Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004014.1 Hibiscus syriacus cultivar Beakdansim tig00008766_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: 67396
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:327 original size:20 final size:20
Alignment explanation
Indices: 298--349 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
288 TTTTGTGGAA
* *
298 GAGGTTAAGACTATATTCTC
1 GAGGTGAAGAATATATTCTC
318 GAGGTGAAGAATATATTC-C
1 GAGGTGAAGAATATATTCTC
*
337 GAAGGTGGAGAAT
1 G-AGGTGAAGAAT
350 TTGTTCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.27
Consensus pattern (20 bp):
GAGGTGAAGAATATATTCTC
Found at i:7932 original size:31 final size:31
Alignment explanation
Indices: 7896--7954 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
7886 AACTTAAAAG
* * *
7896 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
7927 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
7955 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:8005 original size:22 final size:22
Alignment explanation
Indices: 7979--8021 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7969 TAATAAATTA
*
7979 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAACCAATCCATAT
*
8001 TTTAAAATAAACCAATTCATA
1 TTTAAAATAAACCAATCCATA
8022 CTAATAAATT
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:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAACCAATCCATAT
Found at i:8074 original size:80 final size:83
Alignment explanation
Indices: 7969--9033 Score: 703
Period size: 80 Copynumber: 13.0 Consensus size: 83
7959 ACAACTACAA
* *
7969 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAACCAATTCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTAT
8034 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
* * *
8055 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTT
8116 AAAATAAATCAATCCATAC
65 AAAATAAATCAATCCATAC
* * **
8135 TAATAAATTATTTAAAATAAATCAAT-C-TA---TACAACTACAAT-AATAAAT-C-AATCCA-T
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTA-AAATA-AATCAATACATACTAATAAATT
*
8191 ATTTTAAAATAAATCAATTCATAC
61 A-TTTAAAATAAATCAATCCATAC
* **
8215 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATACATACTAATAAA
1 TAATAAA-TA-TT-AAATAAATCAATCCAT---ATTTTAA-AATAAATCAATACATACTAATAAA
8280 TTATTTAAAATAAATCAATCCATA-
59 TTATTTAAAATAAATCAATCCATAC
** * * *
8304 TTTTAAA-A-TAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-
1 TAATAAATATTAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATACATACTAATAAAT
8358 T-TTTAAAATAAATCAA-CCAATAC
60 TATTTAAAATAAATCAATCC-ATAC
* * * **
8381 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C-AATCTA-TA
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATA-AATCAATACATACTAATAAATTA
*
8438 TTTTAAAATAAATCAATTCATAC
62 -TTTAAAATAAATCAATCCATAC
*
8461 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTAT
8526 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
* * * *
8547 -AACTACA-A-T-AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTGTTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTT
8608 AAAATAAATCAATCCATAC
65 AAAATAAATCAATCCATAC
* *
8627 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTAT
* *
8692 TTAAAATAAATTAATTCATA-
63 TTAAAATAAATCAATCCATAC
* ** * ** * * **
8712 T--T---T-TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCTA-TATT
1 TAATAAATATTAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATACATACTAATAAATTA-T
8768 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
* * * * **
8789 TAATAAATTATTTAAAATAAATCAATTCATA----CAACTACAAT-AATAAAT-C-AATCCA-TA
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATA-AATCAATACATACTAATAAATTA
8846 TTTTAAAATAAATCAATCCATAC
62 -TTTAAAATAAATCAATCCATAC
* * * **
8869 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C-AATCCA-TA
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATA-AATCAATACATACTAATAAATTA
8926 TTTTAAAATAAATCAATCCATAC
62 -TTTAAAATAAATCAATCCATAC
* *
8949 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTAT
9014 TTAAAATAAATCAATCCATA
63 TTAAAATAAATCAATCCATA
9034 TTTTAAAATC
Statistics
Matches: 816, Mismatches: 80, Indels: 166
0.77 0.08 0.16
Matches are distributed among these distances:
72 7 0.01
73 3 0.00
75 5 0.01
76 59 0.07
77 17 0.02
78 9 0.01
79 5 0.01
80 394 0.48
81 15 0.02
82 26 0.03
83 11 0.01
84 34 0.04
85 15 0.02
86 162 0.20
87 12 0.01
88 10 0.01
89 6 0.01
90 24 0.03
91 2 0.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (83 bp):
TAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTA
AAATAAATCAATCCATAC
Found at i:8117 original size:32 final size:32
Alignment explanation
Indices: 8081--9033 Score: 504
Period size: 32 Copynumber: 34.7 Consensus size: 32
8071 CAATCCATAT
*
8081 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8113 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
8145 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
8175 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8193 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8225 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
8255 --T--AATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8283 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8305 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8337 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8359 TTTAAAATAAATCAA-CCAATACTAATAAATTA
1 TTTAAAATAAATCAATCC-ATACTAATAAATTA
*
8391 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
8421 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8446 -------TAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8471 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8493 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8525 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
8555 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
8580 -------TAAATCAATTCATACTAATAAATTG
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8605 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8637 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8659 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8691 TTTAAAATAAATTAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8713 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8745 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8767 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
8799 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
8829 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8847 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
8879 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
8909 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8927 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8959 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
8981 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
9013 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
9034 TTTTAAAATC
Statistics
Matches: 731, Mismatches: 38, Indels: 304
0.68 0.04 0.28
Matches are distributed among these distances:
20 3 0.00
22 170 0.23
23 23 0.03
24 13 0.02
25 14 0.02
26 115 0.16
27 10 0.01
28 30 0.04
29 2 0.00
30 14 0.02
31 23 0.03
32 312 0.43
33 2 0.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:8126 original size:54 final size:55
Alignment explanation
Indices: 8064--9009 Score: 521
Period size: 54 Copynumber: 17.4 Consensus size: 55
8054 CAACTACAAT
**
8064 AATAAATCAATCCATA-TTTTAAAATAAATAAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
* * *
8118 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CT-ATACAACTA--CAA
1 AATAAATCAATCCATACTAATAAA--A--T-AAATAAATCCATACTAATA-AATTATTTAA
** * *
8175 TAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 -AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
* *
8230 AATAAATCAATCCATAC-AACTACAATAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATACTAA-T--AA-AATAAATAAATCCATACTAATAAATTATTTAA
** * *
8288 AATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
** *
8342 AATAAATCAATCCATA-TTTTAAAATAAATCAA-CCAATACTAATAAATTATTTAA
1 AATAAATCAATCCATACTAATAAAATAAATAAATCC-ATACTAATAAATTATTTAA
* *
8396 AATAAATCAATCCATAC-AACTACAAT-AATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATACTAA-TAAAATAAATAAATCCATACTAATAAATTATTTAA
* * ** ** **
8444 AATAAATCAATTCATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAA
1 AATAAATCAATCCATACTAATAAAATAAAT-AAATCCATACTAATAAATTA-TTTAA
* * * *
8498 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA--CAA
1 AATAAATCAATCCATACTAATAAA--A--T-AAATAAATCCATACTAATA-AATTATTTAA
* ** * * *
8555 TAATAAATCAATCTATA-TTTTAAAATAAATCAATTCATACTAATAAATTGTTTAA
1 -AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
*
8610 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATACTAATAAA--A--T-AAATAAATCCATACTAATAAATTATTTAA
* ** * * **
8664 AATAAATCAATCCATACTAATAAATTATTTAAAAT--AAATTAATTCA-TATTTTAA
1 AATAAATCAATCCATACTAATAAAATAAAT-AAATCCATACTAATAAATTA-TTTAA
*
8718 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATACTAATAAA--A--T-AAATAAATCCATACTAATAAATTATTTAA
* * * *
8772 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-CA-ATTCATACAACTA--CAA
1 AATAAATCAATCCATACTAATAAA--A--T-AAATAAATCCATACTAATA-AATTATTTAA
** *
8829 TAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 -AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
* * *
8884 AATAAATCAATCCATAC-AACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAA
1 AATAAATCAATCCATACTAA-TAAAATAAATAAATCCATACTAATAAATTATTTAA
* ** ** **
8932 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATTCA-TATTTTAA
1 AATAAATCAATCCATACTAATAAAATAAAT-AAATCCATACTAATAAATTA-TTTAA
8986 AATAAATCAATCCATACTAATAAA
1 AATAAATCAATCCATACTAATAAA
9010 TTATTTAAAA
Statistics
Matches: 721, Mismatches: 88, Indels: 166
0.74 0.09 0.17
Matches are distributed among these distances:
48 52 0.07
49 11 0.02
50 29 0.04
52 35 0.05
53 25 0.03
54 348 0.48
55 34 0.05
56 3 0.00
57 27 0.04
58 118 0.16
59 16 0.02
60 23 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (55 bp):
AATAAATCAATCCATACTAATAAAATAAATAAATCCATACTAATAAATTATTTAA
Found at i:8334 original size:22 final size:22
Alignment explanation
Indices: 8285--8333 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8275 ATAAATTATT
**
8285 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
8307 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
8330 TAAA
1 TAAA
8334 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8426 original size:134 final size:134
Alignment explanation
Indices: 8288--9078 Score: 1029
Period size: 134 Copynumber: 5.9 Consensus size: 134
8278 AATTATTTAA
*
8288 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
8353 CCATATTTTAAAATAAATCAA-CCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
66 CCATATTTTAAAATAAATCAATCC-ATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
8417 ACAAT
130 ACAAT
* *
8422 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
8487 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
8552 CAAT
131 CAAT
* * *
8556 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTGTTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
** * *
8621 CCATACTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATA
66 CCATA-TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
*
8680 CTAA-TAAATTATTT
125 C-AACTACA--A--T
* *
8694 AAAATAAATTAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
8759 ATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAAC
64 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
8824 TACAAT
129 TACAAT
8830 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*** * * * *
8895 CCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-
66 CCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AAC
*
8952 TAAATTATTT
129 TACA--A--T
*
8962 AAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* * *
9027 ATCCATATTTTAAAATCAATCAATCCTTAATAATAAATTATTTAAAATAAAT
64 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
9079 TATTTTAAAA
Statistics
Matches: 578, Mismatches: 43, Indels: 66
0.84 0.06 0.10
Matches are distributed among these distances:
128 24 0.04
129 3 0.01
130 2 0.00
132 3 0.01
133 6 0.01
134 385 0.67
135 18 0.03
136 7 0.01
137 2 0.00
138 6 0.01
139 12 0.02
140 110 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (134 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
CAAT
Found at i:8497 original size:22 final size:22
Alignment explanation
Indices: 8471--8513 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
8461 TAATAAATTA
8471 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
8493 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
8514 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:8522 original size:22 final size:22
Alignment explanation
Indices: 8473--8521 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
8463 ATAAATTATT
**
8473 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
8495 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8518 TAAA
1 TAAA
8522 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8688 original size:22 final size:22
Alignment explanation
Indices: 8639--8687 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8629 ATAAATTATT
* **
8639 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
8661 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8684 TAAA
1 TAAA
8688 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8706 original size:22 final size:22
Alignment explanation
Indices: 8681--8724 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
8671 CAATCCATAC
8681 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
8703 TAATTCATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
8725 CAATCCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:8733 original size:22 final size:22
Alignment explanation
Indices: 8691--8733 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
8681 TAATAAATTA
* *
8691 TTTAAAATAAATTAATTCATAT
1 TTTAAAATAAATCAATCCATAT
8713 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
8734 CTAATAAATT
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:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:8796 original size:22 final size:22
Alignment explanation
Indices: 8747--8795 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8737 ATAAATTATT
* **
8747 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
8769 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8792 TAAA
1 TAAA
8796 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8876 original size:22 final size:22
Alignment explanation
Indices: 8801--8875 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
8791 ATAAATTATT
* *
8801 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
8823 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
8849 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8872 TAAA
1 TAAA
8876 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8956 original size:22 final size:23
Alignment explanation
Indices: 8881--8955 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
8871 ATAAATTATT
8881 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
8903 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
8929 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
8952 TAAA
1 TAAA
8956 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:8985 original size:22 final size:22
Alignment explanation
Indices: 8959--9001 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8949 TAATAAATTA
*
8959 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
8981 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
9002 CTAATAAATT
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:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:9010 original size:22 final size:22
Alignment explanation
Indices: 8961--9009 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8951 ATAAATTATT
* **
8961 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
8983 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
9006 TAAA
1 TAAA
9010 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:9010 original size:54 final size:54
Alignment explanation
Indices: 8422--9130 Score: 716
Period size: 54 Copynumber: 13.1 Consensus size: 54
8412 CAACTACAAT
*
8422 AATAAATCAA-TCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
8476 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *** * * *
8530 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATTCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
8578 AATAAATCAATTCATACTAATAAATTGTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAA-T--T-C--AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
8642 AATAAATCAA-TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
8696 AATAAATTAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
8750 AATAAATCAA-TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** ** * ** *
8804 AATAAATCAATTCATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATTCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
** ** *
8860 AATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAAT-C-AATTCATAT-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
*
8910 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
8964 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * *
9018 AATAAATCAATCCATATTTTAAAATCAATCAATCCTTAATAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
9072 AAT--A--AA-T--TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TTTAA
9124 AATAAAT
1 AATAAAT
9131 TATTTTAAAA
Statistics
Matches: 558, Mismatches: 51, Indels: 91
0.80 0.07 0.13
Matches are distributed among these distances:
47 22 0.04
48 45 0.08
49 6 0.01
50 9 0.02
51 12 0.02
52 13 0.02
53 5 0.01
54 349 0.63
55 17 0.03
56 7 0.01
57 18 0.03
58 32 0.06
59 3 0.01
60 3 0.01
62 1 0.00
63 1 0.00
64 15 0.03
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:9039 original size:22 final size:22
Alignment explanation
Indices: 9013--9115 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
9003 TAATAAATTA
9013 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
9035 TTTAAAATCAATCAATCCTTAAT
1 TTTAAAATAAATCAATCCAT-AT
** * ** * **
9058 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
9082 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
9104 TTTATAATAAAT
1 TTTAAAATAAAT
9116 TATTTTAAAA
Statistics
Matches: 57, Mismatches: 21, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
22 32 0.56
23 12 0.21
24 12 0.21
25 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:9085 original size:15 final size:15
Alignment explanation
Indices: 9053--9242 Score: 220
Period size: 15 Copynumber: 11.7 Consensus size: 15
9043 CAATCAATCC
9053 TTAATAATAAATTA-T
1 TTAA-AATAAATTATT
9068 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9083 TTAAAATAAATCAATCCATATT
1 TTAAAAT--A--AAT---TATT
*
9105 TTATAATAAATTATT
1 TTAAAATAAATTATT
9120 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9135 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9150 TTAAAATAAATCAATCCATATT
1 TTAAAAT--A--AAT---TATT
*
9172 TTATAATAAATTATT
1 TTAAAATAAATTATT
9187 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9202 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9217 TTAAAATAAATTATT
1 TTAAAATAAATTATT
9232 TTAAAATAAAT
1 TTAAAATAAAT
9243 AACATTATTA
Statistics
Matches: 156, Mismatches: 4, Indels: 30
0.82 0.02 0.16
Matches are distributed among these distances:
14 9 0.06
15 111 0.71
17 2 0.01
18 6 0.04
19 6 0.04
20 2 0.01
22 20 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAATAAATTATT
Found at i:9164 original size:67 final size:67
Alignment explanation
Indices: 9004--9227 Score: 371
Period size: 67 Copynumber: 3.3 Consensus size: 67
8994 AATCCATACT
* * * *
9004 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATCAATCAATCCTTAATAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAAT-TAT-TTTAA-AATAAATTAT
9067 TTTAA
63 TTTAA
9072 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
9137 AA
66 AA
9139 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
9204 AA
66 AA
9206 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
9228 TATTTTAAAA
Statistics
Matches: 150, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
66 9 0.06
67 98 0.65
68 11 0.07
69 32 0.21
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
AA
Found at i:9564 original size:51 final size:51
Alignment explanation
Indices: 9488--9592 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
9478 AACTAAGCCT
9488 TAAAGTTACTTATTTCCGACTCACTATTATGTTTTTTAAGCTAATTAATAG
1 TAAAGTTACTTATTTCCGACTCACTATTATGTTTTTTAAGCTAATTAATAG
9539 TAAAGTTACTTATTTCCGACTCACTATTATGTTTTTTAAGCTAATTAATAG
1 TAAAGTTACTTATTTCCGACTCACTATTATGTTTTTTAAGCTAATTAATAG
9590 TAA
1 TAA
9593 TTTGATGGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (51 bp):
TAAAGTTACTTATTTCCGACTCACTATTATGTTTTTTAAGCTAATTAATAG
Found at i:10568 original size:30 final size:29
Alignment explanation
Indices: 10534--10622 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
10524 GTCATGTTAT
*
10534 AATAAGATATTAACAGT-TGAGTAATTAAAA
1 AATAAGA-ATTAA-AATATGAGTAATTAAAA
* *
10564 AATAATAATTAAAATACTGAGTGATTAAAA
1 AATAAGAATTAAAATA-TGAGTAATTAAAA
* *
10594 AATAATAATTAAAATAATGAGTGATTAAA
1 AATAAGAATTAAAAT-ATGAGTAATTAAA
10623 CTGAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.04
29 5 0.09
30 45 0.85
31 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.30
Consensus pattern (29 bp):
AATAAGAATTAAAATATGAGTAATTAAAA
Found at i:10574 original size:14 final size:14
Alignment explanation
Indices: 10555--10607 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
10545 AACAGTTGAG
10555 TAATTAAAAAATAA
1 TAATTAAAAAATAA
* *
10569 TAATTAAAATACTGAG
1 TAATTAAAA-AAT-AA
*
10585 TGATTAAAAAATAA
1 TAATTAAAAAATAA
10599 TAATTAAAA
1 TAATTAAAA
10608 TAATGAGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 18 0.58
15 4 0.13
16 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (14 bp):
TAATTAAAAAATAA
Found at i:10592 original size:16 final size:16
Alignment explanation
Indices: 10571--10622 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
10561 AAAAATAATA
*
10571 ATTAAAATACTGAGTG
1 ATTAAAATAATGAGTG
* *
10587 ATTAAAA-AAT-AATA
1 ATTAAAATAATGAGTG
10601 ATTAAAATAATGAGTG
1 ATTAAAATAATGAGTG
10617 ATTAAA
1 ATTAAA
10623 CTGAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 9 0.31
15 5 0.17
16 15 0.52
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.31
Consensus pattern (16 bp):
ATTAAAATAATGAGTG
Found at i:16416 original size:24 final size:24
Alignment explanation
Indices: 16388--16435 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16378 CAACCAAACT
16388 CAAAATATAACATTCTTTAACAAA
1 CAAAATATAACATTCTTTAACAAA
16412 CAAAATATAACATTCTTTAACAAA
1 CAAAATATAACATTCTTTAACAAA
16436 TATATAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (24 bp):
CAAAATATAACATTCTTTAACAAA
Found at i:16438 original size:19 final size:21
Alignment explanation
Indices: 16388--16442 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 21
16378 CAACCAAACT
16388 CAAAATATAACATTCTTTAACAAA
1 CAAAATATAACATTCTTT---AAA
16412 CAAAATATAACATTCTTT-AA
1 CAAAATATAACATTCTTTAAA
16432 CAAATATATAA
1 CAAA-ATATAA
16443 TCAGGGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.20
21 6 0.20
24 18 0.60
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
CAAAATATAACATTCTTTAAA
Found at i:17792 original size:31 final size:31
Alignment explanation
Indices: 17754--17827 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
17744 TTGCAGTTGA
* *
17754 CATCATCCTTGCTATCTGCCTTGTCAGACAT
1 CATCATCCTTGCTATCTCCCTAGTCAGACAT
17785 CATCATCCTTGCTATCTCCCTAGTCAGACAT
1 CATCATCCTTGCTATCTCCCTAGTCAGACAT
17816 CATCATCCTTGC
1 CATCATCCTTGC
17828 CGTCGATTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.34
Consensus pattern (31 bp):
CATCATCCTTGCTATCTCCCTAGTCAGACAT
Found at i:18243 original size:204 final size:203
Alignment explanation
Indices: 17893--18304 Score: 761
Period size: 204 Copynumber: 2.0 Consensus size: 203
17883 CGAGGTCGTG
*
17893 TAATTCGTCGGTCATTTTTAGTTTGTTGGTTCTTGTTCCAGTGAATTTTCGTTGCAAATTGGTCG
1 TAATTCGTCGGTCATTTTTAGTTTGTTGGCTCTTGTTCCAGTGAATTTTCGTTGCAAATTGGTCG
*
17958 TCTAGTAGAGGTGCAAATGGGTAAGGTTCGACGACGATAAAGGGGATGACTGGAGTAGATTTAGG
66 TCTAATAGAGGTGCAAATGGGTAAGGTTCGACGACGATAAAGGGGATGACTGGAGTAGATTTAGG
* *
18023 GATTGAAATTAAAATTTTAAAATTTTTTAAAGGTTTTTAAAGTTTTTGGACTTTTTAGAAATGAA
131 GATTGAAATTAAAATTTTAAAATTTTTTAAAGGTTTTCAAAGTTTTTGAAC-TTTTAGAAATGAA
18088 TTATAATTA
195 TTATAATTA
18097 TAATTCGTCGGTCATTTTTAGTTTGTTGGCTCTTGTTCCAGTGAATTTTCGTTGCAAATTGGTCG
1 TAATTCGTCGGTCATTTTTAGTTTGTTGGCTCTTGTTCCAGTGAATTTTCGTTGCAAATTGGTCG
*
18162 TCTAATAGAGGTGCAAATGGGTAAGGTTCGACGACGATAAAGGGGATGATTGGAGTAGATTTAGG
66 TCTAATAGAGGTGCAAATGGGTAAGGTTCGACGACGATAAAGGGGATGACTGGAGTAGATTTAGG
*
18227 GATTGAAATTAAAATTTTAGAATTTTTTAAAGGTTTTCAAAGTTTTTGAACTTTTAGAAATGAAT
131 GATTGAAATTAAAATTTTAAAATTTTTTAAAGGTTTTCAAAGTTTTTGAACTTTTAGAAATGAAT
18292 TATAATTA
196 TATAATTA
18300 TAATT
1 TAATT
18305 TTTTATTTGA
Statistics
Matches: 202, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
203 27 0.13
204 175 0.87
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (203 bp):
TAATTCGTCGGTCATTTTTAGTTTGTTGGCTCTTGTTCCAGTGAATTTTCGTTGCAAATTGGTCG
TCTAATAGAGGTGCAAATGGGTAAGGTTCGACGACGATAAAGGGGATGACTGGAGTAGATTTAGG
GATTGAAATTAAAATTTTAAAATTTTTTAAAGGTTTTCAAAGTTTTTGAACTTTTAGAAATGAAT
TATAATTA
Found at i:28386 original size:31 final size:30
Alignment explanation
Indices: 28334--28395 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
28324 CCAATGTTTG
28334 ATTGTATGAATTCATGAATACA-AGTATAT
1 ATTGTATGAATTCATGAATACAGAGTATAT
* *
28363 ATTGATATGATTTCTATGTATACATGAGTATAT
1 ATTG-TATGAATTC-ATGAATACA-GAGTATAT
28396 GCATATGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 8 0.30
31 8 0.30
33 7 0.26
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (30 bp):
ATTGTATGAATTCATGAATACAGAGTATAT
Found at i:28612 original size:45 final size:45
Alignment explanation
Indices: 28491--28612 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
28481 ATGAGAACAA
* *
28491 GATATAAGCTATGTGACAATTACCTATGTGATGACTTGAGAATAT
1 GATATAAGCTATGTGACAATGACCTATGTGATGACTTGAAAATAT
* ** * * * * *
28536 GATATAAGTTATGTGGTATTGACATAAGTGATTA-TATGAAAATGT
1 GATATAAGCTATGTGACAATGACCTATGTGATGACT-TGAAAATAT
* *
28581 TATATAAGCTACGTGACAATGACCTATGTGAT
1 GATATAAGCTATGTGACAATGACCTATGTGAT
28613 ATTGAACTAC
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (45 bp):
GATATAAGCTATGTGACAATGACCTATGTGATGACTTGAAAATAT
Found at i:28745 original size:23 final size:23
Alignment explanation
Indices: 28718--28819 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
28708 GAGTCGAGGG
*
28718 TTCTACGCGGTCCTTCGAGACAA
1 TTCTACGCGGTCATTCGAGACAA
* * *
28741 TTCTATGTGGTCATTCGAGACAT
1 TTCTACGCGGTCATTCGAGACAA
* * * * *
28764 TTCTACACTGTCCTTTGGGACAA
1 TTCTACGCGGTCATTCGAGACAA
* *** * *
28787 TACTATATGGTCATTCAAGACAT
1 TTCTACGCGGTCATTCGAGACAA
28810 TTCTACGCGG
1 TTCTACGCGG
28820 CACTTTGGTG
Statistics
Matches: 54, Mismatches: 25, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCATTCGAGACAA
Found at i:28777 original size:46 final size:46
Alignment explanation
Indices: 28718--28815 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
28708 GAGTCGAGGG
* * * *
28718 TTCTACGCGGTCCTTCGAGACAATTCTATGTGGTCATTCGAGACAT
1 TTCTACACGGTCCTTCGAGACAATACTATATGGTCATTCAAGACAT
* * *
28764 TTCTACACTGTCCTTTGGGACAATACTATATGGTCATTCAAGACAT
1 TTCTACACGGTCCTTCGAGACAATACTATATGGTCATTCAAGACAT
28810 TTCTAC
1 TTCTAC
28816 GCGGCACTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (46 bp):
TTCTACACGGTCCTTCGAGACAATACTATATGGTCATTCAAGACAT
Found at i:28826 original size:46 final size:45
Alignment explanation
Indices: 28718--28827 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 45
28708 GAGTCGAGGG
* * * * *
28718 TTCTACGCGGTCCTTCGAGACAATTCTATGTGGTCATTCGAGACAT
1 TTCTACGCGG-CCTTTGGGACAATACTATATGGTCATTCAAGACAT
* *
28764 TTCTACACTGTCCTTTGGGACAATACTATATGGTCATTCAAGACAT
1 TTCTACGC-GGCCTTTGGGACAATACTATATGGTCATTCAAGACAT
28810 TTCTACGCGGCACTTTGG
1 TTCTACGCGGC-CTTTGG
28828 TGCAATTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
45 2 0.04
46 50 0.94
47 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (45 bp):
TTCTACGCGGCCTTTGGGACAATACTATATGGTCATTCAAGACAT
Found at i:32445 original size:3 final size:3
Alignment explanation
Indices: 32437--32469 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32427 TTTGTATCCT
32437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32470 ATATCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38157 original size:17 final size:17
Alignment explanation
Indices: 38088--38179 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
38078 TTAATTTCTC
38088 TATTTAATTTTCTTAATTT
1 TATTT-ATTTTCTT-ATTT
* ** *
38107 TATTTATTCAT-TTGGTA
1 TATTTATT-TTCTTATTT
*
38124 TATATTATCTTCATTATTT
1 TAT-TTATTTTC-TTATTT
38143 TATTTATTTTCTTATTT
1 TATTTATTTTCTTATTT
38160 TATCTT-TTTAT-TTATTT
1 TAT-TTATTT-TCTTATTT
38177 TAT
1 TAT
38180 CTTCGTTGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 26 0.46
18 19 0.33
19 12 0.21
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTTATTTTCTTATTT
Found at i:38180 original size:17 final size:18
Alignment explanation
Indices: 38137--38182 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
38127 ATTATCTTCA
38137 TTATTTTAT-TTATTTTC
1 TTATTTTATCTTATTTTC
38154 TTATTTTATCTT-TTTAT-
1 TTATTTTATCTTATTT-TC
38171 TTATTTTATCTT
1 TTATTTTATCTT
38183 CGTTGTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 24 0.89
18 3 0.11
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTATCTTATTTTC
Found at i:41605 original size:27 final size:27
Alignment explanation
Indices: 41568--41651 Score: 168
Period size: 27 Copynumber: 3.1 Consensus size: 27
41558 ACATATTTAT
41568 TTTCTCATTTACCCCTATCAATGATCA
1 TTTCTCATTTACCCCTATCAATGATCA
41595 TTTCTCATTTACCCCTATCAATGATCA
1 TTTCTCATTTACCCCTATCAATGATCA
41622 TTTCTCATTTACCCCTATCAATGATCA
1 TTTCTCATTTACCCCTATCAATGATCA
41649 TTT
1 TTT
41652 TTCTATCGAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.43
Consensus pattern (27 bp):
TTTCTCATTTACCCCTATCAATGATCA
Found at i:42451 original size:17 final size:17
Alignment explanation
Indices: 42429--42486 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
42419 GTGGCAGAGC
*
42429 CGGCGCATACTGCGCGA
1 CGGCGCATACTACGCGA
42446 CGGCGCATACTACGCGA
1 CGGCGCATACTACGCGA
42463 CGGCGCATACTACGCGA
1 CGGCGCATACTACGCGA
42480 CGGCGCA
1 CGGCGCA
42487 GGGCCCTACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.21, C:0.36, G:0.33, T:0.10
Consensus pattern (17 bp):
CGGCGCATACTACGCGA
Found at i:42790 original size:24 final size:24
Alignment explanation
Indices: 42754--42801 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
42744 ACAAAGGAAA
42754 AAACACATATTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
* *
42778 AAACGCATGTTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
42802 TTCACAGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
AAACACATATTTCCTTCTTATTAT
Found at i:46937 original size:48 final size:48
Alignment explanation
Indices: 46877--46979 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
46867 GCTCGACTCA
* * * * *
46877 TGCTTGTTAAGAAAATTTGTTGCTCAGCTCATTGCTCATTAAGCTTGT
1 TGCTCGTTAAGAAAAGTTATTGCTCAACTCATTGCTCATTAAGCTCGT
* *
46925 TGCTCGTTAAGAAAAGTTATTGCTCAACTCGTTGCTCGTTAAGCTCGT
1 TGCTCGTTAAGAAAAGTTATTGCTCAACTCATTGCTCATTAAGCTCGT
46973 TGCTCGT
1 TGCTCGT
46980 CTCGTTGCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (48 bp):
TGCTCGTTAAGAAAAGTTATTGCTCAACTCATTGCTCATTAAGCTCGT
Found at i:46964 original size:7 final size:7
Alignment explanation
Indices: 46952--46992 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
46942 TATTGCTCAA
46952 CTCGTTG
1 CTCGTTG
46959 CTCGTTAAG
1 CTCGTT--G
46968 CTCGTTG
1 CTCGTTG
46975 CTCG-T-
1 CTCGTTG
46980 CTCGTTG
1 CTCGTTG
46987 CTCGTT
1 CTCGTT
46993 AAGCTCACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
9 7 0.23
ACGTcount: A:0.05, C:0.29, G:0.24, T:0.41
Consensus pattern (7 bp):
CTCGTTG
Found at i:46973 original size:16 final size:16
Alignment explanation
Indices: 46952--46998 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
46942 TATTGCTCAA
46952 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCGTTAAG
46968 CTCGTTGCTCG-T---
1 CTCGTTGCTCGTTAAG
46980 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCGTTAAG
46996 CTC
1 CTC
46999 ACCAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
15 1 0.04
16 14 0.52
ACGTcount: A:0.09, C:0.30, G:0.23, T:0.38
Consensus pattern (16 bp):
CTCGTTGCTCGTTAAG
Found at i:46977 original size:28 final size:28
Alignment explanation
Indices: 46944--46998 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
46934 AGAAAAGTTA
46944 TTGCTCAACTCGTTGCTCGTTAAGCTCG
1 TTGCTCAACTCGTTGCTCGTTAAGCTCG
**
46972 TTGCTCGTCTCGTTGCTCGTTAAGCTC
1 TTGCTCAACTCGTTGCTCGTTAAGCTC
46999 ACCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.11, C:0.29, G:0.22, T:0.38
Consensus pattern (28 bp):
TTGCTCAACTCGTTGCTCGTTAAGCTCG
Found at i:50824 original size:14 final size:14
Alignment explanation
Indices: 50788--50839 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
50778 CCATTAAAAA
*
50788 ACTAAACCCAAAT-C
1 ACTAAA-CCTAATCC
50802 ACTAAACCTAATCC
1 ACTAAACCTAATCC
*
50816 ACTAAACCT-ACCC
1 ACTAAACCTAATCC
50829 ACTAAACCTAA
1 ACTAAACCTAA
50840 AAAACATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 17 0.50
14 17 0.50
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACTAAACCTAATCC
Found at i:53112 original size:32 final size:32
Alignment explanation
Indices: 53069--53129 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
53059 CTTACCTGTG
*
53069 CTAACTAATTTCTTTTGTTTTGTTTGTGTACA
1 CTAACTAATTTCTTTTCTTTTGTTTGTGTACA
*
53101 CTAACTTATTTCTTTTCTTTTGTTTGTGT
1 CTAACTAATTTCTTTTCTTTTGTTTGTGT
53130 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.61
Consensus pattern (32 bp):
CTAACTAATTTCTTTTCTTTTGTTTGTGTACA
Found at i:53877 original size:15 final size:14
Alignment explanation
Indices: 53844--53880 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
53834 GGCTCAACAT
53844 TTTTGCATC-TTCA
1 TTTTGCATCTTTCA
53857 -TTTGCATCTTTGCA
1 TTTTGCATCTTT-CA
53871 TTTTGCATCT
1 TTTTGCATCT
53881 GCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 2 0.10
14 2 0.10
15 9 0.43
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.54
Consensus pattern (14 bp):
TTTTGCATCTTTCA
Found at i:53885 original size:13 final size:13
Alignment explanation
Indices: 53844--53886 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
53834 GGCTCAACAT
*
53844 TTTTGCATCTTCA
1 TTTTGCATCTGCA
53857 -TTTGCATCTTTGCA
1 TTTTGCATC--TGCA
53871 TTTTGCATCTGCA
1 TTTTGCATCTGCA
53884 TTT
1 TTT
53887 CATTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 8 0.31
13 7 0.27
14 3 0.12
15 8 0.31
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (13 bp):
TTTTGCATCTGCA
Found at i:55102 original size:6 final size:6
Alignment explanation
Indices: 55091--55145 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
55081 AAAGAGCAAA
*
55091 AAAAAG AAAAAG -AAAAG -AAAAG AAAAAG -AACA- AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
55135 -TAAAG AAAAAG
1 AAAAAG AAAAAG
55146 GGATGAGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 20 0.49
6 21 0.51
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:55106 original size:11 final size:11
Alignment explanation
Indices: 55088--55145 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
55078 CAAAAAGAGC
55088 AAAA-AAAAGA
1 AAAAGAAAAGA
55098 AAAAGAAAAG-
1 AAAAGAAAAGA
55108 AAAAGAAAAAGA
1 AAAAG-AAAAGA
*
55120 ACAA-AAAAGA
1 AAAAGAAAAGA
*
55130 AAAAGTAAAGA
1 AAAAGAAAAGA
55141 AAAAG
1 AAAAG
55146 GGATGAGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 18 0.44
11 20 0.49
12 3 0.07
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:55113 original size:16 final size:15
Alignment explanation
Indices: 55088--55145 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 15
55078 CAAAAAGAGC
55088 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
55103 AAAAGAAAAGAAAAAG
1 AAAA-AAAAGAAAAAG
55119 AACAAAAAAGAAAAAG
1 AA-AAAAAAGAAAAAG
55135 TAAAGAAAAAG
1 -AAA-AAAAAG
55146 GGATGAGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.10
16 25 0.64
17 10 0.26
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:56362 original size:34 final size:34
Alignment explanation
Indices: 56318--56471 Score: 245
Period size: 34 Copynumber: 4.5 Consensus size: 34
56308 AAAAAATTTG
* * *
56318 TCTCGCTTGAGATAATTTCCCAAAACAAATTTCA
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
56352 TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
* *
56386 TCTCACTTGAGACAATTTCTCATAACAAATTTCG
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
*
56420 TCTCACTTGAAACAATTTCTCAAAACAAATTTCA
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
*
56454 TCTCGCTTGAGACAATTT
1 TCTCACTTGAGACAATTT
56472 TTCTCTGAGA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 110 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (34 bp):
TCTCACTTGAGACAATTTCTCAAAACAAATTTCA
Found at i:56370 original size:20 final size:20
Alignment explanation
Indices: 56345--56404 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 20
56335 TCCCAAAACA
56345 AATTTCATCTCACTTGAGAC
1 AATTTCATCTCACTTGAGAC
*
56365 AA-TT--TCTCA----AAAC
1 AATTTCATCTCACTTGAGAC
56378 AAATTTCATCTCACTTGAGAC
1 -AATTTCATCTCACTTGAGAC
56399 AATTTC
1 AATTTC
56405 TCATAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 2 0.07
17 10 0.33
19 2 0.07
20 8 0.27
21 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (20 bp):
AATTTCATCTCACTTGAGAC
Found at i:56863 original size:33 final size:33
Alignment explanation
Indices: 56790--56876 Score: 79
Period size: 33 Copynumber: 2.6 Consensus size: 33
56780 AAATTCTGAA
* * *
56790 ATTGTTTCACTTAAAATAAAAATCATCTTTGAG
1 ATTGTTTCACTGAAAACAAAAACCATCTTTGAG
* * *
56823 -TCCGTTTCACTGGAAACAACAACCATCTTTGAG
1 AT-TGTTTCACTGAAAACAAAAACCATCTTTGAG
*
56856 ATTGTTTCTCTTGAAAA-AAAA
1 ATTGTTTCAC-TGAAAACAAAA
56877 TCTTATTTTC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
32 1 0.02
33 34 0.83
34 6 0.15
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (33 bp):
ATTGTTTCACTGAAAACAAAAACCATCTTTGAG
Found at i:57034 original size:35 final size:34
Alignment explanation
Indices: 56986--57105 Score: 108
Period size: 33 Copynumber: 3.6 Consensus size: 34
56976 AATACCCATA
*
56986 TTTGAGTTTGTTTCCCTTGAAACAAAACAAACATC
1 TTTGAGTTCGTTTCCCTTGAAACAAAACAAA-ATC
* *
57021 TTTGA-TATCGTTTCCCTTGAAAC-GAATAAAATC
1 TTTGAGT-TCGTTTCCCTTGAAACAAAACAAAATC
* ** *
57054 TTTGAGTTTGTTTATCTTGAAACAAAAC--CATC
1 TTTGAGTTCGTTTCCCTTGAAACAAAACAAAATC
*
57086 TTTGAG-TC-ATTCCCTTGAAA
1 TTTGAGTTCGTTTCCCTTGAAA
57106 TGAATTTTGT
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
30 9 0.13
31 1 0.01
32 9 0.13
33 21 0.30
34 9 0.13
35 20 0.29
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (34 bp):
TTTGAGTTCGTTTCCCTTGAAACAAAACAAAATC
Found at i:57228 original size:46 final size:45
Alignment explanation
Indices: 57169--57448 Score: 166
Period size: 40 Copynumber: 6.5 Consensus size: 45
57159 TTTCTTTTGA
* *
57169 AACCAT-T-ATCACCCTTGGATGACCTATCGTCCTCATCGCGTAGG
1 AACCATGTCATCACCC-TAGATGACCTATCGTCCTCATCACGTAGG
* * * *
57213 AACCGTGTCATCACCC-----GACTTGATC-TCCTCATCACATAAG
1 AACCATGTCATCACCCTAGATGACCT-ATCGTCCTCATCACGTAGG
* * *
57253 AGCCATGTCA--ACCCCAGATAAACC-AGTCGTCCTCATCACGTAGG
1 AACCATGTCATCACCCTAGAT-GACCTA-TCGTCCTCATCACGTAGG
* * *
57297 AACCATGTTATCAACCTTAGATGACCTACCGTCCTCATCACGTAGG
1 AACCATGTCATC-ACCCTAGATGACCTATCGTCCTCATCACGTAGG
* * * **
57343 AACCGTATCATCA-CC----TGACCTGTTTTCCTCATCACGTAGG
1 AACCATGTCATCACCCTAGATGACCTATCGTCCTCATCACGTAGG
* * *
57383 AACCATGTCA--ACCCCAGATAACC-AGCCGTCCTCATCACGTAGG
1 AACCATGTCATCACCCTAGATGACCTA-TCGTCCTCATCACGTAGG
* *
57426 AACCGTGTTATCACCCTTAGATG
1 AACCATGTCATCACCC-TAGATG
57449 GCCAAGACTC
Statistics
Matches: 176, Mismatches: 36, Indels: 46
0.68 0.14 0.18
Matches are distributed among these distances:
38 5 0.03
39 2 0.01
40 53 0.30
41 3 0.02
42 1 0.01
43 29 0.16
44 29 0.16
45 6 0.03
46 40 0.23
47 8 0.05
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (45 bp):
AACCATGTCATCACCCTAGATGACCTATCGTCCTCATCACGTAGG
Found at i:57424 original size:83 final size:84
Alignment explanation
Indices: 57282--57440 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 84
57272 AAACCAGTCG
** *
57282 TCCTCATCACGTAGGAACCATGTTATCAACCTTAGATGACCTACCGTCCTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACCATG-T-TCAACCCCAGATAACCTACCGTCCTCATCACGTAGGAACC
57347 GTATCATCACCTGACCTGTTT
64 GTATCATCACCTGACCTGTTT
57368 TCCTCATCACGTAGGAACCATG-TCAACCCCAGATAACC-AGCCGTCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAACCATGTTCAACCCCAGATAACCTA-CCGTCCTCATCACGTAGGAACCG
* *
57431 TGTTATCACC
65 TATCATCACC
57441 CTTAGATGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
82 1 0.01
83 44 0.66
86 22 0.33
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (84 bp):
TCCTCATCACGTAGGAACCATGTTCAACCCCAGATAACCTACCGTCCTCATCACGTAGGAACCGT
ATCATCACCTGACCTGTTT
Found at i:57529 original size:127 final size:126
Alignment explanation
Indices: 57217--57832 Score: 689
Period size: 127 Copynumber: 4.8 Consensus size: 126
57207 CGTAGGAACC
* * * * * * * *
57217 GTGTCATCACCCGACTTGATCTCCTCATCACATAAGAGCCATGTCAACCCCAGATAAACCAGTCG
1 GTGTCATCACCTGACCTGATTTTCTCATCACGTAGGAGCCGTGTCAA-CCCAGAT-AACCAGCCG
* * * * * * ** * *
57282 TCCTCATCACGTAGGAACCATGTTATCAACCTTAGATGACCTACCGTCCTCAT-CACGTAGGAAC
64 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC-A-AG-ACTCATGAACAAATGAGC
*
57346 C
126 A
* * *
57347 GTATCATCACCTGACCTG-TTTTCCTCATCACGTAGGAACCATGTCAACCCCAGATAACCAGCCG
1 GTGTCATCACCTGACCTGATTTT-CTCATCACGTAGGAGCCGTGTCAA-CCCAGATAACCAGCCG
57411 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
64 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * *
57474 GTGTCATCACCCGACCTGATTTTCTCATCACGTAGGAACCGTGTCAACAACAGATAACTAGCCGT
1 GTGTCATCACCTGACCTGATTTTCTCATCACGTAGGAGCCGTGTCAAC-CCAGATAACCAGCCGT
*
57539 CCTTATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
65 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * * * * * * * *
57601 GTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCAGATAATCAGTCGT
1 GTGTCATCACCTGACCTGATTTTCTCATCACGT-AGGAGCCGTGTCAACCCAGATAACCAGCCGT
*
57666 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAGATGAGCA
65 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * * * * *
57728 GTGTCATCACCTGACCAGA-TCTCTTCATTATGTAGGAGCTGTGTCAACCCAGATATCCAACCGT
1 GTGTCATCACCTGACCTGATTTTC-TCATCACGTAGGAGCCGTGTCAACCCAGATAACCAGCCGT
* **
57792 CCTCATCACATAGGAACCGTGTTATCACATTTAGATGGCCA
65 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCA
57833 GAACTATTCA
Statistics
Matches: 427, Mismatches: 53, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
126 71 0.17
127 246 0.58
128 18 0.04
129 48 0.11
130 44 0.10
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (126 bp):
GTGTCATCACCTGACCTGATTTTCTCATCACGTAGGAGCCGTGTCAACCCAGATAACCAGCCGTC
CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
Found at i:57902 original size:254 final size:254
Alignment explanation
Indices: 57366--57902 Score: 679
Period size: 254 Copynumber: 2.1 Consensus size: 254
57356 CCTGACCTGT
* * *
57366 TTTCCTCATCACGTAGGAACCATGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCG
1 TTTCCTCATTATGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCG
* *
57431 TGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCCGACCTGATTT
66 TGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCCGACCAGATTC
* * * *
57496 TCTCATCACGTAGGAACCGTGTCAACAACAGATAACTAGCCGTCCTTATCACGTAGGAACCGTGT
131 TCTCATCACGTAGGAACCGTGTCAACAACAGATAACCAACCGTCCTCATCACATAGGAACCGTGT
* *
57561 TATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACATGACCAGA
196 TATCACACTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACACGACCAGA
* * * * * *
57620 TCTCCTCATTATGTAAGGAGCTGTGTCAA-CTCAGATAATCAGTCGTCCTCATCACGTAGGAACC
1 TTTCCTCATTATGT-AGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACC
* *
57684 GTGTTATCACCCTTAGATGGCCAAGACTCATGAACAGATGAGCAGTGTCATCACCTGACCAGA-T
65 GTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCCGACCAGATT
* * * * * *
57748 CTCTTCATTATGTAGGAGCTGTGTCAAC-CCAGATATCCAACCGTCCTCATCACATAGGAACCGT
130 CTC-TCATCACGTAGGAACCGTGTCAACAACAGATAACCAACCGTCCTCATCACATAGGAACCGT
* * ** * * * *
57812 GTTATCACATTTAGATGGCC-AGAACTATTCAT-CACGTATGAGCTGTGTCATTACCCGACTAGA
194 GTTATCACACTTAGATGGCCAAG-AC---TCATGAACAAATGAGCAGTGTCATCACACGACCAGA
*
57875 TTTCCTCATTATGTAGGAATCGTGTCAA
1 TTTCCTCATTATGTAGGAACCGTGTCAA
57903 TCCTTGATAA
Statistics
Matches: 240, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
252 2 0.01
253 53 0.22
254 134 0.56
255 47 0.20
256 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (254 bp):
TTTCCTCATTATGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACCG
TGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCCGACCAGATTC
TCTCATCACGTAGGAACCGTGTCAACAACAGATAACCAACCGTCCTCATCACATAGGAACCGTGT
TATCACACTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACACGACCAGA
Found at i:58618 original size:14 final size:14
Alignment explanation
Indices: 58582--58633 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
58572 TCCATTAAAA
*
58582 ACTAAACCCAAAT-C
1 ACTAAA-CCTAATCC
58596 ACTAAACCTAATCC
1 ACTAAACCTAATCC
*
58610 ACTAAACCT-ACCC
1 ACTAAACCTAATCC
58623 ACTAAACCTAA
1 ACTAAACCTAA
58634 AAAACATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 17 0.50
14 17 0.50
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACTAAACCTAATCC
Found at i:62508 original size:31 final size:29
Alignment explanation
Indices: 62428--62529 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
62418 AAAATTTTGA
*
62428 ATACTTTAAGTACCTATTTTGACCAAAAG
1 ATACTTTAAGTACCTATTTTGACAAAAAG
*
62457 ATACTTTAGGTACCTATTTTGATCAAAAAG
1 ATACTTTAAGTACCTATTTTGA-CAAAAAG
* * *
62487 ATTATTTTAAATACTTATTTTGACTAAAAA-
1 A-TACTTTAAGTACCTATTTTGAC-AAAAAG
*
62517 ATACTTTAGGTAC
1 ATACTTTAAGTAC
62530 TTAAATGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 30 0.49
30 9 0.15
31 22 0.36
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
ATACTTTAAGTACCTATTTTGACAAAAAG
Found at i:62553 original size:60 final size:58
Alignment explanation
Indices: 62393--62567 Score: 151
Period size: 60 Copynumber: 2.9 Consensus size: 58
62383 TGTTATTAAT
* * * * *
62393 TAAAGAATATTTTAGGTACT-AATGAAAAATTTTGA-ATACTTTAAGTACCTATTTTGAC
1 TAAAAAATACTTTAGGTACTAAATGAAAAA--ATGATATATTTTAAGTACTTATTTTGAC
* * ** *
62451 CAAAAGATACTTTAGGTACCTATTTTGATCAAAAA-GAT-TATTTTAAATACTTATTTTGAC
1 TAAAAAATACTTTAGGTA-CTA-AATGA--AAAAATGATATATTTTAAGTACTTATTTTGAC
*
62511 TAAAAAATACTTTAGGTACTTAAATGAAAAAGATGATATATTTTAAGTATTTATTTT
1 TAAAAAATACTTTAGGTAC-TAAATGAAAAA-ATGATATATTTTAAGTACTTATTTT
62568 CTATACCTAA
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
57 4 0.04
58 15 0.16
59 9 0.10
60 56 0.62
61 3 0.03
63 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (58 bp):
TAAAAAATACTTTAGGTACTAAATGAAAAAATGATATATTTTAAGTACTTATTTTGAC
Found at i:62763 original size:16 final size:16
Alignment explanation
Indices: 62727--62771 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
62717 AATTAGTGGA
*
62727 CAGATGGAT-GTGGGG
1 CAGATGGATGGGGGGG
62742 CAGATGGATGGGGGGG
1 CAGATGGATGGGGGGG
*
62758 CGGATGGATGGGGG
1 CAGATGGATGGGGG
62772 CGGGCGGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.18, C:0.07, G:0.60, T:0.16
Consensus pattern (16 bp):
CAGATGGATGGGGGGG
Done.