Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006427.1 Hibiscus syriacus cultivar Beakdansim tig00015516_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: 94931
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3912 original size:21 final size:21
Alignment explanation
Indices: 3886--3943 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
3876 AAATTTTTGC
3886 CTTATGGTATCGATACTCATT
1 CTTATGGTATCGATACTCATT
3907 CTTATGGTATCGATACTCATT
1 CTTATGGTATCGATACTCATT
3928 CTTATGGTATCGATAC
1 CTTATGGTATCGATAC
3944 CCTCACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTATGGTATCGATACTCATT
Found at i:9895 original size:21 final size:21
Alignment explanation
Indices: 9865--9912 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
9855 CCGATTCCCC
*
9865 CCCCCCAAGAGGGTACCGATT
1 CCCCCTAAGAGGGTACCGATT
*
9886 CCCCCTAAGAGGGTATCGATT
1 CCCCCTAAGAGGGTACCGATT
9907 CCCCCT
1 CCCCCT
9913 GAATGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (21 bp):
CCCCCTAAGAGGGTACCGATT
Found at i:15782 original size:21 final size:21
Alignment explanation
Indices: 15757--15820 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
15747 TTGGTGCAGA
15757 GGGAATCGATACCCCCTTGAG
1 GGGAATCGATACCCCCTTGAG
* * **
15778 GGGAACCGATTCCTCCC-ACAG
1 GGGAATCGATACC-CCCTTGAG
*
15799 GGGAATCGATA-CCCGTTGAG
1 GGGAATCGATACCCCCTTGAG
15819 GG
1 GG
15821 TTATGGATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 22 0.69
22 3 0.09
ACGTcount: A:0.23, C:0.28, G:0.31, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTGAG
Found at i:19923 original size:9 final size:9
Alignment explanation
Indices: 19903--19948 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
19893 TCTTCATTCA
19903 TTTTTTTCT
1 TTTTTTTCT
*
19912 TTTTTCT-T
1 TTTTTTTCT
19920 TTTTTTTCT
1 TTTTTTTCT
19929 TTATTTTT-T
1 TT-TTTTTCT
*
19938 TTATTTTCT
1 TTTTTTTCT
19947 TT
1 TT
19949 CCCTTACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
8 11 0.35
9 15 0.48
10 5 0.16
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:19926 original size:18 final size:17
Alignment explanation
Indices: 19903--19948 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
19893 TCTTCATTCA
19903 TTTTTTTCTTT-TTTCTT
1 TTTTTTTCTTTATTT-TT
19920 TTTTTTTCTTTATTTTT
1 TTTTTTTCTTTATTTTT
19937 TTTATTTTCTTT
1 TTT-TTTTCTTT
19949 CCCTTACCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTTCTTTATTTTT
Found at i:26215 original size:19 final size:18
Alignment explanation
Indices: 26187--26225 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
26177 ACTTCATTCA
*
26187 TTTCATTTTTTTGATTTT
1 TTTCATTTTTTTCATTTT
26205 TTTCAATTTTTTTCATTTT
1 TTTC-ATTTTTTTCATTTT
26224 TT
1 TT
26226 AGTAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTCATTTTTTTCATTTT
Found at i:29482 original size:12 final size:12
Alignment explanation
Indices: 29461--29510 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
29451 ACCTGAAAAG
*
29461 ACAAGGAAAATA
1 ACAAGTAAAATA
29473 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
29486 TACAA--AAAATGA
1 -ACAAGTAAAAT-A
29498 ACAAGTAAAATA
1 ACAAGTAAAATA
29510 A
1 A
29511 AAATGCTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:33346 original size:226 final size:232
Alignment explanation
Indices: 33015--33477 Score: 742
Period size: 226 Copynumber: 2.0 Consensus size: 232
33005 AATAACTAGT
*
33015 TGGTGTAGTGAGATGAGGCACTAGTTCCTTTAAGCAAGGTAAGAGATTTAAATTCTAACAATTGC
1 TGGTGTAGTGAGATGAGACACTAGTTCCTTTAAGCAAGGTAAGAGATTTAAATTCTAACAATTGC
*
33080 GAATAGAGTAAAATGGGTTAGGAGAGTTGTCTTTGCCTCTGTAATATCCGATTCGGTGTAGTCAA
66 GAATAGAATAAAATGGGTTAGGAGAGTTGTCTTTGCCTCTGTAATATCCGATTCGGTGTAGTCAA
* * *
33145 TCAATAGATTGGACACCGGTGA-T-T-AT-AA-AAAA-ATAAATTACATAAATAATTATTTGACT
131 ACAATAGATTGAACACCAGTGATTATAATAAATAAAATATAAATTACATAAATAATTATTTGACT
33204 AATAATATTTTCTTTATATCATTTGATTATCAAAAAG
196 AATAATATTTTCTTTATATCATTTGATTATCAAAAAG
* *
33241 TGGTGTAGTGGGATGAGACATTAGTT-CTCTTAAGCAAGGTAAGAGATTTAAATTCTAACAATTG
1 TGGTGTAGTGAGATGAGACACTAGTTCCT-TTAAGCAAGGTAAGAGATTTAAATTCTAACAATTG
33305 CGAATAGAATAAAATGGGTTAGGAGAGTTGTCTTTGCCTCTGTAATATCCGATTCGGTGTAGTCA
65 CGAATAGAATAAAATGGGTTAGGAGAGTTGTCTTTGCCTCTGTAATATCCGATTCGGTGTAGTCA
33370 AACAATAGATTGAACACCAGTGATTATAAAAACATAAATTTAAAATATAAATTACATAAATAATT
130 AACAATAGATTGAACACCAGTGATTAT----A-ATAAA--TAAAATATAAATTACATAAATAATT
33435 ATTTGACTAATAATATTTTCTTTATATCATTTGATTATCAAAA
188 ATTTGACTAATAATATTTTCTTTATATCATTTGATTATCAAAA
33478 GTTATAAAAA
Statistics
Matches: 216, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
225 2 0.01
226 142 0.66
227 1 0.00
228 1 0.00
234 2 0.01
235 2 0.01
238 4 0.02
239 62 0.29
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (232 bp):
TGGTGTAGTGAGATGAGACACTAGTTCCTTTAAGCAAGGTAAGAGATTTAAATTCTAACAATTGC
GAATAGAATAAAATGGGTTAGGAGAGTTGTCTTTGCCTCTGTAATATCCGATTCGGTGTAGTCAA
ACAATAGATTGAACACCAGTGATTATAATAAATAAAATATAAATTACATAAATAATTATTTGACT
AATAATATTTTCTTTATATCATTTGATTATCAAAAAG
Found at i:36347 original size:16 final size:16
Alignment explanation
Indices: 36326--36406 Score: 76
Period size: 16 Copynumber: 4.8 Consensus size: 16
36316 TATGCATACA
36326 ATATAAGTATATACTT
1 ATATAAGTATATACTT
36342 ATATAAGTATATAC-T
1 ATATAAGTATATACTT
*
36357 ATAGATA-TACTATACTT
1 ATATA-AGTA-TATACTT
*
36374 ATAATATATGTATATAATAT
1 AT-ATA-A-GTATATACT-T
36394 ATATAAGTATATA
1 ATATAAGTATATA
36407 TATAAACTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
15 7 0.13
16 20 0.36
17 10 0.18
18 5 0.09
19 8 0.15
20 5 0.09
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATAAGTATATACTT
Found at i:36452 original size:16 final size:15
Alignment explanation
Indices: 36431--36525 Score: 60
Period size: 14 Copynumber: 6.6 Consensus size: 15
36421 TAGAAGTAGA
36431 AGTATATAAACTATAT
1 AGTATATAAA-TATAT
36447 AG--TAT--ATATAT
1 AGTATATAAATATAT
*
36458 AGTATATAAAATATAA
1 AGTATAT-AAATATAT
**
36474 AGCGTATAAACTATA-
1 AGTATATAAA-TATAT
*
36489 A-TATATATATATAT
1 AGTATATAAATATAT
*
36503 A-TATATAAGTATAT
1 AGTATATAAATATAT
*
36517 AATATATAA
1 AGTATATAA
36526 GTATGTAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
11 7 0.11
12 1 0.02
13 7 0.11
14 21 0.33
15 11 0.17
16 16 0.25
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (15 bp):
AGTATATAAATATAT
Found at i:36472 original size:27 final size:27
Alignment explanation
Indices: 36431--36529 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
36421 TAGAAGTAGA
*
36431 AGTATATAAACTATATAGTATATATAT
1 AGTATATAAAATATATAGTATATATAT
* *
36458 AGTATATAAAATATAAAGCGTATAAACTAT
1 AGTATATAAAATATATA--GTATATA-TAT
*
36488 A--ATAT-ATATATATA-TATATATA-
1 AGTATATAAAATATATAGTATATATAT
*
36510 AGTATATAATATATA-AGTAT
1 AGTATATAAAATATATAGTAT
36530 GTAAACTATA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.02
23 2 0.03
24 10 0.17
25 10 0.17
27 22 0.37
28 4 0.07
29 6 0.10
30 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (27 bp):
AGTATATAAAATATATAGTATATATAT
Found at i:36496 original size:2 final size:2
Alignment explanation
Indices: 36485--36524 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
36475 GCGTATAAAC
36485 TA TA -A TA TA TA TA TA TA TA TA TA TA -A GTA TA TA -A 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
36525 AGTATGTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 30 0.88
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:36525 original size:43 final size:42
Alignment explanation
Indices: 36341--36525 Score: 125
Period size: 43 Copynumber: 4.3 Consensus size: 42
36331 AGTATATACT
* *
36341 TATATAAGTATAT--ACTATAGATATACTATACT-TATAATATATG
1 TATATAA-TATATAAACTATATATATA-TATA-TATAT-ATATAAG
* * *
36384 TATATAATATATATAAGTATATATATA-A-ACTATAAAGTAGAAG
1 TATATAATATATA-AACTATATATATATATA-TATATA-TATAAG
* * *
36427 TAGA-AGTATATAAACTATATAGTATATATATAGTATATA-AAA
1 TATATAATATATAAACTATATA-TATATATATA-TATATATAAG
**
36469 TATA-AAGCGTATAAACTATAATATATATATATATATATATAAG
1 TATATAA-TATATAAACTAT-ATATATATATATATATATATAAG
36512 TATATAATATATAA
1 TATATAATATATAA
36526 GTATGTAAAC
Statistics
Matches: 112, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
41 8 0.07
42 32 0.29
43 53 0.47
44 9 0.08
45 10 0.09
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (42 bp):
TATATAATATATAAACTATATATATATATATATATATATAAG
Found at i:36539 original size:15 final size:15
Alignment explanation
Indices: 36326--36529 Score: 69
Period size: 18 Copynumber: 12.7 Consensus size: 15
36316 TATGCATACA
*
36326 ATATAAGTATATACTT
1 ATATAAGTATATA-AT
36342 ATATAAGTATATACTAT
1 ATATAAGTATATA--AT
* * *
36359 AGATATACTATACTTAT
1 ATATA-AGTATA-TAAT
*
36376 AATATATGTATATAATAT
1 -ATATAAGTATAT-A-AT
36394 ATATAAGTATAT-AT
1 ATATAAGTATATAAT
*
36408 ATA-AACTATA-AA-
1 ATATAAGTATATAAT
* * * *
36420 GTAGAAGTAGA-AGT
1 ATATAAGTATATAAT
*
36434 ATATAAACTATATAGTAT
1 ATAT-AAGTATATA--AT
*
36452 ATATATAGTATATAAA
1 ATATA-AGTATATAAT
36468 ATATAAAGCGTATA-AACT
1 ATAT-AA--GTATATAA-T
*
36486 ATAATATATATATATATAT
1 AT-ATA-A-GTATATA-AT
36505 ATATAAGTATATAAT
1 ATATAAGTATATAAT
36520 ATATAAGTAT
1 ATATAAGTAT
36530 GTAAACTATA
Statistics
Matches: 140, Mismatches: 26, Indels: 45
0.66 0.12 0.21
Matches are distributed among these distances:
12 2 0.01
13 13 0.09
14 7 0.05
15 17 0.12
16 27 0.19
17 27 0.19
18 38 0.27
19 8 0.06
20 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (15 bp):
ATATAAGTATATAAT
Found at i:36553 original size:51 final size:51
Alignment explanation
Indices: 36435--36557 Score: 130
Period size: 51 Copynumber: 2.4 Consensus size: 51
36425 AGTAGAAGTA
*
36435 TATAA-AC-TATATAGTATATATATAGTATATAAAATATAAAGCGTATAAAC
1 TATAATACATATATA-TATATATATAGTATATAAAATATAAAGCATATAAAC
* * * *
36485 TATAATATATATATATATATATATAAGTATATAATATAT-AAGTATGTAAAC
1 TATAATACATATATATATATATAT-AGTATATAAAATATAAAGCATATAAAC
36536 TAT-ATGACATA-AGTATATATAT
1 TATAAT-ACATATA-TATATATAT
36558 GCATGTATGT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
50 8 0.13
51 35 0.56
52 19 0.31
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (51 bp):
TATAATACATATATATATATATATAGTATATAAAATATAAAGCATATAAAC
Found at i:36663 original size:15 final size:15
Alignment explanation
Indices: 36643--36672 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36633 TGTATGATCA
36643 ATGATACATGTATGT
1 ATGATACATGTATGT
36658 ATGATACATGTATGT
1 ATGATACATGTATGT
36673 GTGTGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
ATGATACATGTATGT
Found at i:43093 original size:16 final size:16
Alignment explanation
Indices: 43072--43124 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
43062 TGCAACTTAT
43072 AAGTCATGTAAATATC
1 AAGTCATGTAAATATC
* *
43088 AAGTCATATAAATGTC
1 AAGTCATGTAAATATC
** * *
43104 ATCTCATGTCAATAAC
1 AAGTCATGTAAATATC
43120 AAGTC
1 AAGTC
43125 GGATTATTTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (16 bp):
AAGTCATGTAAATATC
Found at i:47440 original size:76 final size:75
Alignment explanation
Indices: 47355--47696 Score: 428
Period size: 76 Copynumber: 4.5 Consensus size: 75
47345 TAAAAATCGG
* *
47355 TTTTT-AAAATATATATATTATATAGCTTTGAAAATGATTTTTGAAAA-TGTATATATATTATAT
1 TTTTTGAAAATATATATAATATATAG-TTTTAAAAT-ATTTTTGAAAACT-TATATATATTATAT
*
47418 AGTTTTTAAAATA
63 AGTTTTTAAAACA
* *
47431 -TTTTGAAAATATATATAATATATAGTTTTTAAATCATTTTTGAAAACTTATATATAATATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTAAAAT-ATTTTTGAAAACTTATATATATTATATAG
47495 TTTTTAAAACA
65 TTTTTAAAACA
**
47506 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAA-A-AATTGAAAACTTATATATATTATAT
1 TTTTTG--AAAATATATATAATATATAG-TTTTAAAATATTTTTGAAAACTTATATATATTATAT
47569 AGTTTTTAAAACA
63 AGTTTTTAAAACA
*
47582 TTTTTGAAAACTTATATATAATATATAGTTTTAAAATATTTTTGAATA-TATATATATATTATAT
1 TTTTTGAAAA--TATATATAATATATAGTTTTAAAATATTTTTGAAAACT-TATATATATTATAT
47646 AGTTTTTTTAAAACA
63 AG--TTTTTAAAACA
47661 -TTTTGAAAACATATATATAATATATAGTTTTTAAAA
1 TTTTTG-AAA-ATATATATAATATATAG-TTTTAAAA
47697 AACATTTTGA
Statistics
Matches: 237, Mismatches: 13, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
74 4 0.02
75 55 0.23
76 84 0.35
77 23 0.10
78 41 0.17
79 29 0.12
80 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (75 bp):
TTTTTGAAAATATATATAATATATAGTTTTAAAATATTTTTGAAAACTTATATATATTATATAGT
TTTTAAAACA
Found at i:47494 original size:39 final size:39
Alignment explanation
Indices: 47364--47709 Score: 415
Period size: 39 Copynumber: 8.9 Consensus size: 39
47354 GTTTTTAAAA
* * * *
47364 TATATATATTATATAGCTTTGAAAATGATTTTTGAAAA-T
1 TATATATAATATATAGTTTTTAAAA-CATTTTTGAAAACT
* *
47403 GTATATATATTATATAGTTTTTAAAATA-TTTTGAAAA--
1 -TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
*
47440 TATATATAATATATAGTTTTTAAATCATTTTTGAAAACT
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
**
47479 TATATATAATATATAGTTTTTAAAACATTTTTGAAAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
**
47518 TATATATAATATATAGTTTTTAAAA-A-AATTGAAAACT
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
*
47555 TATATATATTATATAGTTTTTAAAACATTTTTGAAAACT
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
* *
47594 TATATATAATATATAG-TTTTAAAATATTTTTGAATA-T
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
* *
47631 ATATATATATTATATAGTTTTTTTAAAACA-TTTTGAAAACA
1 -TATATATAATATATAG--TTTTTAAAACATTTTTGAAAACT
47672 TATATATAATATATAGTTTTTAAAAAACA-TTTTGAAAA
1 TATATATAATATATAGTTTTT--AAAACATTTTTGAAAA
47710 TTAAATGGTT
Statistics
Matches: 270, Mismatches: 24, Indels: 24
0.85 0.08 0.08
Matches are distributed among these distances:
36 24 0.09
37 41 0.15
38 49 0.18
39 86 0.32
40 61 0.23
41 9 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (39 bp):
TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
Found at i:48912 original size:6 final size:6
Alignment explanation
Indices: 48903--49014 Score: 50
Period size: 6 Copynumber: 18.5 Consensus size: 6
48893 TTTTTCACTC
* * * * * * *
48903 TTTTTA TTTTGGTT TTTTTA TTTTCA CTATTA TTATTA TTATTA TTATTA
1 TTTTTA TTTT--TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * * *
48953 -ATTTA TTTATA TCTATTTA TTTAT- TTTTTA TTATTA TTTTT- TTTATA
1 TTTTTA TTTTTA T-T-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
49000 TTTTTA TATTTA TTT
1 TTTTTA TTTTTA TTT
49015 ATTTTTCTTT
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
5 11 0.14
6 57 0.72
7 2 0.03
8 9 0.11
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:48951 original size:18 final size:17
Alignment explanation
Indices: 48920--49010 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 17
48910 TTTGGTTTTT
*
48920 TTATTTTCACTATTATTA
1 TTATTTT-ATTATTATTA
*
48938 TTATTATTATTATTAAT-
1 TTATT-TTATTATTATTA
48955 TTATTTATATCTATTTATTTA
1 TTATTT-TAT-TA-TTA-TTA
48976 TT-TTTTATTATTATT-
1 TTATTTTATTATTATTA
*
48991 TT-TTTTA-TATTTTTA
1 TTATTTTATTATTATTA
49006 -TATTT
1 TTATTT
49011 ATTTATTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
14 7 0.11
15 10 0.16
16 3 0.05
17 11 0.18
18 16 0.26
19 8 0.13
20 4 0.07
21 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTATTATTATTA
Found at i:48978 original size:22 final size:20
Alignment explanation
Indices: 48942--49018 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 20
48932 TTATTATTAT
*
48942 TATTA-TTATTAATTTATTTA
1 TATTATTTATTTATTT-TTTA
48962 TATCTATTTATTTATTTTTTA
1 TAT-TATTTATTTATTTTTTA
*
48983 TTATTATTTTTTTTATATTTTTA
1 -TATTA-TTTATTTAT-TTTTTA
49006 TATTTATTTATTT
1 TA-TTATTTATTT
49019 TTCTTTTAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.06
21 8 0.17
22 28 0.58
23 9 0.19
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTATTTATTTATTTTTTA
Found at i:48984 original size:36 final size:37
Alignment explanation
Indices: 48935--49014 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
48925 TTCACTATTA
48935 TTATTATTATTATTATTAATTTATTTATATCTATT-TAT
1 TTATT-TTATTATTATTAATTTATTTATAT-TATTATAT
* * *
48973 TTATTTT-TTATTATTATTTTTTTTATATTTTTATAT
1 TTATTTTATTATTATTAATTTATTTATATTATTATAT
49009 TTATTT
1 TTATTT
49015 ATTTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 3 0.08
36 28 0.74
37 2 0.05
38 5 0.13
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (37 bp):
TTATTTTATTATTATTAATTTATTTATATTATTATAT
Found at i:49020 original size:17 final size:18
Alignment explanation
Indices: 48944--49014 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 18
48934 ATTATTATTA
*
48944 TTATTATTAATTTA-TTT
1 TTATTATTTATTTATTTT
*
48961 ATATCTATTTATTTATTTT
1 TTAT-TATTTATTTATTTT
48980 TTATTA-TTATTT-TTTT
1 TTATTATTTATTTATTTT
*
48996 TATATTTTTATATTTATTT
1 T-TATTATT-TATTTATTT
49015 ATTTTTCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 5 0.11
17 13 0.30
18 12 0.27
19 11 0.25
20 3 0.07
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:49122 original size:19 final size:19
Alignment explanation
Indices: 49100--49166 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
49090 TTTTGACTTT
49100 TTTTA-TTTATTTTTATTTA
1 TTTTATTTTA-TTTTATTTA
*
49119 TTTTATTTTATTTTATTTCC
1 TTTTATTTTATTTTATTT-A
*
49139 TTTGATTTATTATTTTA-TTA
1 TTTTA-TT-TTATTTTATTTA
49159 -TTTATTTT
1 TTTTATTTT
49167 TTTCCTAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 16 0.40
20 8 0.20
21 4 0.10
22 8 0.20
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTTTATTTA
Found at i:49125 original size:5 final size:5
Alignment explanation
Indices: 49100--49136 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
49090 TTTTGACTTT
49100 TTTTA -TTTA TTTT- TATTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTT
49137 CCTTTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 5 0.17
5 23 0.79
6 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:49169 original size:15 final size:14
Alignment explanation
Indices: 49097--49169 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
49087 TCCTTTTGAC
*
49097 TTTT-TTTATTTAT
1 TTTTATTTATTTTT
*
49110 TTTTATTTATTTTA
1 TTTTATTTATTTTT
**
49124 TTTTATTTTATTTCC
1 TTTTA-TTTATTTTT
*
49139 TTTGATTTATTATTT
1 TTTTATTTATT-TTT
*
49154 TATTATTTATTTTT
1 TTTTATTTATTTTT
49168 TT
1 TT
49170 CCTAACATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
13 4 0.09
14 22 0.47
15 21 0.45
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTATTTATTTTT
Found at i:53151 original size:85 final size:85
Alignment explanation
Indices: 52987--53697 Score: 959
Period size: 85 Copynumber: 8.4 Consensus size: 85
52977 TATTTTTTCT
* *
52987 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
53052 CTCAGCTCAAAGGCATATCCA
65 CTCAGCTCAAAGGCATATCCA
** * * * * *
53073 ATTCGCAGCATAGATCAAGGCAAAAAGGGCTATCTGTCGACAAAGACCTTCGAGTTCGATTACAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
53138 TCAGCTCAAAGGCATAT-CA
66 TCAGCTCAAAGGCATATCCA
** * *
53157 ATTTACAATATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
* *
53222 TCAGCTCAAAGGCACATCAA
66 TCAGCTCAAAGGCATATCCA
* *
53242 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTATTAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
53307 CTCAGCTCAAAGGCATAT-CA
65 CTCAGCTCAAAGGCATATCCA
* * *
53327 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGCCCTTCGAGTTCGATTACAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
* *
53392 TCAGCTCAAAGGCACATCAA
66 TCAGCTCAAAGGCATATCCA
* * *
53412 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGT-TACAAAAGACCTTTGAGTTCGATTGCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
*
53476 CTCAACTCAAAGGCATAT-CA
65 CTCAGCTCAAAGGCATATCCA
* * *
53496 ATTTATAGCATAGCTCAAGGCGAGAAGGGATATCTGTCAACTAAGACCTTCGAGTTCGATTACAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
* *
53561 TCAGCTCAAAGACACA-CCGA
66 TCAGCTCAAAGGCATATCC-A
* * * *
53581 ATTTAAAGCATAGCTCAAGACGAGAAGGTTTATCTATCATTA-AAAGACCTTCGAGTTCGATTAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCA--ACAAAGACCTTCGAGTTCGATTAC
*
53645 ACTCAGCTCAAAGGCATATCAA
64 ACTCAGCTCAAAGGCATATCCA
* * *
53667 ATTTGCAGCATAACTCAATGG-GAGAATGGTT
1 ATTTACAGCATAGCTCAA-GGCGAGAAGGGTT
53698 GTAACATCCT
Statistics
Matches: 546, Mismatches: 68, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
84 183 0.34
85 225 0.41
86 135 0.25
87 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (85 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
TCAGCTCAAAGGCATATCCA
Found at i:53608 original size:339 final size:341
Alignment explanation
Indices: 52987--53697 Score: 1070
Period size: 339 Copynumber: 2.1 Consensus size: 341
52977 TATTTTTTCT
* * *
52987 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
* * *
53052 CTCAGCTCAAAGGCATATCCAATTCGCAGCATAGATCAAGGCAAAAAGGGCTATCTGTCGACAAA
66 CTCAGCTCAAAGGCACATCAAATTCACAGCATAGATCAAGGCAAAAAGGGCTATCTGTCGACAAA
* *
53117 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAATTTACAATATAACTCAAGGCGAGA
131 GACCTTCGAGTTCGATTACACTCAACTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAGA
* * *
53182 AGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTA
196 AGGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTTA
* * *
53247 CAGCATAGCTCAAGGCGAGAAGGGTTATCTATTAACAAAAGACCTTCGAGTTCGATTACACTCAG
261 AAGCATAGCTCAAGACGAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTACACTCAG
53312 CTCAAAGGCATATC-A
326 CTCAAAGGCATATCAA
* *
53327 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGCCCTTCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
* * * * * *
53391 CTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGT-TACAAA
66 CTCAGCTCAAAGGCACATCAAATTCACAGCATAGATCAAGGCAAAAAGGGCTATCTGTCGAC-AA
* * * * *
53455 AGACCTTTGAGTTCGATTGCACTCAACTCAAAGGCATATCAATTTATAGCATAGCTCAAGGCGAG
130 AGACCTTCGAGTTCGATTACACTCAACTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAG
* *
53520 AAGGGATATCTGTCAACTAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCGAATTT
195 AAGGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTT
* **
53585 AAAGCATAGCTCAAGACGAGAAGGTTTATCTATCATTAAAAGACCTTCGAGTTCGATTACACTCA
260 AAAGCATAGCTCAAGACGAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTACACTCA
53650 GCTCAAAGGCATATCAA
325 GCTCAAAGGCATATCAA
* *
53667 ATTTGCAGCATAACTCAATGG-GAGAATGGTT
1 ATTTACAGCATAACTCAA-GGCGAGAAGGGTT
53698 GTAACATCCT
Statistics
Matches: 334, Mismatches: 34, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
338 2 0.01
339 264 0.79
340 66 0.20
341 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (341 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCACATCAAATTCACAGCATAGATCAAGGCAAAAAGGGCTATCTGTCGACAAA
GACCTTCGAGTTCGATTACACTCAACTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAGA
AGGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTTA
AAGCATAGCTCAAGACGAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCATATCAA
Found at i:54461 original size:21 final size:21
Alignment explanation
Indices: 54419--54461 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54409 TTTCTAGGCT
* *
54419 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
54440 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
54461 A
1 A
54462 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:54514 original size:20 final size:20
Alignment explanation
Indices: 54489--54526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54479 GAATGCTAGA
*
54489 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
54509 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
54527 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:55688 original size:30 final size:30
Alignment explanation
Indices: 55652--55735 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
55642 ACCTATGGAT
* *
55652 AGGATCTTTATAATCTCTGGATAGTTACCG
1 AGGATCTTTATGACCTCTGGATAGTTACCG
55682 AGGATCTTTATGACCTCTGGATAGTTACCG
1 AGGATCTTTATGACCTCTGGATAGTTACCG
55712 AGGATCTTTATGACCTCTGGATAG
1 AGGATCTTTATGACCTCTGGATAG
55736 GTCATTCGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (30 bp):
AGGATCTTTATGACCTCTGGATAGTTACCG
Found at i:59087 original size:21 final size:21
Alignment explanation
Indices: 59045--59087 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
59035 TTTCTGGGCT
* *
59045 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
59066 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
59087 A
1 A
59088 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:60228 original size:31 final size:31
Alignment explanation
Indices: 60190--60295 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 31
60180 GTCAAAGAAC
60190 TACCTATG-TCTTTCGAGACATATGGACAGT
1 TACCTATGATCTTTCGAGACATATGGACAGT
* *** *
60220 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATGATCTTTCGAGACATATGGACAG-T
* * * *
60252 TACCTAGGTTC-TTCGGGACCTATGGACAGT
1 TACCTATGATCTTTCGAGACATATGGACAGT
*
60282 TACCGATGATCTTT
1 TACCTATGATCTTT
60296 ATGACCTCTG
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
30 10 0.18
31 41 0.72
32 6 0.11
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
TACCTATGATCTTTCGAGACATATGGACAGT
Found at i:60302 original size:30 final size:30
Alignment explanation
Indices: 60268--60370 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
60258 GGTTCTTCGG
* * *
60268 GACCTATGGACAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
60298 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
60328 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
60358 GACCTCTGGATAG
1 GACCTCTGGATAG
60371 GTCCTTCGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:61150 original size:86 final size:86
Alignment explanation
Indices: 60987--61150 Score: 186
Period size: 86 Copynumber: 1.9 Consensus size: 86
60977 TCTGTTAACC
**
60987 AAGACCCTCGAGTTCGATTACACTCAACTCTGAGGCACATCAAATTTACAGCATAGCTCAAGGCG
1 AAGACCCTCGAGTTCGATTACACTCAACTAAGAGGCACATCAAATTTACAGCATAGCTCAAGGCG
**
61052 AGAAGGGCTATCTTTCATTAA
66 AGAAAAGCTATCTTTCATTAA
* * ** * ** * *
61073 AAGACCTTCGAGTTCGATTACACTCAGCTAA-AGGGCATGTCAAATTTGCAGCATTTCTTAAGTC
1 AAGACCCTCGAGTTCGATTACACTCAACTAAGA-GGCACATCAAATTTACAGCATAGCTCAAGGC
*
61137 GAGAAAAGTTATCT
65 GAGAAAAGCTATCT
61151 GTCAACAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
85 1 0.02
86 62 0.98
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (86 bp):
AAGACCCTCGAGTTCGATTACACTCAACTAAGAGGCACATCAAATTTACAGCATAGCTCAAGGCG
AGAAAAGCTATCTTTCATTAA
Found at i:61772 original size:12 final size:12
Alignment explanation
Indices: 61755--61789 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
61745 ATATAGCGTA
61755 GTTTTTGAAAAT
1 GTTTTTGAAAAT
61767 GTTTTTGAAAAT
1 GTTTTTGAAAAT
*
61779 ATTTTTGAAAA
1 GTTTTTGAAAA
61790 ATATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (12 bp):
GTTTTTGAAAAT
Found at i:61966 original size:39 final size:37
Alignment explanation
Indices: 61864--62168 Score: 380
Period size: 39 Copynumber: 7.8 Consensus size: 37
61854 TGAAAATGAT
61864 TTTTTGAAAATGTATATATAATATATAGTTTTTAAAACA
1 TTTTT-AAAAT-TATATATAATATATAGTTTTTAAAACA
* *
61903 -TTTTAAAAATATATATAATATATAGTTTTTAAATCA
1 TTTTTAAAATTATATATAATATATAGTTTTTAAAACA
61939 TTTTTAAACACTTATATATAATATATAGTTTTTAAAACA
1 TTTTTAAA-A-TTATATATAATATATAGTTTTTAAAACA
*
61978 TTTTTGAATATATATATATAATATATAGTTTTTAAAACA
1 TTTTT-AAAAT-TATATATAATATATAGTTTTTAAAACA
*
62017 TTTTTGAAAACTTATATATATTATATAGTTTTTAAAACA
1 TTTTT-AAAA-TTATATATAATATATAGTTTTTAAAACA
* *
62056 TTTTTGAAAACTTATTTATAATATATAGTTTTTAAAATA
1 TTTTT-AAAA-TTATATATAATATATAGTTTTTAAAACA
*
62095 TTTTTGAAAATATATATATATTATATAGTTTTTTTTAAAACA
1 TTTTT-AAAAT-TATATATAATATATAG---TTTTTAAAACA
62137 TTTTGTAAACA-TATATATAATATATAGTTTTT
1 TTTT-TAAA-ATTATATATAATATATAGTTTTT
62169 TTAAAAAAAC
Statistics
Matches: 240, Mismatches: 14, Indels: 25
0.86 0.05 0.09
Matches are distributed among these distances:
36 26 0.11
37 11 0.05
38 12 0.05
39 154 0.64
40 3 0.01
41 15 0.06
42 17 0.07
43 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (37 bp):
TTTTTAAAATTATATATAATATATAGTTTTTAAAACA
Found at i:63440 original size:6 final size:6
Alignment explanation
Indices: 63429--63479 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
63419 TCTCTATTTA
* *
63429 TTTATT TTTATT TTTATT ATTATT ATATTA-T TATATT TTATATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT -T-TTATT TTTATT TT-TATT TTTATT
63479 T
1 T
63480 ATTTTTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 2 0.05
6 25 0.68
7 7 0.19
8 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:66799 original size:14 final size:15
Alignment explanation
Indices: 66774--66804 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
66764 ACAACCTCAC
66774 AACCTCTAAACCATA
1 AACCTCTAAACCATA
66789 AACCT-TAAACCATA
1 AACCTCTAAACCATA
66803 AA
1 AA
66805 TAATAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCTCTAAACCATA
Found at i:67425 original size:3 final size:3
Alignment explanation
Indices: 67417--67454 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
67407 AAGGACTAAT
67417 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
67455 TATATTTTCA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:72140 original size:2 final size:2
Alignment explanation
Indices: 72133--72168 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
72123 TTATCTTATC
*
72133 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72169 AGTCCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:73200 original size:22 final size:22
Alignment explanation
Indices: 73172--73216 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
73162 CCAGACATAG
73172 ACCTGTGATCACTAGCATCACC
1 ACCTGTGATCACTAGCATCACC
73194 ACCTGTGATCACTAGCATCACC
1 ACCTGTGATCACTAGCATCACC
73216 A
1 A
73217 GCCCAGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (22 bp):
ACCTGTGATCACTAGCATCACC
Found at i:77647 original size:166 final size:167
Alignment explanation
Indices: 77342--77653 Score: 371
Period size: 166 Copynumber: 1.9 Consensus size: 167
77332 GTTTCAAGGA
* **
77342 TAATGATTTAGCGGCGTTTTTATATAAACGCCGCAAAATAATAGAACTTTAACGGCGTTGTTATT
1 TAATGATTTAGCGGCGTTTTTATATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTAAG
** * * * * *
77407 AAAACGCCGCTATAAAGTGTTACTTTAGTGTCGTTTTTAAACAAAAATGCCGTAAAATATTTAGA
66 AAAACGCCGCTATAAAGTGTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCCTAAAACATTTAGA
*
77472 CATTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
131 CAGTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
* * * * * *
77509 TAAT-ATTTAGTGGCGTTTTT-TAATCAACGCCGCAATATAATATAACTTTAGCAGCGTTTTTAA
1 TAATGATTTAGCGGCGTTTTTAT-ATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTAA
* * * *
77572 GAAAATGCCGCTATAGAG-GCTTAAGTTAGTGGCGTTTTGAAACACAAACGCCACT-CAACATTT
65 GAAAACGCCGCTATAAAGTG-TTAAGTTAGTGGCGTTTTGAAACAAAAACGCC-CTAAAACATTT
*
77635 GGACAGTAGTGGCGTTTTT
128 AGACAGTAGTGGCGTTTTT
77654 TAAGTAAACG
Statistics
Matches: 120, Mismatches: 22, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
165 2 0.02
166 113 0.94
167 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (167 bp):
TAATGATTTAGCGGCGTTTTTATATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTAAG
AAAACGCCGCTATAAAGTGTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCCTAAAACATTTAGA
CAGTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
Found at i:82024 original size:43 final size:42
Alignment explanation
Indices: 81977--82110 Score: 108
Period size: 43 Copynumber: 3.1 Consensus size: 42
81967 TTTATTGTGA
*
81977 CGTTTGTGATAAAAACGCCGCTAAATATTGACACCAATTGCGG
1 CGTTTGT-ATAAAAACGCCGCTAAATATCGACACCAATTGCGG
* * ** *
82020 CGTTTTTA-AGACAAATGCCGCTAAATATCGGTACCTATTGCGG
1 CGTTTGTATA-A-AAACGCCGCTAAATATCGACACCAATTGCGG
* * * ** * *
82063 CATTTGTTTAACAAACGCCGCTACATATCGTTACCTATTGTGG
1 CGTTTGTATAA-AAACGCCGCTAAATATCGACACCAATTGCGG
82106 CGTTT
1 CGTTT
82111 TTGGTTAACA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 70 0.95
44 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (42 bp):
CGTTTGTATAAAAACGCCGCTAAATATCGACACCAATTGCGG
Found at i:82169 original size:12 final size:14
Alignment explanation
Indices: 82133--82169 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
82123 CGCCGTGAAC
82133 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
82147 TTTCAGCGGCGC-AT
1 TTT-AGCGGCGCTAT
82161 TTT-GCGGCG
1 TTTAGCGGCG
82170 TTTTTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.32
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:87822 original size:20 final size:20
Alignment explanation
Indices: 87797--87842 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
87787 TCTGGCAATG
* *
87797 AACCGGCTGAAAA-TCGGTAA
1 AACCGGCTAAAAACT-GGCAA
87817 AACCGGCTAAAAACTGGCAA
1 AACCGGCTAAAAACTGGCAA
87837 AACCGG
1 AACCGG
87843 TTTGAACCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (20 bp):
AACCGGCTAAAAACTGGCAA
Found at i:88499 original size:24 final size:24
Alignment explanation
Indices: 88435--88489 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
88425 TATGTTGTAA
88435 TTGATTTGAATCATTTTGTTTCAC
1 TTGATTTGAATCATTTTGTTTCAC
88459 TTGATTTGAATCATTTTGTTTCAC
1 TTGATTTGAATCATTTTGTTTCAC
88483 TTGATTT
1 TTGATTT
88490 TATGGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.56
Consensus pattern (24 bp):
TTGATTTGAATCATTTTGTTTCAC
Found at i:90833 original size:141 final size:143
Alignment explanation
Indices: 90551--90833 Score: 462
Period size: 141 Copynumber: 2.0 Consensus size: 143
90541 GTTTCAGAAC
*
90551 AAGAAAGAAAAATATGTCGATTGGTGAAGTCTTTGTATAAAATTAAACAAGCACCAAAACAATGT
1 AAGAAAGAAAAACATGTCGATTGGTGAAGTCTTTGTATAAAATTAAACAAGCACCAAAACAATGT
* **
90616 CATGAGAAGTTCGATAATGTCATGATGACAAATGACTTCAAGATAAATGAGTGTGACAAGTGTAT
66 AATGAGAAGTTCGATAATGTCATGATGACAAACAACTTCAAGATAAATGAGTGTGACAAGTGTAT
*
90681 ATATGTCAAAAAT
131 ATATGTAAAAAAT
* * *
90694 AAGAAAG-AAAACATGTCGATTGGT-AAGTCTTTTTATAGACTTAAACAAGCACCAAAACAATGT
1 AAGAAAGAAAAACATGTCGATTGGTGAAGTCTTTGTATAAAATTAAACAAGCACCAAAACAATGT
* *
90757 AATGAGAAGTTCGATAATGTCATGATGACAAACAACTTCAAGATAAGTGAGTGTGACAAGTGTGT
66 AATGAGAAGTTCGATAATGTCATGATGACAAACAACTTCAAGATAAATGAGTGTGACAAGTGTAT
90822 ATATGTAAAAAA
131 ATATGTAAAAAA
90834 CACATACTTA
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 107 0.82
142 16 0.12
143 7 0.05
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (143 bp):
AAGAAAGAAAAACATGTCGATTGGTGAAGTCTTTGTATAAAATTAAACAAGCACCAAAACAATGT
AATGAGAAGTTCGATAATGTCATGATGACAAACAACTTCAAGATAAATGAGTGTGACAAGTGTAT
ATATGTAAAAAAT
Found at i:91489 original size:22 final size:19
Alignment explanation
Indices: 91423--91468 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
91413 AATGGTACCT
91423 ATACCCCCCATAGGTATCG
1 ATACCCCCCATAGGTATCG
91442 ATACCCCCCATAGGTATCG
1 ATACCCCCCATAGGTATCG
91461 ATACCCCC
1 ATACCCCC
91469 ATGCAATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (19 bp):
ATACCCCCCATAGGTATCG
Done.