Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004724.1 Kokia drynarioides strain JFW-HI SEQ_118301, 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: 113866
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3362 original size:49 final size:49
Alignment explanation
Indices: 3255--3373 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
3245 AGGTTCGCTG
* * * *
3255 TTGCGGCCTCAACCTTTCCCCTTTATATTTCCATGGTACTAGATCCGTCG
1 TTGCGGCCTCAACCTTT-CCCTTCATATTTCCATGGTACCAGATCCATCA
* * *
3305 TTGCGGCCTCAACCTTTCCCTTCATATCTT-CATGGTACCATATTCATTA
1 TTGCGGCCTCAACCTTTCCCTTCATAT-TTCCATGGTACCAGATCCATCA
*
3354 TTGTGGCCTCAATCCTTTCC
1 TTGCGGCCTCAA-CCTTTCC
3374 ATCACATCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 33 0.56
50 26 0.44
ACGTcount: A:0.17, C:0.32, G:0.13, T:0.38
Consensus pattern (49 bp):
TTGCGGCCTCAACCTTTCCCTTCATATTTCCATGGTACCAGATCCATCA
Found at i:4259 original size:4 final size:4
Alignment explanation
Indices: 4242--4272 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4232 TCTCCTTCTT
*
4242 TTTC TTTA TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
4273 TTTGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:11419 original size:21 final size:21
Alignment explanation
Indices: 11364--11412 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
11354 TGGTGTAGAC
11364 TTCTACTC-ATACAAGTGACAA
1 TTCTAC-CAATACAAGTGACAA
*
11385 TTCTACCAATACAAGTGACTA
1 TTCTACCAATACAAGTGACAA
11406 TTCTACC
1 TTCTACC
11413 GAAACAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (21 bp):
TTCTACCAATACAAGTGACAA
Found at i:11616 original size:21 final size:21
Alignment explanation
Indices: 11592--11631 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11582 TACCCTGTAC
* *
11592 TTCTACCGACACATGTAAGGG
1 TTCTACCGAAACAAGTAAGGG
*
11613 TTCTATCGAAACAAGTAAG
1 TTCTACCGAAACAAGTAAG
11632 CAGAATTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAAGTAAGGG
Found at i:12220 original size:50 final size:51
Alignment explanation
Indices: 12165--12275 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 51
12155 ATATGAGCTA
* * * * *
12165 AACAGAATTACGCTCTTACTAACGAGATATAATTTCGCTCTTATAAGCCAG
1 AACAGAATTACACTCTTACGAACCAGATAGAATTACGCTCTTATAAGCCAG
* *
12216 -ACAGAATTACACTCTTACGAGCCAGATAGAATTACGCTCTTATGAGCCAG
1 AACAGAATTACACTCTTACGAACCAGATAGAATTACGCTCTTATAAGCCAG
12266 AATCAGAATT
1 AA-CAGAATT
12276 TCCTCATCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 43 0.84
51 1 0.02
52 7 0.14
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (51 bp):
AACAGAATTACACTCTTACGAACCAGATAGAATTACGCTCTTATAAGCCAG
Found at i:12262 original size:25 final size:25
Alignment explanation
Indices: 12150--12275 Score: 110
Period size: 25 Copynumber: 5.0 Consensus size: 25
12140 GACAAAATAT
* * * *
12150 CGCTCATATGAGCTAAACAGAATTA
1 CGCTCTTATGAGCCAGATAGAATTA
* * * *
12175 CGCTCTTACT-AACGAGATATAATTT
1 CGCTCTTA-TGAGCCAGATAGAATTA
* *
12200 CGCTCTTATAAGCCAGACAGAATTA
1 CGCTCTTATGAGCCAGATAGAATTA
* *
12225 CACTCTTACGAGCCAGATAGAATTA
1 CGCTCTTATGAGCCAGATAGAATTA
12250 CGCTCTTATGAGCCAGAATCAGAATT
1 CGCTCTTATGAGCCAG-AT-AGAATT
12276 TCCTCATCTT
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.01
25 69 0.87
26 3 0.04
27 6 0.08
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (25 bp):
CGCTCTTATGAGCCAGATAGAATTA
Found at i:17649 original size:14 final size:13
Alignment explanation
Indices: 17615--17672 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
17605 AAGAAAATAG
*
17615 AAAAGAAAATGGA
1 AAAAGGAAATGGA
**
17628 AATGGGAAATGGA
1 AAAAGGAAATGGA
*
17641 AAGAAGGAAAAGGA
1 AA-AAGGAAATGGA
*
17655 AAAAGTGAAATAGA
1 AAAAG-GAAATGGA
17669 AAAA
1 AAAA
17673 TAAATTATGA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 15 0.43
14 20 0.57
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.09
Consensus pattern (13 bp):
AAAAGGAAATGGA
Found at i:18676 original size:15 final size:15
Alignment explanation
Indices: 18649--18692 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
18639 TATATCAAAC
*
18649 AATTTTATA-ACTTA
1 AATTTTAAATACTTA
18663 AATTTTAAATACTTA
1 AATTTTAAATACTTA
* *
18678 ATTTTTCAATACTTA
1 AATTTTAAATACTTA
18693 TTTTTTCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTAAATACTTA
Found at i:18697 original size:15 final size:15
Alignment explanation
Indices: 18665--18717 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
18655 ATAACTTAAA
* *
18665 TTTTAAATACTTAAT
1 TTTTCAATACTTATT
18680 TTTTCAATACTTATT
1 TTTTCAATACTTATT
* *
18695 TTTTCAACATTTATT
1 TTTTCAATACTTATT
18710 TTTTCAAT
1 TTTTCAAT
18718 TTATCAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTCAATACTTATT
Found at i:24881 original size:18 final size:18
Alignment explanation
Indices: 24858--24893 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24848 ACTGAACATG
24858 TTTTATAACTAT-TTTCTC
1 TTTTATAA-TATGTTTCTC
24876 TTTTATAATATGTTTCTC
1 TTTTATAATATGTTTCTC
24894 AAGTTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAATATGTTTCTC
Found at i:28492 original size:22 final size:22
Alignment explanation
Indices: 28443--28510 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
28433 TATAATATTC
* * *
28443 AAATAACAACAAAATAGTAGTA
1 AAATAACAGCAAAATGGTAGCA
* * *
28465 ATATAATAGCAAAATGGTGGCA
1 AAATAACAGCAAAATGGTAGCA
* *
28487 AAATAACATCGAAATGGTAGCA
1 AAATAACAGCAAAATGGTAGCA
28509 AA
1 AA
28511 CAACAACAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.19
Consensus pattern (22 bp):
AAATAACAGCAAAATGGTAGCA
Found at i:31842 original size:30 final size:29
Alignment explanation
Indices: 31784--31842 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
31774 TAGAAATTAA
* * *
31784 ATTATTTTTAAGGATTAAATTAAATTTTT
1 ATTATTTTTAAGAATCAAAATAAATTTTT
*
31813 ATTATTTTTGAGAATCAAAATATAATTTTT
1 ATTATTTTTAAGAATCAAAATA-AATTTTT
31843 TAATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (29 bp):
ATTATTTTTAAGAATCAAAATAAATTTTT
Found at i:33306 original size:17 final size:17
Alignment explanation
Indices: 33259--33348 Score: 58
Period size: 18 Copynumber: 5.0 Consensus size: 17
33249 TTATTGCAAA
*
33259 ATTTTTAATTAATAATT
1 ATTTTTAATTTATAATT
* *
33276 -TTAAATTAAGTTATAATT
1 ATT--TTTAATTTATAATT
33294 ATTTTTAATTTATCATAATT
1 ATTTTTAA-TT-T-ATAATT
*
33314 -TTTATTAAATTATAATT
1 ATTT-TTAATTTATAATT
*
33331 ATTTTTAAATGTATAATT
1 ATTTTT-AATTTATAATT
33349 TTTCAATTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.04
17 12 0.21
18 25 0.45
19 7 0.12
20 10 0.18
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTTAATTTATAATT
Found at i:33313 original size:20 final size:17
Alignment explanation
Indices: 33288--33340 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
33278 AAATTAAGTT
33288 ATAATTATTTTTAATTTATC
1 ATAATTATTTTTAA---ATC
*
33308 ATAATT-TTTATTAAATT
1 ATAATTATTT-TTAAATC
33325 ATAATTATTTTTAAAT
1 ATAATTATTTTTAAAT
33341 GTATAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.47
18 3 0.10
19 3 0.10
20 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTTTAAATC
Found at i:33327 original size:37 final size:35
Alignment explanation
Indices: 33259--33338 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 35
33249 TTATTGCAAA
*
33259 ATTTTTAATTAATAATTTTAAATTAAGTTATAATT
1 ATTTTTAATTAATAATTTTAAATTAAATTATAATT
*
33294 ATTTTTAATTTATCATAATTTT-TATTAAATTATAATT
1 ATTTTTAA-TTA--ATAATTTTAAATTAAATTATAATT
33331 ATTTTTAA
1 ATTTTTAA
33339 ATGTATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 8 0.20
36 3 0.08
37 21 0.52
38 8 0.20
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTTTAATTAATAATTTTAAATTAAATTATAATT
Found at i:37665 original size:15 final size:15
Alignment explanation
Indices: 37647--37699 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
37637 TTAGATATTG
37647 AAATTTAATATTTTT
1 AAATTTAATATTTTT
37662 AAATTTAATATTTTT
1 AAATTTAATATTTTT
* *
37677 ATATTTAA-ATTTTC
1 AAATTTAATATTTTT
*
37691 AAGTTTAAT
1 AAATTTAAT
37700 TGTTAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
AAATTTAATATTTTT
Found at i:38237 original size:15 final size:15
Alignment explanation
Indices: 38217--38259 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
38207 CAAAGAATAG
38217 AAGAAAACAAGACAA
1 AAGAAAACAAGACAA
38232 AAGAAAA-AAGACAA
1 AAGAAAACAAGACAA
*
38246 AA-ATAACAAGACAA
1 AAGAAAACAAGACAA
38260 CGAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.62
15 7 0.27
ACGTcount: A:0.74, C:0.12, G:0.12, T:0.02
Consensus pattern (15 bp):
AAGAAAACAAGACAA
Found at i:38244 original size:14 final size:14
Alignment explanation
Indices: 38217--38275 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
38207 CAAAGAATAG
38217 AAGAAAACAAGACAA
1 AAGAAAA-AAGACAA
38232 AAGAAAAAAGACAA
1 AAGAAAAAAGACAA
*
38246 AA-ATAACAAGACAA
1 AAGA-AAAAAGACAA
* *
38260 CGAGAAAAAAAACAA
1 -AAGAAAAAAGACAA
38275 A
1 A
38276 TGTATTGAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 18 0.50
15 16 0.44
16 1 0.03
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAGACAA
Found at i:39375 original size:31 final size:31
Alignment explanation
Indices: 39273--39410 Score: 96
Period size: 31 Copynumber: 4.6 Consensus size: 31
39263 GTTTTAATTC
* * *
39273 AAATTTAATCTTTTTATTGTTT-TTCCCTTTTA
1 AAATTTAACCCTTTTATT-TTTATT-TCTTTTA
* * *
39305 AAA-TTCACCCATTTA-TTCTA-TT-TTTT-
1 AAATTTAACCCTTTTATTTTTATTTCTTTTA
* *
39331 AAATTAAATCCTTTTATTTTTATTT-TTGTTA
1 AAATTTAACCCTTTTATTTTTATTTCTT-TTA
* *
39362 AAATTTAACCCTTTAATTTTTGTTTCTTTTA
1 AAATTTAACCCTTTTATTTTTATTTCTTTTA
39393 AAA-TT-ACCCTTTTATTTT
1 AAATTTAACCCTTTTATTTT
39411 GTTTTTTTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 17
0.72 0.14 0.15
Matches are distributed among these distances:
26 3 0.04
27 12 0.14
28 4 0.05
29 19 0.23
30 5 0.06
31 35 0.42
32 5 0.06
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.59
Consensus pattern (31 bp):
AAATTTAACCCTTTTATTTTTATTTCTTTTA
Found at i:39455 original size:16 final size:17
Alignment explanation
Indices: 39436--39473 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
39426 CCCTTTATAT
*
39436 CTTTTTTAA-TTTAATC
1 CTTTTTAAAGTTTAATC
39452 CTTTTTAAAGTTTAATC
1 CTTTTTAAAGTTTAATC
39469 CTTTT
1 CTTTT
39474 ATCACTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (17 bp):
CTTTTTAAAGTTTAATC
Found at i:42209 original size:24 final size:24
Alignment explanation
Indices: 42174--42232 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
42164 TACAAGTACC
*
42174 CAGACTATCGATACTT-CTATGAA
1 CAGACTACCGATACTTACTATGAA
42197 CAGATCTACCGATACTTACTATG--
1 CAGA-CTACCGATACTTACTATGAA
42220 CA-ACTACCGATAC
1 CAGACTACCGATAC
42233 AACTCAAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 10 0.30
22 1 0.03
23 6 0.18
24 11 0.33
25 5 0.15
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (24 bp):
CAGACTACCGATACTTACTATGAA
Found at i:42821 original size:41 final size:41
Alignment explanation
Indices: 42761--42852 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 41
42751 AGTCGTAAAA
* * *
42761 CTTCCTCTTTAGATGATCTTATACT-TCATAGAATCGTAAGT
1 CTTCCTTTTTAAATAATCTTATACTCT-ATAGAATCGTAAGT
* * * * *
42802 CTTCCTTTTTAAATAATCTTGTGCTCTATCGAGTCGTAGGT
1 CTTCCTTTTTAAATAATCTTATACTCTATAGAATCGTAAGT
42843 CTTCCTTTTT
1 CTTCCTTTTT
42853 TTAAAACATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 41 0.98
42 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (41 bp):
CTTCCTTTTTAAATAATCTTATACTCTATAGAATCGTAAGT
Found at i:42904 original size:42 final size:42
Alignment explanation
Indices: 42856--43061 Score: 193
Period size: 42 Copynumber: 4.9 Consensus size: 42
42846 CCTTTTTTTA
* ** *
42856 AAACATAATCTCACGCTCATTCCGAGACATTTGTCTTTCTTT
1 AAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTT
* * * ** *
42898 AAACATAATCGCATTCTTACCCCAAGACATGAGTCTTCCTTT
1 AAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTT
* *
42940 AAACATAATCTCATTCCCA-TCTCGAGACATGAGTCTTCCTTT
1 AAACATAATCTCATGCTCATTC-CGAGACATGAGTCTTCCTTT
* * * *
42982 AAACAGATTCTCATGCTCATTCCGAGTCACGAGTCTTCCATTT
1 AAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCC-TTT
* *
43025 ATACA-AATTCTCATGCTCAATT-TGAGACATGAGTCTT
1 AAACATAA-TCTCATGCTC-ATTCCGAGACATGAGTCTT
43062 TCATTTATAC
Statistics
Matches: 133, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
41 1 0.01
42 98 0.74
43 31 0.23
44 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (42 bp):
AAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTT
Found at i:48299 original size:12 final size:12
Alignment explanation
Indices: 48282--48331 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
48272 AATTTCACCC
48282 AAAAAGAAGAAG
1 AAAAAGAAGAAG
48294 AAAAAGAAGAAG
1 AAAAAGAAGAAG
48306 AAAAA-AAG--G
1 AAAAAGAAGAAG
*
48315 -AAAAGAAAAAG
1 AAAAAGAAGAAG
48326 AAAAAG
1 AAAAAG
48332 GAAAGGTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
11 4 0.12
12 22 0.67
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:48300 original size:6 final size:6
Alignment explanation
Indices: 48282--48331 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
48272 AATTTCACCC
* * *
48282 AAAAAG AAGAAG AAAAAG AAGAAGAA AAAAAG GAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AA-AA-AG AAAAAG AAAAAG AAAAAG AAAAAG
48332 GAAAGGTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 29 0.81
7 4 0.11
8 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:48709 original size:27 final size:27
Alignment explanation
Indices: 48657--48710 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
48647 CATTTTTTAC
* *
48657 AATGTTTACAATTTTTATCCATTGTTT
1 AATGTTTACAATTTTTATACAATGTTT
*
48684 AATGTTTGCAATTTTT-TAACAATGTTT
1 AATGTTTACAATTTTTAT-ACAATGTTT
48711 GACATTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (27 bp):
AATGTTTACAATTTTTATACAATGTTT
Found at i:49398 original size:50 final size:50
Alignment explanation
Indices: 49306--49415 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
49296 TCTTACCTCT
* *
49306 CTGAAGATACAGTGAAGTAAGATGAAGCTACAACAACGAATATTATC-TC
1 CTGAAGATGCAGTGAAGTAAGATGAAGCTACAACAACAAATATTATCTTC
* ** *** *
49355 CTTGAAGATGCAGTGAGGTAAGATGAATTTACAATGTCAAATATTGTCTTC
1 C-TGAAGATGCAGTGAAGTAAGATGAAGCTACAACAACAAATATTATCTTC
49406 CTGAAGATGC
1 CTGAAGATGC
49416 GGCGAAACAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
49 1 0.02
50 46 0.92
51 3 0.06
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (50 bp):
CTGAAGATGCAGTGAAGTAAGATGAAGCTACAACAACAAATATTATCTTC
Found at i:49643 original size:99 final size:98
Alignment explanation
Indices: 49532--49714 Score: 235
Period size: 99 Copynumber: 1.9 Consensus size: 98
49522 GCTATGACAG
* * * * *
49532 CAAATCTATATCCTTGAAGTTACA-AGGATCAAAGTAAAACAAGTAGC-GAATCTCAATCTCCAC
1 CAAATCTATATCCCTGAAGTTACAGAGGATCAAAGTAAAAAAACTAACAG-ACCTCAATCTCC-C
49595 TGAAGTTGCAGTGGAATGGAGTAAATTCACAACCT
64 TGAAGTTGCAGTGGAATGGAGTAAATTCACAACCT
* * * *
49630 CAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTAAAAAAACTAACAGACCTCAATCTCCCT
1 CAAAT-CTATATCCCTGAAGTTACAGAGGATCAAAGTAAAAAAACTAACAGACCTCAATCTCCCT
*
49695 GAAGTTGTAGTGGAATGGAG
65 GAAGTTGCAGTGGAATGGAG
49715 CGAAGTTACC
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
98 5 0.07
99 38 0.53
100 28 0.39
101 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (98 bp):
CAAATCTATATCCCTGAAGTTACAGAGGATCAAAGTAAAAAAACTAACAGACCTCAATCTCCCTG
AAGTTGCAGTGGAATGGAGTAAATTCACAACCT
Found at i:49766 original size:99 final size:100
Alignment explanation
Indices: 49583--49769 Score: 220
Period size: 99 Copynumber: 1.9 Consensus size: 100
49573 AGTAGCGAAT
*
49583 CTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTAAATTCACAACCTCAAATCCTATATCCCTGA
1 CTCAATCTCCACTGAAGTTGCAGTGGAATGGAGGAAATTCACAACCTCAAATCCTATATCCCTGA
* * *
49648 AGTTGCAGTGGATCAGATTAAAAAAACTAACAGAC
66 AGTTACAGTGAAGCAGATTAAAAAAACTAACAGAC
* * * * * *
49683 CTCAATCTCC-CTGAAGTTGTAGTGGAATGGAGCGAAGTT-ACCATA-C-CAAATTCTATCTTCT
1 CTCAATCTCCACTGAAGTTGCAGTGGAATGGAG-GAAATTCA-CA-ACCTCAAATCCTATATCCC
*
49744 TGAAGTTACAGTGAAGCGGATTAAAA
63 TGAAGTTACAGTGAAGCAGATTAAAA
49770 CTATAGTAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
99 55 0.75
100 17 0.23
101 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (100 bp):
CTCAATCTCCACTGAAGTTGCAGTGGAATGGAGGAAATTCACAACCTCAAATCCTATATCCCTGA
AGTTACAGTGAAGCAGATTAAAAAAACTAACAGAC
Found at i:49966 original size:42 final size:40
Alignment explanation
Indices: 49828--49971 Score: 180
Period size: 40 Copynumber: 3.5 Consensus size: 40
49818 AAGTTACATC
* * * * * *
49828 ACCATCTAATCTTTTGCCCCAACCGGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGAAGATTAAAG
* *
49868 ACCATCCAATCTTTTACCCAAACCAGAGTGAAGATTAAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGAAGATTAAAG
* *
49908 ACCATCCAATATTTTACCCTAACTAGAGGGAAGATTAAAG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGAAGATTAAAG
49948 ACATCATCCAATCTTTTACCCTAA
1 AC--CATCCAATCTTTTACCCTAA
49972 TTAGAAGTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
40 71 0.79
42 19 0.21
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCTAACCAGAGGGAAGATTAAAG
Found at i:49985 original size:42 final size:40
Alignment explanation
Indices: 49859--50008 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
49849 ACCGGAGGGC
* * *
49859 AGATTGAAGACCATCCAATCTTTTACCCAAACCAG-AGTGA
1 AGATTAAAGACCATCCAATCTTTTACCCTAACTAGAAGT-A
* * *
49899 AGATTAAAGACCATCCAATATTTTACCCTAACTAGAGGGA
1 AGATTAAAGACCATCCAATCTTTTACCCTAACTAGAAGTA
* *
49939 AGATTAAAGACATCATCCAATCTTTTACCCTAATTAGAAGTT
1 AGATTAAAGAC--CATCCAATCTTTTACCCTAACTAGAAGTA
* * * * *
49981 AGATTGAAGATCATTCAGTCTTATACCC
1 AGATTAAAGACCATCCAATCTTTTACCC
50009 CAAATCTAGA
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 57 0.63
41 1 0.01
42 33 0.36
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (40 bp):
AGATTAAAGACCATCCAATCTTTTACCCTAACTAGAAGTA
Found at i:50068 original size:47 final size:47
Alignment explanation
Indices: 49999--50251 Score: 278
Period size: 47 Copynumber: 5.4 Consensus size: 47
49989 GATCATTCAG
* *
49999 TCTTATACCCCAAATCTAGAAGGTCAAATTAAAGTCATCCCATCCAA
1 TCTTATACCCCAAATCTAGAAGGGCAAATTAAAGCCATCCCATCCAA
* *
50046 TCTTATACCCAAAATCTAGAAGGGCAAATTGAAGCCATCCCATCCAA
1 TCTTATACCCCAAATCTAGAAGGGCAAATTAAAGCCATCCCATCCAA
* * *
50093 TCTTATACCCCAAATCTA-AGGGGCAGATTAAAGCTATCCCATCCAA
1 TCTTATACCCCAAATCTAGAAGGGCAAATTAAAGCCATCCCATCCAA
* * * * ** **
50139 TCTTTTACCCTAAATCAAAAAGGGCAAATTAAAGTTAT-CCATTTAA
1 TCTTATACCCCAAATCTAGAAGGGCAAATTAAAGCCATCCCATCCAA
** * * * *
50185 TCTTATACCTTAAATCTAG-AGAGGTAGATTGAAGCCATCACATCCAA
1 TCTTATACCCCAAATCTAGAAG-GGCAAATTAAAGCCATCCCATCCAA
*
50232 TCTTATAACCCAAATCTAGA
1 TCTTATACCCCAAATCTAGA
50252 GGGGTAGATT
Statistics
Matches: 170, Mismatches: 32, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
45 2 0.01
46 71 0.42
47 97 0.57
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (47 bp):
TCTTATACCCCAAATCTAGAAGGGCAAATTAAAGCCATCCCATCCAA
Found at i:50138 original size:93 final size:92
Alignment explanation
Indices: 49999--50266 Score: 288
Period size: 93 Copynumber: 2.9 Consensus size: 92
49989 GATCATTCAG
* * *
49999 TCTTATACCCCAAATCTAGAAGGTCAAATTAAAG-TCATCCCATCCAATCTTATACCCAAAATCT
1 TCTTATACCCCAAATCTAGAGGGGCAGATTAAAGCT-ATCCCATCCAATCTTATACCC-AAATCT
50063 AGAAGGGCAAATTGAAGCCATCCCATCCAA
64 AGAAGGGCAAATTGAAGCCAT-CCATCCAA
* *
50093 TCTTATACCCCAAATCTA-AGGGGCAGATTAAAGCTATCCCATCCAATCTTTTACCCTAAATCAA
1 TCTTATACCCCAAATCTAGAGGGGCAGATTAAAGCTATCCCATCCAATCTTATACCC-AAATCTA
* * ** **
50157 AAAGGGCAAATTAAAGTTATCCATTTAA
65 GAAGGGCAAATTGAAGCCATCCATCCAA
** * * * * *
50185 TCTTATACCTTAAATCTAGAGAGGTAGATTGAAGCCATCACATCCAATCTTATAACCCAAATCTA
1 TCTTATACCCCAAATCTAGAGGGGCAGATTAAAGCTATCCCATCCAATCTTAT-ACCCAAATCTA
* * *
50250 GAGGGGTAGATTGAAGC
65 GAAGGGCAAATTGAAGC
50267 TACCAGATTA
Statistics
Matches: 144, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
92 22 0.15
93 99 0.69
94 23 0.16
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (92 bp):
TCTTATACCCCAAATCTAGAGGGGCAGATTAAAGCTATCCCATCCAATCTTATACCCAAATCTAG
AAGGGCAAATTGAAGCCATCCATCCAA
Found at i:50216 original size:139 final size:141
Alignment explanation
Indices: 49999--50268 Score: 366
Period size: 139 Copynumber: 1.9 Consensus size: 141
49989 GATCATTCAG
* * *
49999 TCTTATACCCCAAATCTAGAAGGTCAAATTAAAGTCATCCCATCCAATCTTATACCCAAAATCTA
1 TCTTATACCCCAAATCAAAAAGGGCAAATTAAAGTCATCCCATCCAATCTTATACCCAAAATCTA
* *
50064 GAAGGGCAAATTGAAGCCATCCCATCCAATCTTATACCCCAAATCTA-AGGGGCAGATTAAAGCT
66 GAAGGGCAAATTGAAGCCATCACATCCAATCTTATAACCCAAATCTAGAGGGGCAGATTAAAGCT
50128 ATCCCATCCAA
131 ATCCCATCCAA
* * * ** **
50139 TCTTTTACCCTAAATCAAAAAGGGCAAATTAAAGTTAT-CCATTTAATCTTATACCTTAAATCTA
1 TCTTATACCCCAAATCAAAAAGGGCAAATTAAAGTCATCCCATCCAATCTTATACCCAAAATCTA
* * * *
50203 G-AGAGGTAGATTGAAGCCATCACATCCAATCTTATAACCCAAATCTAGAGGGGTAGATTGAAGC
66 GAAG-GGCAAATTGAAGCCATCACATCCAATCTTATAACCCAAATCTAGAGGGGCAGATTAAAGC
50267 TA
130 TA
50269 CCAGATTAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 2 0.02
139 62 0.55
140 48 0.43
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (141 bp):
TCTTATACCCCAAATCAAAAAGGGCAAATTAAAGTCATCCCATCCAATCTTATACCCAAAATCTA
GAAGGGCAAATTGAAGCCATCACATCCAATCTTATAACCCAAATCTAGAGGGGCAGATTAAAGCT
ATCCCATCCAA
Found at i:50252 original size:47 final size:46
Alignment explanation
Indices: 49952--50266 Score: 211
Period size: 47 Copynumber: 6.9 Consensus size: 46
49942 TTAAAGACAT
* * *
49952 CATCCAATCTT-TTACCCTAAT-TAGAAGTTAGATTGAAG--AT--
1 CATCCAATCTTATAACCCAAATCTAGAAGGTAGATTGAAGCCATCC
* * * * * *
49992 CATTCAGTCTTATACCCCAAATCTAGAAGGTCAAATTAAAGTCATCC
1 CATCCAATCTTATAACCCAAATCTAGAAGGT-AGATTGAAGCCATCC
* *
50039 CATCCAATCTTAT-ACCCAAAATCTAGAAGGGCAAATTGAAGCCATCC
1 CATCCAATCTTATAACCC-AAATCTAGAA-GGTAGATTGAAGCCATCC
* * * * *
50086 CATCCAATCTTATACCCCAAATCTA-AGGGGCAGATTAAAGCTATCC
1 CATCCAATCTTATAACCCAAATCTAGA-AGGTAGATTGAAGCCATCC
* * * * * * **
50132 CATCCAATCTT-TTACCCTAAATCAAAAAGGGCAAATTAAAGTTAT-C
1 CATCCAATCTTATAACCC-AAATCTAGAA-GGTAGATTGAAGCCATCC
** * *
50178 CATTTAATCTTAT-ACCTTAAATCTAGAGAGGTAGATTGAAGCCATCA
1 CATCCAATCTTATAACC-CAAATCTAGA-AGGTAGATTGAAGCCATCC
*
50225 CATCCAATCTTATAACCCAAATCTAGAGGGGTAGATTGAAGC
1 CATCCAATCTTATAACCCAAATCTAGA-AGGTAGATTGAAGC
50267 TACCAGATTA
Statistics
Matches: 216, Mismatches: 40, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
40 9 0.04
41 7 0.03
42 7 0.03
43 7 0.03
45 6 0.03
46 67 0.31
47 105 0.49
48 8 0.04
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (46 bp):
CATCCAATCTTATAACCCAAATCTAGAAGGTAGATTGAAGCCATCC
Found at i:50564 original size:12 final size:11
Alignment explanation
Indices: 50537--50569 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
50527 CCGGCCAATG
50537 AAAAATAAAAC
1 AAAAATAAAAC
50548 AAAAATAAAAC
1 AAAAATAAAAC
50559 ACAAAATAAAA
1 A-AAAATAAAA
50570 ATCCATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:50867 original size:14 final size:14
Alignment explanation
Indices: 50831--50869 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
50821 TTAGATCTGC
50831 AAAGAACAAAAGAAA
1 AAAG-ACAAAAGAAA
50846 ACAAGACAAAAGAAA
1 A-AAGACAAAAGAAA
50861 AAAGACAAA
1 AAAGACAAA
50870 CAACGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 12 0.52
16 3 0.13
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGACAAAAGAAA
Found at i:51976 original size:29 final size:27
Alignment explanation
Indices: 51933--52092 Score: 98
Period size: 30 Copynumber: 5.8 Consensus size: 27
51923 TGTTTTTCCC
* * *
51933 TTTTAAATTTTATCCATTTATTCTAATT
1 TTTTAAAATTAATCCTTTTATTCT-ATT
*
51961 TTTTAAAATTAAATCCTTTTATTTTTATT
1 TTTTAAAATT-AATCCTTTTA-TTCTATT
*
51990 TTGTTAAAATTTAACCCTTTTATT-T-TT
1 TT-TTAAAA-TTAATCCTTTTATTCTATT
*
52017 CTTTTAAAATT-ATCCTTTTATTCTTTTTAT
1 -TTTTAAAATTAATCCTTTTATTC--TAT-T
***
52047 TTTTATTTTTAATCCTTTTATATC--TT
1 TTTTAAAATTAATCCTTTTAT-TCTATT
*
52073 TTTT-AATTTAATCCTTTTAT
1 TTTTAAAATTAATCCTTTTAT
52093 CACTTTATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 27
0.74 0.07 0.18
Matches are distributed among these distances:
25 24 0.22
26 7 0.06
27 9 0.08
28 13 0.12
29 23 0.21
30 29 0.27
31 4 0.04
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTTAAAATTAATCCTTTTATTCTATT
Found at i:51999 original size:30 final size:29
Alignment explanation
Indices: 51944--52038 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 29
51934 TTTAAATTTT
* * *
51944 ATCCATTTATTCTAATTTTTTAAAATTAA
1 ATCCTTTTATTTTTATTTTTTAAAATTAA
*
51973 ATCCTTTTATTTTTATTTTGTTAAAATTTA
1 ATCCTTTTATTTTTATTTT-TTAAAATTAA
* *
52003 ACCCTTTTA-TTTT-TCTTTTAAAATT--
1 ATCCTTTTATTTTTATTTTTTAAAATTAA
52028 ATCCTTTTATT
1 ATCCTTTTATT
52039 CTTTTTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.14
26 1 0.02
27 8 0.14
28 3 0.05
29 20 0.35
30 17 0.30
ACGTcount: A:0.28, C:0.12, G:0.01, T:0.59
Consensus pattern (29 bp):
ATCCTTTTATTTTTATTTTTTAAAATTAA
Found at i:52033 original size:25 final size:27
Alignment explanation
Indices: 51932--52038 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 27
51922 TTGTTTTTCC
* * * *
51932 CTTTTAAATTTTATCCATTTATTCTAAT
1 CTTTTAAAATTAATCCTTTTATT-TTAT
*
51960 TTTTTAAAATTAAATCCTTTTATTTTTAT
1 CTTTTAAAATT-AATCCTTTTA-TTTTAT
* *
51989 TTTGTTAAAATTTAACCCTTTTATTTT-T
1 CTT-TTAAAA-TTAATCCTTTTATTTTAT
52017 CTTTTAAAATT-ATCCTTTTATT
1 CTTTTAAAATTAATCCTTTTATT
52039 CTTTTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
25 10 0.15
26 2 0.03
27 6 0.09
28 12 0.18
29 18 0.27
30 17 0.25
31 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.01, T:0.60
Consensus pattern (27 bp):
CTTTTAAAATTAATCCTTTTATTTTAT
Found at i:52655 original size:13 final size:13
Alignment explanation
Indices: 52637--52670 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52627 CCATGAATTT
52637 TTAGCATTCATCC
1 TTAGCATTCATCC
**
52650 TTAGCATTCATTT
1 TTAGCATTCATCC
52663 TTAGCATT
1 TTAGCATT
52671 TTTTATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (13 bp):
TTAGCATTCATCC
Found at i:61014 original size:17 final size:17
Alignment explanation
Indices: 60991--61046 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
60981 CATCACGTTC
*
60991 TCATTGTCATTACATTT
1 TCATTGTCATTGCATTT
*
61008 T-ATTTGTCACTGCATTT
1 TCA-TTGTCATTGCATTT
61025 TCATTGTCATTGCATTT
1 TCATTGTCATTGCATTT
*
61042 CCATT
1 TCATT
61047 TGTGATTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.52
Consensus pattern (17 bp):
TCATTGTCATTGCATTT
Found at i:61635 original size:17 final size:16
Alignment explanation
Indices: 61613--61646 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61603 CATATATAAA
*
61613 AAAAGAGAAGAGAAAAG
1 AAAAGAAAAGA-AAAAG
61630 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
61646 A
1 A
61647 TAGATGTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:66574 original size:23 final size:23
Alignment explanation
Indices: 66548--66591 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
66538 TAAATATTAT
*
66548 TTTATTAATATTTTAATTAGATA
1 TTTATTAATATCTTAATTAGATA
* *
66571 TTTATTATTATCTTATTTAGA
1 TTTATTAATATCTTAATTAGA
66592 AAATTGTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTAATATCTTAATTAGATA
Found at i:66860 original size:23 final size:23
Alignment explanation
Indices: 66834--66904 Score: 56
Period size: 26 Copynumber: 2.9 Consensus size: 23
66824 TGAAAGTGGA
66834 GAAAAATGAGAAGAAAAAAGATG
1 GAAAAATGAGAAGAAAAAAGATG
*
66857 G-AAAATGGTGAAGAAAAGAA-ATG
1 GAAAAAT-GAGAAGAAAA-AAGATG
*
66880 CATGAAAATGAGGAAGAAAGAAAGA
1 GA--AAAATGA-GAAGAAA-AAAGA
66905 AATTCTTGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
22 5 0.14
23 13 0.35
24 2 0.05
25 1 0.03
26 14 0.38
27 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.28, T:0.10
Consensus pattern (23 bp):
GAAAAATGAGAAGAAAAAAGATG
Found at i:74262 original size:34 final size:34
Alignment explanation
Indices: 74219--74286 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
74209 CGAGACAAAT
74219 GGTCAGCTACTTGATTCTCAGATCCTTTCCTATC
1 GGTCAGCTACTTGATTCTCAGATCCTTTCCTATC
74253 GGTCAGCTACTTGATTCTCAGATCCTTTCCTATC
1 GGTCAGCTACTTGATTCTCAGATCCTTTCCTATC
74287 TCTGATTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (34 bp):
GGTCAGCTACTTGATTCTCAGATCCTTTCCTATC
Found at i:87710 original size:23 final size:23
Alignment explanation
Indices: 87684--87729 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
87674 AGTCAGGACC
87684 ATATCATGTAAGACCTAGTTTGG
1 ATATCATGTAAGACCTAGTTTGG
87707 ATATCATGTAAGACCTAGTTTGG
1 ATATCATGTAAGACCTAGTTTGG
87730 GAGTACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (23 bp):
ATATCATGTAAGACCTAGTTTGG
Found at i:89596 original size:10 final size:10
Alignment explanation
Indices: 89581--89611 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
89571 TTTATAGCAG
89581 TATTTCTTTT
1 TATTTCTTTT
89591 TATTTCTTTT
1 TATTTCTTTT
89601 TATTTCTTTT
1 TATTTCTTTT
89611 T
1 T
89612 TCTTTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTCTTTT
Found at i:89627 original size:17 final size:17
Alignment explanation
Indices: 89585--89627 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
89575 TAGCAGTATT
89585 TCTTTTTATTTCTTTTTA
1 TCTTTTT-TTTCTTTTTA
*
89603 T-TTCTTTTTTCTTTTTC
1 TCTT-TTTTTTCTTTTTA
89620 TCTTTTTT
1 TCTTTTTT
89628 CTATTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
TCTTTTTTTTCTTTTTA
Found at i:89627 original size:27 final size:27
Alignment explanation
Indices: 89583--89638 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
89573 TATAGCAGTA
89583 TTTCTTTTTATTTCTTTT-TATTTCTTT
1 TTTCTTTTTATTTCTTTTCTA-TTCTTT
*
89610 TTTCTTTTTCTCTT-TTTTCTATTCTTT
1 TTTCTTTTTAT-TTCTTTTCTATTCTTT
89637 TT
1 TT
89639 CACATTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTCTTTTTATTTCTTTTCTATTCTTT
Found at i:100120 original size:30 final size:28
Alignment explanation
Indices: 100051--100104 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
100041 TGATAAGTGA
*
100051 AAGCCTTTGTGGTTGCTTTGATATGTAG
1 AAGCCTTTGTGGTGGCTTTGATATGTAG
*
100079 AAGCCTTTGTGGTGGCTTTGTTATGT
1 AAGCCTTTGTGGTGGCTTTGATATGT
100105 GTGTGAGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (28 bp):
AAGCCTTTGTGGTGGCTTTGATATGTAG
Found at i:103527 original size:30 final size:30
Alignment explanation
Indices: 103391--103535 Score: 123
Period size: 29 Copynumber: 4.9 Consensus size: 30
103381 TTTTAAGGAT
* * *
103391 AGTGGTAAAATTGTAAAATTTGGAAAAAT-
1 AGTGGCAAAATTGTAAAATCTAGAAAAATC
* * *
103420 AATGGCAGAATTGTAAAATCTCGAAAAA-C
1 AGTGGCAAAATTGTAAAATCTAGAAAAATC
* * * * *
103449 AGCGGCAAAACTATAAAATCTGGAAAAGAAC
1 AGTGGCAAAATTGTAAAATCTAGAAAA-ATC
* * *
103480 AGTGGTAAAATTCTAAAATTTAGAAAAATC
1 AGTGGCAAAATTGTAAAATCTAGAAAAATC
* *
103510 AGTGGAAAAACTGTAAAATCTAGAAA
1 AGTGGCAAAATTGTAAAATCTAGAAA
103536 TATAATGACA
Statistics
Matches: 91, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
29 44 0.48
30 25 0.27
31 22 0.24
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (30 bp):
AGTGGCAAAATTGTAAAATCTAGAAAAATC
Found at i:104466 original size:35 final size:34
Alignment explanation
Indices: 104422--104490 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
104412 ATAGTTTTAA
* *
104422 AATTCCAATTCATTCACATATTATAAACAATCAAG
1 AATTCCAATTAATTCACA-ATCATAAACAATCAAG
* *
104457 AATTTCAATTAATTCATAATCATAAACAATCAAG
1 AATTCCAATTAATTCACAATCATAAACAATCAAG
104491 TAAGTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (34 bp):
AATTCCAATTAATTCACAATCATAAACAATCAAG
Found at i:105059 original size:3 final size:3
Alignment explanation
Indices: 105051--105113 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
105041 ATAAAACGAA
105051 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
105099 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
105114 CAATCAATCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:106387 original size:29 final size:28
Alignment explanation
Indices: 106355--106497 Score: 97
Period size: 29 Copynumber: 4.8 Consensus size: 28
106345 AAATAGTTAT
106355 AAAACTGTAAAATTTGCAAAACTAGTGGC
1 AAAACTGTAAAATTTG-AAAACTAGTGGC
* * *
106384 AAAACTGTAAAATCTAGAAAAAAAAATAATGGC
1 AAAACTGTAAAAT-TTG----AAAACTAGTGGC
* * *
106417 AAAATTCTAAAATCTAGAAAACTAGTGGC
1 AAAACTGTAAAAT-TTGAAAACTAGTGGC
* * *
106446 AAAATTGTAAAATTTGGAAAATTTAGTGAC
1 AAAACTGTAAAATTT-GAAAA-CTAGTGGC
* *
106476 AGAACTGTAAAATCTGTAAAAC
1 AAAACTGTAAAATTTG-AAAAC
106498 GGTGGTACAT
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
28 1 0.01
29 41 0.45
30 24 0.26
33 25 0.27
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.24
Consensus pattern (28 bp):
AAAACTGTAAAATTTGAAAACTAGTGGC
Found at i:106466 original size:62 final size:62
Alignment explanation
Indices: 106315--106466 Score: 180
Period size: 62 Copynumber: 2.5 Consensus size: 62
106305 TTTTTAAGAA
* * * * * * *
106315 TAGTGACAAAATTGTAAAATCTGAAAAAAAAAATAGTTATAAAACTGTAAAATTTGCAAAAC
1 TAGTGGCAAAATTGTAAAATCTGGAAAAAAAAATAATGACAAAACTCTAAAATTAGCAAAAC
* * * *
106377 TAGTGGCAAAACTGTAAAATCTAGAAAAAAAAATAATGGCAAAATTCTAAAATCTAG-AAAAC
1 TAGTGGCAAAATTGTAAAATCTGGAAAAAAAAATAATGACAAAACTCTAAAAT-TAGCAAAAC
*
106439 TAGTGGCAAAATTGTAAAATTTGGAAAA
1 TAGTGGCAAAATTGTAAAATCTGGAAAA
106467 TTTAGTGACA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
62 73 0.97
63 2 0.03
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (62 bp):
TAGTGGCAAAATTGTAAAATCTGGAAAAAAAAATAATGACAAAACTCTAAAATTAGCAAAAC
Found at i:106932 original size:27 final size:26
Alignment explanation
Indices: 106892--106948 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
106882 AAGAAAGATA
106892 AATTCTATTAGGATTTGAAAAGGAGT
1 AATTCTATTAGGATTTGAAAAGGAGT
* *
106918 AATTCTAGTTAGGATTTTAAAAGGATT
1 AATTCTA-TTAGGATTTGAAAAGGAGT
106945 AATT
1 AATT
106949 TAGGATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (26 bp):
AATTCTATTAGGATTTGAAAAGGAGT
Found at i:107217 original size:131 final size:128
Alignment explanation
Indices: 107081--107339 Score: 317
Period size: 131 Copynumber: 2.0 Consensus size: 128
107071 AGAATGACAA
* * * * **
107081 TTCATACTGCAAAAAC-ATTGTTCGTTGTGT-ATTCACAGCCTTAATAGATTCCAACTGTGACTT
1 TTCATACT-AAAAAACGAATGTTCGTTGTGTAATT-ACAGCCTTAACAGATTCCAAATGCAACTT
* * * *
107144 TATTTACTGGGT-ATCCACGATCCCTCTGACAACTTTTTTTTTTTGCGAGTGGTTGTGGATCCTC
64 TATTTACTGGGTGA-CCACGATCCCTCTGACAAC---TTCTATCTGCGAGTGGTTGTGAATCCTC
107208 AGCC
125 AGCC
*
107212 TTCATACTAAAAAACGAATGTTCGTTGTGTAATTACAGCCTTAGCAGATTCCAAATGCAACTTTA
1 TTCATACTAAAAAACGAATGTTCGTTGTGTAATTACAGCCTTAACAGATTCCAAATGCAACTTTA
* * *
107277 TTTATTGGGTGACCACTATCCCTCTGACAGCTTCTATCTGCGAGTGGTTGTGAATCCTCAGCC
66 TTTACTGGGTGACCACGATCCCTCTGACAACTTCTATCTGCGAGTGGTTGTGAATCCTCAGCC
107340 AAATAACAGC
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 28 0.25
130 6 0.05
131 73 0.66
132 4 0.04
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (128 bp):
TTCATACTAAAAAACGAATGTTCGTTGTGTAATTACAGCCTTAACAGATTCCAAATGCAACTTTA
TTTACTGGGTGACCACGATCCCTCTGACAACTTCTATCTGCGAGTGGTTGTGAATCCTCAGCC
Found at i:112669 original size:30 final size:29
Alignment explanation
Indices: 112628--112745 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 29
112618 CGAACATCCA
*
112628 GGGGT-AAAATGGTAATTTTTTGAAG-TTC
1 GGGGTAAAAATGG-AATTTTTAGAAGTTTC
112656 GAGGGTAAAAATGGAA-TTTTAGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTA-GAAGTTTC
*
112686 GGGGGTCAAAAAT-GAGATTTTTAGAAGTTTT
1 -GGGGT-AAAAATGGA-ATTTTTAGAAGTTTC
* *
112717 GGGGTAAAAATAGAATTTTTGGACAGTTT
1 GGGGTAAAAATGGAATTTTTAGA-AGTTT
112746 AGGGACCTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
28 5 0.06
29 24 0.31
30 28 0.36
31 15 0.19
32 5 0.06
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTAGAAGTTTC
Done.