Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006184.1 Hibiscus syriacus cultivar Beakdansim tig00014710_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: 88191
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2783 original size:24 final size:24
Alignment explanation
Indices: 2753--2810 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
2743 GGACTCATTC
2753 ACTGCAAAAGCAAAAGCCTCGTCT
1 ACTGCAAAAGCAAAAGCCTCGTCT
* *
2777 GCTGCAAAAGCACAAGCCTCGTCT
1 ACTGCAAAAGCAAAAGCCTCGTCT
*
2801 ACTGTAAAAG
1 ACTGCAAAAG
2811 TACAGACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (24 bp):
ACTGCAAAAGCAAAAGCCTCGTCT
Found at i:10584 original size:21 final size:21
Alignment explanation
Indices: 10558--10597 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10548 CCCCCTTTGA
*
10558 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
10579 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
10598 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:17166 original size:9 final size:9
Alignment explanation
Indices: 17152--17185 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17142 TATGCACACA
17152 TATCATTAT
1 TATCATTAT
17161 TATCATTAT
1 TATCATTAT
* *
17170 TAACATTCT
1 TATCATTAT
17179 TATCATT
1 TATCATT
17186 TATTCATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (9 bp):
TATCATTAT
Found at i:17457 original size:28 final size:28
Alignment explanation
Indices: 17418--17486 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
17408 TAGGATTTTC
17418 CCCGAAGGACCACATATAACACATATGT
1 CCCGAAGGACCACATATAACACATATGT
*
17446 CCCGAAGGACCATATATAACACATATGT
1 CCCGAAGGACCACATATAACACATATGT
* *
17474 CCCAAATGACCAC
1 CCCGAAGGACCAC
17487 TCTTTAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.17
Consensus pattern (28 bp):
CCCGAAGGACCACATATAACACATATGT
Found at i:18541 original size:21 final size:19
Alignment explanation
Indices: 18512--18551 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
18502 ATTGCCTTGT
*
18512 AGTATCGATACTTACTCAACC
1 AGTACCGATAC-TAC-CAACC
18533 AGTACCGATACTACCAACC
1 AGTACCGATACTACCAACC
18552 CATAATCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.23
Consensus pattern (19 bp):
AGTACCGATACTACCAACC
Found at i:21386 original size:9 final size:9
Alignment explanation
Indices: 21372--21405 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
21362 TATGCACACA
21372 TATCATTAT
1 TATCATTAT
21381 TATCATTAT
1 TATCATTAT
* *
21390 TAACATTCT
1 TATCATTAT
21399 TATCATT
1 TATCATT
21406 TATTTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (9 bp):
TATCATTAT
Found at i:21782 original size:23 final size:21
Alignment explanation
Indices: 21734--21786 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
21724 CGAAGTACAG
* *
21734 CATATATGTTCCAAAGGATTA
1 CATATATATCCCAAAGGATTA
21755 CATATATATCCCAAAGGATTA
1 CATATATATCCCAAAGGATTA
21776 CATATATATCC
1 CATATATATCC
21787 GAATGACCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
CATATATATCCCAAAGGATTA
Found at i:23194 original size:3 final size:3
Alignment explanation
Indices: 23186--23223 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
23176 AGACTAACGG
23186 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
23224 CAAGAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27510 original size:34 final size:35
Alignment explanation
Indices: 27467--27598 Score: 142
Period size: 37 Copynumber: 3.7 Consensus size: 35
27457 AAAACATATT
* *
27467 TTTTTAAAACGTATAATATATAG-TTAAAAAATGA
1 TTTTGAAAACGTATAATATATAGTTTAAAAAATGG
*
27501 TTTTGAAAACTTATAATATATAGTTTTAAAAAATGG
1 TTTTGAAAACGTATAATATATAG-TTTAAAAAATGG
* * *
27537 TTTTGAAAAACGTTTAATGTATAGTTTTAAAAAACGG
1 TTTTG-AAAACGTATAATATATAG-TTTAAAAAATGG
** *
27574 TTTCAAAAAAGTATAATATAT-GTTT
1 TTTTGAAAACGTATAATATATAGTTT
27599 TTTTTAAACA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 24 0.29
35 1 0.01
36 28 0.34
37 30 0.36
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (35 bp):
TTTTGAAAACGTATAATATATAGTTTAAAAAATGG
Found at i:27630 original size:36 final size:35
Alignment explanation
Indices: 27579--27713 Score: 113
Period size: 33 Copynumber: 3.9 Consensus size: 35
27569 AACGGTTTCA
* * **
27579 AAAAAGTATAATATATGTTTTTTTTAAACAATTTT-G
1 AAAACGTATAATATATG-GTTTTGAAAAC-ATTTTGG
*
27615 AAAACGTATAGTATATGGTTTTGAAAACATTTTGG
1 AAAACGTATAATATATGGTTTTGAAAACATTTTGG
*
27650 AAAACGTAT-A-ATATGGTTTTGAAAATGATTTT--
1 AAAACGTATAATATATGGTTTTGAAAA-CATTTTGG
*
27682 TAAACGTATAATATGAT--TTTTGAAAACGATTT
1 AAAACGTATAATAT-ATGGTTTTGAAAAC-ATTT
27714 ATGAAAATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
32 8 0.10
33 29 0.35
34 12 0.14
35 20 0.24
36 15 0.18
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.41
Consensus pattern (35 bp):
AAAACGTATAATATATGGTTTTGAAAACATTTTGG
Found at i:27669 original size:33 final size:33
Alignment explanation
Indices: 27604--27720 Score: 130
Period size: 33 Copynumber: 3.5 Consensus size: 33
27594 TGTTTTTTTT
27604 AAACAATTTTGAAAACGTATAGTATATGGTTTTGA
1 AAACAATTTTGAAAACGTATA--ATATGGTTTTGA
27639 AAAC-ATTTTGGAAAACGTATAATATGGTTTTGA
1 AAACAATTTT-GAAAACGTATAATATGGTTTTGA
** * *
27672 AAATGATTTT-TAAACGTATAATATGATTTTTGA
1 AAACAATTTTGAAAACGTATAATATG-GTTTTGA
*
27705 AAACGATTTATGAAAA
1 AAACAATTT-TGAAAA
27721 TATATTAACA
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
32 14 0.19
33 29 0.40
34 11 0.15
35 18 0.25
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (33 bp):
AAACAATTTTGAAAACGTATAATATGGTTTTGA
Found at i:27763 original size:22 final size:22
Alignment explanation
Indices: 27730--27779 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
27720 ATATATTAAC
27730 ATATATAATTTTTGAAAACATA
1 ATATATAATTTTTGAAAACATA
* * * *
27752 TTATATAGTTTTTGGAAATATA
1 ATATATAATTTTTGAAAACATA
27774 ATATAT
1 ATATAT
27780 GTTATATAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
ATATATAATTTTTGAAAACATA
Found at i:27800 original size:3 final size:3
Alignment explanation
Indices: 27794--27865 Score: 55
Period size: 3 Copynumber: 23.7 Consensus size: 3
27784 TATAGTTTTT
27794 TTA TTA TTA TTA TT- TATA TTA TTTA TTA TTA TT- TTA TATA TTA GGTTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA T-TA TTA --TTA
27842 -TA TTA TTA TTTA TT- TTA TT- TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TT
27866 TTTAATAGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 22
0.73 0.00 0.28
Matches are distributed among these distances:
2 9 0.16
3 36 0.62
4 10 0.17
5 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27864 original size:22 final size:23
Alignment explanation
Indices: 27792--27865 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 23
27782 TATATAGTTT
27792 TTTTATTATTATTATTTATATTA
1 TTTTATTATTATTATTTATATTA
27815 -TTTATTATTATT-TTATATATTA
1 TTTTATTATTATTATT-TATATTA
** *
27837 GGTTA-TATTATTATTTATTTTA
1 TTTTATTATTATTATTTATATTA
27859 TTTTATT
1 TTTTATT
27866 TTTAATAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.05
22 35 0.81
23 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (23 bp):
TTTTATTATTATTATTTATATTA
Found at i:27867 original size:10 final size:10
Alignment explanation
Indices: 27797--27861 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 10
27787 AGTTTTTTTA
27797 TTATTATTAT
1 TTATTATTAT
27807 TTA-TATTAT
1 TTATTATTAT
27816 TTATTATTATT
1 TTATTATTA-T
27827 TTATATATTAGGT
1 TTAT-TATTA--T
27840 TATATTATTAT
1 T-TATTATTAT
27851 TTATT-TTAT
1 TTATTATTAT
27860 TT
1 TT
27862 TATTTTTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
9 15 0.31
10 12 0.24
11 7 0.14
12 5 0.10
13 7 0.14
14 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTATTATTAT
Found at i:30691 original size:28 final size:27
Alignment explanation
Indices: 30632--30697 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
30622 AGTCATAACC
*
30632 ATTTTTTAAAAAACAATTATGATTATT
1 ATTTTTTAAAAAACAATTATGACTATT
* *
30659 ATTTTATAACAAAATAATTATGACT-TT
1 ATTTTTTAA-AAAACAATTATGACTATT
*
30686 ATTTTTGAAAAA
1 ATTTTTTAAAAA
30698 TTGGTGATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 17 0.52
28 13 0.39
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (27 bp):
ATTTTTTAAAAAACAATTATGACTATT
Found at i:31348 original size:2 final size:2
Alignment explanation
Indices: 31341--31378 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31331 ATTTCGAAAG
31341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31379 GGAAACAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33361 original size:2 final size:2
Alignment explanation
Indices: 33354--33434 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
33344 ATTTTGAAAG
33354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
33396 TA TA TA TA TA TA TA TA TA TA TA GA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33435 TAAGGAAACG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35188 original size:2 final size:2
Alignment explanation
Indices: 35181--35214 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35171 TGTAAATAAA
35181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35215 TTTAGACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37066 original size:2 final size:2
Alignment explanation
Indices: 37059--37098 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
37049 AGAGAATTAC
*
37059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37099 GTTGAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:37872 original size:21 final size:20
Alignment explanation
Indices: 37834--37874 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
37824 CAAAGGTGAC
*
37834 GAAAATAAATTAAAAATAAA
1 GAAAATAAAATAAAAATAAA
*
37854 GAAACTAAAATAAATAATAAA
1 GAAAATAAAATAAA-AATAAA
37875 TAAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (20 bp):
GAAAATAAAATAAAAATAAA
Found at i:38025 original size:24 final size:23
Alignment explanation
Indices: 37998--38062 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
37988 GGAACAAATG
37998 TAAATAAATAAAATACGACAA-AAA
1 TAAATAAATAAAATA--ACAAGAAA
*
38022 TAAATAAATTAAATAACAAGAAA
1 TAAATAAATAAAATAACAAGAAA
*
38045 TAAAAAAAAGTAAAATAA
1 T-AAATAAA-TAAAATAA
38063 GACGAGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 20 0.57
25 7 0.20
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (23 bp):
TAAATAAATAAAATAACAAGAAA
Found at i:38092 original size:2 final size:2
Alignment explanation
Indices: 38085--38119 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38075 AAGATAAAAC
38085 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
38120 AAATATAACT
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:38263 original size:19 final size:18
Alignment explanation
Indices: 38223--38265 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
38213 CACATATATG
38223 TAAAAAATAAAATACTAGA
1 TAAAAAATAAAATACTA-A
38242 TAAAAAACTAATAATACT-A
1 TAAAAAA-TAA-AATACTAA
38261 TAAAA
1 TAAAA
38266 TATATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.59
20 3 0.14
21 6 0.27
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAAATAAAATACTAA
Found at i:39409 original size:2 final size:2
Alignment explanation
Indices: 39402--39452 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
39392 ATAAATAAAT
39402 TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TGA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
39442 TA TA TA -A TA TA
1 TA TA TA TA TA TA
39453 ACATTAGAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.09
2 38 0.86
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40262 original size:105 final size:105
Alignment explanation
Indices: 39944--40711 Score: 1230
Period size: 105 Copynumber: 7.3 Consensus size: 105
39934 TGTTCCGAGG
** * * * * *
39944 CCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAG
* * *
40009 CGGTCCCTTCATCGTAAAGTTGAACTTGCGTTGTCTTGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
40050 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAATCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTATTGACAACCAG
*
40115 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
40156 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
40221 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
40261 CCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
* *
40326 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGC
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
40366 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCAATTGAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
*
40431 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
40471 CCAATACCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
* *
40536 GGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTAGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
40576 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAG
*
40641 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
40682 CCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTG
40712 ACTTTGGGTA
Statistics
Matches: 615, Mismatches: 45, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
105 392 0.64
106 223 0.36
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:48155 original size:21 final size:22
Alignment explanation
Indices: 48109--48156 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
48099 TCTTTAATTG
*
48109 ATCTTCTAATATTTTTATCTTT
1 ATCTTCTAATATTTTTAGCTTT
* *
48131 -TCTTC-AATCTTTTTGGCTTT
1 ATCTTCTAATATTTTTAGCTTT
48151 ATCTTC
1 ATCTTC
48157 CTCATCAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.17, C:0.19, G:0.04, T:0.60
Consensus pattern (22 bp):
ATCTTCTAATATTTTTAGCTTT
Found at i:53487 original size:2 final size:2
Alignment explanation
Indices: 53480--53526 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
53470 ATAAATAAAT
53480 TA TA TA TA TA TA TA TA T- TA TA -A TA TGA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
53520 TA -A TA TA
1 TA TA TA TA
53527 ACATTAGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 34 0.85
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:53919 original size:22 final size:23
Alignment explanation
Indices: 53894--53973 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 23
53884 TTATTTATTA
53894 ATATTTATAATAATATAATAT-T
1 ATATTTATAATAATATAATATAT
*
53916 ATATTTTTAATATTATATAA-ATAAT
1 ATATTTATAATA--ATATAATAT-AT
*
53941 CAATTATATTATAATAATATAAGATAT
1 --A-TAT-TTATAATAATATAATATAT
53968 ATATTT
1 ATATTT
53974 TTATTTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
22 11 0.23
23 4 0.09
24 9 0.19
25 2 0.04
27 9 0.19
28 5 0.11
29 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTTATAATAATATAATATAT
Found at i:53947 original size:30 final size:32
Alignment explanation
Indices: 53881--53960 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
53871 AAATATTATT
53881 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
53912 TATTATATTT-TTAATA-TTAT-ATAA-ATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
53940 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
53961 AAGATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 12 0.29
31 11 0.26
32 10 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:54012 original size:30 final size:30
Alignment explanation
Indices: 53944--54056 Score: 103
Period size: 28 Copynumber: 3.8 Consensus size: 30
53934 AAATAATCAA
*
53944 TTATATTATAATAATATA-AGATATA-TATTT
1 TTATATT-TAATAATATATA-ATAAATTATTT
*
53974 TTAT-TTTAATAATATATAATAAATTTTTT
1 TTATATTTAATAATATATAATAAATTATTT
54003 TTATATTTAATAATGA-ATAAT--ATTATTT
1 TTATATTTAATAAT-ATATAATAAATTATTT
* *
54031 ATATATTTTAATAATATTTTAATAAA
1 TTATA-TTTAATAATA-TATAATAAA
54057 GATATTTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
28 25 0.36
29 20 0.29
30 22 0.32
31 1 0.01
32 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTATATTTAATAATATATAATAAATTATTT
Found at i:54063 original size:14 final size:11
Alignment explanation
Indices: 54018--54055 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54008 TTTAATAATG
54018 AATAATATTATT
1 AATAATATT-TT
*
54030 TAT-ATATTTT
1 AATAATATTTT
54040 AATAATATTTT
1 AATAATATTTT
54051 AATAA
1 AATAA
54056 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:54076 original size:23 final size:23
Alignment explanation
Indices: 54050--54094 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54040 AATAATATTT
54050 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
54073 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
54095 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:54242 original size:27 final size:27
Alignment explanation
Indices: 54187--54242 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
54177 ATTATAAAAA
*
54187 TAATATTTAATAATAAATAAATTATTT
1 TAATATTTAATAATAAATAAATTAGTT
54214 TAATATTTAA-AAT-AATAATATTAAGTT
1 TAATATTTAATAATAAATAA-ATT-AGTT
54241 TA
1 TA
54243 TGATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 6 0.23
27 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TAATATTTAATAATAAATAAATTAGTT
Found at i:54425 original size:13 final size:14
Alignment explanation
Indices: 54384--54426 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54374 AATGTCATTC
* *
54384 ATTTTACGAAAAAC
1 ATTTTCCGAAAAAT
*
54398 ATTTTCCGTAAAAT
1 ATTTTCCGAAAAAT
54412 ATTTTCC-AAAAAT
1 ATTTTCCGAAAAAT
54425 AT
1 AT
54427 AATTCATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (14 bp):
ATTTTCCGAAAAAT
Found at i:54459 original size:15 final size:15
Alignment explanation
Indices: 54441--54476 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54431 CATTTTCTAG
* *
54441 AATTTAAATTTCAGT
1 AATTCAAATTCCAGT
54456 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
54471 AATTCA
1 AATTCA
54477 TTTTTCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:60146 original size:49 final size:49
Alignment explanation
Indices: 60080--60173 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
60070 TGATTTCTTT
* * *
60080 GTTTAAATTGGTTAAAAGATTATTAGATTGAATACTAAAATCAATTTCA
1 GTTTAAACTGGTTAAAAGATCATTAAATTGAATACTAAAATCAATTTCA
* *
60129 GTTTAAACTGGTTAAAAGATCATTAAATTGAATATTGAAATCAAT
1 GTTTAAACTGGTTAAAAGATCATTAAATTGAATACTAAAATCAAT
60174 ATGTCAGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (49 bp):
GTTTAAACTGGTTAAAAGATCATTAAATTGAATACTAAAATCAATTTCA
Found at i:60270 original size:36 final size:36
Alignment explanation
Indices: 60217--60287 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
60207 GGCCTTGCTA
*
60217 AAAAAAACCTTCTATATTCGAGTCAAATCAAAATTC
1 AAAAAAACCTTCTATATTCGAATCAAATCAAAATTC
* *
60253 AAAAAACCCTT-TCATATTTGAATCAAATCAAAATT
1 AAAAAAACCTTCT-ATATTCGAATCAAATCAAAATT
60288 TAATATCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (36 bp):
AAAAAAACCTTCTATATTCGAATCAAATCAAAATTC
Found at i:62412 original size:9 final size:9
Alignment explanation
Indices: 62398--62425 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62388 ATCTAATACT
62398 TTTGAGCAC
1 TTTGAGCAC
62407 TTTGAGCAC
1 TTTGAGCAC
62416 TTTGAGCAC
1 TTTGAGCAC
62425 T
1 T
62426 CACTCTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (9 bp):
TTTGAGCAC
Found at i:65162 original size:40 final size:40
Alignment explanation
Indices: 65118--65299 Score: 129
Period size: 39 Copynumber: 4.7 Consensus size: 40
65108 TATAATTTAC
65118 AAATGTTTTTGAAATACATATAATATATATATAGTTTTGA
1 AAATGTTTTTGAAATACATATAATATATATATAGTTTTGA
* * *
65158 AAATGATTTTTGGAAATATATATATTATATA-AT-G-TTTGG
1 AAATG-TTTTT-GAAATACATATAATATATATATAGTTTTGA
*
65197 AAA-GATTTTTG-AA-ACATAT-ATA-ATATATGGTTTTTGA
1 AAATG-TTTTTGAAATACATATAATATATATATAG-TTTTGA
* * *
65234 AAAT-ATTTT-AAATATATATATATATATAATATAATTTT-A
1 AAATGTTTTTGAAATACATATA-ATATAT-ATATAGTTTTGA
** *
65273 AAACATTTTTGAAAT--TTATAATATATA
1 AAATGTTTTTGAAATACATATAATATATA
65300 ATTTTAAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
33 3 0.03
34 4 0.04
35 6 0.05
36 8 0.07
37 14 0.12
38 13 0.11
39 18 0.16
40 16 0.14
41 15 0.13
42 17 0.15
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (40 bp):
AAATGTTTTTGAAATACATATAATATATATATAGTTTTGA
Found at i:65216 original size:37 final size:37
Alignment explanation
Indices: 65098--65263 Score: 128
Period size: 37 Copynumber: 4.4 Consensus size: 37
65088 TTTTCGCCTG
**
65098 ATATATATTATATAA-TTTACAAATG-TTTTTGAAATAC
1 ATATATATTATATAATTTTGGAAATGATTTTTG-AA-AC
* * *
65135 ATATAATATATATATAGTTTTGAAAATGATTTTTGGAAAT
1 ATAT-ATAT-TATATAATTTTGGAAATGATTTTT-GAAAC
65175 ATATATATTATATAATGTTTGGAAA-GATTTTTGAAAC
1 ATATATATTATATAAT-TTTGGAAATGATTTTTGAAAC
* ** * *
65212 ATATATAATATATGGTTTTTGAAA--ATATTTT-AAAT
1 ATATATATTATATAATTTTGGAAATGAT-TTTTGAAAC
65247 ATATATATATATATAAT
1 ATATATAT-TATATAAT
65264 ATAATTTTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
35 12 0.11
36 17 0.16
37 21 0.20
38 18 0.17
39 17 0.16
40 13 0.12
41 7 0.07
42 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (37 bp):
ATATATATTATATAATTTTGGAAATGATTTTTGAAAC
Found at i:65251 original size:35 final size:37
Alignment explanation
Indices: 65124--65261 Score: 133
Period size: 36 Copynumber: 3.6 Consensus size: 37
65114 TTACAAATGT
65124 TTTTGAAATACATATAATATATATATAG-TTTTGAAAATGA
1 TTTTGAAAT--ATAT-ATATATATATAGTTTTTGAAAAT-A
* *
65164 TTTTTGGAAATATATATAT-TATATAATGTTTGGAAAGAT-
1 -TTTT-GAAATATATATATATATATAGT-TTTTGAAA-ATA
* *
65203 TTTTGAAACATATATA-ATATATGGTTTTTGAAAATA
1 TTTTGAAATATATATATATATATAGTTTTTGAAAATA
65239 TTTT-AAATATATATATATATATA
1 TTTTGAAATATATATATATATATA
65262 ATATAATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
35 12 0.15
36 17 0.21
37 17 0.21
38 10 0.12
39 4 0.05
40 11 0.13
41 6 0.07
42 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (37 bp):
TTTTGAAATATATATATATATATAGTTTTTGAAAATA
Found at i:65320 original size:38 final size:36
Alignment explanation
Indices: 65251--65451 Score: 155
Period size: 35 Copynumber: 5.5 Consensus size: 36
65241 TTAAATATAT
65251 ATATATATATAATATAATTTT--AAAACA-TTTTTGAA
1 ATATATA-AT-ATATAATTTTAAAAAACATTTTTTGAA
*
65286 ATTTATAATATATAATTTTAAAAAAACATTTTTTTGAAA
1 ATATATAATATATAATTTT-AAAAAACA-TTTTTTG-AA
* * *
65325 ACATATAAAATAT-AGTTT-AAAAACA-TTTTTGAAA
1 ATATATAATATATAATTTTAAAAAACATTTTTTG-AA
* *
65359 ACTATATAATATATAA-TTTAAAAAAGATTTTTTAAA
1 A-TATATAATATATAATTTTAAAAAACATTTTTTGAA
* ** * *
65395 ATATATAATATATAGTTTTTTTAAAATATTTTTTTAAA
1 ATATATAATATATA-ATTTTAAAAAACA-TTTTTTGAA
* *
65433 AGATATATTATATAATTTT
1 ATATATAATATATAATTTT
65452 TTGAAAATAT
Statistics
Matches: 137, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
33 10 0.07
34 12 0.09
35 32 0.23
36 23 0.17
37 17 0.12
38 31 0.23
39 12 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATATAATATATAATTTTAAAAAACATTTTTTGAA
Found at i:65352 original size:72 final size:70
Alignment explanation
Indices: 65255--65412 Score: 203
Period size: 72 Copynumber: 2.2 Consensus size: 70
65245 ATATATATAT
* * * *
65255 ATATATAATATAATTTTAAAACATTTTTG-AAA-TTTATAATATATAATTTTAAAAAAACATTTT
1 ATATAAAATATAGTTTAAAAACATTTTTGAAAACTATATAATATATAA-TTT-AAAAAACA-TTT
65318 TTTGAAAAC
63 TTT-AAAAC
*
65327 ATATAAAATATAGTTTAAAAACATTTTTGAAAACTATATAATATATAATTTAAAAAAGATTTTTT
1 ATATAAAATATAGTTTAAAAACATTTTTGAAAACTATATAATATATAATTTAAAAAACATTTTTT
*
65392 AAAAT
66 AAAAC
*
65397 ATATAATATATAGTTT
1 ATATAAAATATAGTTT
65413 TTTTAAAATA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
70 19 0.25
71 6 0.08
72 33 0.43
73 6 0.08
74 13 0.17
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (70 bp):
ATATAAAATATAGTTTAAAAACATTTTTGAAAACTATATAATATATAATTTAAAAAACATTTTTT
AAAAC
Found at i:65366 original size:35 final size:35
Alignment explanation
Indices: 65251--65408 Score: 169
Period size: 35 Copynumber: 4.4 Consensus size: 35
65241 TTAAATATAT
*
65251 ATATATATATAATATAATTT-TAAAACATTTTTG-AA
1 ATATATA-AT-ATATAATTTAAAAAACATTTTTGAAA
*
65286 ATTTATAATATATAATTTTAAAAAAACATTTTTTTGAAA
1 ATATATAATATATAA-TTT-AAAAAACA--TTTTTGAAA
* * *
65325 ACATATAAAATATAGTTT-AAAAACATTTTTGAAA
1 ATATATAATATATAATTTAAAAAACATTTTTGAAA
* *
65359 ACTATATAATATATAATTTAAAAAAGATTTTTTAAA
1 A-TATATAATATATAATTTAAAAAACATTTTTGAAA
65395 ATATATAATATATA
1 ATATATAATATATA
65409 GTTTTTTTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
33 6 0.06
34 15 0.14
35 33 0.32
36 28 0.27
38 9 0.09
39 13 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (35 bp):
ATATATAATATATAATTTAAAAAACATTTTTGAAA
Found at i:65452 original size:38 final size:38
Alignment explanation
Indices: 65135--65465 Score: 127
Period size: 38 Copynumber: 8.8 Consensus size: 38
65125 TTTGAAATAC
* ** *
65135 ATATAATATATATATAGTTTTGAAAATGATTTTTGGAAATAT
1 ATATAATATATA-AT-TTTTTGAAAAT-ATTTTTTTAAA-AG
* * * * * *
65177 ATATATTATATAA-TGTTTGGAAAGA-TTTTTGAAACAT
1 ATATAATATATAATTTTTTGAAAATATTTTTTTAAA-AG
** *
65214 ATATAATATAT-GGTTTTTGAAAATA---TTTTAAATAT
1 ATATAATATATAATTTTTTGAAAATATTTTTTTAAA-AG
* * *
65249 ATATATATATATAATATAATTTT-AAAACA--TTTTTGAAAT
1 ATATA-ATATATAAT-T--TTTTGAAAATATTTTTTTAAAAG
* *** * *
65288 TTATAATATATAATTTTAAAAAAACATTTTTTTGAAAAC
1 ATATAATATATAATTTTTTGAAAATATTTTTTT-AAAAG
** * * * *
65327 ATATAA-A-AT-ATAGTTTAAAAACA-TTTTTGAAAACT
1 ATATAATATATAATTTTTTGAAAATATTTTTTTAAAA-G
** * *
65362 ATATAATATATAA--TTTAAAAAAGA-TTTTTTAAAAT
1 ATATAATATATAATTTTTTGAAAATATTTTTTTAAAAG
* *
65397 ATATAATATATAGTTTTTTTAAAATATTTTTTTAAAAG
1 ATATAATATATAATTTTTTGAAAATATTTTTTTAAAAG
*
65435 ATATATTATATAATTTTTTGAAAATATTTTT
1 ATATAATATATAATTTTTTGAAAATATTTTT
65466 GTATATAATA
Statistics
Matches: 229, Mismatches: 42, Indels: 40
0.74 0.14 0.13
Matches are distributed among these distances:
34 4 0.02
35 39 0.17
36 40 0.17
37 42 0.18
38 56 0.24
39 26 0.11
40 10 0.04
41 1 0.00
42 11 0.05
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATAATATATAATTTTTTGAAAATATTTTTTTAAAAG
Found at i:65494 original size:13 final size:13
Alignment explanation
Indices: 65476--65516 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
65466 GTATATAATA
65476 TATTATTATTATT
1 TATTATTATTATT
65489 TATTATTATTATT
1 TATTATTATTATT
*
65502 TCTTA-T-TTATT
1 TATTATTATTATT
65513 TATT
1 TATT
65517 TCCATTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 8 0.31
12 1 0.04
13 17 0.65
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:66628 original size:14 final size:14
Alignment explanation
Indices: 66580--66635 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
66570 TTACGCATAT
*
66580 TTTATTGTTA-TTA
1 TTTATTTTTATTTA
66593 TATTATTGTTT-TTT-
1 T-TTATT-TTTATTTA
*
66607 TCTATTTTTATTTA
1 TTTATTTTTATTTA
66621 TTTATTTTTATTTA
1 TTTATTTTTATTTA
66635 T
1 T
66636 CATTCTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
12 3 0.09
13 8 0.23
14 20 0.57
15 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:66791 original size:22 final size:24
Alignment explanation
Indices: 66766--66833 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
66756 ATTATTTAGC
66766 ATTTTATTTATTATTTTTCC-TTA
1 ATTTTATTTATTATTTTTCCTTTA
* *
66789 TTTTTATTT-TTATTTTCCCTTTGA
1 ATTTTATTTATTATTTTTCCTTT-A
66813 ATTATTATTTTATTATTTTTC
1 ATT-TTA-TTTATTATTTTTC
66834 ATTTTTATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 9 0.25
23 10 0.28
24 3 0.08
25 3 0.08
26 3 0.08
27 8 0.22
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.71
Consensus pattern (24 bp):
ATTTTATTTATTATTTTTCCTTTA
Found at i:66849 original size:16 final size:17
Alignment explanation
Indices: 66820--66856 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
66810 TGAATTATTA
66820 TTTTATTATTTTTCAT-
1 TTTTATTATTTTTCATG
66836 TTTTATTCA-TTTTCATG
1 TTTTATT-ATTTTTCATG
66853 TTTT
1 TTTT
66857 TTTACTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTTTCATG
Found at i:70349 original size:95 final size:95
Alignment explanation
Indices: 70173--70415 Score: 274
Period size: 95 Copynumber: 2.5 Consensus size: 95
70163 TATTATTATG
* ** * *
70173 TATACAATAAAGCTTGAACTGTCCCTCTAGAGCAATTGGTTAAACCCCCCGGCTTTATGGATAAG
1 TATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAG
* * *
70238 ATTCATCTAACTTGATAAAGG-GAATTATAA
66 ATTAAGCTAACCTGATAAAGGTG-ATTATAA
* * *
70268 TATACAATAAAGTTTGAGTTATCCCTATAGAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAT
1 TATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAG
* *
70333 ATTAAGCTAGCCTGATAAAGGTGATTATAT
66 ATTAAGCTAACCTGATAAAGGTGATTATAA
* * **
70363 TAT-CTATACAATGATATTAAGTTGTCCCTCTAGAAAAATTGGTTAAACGCCCC
1 TATACAATA-AA-G-T-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCC
70416 AACTTTATGA
Statistics
Matches: 124, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
94 4 0.03
95 85 0.69
96 2 0.02
97 1 0.01
98 32 0.26
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (95 bp):
TATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAG
ATTAAGCTAACCTGATAAAGGTGATTATAA
Found at i:71999 original size:31 final size:31
Alignment explanation
Indices: 71957--72020 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
71947 GTATTCTAAA
* * * *
71957 CACAAGTAGTGAATTTCGACAGGAATACTAG
1 CACAAGCAGTGAATTTCGAAAGCAACACTAG
*
71988 CACAAGCAGTGAGTTTCGAAAGCAACACTAG
1 CACAAGCAGTGAATTTCGAAAGCAACACTAG
72019 CA
1 CA
72021 GTCCATAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (31 bp):
CACAAGCAGTGAATTTCGAAAGCAACACTAG
Found at i:81329 original size:8 final size:8
Alignment explanation
Indices: 81316--81343 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
81306 AGATCCTCTC
81316 ATATGTAT
1 ATATGTAT
81324 ATATGTAT
1 ATATGTAT
81332 ATATGTAT
1 ATATGTAT
81340 ATAT
1 ATAT
81344 ATATTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:84846 original size:7 final size:7
Alignment explanation
Indices: 84836--84893 Score: 61
Period size: 7 Copynumber: 8.4 Consensus size: 7
84826 AGAAAAAAAT
84836 AAAATGAA
1 AAAATG-A
84844 AAAATGA
1 AAAATGA
84851 GAAAATGA
1 -AAAATGA
84859 AAAA-GA
1 AAAATGA
84865 AAAA-G-
1 AAAATGA
84870 AAAA-GAA
1 AAAATG-A
84877 AAAATGA
1 AAAATGA
84884 AAAATGA
1 AAAATGA
84891 AAA
1 AAA
84894 GGAAAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.11
6 7 0.15
7 20 0.43
8 14 0.30
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (7 bp):
AAAATGA
Found at i:84847 original size:8 final size:8
Alignment explanation
Indices: 84836--84893 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
84826 AGAAAAAAAT
84836 AAAATGAA
1 AAAATGAA
*
84844 AAAATGAG
1 AAAATGAA
84852 AAAATGAA
1 AAAATGAA
*
84860 AAAGA-AAA
1 AAA-ATGAA
*
84868 AGAAAAGAA
1 A-AAATGAA
84877 AAAATG-A
1 AAAATGAA
84884 AAAATGAA
1 AAAATGAA
84892 AA
1 AA
84894 GGAAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 7 0.17
8 28 0.68
9 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (8 bp):
AAAATGAA
Found at i:84885 original size:19 final size:18
Alignment explanation
Indices: 84858--84909 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 18
84848 TGAGAAAATG
84858 AAAAAGAAAAAGAAAAGA
1 AAAAAGAAAAAGAAAAGA
*
84876 AAAAATGAAAAATGAAAAGG
1 AAAAA-GAAAAA-GAAAAGA
84896 AAAAAGAAGAAAGA
1 AAAAAGAA-AAAGA
84910 GTAAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 14 0.47
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAGA
Found at i:84888 original size:32 final size:34
Alignment explanation
Indices: 84830--84903 Score: 116
Period size: 32 Copynumber: 2.2 Consensus size: 34
84820 TTAAAGAGAA
*
84830 AAAAATAAAATGAAAAAATGAGAAAATGAAAAAG
1 AAAAAGAAAATGAAAAAATGAGAAAATGAAAAAG
*
84864 AAAAAGAAAA-GAAAAAATGA-AAAATGAAAAGG
1 AAAAAGAAAATGAAAAAATGAGAAAATGAAAAAG
84896 AAAAAGAA
1 AAAAAGAA
84904 GAAAGAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 19 0.50
33 10 0.26
34 9 0.24
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (34 bp):
AAAAAGAAAATGAAAAAATGAGAAAATGAAAAAG
Found at i:86286 original size:38 final size:37
Alignment explanation
Indices: 86195--86301 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 37
86185 TCGAAACAAG
* * * * *
86195 TCAATTTTAAGCCTTCATGAAATAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGGAATAGTAGTGAAGCAAA
*
86232 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAA
1 TCAATCTTAAGCCTTCACGGAATAGTAGTGAAGC-AAA
86270 TC-ATCTATAAGCCTTCACGGAATAGTAGTGAA
1 TCAATCT-TAAGCCTTCACGGAATAGTAGTGAA
86302 ACATATTCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
37 33 0.54
38 28 0.46
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAATAGTAGTGAAGCAAA
Found at i:86388 original size:55 final size:55
Alignment explanation
Indices: 86322--86734 Score: 431
Period size: 55 Copynumber: 7.5 Consensus size: 55
86312 TTTATGAAGA
* * * * *
86322 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTAGTTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
86377 TTGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTAGTTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * * *
86432 TTGAGTTCTATACTCCCTAAAGGAATAGGGAGCAGA-CCATTTTTATGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * * ** *
86487 TCGAGTTTTATACTCCCTGAACGAATAGGGGGTGGACCTATTTTGCTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACC-CGTTTGTTGAAGATTGT
* * * * * *
86543 TTGAGTTCTATACTCCCTAAATGAATAGGGAG-TGACCCATTTTTATGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* *
86598 TCGAGTTCTATAGTCCCTGAACG-ATAGGGAGTGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * * *
86652 TCAAGTCCTATACTCTCTGAAGGAAGAGGGAGCGGACCCG-TT-TTGAAGATTAT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
86705 TCGAGTCCTATACTCTCTGAATGAATAGGG
1 TCGAGTTCTATACTCCCTGAACGAATAGGG
86735 GGAAGAGAAT
Statistics
Matches: 302, Mismatches: 50, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
53 37 0.12
54 46 0.15
55 178 0.59
56 38 0.13
57 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:86481 original size:110 final size:109
Alignment explanation
Indices: 86324--86734 Score: 477
Period size: 110 Copynumber: 3.8 Consensus size: 109
86314 TATGAAGATC
* * * ** *
86324 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTAGTTGAAGATTGTTTGAGTTCTATA
1 GAGTCCTATACTCCCTAAAGGAATAGGGAGCGGAC-CATTTTTTGAAGATTGTTCGAGTTCTATA
** *
86389 CTCCCTGAACGAATAGGGAGCAGACCCGTTAGTTGAAGATTGTTT
65 CTCCCTGAACGAATAGGGAGTGGACCCGTTTGTTGAAGATTGTTT
* * *
86434 GAGTTCTATACTCCCTAAAGGAATAGGGAGCAGACCATTTTTATGAAGATTGTTCGAGTTTTATA
1 GAGTCCTATACTCCCTAAAGGAATAGGGAGCGGACCATTTTT-TGAAGATTGTTCGAGTTCTATA
* ** *
86499 CTCCCTGAACGAATAGGGGGTGGACCTATTTTGCTGAAGATTGTTT
65 CTCCCTGAACGAATAGGGAGTGGACC-CGTTTGTTGAAGATTGTTT
* * *
86545 GAGTTCTATACTCCCTAAATGAATAGGGAG-TGACCCATTTTTATGAAGATTGTTCGAGTTCTAT
1 GAGTCCTATACTCCCTAAAGGAATAGGGAGCGGA-CCATTTTT-TGAAGATTGTTCGAGTTCTAT
* *
86609 AGTCCCTGAACG-ATAGGGAGTGGACCCGTTTGTTGAAGATTGTTC
64 ACTCCCTGAACGAATAGGGAGTGGACCCGTTTGTTGAAGATTGTTT
* * * * ** * *
86654 AAGTCCTATACTCTCTGAAGGAAGAGGGAGCGGACC-CGTTTTGAAGATTATTCGAGTCCTATAC
1 GAGTCCTATACTCCCTAAAGGAATAGGGAGCGGACCATTTTTTGAAGATTGTTCGAGTTCTATAC
* *
86718 TCTCTGAATGAATAGGG
66 TCCCTGAACGAATAGGG
86735 GGAAGAGAAT
Statistics
Matches: 257, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
107 28 0.11
108 9 0.04
109 45 0.18
110 91 0.35
111 84 0.33
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (109 bp):
GAGTCCTATACTCCCTAAAGGAATAGGGAGCGGACCATTTTTTGAAGATTGTTCGAGTTCTATAC
TCCCTGAACGAATAGGGAGTGGACCCGTTTGTTGAAGATTGTTT
Found at i:87719 original size:84 final size:83
Alignment explanation
Indices: 87597--87781 Score: 230
Period size: 84 Copynumber: 2.2 Consensus size: 83
87587 GTTGACTTGT
* * * *
87597 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA-TTGCAA-CATAACTCAAGG
1 CAAAAGACCTTCGAGTTCAACTACACTCAACTCAAAGGCACATCATTTG-AAGC-TAACTCAAGG
*
87660 AAAGAAGGGTTATCTTGCCAA
64 AAAGAAGGGCTATC-TGCCAA
* * ***
87681 CAAAAGACCTTTGAGTTCAACTACACTCAACTCAAAGGCACATCATTTGAAGCTAACTTAAGTCG
1 CAAAAGACCTTCGAGTTCAACTACACTCAACTCAAAGGCACATCATTTGAAGCTAACTCAAGGAA
87746 AGAAGGGCTATCTGCCAA
66 AGAAGGGCTATCTGCCAA
*
87764 CCAAAGACCTTCGAGTTC
1 CAAAAGACCTTCGAGTTC
87782 GACTCGTGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
83 22 0.25
84 61 0.70
85 4 0.05
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (83 bp):
CAAAAGACCTTCGAGTTCAACTACACTCAACTCAAAGGCACATCATTTGAAGCTAACTCAAGGAA
AGAAGGGCTATCTGCCAA
Done.