Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015329.1 Kokia drynarioides strain JFW-HI SEQ_130376, 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: 69773
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:413 original size:13 final size:13
Alignment explanation
Indices: 395--422 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
385 CTTTTATAAC
395 CTTTTCATCATTT
1 CTTTTCATCATTT
408 CTTTTCATCATTT
1 CTTTTCATCATTT
421 CT
1 CT
423 CTAGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTTTCATCATTT
Found at i:3848 original size:61 final size:61
Alignment explanation
Indices: 3750--3922 Score: 240
Period size: 61 Copynumber: 2.8 Consensus size: 61
3740 TCGACAAATT
* *
3750 AGAAAGCCTTTGTGGTGAGTAATAAATGTTAATGAACGCCTTTATGGAAAAACTCTAGACA
1 AGAAAACCTTTGTGGTGAGTAATAAATGTTAAGGAACGCCTTTATGGAAAAACTCTAGACA
* * * *
3811 AGAAAACCTTTTTGGTGAGTACTAAATGTTAAGGAACGCCTTTGTGGCAAAACTCTAGACA
1 AGAAAACCTTTGTGGTGAGTAATAAATGTTAAGGAACGCCTTTATGGAAAAACTCTAGACA
* * * *
3872 A-AAAAGCCTTTGTGGCGAGTATTGAATGTTAAGGAACACCTTTATGGAAAA
1 AGAAAA-CCTTTGTGGTGAGTAATAAATGTTAAGGAACGCCTTTATGGAAAA
3923 TTTCTAAAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
60 4 0.04
61 94 0.96
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (61 bp):
AGAAAACCTTTGTGGTGAGTAATAAATGTTAAGGAACGCCTTTATGGAAAAACTCTAGACA
Found at i:4042 original size:28 final size:28
Alignment explanation
Indices: 3963--4059 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
3953 ACTGAATGGA
* * *
3963 AAAGGAA-GCCTTCGTGGTTGTCTCTAT
1 AAAGGAATGCCTTCGTGGCTATCTCTGT
* * *
3990 AAAGGAAATGCCTTTGTGACAATCTCTGTT
1 AAAGG-AATGCCTTCGTGGCTATCTCTG-T
**
4020 AAAGGAA-GCCTTCGTGGCTATCTAAGT
1 AAAGGAATGCCTTCGTGGCTATCTCTGT
4047 AAAGGAATGCCTT
1 AAAGGAATGCCTT
4060 AATGGCGAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
27 13 0.24
28 21 0.38
29 15 0.27
30 6 0.11
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (28 bp):
AAAGGAATGCCTTCGTGGCTATCTCTGT
Found at i:11614 original size:27 final size:27
Alignment explanation
Indices: 11583--11641 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
11573 GCGAACTTCA
*
11583 AAGAAGACGT-CATTTTGGCAAACTCTG
1 AAGAAGA-GTCCATTGTGGCAAACTCTG
* *
11610 AAGAAGATTCCATTGTGGCACACTCTG
1 AAGAAGAGTCCATTGTGGCAAACTCTG
11637 AAGAA
1 AAGAA
11642 ATGGTACTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
AAGAAGAGTCCATTGTGGCAAACTCTG
Found at i:12074 original size:23 final size:23
Alignment explanation
Indices: 12043--12089 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12033 AGATGTGAAG
*
12043 GGTAAGACAAGATTTCAAGGTAA
1 GGTAAGACAAGATTTCAAAGTAA
* * *
12066 GGTATGACATGTTTTCAAAGTAA
1 GGTAAGACAAGATTTCAAAGTAA
12089 G
1 G
12090 TACGACGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (23 bp):
GGTAAGACAAGATTTCAAAGTAA
Found at i:13270 original size:20 final size:20
Alignment explanation
Indices: 13243--13282 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
13233 TATCATAATG
*
13243 TAAAAAAATATTTAAAATTAA
1 TAAAAAAA-ATTAAAAATTAA
13264 TAAAAAAAATTAAAAATTA
1 TAAAAAAAATTAAAAATTA
13283 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAAATTAAAAATTAA
Found at i:15181 original size:32 final size:31
Alignment explanation
Indices: 15145--15211 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
15135 AGTGAACTGT
15145 GAGGATTGAG-TGAAATTAAAAGAGAATTGAGA
1 GAGGATTGAGAT-AAATTAAAAGAGAATT-AGA
* *
15177 GAGGATTGAGAATAAATTGAAAGAGAGTTAGA
1 GAGGATTGAG-ATAAATTAAAAGAGAATTAGA
15209 GAG
1 GAG
15212 TGAATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 16 0.52
33 14 0.45
34 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.21
Consensus pattern (31 bp):
GAGGATTGAGATAAATTAAAAGAGAATTAGA
Found at i:15410 original size:29 final size:30
Alignment explanation
Indices: 15363--15425 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
15353 CCCTCTCTCC
*
15363 AAATCGACCTAATCCGATAAATTTAA-AAA
1 AAATCAACCTAATCCGATAAATTTAATAAA
** *
15392 AAATCAACCTAATTTGATAATTTTAATAAA
1 AAATCAACCTAATCCGATAAATTTAATAAA
15422 AAAT
1 AAAT
15426 GAGCATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATCAACCTAATCCGATAAATTTAATAAA
Found at i:17609 original size:33 final size:33
Alignment explanation
Indices: 17539--17609 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
17529 TTCATGTACC
** **
17539 AATTAAATATTTTTTTTGACAAATTTAAGTAGT
1 AATTAAATATTTTTTTTGACAAATTTAAAAACA
*
17572 AATTAAATA-TTTTTTTGAGAAATTTAAAAAACA
1 AATTAAATATTTTTTTTGACAAATTT-AAAAACA
17605 AATTA
1 AATTA
17610 CATTAACTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (33 bp):
AATTAAATATTTTTTTTGACAAATTTAAAAACA
Found at i:17760 original size:7 final size:7
Alignment explanation
Indices: 17748--17773 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17738 TACATGCAGA
17748 AAGGTTG
1 AAGGTTG
17755 AAGGTTG
1 AAGGTTG
17762 AAGGTTG
1 AAGGTTG
17769 AAGGT
1 AAGGT
17774 GATTCCAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (7 bp):
AAGGTTG
Found at i:21191 original size:31 final size:32
Alignment explanation
Indices: 21155--21235 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 32
21145 TTTGTGTTAG
21155 GACTAAAATT-TCAAAATTCAAAAAGTA-AAGA
1 GACTAAAATTGTC-AAATTCAAAAAGTATAAGA
*
21186 GACTAAAATTGTCCAATTCAAAAAGTATAAGA
1 GACTAAAATTGTCAAATTCAAAAAGTATAAGA
*
21218 -TCTAAAATTGATCAAATT
1 GACTAAAATTG-TCAAATT
21236 AAAGTATAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 32 0.73
32 12 0.27
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (32 bp):
GACTAAAATTGTCAAATTCAAAAAGTATAAGA
Found at i:21381 original size:35 final size:35
Alignment explanation
Indices: 21304--21382 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
21294 AACCAACTTT
21304 TAAAGT-AT-ATTATTTTTAAAATAATATAAAAGG
1 TAAAGTGATAATTATTTTTAAAATAATATAAAAGG
* * * * *
21337 TTAATTGATAATTATTATTTTAAA-AATATTACAGG
1 TAAAGTGATAATTATT-TTTAAAATAATATAAAAGG
21372 TAAAGTGATAA
1 TAAAGTGATAA
21383 AAAATACATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
33 4 0.11
34 2 0.06
35 24 0.67
36 6 0.17
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (35 bp):
TAAAGTGATAATTATTTTTAAAATAATATAAAAGG
Found at i:29569 original size:16 final size:15
Alignment explanation
Indices: 29529--29584 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
29519 AATGTAATCC
29529 AAAA-AAAAA-ATTA
1 AAAATAAAAATATTA
29542 AAAATATAAAATATTA
1 AAAATA-AAAATATTA
29558 ATAAATAAAAATCATATGA
1 A-AAATAAAAAT-AT-T-A
29577 AAAATAAA
1 AAAATAAA
29585 TTAATTTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.11
14 1 0.03
15 4 0.11
16 10 0.28
17 7 0.19
18 8 0.22
19 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAATAAAAATATTA
Found at i:31311 original size:21 final size:21
Alignment explanation
Indices: 31287--31326 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31277 ACTCTCTCCC
*
31287 AAATCT-ATAAATTTCTCAATT
1 AAATCTCA-AAATCTCTCAATT
31308 AAATCTCAAAATCTCTCAA
1 AAATCTCAAAATCTCTCAA
31327 ATATTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATCTCAAAATCTCTCAATT
Found at i:31340 original size:12 final size:12
Alignment explanation
Indices: 31319--31352 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31309 AATCTCAAAA
*
31319 TCTCTCAAATAT
1 TCTCTTAAATAT
31331 TCTCTTAAATAT
1 TCTCTTAAATAT
*
31343 TTTCTTAAAT
1 TCTCTTAAAT
31353 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTTAAATAT
Found at i:33966 original size:30 final size:30
Alignment explanation
Indices: 33930--34296 Score: 320
Period size: 30 Copynumber: 12.3 Consensus size: 30
33920 GGAGAATTTG
* * *
33930 GGGTTAAAATATAATTTTGGAAAAATTTAA
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
* *
33960 GGGTTAAAATAT-ATTTTAGGAAAA-TTTGA
1 GGGTTAAAATGTGATTTT-GGAAAAGTTTAA
* *
33989 GGGTCAAAATGTGATTTT-GAGAAGGTTTAA
1 GGGTTAAAATGTGATTTTGGA-AAAGTTTAA
* * * * *
34019 AGGTCAAAATTTGATTTTAGGGAAA-TTTAG
1 GGGTTAAAATGTGATTTT-GGAAAAGTTTAA
*
34049 GGGGTAAAATGTGATTTTAGG-AAAGTTT-A
1 GGGTTAAAATGTGATTTT-GGAAAAGTTTAA
* *
34078 GGGTTAAGATGTGATTTT-AAGAAAGTTTAA
1 GGGTTAAAATGTGATTTTGGA-AAAGTTTAA
* * * *
34108 GGGTGAAAATGTGATTTTCGTAAAGTTTAT
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
* *
34138 GGGTCAAAATGTGATTTTGGAAAAGTTTTGA
1 GGGTTAAAATGTGATTTTGGAAAAG-TTTAA
*
34169 GGGTTAAAATGTAATTTTGGAAAAGTTT-A
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
** * *
34198 GTTTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
* * * * *
34228 GGGTGAAAACGTAATTTTGGAAAGGTTT-G
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
* *
34257 GGGTTAAAATGTGATTTTAGAAAAGTTTGA
1 GGGTTAAAATGTGATTTTGGAAAAGTTTAA
34287 GGGTTAAAAT
1 GGGTTAAAAT
34297 ATAATTTTTA
Statistics
Matches: 279, Mismatches: 44, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.01
29 98 0.35
30 150 0.54
31 28 0.10
32 1 0.00
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTGGAAAAGTTTAA
Found at i:34007 original size:59 final size:59
Alignment explanation
Indices: 33924--34304 Score: 339
Period size: 59 Copynumber: 6.4 Consensus size: 59
33914 AGTTTCGGAG
* * *
33924 AATTTG-GGGTTAAAATATAATTTTGGAAAAATTTAAGGGTTAAAATAT-ATTTTAGGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATGTGATTTTAGGAA
* * * * * * *
33982 AATTTGAGGGTCAAAATGTGATTTT-GAGAAGGTTTAAAGGTCAAAATTTGATTTTAGGGA
1 AATTTGAGGGTTAAAATGTAATTTTGGA-AAAGTTT-AGGGTTAAAATGTGATTTTAGGAA
* * * *
34042 AATTT-AGGGGGTAAAATGTGATTTTAGG-AAAGTTTAGGGTTAAGATGTGATTTTAAGAA
1 AATTTGA-GGGTTAAAATGTAATTTT-GGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAA
* * * * * * *
34101 AGTTTAAGGGTGAAAATGTGATTTTCGTAAAGTTTATGGGTCAAAATGTGATTTT-GGAA
1 AATTTGAGGGTTAAAATGTAATTTTGGAAAAGTTTA-GGGTTAAAATGTGATTTTAGGAA
** *
34160 AAGTTTTGAGGGTTAAAATGTAATTTTGGAAAAGTTTAGTTTTAAAATGTAATTTT-GGAA
1 AA--TTTGAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAA
* * * *
34220 AAGTTT-AGGGGTGAAAACGTAATTTTGGAAAGGTTTGGGGTTAAAATGTGATTTTA-GAA
1 AA-TTTGA-GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAA
*
34279 AAGTTTGAGGGTTAAAATATAATTTT
1 AA-TTTGAGGGTTAAAATGTAATTTT
34305 TAAATAAAAT
Statistics
Matches: 263, Mismatches: 46, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
58 10 0.04
59 149 0.57
60 74 0.28
61 29 0.11
62 1 0.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.37
Consensus pattern (59 bp):
AATTTGAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAA
Found at i:34045 original size:89 final size:89
Alignment explanation
Indices: 33952--34284 Score: 290
Period size: 89 Copynumber: 3.7 Consensus size: 89
33942 AATTTTGGAA
* * *
33952 AAATTTAAGGGTTAAAATAT-ATTTTAGGAAAATTTGAGGGTCAAAATGTGATTTTGAGAAGGTT
1 AAATTTAAGGGTTAAAATGTGATTTTAGGAAAATTTGAGGGTTAAAATGTGATTTTGAGAAAGTT
* *
34016 TAAAGGTCAAAATTTGATTTTAGGG
66 TAAAGGTCAAAATGTGATTTT-CGG
* * * * *
34041 AAATTTAGGGGGTAAAATGTGATTTTAGGAAAGTTT-AGGGTTAAGATGTGATTTTAAGAAAGTT
1 AAATTTAAGGGTTAAAATGTGATTTTAGGAAAATTTGAGGGTTAAAATGTGATTTTGAGAAAGTT
* * *
34105 TAAGGGTGAAAATGTGATTTTCGT
66 TAAAGGTCAAAATGTGATTTTCGG
* * *
34129 AAAGTTTATGGGTCAAAATGTGATTTT-GGAAAAGTTTTGAGGGTTAAAATGTAATTTTG-GAAA
1 AAA-TTTAAGGGTTAAAATGTGATTTTAGGAAAA--TTTGAGGGTTAAAATGTGATTTTGAG-AA
* * *
34192 AGTTT--AGTTTTAAAATGTAATTTT-GG
62 AGTTTAAAG-GTCAAAATGTGATTTTCGG
* * * * *
34218 AAAAGTTTAGGGGTGAAAACGTAATTTT-GGAAAGGTTTG-GGGTTAAAATGTGATTTT-AGAAA
1 -AAA-TTTAAGGGTTAAAATGTGATTTTAGGAAA-ATTTGAGGGTTAAAATGTGATTTTGAG-AA
34280 AGTTT
62 AGTTT
34285 GAGGGTTAAA
Statistics
Matches: 203, Mismatches: 31, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
88 35 0.17
89 85 0.42
90 59 0.29
91 24 0.12
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (89 bp):
AAATTTAAGGGTTAAAATGTGATTTTAGGAAAATTTGAGGGTTAAAATGTGATTTTGAGAAAGTT
TAAAGGTCAAAATGTGATTTTCGG
Found at i:35317 original size:13 final size:12
Alignment explanation
Indices: 35295--35341 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
35285 CGTTTTCTGC
35295 AATA-AATAATA
1 AATATAATAATA
35306 AATGATAATAAT-
1 AAT-ATAATAATA
35318 AATATAATAAATA
1 AATATAAT-AATA
*
35331 AATATATTAAT
1 AATATAATAAT
35342 GTGTATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 8 0.26
12 10 0.32
13 13 0.42
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AATATAATAATA
Found at i:36796 original size:49 final size:49
Alignment explanation
Indices: 36738--37168 Score: 337
Period size: 49 Copynumber: 8.7 Consensus size: 49
36728 ATATTTCTAA
* * * * *
36738 GGTATCGGGTTCACCGTTGCAGCTTCAACCTTTCCCTTCATATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
** * *
36787 GGTACCGGGTTTACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTC-AT
* * * * * *
36837 GGTACCAGATTCGTCATTGTGGCCTCAATCC-TTCCCTTCAAATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCACATCTTCAT
** * * * * *
36886 GGTACCGGGTTCGCCGCAGCAGCCTTAACCTTTCCCATCACATCTTTTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC-TTCAT
* ** * * *
36936 GGTACTGGGTTCGTTGTTGTGGCCTCAACCTTTCCCTTCATATGTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* * * * *
36985 GGTATCGGGTTTGCCGTTGCGACCTCAACTTTTCCCATT-ACATCTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC-TTCACATCTTC-AT
* * * * * * * *
37035 GGTATCGGATTCGCAGTTGCAGCCTCAATCC-TTCCCTTTAAACCCTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCACATCTTCAT
* * * *
37084 GGTACCGGGTTCACCGTTGCGGCATCCACCTTTCCCTTCATATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
** * **
37133 GGTATAGGGTTTGCTATTGCGGCCTCAACCTTTCCC
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
37169 ATCGCGCCGT
Statistics
Matches: 290, Mismatches: 83, Indels: 18
0.74 0.21 0.05
Matches are distributed among these distances:
48 4 0.01
49 175 0.60
50 108 0.37
51 3 0.01
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (49 bp):
GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
Found at i:36916 original size:99 final size:98
Alignment explanation
Indices: 36769--37130 Score: 395
Period size: 99 Copynumber: 3.7 Consensus size: 98
36759 GCTTCAACCT
* **
36769 TTCCCTTCATATCTTCATGGTACCGGGTTTACCGTTGCGGCCTCAACCTTTCCCATCACATCTTC
1 TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGC-GCCTCAACCTTTCCCATCACATCTTC
*
36834 TAAGGTACCAGATTCGTCATTGTGGCCTCAATCC
65 TAAGGTACCGGATTCGTCATTGTGGCCTCAATCC
** * *
36868 TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGCAGCAGCCTTAACCTTTCCCATCACATCTTT
1 TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGC-GCCTCAACCTTTCCCATCACATCTTC
* * **
36933 TAAGGTACTGGGTTCGTTGTTGTGGCCTCAA-CC
65 TAAGGTACCGGATTCGTCATTGTGGCCTCAATCC
* * * * * *
36966 TTTCCCTTCATATGTTCATGGTATCGGGTTTGCCGTTGCGACCTCAACTTTTCCCATTACATCTT
1 -TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCG-CCTCAACCTTTCCCATCACATCTT
* **
37031 CTAAGGTATCGGATTCG-CAGTTGCAGCCTCAATCC
64 CTAAGGTACCGGATTCGTCA-TTGTGGCCTCAATCC
* * * * * * * *
37066 TTCCCTTTAAACCCTCATGGTACCGGGTTCACCGTTGCGGCATCCACCTTTCCCTTCATATCTTC
1 TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGC-GCCTCAACCTTTCCCATCACATCTTC
37131 ATGGTATAGG
Statistics
Matches: 214, Mismatches: 44, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
98 3 0.01
99 208 0.97
100 3 0.01
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (98 bp):
TTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCGCCTCAACCTTTCCCATCACATCTTCT
AAGGTACCGGATTCGTCATTGTGGCCTCAATCC
Found at i:37030 original size:148 final size:148
Alignment explanation
Indices: 36787--37170 Score: 328
Period size: 148 Copynumber: 2.6 Consensus size: 148
36777 ATATCTTCAT
* * * * * * * * *
36787 GGTACCGGGTTTACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCA-GATTCGT
1 GGTACCGGGTTCACCGTTGCGGCATCAACCTTTCCCTTCATATCTTC-ATGGTA-TAGGGTTTGC
* * * * * * *
36851 CATTGTGGCCTCAATCC-TTCCC-TTCAAATCTTC-ATGGTACCGGGTTCGCCGCAGCAGCCTTA
64 CATTGCGACCTCAA-CCTTTCCCATT-ACATCTTCTAAGGTACCGGATTCGCAGCAGCAGCCTCA
* ** *
36913 A-CCTTTCCCATCACATCTTTTAA
127 ATCC-TTCCCATCA-AACCCTCAA
* *** * * * * *
36936 GGTACTGGGTTCGTTGTTGTGGCCTCAACCTTTCCCTTCATATGTTCATGGTATCGGGTTTGCCG
1 GGTACCGGGTTCACCGTTGCGGCATCAACCTTTCCCTTCATATCTTCATGGTATAGGGTTTGCCA
* * **
37001 TTGCGACCTCAACTTTTCCCATTACATCTTCTAAGGTATCGGATTCGCAGTTGCAGCCTCAATCC
66 TTGCGACCTCAACCTTTCCCATTACATCTTCTAAGGTACCGGATTCGCAGCAGCAGCCTCAATCC
* * *
37066 TTCCCTTTAAACCCTCAT
131 TTCCCATCAAACCCTCAA
* *
37084 GGTACCGGGTTCACCGTTGCGGCATCCACCTTTCCCTTCATATCTTCATGGTATAGGGTTTGCTA
1 GGTACCGGGTTCACCGTTGCGGCATCAACCTTTCCCTTCATATCTTCATGGTATAGGGTTTGCCA
*
37149 TTGCGGCCTCAACCTTTCCCAT
66 TTGCGACCTCAACCTTTCCCAT
37171 CGCGCCGTTA
Statistics
Matches: 183, Mismatches: 47, Indels: 11
0.76 0.20 0.05
Matches are distributed among these distances:
147 1 0.01
148 110 0.60
149 70 0.38
150 2 0.01
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.33
Consensus pattern (148 bp):
GGTACCGGGTTCACCGTTGCGGCATCAACCTTTCCCTTCATATCTTCATGGTATAGGGTTTGCCA
TTGCGACCTCAACCTTTCCCATTACATCTTCTAAGGTACCGGATTCGCAGCAGCAGCCTCAATCC
TTCCCATCAAACCCTCAA
Found at i:37117 original size:198 final size:197
Alignment explanation
Indices: 36762--37168 Score: 521
Period size: 198 Copynumber: 2.1 Consensus size: 197
36752 CGTTGCAGCT
*
36762 TCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTTACCGTTGCGGCCTCAACCTTTCCCATCA
1 TCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTTACCGTTGCGACCTCAACCTTTCCCATCA
** * *
36827 CATCTTCTAAGGTACCAGATTCGTCATTGTGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACC
66 CATCTTCTAAGGTACCAGATTCGTCATTGCAGCCTCAATCCTTCCCTTCAAACCCTCATGGTACC
* * * * * * *
36892 GGGTTCGCCGCAGCAGCCTTAACCTTTCCCATCACATCTTTTAAGGTACT-GGGTTCGTTGTTGT
131 GGGTTCACCGCAGCAGCATCAACCTTTCCCATCACATC-TTCAAGGTA-TAGGGTTCGCTATTGC
36956 GGCC
194 GGCC
* * * * *
36960 TCAACCTTTCCCTTCATATGTTCATGGTATCGGGTTTGCCGTTGCGACCTCAACTTTTCCCATTA
1 TCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTTACCGTTGCGACCTCAACCTTTCCCATCA
* * *
37025 CATCTTCTAAGGTATCGGATTCG-CAGTTGCAGCCTCAATCCTTCCCTTTAAACCCTCATGGTAC
66 CATCTTCTAAGGTACCAGATTCGTCA-TTGCAGCCTCAATCCTTCCCTTCAAACCCTCATGGTAC
** * * * * * *
37089 CGGGTTCACCGTTGCGGCATCCACCTTTCCCTTCATATCTTCATGGTATAGGGTTTGCTATTGCG
130 CGGGTTCACCGCAGCAGCATCAACCTTTCCCATCACATCTTCAAGGTATAGGGTTCGCTATTGCG
37154 GCC
195 GCC
37157 TCAACCTTTCCC
1 TCAACCTTTCCC
37169 ATCGCGCCGT
Statistics
Matches: 179, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
196 1 0.01
197 35 0.20
198 143 0.80
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (197 bp):
TCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTTACCGTTGCGACCTCAACCTTTCCCATCA
CATCTTCTAAGGTACCAGATTCGTCATTGCAGCCTCAATCCTTCCCTTCAAACCCTCATGGTACC
GGGTTCACCGCAGCAGCATCAACCTTTCCCATCACATCTTCAAGGTATAGGGTTCGCTATTGCGG
CC
Found at i:41709 original size:30 final size:30
Alignment explanation
Indices: 41673--41734 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
41663 GAGGTCCAAA
*
41673 GAATAGATAAATTTGAGAATGGTGTGATAT
1 GAATAGATAAATTTGAGAATGGTATGATAT
41703 GAATAGATAAATTTGAGAATGGTATGATAT
1 GAATAGATAAATTTGAGAATGGTATGATAT
41733 GA
1 GA
41735 GTATGAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (30 bp):
GAATAGATAAATTTGAGAATGGTATGATAT
Found at i:46177 original size:30 final size:29
Alignment explanation
Indices: 46103--46478 Score: 251
Period size: 30 Copynumber: 12.5 Consensus size: 29
46093 TTTCGAAGAA
* *
46103 TTTAGGGTCAAAATGTAATTTTAGAAAAAAA
1 TTTAGGGTTAAAATGTAATTTTAG--AAAAG
**
46134 AATAGGGGTTAAAATGTAATTTTAGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTAGAAAAG
* *
46164 TTTAGGTGTTAAAATATGATTTTAGGAAAA-
1 TTTAGG-GTTAAAATGTAATTTTA-GAAAAG
*
46194 TTTAAGGG-TAAAATG-AGATTTTAGGAAAG
1 TTT-AGGGTTAAAATGTA-ATTTTAGAAAAG
* * *
46223 TTTGAGGGTTAAAATGTGATTTTGGGAAAG
1 TTT-AGGGTTAAAATGTAATTTTAGAAAAG
* * * * *
46253 TTCAAGGGTGACAATATGATTTT-GAGAAAG
1 TT-TAGGGTTAAAATGTAATTTTAGA-AAAG
* * * * *
46283 TTTCGAGTTAAAATATGATTTTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
* * *
46312 TTTGGGGGTGAAAATGTAATTTTGGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTAGAAAAG
*
46342 TTTTAGTGGTTAAAATGTAATTTTGGAAAAG
1 -TTTAG-GGTTAAAATGTAATTTTAGAAAAG
* *
46373 TTTAGGGGTCAAAATGTAATTTT-GCAAAAAT
1 TTTA-GGGTTAAAATGTAATTTTAG--AAAAG
* *
46404 TTTAGTGGTGAAAATGTAATTTTAGAAAGG
1 TTTAG-GGTTAAAATGTAATTTTAGAAAAG
* *
46434 TTT-GGGTGTCAAAATGTGATTTTAGAAAGG
1 TTTAGGGT-T-AAAATGTAATTTTAGAAAAG
*
46464 TTTGGAGGTTAAAAT
1 TTTAG-GGTTAAAAT
46479 ATAGCTTTTA
Statistics
Matches: 284, Mismatches: 38, Indels: 47
0.77 0.10 0.13
Matches are distributed among these distances:
28 7 0.02
29 46 0.16
30 145 0.51
31 63 0.22
32 23 0.08
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:46215 original size:59 final size:60
Alignment explanation
Indices: 46139--46480 Score: 258
Period size: 59 Copynumber: 5.7 Consensus size: 60
46129 AAAAAAATAG
*
46139 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGTGTTAAAATATGATTTTAGGAAAA-TTTAA
1 GGGTGAAAATGTAATTTTAGAAAAGTTTAGGTGTTAAAATATGATTTT-GGAAAAGTTTAA
* * * *
46199 GGGT-AAAATG-AGATTTTAGGAAAGTTTGAGG-GTTAAAATGTGATTTTGGGAAAGTTCAA
1 GGGTGAAAATGTA-ATTTTAGAAAAGTTT-AGGTGTTAAAATATGATTTTGGAAAAGTTTAA
* * * * * **
46258 GGGTGACAATATGATTTT-GAGAAAGTTT-CGAGTTAAAATATGATTTTGGAAAAGTTTGG
1 GGGTGAAAATGTAATTTTAGA-AAAGTTTAGGTGTTAAAATATGATTTTGGAAAAGTTTAA
* * * *
46317 GGGTGAAAATGTAATTTTGGAAAAGTTTTA-GTGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTGAAAATGTAATTTTAGAAAAG-TTTAGGT-GTTAAAATATGATTTTGGAAAAGTTTAA
* * * * * * *
46378 GGGTCAAAATGTAATTTT-GCAAAAATTTTA-GTGGTGAAAATGTAATTTTAGAAAGGTTT--
1 GGGTGAAAATGTAATTTTAG--AAAAGTTTAGGT-GTTAAAATATGATTTTGGAAAAGTTTAA
* * *
46437 GGGTGTCAAAATGTGATTTTAGAAAGGTTT-GGAGGTTAAAATAT
1 GGGTG--AAAATGTAATTTTAGAAAAGTTTAGG-TGTTAAAATAT
46481 AGCTTTTAAA
Statistics
Matches: 231, Mismatches: 33, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
58 7 0.03
59 90 0.39
60 45 0.19
61 84 0.36
62 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (60 bp):
GGGTGAAAATGTAATTTTAGAAAAGTTTAGGTGTTAAAATATGATTTTGGAAAAGTTTAA
Found at i:46372 original size:61 final size:60
Alignment explanation
Indices: 46136--46466 Score: 291
Period size: 61 Copynumber: 5.5 Consensus size: 60
46126 GAAAAAAAAA
* * *
46136 TAGGGGTTAAAATGTAATTTTAGAAAAG-TTTAGGTGTTAAAATATGATTTTAGGAAAA-TT
1 TAGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGG-GTTAAAATGTGATTTT-GGAAAAGTT
* * *
46196 TAAGGGT-AAAATG-AGATTTTAGG-AAAGTTTGAGGGTTAAAATGTGATTTTGGGAAAGTT
1 TAGGGGTCAAAATGTA-ATTTT-GGAAAAGTTTTAGGGTTAAAATGTGATTTTGGAAAAGTT
* * * * * * * * *
46255 CAAGGGTGACAATATGATTTT-GAGAAAG-TTTCGAGTTAAAATATGATTTTGGAAAAGTT
1 TAGGGGTCAAAATGTAATTTTGGA-AAAGTTTTAGGGTTAAAATGTGATTTTGGAAAAGTT
* * *
46314 TGGGGGTGAAAATGTAATTTTGGAAAAGTTTTAGTGGTTAAAATGTAATTTTGGAAAAGTT
1 TAGGGGTCAAAATGTAATTTTGGAAAAGTTTTAG-GGTTAAAATGTGATTTTGGAAAAGTT
* * * * * *
46375 TAGGGGTCAAAATGTAATTTTGCAAAAATTTTAGTGGTGAAAATGTAATTTTAGAAAGGTT
1 TAGGGGTCAAAATGTAATTTTGGAAAAGTTTTAG-GGTTAAAATGTGATTTTGGAAAAGTT
* * *
46436 T-GGGTGTCAAAATGTGATTTTAGAAAGGTTT
1 TAGGG-GTCAAAATGTAATTTTGGAAAAGTTT
46467 GGAGGTTAAA
Statistics
Matches: 223, Mismatches: 36, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
58 7 0.03
59 83 0.37
60 34 0.15
61 99 0.44
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (60 bp):
TAGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTGATTTTGGAAAAGTT
Found at i:47439 original size:13 final size:13
Alignment explanation
Indices: 47421--47445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47411 TTCTTTTTAG
47421 TATTTATTATATA
1 TATTTATTATATA
47434 TATTTATTATAT
1 TATTTATTATAT
47446 GTTTTTTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATTATATA
Found at i:50223 original size:14 final size:15
Alignment explanation
Indices: 50204--50233 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50194 AGTTTGGTTG
50204 AAAATAA-AGAAATA
1 AAAATAATAGAAATA
50218 AAAATAATAGAAATA
1 AAAATAATAGAAATA
50233 A
1 A
50234 TGGATATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATAATAGAAATA
Found at i:50822 original size:18 final size:18
Alignment explanation
Indices: 50801--50838 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
50791 TAAATTTTCG
50801 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
50819 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
50837 AA
1 AA
50839 AATTGTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:62936 original size:6 final size:6
Alignment explanation
Indices: 62925--62975 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
62915 ACAATTCATA
* * * *
62925 TCACTT TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCCCTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
62973 TCA
1 TCA
62976 ATTTTGATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:66252 original size:18 final size:20
Alignment explanation
Indices: 66229--66267 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
66219 GAGGAAGGGG
66229 AGGAAG-AAGAGAAA-AGAA
1 AGGAAGAAAGAGAAAGAGAA
66247 AGGAAGAAAGAGAAAGAGAA
1 AGGAAGAAAGAGAAAGAGAA
66267 A
1 A
66268 AGAATAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AGGAAGAAAGAGAAAGAGAA
Done.