Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006736.1 Hibiscus syriacus cultivar Beakdansim tig00016904_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: 64517
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:732 original size:64 final size:65
Alignment explanation
Indices: 591--747 Score: 273
Period size: 65 Copynumber: 2.4 Consensus size: 65
581 CATTCCTTAT
* *
591 GCCCGCACGGTGAAT-AATTCACACGAAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAG
1 GCCCGCACGGTGAATAAATTCACACGAAGACATAAGGTATATGAATACCGAAGGCTACTTGCTAG
655 GCCCGCACGGTGAATAAATTCACACGAAGACATAAGGTATATGAATACCGAAGGCTACTTGCTAG
1 GCCCGCACGGTGAATAAATTCACACGAAGACATAAGGTATATGAATACCGAAGGCTACTTGCTAG
*
720 GCCCACAC-GTGAATAAATTCACACGAAG
1 GCCCGCACGGTGAATAAATTCACACGAAG
748 CGTCGCTTTT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
64 35 0.39
65 54 0.61
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (65 bp):
GCCCGCACGGTGAATAAATTCACACGAAGACATAAGGTATATGAATACCGAAGGCTACTTGCTAG
Found at i:1236 original size:10 final size:10
Alignment explanation
Indices: 1223--1252 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1213 TTGCGAAAAT
1223 TTAAATTTAA
1 TTAAATTTAA
1233 TTAAATTTAA
1 TTAAATTTAA
1243 TTAAATTTAA
1 TTAAATTTAA
1253 AAACTTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:1401 original size:8 final size:8
Alignment explanation
Indices: 1388--1423 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
1378 GAAGGAAAAG
1388 AAATAATA
1 AAATAATA
1396 AAATAATA
1 AAATAATA
1404 AAATAAATA
1 AAAT-AATA
1413 AAATAATA
1 AAATAATA
1421 AAA
1 AAA
1424 CCAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:1414 original size:17 final size:16
Alignment explanation
Indices: 1388--1423 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
1378 GAAGGAAAAG
1388 AAATAATAAAATAATA
1 AAATAATAAAATAATA
1404 AAATAAATAAAATAATA
1 AAAT-AATAAAATAATA
1421 AAA
1 AAA
1424 CCAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAATAAAATAATA
Found at i:1429 original size:17 final size:17
Alignment explanation
Indices: 1392--1435 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1382 GAAAAGAAAT
*
1392 AATAAAATAATAAAATA
1 AATAAAATAATAAAACA
*
1409 AATAAAATAATAAAACC
1 AATAAAATAATAAAACA
1426 AATAATAATA
1 AATAA-AATA
1436 TTAGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAAAATAATAAAACA
Found at i:2823 original size:5 final size:5
Alignment explanation
Indices: 2815--2854 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
2805 AAAAATAATG
2815 AAATT AAATT -AA-T AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AA
2855 TATATAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 28 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:2901 original size:28 final size:26
Alignment explanation
Indices: 2870--2932 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
2860 AAACTATATA
*
2870 TATATATTTCAAAAATA-TTTTTAGAAAC
1 TATATATTT-AAAAA-AGTTTTCA-AAAC
2898 TATATACTTTAAAAAAGTTTTCAAAAC
1 TATATA-TTTAAAAAAGTTTTCAAAAC
2925 TATATATT
1 TATATATT
2933 ACATAGTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 2 0.06
27 11 0.34
28 16 0.50
29 3 0.09
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (26 bp):
TATATATTTAAAAAAGTTTTCAAAAC
Found at i:3023 original size:36 final size:35
Alignment explanation
Indices: 2908--3198 Score: 146
Period size: 37 Copynumber: 8.1 Consensus size: 35
2898 TATATACTTT
* * **
2908 AAAAAA-GTTTTCAAAACTATATATTACATAGTTC
1 AAAAAATGTTTTTAAAACTATATATTATATTTTTC
* *
2942 -CAAAATGTTTTTAAAA-TAT-TA-TATAAGTTTTC
1 AAAAAATGTTTTTAAAACTATATATTAT-ATTTTTC
2974 AAAAAAAATGTTTTTAAAACTATATATTATATTTTTAC
1 --AAAAAATGTTTTTAAAACTATATATTATATTTTT-C
3012 AAAAAATGTTTTTAAAAACTATATACTATATATGTTTTC
1 AAAAAATGTTTTT-AAAACTATATA-T-TATAT-TTTTC
* * *
3051 --AAAATGTTTTAAAAACTATATAATTTTAAACGTTTTC
1 AAAAAATGTTTTTAAAACTATAT-A--TTATA-TTTTTC
*
3088 ---AAATGTTTTCAAAACTATATATTACGTA-TTTTC
1 AAAAAATGTTTTTAAAACTATATATTA--TATTTTTC
*
3121 --AAAATGTTTTCAAAAAAACTATATAATATATAAATGTTTTC
1 AAAAAATGTTTT---TAAAACTATAT-AT-TAT--AT-TTTTC
* * *
3162 --AACATGTTTTCAAAACTATATATTATA-TATTC
1 AAAAAATGTTTTTAAAACTATATATTATATTTTTC
3194 AAAAA
1 AAAAA
3199 CCATTTGCAA
Statistics
Matches: 208, Mismatches: 19, Indels: 60
0.72 0.07 0.21
Matches are distributed among these distances:
31 2 0.01
32 10 0.05
33 15 0.07
34 21 0.10
35 17 0.08
36 48 0.23
37 50 0.24
38 18 0.09
39 9 0.04
40 4 0.02
41 14 0.07
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (35 bp):
AAAAAATGTTTTTAAAACTATATATTATATTTTTC
Found at i:3030 original size:37 final size:36
Alignment explanation
Indices: 2908--3072 Score: 141
Period size: 36 Copynumber: 4.7 Consensus size: 36
2898 TATATACTTT
* * **
2908 AAAAAA-GTTTTCAAAACTATATATTACATAGTT-C
1 AAAAAATGTTTTTAAAACTATATATTATATTTTTAC
* * *
2942 -CAAAATGTTTTTAAAA-TAT-TA-TATAAGTTTTCAA
1 AAAAAATGTTTTTAAAACTATATATTAT-A-TTTTTAC
2976 AAAAAATGTTTTTAAAACTATATATTATATTTTTAC
1 AAAAAATGTTTTTAAAACTATATATTATATTTTTAC
3012 AAAAAATGTTTTTAAAAACTATATACTATATATGTTTT-C
1 AAAAAATGTTTTT-AAAACTATATA-T-TATAT-TTTTAC
*
3051 --AAAATGTTTTAAAAACTATATA
1 AAAAAATGTTTTTAAAACTATATA
3073 ATTTTAAACG
Statistics
Matches: 108, Mismatches: 11, Indels: 22
0.77 0.08 0.16
Matches are distributed among these distances:
31 2 0.02
32 3 0.03
33 9 0.08
34 9 0.08
35 15 0.14
36 32 0.30
37 24 0.22
38 4 0.04
39 6 0.06
40 4 0.04
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAAAATGTTTTTAAAACTATATATTATATTTTTAC
Found at i:3106 original size:109 final size:108
Alignment explanation
Indices: 2979--3183 Score: 281
Period size: 109 Copynumber: 1.9 Consensus size: 108
2969 TTTTCAAAAA
* * *
2979 AAATGTTTTTAAAACTATATATTA-TATTTTTACAAAAAATGTTTT-TAAAAACTATATACTATA
1 AAATGTTTTCAAAACTATATATTACTA-TTTT-C--AAAATGTTTTAAAAAAACTATATAATATA
3042 T-ATGTTTTCAAAATGTTTTAAAAACTATATAATTTTAAACGTTTTC
62 TAATGTTTTCAAAATGTTTTAAAAACTATATAATTTTAAACGTTTTC
3088 AAATGTTTTCAAAACTATATATTACGTATTTTCAAAATGTTTTCAAAAAAACTATATAATATATA
1 AAATGTTTTCAAAACTATATATTAC-TATTTTCAAAATGTTTT-AAAAAAACTATATAATATAT-
* *
3153 AATGTTTTCAACATGTTTTCAAAACTATATA
63 AATGTTTTCAAAATGTTTTAAAAACTATATA
3184 TTATATATTC
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
107 10 0.12
109 41 0.48
110 4 0.05
111 30 0.35
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (108 bp):
AAATGTTTTCAAAACTATATATTACTATTTTCAAAATGTTTTAAAAAAACTATATAATATATAAT
GTTTTCAAAATGTTTTAAAAACTATATAATTTTAAACGTTTTC
Found at i:3180 original size:75 final size:70
Alignment explanation
Indices: 3046--3186 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 70
3036 ACTATATATG
*
3046 TTTTCAAAATGTTTTAAAAACTATATAATTTTAAACGTTTTCAAATGTTTTCAAAACTATATATT
1 TTTTCAAAATGTTTTAAAAACTATATAATTATAAACGTTTTCAAATGTTTTCAAAACTATATATT
3111 ACGTA
66 ACGTA
*
3116 TTTTCAAAATGTTTTCAAAAAAACTATATAATATATAAATGTTTTCAACATGTTTTCAAAACTAT
1 TTTTCAAAATGTTTT---AAAAACTATATAAT-TATAAACGTTTTCAA-ATGTTTTCAAAACTAT
3181 ATATTA
61 ATATTA
3187 TATATTCAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
70 15 0.23
73 14 0.22
74 13 0.20
75 22 0.34
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (70 bp):
TTTTCAAAATGTTTTAAAAACTATATAATTATAAACGTTTTCAAATGTTTTCAAAACTATATATT
ACGTA
Found at i:3218 original size:73 final size:73
Alignment explanation
Indices: 3061--3209 Score: 194
Period size: 75 Copynumber: 2.0 Consensus size: 73
3051 AAAATGTTTT
* *
3061 AAAAACTATATAAT-TTTAAACGTTTTCAAATGTTTTCAAAACTATATATTACGTATTTTCAAAA
1 AAAAACTATATAATATATAAACGTTTTCAAATGTTTTCAAAACTATATATTAC-TATATTCAAAA
** *
3125 TGTTTTCAA
65 CATTTGCAA
*
3134 AAAAACTATATAATATATAAATGTTTTCAACATGTTTTCAAAACTATATATTA-TATATTCAAAA
1 AAAAACTATATAATATATAAACGTTTTCAA-ATGTTTTCAAAACTATATATTACTATATTC-AAA
3198 ACCATTTGCAA
64 A-CATTTGCAA
3209 A
1 A
3210 TTATATATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
73 20 0.30
74 17 0.26
75 29 0.44
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (73 bp):
AAAAACTATATAATATATAAACGTTTTCAAATGTTTTCAAAACTATATATTACTATATTCAAAAC
ATTTGCAA
Found at i:7496 original size:22 final size:23
Alignment explanation
Indices: 7468--7511 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
7458 AAAAATTCAG
*
7468 AATCGAAAAAC-CTGTTTACCAT
1 AATCGAAAAACTATGTTTACCAT
7490 AATCGAAAAACTATGTTTACCA
1 AATCGAAAAACTATGTTTACCA
7512 GAACCAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (23 bp):
AATCGAAAAACTATGTTTACCAT
Found at i:7882 original size:22 final size:22
Alignment explanation
Indices: 7857--7901 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
7847 CTTCCCGTTT
* *
7857 CGTTGTTTGGTACTTGTTCCAC
1 CGTTATTTGGTACCTGTTCCAC
7879 CGTTATTTGGTACCTGTTCCAC
1 CGTTATTTGGTACCTGTTCCAC
7901 C
1 C
7902 ACTGTTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (22 bp):
CGTTATTTGGTACCTGTTCCAC
Found at i:12472 original size:23 final size:23
Alignment explanation
Indices: 12446--12502 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
12436 ATAATTACAT
12446 AATCGAAAAACCATGTTTACCAG
1 AATCGAAAAACCATGTTTACCAG
***
12469 AATCGAAAAATTTTGTTTACCAG
1 AATCGAAAAACCATGTTTACCAG
* *
12492 AACCGGAAAAC
1 AATCGAAAAAC
12503 TCTATTTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (23 bp):
AATCGAAAAACCATGTTTACCAG
Found at i:16718 original size:19 final size:19
Alignment explanation
Indices: 16694--16738 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
16684 TTTGCTAGTA
16694 TGCCTCATGTTGCAGACCT
1 TGCCTCATGTTGCAGACCT
16713 TGCCTCATGTTGCAGACCT
1 TGCCTCATGTTGCAGACCT
16732 TGCCTCA
1 TGCCTCA
16739 AAGGCTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.33, G:0.20, T:0.31
Consensus pattern (19 bp):
TGCCTCATGTTGCAGACCT
Found at i:18441 original size:2 final size:2
Alignment explanation
Indices: 18434--18542 Score: 218
Period size: 2 Copynumber: 54.5 Consensus size: 2
18424 AAAAGAGTGT
18434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18518 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 T
18543 GCTTTGAATA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19054 original size:2 final size:2
Alignment explanation
Indices: 19042--19074 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
19032 CTTTAATCAA
19042 AT AT GAT 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
19075 TTCACATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19303 original size:14 final size:13
Alignment explanation
Indices: 19283--19323 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
19273 TCTTATATTT
19283 ATTTAAACTTTAA
1 ATTTAAACTTTAA
*
19296 ACTTTAAATTTTAA
1 A-TTTAAACTTTAA
19310 ATTT-AA-TTTAA
1 ATTTAAACTTTAA
19321 ATT
1 ATT
19324 AACTTTACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 8 0.31
12 2 0.08
13 4 0.15
14 12 0.46
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTAAACTTTAA
Found at i:21049 original size:2 final size:2
Alignment explanation
Indices: 21038--21066 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21028 CAGGCGATTA
21038 AT AT -T 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
21067 GATGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:22148 original size:22 final size:22
Alignment explanation
Indices: 22117--22187 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
22107 ATTCACAAAT
*
22117 GTGTTCATTTAGCATTCGTTTA
1 GTGTTCATTTAGCATTCATTTA
* *
22139 GTG-TCTATTTAGCGTTTATTTA
1 GTGTTC-ATTTAGCATTCATTTA
*
22161 GTGTTCGTTTAGCATTCATTTA
1 GTGTTCATTTAGCATTCATTTA
22183 GTGTT
1 GTGTT
22188 TGTTTATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (22 bp):
GTGTTCATTTAGCATTCATTTA
Found at i:22168 original size:33 final size:32
Alignment explanation
Indices: 22131--22204 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
22121 TCATTTAGCA
22131 TTCGTTTAG-TGTCTATTTAGCGTTTATTTAGTG
1 TTCGTTTAGAT-TC-ATTTAGCGTTTATTTAGTG
* * *
22164 TTCGTTTAGCATTCATTTAGTGTTTGTTTATTG
1 TTCGTTTAG-ATTCATTTAGCGTTTATTTAGTG
22197 TTCGTTTA
1 TTCGTTTA
22205 TCATTCGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 33 0.92
34 2 0.06
35 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.19, T:0.57
Consensus pattern (32 bp):
TTCGTTTAGATTCATTTAGCGTTTATTTAGTG
Found at i:22171 original size:11 final size:11
Alignment explanation
Indices: 22117--22187 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
22107 ATTCACAAAT
22117 GTGTTCATTTA
1 GTGTTCATTTA
** *
22128 GCATTCGTTTA
1 GTGTTCATTTA
22139 GTG-TCTATTTA
1 GTGTTC-ATTTA
* *
22150 GCGTTTATTTA
1 GTGTTCATTTA
*
22161 GTGTTCGTTTA
1 GTGTTCATTTA
**
22172 GCATTCATTTA
1 GTGTTCATTTA
22183 GTGTT
1 GTGTT
22188 TGTTTATTGT
Statistics
Matches: 42, Mismatches: 16, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
10 2 0.05
11 39 0.93
12 1 0.02
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (11 bp):
GTGTTCATTTA
Found at i:22193 original size:11 final size:11
Alignment explanation
Indices: 22117--22204 Score: 52
Period size: 11 Copynumber: 8.0 Consensus size: 11
22107 ATTCACAAAT
*
22117 GTGTTCATTTA
1 GTGTTCGTTTA
**
22128 GCATTCGTTTA
1 GTGTTCGTTTA
*
22139 GTG-TCTATTTA
1 GTGTTC-GTTTA
* **
22150 GCGTTTATTTA
1 GTGTTCGTTTA
22161 GTGTTCGTTTA
1 GTGTTCGTTTA
** *
22172 GCATTCATTTA
1 GTGTTCGTTTA
*
22183 GTGTTTGTTTA
1 GTGTTCGTTTA
*
22194 TTGTTCGTTTA
1 GTGTTCGTTTA
22205 TCATTCGTTT
Statistics
Matches: 55, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
10 2 0.04
11 52 0.95
12 1 0.02
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (11 bp):
GTGTTCGTTTA
Found at i:22210 original size:33 final size:33
Alignment explanation
Indices: 22145--22215 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
22135 TTTAGTGTCT
22145 ATTTAGCGTTTATTTAGTGTTCGTTTAGCATTC
1 ATTTAGCGTTTATTTAGTGTTCGTTTAGCATTC
* * * *
22178 ATTTAGTGTTTGTTTATTGTTCGTTTATCATTC
1 ATTTAGCGTTTATTTAGTGTTCGTTTAGCATTC
*
22211 GTTTA
1 ATTTA
22216 TATATTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.56
Consensus pattern (33 bp):
ATTTAGCGTTTATTTAGTGTTCGTTTAGCATTC
Found at i:23751 original size:21 final size:20
Alignment explanation
Indices: 23704--23751 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23694 TTTTGTAAAG
23704 CGCTACCGAAAATATTATTT
1 CGCTACCGAAAATATTATTT
*** *
23724 TTTTACCGAAAATGTTAATTT
1 CGCTACCGAAAATATT-ATTT
23745 CGCTACC
1 CGCTACC
23752 TAATTTTTGG
Statistics
Matches: 20, Mismatches: 7, Indels: 1
0.71 0.25 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
CGCTACCGAAAATATTATTT
Found at i:26622 original size:82 final size:82
Alignment explanation
Indices: 26485--26727 Score: 333
Period size: 82 Copynumber: 3.0 Consensus size: 82
26475 TAGAATAACC
* * * *
26485 TCATTTGCTTTTCATTGACATTTCACATCAACTCAAATAAAATGAAAAATTTTAGAGAGTCAGAT
1 TCATTTACTTTTCATTGACATTTCACATCAACTCAAATAAACTTAAAAATTTTAGAGAGTCAGAG
* *
26550 AATCTATACTATTCACG
66 AATCTACACTATTCACA
* * * *
26567 TCATTTATTTTTCATTGATATTTCACATCAACTCAGATAAACTTAAAAATTTTAGAGAGTCCGAG
1 TCATTTACTTTTCATTGACATTTCACATCAACTCAAATAAACTTAAAAATTTTAGAGAGTCAGAG
*
26632 AATCTACACTATTTACA
66 AATCTACACTATTCACA
* * * * *
26649 TCTTTTGCTTTTCATTGACATTTCACATCAACACATATAAACTTAAAAAATTTAGAGAGTCAGAG
1 TCATTTACTTTTCATTGACATTTCACATCAACTCAAATAAACTTAAAAATTTTAGAGAGTCAGAG
*
26714 AATCTACATTATTC
66 AATCTACACTATTC
26728 TACAAAATTA
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 140 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (82 bp):
TCATTTACTTTTCATTGACATTTCACATCAACTCAAATAAACTTAAAAATTTTAGAGAGTCAGAG
AATCTACACTATTCACA
Found at i:28603 original size:10 final size:10
Alignment explanation
Indices: 28570--28604 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
28560 AATTTTTTCA
28570 AAATTAAAAT
1 AAATTAAAAT
*
28580 AAAATAAAAT
1 AAATTAAAAT
*
28590 AAATTAAATT
1 AAATTAAAAT
28600 AAATT
1 AAATT
28605 TACTGTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:40552 original size:20 final size:21
Alignment explanation
Indices: 40523--40563 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40513 TTTGGGAAAA
*
40523 ATCGG-TTTTTTTTTAACCGG
1 ATCGGATTTTTTTTAAACCGG
40543 ATCGGATTTTTTTTAAACCGG
1 ATCGGATTTTTTTTAAACCGG
40564 TTTGGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (21 bp):
ATCGGATTTTTTTTAAACCGG
Found at i:42972 original size:21 final size:21
Alignment explanation
Indices: 42948--42987 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42938 TTTATTTTAT
42948 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
42969 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
42988 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:43262 original size:21 final size:21
Alignment explanation
Indices: 43210--43264 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
43200 TGGAGCGTGG
*
43210 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
43231 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
43252 GGGAATCGGTTCC
1 GGGAATCGGTTCC
43265 TTAAGTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:43484 original size:17 final size:17
Alignment explanation
Indices: 43434--43484 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
43424 CTGGAATATT
*
43434 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
* **
43449 ATAACCGGTTTTTAAAA
1 AAAACCGGTTTTTTTAA
43466 AAAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
43483 AA
1 AA
43485 CCGAAACCGG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
17 16 0.59
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:43486 original size:15 final size:15
Alignment explanation
Indices: 43432--43487 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
43422 ATCTGGAATA
*
43432 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
43447 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
**
43462 AAAAAAAACCGGTTTTT
1 --TTAAAACCGGTTTTT
43479 TTAAAACCG
1 TTAAAACCG
43488 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:43604 original size:15 final size:17
Alignment explanation
Indices: 43578--43609 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43568 TTCTATGAGA
43578 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
43594 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
43610 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:43784 original size:25 final size:27
Alignment explanation
Indices: 43738--43794 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
43728 GTAATTGGGT
**
43738 AAAAACTAAAATATTATTAAATT-TTA
1 AAAAACTAAAATATTACCAAATTATTA
*
43764 AAAAACTAAGATA-TACCAAATTATTA
1 AAAAACTAAAATATTACCAAATTATTA
*
43790 TAAAA
1 AAAAA
43795 TTTAATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAACTAAAATATTACCAAATTATTA
Found at i:44777 original size:11 final size:11
Alignment explanation
Indices: 44761--44785 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44751 TATATTATAG
44761 TTTTGAAAACA
1 TTTTGAAAACA
44772 TTTTGAAAACA
1 TTTTGAAAACA
44783 TTT
1 TTT
44786 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:44849 original size:71 final size:73
Alignment explanation
Indices: 44731--44872 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 73
44721 TTTTTTAAAA
* * *
44731 AAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATA
1 AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
44796 TAGTTTTT
66 TAGTTTTT
* * * *
44804 AAAACGTTTTTG-AAA-ACTTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATA
1 AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
44867 TAGTTT
66 TAGTTT
44873 AAGAAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 48 0.77
72 3 0.05
73 11 0.18
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (73 bp):
AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
TAGTTTTT
Found at i:44903 original size:71 final size:70
Alignment explanation
Indices: 44729--44902 Score: 172
Period size: 71 Copynumber: 2.4 Consensus size: 70
44719 AGTTTTTTAA
* * * *
44729 AAAAAAC-ATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATT
1 AAAAAACGA-TTTTG-AAA-ACTTATA-TATATTTTTGAAAACATGTTGAAAACATTCATATATT
44793 ATATAGTTT
62 ATATAGTTT
** * *
44802 TTAAAACGTTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATA
1 AAAAAACGATTTTGAAAACTTATAT-ATATTTTTGAAAACATGTTGAAAACATTCATATATTATA
44867 TAGTTT
65 TAGTTT
*
44873 AAGAAAAAAAC-ATTTTGAAAATTTATATAT
1 ----AAAAAACGATTTTGAAAACTTATATAT
44903 TATATGTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
70 1 0.01
71 47 0.57
72 3 0.04
73 12 0.14
74 15 0.18
75 5 0.06
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (70 bp):
AAAAAACGATTTTGAAAACTTATATATATTTTTGAAAACATGTTGAAAACATTCATATATTATAT
AGTTT
Found at i:44943 original size:3 final size:3
Alignment explanation
Indices: 44935--44966 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
44925 TGTATATATA
44935 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
44967 TTCATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:44967 original size:22 final size:22
Alignment explanation
Indices: 44919--44963 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
44909 TTTTTGAAAA
44919 TATTTATGTATATATATATTAT
1 TATTTATGTATATATATATTAT
44941 TATTTAT-TAT-TAT-TATTAT
1 TATTTATGTATATATATATTAT
44960 TATT
1 TATT
44964 ATTTTCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 3 0.13
22 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTATGTATATATATATTAT
Found at i:46214 original size:11 final size:11
Alignment explanation
Indices: 46198--46231 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
46188 ATATTTTTCT
46198 TATTTATTTAA
1 TATTTATTTAA
46209 TATTTATTTAA
1 TATTTATTTAA
46220 T-TTTAATTTAA
1 TATTT-ATTTAA
46231 T
1 T
46232 TTCTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:46272 original size:3 final size:3
Alignment explanation
Indices: 46264--46304 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
46254 TCATTTACTT
46264 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
46305 TTGATTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48053 original size:18 final size:19
Alignment explanation
Indices: 48032--48076 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
48022 ATTTAGACAT
48032 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTATTATTTTC
48050 TTTGCATTTTATTATTTTC
1 TTTGCATTTTATTATTTTC
*
48069 TCTGCATT
1 TTTGCATT
48077 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTATTATTTTC
Found at i:51656 original size:85 final size:83
Alignment explanation
Indices: 51416--52015 Score: 624
Period size: 85 Copynumber: 7.2 Consensus size: 83
51406 GCTCAAGGCC
* * *
51416 AGAAGGGCTATCTGCCCACCAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACAAAGACCCTT-GAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
* * *
51480 TGCAGAATAGCTTAAGTCG
65 TGCAGTATAACTTAAGTCA
* *
51499 AGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATT
51561 TGCAGTATAACTTAAGTCA
65 TGCAGTATAACTTAAGTCA
* * * * * *
51580 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATATCAT
1 AGAAGGGCTATCTGCCAAC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * * * * *
51645 CTACAGCATAACTCAAGGCT
64 TTGCAGTATAACTTAAGTCA
* * * * *
51665 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTGCCAACAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* * *
51730 GCAGAATAGCTTAAGTCG
66 GCAGTATAACTTAAGTCA
* *
51748 AGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATT
51810 TGCAGTATAACTTAAGTCA
65 TGCAGTATAACTTAAGTCA
* * * * * *
51829 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCAT
1 AGAAGGGCTATCTGCCAAC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * * *
51894 TTACAGCATAACTCAAGGCTA
64 TTGCAGTATAACTTAAGTC-A
* ** * * *
51915 A-AAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCAT
1 AGAAGGGCTATCTGCCAAC-AAAGACCCTT-GAGTTCGACTACGCTCAGCTTCAAGGCACATCAT
*
51978 TTGCAGTATAGCTTAAGTCA
64 TTGCAGTATAACTTAAGTCA
51998 AGAAGGGCTATCTGCCAA
1 AGAAGGGCTATCTGCCAA
52016 AGACTCCCGA
Statistics
Matches: 424, Mismatches: 77, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
80 54 0.13
81 87 0.21
82 4 0.01
83 51 0.12
84 73 0.17
85 153 0.36
86 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
AGAAGGGCTATCTGCCAACAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
GCAGTATAACTTAAGTCA
Found at i:51845 original size:249 final size:249
Alignment explanation
Indices: 51407--52060 Score: 1105
Period size: 249 Copynumber: 2.6 Consensus size: 249
51397 TGCAGCTTAG
* * *
51407 CTCAAGGCCAGAAGGGCTATCTGCCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
51471 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
51536 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
130 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
51601 AAGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATATCATCTACAGCATAA
195 AAGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATATCATCTACAGCATAA
*
51656 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
51721 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
51786 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
131 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
* * *
51851 AGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCATTTACAGCATAA
196 AGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATATCATCTACAGCATAA
* * *
51905 CTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
51970 CACATCATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATT
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-CCTCGAGTTCGACT
** * * *
52034 ACACTCAACTTCGAAGTCATATCATTT
129 ACGTTCAGCTTCGAAGGCACATCATTT
52061 ATCATGGCAA
Statistics
Matches: 383, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
248 4 0.01
249 263 0.69
250 114 0.30
251 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (249 bp):
CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
AGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATATCATCTACAGCATAA
Found at i:52015 original size:169 final size:164
Alignment explanation
Indices: 51436--52014 Score: 612
Period size: 169 Copynumber: 3.5 Consensus size: 164
51426 TCTGCCCACC
* * *
51436 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAG
* *
51501 AAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGC
66 AAGGGCTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGC
* ** *
51564 AGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
130 AGAATAACTTAAGTCAA-AAGGGTTATCTG-TGACCA
* * * * * * * * * * * *
51601 AAGACCCTT-AAGTTCGATTACACTCAACTTCAAGGGCATATCATCTACAGCATAACTCAAGGCT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGTATAACTTAAGTCA
* * * *
51665 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
64 AGAAGGGCTATCTGCCA-CAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* * *
51730 GCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CCA
128 GCAGAATAACTTAAGTC-AAAAGGGTTATCTGTGACCA
* * *
51765 AAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAACTTAAGTCAA
* * * * * *
51830 GAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCATT
65 GAAGGGCTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCATT
* * * *
51895 TACAGCATAACTCAAGGCTAAAAGGGTTATCTGTGACCAA
127 TGCAGAATAACTTAAGTC-AAAAGGGTTATCTGTGACC-A
* *
51935 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAG
52000 AAGGGCTATCTGCCA
66 AAGGGCTATCTGCCA
52015 AAGACTCCCG
Statistics
Matches: 337, Mismatches: 62, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
163 3 0.01
164 59 0.18
165 55 0.16
166 72 0.21
167 1 0.00
168 41 0.12
169 80 0.24
170 26 0.08
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAG
AAGGGCTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCA
GAATAACTTAAGTCAAAAGGGTTATCTGTGACCA
Found at i:52783 original size:11 final size:11
Alignment explanation
Indices: 52767--52791 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52757 TATATTATAG
52767 TTTTGAAAACA
1 TTTTGAAAACA
52778 TTTTGAAAACA
1 TTTTGAAAACA
52789 TTT
1 TTT
52792 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:52855 original size:71 final size:73
Alignment explanation
Indices: 52737--52872 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 73
52727 TTTTTTAAAA
* * *
52737 AAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATA
1 AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
52802 TAGTTTTT
66 TAGTTTTT
* * * *
52810 AAAACGTTTTTG-AAA-ACTTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATA
1 AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
52873 GTTTAAGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 42 0.75
72 3 0.05
73 11 0.20
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (73 bp):
AAAACATTTTTGAAAACACATATATAATAGTTTTGAAAACATGTTGAAAACATTCATATATTATA
TAGTTTTT
Found at i:52887 original size:73 final size:71
Alignment explanation
Indices: 52734--52920 Score: 173
Period size: 71 Copynumber: 2.5 Consensus size: 71
52724 TAGTTTTTTA
* * * * *
52734 AAAAAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATT
1 AAAAAAAC-TTTTTG-AAA-ACTTATATAATATTTTTGAAAACATGTTGAAAACATTCATATATT
52799 ATATAGTTT
63 ATATAGTTT
** *
52808 -TTAAAACGTTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATA-T-T
1 AAAAAAAC-TTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTCATATATTAT
52870 ATAGTTT
65 ATAGTTT
* * *
52877 AAGAAAAAAACATTTTGAAAATTTATATATTATGTTTTTGAAAA
1 ---AAAAAAACTTTTTGAAAACTTATATA--ATATTTTTGAAAA
52921 TATTTATGTA
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
69 8 0.09
70 1 0.01
71 37 0.40
72 19 0.20
73 16 0.17
74 12 0.13
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (71 bp):
AAAAAAACTTTTTGAAAACTTATATAATATTTTTGAAAACATGTTGAAAACATTCATATATTATA
TAGTTT
Found at i:52945 original size:19 final size:16
Alignment explanation
Indices: 52921--52968 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
52911 TTTTTGAAAA
52921 TATTTATGTATATATATAT
1 TATTTAT-TAT-TAT-TAT
52940 TATTTATTATTATTAT
1 TATTTATTATTATTAT
52956 TA-TTATTATTATT
1 TATTTATTATTATT
52969 CATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.38
16 5 0.17
17 3 0.10
18 3 0.10
19 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:52949 original size:3 final size:3
Alignment explanation
Indices: 52937--52968 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
52927 TGTATATATA
52937 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
52969 CATTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:54209 original size:11 final size:11
Alignment explanation
Indices: 54193--54226 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
54183 ATATTTTTCT
54193 TATTTATTTAA
1 TATTTATTTAA
54204 TATTTATTTAA
1 TATTTATTTAA
54215 T-TTTAATTTAA
1 TATTT-ATTTAA
54226 T
1 T
54227 TTCTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:54267 original size:3 final size:3
Alignment explanation
Indices: 54259--54296 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54249 TCATTTACTT
54259 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54297 TTGATTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58086 original size:16 final size:14
Alignment explanation
Indices: 58060--58102 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
58050 AGTTCGTTTG
*
58060 ATATTTCGTTATAA
1 ATATTTTGTTATAA
58074 AGTAATTTTGTTAT-A
1 A-T-ATTTTGTTATAA
58089 ATATTTTGTTATAA
1 ATATTTTGTTATAA
58103 TTATATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 3 0.12
16 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (14 bp):
ATATTTTGTTATAA
Found at i:58831 original size:24 final size:24
Alignment explanation
Indices: 58804--58858 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
58794 GGTATCGTCA
58804 CATCAACTTCAATGGGGAGACATT
1 CATCAACTTCAATGGGGAGACATT
58828 CATCAACTTCAATGGGGAGACATT
1 CATCAACTTCAATGGGGAGACATT
58852 CATCAAC
1 CATCAAC
58859 AACTCCTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (24 bp):
CATCAACTTCAATGGGGAGACATT
Found at i:62913 original size:26 final size:25
Alignment explanation
Indices: 62884--62932 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
62874 TAGCTATGTG
62884 AATATATGAAATGACATAGAATATGC
1 AATATATGAAATGACAT-GAATATGC
* * *
62910 AATATGTGATATGATATGAATAT
1 AATATATGAAATGACATGAATAT
62933 ATGGTTTACG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (25 bp):
AATATATGAAATGACATGAATATGC
Done.