Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001538.1 Hibiscus syriacus cultivar Beakdansim tig00003020_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: 120532
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:978 original size:17 final size:17
Alignment explanation
Indices: 956--990 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
946 TGTGTTTCTT
956 TTTATTTTTTATAACAA
1 TTTATTTTTTATAACAA
973 TTTATTTTTTATAACAA
1 TTTATTTTTTATAACAA
990 T
1 T
991 GAAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTTTTTATAACAA
Found at i:3678 original size:19 final size:19
Alignment explanation
Indices: 3654--3690 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3644 ACCTTACTAA
3654 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
3673 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
3691 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:6280 original size:183 final size:183
Alignment explanation
Indices: 5972--6508 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
5962 ATTAAATCCG
5972 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
6037 ATAGATTATGTTCAAACTATGACACTGCTCGAACACTTGGCAATTTGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
6102 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
6155 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
6220 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * * *
6285 TTGTCAGGCCAAAGACTTTGTGATGAGACGAATCCTTTAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
*
6338 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGTCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
6403 ATAGATTACATTCATA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
6467 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
6509 TAAACCTGAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 337 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
Found at i:7702 original size:36 final size:34
Alignment explanation
Indices: 7662--7775 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
7652 CACTCAAATT
7662 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
7698 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
7734 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
7770 CGTTTT
1 TGTTTT
7776 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:7738 original size:72 final size:76
Alignment explanation
Indices: 7646--7807 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 76
7636 ATGCAGATGA
* * * *
7646 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
7708 GAAAGAA-G-AT
65 GAAAGAAGGCAT
*
7718 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
7782 AAAGAAGGCAT
66 AAAGAAGGCAT
7793 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
7808 GCTATTTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.63
73 11 0.14
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
AAAGAAGGCAT
Found at i:7855 original size:73 final size:72
Alignment explanation
Indices: 7685--7857 Score: 165
Period size: 73 Copynumber: 2.4 Consensus size: 72
7675 ACATACTTTG
* * * * *
7685 TCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTATTTTTCTT-AAAC
*
7749 AAGATTTG
65 AAGATTTA
* *
7757 TCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCAAGGCTATTTTT-TT-A
1 TCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTATTTTTCTTAA
*
7820 AGAAGATTTTA
63 ACAAGA-TTTA
* * *
7831 TCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TCTCGCTTGAGACAGTTTTCACTCGAAA
7858 CAGAACATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
72 17 0.20
73 27 0.32
74 16 0.19
75 6 0.07
76 18 0.21
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (72 bp):
TCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTATTTTTCTTAAACA
AGATTTA
Found at i:7971 original size:39 final size:39
Alignment explanation
Indices: 7914--7988 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
7904 CCTTGAAATT
* *
7914 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* *
7953 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
7989 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:7999 original size:104 final size:104
Alignment explanation
Indices: 7891--8208 Score: 525
Period size: 104 Copynumber: 3.1 Consensus size: 104
7881 ACAGTTTCTC
* *
7891 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
7956 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
7995 TTGAAAACATTTCCATTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
8060 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
8099 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
8161 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
8200 TTGAAAACA
1 TTGAAAACA
8209 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 153 0.76
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:8155 original size:36 final size:36
Alignment explanation
Indices: 8108--8183 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
8098 ATTGAAAACA
* * *
8108 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
8144 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
8180 TTTC
1 TTTC
8184 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:8583 original size:105 final size:105
Alignment explanation
Indices: 8383--8907 Score: 862
Period size: 105 Copynumber: 5.0 Consensus size: 105
8373 ATATCGTGAC
* * * * *
8383 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
8448 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
8489 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
8554 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
8594 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGCTTGTCAACAAAAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
8659 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
8699 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
8764 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
8804 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
8865 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
8904 ACTC
1 ACTC
8908 GGAACAATGC
Statistics
Matches: 399, Mismatches: 20, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
100 39 0.10
101 1 0.00
102 1 0.00
103 2 0.01
104 2 0.01
105 306 0.77
106 48 0.12
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:9503 original size:37 final size:37
Alignment explanation
Indices: 9450--9554 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
9440 CATTTTCGTC
9450 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
9487 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
9524 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
9555 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:9954 original size:18 final size:17
Alignment explanation
Indices: 9915--9957 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
9905 ATTATATGAA
9915 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
9931 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
9949 TATTATTAT
1 TATTATTAT
9958 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:9966 original size:2 final size:2
Alignment explanation
Indices: 9959--9985 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9949 TATTATTATG
9959 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9986 TAAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10024 original size:49 final size:51
Alignment explanation
Indices: 9966--10086 Score: 133
Period size: 49 Copynumber: 2.4 Consensus size: 51
9956 ATGTATATAT
* * * *
9966 ATATATATATATATATATATTAAATTAT-TTTCATTTTTTAC-TAT-ATTTTA
1 ATAT-TATATATATATATATTAAATT-TCTTTAATATTTTACTTATAAGTCTA
* *
10016 TTATTATATATATATATA-TATATTTCTTTAATATTTTACTTATAAGTCTA
1 ATATTATATATATATATATTAAATTTCTTTAATATTTTACTTATAAGTCTA
10066 ATATTACTATATATATATATT
1 ATATTA-TATATATATATATT
10087 GTAATTATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
47 1 0.02
48 16 0.27
49 17 0.29
50 12 0.20
51 12 0.20
52 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (51 bp):
ATATTATATATATATATATTAAATTTCTTTAATATTTTACTTATAAGTCTA
Found at i:10262 original size:14 final size:15
Alignment explanation
Indices: 10240--10269 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10230 TTCGTTTTTT
10240 TATTCATTATTATTA
1 TATTCATTATTATTA
10255 TATT-ATTATTATTA
1 TATTCATTATTATTA
10269 T
1 T
10270 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTCATTATTATTA
Found at i:10468 original size:2 final size:2
Alignment explanation
Indices: 10461--10536 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
10451 TAATACTTTG
10461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
10503 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10537 TTTTTCTTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16273 original size:3 final size:3
Alignment explanation
Indices: 16265--16307 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
16255 ATTCCTATCA
16265 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16308 TTCTCTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16322 original size:16 final size:16
Alignment explanation
Indices: 16303--16346 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
16293 ATTATTATTA
16303 TTATTTTCTCTTATCT
1 TTATTTTCTCTTATCT
16319 TTATTTTCTCTTATCT
1 TTATTTTCTCTTATCT
16335 TTATTTTCTCTT
1 TTATTTTCTCTT
16347 TATTGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTCTCTTATCT
Found at i:20457 original size:103 final size:103
Alignment explanation
Indices: 20224--20441 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
20214 GTTGAGGGTC
*
20224 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
20289 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* *
20327 TATGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
20392 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
20430 TATGTGGTCCTT
1 TATGTGGTCCTT
20442 ATGGACAGTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:20524 original size:23 final size:23
Alignment explanation
Indices: 20457--20525 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
20447 CAGTATTATA
* **
20457 TGGCACTACGGTGCAATTCTACA
1 TGGCACTACGGTGCAATTATATG
* *
20480 CGGCACTCCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
*
20503 TGGCACTTCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
20526 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATATG
Found at i:24071 original size:64 final size:64
Alignment explanation
Indices: 23960--24118 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
23950 TTGAAGGTGT
** *** * *
23960 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAAAATAAAAACATCGAATGTAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAAAATAAAAACATCAAATGCAATTCATGC
* * *
24024 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAAT-ACAACATCAAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAA-AATAAAAACATCAAATGCAATTCATGC
* *
24088 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
24119 TTTCATTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 77 0.95
65 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAAAATAAAAACATCAAATGCAATTCATGC
Found at i:24798 original size:31 final size:31
Alignment explanation
Indices: 24760--24915 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
24750 AGGGTCGAGG
24760 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
24791 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
24822 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
24853 GTTTACCTATGTTCTTTGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
24884 GTTTACCTAGGTTCTTTGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
24915 G
1 G
24916 GTCATTCGGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:28503 original size:64 final size:64
Alignment explanation
Indices: 28434--28591 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
28424 TTGAAGGTGT
** *** *
28434 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACACCGAATGCAATTCATG
28497 C
64 C
* * *
28498 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACACCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACACCGAATGCAATTCATGC
* *
28562 ACCGATGCATCAGTAGTGCATCGATGCATA
1 ATCGATGCATAAGTAGTGCATCGATGCATA
28592 TTTTCATTGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 77 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACACCGAATGCAATTCATGC
Found at i:29285 original size:31 final size:31
Alignment explanation
Indices: 29247--29340 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
29237 AGGGTCGAGG
29247 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
29278 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
29309 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
29340 G
1 G
29341 GTCCTTCGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:31939 original size:42 final size:42
Alignment explanation
Indices: 31887--32006 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
31877 TTTCCCCGAA
* * *
31887 TTCCCTTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
31929 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
31971 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
32007 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:32241 original size:22 final size:23
Alignment explanation
Indices: 32194--32254 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
32184 TAATTATTAA
* *
32194 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
32215 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
32238 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
32255 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:32250 original size:52 final size:52
Alignment explanation
Indices: 32194--32345 Score: 145
Period size: 52 Copynumber: 2.9 Consensus size: 52
32184 TAATTATTAA
32194 AATATTTAAAATAT-ATTTATTAATATTTATAATAATATAATATTATATTTTT
1 AATATTTAAAATATAATTTATT-ATATTTATAATAATATAATATTATATTTTT
**
32246 AATATTATATAAA-ATAATCAATTATA-TTATAATAATATAAGATATTATATTTTT
1 AATATT-TA-AAATATAATTTATTATATTTATAATAATAT-A-ATATTATATTTTT
* * *
32300 -AT-TTTAATAATATAATTTTTTTTTATTTAATAATGA-ATAATATTAT
1 AATATTTAA-AATATAA-TTTATTATATTT-ATAATAATATAATATTAT
32346 TTATATATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
50 1 0.01
51 4 0.05
52 31 0.37
53 16 0.19
54 25 0.30
55 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (52 bp):
AATATTTAAAATATAATTTATTATATTTATAATAATATAATATTATATTTTT
Found at i:32270 original size:31 final size:32
Alignment explanation
Indices: 32205--32283 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
32195 ATATTTAAAA
32205 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
*
32237 TATATTT-TTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
32268 TATATTATAATAATAT
1 TATATT-TATTAATAT
32284 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.35
32 8 0.20
33 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:32608 original size:20 final size:20
Alignment explanation
Indices: 32530--32599 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
32520 TTTCCAGATG
32530 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
32550 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
32570 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
32590 TTTTCCAGAA
1 TTTTCCAGAA
32600 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:32608 original size:40 final size:40
Alignment explanation
Indices: 32530--32608 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
32520 TTTCCAGATG
* **
32530 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
32570 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
32609 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:32618 original size:15 final size:15
Alignment explanation
Indices: 32582--32663 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
32572 TTACAGAAAT
**
32582 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
32597 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
32611 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
32626 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
32641 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
32656 GTAATTCA
1 GTAATTCA
32664 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:32634 original size:30 final size:30
Alignment explanation
Indices: 32582--32663 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
32572 TTACAGAAAT
32582 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
32611 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
32641 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
32664 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:32656 original size:45 final size:44
Alignment explanation
Indices: 32582--32668 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
32572 TTACAGAAAT
**
32582 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
32626 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
32669 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:34073 original size:103 final size:103
Alignment explanation
Indices: 33894--34111 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
33884 GTCGAGGGTC
33894 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
33959 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
33997 TATGTGGTCCTTCGGGAGATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
34062 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
34100 TATGTGGTCCTT
1 TATGTGGTCCTT
34112 ATGGATAGTA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:34194 original size:23 final size:23
Alignment explanation
Indices: 34135--34195 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
34125 TATGGAACTA
* *
34135 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTATATGTGGCACTC
*
34158 CGGTGCAATTATATGTGGCACTT
1 CGGTGCAATTATATGTGGCACTC
*
34181 CGGTGAAATTATATG
1 CGGTGCAATTATATG
34196 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
CGGTGCAATTATATGTGGCACTC
Found at i:37032 original size:102 final size:106
Alignment explanation
Indices: 36917--37126 Score: 374
Period size: 102 Copynumber: 2.0 Consensus size: 106
36907 ATTTCTTAAT
36917 GAAAAAGGGGAGCTTAACATTTTCATATATTTTCAAACAATTGGTAACAATTGATATCATTTTGT
1 GAAAAAGGGGAGCTTAACATTTTCATATATTTTCAAACAATTGGTAACAATTGATATCATTTTGT
*
36982 TAACAATTGGT-T-TTTTT-ATTAAACATTTTATT-AGGGG
66 TAACAATTGATATCTTTTTCATTAAACATTTTATTAAGGGG
*
37019 GAAAAGGGGGAGCTTAACATTTTCATATATTTTCAAACAATTGGTAACAATTGATATCATTTTGT
1 GAAAAAGGGGAGCTTAACATTTTCATATATTTTCAAACAATTGGTAACAATTGATATCATTTTGT
37084 TAACAATTGATATCTTTTTCATTAAACATTTTATTAAGGGG
66 TAACAATTGATATCTTTTTCATTAAACATTTTATTAAGGGG
37125 GA
1 GA
37127 GTTTTGTCAA
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
102 74 0.73
103 1 0.01
104 5 0.05
105 15 0.15
106 7 0.07
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (106 bp):
GAAAAAGGGGAGCTTAACATTTTCATATATTTTCAAACAATTGGTAACAATTGATATCATTTTGT
TAACAATTGATATCTTTTTCATTAAACATTTTATTAAGGGG
Found at i:37089 original size:21 final size:21
Alignment explanation
Indices: 37063--37102 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37053 AAACAATTGG
37063 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
37084 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
37103 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:37377 original size:23 final size:20
Alignment explanation
Indices: 37326--37404 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
37316 AGGGTGTCAA
* * *
37326 AGTGCATCCATGAACCCCTGC
1 AGTGCATCCATGCA-CCATGT
37347 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCATG----T
*
37370 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
37390 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
37405 TCCATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 2 0.04
20 17 0.35
21 13 0.27
23 15 0.31
24 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:38955 original size:32 final size:34
Alignment explanation
Indices: 38888--38955 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
38878 TAACTCAACA
* * *
38888 GAAAGGTTCTAGCTTATCCCGTGTAAAAGCTAGG
1 GAAAAGTTCTAGCTTAGCCCGTGTAAAAACTAGG
*
38922 GAAAAGTTCTAGTTTAGCCCG-G-AAAAACTAGG
1 GAAAAGTTCTAGCTTAGCCCGTGTAAAAACTAGG
38954 GA
1 GA
38956 GTTGTAAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 11 0.37
33 1 0.03
34 18 0.60
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (34 bp):
GAAAAGTTCTAGCTTAGCCCGTGTAAAAACTAGG
Found at i:39709 original size:22 final size:24
Alignment explanation
Indices: 39684--39737 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 24
39674 TTTAGTTAAC
39684 TTTTATAATACTTTTA-T-AAATA
1 TTTTATAATACTTTTATTAAAATA
*
39706 -TTT-TAATATTTTTATTAAAATA
1 TTTTATAATACTTTTATTAAAATA
39728 TTTTAATAAT
1 TTTT-ATAAT
39738 GTCTTAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 10 0.38
21 4 0.15
22 5 0.19
23 3 0.12
25 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAATACTTTTATTAAAATA
Found at i:39718 original size:20 final size:22
Alignment explanation
Indices: 39689--39735 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
39679 TTAACTTTTA
39689 TAATACTTTTA-T-AAATATTT
1 TAATACTTTTATTAAAATATTT
*
39709 TAATATTTTTATTAAAATATTT
1 TAATACTTTTATTAAAATATTT
39731 TAATA
1 TAATA
39736 ATGTCTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATACTTTTATTAAAATATTT
Found at i:39941 original size:21 final size:21
Alignment explanation
Indices: 39917--39973 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
39907 CATTATCATG
* *
39917 AATTATCACAATAATATAATA
1 AATTATCACATTAATAAAATA
*
39938 AATTATTACATTAATAAAATA
1 AATTATCACATTAATAAAATA
*
39959 AAATATCACATTAAT
1 AATTATCACATTAAT
39974 TAACAGTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTATCACATTAATAAAATA
Found at i:51101 original size:20 final size:21
Alignment explanation
Indices: 51070--51123 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
51060 TATTCTTGAC
51070 AATCGCAATGCGATTTT-CAT
1 AATCGCAATGCGATTTTCCAT
* *
51090 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTTCCAT
*
51111 AATCGCAACGCGA
1 AATCGCAATGCGA
51124 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAT
Found at i:51205 original size:20 final size:20
Alignment explanation
Indices: 51111--51339 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
51101 GATTTTCCAT
* ** *
51111 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
51131 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
51151 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51171 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
51191 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51211 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51231 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51251 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
51271 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
51291 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
51311 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
51331 AATCACAAC
1 AATCGCAAC
51340 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:52070 original size:24 final size:24
Alignment explanation
Indices: 52031--52077 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
52021 AAATTTGGTC
52031 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
52055 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
52078 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:52269 original size:12 final size:12
Alignment explanation
Indices: 52252--52276 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52242 ATATAATCCT
52252 GAAGAAGAAAAA
1 GAAGAAGAAAAA
52264 GAAGAAGAAAAA
1 GAAGAAGAAAAA
52276 G
1 G
52277 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:54644 original size:19 final size:19
Alignment explanation
Indices: 54575--54750 Score: 228
Period size: 19 Copynumber: 9.7 Consensus size: 19
54565 GCAACGAGAG
54575 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
54594 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
54608 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
54628 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
54647 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
54666 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
54685 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
54699 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
54719 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
54738 AATCGCATTGCGA
1 AATCGCAATGCGA
54751 TTCTCTCGTT
Statistics
Matches: 138, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
14 20 0.14
15 3 0.02
16 2 0.01
17 3 0.02
19 83 0.60
20 27 0.20
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:54661 original size:72 final size:70
Alignment explanation
Indices: 54575--54741 Score: 216
Period size: 72 Copynumber: 2.3 Consensus size: 70
54565 GCAACGAGAG
54575 AATCGCAATGCGAAATGAAAATCCCAA-C-AA-GAAAATCGCAATGCGGAAATGAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCCCAAGCAAATGAAAATCGCAA--C-G--A-GAAAATCGCAAT
54637 GC-GAAATGAA
60 GCGGAAATGAA
* *
54647 AATCGCAATGCGAAATGAAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCCCAA-GC-AAATGAAAATCGCAACGAGAAAATCGCAATGCGG
54712 AAATGAA
64 AAATGAA
54719 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
54742 GCATTGCGAT
Statistics
Matches: 87, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
71 13 0.15
72 58 0.67
74 2 0.02
75 1 0.01
76 2 0.02
77 11 0.13
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.14
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCCCAAGCAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAA
ATGAA
Found at i:54730 original size:91 final size:91
Alignment explanation
Indices: 54575--54750 Score: 307
Period size: 91 Copynumber: 1.9 Consensus size: 91
54565 GCAACGAGAG
*
54575 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCAAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
54640 AAATGAAAATCGCAATGCGAAATGAA
66 AAATGAAAATCGCAATGCGAAATGAA
* * *
54666 AATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCAAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
54731 AAATGAAAATCGCATTGCGA
66 AAATGAAAATCGCAATGCGA
54751 TTCTCTCGTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (91 bp):
AATCGCAATGCAAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAATGCGAAATGAA
Found at i:54784 original size:53 final size:52
Alignment explanation
Indices: 54721--54836 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
54711 GAAATGAAAA
*
54721 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
54773 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
54826 TCGCATTGCGA
1 TCGCATTGCGA
54837 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:54799 original size:19 final size:19
Alignment explanation
Indices: 54759--54846 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
54749 GATTCTCTCG
54759 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
54779 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
54798 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
54812 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
54831 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
54847 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:54956 original size:14 final size:14
Alignment explanation
Indices: 54937--54973 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54927 CATCAATTAC
54937 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
54951 ACAAATCATCTTTT
1 ACAAATCAACTTTT
54965 ACAAATCAA
1 ACAAATCAA
54974 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:56940 original size:19 final size:19
Alignment explanation
Indices: 56898--57046 Score: 129
Period size: 19 Copynumber: 8.3 Consensus size: 19
56888 TAGTTTACTT
* *
56898 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
56918 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
56937 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
56956 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
56975 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
**
56989 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
57008 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
57022 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
57041 TCGCAA
1 TCGCAA
57047 TGCAATTTTG
Statistics
Matches: 103, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
14 17 0.17
15 1 0.01
16 7 0.07
17 6 0.06
18 1 0.01
19 59 0.57
20 12 0.12
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:56992 original size:14 final size:14
Alignment explanation
Indices: 56973--57029 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
56963 GCGAAATGAA
56973 AATCGCAACGACAG
1 AATCGCAACGACAG
*
56987 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
57006 AATCGCAACGAGAG
1 AATCGCAACGACAG
57020 AATCGCAACG
1 AATCGCAACG
57030 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.28, G:0.21, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:56996 original size:33 final size:33
Alignment explanation
Indices: 56916--57046 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
56906 CGAAACTTAA
* *
56916 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
56954 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
** *
56987 AATCGCAACGCGAAACCAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
57020 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
57047 TGCAATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.66
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:57043 original size:52 final size:51
Alignment explanation
Indices: 56915--57046 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 51
56905 ACGAAACTTA
* *
56915 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAACGAGAAACCAAAATCGCAACGAG
* ** * * *
56966 AAAT-GAAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAACGAGAAACCAAAATCGCAACGAG
57018 AGAATCGCAACGCGAAATGAAAATCGCAA
1 A-AATCGCAACGCGAAATGAAAATCGCAA
57047 TGCAATTTTG
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
50 9 0.14
51 4 0.06
52 38 0.59
53 4 0.06
54 9 0.14
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.08
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAGAAACCAAAATCGCAACGAG
Found at i:57073 original size:19 final size:18
Alignment explanation
Indices: 57051--57138 Score: 75
Period size: 19 Copynumber: 5.2 Consensus size: 18
57041 TCGCAATGCA
57051 ATTTTGGTTTCGCGTTGCG
1 ATTTT-GTTTCGCGTTGCG
57070 ATTTTG--T--CGTTGCG
1 ATTTTGTTTCGCGTTGCG
57084 ATTTTGGTTTCGCGTTGCG
1 ATTTT-GTTTCGCGTTGCG
*
57103 ATTCTG--T--CGTTGCG
1 ATTTTGTTTCGCGTTGCG
*
57117 ATTTTCATTTCGCGTTGCG
1 ATTTT-GTTTCGCGTTGCG
57136 ATT
1 ATT
57139 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
14 23 0.41
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 26 0.46
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.48
Consensus pattern (18 bp):
ATTTTGTTTCGCGTTGCG
Found at i:57082 original size:14 final size:14
Alignment explanation
Indices: 57063--57121 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
57053 TTTGGTTTCG
57063 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
57077 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
57094 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
57110 CGTTGCGATTTT
1 CGTTGCGATTTT
57122 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:57093 original size:33 final size:33
Alignment explanation
Indices: 57051--57170 Score: 177
Period size: 33 Copynumber: 3.6 Consensus size: 33
57041 TCGCAATGCA
*
57051 ATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
57084 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
** *
57117 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
* *
57150 ATTTTAAGTTTCGTGTTGCGA
1 ATTTT-GGTTTCGCGTTGCGA
57171 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 67 0.85
34 12 0.15
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
Found at i:57148 original size:14 final size:14
Alignment explanation
Indices: 57096--57152 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
57086 TTTGGTTTCG
*
57096 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
57110 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57129 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57143 CGTTGCGATT
1 CGTTGCGATT
57153 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57501 original size:92 final size:93
Alignment explanation
Indices: 57268--57582 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
57258 TCAGGGTATT
*
57268 AGTTTAGCAGAATTGGCAGCAACCAAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
57333 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
57361 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
57426 TACTATTTCACAGTGTT-AAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
57453 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
57518 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
57546 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
57583 AAGCAATCTA
Statistics
Matches: 219, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 92 0.42
93 127 0.58
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:59338 original size:21 final size:21
Alignment explanation
Indices: 59282--59346 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
59272 TCTTTTGGTT
59282 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
59303 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
59323 GAAATAAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
59344 GAA
1 GAA
59347 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:59407 original size:14 final size:14
Alignment explanation
Indices: 59388--59477 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
59378 TTTGGTTTCG
59388 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
59402 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
59419 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
*
59435 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
59454 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
59468 CGTTGCGATT
1 CGTTGCGATT
59478 TTCATTTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
16 9 0.15
17 9 0.15
19 17 0.27
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:59413 original size:33 final size:33
Alignment explanation
Indices: 59371--59484 Score: 201
Period size: 33 Copynumber: 3.5 Consensus size: 33
59361 CAAAATCGCA
**
59371 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
59404 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
59437 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
59470 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
59485 TTCTCGTTGC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:59490 original size:21 final size:21
Alignment explanation
Indices: 59465--59538 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
59455 GTTGCGATTC
59465 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
59486 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
59507 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
59528 TCTCGTTGCGA
1 TCTCGTTGCGA
59539 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:59660 original size:33 final size:33
Alignment explanation
Indices: 59618--59688 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
59608 AATACTAACT
59618 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
59651 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
59684 TGAAA
1 TGAAA
59689 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:60092 original size:20 final size:20
Alignment explanation
Indices: 60067--60218 Score: 198
Period size: 20 Copynumber: 7.6 Consensus size: 20
60057 CTTTAAAAAT
60067 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
60087 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
60107 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
60127 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
60147 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
60167 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
60187 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
60207 CGCGTTGCGATT
1 CGCGTTGCGATT
60219 ATGGAAAATC
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
20 115 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:60236 original size:21 final size:20
Alignment explanation
Indices: 60212--60259 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
60202 ATATTCGCGT
60212 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
60233 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
60253 TGCGATT
1 TGCGATT
60260 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:60665 original size:8 final size:8
Alignment explanation
Indices: 60654--60683 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
60644 TGAAAATAAA
60654 AAAAAAAT
1 AAAAAAAT
60662 AAAAAAAT
1 AAAAAAAT
60670 AAAAAAAT
1 AAAAAAAT
60678 AAAAAA
1 AAAAAA
60684 TTATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:73008 original size:272 final size:274
Alignment explanation
Indices: 72522--73067 Score: 1006
Period size: 272 Copynumber: 2.0 Consensus size: 274
72512 GAAAACCAGA
*
72522 ATGCTATGAGTTTACAGATCCTACTGGGATGAAAACAAGCTTTATGTTTGTTAGAGAAAGAGACA
1 ATGCTATGAGTTTACAGATCCTACAGGGATGAAAACAAGCTTTATGTTTGTTAGAGAAAGAGACA
72587 CGAATAATGTTTTTTCCTCAATATCTCCTTTGTAGTAGTCCCAAGGGATGACTGACATTAGCTGG
66 CGAATAATGTTTTTTCCTCAATATCTCCTTTGTAGTAGTCCCAAGGGATGACTGACATTAGCTGG
* *
72652 TACAAGCCACAAAAGATAAACAGAAAAGGTGAATTTGTCAAGATAGTGAATATCAAAATGCGCAA
131 TACAAGCCACAAAAGATAAACACAAAAGGTGAATTTGTCAAGATAGTGAATATCAAAATGCCCAA
*
72717 CATCATACAGGTTTTTTTTT-AAAAAGAAGTCA-TTTTTCCACTAAAATGGCTTGCAGAACCCAA
196 CATCATACAGGTTTTTTTTTAAAAAAGAAATCATTTTTTCCACTAAAATGGCTTGCAGAACCCAA
72780 CAAAACAGAACAAT
261 CAAAACAGAACAAT
72794 ATGCTATGAGTTTACAGATCCTACAGGGATGAAAACAAGCTTTATGTTTGTTAGAGAAAGAGACA
1 ATGCTATGAGTTTACAGATCCTACAGGGATGAAAACAAGCTTTATGTTTGTTAGAGAAAGAGACA
*
72859 CGAATAATGTTTTTTCCTCAATATCTCCTTTGTAGTAGTCCCAAGGGATGAGTGACATTAGCTGG
66 CGAATAATGTTTTTTCCTCAATATCTCCTTTGTAGTAGTCCCAAGGGATGACTGACATTAGCTGG
*
72924 TACAAGCCACAAAAGATAAACACAAAAGGTGAATTTGTCAAGATAGTGGATATCAAAATGCCCAA
131 TACAAGCCACAAAAGATAAACACAAAAGGTGAATTTGTCAAGATAGTGAATATCAAAATGCCCAA
72989 CATCATACAGGTTTTTTTTTAAAAAAAGAAATCATTTTTTCCACTAAAATGGCTTGCAGAACCCA
196 CATCATACAGGTTTTTTTTT-AAAAAAGAAATCATTTTTTCCACTAAAATGGCTTGCAGAACCCA
*
73054 ACAAAGCAGAACAA
260 ACAAAACAGAACAA
73068 GGGGGAATAT
Statistics
Matches: 264, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
272 210 0.80
274 11 0.04
275 43 0.16
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (274 bp):
ATGCTATGAGTTTACAGATCCTACAGGGATGAAAACAAGCTTTATGTTTGTTAGAGAAAGAGACA
CGAATAATGTTTTTTCCTCAATATCTCCTTTGTAGTAGTCCCAAGGGATGACTGACATTAGCTGG
TACAAGCCACAAAAGATAAACACAAAAGGTGAATTTGTCAAGATAGTGAATATCAAAATGCCCAA
CATCATACAGGTTTTTTTTTAAAAAAGAAATCATTTTTTCCACTAAAATGGCTTGCAGAACCCAA
CAAAACAGAACAAT
Found at i:74831 original size:31 final size:31
Alignment explanation
Indices: 74796--74857 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
74786 ATTAAAAAAG
74796 TAATTAAACATAATTA-ATTTTTTCAAGAAAT
1 TAATTAAACATAATTACA-TTTTTCAAGAAAT
*
74827 TAATTGAACATAATTACATTTTTCAAGAAAT
1 TAATTAAACATAATTACATTTTTCAAGAAAT
74858 GAGGAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (31 bp):
TAATTAAACATAATTACATTTTTCAAGAAAT
Found at i:83165 original size:23 final size:24
Alignment explanation
Indices: 83112--83167 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
83102 TATCCTGAAT
*
83112 GACTACATAGTTTTGTCCCGAAAG
1 GACTACATAGTTTTGTACCGAAAG
*
83136 AAC-ACATAGTTTTGTACCG-AAG
1 GACTACATAGTTTTGTACCGAAAG
83158 GACTACATAG
1 GACTACATAG
83168 AACCCACGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 21 0.75
24 2 0.07
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (24 bp):
GACTACATAGTTTTGTACCGAAAG
Found at i:93837 original size:23 final size:23
Alignment explanation
Indices: 93793--93837 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
93783 ATTATTATAT
*
93793 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* * *
93816 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTACAATTATACG
93838 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:100598 original size:15 final size:14
Alignment explanation
Indices: 100572--100602 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
100562 ATTTATCATT
100572 TTAAAAACACACAC
1 TTAAAAACACACAC
100586 TTAAAACACACACAC
1 TTAAAA-ACACACAC
100601 TT
1 TT
100603 TCTCCCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
TTAAAAACACACAC
Found at i:102898 original size:21 final size:21
Alignment explanation
Indices: 102816--102899 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
102806 CAAAACCCCA
*
102816 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
102835 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
102860 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
102881 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
102900 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:110316 original size:23 final size:23
Alignment explanation
Indices: 110272--110316 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
110262 ATTATTATAT
*
110272 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* * *
110295 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTACAATTATACG
110317 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:113758 original size:34 final size:34
Alignment explanation
Indices: 113715--113807 Score: 145
Period size: 34 Copynumber: 2.7 Consensus size: 34
113705 ATAATAAGAG
113715 AAAAAAAAAGAAAGAAAAAGAAAAAAAA-AAAAAA
1 AAAAAAAAAGAAA-AAAAAGAAAAAAAAGAAAAAA
*
113749 AAAAAAAAAGAAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAG-AAAAAAAAGAAAAAAAAGAAAAAA
113784 AAAAAAAAAG-AAAAAAAGAAAAAA
1 AAAAAAAAAGAAAAAAAAGAAAAAA
113808 CGAAAATGGA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
33 13 0.24
34 23 0.42
35 19 0.35
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAA
Found at i:113776 original size:43 final size:44
Alignment explanation
Indices: 113713--113807 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 44
113703 AAATAATAAG
*
113713 AGAAAAAAAAAGAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AGAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
*
113757 AGAAAAAAAAA-AAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAA
1 AGAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
113800 AGAAAAAA
1 AGAAAAAA
113808 CGAAAATGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 38 0.78
44 11 0.22
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (44 bp):
AGAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
Found at i:113823 original size:1 final size:1
Alignment explanation
Indices: 113715--113807 Score: 123
Period size: 1 Copynumber: 93.0 Consensus size: 1
113705 ATAATAAGAG
* * * * *
113715 AAAAAAAAAGAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
113780 AAAAAAAAAAAAAGAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
113808 CGAAAATGGA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:116920 original size:30 final size:30
Alignment explanation
Indices: 116849--116931 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
116839 CCCGAAGGAC
* *
116849 CTATCCAGAGGTCACAAAG-ACCCCGATAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
*
116878 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
* * *
116908 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
116932 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 18 0.39
30 28 0.61
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGACAA
Found at i:116960 original size:31 final size:31
Alignment explanation
Indices: 116906--117031 Score: 139
Period size: 31 Copynumber: 4.1 Consensus size: 31
116896 GAACCTCGAC
* * * *
116906 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* *
116937 AACTGTCTATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * *
116968 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCATAGAACATAGGTA
*
116999 AACTGTCCATA-GTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
117029 AAC
1 AAC
117032 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.05
30 14 0.18
31 56 0.72
32 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:116997 original size:62 final size:61
Alignment explanation
Indices: 116907--117028 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 61
116897 AACCTCGACA
* * *
116907 ACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCTATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATA-GTTCCGTAGAACATAGGTAT
* *
116969 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAACTGTCCATAGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTC-CCAAAGAACATAGGTAAACTGTCCATAGTTCCGTAGAACATAGGTA
117029 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 18 0.33
62 31 0.57
63 5 0.09
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (61 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATAGTTCCGTAGAACATAGGTAT
Done.