Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007118.1 Hibiscus syriacus cultivar Beakdansim tig00018603_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: 49846
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Found at i:3878 original size:14 final size:14
Alignment explanation
Indices: 3859--3904 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
3849 CTCATATTAT
3859 ATAAATAATAATAA
1 ATAAATAATAATAA
3873 ATAAATAATAAT-A
1 ATAAATAATAATAA
*
3886 AT-AATAAT-ATAT
1 ATAAATAATAATAA
3898 ATAAATA
1 ATAAATA
3905 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.07
12 8 0.28
13 7 0.24
14 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATAATAATAA
Found at i:3985 original size:36 final size:36
Alignment explanation
Indices: 3921--4312 Score: 350
Period size: 36 Copynumber: 10.9 Consensus size: 36
3911 ATTATTTTTT
* *
3921 AAACTATAT-ATATATATGCCTTTAAAAATTGTTTTCA
1 AAACTATATAATATATAT--TTTTCAAAATTGTTTTCA
* *
3958 AAACCATATAATATATATTTTTCAAAATTATTTT-A
1 AAACTATATAATATATATTTTTCAAAATTGTTTTCA
*
3993 AAACTATATAATATATA--TTTCGAAATTGTTTT-A
1 AAACTATATAATATATATTTTTCAAAATTGTTTTCA
4026 AAACTATATAATATATA-TTTTCAAAAATTGTTTT-A
1 AAACTATATAATATATATTTTTC-AAAATTGTTTTCA
* *
4061 AAAC--TAT-ATATATA-TTTTCAAAAATATTTTCA
1 AAACTATATAATATATATTTTTCAAAATTGTTTTCA
* *
4093 AAACTATAT-ATATATACATTTTCAAAA-TATTTTCAA
1 AAACTATATAATATATA-TTTTTCAAAATTGTTTTC-A
** *
4129 AAACTATATTTTATATA-TATTCAAAATTGTTTTCAA
1 AAACTATATAATATATATTTTTCAAAATTGTTTTC-A
* *
4165 AAACTATATATTATATATATTTTCAAAAATGTTTTCAA
1 AAACTATATAATATATAT-TTTTCAAAATTGTTTTC-A
****
4203 AAACTATATATTATATATATGTTTTCAAAA-AAAATTCA
1 AAACTATATA--ATATATAT-TTTTCAAAATTGTTTTCA
**
4241 AAACTATATAATATATATATTTTCGAAAACCGTTTTC-
1 AAACTATATAATATATAT-TTTTC-AAAATTGTTTTCA
4278 AAACTATATAATATATA-TTTTCAAAAATTGATTTT
1 AAACTATATAATATATATTTTTC-AAAATTG-TTTT
4313 ATAGTATAAA
Statistics
Matches: 307, Mismatches: 30, Indels: 37
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.03
32 17 0.06
33 34 0.11
34 14 0.05
35 57 0.19
36 73 0.24
37 35 0.11
38 49 0.16
39 3 0.01
40 16 0.05
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (36 bp):
AAACTATATAATATATATTTTTCAAAATTGTTTTCA
Found at i:4651 original size:15 final size:16
Alignment explanation
Indices: 4633--4662 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4623 CATTTACACA
4633 TTTATCA-GTTATTTT
1 TTTATCATGTTATTTT
4648 TTTATCATGTTATTT
1 TTTATCATGTTATTT
4663 ATATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTATCATGTTATTTT
Found at i:7912 original size:16 final size:17
Alignment explanation
Indices: 7893--7925 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
7883 AAAACCATAA
7893 ATTATA-TATTTTTAAT
1 ATTATATTATTTTTAAT
7909 ATTATATTTATTTTTAA
1 ATTATA-TTATTTTTAA
7926 AACTATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATATTATTTTTAAT
Found at i:7928 original size:41 final size:42
Alignment explanation
Indices: 7879--7983 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
7869 ATATATAAAC
* *
7879 TTTCAAAACCATAA-ATTATATATTTTT-AATATTATATTTAT
1 TTTCAAAACCATAATA-TATATATTTTTCAAAACTATATTTAT
* * *
7920 TTTTAAAACTATGATATATATATTTTTCAAAACTATATTTAT
1 TTTCAAAACCATAATATATATATTTTTCAAAACTATATTTAT
* *
7962 TTTCAAAACTATACTATATATA
1 TTTCAAAACCATAATATATATA
7984 ACCAAAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 22 0.41
42 32 0.59
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.49
Consensus pattern (42 bp):
TTTCAAAACCATAATATATATATTTTTCAAAACTATATTTAT
Found at i:7937 original size:23 final size:23
Alignment explanation
Indices: 7911--7963 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
7901 TTTTTAATAT
7911 TATATTTATTTTT-AAAACTATGA
1 TATATTTATTTTTCAAAACTAT-A
*
7934 TATATATATTTTTCAAAACTATA
1 TATATTTATTTTTCAAAACTATA
*
7957 TTTATTT
1 TATATTT
7964 TCAAAACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATTTATTTTTCAAAACTATA
Found at i:7970 original size:42 final size:41
Alignment explanation
Indices: 7895--7983 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 41
7885 AACCATAAAT
* * *
7895 TATATATTTTTAATATTATATTTATTTTTAAAACTATGA-TA
1 TATATATTTTTAAAACTATATTTATTTTCAAAACTAT-ACTA
7936 TATATATTTTTCAAAACTATATTTATTTTCAAAACTATACTA
1 TATATATTTTT-AAAACTATATTTATTTTCAAAACTATACTA
7978 TATATA
1 TATATA
7984 ACCAAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (41 bp):
TATATATTTTTAAAACTATATTTATTTTCAAAACTATACTA
Found at i:8016 original size:15 final size:16
Alignment explanation
Indices: 7987--8020 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7977 ATATATAACC
7987 AAAATAAAATAAAACA
1 AAAATAAAATAAAACA
*
8003 AAAATAAACT-AAACA
1 AAAATAAAATAAAACA
8018 AAA
1 AAA
8021 GGAAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAATAAAACA
Found at i:8478 original size:40 final size:40
Alignment explanation
Indices: 8405--8554 Score: 147
Period size: 40 Copynumber: 3.7 Consensus size: 40
8395 AATTTGATCC
* ** * *
8405 ACTTCGTTGCTCTTCAGGGAAGATTAAACCGAACATGATTT
1 ACTTCGCTGCTCTTCA-GGAAGACCAAATCGAACTTGATTT
* * * * *
8446 CCTTCGCTGCACTTTAGGAAGACCAATTCGAACTTTATTT
1 ACTTCGCTGCTCTTCAGGAAGACCAAATCGAACTTGATTT
* * * *
8486 GCTTTGTTGCTCTTCAGGAGGACCAAATCGAACTTGATTT
1 ACTTCGCTGCTCTTCAGGAAGACCAAATCGAACTTGATTT
* *
8526 AGTTCACTGCTCTTCAGGAAGACCAAATC
1 ACTTCGCTGCTCTTCAGGAAGACCAAATC
8555 TGAAAGAATG
Statistics
Matches: 85, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
40 73 0.86
41 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (40 bp):
ACTTCGCTGCTCTTCAGGAAGACCAAATCGAACTTGATTT
Found at i:8692 original size:29 final size:29
Alignment explanation
Indices: 8650--10327 Score: 189
Period size: 29 Copynumber: 50.9 Consensus size: 29
8640 CATACTTAGA
* * *
8650 GATTGATTTCTCTTCATGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* *
8679 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
** *
8717 GATTGACTTATCTTCACGAGGAACTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
8746 GATTGACTCCTCTTCACGAGGGATTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* * *
8784 GATTGACTTCTCTTCACGAGAAAGTCGAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
8813 GATTGACTCCTCTTCACGAGGGGGAA-TAACAAA
1 GATTGACTCCTCTTCACGA---GGAAGT--CAAG
*
8846 GATTGACTACTCTTCACGAGGAAGT-AATG
1 GATTGACTCCTCTTCACGAGGAAGTCAA-G
* * *
8875 GATTGACTCATCTCCGCGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
** * *
8904 GATTGACTCCTC-TCTGTGAGGAAGTTAAT
1 GATTGACTCCTCTTC-ACGAGGAAGTCAAG
** * * * *
8933 GATTGACTATTTTTTACGAGAGAGCCAGGAATAAAAAA
1 GATTGACTCCTCTTCACGAG-GA---A-G--T--CAAG
* * *
8971 GATTGACTTCTCTTCACGAGAAAGTCAAT
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* ** *
9000 GATTGACTCATCTTCGTGAGGGAGCCAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* * * *
9038 GATTGAATTCTCTTCACAAGGAAGTCAAT
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* *
9067 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAAAAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
** *
9105 GATTGACTTTTCTTCACAAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
9134 GATTGACTCCTCTTCACGAGGGAGTTAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* * * * *
9172 GACTGACTTCTCTTTACGAGAAAGTCGAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * *
9201 GATTGACT-CTCTCCACGAAGGAGTCAATAATAACAAA
1 GATTGACTCCTCTTCACG-A-G-G---A-AGT--CAAG
* *
9238 AATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * * * *
9267 GATTGAATCCTTTTTGCGAGGGAGTCAAGAATAACAAA
1 GATTGACTCC-TCTT-C-A-CGAG-GAAG--T--CAAG
* *
9305 GATTGACTTCTCTTCACGAGGAATTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
9334 GATTGACTCCTCTTCACGAGGGAGTTAAGAATAACAAA
1 GATTGACTCCTCTTCACGA--G-G--AAG--T--CAAG
** * *
9372 GATTGACTTGTTTTCATGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
9401 GATTGACTCCTCTTCACGAGTGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGAG-GA---A-G--T--CAAG
* * ** * * * *
9439 TATTGATTTATCTTCTCAAGGAAGTCGAT
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * *
9468 GATTGACTCCTCTTAACAAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
*
9506 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * * *
9535 GATTGACTCATATTCATGAGGGAGTCAAAAATAACAAG
1 GATTGACTCCTCTTCACGA--G-G----AAGT--CAAG
*
9573 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * * *
9602 GATTGACTCGTCTTCATGAATGAGTCAGGAATAACAAT
1 GATTGACTCCTCTTCACG-A-G-G--A--AGT--CAAG
* * * * * *
9640 TATTGATTTCTTTTCACAAGCAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* ** *
9669 GATTGACTCATCTTCATTAGGGATTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* * *
9707 GATTGACTTCTCTTCATGAGGAAGTTAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* *
9736 GATTGACTCCTCTTCGCGAGGGAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
9765 AATTATAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
1 ---------GATTGACTCCTCTTCACGAGGAAGTCAAG
* * * * * *
9803 GATTTAATCCTCTTTGCGAGGGAATAAAGAAGAACAAA
1 GATTGACTCCTC-TT-C-A-CG----AGGAAG-TCAAG
*
9841 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * *
9870 GATTGGCTCCTCTTCACGATGGAGTCATGAATAAAAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* * * *
9908 GTTTGACTTCTTTTTACGAGGAAGTC-AG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
9936 TGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
1 -GATTGACTCCTCTTCACGA--G-G--AAG--T--CAAG
* *
9975 GATTGACTTCTCTTAACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
10004 GATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
1 GATTGACTCCTCTTCACGA--G-G--AAG--T--CAAG
* *
10042 GATTGACTTCTCTTCACAAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
10071 GATTGACTCCTCTTCACGAGGGATTCAAGAATAACAAT
1 GATTGACTCCTCTTCACGA-GG----AAG--T--CAAG
* * * **
10109 GATTGACTTCTTTTCACAATAAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* *
10138 GATTGACTCCTCTTCACGAGGGAGTTAGGAATAATAAA
1 GATTGACTCCTCTTCACGA-GGA---A-G--T--CAAG
* *
10176 GATTGAATTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
10205 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * *
10234 GATTGACTCCTCTTCGTGAGGGAGTCAAGAATTACAAA
1 GATTGACTCCTCTTC---A-CGAG----GAAGT-CAAG
*
10272 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
* * *
10301 GATTAACTCCTCTTCGCGAGGGAGTCA
1 GATTGACTCCTCTTCACGAGGAAGTCA
10328 TGAATAACAA
Statistics
Matches: 1180, Mismatches: 258, Indels: 422
0.63 0.14 0.23
Matches are distributed among these distances:
28 11 0.01
29 491 0.42
30 52 0.04
31 32 0.03
32 12 0.01
33 63 0.05
34 44 0.04
35 10 0.01
36 29 0.02
37 53 0.04
38 382 0.32
39 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (29 bp):
GATTGACTCCTCTTCACGAGGAAGTCAAG
Found at i:8721 original size:38 final size:38
Alignment explanation
Indices: 8679--8803 Score: 124
Period size: 38 Copynumber: 3.5 Consensus size: 38
8669 GGAAGTCAAG
*
8679 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
** * *
8717 GATTGACTTATCTTCACGA--G-G--A--ACT--CAAG
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
*
8746 GATTGACTCCTCTTCACGAGGGATTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
*
8784 GATTGACTTCTCTTCACGAG
1 GATTGACTCCTCTTCACGAG
8804 AAAGTCGAGG
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
29 20 0.30
31 3 0.04
33 1 0.01
34 1 0.01
35 1 0.01
36 3 0.04
38 38 0.57
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (38 bp):
GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
Found at i:8757 original size:67 final size:67
Alignment explanation
Indices: 8649--10231 Score: 1888
Period size: 67 Copynumber: 23.9 Consensus size: 67
8639 CCATACTTAG
* * *
8649 AGATTGATTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
8714 AA
66 AA
* * *
8716 AGATTGACTTATCTTCACGAGGAACTCAAGGATTGACTCCTCTTCACGAGGGATTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
8781 AA
66 AA
* *
8783 AGATTGACTTCTCTTCACGAGAAAGTCGAGGATTGACTCCTCTTCACGA-GG-G---GGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
8843 AA
66 AA
* * * *
8845 AGATTGACTACTCTTCACGAGGAAGT-AATGGATTGACTCATCTCCGCGA-GGA---A-G--T--
1 AGATTGACTTCTCTTCACGAGGAAGTCAA-GGATTGACTCCTCTTCACGAGGGAGTCAGGAATAA
8900 CAA
65 CAA
* * ** * * ** * * * *
8903 GGATTGACTCCTC-TCTGTGAGGAAGTTAATGATTGACTATTTTTTACGAGAGAGCCAGGAATAA
1 AGATTGACTTCTCTTC-ACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAA
*
8967 AAA
65 CAA
* * * ** *
8970 AGATTGACTTCTCTTCACGAGAAAGTCAATGATTGACTCATCTTCGTGAGGGAGCCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9035 AA
66 AA
* * * *
9037 AGATTGAATTCTCTTCACAAGGAAGTCAATGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9102 AA
66 AA
* * *
9104 AGATTGACTTTTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTTAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9169 AA
66 AA
* * * * * * **
9171 AGACTGACTTCTCTTTACGAGAAAGTCGAGGATTGACT-CTCTCCACGAAGGAGTCAATAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9235 AA
66 AA
* * * ** *
9237 AAATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTTTTTGCGAGGGAGTCAAGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9302 AA
66 AA
* * *
9304 AGATTGACTTCTCTTCACGAGGAATTCAAGGATTGACTCCTCTTCACGAGGGAGTTAAGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9369 AA
66 AA
* * * *
9371 AGATTGACTTGTTTTCATGAGGAAGTCAAGGATTGACTCCTCTTCACGAGTGAGTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9436 AA
66 AA
* * * * * * * * *
9438 ATATTGATTTATCTTCTCAAGGAAGTCGATGATTGACTCCTCTTAACAAGGGAGTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9503 AA
66 AA
* * * **
9505 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCATATTCATGAGGGAGTCAAAAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9570 AA
66 AA
* * * **
9572 GGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCGTCTTCATGAATGAGTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9637 AA
66 AA
** * * * * * ** *
9639 TTATTGATTTCTTTTCACAAGCAAGTCAAGGATTGACTCATCTTCATTAGGGATTCAGGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9704 AA
66 AA
* * * * * *
9706 AGATTGACTTCTCTTCATGAGGAAGTTAAGGATTGACTCCTCTTCGCGAGGGAGTCAAGAATTAT
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9771 AA
66 AA
* * ** * * * *
9773 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTTAATCCTCTTTGCGAGGGAATAAAGAAGAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9838 AA
66 AA
* * * *
9840 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGCTCCTCTTCACGATGGAGTCATGAATAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
9905 AA
66 AA
* * * *
9907 AGTTTGACTTCTTTTTACGAGGAAGTC-AGTGATTGACTCCTCTTCACGAGGGAGTCAAGAATAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAG-GATTGACTCCTCTTCACGAGGGAGTCAGGAATAA
9971 CAA
65 CAA
* *
9974 AGATTGACTTCTCTTAACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
10039 AA
66 AA
* * *
10041 AGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGATTCAAGAATAAC
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
10106 AA
66 AA
* * * ** * *
10108 TGATTGACTTCTTTTCACAATAAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTTAGGAATAAT
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
10173 AA
66 AA
* * *
10175 AGATTGAATTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTCACGAGGAAGTCA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCA
10232 AGGATTGACT
Statistics
Matches: 1293, Mismatches: 205, Indels: 36
0.84 0.13 0.02
Matches are distributed among these distances:
57 2 0.00
58 35 0.03
59 4 0.00
60 1 0.00
61 1 0.00
62 55 0.04
63 1 0.00
65 1 0.00
66 59 0.05
67 1130 0.87
68 4 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (67 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAAC
AA
Found at i:10010 original size:96 final size:96
Alignment explanation
Indices: 9910--10327 Score: 370
Period size: 96 Copynumber: 4.3 Consensus size: 96
9900 ATAAAAAAGT
* *
9910 TTGACTTCTTTTTACGAGGAAGTC-AGTGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAA
1 TTGACTTCTCTTCACGAGGAAGTCAAG-GATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAA
*
9974 AGATTGACTTCTCTTAACGAGGAAGTCAAGGA
65 AGATTGACTTCTCTTCACGAGGAAGTCAAGGA
* * * *
10006 TTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCAC-A---AG-GAAG
1 TTGACTTCTCTTCACGA--G-G--AAG--T--CAAGGATTGACTCCTCTTCACGAGGGAGTCAAG
* * *
10066 --T--CAAGGATTGACTCCTCTTCACGAGGGATTCAAGAATAACAATGA
57 AATAACAAAGATTGACTTCTCTTCACGA-GG----AAG--T--CAAGGA
* * ** * * *
10111 TTGACTTCTTTTCACAATAAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTTAGGAATAATAAA
1 TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
*
10176 GATTGAATTCTCTTCACGAGGAAGTCAAGGA
66 GATTGACTTCTCTTCACGAGGAAGTCAAGGA
** *
10207 TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAAGAATTACAAA
1 TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
10272 GATTGACTTCTCTTCACGAGGAAGTCAAGGA
66 GATTGACTTCTCTTCACGAGGAAGTCAAGGA
* * * *
10303 TTAACTCCTCTTCGCGAGGGAGTCA
1 TTGACTTCTCTTCACGAGGAAGTCA
10328 TGAATAACAA
Statistics
Matches: 255, Mismatches: 39, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
96 164 0.64
97 3 0.01
98 4 0.02
99 1 0.00
100 11 0.04
101 10 0.04
103 3 0.01
104 3 0.01
105 55 0.22
106 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (96 bp):
TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAA
GATTGACTTCTCTTCACGAGGAAGTCAAGGA
Found at i:10276 original size:67 final size:67
Alignment explanation
Indices: 10205--10358 Score: 245
Period size: 67 Copynumber: 2.3 Consensus size: 67
10195 GGAAGTCAAG
* * *
10205 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAAGAATTACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGCGAGGGAGTCAAGAATAACA
10270 AA
66 AA
*
10272 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGCGAGGGAGTCATGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGCGAGGGAGTCAAGAATAACA
10337 AA
66 AA
* * *
10339 GATTGAATCCTCTTCGCGAG
1 GATTGACTTCTCTTCACGAG
10359 AGATTCAAGT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 80 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (67 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGCGAGGGAGTCAAGAATAACA
AA
Found at i:10315 original size:163 final size:163
Alignment explanation
Indices: 10042--10358 Score: 481
Period size: 163 Copynumber: 1.9 Consensus size: 163
10032 GAATAACAAA
*
10042 GATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGATTCAAGAATAACA
1 GATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACA
* * * * *
10107 ATGATTGACTTCTTTTCACAATAAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTTAGGAATAA
66 AAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTAACTCCTCTTCACGAGGGAGTCAGGAATAA
* *
10172 TAAAGATTGAATTCTCTTCACGAGGAAGTCAAG
131 CAAAGATTGAATCCTCTTCACGAGGAAGTCAAG
* ** *
10205 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAAGAATTACA
1 GATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACA
* * * *
10270 AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGCGAGGGAGTCATGAATAA
66 AAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTAACTCCTCTTCACGAGGGAGTCAGGAATAA
*
10335 CAAAGATTGAATCCTCTTCGCGAG
131 CAAAGATTGAATCCTCTTCACGAG
10359 AGATTCAAGT
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
163 137 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (163 bp):
GATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACA
AAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTAACTCCTCTTCACGAGGGAGTCAGGAATAA
CAAAGATTGAATCCTCTTCACGAGGAAGTCAAG
Found at i:11964 original size:54 final size:54
Alignment explanation
Indices: 11897--12115 Score: 316
Period size: 54 Copynumber: 4.1 Consensus size: 54
11887 CATTATAAGT
* * *
11897 TTTC-TGGGGTGCACACGTAGTGCCGATACGGTCGTTCATAAACATATTATGAA
1 TTTCATGGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAA
* * *
11950 TTTCGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAA
1 TTTCATGGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAA
*
12004 TTTCATGGGTTGCACACTTAGTGCCGATAAGGTCATTCATAAACATATTATGAA
1 TTTCATGGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAA
* ** *
12058 TTTCATGGGTTGCACACTTAGTGCC-ACTATGGAAATTCATAAACTTATTATGAA
1 TTTCATGGGTTGCACACTTAGTGCCGA-TACGGTCATTCATAAACATATTATGAA
12112 TTTC
1 TTTC
12116 TTAGGTTAAA
Statistics
Matches: 153, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
53 5 0.03
54 148 0.97
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
TTTCATGGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAA
Found at i:12137 original size:54 final size:54
Alignment explanation
Indices: 12042--12298 Score: 307
Period size: 54 Copynumber: 4.8 Consensus size: 54
12032 AAGGTCATTC
* * ** * ** * * * *
12042 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGCCACTATGGAAATTC
1 ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCCAATACGAAAATTT
* * *
12096 ATAAACTTATTATGAATTTCTTAGGTTAAACACACAATGCCAATACGAAAATTT
1 ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCCAATACGAAAATTT
* * *
12150 ATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGTCAATACGGAAATTT
1 ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCCAATACGAAAATTT
* * **
12204 ATAAACTTGTTATGAATTTCTTAAGTTGGACACACAGTGCCAATATAAAAATTT
1 ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCCAATACGAAAATTT
* *
12258 ATAAACCTATTATGAATTTCTTAAGTTGAACACATAGTGCC
1 ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCC
12299 CATTCTATAA
Statistics
Matches: 175, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 175 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (54 bp):
ATAAACTTATTATGAATTTCTTAAGTTGAACACACAGTGCCAATACGAAAATTT
Found at i:12154 original size:108 final size:107
Alignment explanation
Indices: 11934--12277 Score: 357
Period size: 108 Copynumber: 3.2 Consensus size: 107
11924 ACGGTCGTTC
* * *** *
11934 ATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATT
1 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG-CCATACGGAAATTCATAAACTTATT
* * * ** * *** *
11999 ATGAATTTCATGGGTTGCACACTTAGTGCCGATAAGGTCATTC
65 ATGAATTTCTTAGGTTGAACACACAGTGCCAATAAGAAAATTT
*
12042 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGCCACTATGGAAATTCATAAACTTATT
1 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGCCA-TACGGAAATTCATAAACTTATT
* * *
12107 ATGAATTTCTTAGGTTAAACACACAATGCCAATACGAAAATTT
65 ATGAATTTCTTAGGTTGAACACACAGTGCCAATAAGAAAATTT
* * ** ** * * *
12150 ATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGTCAATACGGAAATTTATAAACTTGTT
1 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG-CCATACGGAAATTCATAAACTTATT
* *
12215 ATGAATTTCTTAAGTTGGACACACAGTGCCAATATA-AAAATTT
65 ATGAATTTCTTAGGTTGAACACACAGTGCCAATA-AGAAAATTT
*
12258 ATAAACCTATTATGAATTTC
1 ATAAACATATTATGAATTTC
12278 TTAAGTTGAA
Statistics
Matches: 197, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
107 2 0.01
108 193 0.98
109 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (107 bp):
ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGCCATACGGAAATTCATAAACTTATTA
TGAATTTCTTAGGTTGAACACACAGTGCCAATAAGAAAATTT
Found at i:12180 original size:162 final size:162
Alignment explanation
Indices: 11988--12291 Score: 365
Period size: 162 Copynumber: 1.9 Consensus size: 162
11978 ACGGTCGTTC
** ** * **
11988 ATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGCCGATAAGGTCATTCATAAACATATT
1 ATAAACATATTATGAATTTCATAAGTTGCACACACAGTGCCAATAAGGAAATTCATAAACATATT
** ** * ** *
12053 ATGAATTTCATGGGTTGCACACTTAGTGCCACTATGGAAATTCATAAACTTATTATGAATTTCTT
66 ATGAATTTCATAAGTTGCACACACAGTGCCAATATAAAAATTCATAAACCTATTATGAATTTCTT
*
12118 AGGTTAAACACACAATGCCAATACGAAAATTT
131 AAGTTAAACACACAATGCCAATACGAAAATTT
* * * * * * *
12150 ATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGTCAATACGGAAATTTATAAACTTGTT
1 ATAAACATATTATGAATTTCATAAGTTGCACACACAGTGCCAATAAGGAAATTCATAAACATATT
* * *
12215 ATGAATTTCTTAAGTTGGACACACAGTGCCAATATAAAAATTTATAAACCTATTATGAATTTCTT
66 ATGAATTTCATAAGTTGCACACACAGTGCCAATATAAAAATTCATAAACCTATTATGAATTTCTT
*
12280 AAGTTGAACACA
131 AAGTTAAACACA
12292 TAGTGCCCAT
Statistics
Matches: 115, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
162 115 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (162 bp):
ATAAACATATTATGAATTTCATAAGTTGCACACACAGTGCCAATAAGGAAATTCATAAACATATT
ATGAATTTCATAAGTTGCACACACAGTGCCAATATAAAAATTCATAAACCTATTATGAATTTCTT
AAGTTAAACACACAATGCCAATACGAAAATTT
Found at i:12740 original size:18 final size:18
Alignment explanation
Indices: 12717--12761 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
12707 TAATCCATGG
12717 TATCGATACCCACATCAA
1 TATCGATACCCACATCAA
12735 TATCGATACCCACATCAA
1 TATCGATACCCACATCAA
12753 TATCGATAC
1 TATCGATAC
12762 TAATTGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.31, G:0.07, T:0.24
Consensus pattern (18 bp):
TATCGATACCCACATCAA
Found at i:23307 original size:3 final size:3
Alignment explanation
Indices: 23299--23324 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23289 GAATTGGGTT
23299 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
23325 ATCACCAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:25107 original size:24 final size:23
Alignment explanation
Indices: 25078--25147 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
25068 AGCAGAACAG
25078 GAACAACAAAGAAGCAGTATA-CCA
1 GAACAAC-AAGAAGCAGTA-AGCCA
*
25102 GAACAATGAAGAAGCAGTAAGCCA
1 GAACAA-CAAGAAGCAGTAAGCCA
* *
25126 GACCAATCAAGAAGCAGCAAGC
1 GAACAA-CAAGAAGCAGTAAGC
25148 ACAAATCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.07
Consensus pattern (23 bp):
GAACAACAAGAAGCAGTAAGCCA
Found at i:29361 original size:16 final size:16
Alignment explanation
Indices: 29340--29371 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29330 AAAATTTTAA
*
29340 TTTAAACTTTTAAATT
1 TTTAAAATTTTAAATT
29356 TTTAAAATTTTAAATT
1 TTTAAAATTTTAAATT
29372 GACCCCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAAATTTTAAATT
Found at i:29915 original size:16 final size:19
Alignment explanation
Indices: 29894--29938 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
29884 AAGAAATTTA
29894 TTTTTATATTAG-TA-T-T
1 TTTTTATATTAGTTATTAT
*
29910 TTTTTA-AATAGTTATTAT
1 TTTTTATATTAGTTATTAT
29928 TTTTTATATTA
1 TTTTTATATTA
29939 ATATATTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 1 0.04
18 7 0.30
19 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTATATTAGTTATTAT
Found at i:29935 original size:34 final size:33
Alignment explanation
Indices: 29889--29992 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 33
29879 GTGGTAAGAA
* * *
29889 ATTTATTTTTATATTAGTAT-TTTTTTAAATAGTT
1 ATTT-TTTTTATATTAATATATTATGTAAATA-TT
29923 ATTATTTTTTATATTAATATATTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTATGTAAATATT
* *
29957 ATTTTTTATTA-AATAATAT-TTATAT-AATCATT
1 ATTTTTT-TTATATTAATATATTATGTAAAT-ATT
29989 ATTT
1 ATTT
29993 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.05
32 12 0.20
33 11 0.18
34 25 0.41
35 10 0.16
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (33 bp):
ATTTTTTTTATATTAATATATTATGTAAATATT
Found at i:29971 original size:17 final size:18
Alignment explanation
Indices: 29944--29977 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29934 TATTAATATA
*
29944 TTATGTAAATATTATTTT
1 TTATGTAAATAATATTTT
29962 TTAT-TAAATAATATTT
1 TTATGTAAATAATATTT
29978 ATATAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATGTAAATAATATTTT
Found at i:29990 original size:32 final size:31
Alignment explanation
Indices: 29922--29997 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
29912 TTTAAATAGT
* *
29922 TATTATTTTTTATATTAATATATTATGTAAA
1 TATTATTTTTTATAATAATATATTATATAAA
29953 TATTATTTTTTATTAAATAATAT-TTATAT-AA
1 TATTATTTTTTA-T-AATAATATATTATATAAA
29984 TCATTATTTATTTA
1 T-ATTATTT-TTTA
29998 GAATTATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 15 0.38
32 13 0.33
33 11 0.28
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
TATTATTTTTTATAATAATATATTATATAAA
Found at i:31751 original size:21 final size:21
Alignment explanation
Indices: 31721--31768 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31711 GCAGGGGTAC
* *
31721 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
31742 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
31763 ATGCCA
1 ATGCCA
31769 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:31798 original size:21 final size:21
Alignment explanation
Indices: 31772--31865 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
31762 TATGCCATCT
* *
31772 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
31793 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
31814 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
31835 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
31856 CCGCAGGGTT
1 CCGCAGGGTT
31866 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:32447 original size:33 final size:34
Alignment explanation
Indices: 32388--32484 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
32378 AAATGTTTTT
*
32388 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
32422 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
32455 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
32485 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:32491 original size:34 final size:33
Alignment explanation
Indices: 32386--32491 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
32376 ATAAATGTTT
*
32386 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
32420 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
32452 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
32487 TTAAA
1 TTAAA
32492 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:33101 original size:128 final size:128
Alignment explanation
Indices: 32871--33482 Score: 1158
Period size: 128 Copynumber: 4.8 Consensus size: 128
32861 TTTAAGTTAT
*
32871 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
32934 GCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
32997 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
33062 GCGCGCCCCCGGGAACGAGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
33125 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
33189 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
33252 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
* *
33317 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTTAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
33380 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
33445 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
33483 CCGATTATAG
Statistics
Matches: 476, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
126 50 0.11
127 126 0.26
128 300 0.63
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (128 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
Found at i:33322 original size:255 final size:256
Alignment explanation
Indices: 32871--33482 Score: 1158
Period size: 255 Copynumber: 2.4 Consensus size: 256
32861 TTTAAGTTAT
*
32871 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
32934 GCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTC
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTC
32999 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
131 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
33064 GCGCCCCCGGGAACGAGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
196 GCGCCCCCGGGAACGAGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
33125 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
33189 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTC
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTC
33254 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
131 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
* * *
33319 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTTAAATAATAGGTACTGATATATCTAGTG
196 GCGCCCCCGGGAACGAGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
33380 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
33445 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
33483 CCGATTATAG
Statistics
Matches: 350, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
253 48 0.14
254 1 0.00
255 200 0.57
256 101 0.29
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (256 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTGTC
CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGAGCCTTCATGTGAATAGTGAAATAATAGGTAATGATATATCTAGTG
Found at i:33563 original size:8 final size:8
Alignment explanation
Indices: 33550--33589 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
33540 TCACAATCTT
33550 TCAAATTC
1 TCAAATTC
33558 TCAAATTC
1 TCAAATTC
* *
33566 CCAAACTC
1 TCAAATTC
33574 T-AAATTC
1 TCAAATTC
33581 TCAAATTC
1 TCAAATTC
33589 T
1 T
33590 TTGAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (8 bp):
TCAAATTC
Found at i:36575 original size:12 final size:13
Alignment explanation
Indices: 36542--36579 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
36532 AAATACATAA
36542 ATATATTTAATAT
1 ATATATTTAATAT
*
36555 ATTTATTTAATAT
1 ATATATTTAATAT
36568 A-ATATTTAATAT
1 ATATATTTAATAT
36580 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:38827 original size:22 final size:24
Alignment explanation
Indices: 38795--38853 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
38785 GGCATGTGAA
* * *
38795 ATATGTCCCGAATGA-C-CTATGC
1 ATATGTTCCGAAGGACCACTATCC
38817 ATATGTTCCGAAGGACCACTATCC
1 ATATGTTCCGAAGGACCACTATCC
*
38841 ATATGTTCTGAAG
1 ATATGTTCCGAAG
38854 AACATAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 13 0.42
23 1 0.03
24 17 0.55
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (24 bp):
ATATGTTCCGAAGGACCACTATCC
Found at i:38915 original size:32 final size:30
Alignment explanation
Indices: 38838--38926 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 30
38828 AGGACCACTA
* *
38838 TCCATATGT-TCTGAAGAACATAAGTAATTG
1 TCCATATGTCTC-GAAGGACATAGGTAATTG
* *
38868 TCTATATGTCCCGAAGGACATAGGTAATCCTG
1 TCCATATGTCTCGAAGGACATAGGTAAT--TG
38900 TCCATATGTCTCGAAGGACATAGGTAA
1 TCCATATGTCTCGAAGGACATAGGTAA
38927 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.44
31 1 0.02
32 27 0.54
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (30 bp):
TCCATATGTCTCGAAGGACATAGGTAATTG
Found at i:42723 original size:18 final size:19
Alignment explanation
Indices: 42697--42732 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42687 CCACACATGT
42697 ATATAATTATC-TTAATTA
1 ATATAATTATCATTAATTA
*
42715 ATATCATTATCATTAATT
1 ATATAATTATCATTAATT
42733 CATTTTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATTATCATTAATTA
Found at i:42769 original size:13 final size:14
Alignment explanation
Indices: 42751--42792 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
42741 CGTATAATCC
42751 TATACATATCAT-T
1 TATACATATCATAT
*
42764 TATACACATCATAT
1 TATACATATCATAT
*
42778 CATATCATATCATAT
1 TATA-CATATCATAT
42793 CACCAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (14 bp):
TATACATATCATAT
Found at i:43075 original size:32 final size:31
Alignment explanation
Indices: 42991--43079 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
42981 CAAAGGACCA
* *
42991 CTATCCATATGTTCTGAAAAACATAGGTAAT
1 CTATCCATATGTCCTGAAAGACATAGGTAAT
* * ** *
43022 -TGTCCATATGCCCCAAAAGACATTGGTAAT
1 CTATCCATATGTCCTGAAAGACATAGGTAAT
*
43052 CCTATCCATATGTCCTGATAGACATAGG
1 -CTATCCATATGTCCTGAAAGACATAGG
43080 CAACCCTCGA
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
30 23 0.53
32 20 0.47
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (31 bp):
CTATCCATATGTCCTGAAAGACATAGGTAAT
Found at i:46239 original size:25 final size:25
Alignment explanation
Indices: 46211--46271 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
46201 ATCATCATCA
* *
46211 TAATTCTATTATAACGTAATAATCT
1 TAATTCTATTATAACATAATAATCG
46236 TAATTCTATTATAACATAATAATCG
1 TAATTCTATTATAACATAATAATCG
46261 TAATTCTATTA
1 TAATTCTATTA
46272 GCAAGACAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (25 bp):
TAATTCTATTATAACATAATAATCG
Found at i:47148 original size:24 final size:22
Alignment explanation
Indices: 47100--47148 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
47090 GGCATGTGAA
* *
47100 ATATGTCCCGAAGGACCTATGC
1 ATATGACCCGAAGGACCTATCC
47122 ATATGACCCGAAGGACCACTATCC
1 ATATGACCCGAAGGA-C-CTATCC
47146 ATA
1 ATA
47149 AGAACATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 1 0.04
24 8 0.35
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (22 bp):
ATATGACCCGAAGGACCTATCC
Found at i:47203 original size:32 final size:30
Alignment explanation
Indices: 47152--47224 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 30
47142 ATCCATAAGA
* *
47152 ACATAGGTAACTGTCCATATGTCTCAAATG
1 ACATAGGTAACTGTCCATATGTCCCAAAGG
*
47182 ACATAGGTAATCCTGTCCATATGTCCCGAAGG
1 ACATAGGTAA--CTGTCCATATGTCCCAAAGG
47214 ACATAGGTAAC
1 ACATAGGTAAC
47225 CCTCGACTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.29
32 27 0.71
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (30 bp):
ACATAGGTAACTGTCCATATGTCCCAAAGG
Done.