Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002461.1 Hibiscus syriacus cultivar Beakdansim tig00005037_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: 244757
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:166525 original size:33 final size:33
Alignment explanation
Indices: 166485--166565 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
166475 CGCAACGAGA
166485 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
166518 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
166551 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
166566 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:166583 original size:19 final size:19
Alignment explanation
Indices: 166561--166658 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
166551 GAAACCAAAA
*
166561 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
166580 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
166594 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
166613 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
166627 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
166646 TCGCGTTGCGATT
1 TCGCGTTGCGATT
166659 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:166602 original size:14 final size:14
Alignment explanation
Indices: 166583--166668 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
166573 TTTCATTTCG
166583 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
166597 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
166616 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
166630 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
166649 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
166663 CGTTGC
1 CGTTGC
166669 AATTTTCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 26 0.45
15 1 0.02
16 5 0.09
17 5 0.09
18 1 0.02
19 20 0.34
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:166608 original size:33 final size:33
Alignment explanation
Indices: 166566--166680 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
166556 CAAAATCGCA
166566 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
166599 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
166632 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
166665 TTGCAATTTTCATTTC
1 TTGCGATTTTCATTTC
166681 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:167607 original size:14 final size:14
Alignment explanation
Indices: 167588--167623 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
167578 ATTGTTTAAT
167588 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
167602 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
167616 TGATTTGT
1 TGATTTGT
167624 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:167790 original size:33 final size:33
Alignment explanation
Indices: 167748--167865 Score: 164
Period size: 33 Copynumber: 3.4 Consensus size: 33
167738 GCGAAATGAA
167748 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
167781 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAG
167820 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
167854 AATCGCAATGCG
1 AATCGCAATGCG
167866 TTTATAATTT
Statistics
Matches: 76, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
33 28 0.37
34 13 0.17
35 2 0.03
36 1 0.01
37 1 0.01
38 2 0.03
39 13 0.17
40 16 0.21
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:167817 original size:20 final size:19
Alignment explanation
Indices: 167730--167847 Score: 174
Period size: 19 Copynumber: 6.4 Consensus size: 19
167720 AAAAATGACT
167730 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
167749 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
167768 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
167782 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
167801 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
167821 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
167841 ATCGCAA
1 ATCGCAA
167848 CGAGAGAATC
Statistics
Matches: 91, Mismatches: 2, Indels: 11
0.88 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 39 0.43
20 36 0.40
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:167879 original size:73 final size:72
Alignment explanation
Indices: 167730--167865 Score: 256
Period size: 73 Copynumber: 1.9 Consensus size: 72
167720 AAAAATGACT
167730 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
167794 AATGAAA
66 AATGAAA
167801 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCG
167866 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 10 0.16
72 19 0.30
73 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAAA
Found at i:167909 original size:33 final size:33
Alignment explanation
Indices: 167872--168024 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
167862 TGCGTTTATA
167872 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
167905 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
167945 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
167976 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
168009 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
168025 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:167918 original size:19 final size:19
Alignment explanation
Indices: 167894--168110 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
167884 GATTCTCTCG
167894 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
167913 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
167932 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
167946 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
167965 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
167984 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
167998 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
168017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
168036 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
168050 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
168070 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
168084 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
168103 TTGCGATT
1 TTGCGATT
168111 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:167929 original size:52 final size:52
Alignment explanation
Indices: 167872--168082 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
167862 TGCGTTTATA
167872 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
167924 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
167976 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
168028 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
168081 AT
1 AT
168083 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:168132 original size:33 final size:33
Alignment explanation
Indices: 167913--168124 Score: 234
Period size: 33 Copynumber: 6.2 Consensus size: 33
167903 TCATTTCGCA
167913 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
167946 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
167982 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
168017 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
168050 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
168084 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
168117 TTGCGATT
1 TTGCGATT
168125 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 73 0.49
34 29 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:170639 original size:24 final size:24
Alignment explanation
Indices: 170605--170651 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
170595 CTGAAACATC
170605 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
170629 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
170652 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:171362 original size:20 final size:20
Alignment explanation
Indices: 171334--171583 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
171324 AAATTTCAGT
* *
171334 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
171354 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
171374 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
171394 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
171414 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
171434 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
171454 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
171474 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* ** * *
171494 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCTC
* *
171514 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
171534 GTTGAGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
171554 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
171574 GTTGCGATTT
1 GTTGCGATTT
171584 TAATATTCGC
Statistics
Matches: 200, Mismatches: 29, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:171592 original size:20 final size:20
Alignment explanation
Indices: 171570--171667 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
171560 ATTTATGTGT
*
171570 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
171590 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
171611 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
171632 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
171653 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
171668 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:171663 original size:42 final size:43
Alignment explanation
Indices: 171570--171668 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
171560 ATTTATGTGT
* *
171570 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
171611 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
171653 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
171669 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:171879 original size:24 final size:23
Alignment explanation
Indices: 171834--171956 Score: 122
Period size: 24 Copynumber: 5.2 Consensus size: 23
171824 TTTACGATCA
* *
171834 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCGTTCATTGTGTTCG
*
171857 TTTAAGTTCGTTCACTTGTGTTCG
1 TTTATGTTCGTTCA-TTGTGTTCG
* * *
171881 TTTACGTTCATTTATTGTGTTCG
1 TTTATGTTCGTTCATTGTGTTCG
* *
171904 TTTATGTTCGTTTA-TGTTCGTTCA
1 TTTATGTTCGTTCATTG-T-GTTCG
*
171928 TTTGTGTTCGTTCATTTGTGTTCG
1 TTTATGTTCGTTCA-TTGTGTTCG
171952 TTTAT
1 TTTAT
171957 CATTTAAATG
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.02
23 33 0.40
24 44 0.54
25 1 0.01
26 2 0.02
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
TTTATGTTCGTTCATTGTGTTCG
Found at i:171889 original size:10 final size:10
Alignment explanation
Indices: 171875--171925 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
171865 CGTTCACTTG
171875 TGTTCGTTTA
1 TGTTCGTTTA
* *
171885 CGTTCATTTA
1 TGTTCGTTTA
171895 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
171908 TGTTCGTTTA
1 TGTTCGTTTA
171918 TGTTCGTT
1 TGTTCGTT
171926 CATTTGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 26 0.76
13 8 0.24
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:171916 original size:33 final size:34
Alignment explanation
Indices: 171875--171939 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
171865 CGTTCACTTG
*
171875 TGTTCGTTTACGTTCATTTA-TTGTGTTCGTTTA
1 TGTTCGTTTACGTTCATTCATTTGTGTTCGTTTA
* *
171908 TGTTCGTTTATGTTCGTTCATTTGTGTTCGTT
1 TGTTCGTTTACGTTCATTCATTTGTGTTCGTT
171940 CATTTGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.58
Consensus pattern (34 bp):
TGTTCGTTTACGTTCATTCATTTGTGTTCGTTTA
Found at i:171935 original size:14 final size:14
Alignment explanation
Indices: 171918--171953 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
171908 TGTTCGTTTA
171918 TGTTCGTTCATTTG
1 TGTTCGTTCATTTG
171932 TGTTCGTTCATTTG
1 TGTTCGTTCATTTG
171946 TGTTCGTT
1 TGTTCGTT
171954 TATCATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.06, C:0.14, G:0.22, T:0.58
Consensus pattern (14 bp):
TGTTCGTTCATTTG
Found at i:172539 original size:28 final size:28
Alignment explanation
Indices: 172507--172565 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
172497 TTACGAGGAT
*
172507 AATAATATATTATTAATA-AAAAT-ATTTA
1 AATAA-ATATT-TAAATATAAAATAATTTA
172535 AATAAATATTTAAATATAAAATAATTTA
1 AATAAATATTTAAATATAAAATAATTTA
172563 AAT
1 AAT
172566 TTTAAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 10 0.36
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATAAATATTTAAATATAAAATAATTTA
Found at i:172541 original size:12 final size:12
Alignment explanation
Indices: 172526--172550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
172516 TTATTAATAA
172526 AAATATTTAAAT
1 AAATATTTAAAT
172538 AAATATTTAAAT
1 AAATATTTAAAT
172550 A
1 A
172551 TAAAATAATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATTTAAAT
Found at i:174445 original size:159 final size:158
Alignment explanation
Indices: 174134--174559 Score: 609
Period size: 159 Copynumber: 2.7 Consensus size: 158
174124 GAAAAACTCG
* * **
174134 AGAATACATGTTTACTTTCAATTCATCTTTTTGATAACAAATTTTTATTTTTCAATTTAGTTATT
1 AGAATACATGTGTAC-TTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTT
* * ** *
174199 CAATTTTTCATAATCTCCTTATTTATTCAATTCGTCATTTA-TTTAAGACTGTTTTTTTTACCAA
65 CAATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTTATTTTTTTTACCAA
174263 ATTTGAGTCACATGATCCTAAACCATAGT
130 ATTTGAGTCACATGATCCTAAACCATAGT
*
174292 AGAATACATGTGTAATATCAATTCCT-TTTCTTGATAACAAATTTTTTATTTTTCAATTTAGTCC
1 AGAATACATGTGTACT-TCAATTCCTCTTT-TTGATAACAAA-TTTTTATTTTTCAATTTAGTCC
* *
174356 TTCAATTTTT-ATAGTCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTTATTTTTTTTATC
63 TTCAATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTTATTTTTTTTACC
**
174420 AAATTTGAGTCACATTCTCCTAAACCATAGT
128 AAATTTGAGTCACATGATCCTAAACCATAGT
174451 AGAATACATGTGTACCTTCAATTCCTCTTTTTGAT----AA-TTTT-TTTTTCAATTTAGTCCTT
1 AGAATACATGTGTA-CTTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTT
*
174510 CAATTTTTCATAATCTCCTTATTCCTTCAATTTGTCATTTATTTTAAGTT
65 CAATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTT
174560 CGATTTTTAC
Statistics
Matches: 244, Mismatches: 17, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
152 26 0.11
153 43 0.18
155 2 0.01
157 4 0.02
158 61 0.25
159 104 0.43
160 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (158 bp):
AGAATACATGTGTACTTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTC
AATTTTTCATAATCTCCTTATTTCTTCAATTTGTCATTTATTTTAAGTTTATTTTTTTTACCAAA
TTTGAGTCACATGATCCTAAACCATAGT
Found at i:183402 original size:15 final size:16
Alignment explanation
Indices: 183384--183414 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
183374 TGAGTTTATA
183384 AAAATCGAG-TAGAGT
1 AAAATCGAGTTAGAGT
183399 AAAATCGAGTTAGAGT
1 AAAATCGAGTTAGAGT
183415 TGTTAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
AAAATCGAGTTAGAGT
Found at i:185842 original size:18 final size:21
Alignment explanation
Indices: 185803--185852 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 21
185793 TGTTCGCTTC
185803 TTCTTCTTCCTCTCATCTCAT
1 TTCTTCTTCCTCTCATCTCAT
185824 TTCTTC-TCCT-TCATC-CA-
1 TTCTTCTTCCTCTCATCTCAT
*
185841 TTATTCTTCCTC
1 TTCTTCTTCCTC
185853 CTCCTCTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 5 0.19
20 4 0.15
21 6 0.23
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (21 bp):
TTCTTCTTCCTCTCATCTCAT
Found at i:186759 original size:31 final size:31
Alignment explanation
Indices: 186724--186785 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
186714 AAAATGTAAG
186724 AACAATCATCAGAATTCTATAAAACAGTTTC
1 AACAATCATCAGAATTCTATAAAACAGTTTC
186755 AACAATCATCAGAATTCTATAAAACAGTTTC
1 AACAATCATCAGAATTCTATAAAACAGTTTC
186786 CTTTCAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (31 bp):
AACAATCATCAGAATTCTATAAAACAGTTTC
Found at i:187195 original size:29 final size:29
Alignment explanation
Indices: 187116--187195 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
187106 CCCAGCATAA
* * * *
187116 GTCGCCATGCCCTCCGGGCGACCTTGTAG
1 GTCGCCATGCACGCCGGGCGACATGGTAG
* *
187145 GTCGCCATGCACGCCAGACGACATGGTAG
1 GTCGCCATGCACGCCGGGCGACATGGTAG
* *
187174 GTCGTCATGCACGCTGGGCGAC
1 GTCGCCATGCACGCCGGGCGAC
187196 CTTGTCCTGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (29 bp):
GTCGCCATGCACGCCGGGCGACATGGTAG
Found at i:187314 original size:31 final size:31
Alignment explanation
Indices: 187279--187340 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
187269 TATGGCACAT
*
187279 GCAAAGCTTCATCCTCTCGTCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
*
187310 GCAAAGCTTTATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
187341 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
Found at i:188848 original size:22 final size:22
Alignment explanation
Indices: 188816--188871 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
188806 TATTCGTGTT
* *
188816 TATTCGTTTAA-AATTCTCGAATA
1 TATTC-TTTAACAATTAT-GAACA
188839 TATTCTTTAACAATTATGAACA
1 TATTCTTTAACAATTATGAACA
*
188861 TATTTTTTAAC
1 TATTCTTTAAC
188872 TTTGTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (22 bp):
TATTCTTTAACAATTATGAACA
Found at i:190712 original size:15 final size:16
Alignment explanation
Indices: 190692--190721 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
190682 TTAGGGGTAC
190692 TTTTTA-CATTATGCA
1 TTTTTATCATTATGCA
190707 TTTTTATCATTATGC
1 TTTTTATCATTATGC
190722 TTACTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTTATCATTATGCA
Found at i:194149 original size:22 final size:22
Alignment explanation
Indices: 194123--194167 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
194113 AAAGAATAAA
194123 TTACTATAAGAAATTAGAAAAT
1 TTACTATAAGAAATTAGAAAAT
194145 TTACTATAAGAAATTAGAAAAT
1 TTACTATAAGAAATTAGAAAAT
194167 T
1 T
194168 CTCACAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (22 bp):
TTACTATAAGAAATTAGAAAAT
Found at i:205180 original size:2 final size:2
Alignment explanation
Indices: 205168--205201 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
205158 TCATTTATCG
*
205168 AT AT AT GT 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
205202 CCTTTGTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206482 original size:32 final size:32
Alignment explanation
Indices: 206406--206499 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
206396 ATCAATGAGG
* * ** *
206406 AATAATGGGGCATCTTTAAAGATTCAACAGTA
1 AATATTGGGGCATATTTGGAGATTCAACATTA
* *
206438 AATGTTGGGGCATATTTGGAGATTCAACATTG
1 AATATTGGGGCATATTTGGAGATTCAACATTA
* * *
206470 AATATTGTGGCATATTTGGGGATTTAACAT
1 AATATTGGGGCATATTTGGAGATTCAACAT
206500 CCTGATGCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (32 bp):
AATATTGGGGCATATTTGGAGATTCAACATTA
Found at i:206897 original size:43 final size:43
Alignment explanation
Indices: 206849--206993 Score: 209
Period size: 43 Copynumber: 3.4 Consensus size: 43
206839 TAAAGGGGTC
*
206849 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAT
1 ATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACAT
*
206892 ATCCACGATTTCAACTCCACGACAGAGGATATTGTACCAACAT
1 ATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACAT
* ** * * * *
206935 ATCCACGTTTTCAACTCCATAACAGAGGATATCGTGCCCATAC
1 ATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACAT
206978 ATCCACGATTTCAACT
1 ATCCACGATTTCAACT
206994 TCACAGCGAA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACAT
Found at i:207325 original size:43 final size:43
Alignment explanation
Indices: 207226--207328 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
207216 ATGAAGGGGC
* *
207226 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGAAGGAGGATATCGTACCAACA
* * * *
207269 GATCCACAATTTCAACTCCACGAAGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGAAGGAGGATATCGTACCAACA
* *
207312 CATCCATGGTTTCAACT
1 CATCCACGATTTCAACT
207329 TCACAACGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGAAGGAGGATATCGTACCAACA
Found at i:207383 original size:335 final size:337
Alignment explanation
Indices: 206892--207600 Score: 969
Period size: 335 Copynumber: 2.1 Consensus size: 337
206882 GTACCAACAT
* * * ** *
206892 ATCCACGATTTCAACTCCACGACAGAGGATATTGTACCAACATATCCACGTTTTCAACTCCATAA
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAGATCCACAATTTCAACTCCAGAA
* * * *
206957 CAGAGGATATCGTGCCCATACATCCACGATTTCAACTTCACAGCGAAGGCAATCGTATACACGAG
66 CAGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAACGAAGGCAATCGTACACACAAG
* * *
207022 CAATATCCATTTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTA
131 CAACATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTA
207087 CCTGTCAATAAA-ATTTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG
196 CCTGTCAATAAACA-TTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG
* * *
207151 AAACAA-C-AC-AAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAATGCTAAACTTT
260 AAACAAGCAACTAA-CTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTTC
*
207213 ACGATGAAGGGGCC
324 ACGACGAAGGGGCC
*
207227 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACGGATCCACAATTTCAACTCCACGA
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAGATCCACAATTTCAACTCCA-GA
* * * *
207292 A-GGAGGATATCGTGCCCACACATCCATGGTTTCAACTTCACAACGAAGGGAATCGTACACACAA
65 ACAGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAACGAAGGCAATCGTACACACAA
* * * *
207356 GCAGCATCTATCTCTAGTTTTGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGT
130 GCAACATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGT
*** * * *
207421 GTTTGTCAATAAACATTCCAGTTTCAGAGTCAATTTCAACTTCACGGCTAAGGATATTGGCCTCG
195 ACCTGTCAATAAACATTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG
* * *
207486 AAACAATGCAACTTAACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGTTCAACTT
260 AAACAA-GCAAC-TAACTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTT
* * * *
207551 CATGACGAATGTGTC
323 CACGACGAAGGGGCC
* *
207566 ATCCACGATTTCAACTTCACGACGAAGGATATCGT
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGT
207601 GTCCACCAGC
Statistics
Matches: 326, Mismatches: 41, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
335 232 0.71
336 3 0.01
337 1 0.00
338 2 0.01
339 86 0.26
340 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (337 bp):
ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAGATCCACAATTTCAACTCCAGAA
CAGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAACGAAGGCAATCGTACACACAAG
CAACATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTA
CCTGTCAATAAACATTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGA
AACAAGCAACTAACTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTTCAC
GACGAAGGGGCC
Found at i:207552 original size:34 final size:34
Alignment explanation
Indices: 207509--207598 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 34
207499 TAACTTGGAT
*
207509 TTCAACTTCACGACGAAGGATATCCAATTCA-AAG
1 TTCAACTTCACGACGAAGGATATCC-ATCCACAAG
* * * * *
207543 TTCAACTTCATGACGAATG-TGT-CATCCACGAT
1 TTCAACTTCACGACGAAGGATATCCATCCACAAG
207575 TTCAACTTCACGACGAAGGATATC
1 TTCAACTTCACGACGAAGGATATC
207599 GTGTCCACCA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 4 0.09
32 19 0.43
33 4 0.09
34 17 0.39
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (34 bp):
TTCAACTTCACGACGAAGGATATCCATCCACAAG
Found at i:207659 original size:121 final size:121
Alignment explanation
Indices: 207502--207843 Score: 549
Period size: 121 Copynumber: 2.8 Consensus size: 121
207492 TGCAACTTAA
* *
207502 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGTGTCA
1 CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGGGTCA
207567 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACAATGCAACC
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACAATGCAACC
207623 CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGGGTCA
1 CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGGGTCA
* * *
207688 TCCACGATTTCAACTTCATGACGAAGGATATCGTGTCCACTAGCAACAATGCAATC
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACAATGCAACC
* * * * * * ** *
207744 CTTGGATTTCAATTTCATGACAAATGATATCCAATTCGATGCTCAACTTCACAATGAATGGGTCA
1 CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGGGTCA
*
207809 TTCACGATTTCAACTTCACGACGAAGGATATCGTG
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTG
207844 CTCATTTGCA
Statistics
Matches: 205, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 205 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (121 bp):
CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAAGTTCAACTTCATGACGAATGGGTCA
TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACAATGCAACC
Found at i:207679 original size:34 final size:30
Alignment explanation
Indices: 207630--207719 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 30
207620 ACCCTTGGAT
* *
207630 TTCAATTTCACGACGAAGGATATCCAATTCAAAG
1 TTCAACTTCATGACGAAGGATATCC-A--C-AAG
* * *
207664 TTCAACTTCATGACGAATGGGTCATCCACGAT
1 TTCAACTTCATGACGAA-GGAT-ATCCACAAG
207696 TTCAACTTCATGACGAAGGATATC
1 TTCAACTTCATGACGAAGGATATC
207720 GTGTCCACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 18 0.38
33 1 0.02
34 15 0.31
35 4 0.08
36 4 0.08
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAACTTCATGACGAAGGATATCCACAAG
Found at i:207988 original size:84 final size:84
Alignment explanation
Indices: 207845--208518 Score: 881
Period size: 84 Copynumber: 8.0 Consensus size: 84
207835 GATATCGTGC
* * * * * * * * *
207845 TCATTTGCAGCTTAGCTCAAGGCAAGAAGGGCTATCTGCTAACAAAAGTCCTTCGAGTTCTATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
207910 CACTCAACTCAAAGGCACA
66 CACTCAGCTCAAAGGCACA
* *
207929 TAATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
207994 CACTCAGCTCCAAGGCACA
66 CACTCAGCTCAAAGGCACA
208013 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
208078 -AGCTCAGCTTC-AAGGCACA
66 CA-CTCAGC-TCAAAGGCACA
* *
208097 TCACTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
208162 CGCTCAGCTCCAAGGCACA
66 CACTCAGCTCAAAGGCACA
* *
208181 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * *
208246 CGCTCAGCTCCAAGACACA
66 CACTCAGCTCAAAGGCACA
* * *
208265 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTACC-ACCAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
208329 CACTCAGCTCAAAGGCACA
66 CACTCAGCTCAAAGGCACA
* * * * *
208348 TCAGTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
208412 CACTCACCTCAAAGGCATA
66 CACTCAGCTCAAAGGCACA
* * * * ** * *
208431 TCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTC-ATGAAAGACCTTTGAGTTCGAT
1 TC--ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGAC
* * * *
208495 TTCATTCAGCTCATAGGCATA
64 TACACTCAGCTCAAAGGCACA
208516 TCA
1 TCA
208519 ACCGCATGGT
Statistics
Matches: 537, Mismatches: 45, Indels: 17
0.90 0.08 0.03
Matches are distributed among these distances:
83 117 0.22
84 346 0.64
85 74 0.14
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CACTCAGCTCAAAGGCACA
Found at i:212960 original size:33 final size:31
Alignment explanation
Indices: 212883--212972 Score: 128
Period size: 31 Copynumber: 2.8 Consensus size: 31
212873 ATACCTAATG
*
212883 TTTACTTTTTGTTTCATTTTAGTACCCGACA
1 TTTACTTTTTGTTTCGTTTTAGTACCCGACA
*
212914 TTTACTTTTTGTTTCGTTTTAGTACCC-CCA
1 TTTACTTTTTGTTTCGTTTTAGTACCCGACA
212944 TTGTTAGCTTTTTGTTTCGTTTTAGTACC
1 -T-TTA-CTTTTTGTTTCGTTTTAGTACC
212973 TAATTTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.04
31 27 0.50
32 3 0.06
33 22 0.41
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.54
Consensus pattern (31 bp):
TTTACTTTTTGTTTCGTTTTAGTACCCGACA
Found at i:216527 original size:31 final size:31
Alignment explanation
Indices: 216489--216553 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
216479 GGTTATTCTA
216489 CATGATTTAGGGGTTATAAGTTTTAGGATCT
1 CATGATTTAGGGGTTATAAGTTTTAGGATCT
216520 CATGATTTAGGGGTTATAAGTTTTAGGATCT
1 CATGATTTAGGGGTTATAAGTTTTAGGATCT
216551 CAT
1 CAT
216554 AATGAGGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (31 bp):
CATGATTTAGGGGTTATAAGTTTTAGGATCT
Found at i:217082 original size:14 final size:14
Alignment explanation
Indices: 217063--217090 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
217053 ATCAAGTGAC
217063 TCTTAAGCTTAAGG
1 TCTTAAGCTTAAGG
217077 TCTTAAGCTTAAGG
1 TCTTAAGCTTAAGG
217091 AAAGCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TCTTAAGCTTAAGG
Found at i:217585 original size:102 final size:102
Alignment explanation
Indices: 217407--217610 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
217397 GTTGAGCTAA
*
217407 AAAGAAAGTGAATTTCATGCTTTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
1 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
*
217472 TGTACCGATGCACTCTCAAACAAATAAACATCGAATG
66 TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
217509 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
1 AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
*
217574 TGTATCAATGCACTCTCAAACAAATAAACATCGAATG
66 TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
217611 CAATTAGTGC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (102 bp):
AAAGAAAGTGAATTTCATGCTCTAACTGGAATTTCTGGGTTGTGTGCATCGATGCACATTCAATG
TGTACCAATGCACTCTCAAACAAATAAACATCGAATG
Found at i:217717 original size:15 final size:15
Alignment explanation
Indices: 217697--217727 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
217687 CGATGCATAG
217697 ATAGTGCATCGATGC
1 ATAGTGCATCGATGC
217712 ATAGTGCATCGATGC
1 ATAGTGCATCGATGC
217727 A
1 A
217728 CTCGTTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (15 bp):
ATAGTGCATCGATGC
Found at i:218613 original size:31 final size:31
Alignment explanation
Indices: 218575--218665 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 31
218565 AGAGTTGAGG
218575 GTTTACCTATG-TCTTTCGGGACATATGGATA
1 GTTTACCTATGTTC-TTCGGGACATATGGATA
* *
218606 GTTTACCTATATTCTACGGGACATATGGATA
1 GTTTACCTATGTTCTTCGGGACATATGGATA
* *
218637 GTTTACCTAGGTTCTTCGGGACCTATGGA
1 GTTTACCTATGTTCTTCGGGACATATGGA
218666 CAATTGTCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 51 0.96
32 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATA
Found at i:229325 original size:12 final size:12
Alignment explanation
Indices: 229308--229332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
229298 AGTCACCGGC
229308 GGCGTCGCCGAA
1 GGCGTCGCCGAA
229320 GGCGTCGCCGAA
1 GGCGTCGCCGAA
229332 G
1 G
229333 AAATCTCCGC
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:0.16, C:0.32, G:0.44, T:0.08
Consensus pattern (12 bp):
GGCGTCGCCGAA
Found at i:231349 original size:18 final size:18
Alignment explanation
Indices: 231328--231405 Score: 94
Period size: 18 Copynumber: 4.5 Consensus size: 18
231318 AAAATATTAT
231328 ATATATAATTAATATAAA
1 ATATATAATTAATATAAA
231346 ATATATAA--AATATAAA
1 ATATATAATTAATATAAA
231362 ATATATAATTAATATAAA
1 ATATATAATTAATATAAA
*
231380 A-ATATTATATT-ATAT-AT
1 ATATA-TA-ATTAATATAAA
231397 ATATATAAT
1 ATATATAAT
231406 CGGGGCGGGG
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
16 18 0.33
17 7 0.13
18 26 0.48
19 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATAATTAATATAAA
Found at i:231356 original size:34 final size:33
Alignment explanation
Indices: 231318--231399 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 33
231308 CCCGAACCAA
231318 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAA-ATAT
* *
231352 AAAATATAAAATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
*
231385 --TATATTATATATATA
1 AAAATATTATATATATA
231400 TATAATCGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.28
33 4 0.09
34 27 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:235002 original size:19 final size:19
Alignment explanation
Indices: 234978--235016 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
234968 TAAGGAGGAT
234978 GAACTAAAATTTCAAGGGG
1 GAACTAAAATTTCAAGGGG
234997 GAACTAAAATTTCAAGGGG
1 GAACTAAAATTTCAAGGGG
235016 G
1 G
235017 CGAAACAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (19 bp):
GAACTAAAATTTCAAGGGG
Found at i:235561 original size:20 final size:20
Alignment explanation
Indices: 235520--235563 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
235510 ACATTAAAAA
* *
235520 TATGGCATGTGACATGAGAT
1 TATGGCATGTGAAATGACAT
235540 TATGGACATGTGAAATG-CAT
1 TATGG-CATGTGAAATGACAT
235560 TATG
1 TATG
235564 ATATCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (20 bp):
TATGGCATGTGAAATGACAT
Found at i:237996 original size:40 final size:40
Alignment explanation
Indices: 237947--238022 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
237937 TATTAACAAG
*
237947 ATTTTATGTTTAATTAATTAAATGAACGAACATGAATAAA
1 ATTTTATGTTCAATTAATTAAATGAACGAACATGAATAAA
* * *
237987 ATTTTATGTTCATTTAATTAAATGAGCGAATATGAA
1 ATTTTATGTTCAATTAATTAAATGAACGAACATGAA
238023 CAAATGGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (40 bp):
ATTTTATGTTCAATTAATTAAATGAACGAACATGAATAAA
Found at i:238303 original size:14 final size:14
Alignment explanation
Indices: 238284--238326 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
238274 AACTCAAATC
238284 ATTTATGTTTGTTT
1 ATTTATGTTTGTTT
*
238298 ATTTATGTTCGTTT
1 ATTTATGTTTGTTT
* *
238312 GTTTATTTTTGTTT
1 ATTTATGTTTGTTT
238326 A
1 A
238327 CGTTCGTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.02, G:0.14, T:0.70
Consensus pattern (14 bp):
ATTTATGTTTGTTT
Found at i:238340 original size:24 final size:24
Alignment explanation
Indices: 238299--238350 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
238289 TGTTTGTTTA
* ** * *
238299 TTTATGTTCGTTTGTTTATTTTTG
1 TTTACGTTCGTTCATTTATGTTCG
238323 TTTACGTTCGTTCATTTATGTTCG
1 TTTACGTTCGTTCATTTATGTTCG
238347 TTTA
1 TTTA
238351 TCATTTCAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.15, T:0.63
Consensus pattern (24 bp):
TTTACGTTCGTTCATTTATGTTCG
Found at i:244725 original size:15 final size:15
Alignment explanation
Indices: 244689--244730 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
244679 TTAGGATTAG
*
244689 TATTCTAACTTCCGA
1 TATTCTAACTACCGA
*
244704 TATTTCTAACTACTGA
1 TA-TTCTAACTACCGA
244720 TATTCTAACTA
1 TATTCTAACTA
244731 ATCCTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (15 bp):
TATTCTAACTACCGA
Done.