Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005033.1 Hibiscus syriacus cultivar Beakdansim tig00011301_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: 74456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2671 original size:36 final size:36
Alignment explanation
Indices: 2598--2702 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2588 ATTTATAAGT
* *
2598 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
2633 TGGTGATGATATAGGCGTGATAATGGTAATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
2669 TGGTGATGATATAGGAGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2703 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:6668 original size:35 final size:37
Alignment explanation
Indices: 6593--6672 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
6583 ATACTATTTC
* * *
6593 CATCACCATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATGATCACGCCTATAT
*
6630 CATCACCATAGTCCATC-ACCA-GATCACGCCTATAT
1 CATCACCATAATCCATCTACCATGATCACGCCTATAT
6665 CATCACCA
1 CATCACCA
6673 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATGATCACGCCTATAT
Found at i:12789 original size:11 final size:13
Alignment explanation
Indices: 12768--12799 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12758 GAGTGCTTTA
12768 ATTTCTTTTC-TG
1 ATTTCTTTTCTTG
12780 ATTT-TTTTCTTG
1 ATTTCTTTTCTTG
12792 ATTTCTTT
1 ATTTCTTT
12800 GACTTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 10 0.56
13 3 0.17
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.72
Consensus pattern (13 bp):
ATTTCTTTTCTTG
Found at i:15711 original size:46 final size:46
Alignment explanation
Indices: 15661--16109 Score: 583
Period size: 46 Copynumber: 9.8 Consensus size: 46
15651 AAATGAATGA
* * *
15661 ATAAATGAAAATGTATAATGGTGCATTATCGGCATAAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
15707 ATAAATGAAAATGAATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
15753 ATAAATTAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * **
15799 ATAAATGAAAATGCATAACGATGCCTTATCCTCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
15845 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGAAGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
15891 ATAAATGAAAATGCATAACGGCGCATTATCGGTATGAAAGGAAGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **** *
15937 ATAAATGAAAATGCATAACGGTACATTATCAATGTGAAACGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **
15983 ATAAATGAAAATGCATAACGATGCATTATCAACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * ** *
16029 ATAAATTAAAATGCACAGTGGTGCATTATCGGCATGAATGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** * * *
16075 ACAGTTGAAAATGTACAACGGTGCATTAACGGCAT
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCAT
16110 AAATGGTTCC
Statistics
Matches: 357, Mismatches: 46, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 357 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:18862 original size:8 final size:9
Alignment explanation
Indices: 18838--18862 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18828 TTCAAAACGA
18838 AAGAAAAAT
1 AAGAAAAAT
18847 AAGAAAAAT
1 AAGAAAAAT
18856 AAGAAAA
1 AAGAAAA
18863 GGAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAGAAAAAT
Found at i:24031 original size:2 final size:2
Alignment explanation
Indices: 24026--24068 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
24016 TTATAACTCT
24026 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
24068 A
1 A
24069 TATATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25326 original size:13 final size:13
Alignment explanation
Indices: 25304--25341 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
25294 ATTCCATTAT
25304 CATCCATCATCAA
1 CATCCATCATCAA
*
25317 CATCCTTCATCAA
1 CATCCATCATCAA
*
25330 GA-CCATCATCAA
1 CATCCATCATCAA
25342 TTCCATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.24
Consensus pattern (13 bp):
CATCCATCATCAA
Found at i:25402 original size:23 final size:23
Alignment explanation
Indices: 25372--25449 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 23
25362 CTCTATCCTT
25372 TCTTTATTTCTATTCATTTCTTA
1 TCTTTATTTCTATTCATTTCTTA
* *
25395 TCTTTA-TTAT-TTCATTTATTA
1 TCTTTATTTCTATTCATTTCTTA
25416 TTTCTTTATTAATCATATTCATTTTCTTA
1 --TCTTTATT--TC-TATTCA-TTTCTTA
25445 TCTTT
1 TCTTT
25450 GTTGCAGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 10 0.23
22 3 0.07
23 12 0.28
24 1 0.02
26 1 0.02
27 6 0.14
28 4 0.09
29 6 0.14
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.65
Consensus pattern (23 bp):
TCTTTATTTCTATTCATTTCTTA
Found at i:25410 original size:21 final size:22
Alignment explanation
Indices: 25384--25426 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
25374 TTTATTTCTA
*
25384 TTCATTTCTTA-TCTTTATTAT
1 TTCATTTATTATTCTTTATTAT
25405 TTCATTTATTATTTCTTTATTA
1 TTCATTTATTA-TTCTTTATTA
25427 ATCATATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCATTTATTATTCTTTATTAT
Found at i:25414 original size:12 final size:11
Alignment explanation
Indices: 25395--25426 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
25385 TCATTTCTTA
25395 TCTTTATTATT
1 TCTTTATTATT
25406 TCATTTATTATT
1 TC-TTTATTATT
25418 TCTTTATTA
1 TCTTTATTA
25427 ATCATATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTATTATT
Found at i:29538 original size:195 final size:195
Alignment explanation
Indices: 29206--29596 Score: 692
Period size: 195 Copynumber: 2.0 Consensus size: 195
29196 ATTCGGCCAA
*
29206 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
1 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATAAAGGGTTAGCCAAGCTATCA
* ** *
29271 CAAGCCCAAAGGACTTAATCATTCATTTGAAGTGTTGTGACCATTCGACCAAGCCCTCTCATTTC
66 CAAGCCCAAAGGACTTAATCATTCATTTAAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
*
29336 CTATGAATAGAGTGGATTGCCTTCATTTGCACTTATCTCATCTTATATATAAAAATTACTCTTGT
131 CTATGAATAGAGTGGATTGCCTTCATTTGCACTTATCTCATCTCATATATAAAAATTACTCTTGT
*
29401 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCTTAAAGGGTTAGCCAAGCTATCA
1 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATAAAGGGTTAGCCAAGCTATCA
29466 CAAGCCCAAAGGACTTAATCATTCATTTAAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
66 CAAGCCCAAAGGACTTAATCATTCATTTAAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
* * *
29531 CTATGAATAGAGTGGCTTGCCTTCATTTGTACTTATCTCGTCTCATATATAAAAATTACTCTTGT
131 CTATGAATAGAGTGGATTGCCTTCATTTGCACTTATCTCATCTCATATATAAAAATTACTCTTGT
29596 G
1 G
29597 TGTTATTTCT
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 186 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (195 bp):
GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATAAAGGGTTAGCCAAGCTATCA
CAAGCCCAAAGGACTTAATCATTCATTTAAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
CTATGAATAGAGTGGATTGCCTTCATTTGCACTTATCTCATCTCATATATAAAAATTACTCTTGT
Found at i:30278 original size:24 final size:24
Alignment explanation
Indices: 30222--30285 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
30212 TTCATCTCTT
* *
30222 TCATTTCATTACTTATATTATTTATC
1 TCATTTC-TTA-TTTTATTATTAATC
30248 -CATTTCTTATTTTATTATTAATC
1 TCATTTCTTATTTTATTATTAATC
30271 TCATTTCTT-TTTTAT
1 TCATTTCTTATTTTAT
30286 CTTTGTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 18 0.51
24 11 0.31
25 6 0.17
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.62
Consensus pattern (24 bp):
TCATTTCTTATTTTATTATTAATC
Found at i:33609 original size:20 final size:20
Alignment explanation
Indices: 33567--33615 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33557 TGAAAGGGAT
* *
33567 TATCGGTACCATGATATAAG
1 TATCGATACCATGATAGAAG
**
33587 TATCGATACCATGATAGGGG
1 TATCGATACCATGATAGAAG
33607 TATCGATAC
1 TATCGATAC
33616 TATTGAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
TATCGATACCATGATAGAAG
Found at i:34073 original size:46 final size:46
Alignment explanation
Indices: 34023--34318 Score: 378
Period size: 46 Copynumber: 6.4 Consensus size: 46
34013 AGTTGAATGA
* *
34023 ATAAATGAAAATGCCTAACGGTG-ACTTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCA-TTATCGGCATGAAAGGATGCC
* * * *
34069 ATAAATGAAAATGCATAATGGTGCATTATCAGCGTGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
34115 ATAAATGAAAATGCATAACGGTGCATTATCAGCATAAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * **
34161 ATAAATGAAAATGCATAACGATACATTATTGGCATGAAAGGATTTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
34207 ATAAATGAAAATGCATAACGGTGAATTATCGGCCTGAAAAGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
34253 ATAAATGGAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **
34299 AAAAATGAAAAAACATAACG
1 ATAAATGAAAATGCATAACG
34319 ATCCATTAAC
Statistics
Matches: 214, Mismatches: 35, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
46 213 1.00
47 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:34215 original size:138 final size:138
Alignment explanation
Indices: 34023--34326 Score: 421
Period size: 138 Copynumber: 2.2 Consensus size: 138
34013 AGTTGAATGA
* * *
34023 ATAAATGAAAATGCCTAACGGTGAC-TTATCGGCATGAAATGATGCCATAAATGAAAATGCATAA
1 ATAAATGAAAATGCATAACGAT-ACATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA
* * * * *
34087 TGGTGCATTATCAGCGTGAAAGGATGTCATAAATGAAAATGCATAACGGTGCATTATCAGCATAA
65 CGGTGAATTATCAGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATAA
34152 AAGGATGCC
130 AAGGATGCC
* **
34161 ATAAATGAAAATGCATAACGATACATTATTGGCATGAAAGGATTTCATAAATGAAAATGCATAAC
1 ATAAATGAAAATGCATAACGATACATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
34226 GGTGAATTATCGGCCTGAAAAGATGTCATAAATGGAAATGCATAACAGTGCATTATCGGCATGAA
66 GGTGAATTATCAGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATAAA
34291 AGGATGCC
131 AGGATGCC
* ** *
34299 AAAAATGAAAAAACATAACGATCCATTA
1 ATAAATGAAAATGCATAACGATACATTA
34327 ACGACATAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
137 2 0.01
138 144 0.99
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (138 bp):
ATAAATGAAAATGCATAACGATACATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
GGTGAATTATCAGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATAAA
AGGATGCC
Found at i:41376 original size:21 final size:21
Alignment explanation
Indices: 41351--41397 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
41341 TAAATACAAG
41351 AGCTAA-CATAAACATAATATA
1 AGCTAAGCATAAACAT-ATATA
**
41372 AGCTAAGCATAAATGTATATA
1 AGCTAAGCATAAACATATATA
41393 AGCTA
1 AGCTA
41398 TGGAAACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.26
Consensus pattern (21 bp):
AGCTAAGCATAAACATATATA
Found at i:43711 original size:21 final size:21
Alignment explanation
Indices: 43664--43711 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
43654 CATAGATAAA
43664 ATGT-ACATATATGAATATAT
1 ATGTAACATATATGAATATAT
* *
43684 CTATAACATAT-TGAATGATAT
1 ATGTAACATATATGAAT-ATAT
43705 ATGTAAC
1 ATGTAAC
43712 GAATATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (21 bp):
ATGTAACATATATGAATATAT
Found at i:46767 original size:21 final size:20
Alignment explanation
Indices: 46738--46785 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
46728 TTAGAAATTG
* *
46738 AAATAAAATAAAAACTTAAGT
1 AAATGAAATAAAAA-TGAAGT
*
46759 AAATGAAATAGAAATGAAGT
1 AAATGAAATAAAAATGAAGT
46779 -AATGAAA
1 AAATGAAA
46786 GAGTTGGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 5 0.21
21 12 0.50
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (20 bp):
AAATGAAATAAAAATGAAGT
Found at i:55563 original size:21 final size:18
Alignment explanation
Indices: 55529--55572 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
55519 TGAAGAAATG
55529 TTATATGATTATTATCTCT
1 TTATATGATTATTAT-TCT
*
55548 TTATATTGATTTATTATTTT
1 TTATA-TGA-TTATTATTCT
55568 TTATA
1 TTATA
55573 AAATCAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTATATGATTATTATTCT
Found at i:59653 original size:45 final size:45
Alignment explanation
Indices: 59556--59932 Score: 303
Period size: 45 Copynumber: 8.6 Consensus size: 45
59546 ACCTTCATTC
* * * *
59556 ATGTTTATAATGCA-CCATTATGCATTTTTAACTATAGCATACTTTT
1 ATGTTGATAATGCACCCA-TATGCA-TTTCAACTATCGCATAATTTT
** * *
59602 CGGTTGATAACGCACCCACATGCATTTCAACTATCGCATAATTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
* * *
59647 GTGTTGATAATTCACTCATATGCATTTCAACTATCGCAT-ATTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
* * * *
59691 CTGTTGATAATGCATCCATATG-----C-A--AGC-CACAATTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
* * *
59727 ATGTTGAAAATGCACCCATATGCATTTCAACTATCACATATTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
* * *
59772 TTATTGATAATGCACCCATATGCATTTCAACTA-AGCCATAATTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCG-CATAATTTT
* * *
59817 ATGTTGAAAATGCACCCATATGCATTTCAACTATAGCATACTTTT
1 ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
* ** * * * ** *
59862 CA-ATTGACCATGCACTCGTATGCATTTCAACTATGGCATCCTTTC
1 -ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
***
59907 ATGCCAATAATGCACCCATATGCATT
1 ATGTTGATAATGCACCCATATGCATT
59933 ATTATTTTCA
Statistics
Matches: 264, Mismatches: 52, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
35 2 0.01
36 26 0.10
38 1 0.00
39 1 0.00
41 1 0.00
42 1 0.00
44 26 0.10
45 185 0.70
46 18 0.07
47 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (45 bp):
ATGTTGATAATGCACCCATATGCATTTCAACTATCGCATAATTTT
Found at i:59797 original size:125 final size:126
Alignment explanation
Indices: 59604--59840 Score: 334
Period size: 125 Copynumber: 1.9 Consensus size: 126
59594 ATACTTTTCG
* * * * *
59604 GTTGATAACGCACCCACATGCATTTCAACTATCGCATAATTTTGTGTTGATAATTCACTCATATG
1 GTTGAAAACGCACCCACATGCATTTCAACTATCACATAATTTTGTATTGATAATGCACCCATATG
* * * *
59669 CATTTCAACT-ATCGCAT-ATTTTCTGTTGATAATGCATCCATATGCAAGCCACAATTTTAT
66 CATTTCAACTAAGC-CATAATTTTATGTTGAAAATGCACCCATATGCAAGCCACAATTTTAT
* * * *
59729 GTTGAAAATGCACCCATATGCATTTCAACTATCACATATTTTTTTATTGATAATGCACCCATATG
1 GTTGAAAACGCACCCACATGCATTTCAACTATCACATAATTTTGTATTGATAATGCACCCATATG
59794 CATTTCAACTAAGCCATAATTTTATGTTGAAAATGCACCCATATGCA
66 CATTTCAACTAAGCCATAATTTTATGTTGAAAATGCACCCATATGCA
59841 TTTCAACTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
125 69 0.71
126 28 0.29
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (126 bp):
GTTGAAAACGCACCCACATGCATTTCAACTATCACATAATTTTGTATTGATAATGCACCCATATG
CATTTCAACTAAGCCATAATTTTATGTTGAAAATGCACCCATATGCAAGCCACAATTTTAT
Found at i:60470 original size:22 final size:21
Alignment explanation
Indices: 60423--60476 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
60413 TGATGTTTCC
*
60423 TGGTATTGATA-TCCTTACCA
1 TGGTATTGATACTCCATACCA
*
60443 TGGTATTGATACTACCATACTA
1 TGGTATTGATACT-CCATACCA
*
60465 TGGTATCGATAC
1 TGGTATTGATAC
60477 CCCCTTACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
22 17 0.59
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (21 bp):
TGGTATTGATACTCCATACCA
Found at i:60565 original size:20 final size:20
Alignment explanation
Indices: 60542--60594 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
60532 CTTATAATGT
60542 TATCGATACTACTTCAA-CAG
1 TATCGATACTA-TTCAATCAG
*
60562 TATCGATACTGATTGAATCAG
1 TATCGATACT-ATTCAATCAG
60583 TATCGATACTAT
1 TATCGATACTAT
60595 CCAGCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (20 bp):
TATCGATACTATTCAATCAG
Found at i:66365 original size:45 final size:45
Alignment explanation
Indices: 66280--66582 Score: 317
Period size: 45 Copynumber: 6.7 Consensus size: 45
66270 CCTTTATTCA
* * * *
66280 TGTTTATAATGTA-CCATTATGCATTTTGAACTATATCATACTTTTC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTTC
* * * *
66326 TATTGATAATTCACCCATATACATTTCAACTATAGCATACCTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * * *
66371 TGTTGAGAATACACCCATATGCATTTCAACTATCGCATATTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * *
66416 TGTTGATAATGCACCCATATGTATTTCAACTATCGCATATTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
** *
66461 TGTTGATAATGCATACATATGCATTTCATCTAT-GCCATGA-TTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAG-CAT-ACTTTTC
* *
66506 TGTTGAAAATGCACCCATATGCATTTTAACTATAGCATAC-TTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * ** *
66550 AGTTAACCATTCACCCATATGCATTTCAACTAT
1 TGTTGATAATGCACCCATATGCATTTCAACTAT
66583 GGTATCCTTT
Statistics
Matches: 219, Mismatches: 33, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
44 33 0.15
45 167 0.76
46 16 0.07
47 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
Done.