Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007363.1 Hibiscus syriacus cultivar Beakdansim tig00019756_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: 107791
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:10053 original size:16 final size:16
Alignment explanation
Indices: 10004--10068 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
9994 ATTAATATAA
10004 TTATATAAA-TATTAT
1 TTATATAAATTATTAT
* * *
10019 TTTTCATTAAAATAATAT
1 TTAT-A-TAAATTATTAT
10037 TTATATAAATTATTAT
1 TTATATAAATTATTAT
*
10053 TTATTTAAATTTATTA
1 TTATATAAA-TTATTA
10069 ATTAATTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 3 0.08
16 18 0.45
17 11 0.28
18 8 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATAAATTATTAT
Found at i:10717 original size:60 final size:60
Alignment explanation
Indices: 10607--10721 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
10597 AACATACCAC
* *
10607 CGTGTCACCTGAGTCAGCAAAACCCCATGAAGGCGCGTCCCTGGGTATGCGCCTTTCACA
1 CGTGTCACCTGAGTCAGCAAAACCCCATGAAAGCGCGTCCCCGGGTATGCGCCTTTCACA
* **
10667 CGTGTCACCTGAGTCGGCATAAA-TTCATGGAAAGCGCGTCCCCGGG-ATGCGCCTT
1 CGTGTCACCTGAGTCAGCA-AAACCCCAT-GAAAGCGCGTCCCCGGGTATGCGCCTT
10722 CCGCCACCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 30 0.62
61 18 0.38
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.21
Consensus pattern (60 bp):
CGTGTCACCTGAGTCAGCAAAACCCCATGAAAGCGCGTCCCCGGGTATGCGCCTTTCACA
Found at i:11251 original size:15 final size:14
Alignment explanation
Indices: 11199--11285 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 14
11189 TAAAAAAATG
11199 AAAAT-TTAAATAT
1 AAAATATTAAATAT
*
11212 GAAAATACTCAAATAATT
1 -AAAATA-TTAAAT-A-T
11230 AAAATATTAAATAT
1 AAAATATTAAATAT
*
11244 AGAAATATTAAAAAT
1 A-AAATATTAAATAT
*
11259 AAAA-AATAAAT-T
1 AAAATATTAAATAT
11271 AAAAATTATTAAATA
1 -AAAA-TATTAAATA
11286 AATATTATCT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
12 1 0.02
13 9 0.16
14 10 0.17
15 20 0.34
16 10 0.17
17 7 0.12
18 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAATATTAAATAT
Found at i:17964 original size:38 final size:37
Alignment explanation
Indices: 17929--17999 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
17919 TACAAATTGT
17929 AAAATATTTATAT-ATTTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTT-TTTAAAAAATTAAATTC
* *
17966 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTTAAAAAATTAAA
18000 AATATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTTTTTAAAAAATTAAATTC
Found at i:18340 original size:31 final size:31
Alignment explanation
Indices: 18305--18371 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
18295 CCAGGAATGA
*
18305 GATTCCCGATCAACTAAACATGGAAATGTAG
1 GATTCCCGATCAACTAAAAATGGAAATGTAG
* * *
18336 GATTCCCGGTCAACTAAAAATGGGAATGTGG
1 GATTCCCGATCAACTAAAAATGGAAATGTAG
18367 GATTC
1 GATTC
18372 TCATCCCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (31 bp):
GATTCCCGATCAACTAAAAATGGAAATGTAG
Found at i:20536 original size:32 final size:33
Alignment explanation
Indices: 20464--20559 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 33
20454 TATAGTATAA
* * *
20464 AATT-AAATATAACATTTGATTATAACTAAAAATTT
1 AATTCAAATATAAC-TTTAAATAT-ACT-AAAAGTT
20499 AATTCAAATATAA-TATTAAATAT-CTAAAAGTT
1 AATTCAAATATAACT-TTAAATATACTAAAAGTT
**
20531 AATTCAGCTATAACTTTAAATATACTAAA
1 AATTCAAATATAACTTTAAATATACTAAA
20560 TTAATATAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
32 25 0.48
33 8 0.15
34 1 0.02
35 10 0.19
36 8 0.15
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (33 bp):
AATTCAAATATAACTTTAAATATACTAAAAGTT
Found at i:21014 original size:21 final size:21
Alignment explanation
Indices: 20966--21026 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
20956 ATATGCCTCG
**
20966 ACGGGCTCGACATGTAACCTA
1 ACGGGCTCGACATGTAAATTA
* * *
20987 ACAGGCTCGACATGCAAATTT
1 ACGGGCTCGACATGTAAATTA
*
21008 ACGGGCTCAACATGTAAAT
1 ACGGGCTCGACATGTAAAT
21027 CAGTGGGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
ACGGGCTCGACATGTAAATTA
Found at i:22857 original size:20 final size:20
Alignment explanation
Indices: 22813--22858 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
22803 TTAGGGCTTT
* *
22813 GGTTTAAGGTTTGATTTTAG
1 GGTTTAAGGTTTGAGTCTAG
* *
22833 TGTTTAAGTTTTGAGTCTAG
1 GGTTTAAGGTTTGAGTCTAG
22853 GGTTTA
1 GGTTTA
22859 TAAAAATGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (20 bp):
GGTTTAAGGTTTGAGTCTAG
Found at i:23939 original size:14 final size:14
Alignment explanation
Indices: 23922--23951 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23912 TTTAGAAAAC
23922 TATTTTTATTTATT
1 TATTTTTATTTATT
23936 TATTTTTATTTATT
1 TATTTTTATTTATT
23950 TA
1 TA
23952 AAGTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTATTTATT
Found at i:24636 original size:14 final size:14
Alignment explanation
Indices: 24595--24639 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
24585 GTTCATGAAC
*
24595 GTTCGGTTATGTTC
1 GTTCGGTTATGTTT
24609 GTTCGGTTATGTTT
1 GTTCGGTTATGTTT
24623 GTTCGGTTATGTTT
1 GTTCGGTTATGTTT
24637 GTT
1 GTT
24640 TATGTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.07, C:0.09, G:0.29, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTT
Found at i:24651 original size:24 final size:24
Alignment explanation
Indices: 24615--24684 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
24605 GTTCGTTCGG
**
24615 TTATGTTTGTTCGGTTATGTTTGT
1 TTATGTTCATTCGGTTATGTTTGT
* * *
24639 TTATGTTCATTCGGTAATATTCGT
1 TTATGTTCATTCGGTTATGTTTGT
**
24663 TTATGTTCATTCATTTATGTTT
1 TTATGTTCATTCGGTTATGTTT
24685 AACCCAATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (24 bp):
TTATGTTCATTCGGTTATGTTTGT
Found at i:25422 original size:10 final size:10
Alignment explanation
Indices: 25407--25481 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
25397 GGGTCTCCAA
25407 CGTTTATGTT
1 CGTTTATGTT
25417 CGTTTATGTT
1 CGTTTATGTT
25427 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
25438 ATGTTCGTGTT
1 -CGTTTATGTT
25449 CGTTTATGTT
1 CGTTTATGTT
25459 CG----TGTT
1 CGTTTATGTT
*
25465 TGTTTATGTT
1 CGTTTATGTT
25475 CGTTTAT
1 CGTTTAT
25482 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:25438 original size:16 final size:16
Alignment explanation
Indices: 25413--25477 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
25403 CCAACGTTTA
25413 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
25429 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
25445 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
25461 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
25477 T
1 T
25478 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:25572 original size:16 final size:16
Alignment explanation
Indices: 25547--25587 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
25537 AAAAAAAATT
25547 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
25563 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
25579 T-TT-ATTTAT
1 TGTTCATTTAT
25588 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:26234 original size:16 final size:18
Alignment explanation
Indices: 26204--26244 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
26194 GATTATTCGT
*
26204 GAGAATATAAGATTATTA
1 GAGAATATAAGATTACTA
26222 GAGAATA-AA-ATTACTA
1 GAGAATATAAGATTACTA
26238 -AGAATAT
1 GAGAATAT
26245 TGTATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 2 0.10
18 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (18 bp):
GAGAATATAAGATTACTA
Found at i:28734 original size:20 final size:20
Alignment explanation
Indices: 28709--28821 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
28699 TTTTCTCAAT
*
28709 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
28729 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
28749 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
28770 TCGCAACGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
* *
28790 TCGCAACGCGAATTGAGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
28811 TCGCAATGCGA
1 TCGCAACGCGA
28822 TACTGACTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
20 47 0.59
21 32 0.41
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:28812 original size:41 final size:41
Alignment explanation
Indices: 28706--28821 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
28696 CGATTTTCTC
**
28706 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGGA
*
28747 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGTA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGGA
* * * *
28788 AA-TCGCAACGCGAATTGAGAAAATCGCAATGCGA
1 AATTCGCAATGCGAA-TAAGTAAATCGCAACGCGA
28822 TACTGACTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 11 0.16
41 56 0.84
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGGA
Found at i:28834 original size:41 final size:41
Alignment explanation
Indices: 28789--28884 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
28779 GAATAAGTAA
* * * *
28789 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-AAAAAATCGCAACGAGATACTGACT
* *
28830 ATCGCAATGCGATAATAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
*
28871 TTCGCAACGCGATA
1 ATCGCAACGCGATA
28885 CTGACTTTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
Found at i:28835 original size:20 final size:20
Alignment explanation
Indices: 28810--28904 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
28800 AATTGAGAAA
*
28810 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
28830 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
28851 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
28871 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
28891 TTCGCAACGCGATA
1 ATCGCAACGCGATA
28905 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:29120 original size:22 final size:22
Alignment explanation
Indices: 29092--29135 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29082 CACTCTCTCA
29092 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
29114 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
29136 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:29424 original size:20 final size:20
Alignment explanation
Indices: 29399--29436 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29389 CGATTCTCTC
29399 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
29419 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
29437 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:30777 original size:18 final size:18
Alignment explanation
Indices: 30756--30800 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
30746 TCCACTTCGG
*
30756 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
30774 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
30792 GAGCCATCA
1 GAGCCATCA
30801 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:31326 original size:19 final size:20
Alignment explanation
Indices: 31272--31338 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
31262 TAGTTTACTT
* *
31272 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
31292 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
31312 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
31331 TCGCAACG
1 TCGCAACG
31339 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:31346 original size:14 final size:14
Alignment explanation
Indices: 31327--31384 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
31317 ATGCGAAATG
31327 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31341 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
31357 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
31373 AAAATCGCAACG
1 AAAATCGCAACG
31385 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:31369 original size:32 final size:33
Alignment explanation
Indices: 31311--31401 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
31301 GGAAATGGCT
*
31311 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
31344 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
31376 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
31402 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:31395 original size:19 final size:19
Alignment explanation
Indices: 31272--31406 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
31262 TAGTTTACTT
* **
31272 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
31292 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
31312 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31331 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
31345 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
31363 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
31377 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31396 TCGCAATGCGA
1 TCGCAACGCGA
31407 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:31437 original size:14 final size:14
Alignment explanation
Indices: 31418--31507 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
31408 TTGTGTTTCG
31418 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
31432 CGTTGCGATTTCATCT
1 CGTTGCGATTT--TGT
31448 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
31464 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
31480 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
31496 CGTTGCGATTTT
1 CGTTGCGATTTT
31508 CATTTTGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 34 0.53
16 8 0.12
18 22 0.34
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:31454 original size:32 final size:32
Alignment explanation
Indices: 31415--31506 Score: 175
Period size: 32 Copynumber: 2.9 Consensus size: 32
31405 GATTTGTGTT
31415 TCGCGTTGCGATTTTGTCGTTGCGATTTCATC
1 TCGCGTTGCGATTTTGTCGTTGCGATTTCATC
*
31447 TCGCGTTGCGATTTTGTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTTGTCGTTGCGATTTCATC
31479 TCGCGTTGCGATTTTGTCGTTGCGATTT
1 TCGCGTTGCGATTTTGTCGTTGCGATTT
31507 TCATTTTGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.46
Consensus pattern (32 bp):
TCGCGTTGCGATTTTGTCGTTGCGATTTCATC
Found at i:31455 original size:18 final size:18
Alignment explanation
Indices: 31432--31492 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
31422 GCGATTTTGT
31432 CGTTGCGATTTCATCTCG
1 CGTTGCGATTTCATCTCG
*
31450 CGTTGCGATTT--TGT--
1 CGTTGCGATTTCATCTCG
*
31464 CGTTGCGATTTCATTTCG
1 CGTTGCGATTTCATCTCG
31482 CGTTGCGATTT
1 CGTTGCGATTT
31493 TGTCGTTGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 11 0.30
16 4 0.11
18 22 0.59
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (18 bp):
CGTTGCGATTTCATCTCG
Found at i:31542 original size:20 final size:19
Alignment explanation
Indices: 31517--31562 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
31507 TCATTTTGCA
31517 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTT-CGCG
*
31537 TTGCGATAGTCATTTCGCG
1 TTGCGATAGCCATTTCGCG
31556 TTGCGAT
1 TTGCGAT
31563 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (19 bp):
TTGCGATAGCCATTTCGCG
Found at i:33451 original size:14 final size:14
Alignment explanation
Indices: 33432--33467 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
33422 ATTGTTTAAT
33432 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
33446 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
33460 TGATTTGT
1 TGATTTGT
33468 TTAATTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33606 original size:19 final size:19
Alignment explanation
Indices: 33584--33651 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
33574 ATCGCAACGA
33584 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33603 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33622 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
33636 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
33652 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:33695 original size:20 final size:20
Alignment explanation
Indices: 33670--33726 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
33660 TCGCATTGCG
*
33670 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
33690 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
33710 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
33727 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:34113 original size:14 final size:14
Alignment explanation
Indices: 34094--34129 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
34084 ATTGTTTAAT
34094 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
34108 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
34122 TGATTTGT
1 TGATTTGT
34130 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:35724 original size:20 final size:19
Alignment explanation
Indices: 35679--35797 Score: 51
Period size: 20 Copynumber: 6.7 Consensus size: 19
35669 TCTTTTGGTT
35679 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
35698 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
35719 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
35738 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
35752 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
35771 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
35785 GAAATGAAAATCG
1 GAAATGAAAATCG
35798 GAATGCGATT
Statistics
Matches: 71, Mismatches: 17, Indels: 24
0.63 0.15 0.21
Matches are distributed among these distances:
14 18 0.25
16 4 0.06
17 4 0.06
19 17 0.24
20 26 0.37
21 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:35761 original size:33 final size:33
Alignment explanation
Indices: 35704--35791 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
35694 ACGAGATAAT
* *
35704 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
35738 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
35771 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
35792 AAATCGGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:35823 original size:19 final size:19
Alignment explanation
Indices: 35801--35867 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
35791 AAAATCGGAA
*
35801 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
35820 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
35839 TGCGATAGTT-ATTTCCGCTT
1 TGCGAT-TTTGATTT-CGCGT
35859 TGCGATTTT
1 TGCGATTTT
35868 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:36457 original size:21 final size:21
Alignment explanation
Indices: 36424--36503 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
36414 TGCGAAAGTA
* * *
36424 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
36445 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
36465 AGTATCGCATTGCGATTTTTCC
1 AGTATCGCATTGCGATTTTT-C
* *
36487 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
36504 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 27 0.59
22 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:36480 original size:20 final size:20
Alignment explanation
Indices: 36387--36480 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
36377 CGCTAAGTAA
*
36387 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
36407 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
36427 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
36448 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
36468 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
36481 TTTTCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:36499 original size:41 final size:41
Alignment explanation
Indices: 36408--36542 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
36398 AAAGTCAGTA
* * * * *
36408 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTT-TATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTTCCAAT
* *
36448 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTTCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTTCCAAT
* ** * *
36490 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTTCCAAT
36531 TCGCGTTGCGAT
1 TCGCGTTGCGAT
36543 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTTCCAAT
Found at i:36532 original size:21 final size:21
Alignment explanation
Indices: 36469--36564 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 21
36459 ATAGTCAGTA
* *
36469 TCGCATTGCGATTTTTCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
36490 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
*
36510 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
36531 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
36551 TCGCATTGCGAATT
1 TCGCATTGCGAATT
36565 GGGAAAATCG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 31 0.53
21 28 0.47
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGAATTTACCAAT
Found at i:36543 original size:41 final size:41
Alignment explanation
Indices: 36469--36564 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
36459 ATAGTCAGTA
* *
36469 TCGCATTGCGATTTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
36510 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
36551 TCGCATTGCGAATT
1 TCGCATTGCGAATT
36565 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:36902 original size:7 final size:7
Alignment explanation
Indices: 36890--36930 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
36880 AACTTAAAAT
36890 CCTAAAC
1 CCTAAAC
36897 CCTAAAC
1 CCTAAAC
36904 CCTAAAC
1 CCTAAAC
36911 CCTAAAC
1 CCTAAAC
36918 CCTAAAC
1 CCTAAAC
36925 CCTAAA
1 CCTAAA
36931 TATAAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:38173 original size:22 final size:23
Alignment explanation
Indices: 38140--38188 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
38130 ACAAAGTGCG
38140 TAATTTTCTAGGGT-AAATTAAA
1 TAATTTTCTAGGGTGAAATTAAA
*
38162 TAATATTT-TAGGTTGAAATTAAA
1 TAAT-TTTCTAGGGTGAAATTAAA
38185 -AATT
1 TAATT
38189 GAATGTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 12 0.50
23 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (23 bp):
TAATTTTCTAGGGTGAAATTAAA
Found at i:39034 original size:21 final size:21
Alignment explanation
Indices: 39010--39053 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39000 CAAATGATAT
39010 TATAAATTATTTTATTATTTG
1 TATAAATTATTTTATTATTTG
39031 TATAAATTATTTTATTATTTG
1 TATAAATTATTTTATTATTTG
39052 TA
1 TA
39054 GGCACGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATAAATTATTTTATTATTTG
Found at i:41229 original size:2 final size:2
Alignment explanation
Indices: 41224--41268 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
41214 CGTTTTTTCT
*
41224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41264 TA TA T
1 TA TA T
41269 TCTTTCGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:55235 original size:160 final size:163
Alignment explanation
Indices: 55049--55346 Score: 435
Period size: 160 Copynumber: 1.8 Consensus size: 163
55039 AAAAACAAAA
*
55049 AAAAAGACTTAATAAAAATAAGTTTTTTAATGAATTAAAAATGATAAAATC-AAAATATTTAAAT
1 AAAAAGACTAAATAAAAATAAGTTTTTTAATGAATT-AAAATGATAAAATCAAAAAT-TTTAAAT
* *
55113 TATAGCATGAATTA-TTTTT-AAAAAGGT-GATTAATTTATTTTTAAT-ATTTTATATACAATTG
64 TATAACATGAATTATTTTTTAAAAAAAGTAGATTAATTTATTTTTAATAATTTTATATACAATTG
*
55174 TTTTAAAAACGGGTATCAAATTAATTCATTTTAAG
129 TCTTAAAAACGGGTATCAAATTAATTCATTTTAAG
* * * *
55209 AAAAGGACTAAATAAAAATAAGTTTTTTAATGTATTAAAATGATAAAATTAAAAATTTTAAATTC
1 AAAAAGACTAAATAAAAATAAGTTTTTTAATGAATTAAAATGATAAAATCAAAAATTTTAAATTA
* * *
55274 TAATATGAATTATTTTTTAAAAAAAATTATATTAATTTATTTTTAATAATTTTATATACAATTGT
66 TAACATGAATTATTTTTT-AAAAAAAGTAGATTAATTTATTTTTAATAATTTTATATACAATTGT
55339 CTTAAAAA
130 CTTAAAAA
55347 ATGAGTATCA
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
159 31 0.26
160 43 0.36
162 6 0.05
163 17 0.14
164 24 0.20
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.42
Consensus pattern (163 bp):
AAAAAGACTAAATAAAAATAAGTTTTTTAATGAATTAAAATGATAAAATCAAAAATTTTAAATTA
TAACATGAATTATTTTTTAAAAAAAGTAGATTAATTTATTTTTAATAATTTTATATACAATTGTC
TTAAAAACGGGTATCAAATTAATTCATTTTAAG
Found at i:55502 original size:2 final size:2
Alignment explanation
Indices: 55427--55486 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
55417 AAAGCAAATA
55427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
55469 AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
55487 CCTCCTACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64919 original size:18 final size:18
Alignment explanation
Indices: 64896--64930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64886 TTCCATCCGG
*
64896 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
64914 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
64931 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:67639 original size:2 final size:2
Alignment explanation
Indices: 67632--67665 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
67622 AGAAAATGTC
*
67632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67666 AACATTGGAT
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:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:71333 original size:21 final size:21
Alignment explanation
Indices: 71309--71357 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
71299 TAAATGTTCG
*
71309 ATTCGAATTGGTTCGACTTGA
1 ATTCGAATTGGTTCGACTCGA
71330 ATTCGAATTGGTTCGACTCGA
1 ATTCGAATTGGTTCGACTCGA
71351 ATTCGAA
1 ATTCGAA
71358 CTCGAATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTCGAATTGGTTCGACTCGA
Found at i:71592 original size:39 final size:41
Alignment explanation
Indices: 71499--71595 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 41
71489 AAATAATAAT
*
71499 TATTAATTTATTAATAAATAATAAAAATAATAAGTTAACTACTC
1 TATT-ATTT-TTAATAAATAATAAAAATAATAAGTTAACTAC-A
*
71543 TATTATTTTTAATAAATAATAAAATATTATTAA-TTAA-TA-A
1 TATTATTTTTAATAAATAATAAAA-A-TAATAAGTTAACTACA
71583 TATTA-TTTTAATA
1 TATTATTTTTAATA
71596 CAAAAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
39 8 0.16
40 5 0.10
42 18 0.37
43 9 0.18
44 9 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (41 bp):
TATTATTTTTAATAAATAATAAAAATAATAAGTTAACTACA
Found at i:71593 original size:18 final size:18
Alignment explanation
Indices: 71543--71595 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
71533 TTAACTACTC
71543 TATTATTTTTAATAAATAA
1 TATTA-TTTTAATAAATAA
* *
71562 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
71583 TATTATTTTAATA
1 TATTATTTTAATA
71596 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 2 0.07
21 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:76420 original size:13 final size:13
Alignment explanation
Indices: 76402--76427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76392 TAAACGCACT
76402 ATAAATAATAATG
1 ATAAATAATAATG
76415 ATAAATAATAATG
1 ATAAATAATAATG
76428 GTGTTGATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAAATAATAATG
Found at i:76620 original size:46 final size:46
Alignment explanation
Indices: 76538--76625 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
76528 AAGGCGTCCA
* * *
76538 AAATTTTTTAATCCAAATTAATTCATGAACAGTGTAGGCGCCTCTT
1 AAATTTTTTAATCCAAATAAATTCATGAACAATGTAGACGCCTCTT
* * *
76584 AAATTTTTTAATTCAAATAAATTCGTGAATAATGTAGACGCC
1 AAATTTTTTAATCCAAATAAATTCATGAACAATGTAGACGCC
76626 ATGCATTCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (46 bp):
AAATTTTTTAATCCAAATAAATTCATGAACAATGTAGACGCCTCTT
Found at i:88130 original size:12 final size:11
Alignment explanation
Indices: 88109--88139 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
88099 TTTTTAACTT
88109 TTTAATTATTA
1 TTTAATTATTA
88120 TTTATATTATTA
1 TTTA-ATTATTA
88132 TTTAATTA
1 TTTAATTA
88140 ATTTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:89207 original size:14 final size:14
Alignment explanation
Indices: 89188--89218 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
89178 CAAGTTGGCA
*
89188 ATGCCATGGTTTAC
1 ATGCCACGGTTTAC
89202 ATGCCACGGTTTAC
1 ATGCCACGGTTTAC
89216 ATG
1 ATG
89219 GTTCTTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (14 bp):
ATGCCACGGTTTAC
Found at i:100214 original size:29 final size:29
Alignment explanation
Indices: 100172--100234 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
100162 GTGATCGCCA
*
100172 TAGGTCGCCATGTAGTCCCGGCGACCTTG
1 TAGGTCGCCATGTAATCCCGGCGACCTTG
100201 TAGGTCGCCATGTAATCCCGGCGACCTTG
1 TAGGTCGCCATGTAATCCCGGCGACCTTG
*
100230 GAGGT
1 TAGGT
100235 ATTTTGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTAATCCCGGCGACCTTG
Found at i:100815 original size:27 final size:27
Alignment explanation
Indices: 100781--100849 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
100771 AATTAGTTTG
*
100781 TTAG-TATAAATTATTAGTTTGTTAGT
1 TTAGTTATAAATTATTAGTTTATTAGT
*
100807 TTAGTTAT-ATTATATTAGTTTATTAGT
1 TTAGTTATAAAT-TATTAGTTTATTAGT
*
100834 TTAAGTTATATATTAT
1 TT-AGTTATAAATTAT
100850 ATTATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.17
27 19 0.54
28 9 0.26
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.57
Consensus pattern (27 bp):
TTAGTTATAAATTATTAGTTTATTAGT
Found at i:101277 original size:17 final size:16
Alignment explanation
Indices: 101254--101289 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
101244 TAATTTCCGT
101254 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
101270 TTT-AAAAATATTTTG
1 TTTAAAAAATATTGTG
101285 TTTAA
1 TTTAA
101290 TTTACATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:101582 original size:26 final size:25
Alignment explanation
Indices: 101553--101611 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
101543 AAATCATATT
*
101553 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
101579 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
101605 ATTATTA
1 ATTATTA
101612 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:101988 original size:12 final size:12
Alignment explanation
Indices: 101971--101996 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
101961 TCAGATATGC
101971 TGCAGTTCCACT
1 TGCAGTTCCACT
101983 TGCAGTTCCACT
1 TGCAGTTCCACT
101995 TG
1 TG
101997 AAGAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.19, T:0.35
Consensus pattern (12 bp):
TGCAGTTCCACT
Found at i:104749 original size:26 final size:26
Alignment explanation
Indices: 104425--104517 Score: 143
Period size: 26 Copynumber: 3.6 Consensus size: 26
104415 GATGATTTAG
*
104425 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
104451 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
104477 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
104503 AAATGATTTAATAAT
1 TAATGATTTGATAAT
104518 GATTTAAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
25 1 0.02
26 61 0.97
27 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:106831 original size:15 final size:14
Alignment explanation
Indices: 106808--106838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
106798 TACAACACTA
106808 AACTTTAATATAAT
1 AACTTTAATATAAT
106822 AACTTATAATATAAT
1 AACTT-TAATATAAT
106837 AA
1 AA
106839 ACTAATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:107317 original size:26 final size:24
Alignment explanation
Indices: 107280--107350 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 24
107270 AAAAAATTTA
107280 CCTTATCT-CCTTTCTTCTTCTACTTT
1 CCTT-TCTCCCTTTCTTCTT-T-CTTT
107306 CCTTTCTCCC--T-TTCTTTCTTT
1 CCTTTCTCCCTTTCTTCTTTCTTT
107327 CCTTTCTCTCCTTTCTTTCTTTCT
1 CCTTTCTC-CCTTTC-TTCTTTCT
107351 CGGCTGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
21 12 0.31
22 3 0.08
23 5 0.13
24 2 0.05
25 3 0.08
26 14 0.36
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (24 bp):
CCTTTCTCCCTTTCTTCTTTCTTT
Found at i:107330 original size:13 final size:13
Alignment explanation
Indices: 107287--107350 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
107277 TTACCTTATC
107287 TCCTTTC-TTCTT
1 TCCTTTCTTTCTT
*
107299 CTACTTTCCTTTC-T
1 -TCCTTT-CTTTCTT
*
107313 CCCTTTCTTTCTT
1 TCCTTTCTTTCTT
*
107326 TCCTTTCTCTCCTT
1 TCCTTTCT-TTCTT
107340 T-CTTTCTTTCT
1 TCCTTTCTTTCT
107351 CGGCTGCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.20
13 23 0.56
14 7 0.17
15 3 0.07
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (13 bp):
TCCTTTCTTTCTT
Found at i:107342 original size:22 final size:21
Alignment explanation
Indices: 107302--107349 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 21
107292 TCTTCTTCTA
107302 CTTTCCTTTCTCCCTTTCTTT
1 CTTTCCTTTCTCCCTTTCTTT
107323 CTTTCCTTTCTCTCCTTTCTTT
1 CTTTCCTTTCTC-CCTTTCTTT
107345 CTTTC
1 CTTTC
107350 TCGGCTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (21 bp):
CTTTCCTTTCTCCCTTTCTTT
Found at i:107401 original size:23 final size:23
Alignment explanation
Indices: 107354--107398 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
107344 TCTTTCTCGG
107354 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
107377 CTGC-ATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
107399 TCTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.07, C:0.40, G:0.04, T:0.49
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:107545 original size:27 final size:27
Alignment explanation
Indices: 107515--107570 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
107505 AATAATTCAC
107515 GGCTCAAACGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
*
107542 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
107569 GG
1 GG
107571 GAGCTGTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (27 bp):
GGCTCAAACGGTTCACATGCATGCATT
Found at i:107670 original size:28 final size:29
Alignment explanation
Indices: 107638--107716 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
107628 ATGGGAATGG
*
107638 CGCCGGGACTACATGGCGACCTA-GAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
107666 CGCCGGGAATACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
107695 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
107717 CTCTATTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 22 0.50
29 20 0.45
30 2 0.05
ACGTcount: A:0.22, C:0.30, G:0.33, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:107766 original size:13 final size:13
Alignment explanation
Indices: 107748--107774 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
107738 TCGTATATGG
107748 CTCGTATGTCACC
1 CTCGTATGTCACC
107761 CTCGTATGTCACC
1 CTCGTATGTCACC
107774 C
1 C
107775 CATATGGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (13 bp):
CTCGTATGTCACC
Done.