTTCAACTTCTCCCCAAAA-TATTTTTTAGAAACTTTAATTTCAAG
1 AAAATTGATACTTTCAACTTTTCCTAAAAACT-TTTTTTA-AAAATTTATTTTTAAG
* *
21352174 AGAAATTGATACTTTCAACTTTTCCTAAAAAAAAATCTTTTTTTTTGAAAATTTATTCTTAAAG
1 A-AAATTGATACTTTCAACTTTTCCT----AAAAA-C--TTTTTTTAAAAATTTATT-TTTAAG
*
21352238 AAAATTGATACTTTCAACTTTTCCTCAAAACGTTTTTTTAAAAATTTATTTTTAAG
1 AAAATTGATACTTTCAACTTTTCCTAAAAAC-TTTTTTTAAAAATTTATTTTTAAG
* ** *
21352294 AAAAATTGATACTTTCAACTTTTTCCTAAAAA-TATTTTTTGAAAACTTTAGTTTCGAGG
1 -AAAATTGATACTTTCAAC-TTTTCCTAAAAACT-TTTTTT-AAAAATTTA-TTTTTAAG
* *
21352353 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTGAAAATTTATTTTTAAG
1 AAAATTGATACTTTCAACTTTTCCT----AAAAACTTTTTTTAAAAATTTATTTTTAAG
* *
21352412 AAAAATTGATACTTGCAACTTATCTCTAAAAA
1 -AAAATTGATACTTTCAACTTTTC-CTAAAAA
21352444 TATAACTTAT
Statistics
Matches: 224, Mismatches: 24, Indels: 43
0.77 0.08 0.15
Matches are distributed among these distances:
56 7 0.03
57 75 0.33
58 38 0.17
59 14 0.06
60 28 0.12
61 17 0.08
63 32 0.14
64 12 0.05
65 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (55 bp):
AAAATTGATACTTTCAACTTTTCCTAAAAACTTTTTTTAAAAATTTATTTTTAAG
Found at i:21352300 original size:120 final size:117
Alignment explanation
Indices: 21352118--21352443 Score: 351
Period size: 120 Copynumber: 2.7 Consensus size: 117
21352108 TTGTATAGAA
* * * * * *
21352118 AAAATTGATACTTTCAACTTCTCCCCAAAA-TATTTTTTAGAAACTTTAATTTCAAGAGAAATTG
1 AAAATTGATACTTTCAACTTTTCCTCAAAACT-TTTTTTA-AAAATTTATTTTTAAGAAAAATTG
* *
21352182 ATACTTTCAACTTTTCCTAAAAAAAAATCTTTTTTTTTGAAAA-TTTA-TTCTTAAAG
64 ATACTTTCAACTTTTCCTAAAAAAAAA---TATTTTTTGAAAACTTTAGTT-TCAAAG
21352238 AAAATTGATACTTTCAACTTTTCCTCAAAACGTTTTTTTAAAAATTTATTTTTAAGAAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAC-TTTTTTTAAAAATTTATTTTTAAGAAAAATTGA
* *
21352303 TACTTTCAACTTTTTCCT----AAAAATATTTTTTGAAAACTTTAGTTTCGAGG
65 TACTTTCAAC-TTTTCCTAAAAAAAAATATTTTTTGAAAACTTTAGTTTCAAAG
* * *
21352353 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTGAAAATTTATTTTTAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCCT----CAAAACTTTTTTTAAAAATTTATTTTTAAGAAAAAT
* *
21352418 TGATACTTGCAACTTATCTCTAAAAA
62 TGATACTTTCAACTTTTC-CTAAAAA
21352444 TATAACTTAT
Statistics
Matches: 177, Mismatches: 15, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
114 12 0.07
115 32 0.18
116 2 0.01
117 9 0.05
118 42 0.24
119 5 0.03
120 59 0.33
121 14 0.08
122 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (117 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAACTTTTTTTAAAAATTTATTTTTAAGAAAAATTGAT
ACTTTCAACTTTTCCTAAAAAAAAATATTTTTTGAAAACTTTAGTTTCAAAG
Found at i:21352452 original size:19 final size:19
Alignment explanation
Indices: 21352428--21352465 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21352418 TGATACTTGC
21352428 AACTTATCTCTAAAAATAT
1 AACTTATCTCTAAAAATAT
21352447 AACTTATCTCTAAAAATAT
1 AACTTATCTCTAAAAATAT
21352466 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
AACTTATCTCTAAAAATAT
Found at i:21352583 original size:15 final size:14
Alignment explanation
Indices: 21352541--21352589 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
21352531 GAATTTTATT
21352541 TAAAGAAAATAAAA
1 TAAAGAAAATAAAA
*
21352555 T-AATAAAATAAAAA
1 TAAAGAAAAT-AAAA
21352569 TAAAGAAAAGTAAAA
1 TAAAGAAAA-TAAAA
21352584 TAAAGA
1 TAAAGA
21352590 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 16 0.53
16 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
TAAAGAAAATAAAA
Found at i:21352603 original size:28 final size:28
Alignment explanation
Indices: 21352541--21352599 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
21352531 GAATTTTATT
21352541 TAAAGAAAATAAAATAATAAAATAAAAA
1 TAAAGAAAATAAAATAATAAAATAAAAA
*
21352569 TAAAGAAAAGTAAAAT-A-AAGATAAAAA
1 TAAAGAAAA-TAAAATAATAAAATAAAAA
21352596 TAAA
1 TAAA
21352600 AGAATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 13 0.45
28 10 0.34
29 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (28 bp):
TAAAGAAAATAAAATAATAAAATAAAAA
Found at i:21352649 original size:4 final size:4
Alignment explanation
Indices: 21352640--21352665 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21352630 ATAATAATAA
21352640 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
21352666 TCTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:21353050 original size:17 final size:16
Alignment explanation
Indices: 21353014--21353153 Score: 73
Period size: 16 Copynumber: 8.9 Consensus size: 16
21353004 TAAATATATT
*
21353014 AATAGAT-AACAAAAA
1 AATAGATAAATAAAAA
21353029 AATAGATAAATAAAAGA
1 AATAGATAAATAAAA-A
**
21353046 AATAGATAAAT--ACT
1 AATAGATAAATAAAAA
*
21353060 AATA-A-AAA-ATAAA
1 AATAGATAAATAAAAA
21353073 AATAGATAAATAATAAA
1 AATAGATAAATAA-AAA
* *
21353090 AATATTAATAGATAAAAA
1 AATA--GATAAATAAAAA
* *
21353108 AATAAAAAAATAAAAA
1 AATAGATAAATAAAAA
* *
21353124 ATATA-TTAAATAATGAA
1 A-ATAGATAAATAA-AAA
21353141 AATA-A-AAATAAAA
1 AATAGATAAATAAAA
21353154 GCCCATTGGG
Statistics
Matches: 98, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
12 3 0.03
13 6 0.06
14 6 0.06
15 17 0.17
16 27 0.28
17 25 0.26
18 7 0.07
19 7 0.07
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.21
Consensus pattern (16 bp):
AATAGATAAATAAAAA
Found at i:21353086 original size:24 final size:25
Alignment explanation
Indices: 21353027--21353150 Score: 103
Period size: 27 Copynumber: 4.9 Consensus size: 25
21353017 AGATAACAAA
*
21353027 AAAATAGATAAATAAA-AGAAATAGAT
1 AAAATA-ATAAA-AAATAAAAATAGAT
21353053 AAATACTAATAAAAAATAAAAATAGAT
1 AAA-A-TAATAAAAAATAAAAATAGAT
**
21353080 -AAATAAT-AAAAATATTAATAGAT
1 AAAATAATAAAAAATAAAAATAGAT
* *
21353103 AAAAAAATAAAAAAATAAAAAATATAT
1 AAAATAAT-AAAAAAT-AAAAATAGAT
* *
21353130 TAAATAAT-GAAAATAAAAATA
1 AAAATAATAAAAAATAAAAATA
21353151 AAAGCCCATT
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
23 14 0.17
24 17 0.21
25 6 0.07
26 14 0.17
27 28 0.35
28 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.23
Consensus pattern (25 bp):
AAAATAATAAAAAATAAAAATAGAT
Found at i:21353117 original size:9 final size:8
Alignment explanation
Indices: 21353063--21353124 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
21353053 AAATACTAAT
21353063 AAAAAATA
1 AAAAAATA
21353071 AAAATAGAT-
1 AAAA-A-ATA
*
21353080 AAATAATA
1 AAAAAATA
* *
21353088 AAAATATT
1 AAAAAATA
* *
21353096 AATAGATA
1 AAAAAATA
21353104 AAAAAATA
1 AAAAAATA
21353112 AAAAAATA
1 AAAAAATA
21353120 AAAAA
1 AAAAA
21353125 TATATTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
7 2 0.05
8 34 0.81
9 4 0.10
10 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (8 bp):
AAAAAATA
Found at i:21353148 original size:39 final size:36
Alignment explanation
Indices: 21353027--21353153 Score: 109
Period size: 35 Copynumber: 3.4 Consensus size: 36
21353017 AGATAACAAA
* *
21353027 AAAATAGATAAATAAAAGAAATAGAT--AAATACTAATAA
1 AAAATA-A-AAATAAAA-AAATA-ATAAAAATATTAATAG
* *
21353065 AAAATAAAAATAGATAAATAATAAAAATATTAATAG
1 AAAATAAAAATAAAAAAATAATAAAAATATTAATAG
*
21353101 ATAA-AAAAATAAAAAAATAA-AAAATATATTAAATAATG
1 AAAATAAAAATAAAAAAATAATAAAA-ATATT-AAT-A-G
21353139 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
21353154 GCCCATTGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
34 6 0.08
35 24 0.32
36 22 0.30
37 2 0.03
38 10 0.14
39 10 0.14
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (36 bp):
AAAATAAAAATAAAAAAATAATAAAAATATTAATAG
Found at i:21353557 original size:42 final size:42
Alignment explanation
Indices: 21353413--21353916 Score: 561
Period size: 42 Copynumber: 11.9 Consensus size: 42
21353403 CTCATTTAAG
* * **
21353413 CAGAGGCTTAACGACTTTGAGAAACATAAACAAAGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTG-GAAAAAT-AA-ATGGCTCCTCTAAT
* * *
21353458 CAGAGGCTCAATGACTTTTGAAAAATAAACAAGGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAAT-AA-ATGGCTCCTCTAAT
* *
21353502 CAGAGGCTCAACGATTTTGGAAAAATAAATGGCTTCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* *
21353544 CAGAGGCTTAACGACTTTTGAAAAATAAATAAGGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAAT--GGCTCCTCTAAT
* *
21353588 CAGAGGCTCAACGATTTTGGAAAAATAAATGACTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* *
21353630 CAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* * *
21353672 CAAAGGCTCAACAACTTT-GAAAAGTAAATGGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* ** * *
21353713 CAGAGGTTCAAATATTTTGAAAAAATAAATGGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* * *
21353755 AAGAGGCTCAACAACTTTGAAAATAACTAAA--GCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAA-AA-TAAATGGCTCCTCTAAT
* * *
21353797 CAGAGGCTCAACGACTTTTGAAAAGTAAATAGCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
* *
21353839 CAGAGGCTCAAAGACTTTGAAAATAACTAAA--GCTCCTCTAAT
1 CAGAGGCTCAACGACTTTGGAAA-AA-TAAATGGCTCCTCTAAT
* * *
21353881 AAGAGGCTCAACGACTTT-GAAAAGTAAATTGCTCCT
1 CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCT
21353917 TGACAATCAT
Statistics
Matches: 398, Mismatches: 50, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.01
40 5 0.01
41 44 0.11
42 232 0.58
43 5 0.01
44 92 0.23
45 16 0.04
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (42 bp):
CAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTCTAAT
Done.