Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002604.1 Kokia drynarioides strain JFW-HI SEQ_114817, 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: 130487
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2516 original size:18 final size:17
Alignment explanation
Indices: 2468--2516 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2458 ATTCAAGAAA
*
2468 ATAAAAATTCAAAATTC
1 ATAAAATTTCAAAATTC
*
2485 AAAAAATTAT-AAAAGTTC
1 ATAAAATT-TCAAAA-TTC
2503 ATAAAATTTCAAAA
1 ATAAAATTTCAAAA
2517 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAATTTCAAAATTC
Found at i:8767 original size:2 final size:2
Alignment explanation
Indices: 8756--8787 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8746 AACTTTATTT
8756 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8788 TAAGATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16812 original size:25 final size:27
Alignment explanation
Indices: 16766--16831 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 27
16756 GATTCCTATA
*
16766 TTTTTTTCCTTTTAAGCAATTT-AA-T
1 TTTTTTTTCTTTTAAGCAATTTGAACT
* **
16791 TTTTTTTTCTTTTATGTTATTTGAACT
1 TTTTTTTTCTTTTAAGCAATTTGAACT
*
16818 TTTCTTCTTCTTTT
1 TTT-TTTTTCTTTT
16832 TTTTCCCCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 18 0.55
26 2 0.06
27 4 0.12
28 9 0.27
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (27 bp):
TTTTTTTTCTTTTAAGCAATTTGAACT
Found at i:19814 original size:23 final size:25
Alignment explanation
Indices: 19790--19875 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 25
19780 TTTACAAGAA
19790 TTTATA-AAATAAATTTCATTTAAT
1 TTTATATAAATAAATTTCATTTAAT
* **
19814 TTTATATATATATTAACTTTACA-AGAA-
1 TTTATATA-A-A-TAAATTT-CATTTAAT
19841 TTTATA-AAATAAATTTCATTTAAT
1 TTTATATAAATAAATTTCATTTAAT
19865 TTTATATAAAT
1 TTTATATAAAT
19876 TAACATAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
24 13 0.27
25 6 0.12
26 2 0.04
27 7 0.15
28 8 0.17
29 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (25 bp):
TTTATATAAATAAATTTCATTTAAT
Found at i:19823 original size:28 final size:28
Alignment explanation
Indices: 19792--19872 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
19782 TACAAGAATT
19792 TATAAAATAAATTTCATTTAATTTTATA
1 TATAAAATAAATTTCATTTAATTTTATA
* * * **
19820 TATATATTAACTTTACA-AGAA---T-T-
1 TATAAAATAAATTT-CATTTAATTTTATA
19843 TATAAAATAAATTTCATTTAATTTTATA
1 TATAAAATAAATTTCATTTAATTTTATA
19871 TA
1 TA
19873 AATTAACATA
Statistics
Matches: 36, Mismatches: 10, Indels: 14
0.60 0.17 0.23
Matches are distributed among these distances:
22 2 0.06
23 13 0.36
24 1 0.03
25 1 0.03
26 1 0.03
27 1 0.03
28 15 0.42
29 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (28 bp):
TATAAAATAAATTTCATTTAATTTTATA
Found at i:19842 original size:51 final size:51
Alignment explanation
Indices: 19770--19879 Score: 206
Period size: 51 Copynumber: 2.2 Consensus size: 51
19760 AGTTCACTTG
19770 ATATATTAACTTTACAAGAATTTATAAAATAAATTTCATTTAATTTTATAT
1 ATATATTAACTTTACAAGAATTTATAAAATAAATTTCATTTAATTTTATAT
19821 ATATATTAACTTTACAAGAATTTATAAAATAAATTTCATTTAATTTTATAT
1 ATATATTAACTTTACAAGAATTTATAAAATAAATTTCATTTAATTTTATAT
19872 A-A-ATTAAC
1 ATATATTAAC
19880 ATAATATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 6 0.10
50 1 0.02
51 52 0.88
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (51 bp):
ATATATTAACTTTACAAGAATTTATAAAATAAATTTCATTTAATTTTATAT
Found at i:21925 original size:15 final size:16
Alignment explanation
Indices: 21905--21941 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
21895 TTATTAAACA
21905 AAAATAT-TTTTAATT
1 AAAATATATTTTAATT
21920 AAAATATCATTTTAATT
1 AAAATAT-ATTTTAATT
21937 AAAAT
1 AAAAT
21942 TTTAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
17 13 0.65
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATATATTTTAATT
Found at i:22408 original size:18 final size:19
Alignment explanation
Indices: 22366--22410 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
22356 ATACTTTCAT
*
22366 ATATTTTGA-AATTTTTCTG
1 ATATTTT-ATAATTTTTCTA
22385 AT-TTTTATAATTTTT-TA
1 ATATTTTATAATTTTTCTA
22402 ATATTTTAT
1 ATATTTTAT
22411 GAAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 17 0.74
19 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
ATATTTTATAATTTTTCTA
Found at i:24124 original size:11 final size:12
Alignment explanation
Indices: 24103--24137 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
24093 TCTTTATGTA
24103 TTCAATTTTAAT
1 TTCAATTTTAAT
*
24115 TT-ATTTTTAAT
1 TTCAATTTTAAT
24126 TTCAATTTTAAT
1 TTCAATTTTAAT
24138 GCAAAATCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCAATTTTAAT
Found at i:24451 original size:28 final size:29
Alignment explanation
Indices: 24410--24465 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
24400 ATTTAACTGA
*
24410 AAAATTATAGTTTATT-CTTTTTCTTTTG
1 AAAAGTATAGTTTATTCCTTTTTCTTTTG
* *
24438 AAAAGTATATTTTATTCCTTTTTTTTTT
1 AAAAGTATAGTTTATTCCTTTTTCTTTT
24466 TTTTTTAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (29 bp):
AAAAGTATAGTTTATTCCTTTTTCTTTTG
Found at i:33269 original size:19 final size:19
Alignment explanation
Indices: 33242--33290 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
33232 TAAACGTCCC
33242 TAAACTATTGCT-TAAACTT
1 TAAACTATT-CTCTAAACTT
*
33261 TAAATTATTCTCTAAACTT
1 TAAACTATTCTCTAAACTT
* *
33280 CAAAGTATTCT
1 TAAACTATTCT
33291 AATCAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (19 bp):
TAAACTATTCTCTAAACTT
Found at i:39521 original size:4 final size:4
Alignment explanation
Indices: 39500--39571 Score: 117
Period size: 4 Copynumber: 18.0 Consensus size: 4
39490 CCGCTTAAAT
* * *
39500 CATA CGTA CGTA CGTA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
39548 CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA
39572 TATATATATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:40354 original size:29 final size:29
Alignment explanation
Indices: 40312--40368 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
40302 TCAACATGCA
* *
40312 ATAACACAATACAAATTAAAATCACACAG
1 ATAACACAAAACAAAATAAAATCACACAG
*
40341 ATAACACAAAACAAAATAATATCACACA
1 ATAACACAAAACAAAATAAAATCACACA
40369 AGGTGTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.21, G:0.02, T:0.16
Consensus pattern (29 bp):
ATAACACAAAACAAAATAAAATCACACAG
Found at i:40433 original size:30 final size:29
Alignment explanation
Indices: 40385--40448 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
40375 GAAACACCGC
*
40385 CACACAACAAAATGTAGCAC-AAGAAGAAA
1 CACACAACAAAATGTAGCACGAACAA-AAA
*
40414 CACACAACAAATCTGTAGCACGAACAAAAA
1 CACACAACAAA-ATGTAGCACGAACAAAAA
40444 CACAC
1 CACAC
40449 TGTAACACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 11 0.35
30 16 0.52
31 4 0.13
ACGTcount: A:0.55, C:0.27, G:0.11, T:0.08
Consensus pattern (29 bp):
CACACAACAAAATGTAGCACGAACAAAAA
Found at i:40447 original size:28 final size:28
Alignment explanation
Indices: 40386--40447 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
40376 AAACACCGCC
* *
40386 ACACAACAAAATGTAGCACAAGAAGAAAC
1 ACACAACAAAATGTAGCAC-AGAACAAAA
*
40415 ACACAACAAATCTGTAGCAC-GAACAAAA
1 ACACAACAAA-ATGTAGCACAGAACAAAA
40443 ACACA
1 ACACA
40448 CTGTAACACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 10 0.34
30 8 0.28
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.08
Consensus pattern (28 bp):
ACACAACAAAATGTAGCACAGAACAAAA
Found at i:41071 original size:22 final size:22
Alignment explanation
Indices: 41043--41116 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
41033 ACTGGGGAAA
41043 CAGAAGCGCACACAGTGCTGAT
1 CAGAAGCGCACACAGTGCTGAT
41065 CAGAAGCGCACACAGTGCTGAT
1 CAGAAGCGCACACAGTGCTGAT
* *
41087 CAGAAGCACACACAATGCTGAT
1 CAGAAGCGCACACAGTGCTGAT
41109 CAGAAGCG
1 CAGAAGCG
41117 TGCTAGCGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.35, C:0.27, G:0.26, T:0.12
Consensus pattern (22 bp):
CAGAAGCGCACACAGTGCTGAT
Found at i:41346 original size:14 final size:15
Alignment explanation
Indices: 41327--41355 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41317 TTATAATTAA
41327 ACACATA-ATTTTTC
1 ACACATACATTTTTC
41341 ACACATACATTTTTC
1 ACACATACATTTTTC
41356 TCAGATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (15 bp):
ACACATACATTTTTC
Found at i:44444 original size:22 final size:21
Alignment explanation
Indices: 44402--44443 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
44392 TAGTTTTAAG
44402 AAAAAAATATTAAATCATTTT
1 AAAAAAATATTAAATCATTTT
44423 AAAAAAATCATTAAAT-ATTTT
1 AAAAAAAT-ATTAAATCATTTT
44444 TTTACTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAATATTAAATCATTTT
Found at i:48665 original size:3 final size:3
Alignment explanation
Indices: 48659--48695 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48649 ATCAATCTTT
48659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48696 CAAAAGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49646 original size:23 final size:20
Alignment explanation
Indices: 49606--49648 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
49596 AAATTCATGG
49606 TTATATTTTGAGCTTGAGTA
1 TTATATTTTGAGCTTGAGTA
49626 TTATGATTTTGAATGCTTGAGTA
1 TTAT-ATTTTG-A-GCTTGAGTA
49649 AGAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 1 0.05
23 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (20 bp):
TTATATTTTGAGCTTGAGTA
Found at i:51410 original size:24 final size:24
Alignment explanation
Indices: 51375--51438 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
51365 CTAATAAGTG
*
51375 TTTAACTCAAACAAATAAATAAAA
1 TTTAACTGAAACAAATAAATAAAA
* * *
51399 TTTAATTGAAACAATTAAATATAA
1 TTTAACTGAAACAAATAAATAAAA
51423 TTTAACTGAAA-AAATA
1 TTTAACTGAAACAAATA
51439 TTTTTCAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (24 bp):
TTTAACTGAAACAAATAAATAAAA
Found at i:68323 original size:54 final size:54
Alignment explanation
Indices: 68237--68342 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
68227 GTGTACCTGA
* *
68237 TTCAATTGATTCTCCTAAAACGGAAATCTGTGAGAAGGATTTATCTACAAGTGT
1 TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGTGT
* * *
68291 TTCAATTGATTCTCCTAAAAAGGAACTTTGTGAGAAGGATCTATCTAGAAGT
1 TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGT
68343 TTTGAACTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (54 bp):
TTCAATTGATTCTCCTAAAAAGGAAATCTGTGAGAAGGATCTATCTACAAGTGT
Found at i:71596 original size:33 final size:33
Alignment explanation
Indices: 71558--71624 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
71548 ATCTGCTTTG
71558 TAAAATAATATTTGAAGTTTATCTATTTGTATC
1 TAAAATAATATTTGAAGTTTATCTATTTGTATC
* * * * *
71591 TAAAATACTGTTTGAAGTTTGTTTGTTTGTATC
1 TAAAATAATATTTGAAGTTTATCTATTTGTATC
71624 T
1 T
71625 CTCTTTCACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (33 bp):
TAAAATAATATTTGAAGTTTATCTATTTGTATC
Found at i:79328 original size:6 final size:6
Alignment explanation
Indices: 79317--79349 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
79307 CTTTTCACAG
79317 TACTAT TACTAT TACTAT TACTAT TACTAT TAC
1 TACTAT TACTAT TACTAT TACTAT TACTAT TAC
79350 AAGAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (6 bp):
TACTAT
Found at i:86232 original size:22 final size:22
Alignment explanation
Indices: 86206--86256 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
86196 TTATAAAAAA
86206 TAAATAATGCTTATTATTTTAT
1 TAAATAATGCTTATTATTTTAT
86228 TAAATAATGCTTATTATTTTAT
1 TAAATAATGCTTATTATTTTAT
86250 TAAATAA
1 TAAATAA
86257 AATTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
TAAATAATGCTTATTATTTTAT
Found at i:86269 original size:22 final size:22
Alignment explanation
Indices: 86206--86268 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
86196 TTATAAAAAA
** *
86206 TAAATAATGCTTATTATTTTAT
1 TAAATAATAATTATAATTTTAT
** *
86228 TAAATAATGCTTATTATTTTAT
1 TAAATAATAATTATAATTTTAT
86250 TAAATAA-AATTATAATTTT
1 TAAATAATAATTATAATTTT
86269 TCATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 9 0.24
22 29 0.76
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
TAAATAATAATTATAATTTTAT
Found at i:93470 original size:29 final size:29
Alignment explanation
Indices: 93401--93472 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
93391 TTGTGTTTAT
* *
93401 TGGTCAGGTCGCCATACTCATCAACAACC
1 TGGTCGGGTTGCCATACTCATCAACAACC
* ** ** *
93430 TAGTCGATTTGCCATACTTGTCAACAACG
1 TGGTCGGGTTGCCATACTCATCAACAACC
93459 TGGTCGGGTTGCCA
1 TGGTCGGGTTGCCA
93473 AACCCGTCAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (29 bp):
TGGTCGGGTTGCCATACTCATCAACAACC
Found at i:95604 original size:50 final size:50
Alignment explanation
Indices: 95523--95698 Score: 201
Period size: 50 Copynumber: 3.5 Consensus size: 50
95513 ATGATCATTG
* * *
95523 CGTTTACGCTTGTCAGC-TATATATACGTTTACGCTGGCCAACTTGGACA
1 CGTTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAACTTGGACA
* * * *
95572 CGTTTACACTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTGTACA
1 CGTTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAACTTGGACA
* * * ** *
95622 CGTTTACGCTCGTCAGCTTATATATGCATTTACGCTCGTCAGCTTATATA
1 CGTTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAACTTGGACA
*
95672 TGCGTTTACGCTCGCCAGCTTATATAT
1 --CGTTTACGCTCGTCAGCTTATATAT
95699 ATATATACGT
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
49 15 0.13
50 73 0.65
52 24 0.21
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (50 bp):
CGTTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAACTTGGACA
Found at i:95609 original size:26 final size:26
Alignment explanation
Indices: 95521--95731 Score: 207
Period size: 26 Copynumber: 8.1 Consensus size: 26
95511 ACATGATCAT
*
95521 TGCGTTTACGCTTGTCAGC-TATATA
1 TGCGTTTACGCTCGTCAGCTTATATA
* * * * ** *
95546 TACGTTTACGCTGGCCAACTTGGACA
1 TGCGTTTACGCTCGTCAGCTTATATA
*
95572 --CGTTTACACTCGTCAGCTTATATA
1 TGCGTTTACGCTCGTCAGCTTATATA
* *
95596 TGCGTTTACGCTCGTCAGCTTGTACA
1 TGCGTTTACGCTCGTCAGCTTATATA
95622 --CGTTTACGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGTCAGCTTATATA
*
95646 TGCATTTACGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGTCAGCTTATATA
*
95672 TGCGTTTACGCTCGCCAGCTTATATATATATA
1 TGCGTTTACGCTCGTCAGC-----T-TATATA
*
95704 TACGTTTACGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGTCAGCTTATATA
95730 TG
1 TG
95732 TGTGTATATA
Statistics
Matches: 150, Mismatches: 25, Indels: 21
0.77 0.13 0.11
Matches are distributed among these distances:
24 39 0.26
25 15 0.10
26 71 0.47
27 1 0.01
31 1 0.01
32 23 0.15
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (26 bp):
TGCGTTTACGCTCGTCAGCTTATATA
Found at i:95704 original size:32 final size:32
Alignment explanation
Indices: 95666--95730 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
95656 CTCGTCAGCT
*
95666 TATATATGCGTTTACGCTCGCCAGCTTATATA
1 TATATATACGTTTACGCTCGCCAGCTTATATA
*
95698 TATATATACGTTTACGCTCGTCAGCTTATATA
1 TATATATACGTTTACGCTCGCCAGCTTATATA
95730 T
1 T
95731 GTGTGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (32 bp):
TATATATACGTTTACGCTCGCCAGCTTATATA
Found at i:95726 original size:58 final size:52
Alignment explanation
Indices: 95521--95731 Score: 189
Period size: 50 Copynumber: 4.0 Consensus size: 52
95511 ACATGATCAT
* * * * * * ** *
95521 TGCGTTTACGCTTGTCAGC-TATATATACGTTTACGCTGGCCAACTTGGACA
1 TGCGTTTACGCTCGCCAGCTTATATATGCGTTTACGCTCGTCAGCTTATATA
* * * *
95572 --CGTTTACACTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTGTACA
1 TGCGTTTACGCTCGCCAGCTTATATATGCGTTTACGCTCGTCAGCTTATATA
* *
95622 --CGTTTACGCTCGTCAGCTTATATATGCATTTACGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGCCAGCTTATATATGCGTTTACGCTCGTCAGCTTATATA
*
95672 TGCGTTTACGCTCGCCAGCTTATATATATATATACGTTTACGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGCCAGC-----T-TATATATGCGTTTACGCTCGTCAGCTTATATA
95730 TG
1 TG
95732 TGTGTATATA
Statistics
Matches: 137, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
49 15 0.11
50 73 0.53
52 16 0.12
57 1 0.01
58 32 0.23
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCGTTTACGCTCGCCAGCTTATATATGCGTTTACGCTCGTCAGCTTATATA
Found at i:95741 original size:2 final size:2
Alignment explanation
Indices: 95736--95772 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
95726 TATATGTGTG
*
95736 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95773 GTCGACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:95780 original size:18 final size:18
Alignment explanation
Indices: 95743--95782 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
95733 GTGTATATAT
*
95743 ATATATATATATATATAC
1 ATATATATATATATAGAC
* *
95761 ATATATATATATGTCGAC
1 ATATATATATATATAGAC
95779 ATAT
1 ATAT
95783 GAATAACAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (18 bp):
ATATATATATATATAGAC
Found at i:96590 original size:47 final size:47
Alignment explanation
Indices: 96521--96622 Score: 195
Period size: 47 Copynumber: 2.1 Consensus size: 47
96511 CAACAACTAT
96521 TACCTATGGGGGTAGCCTGCAAATGATCTCGAGATATGATCACTTTA
1 TACCTATGGGGGTAGCCTGCAAATGATCTCGAGATATGATCACTTTA
96568 TACCTATGGGGGTAGCCTGCAAATGATCTCGAGATATGATCACTTTA
1 TACCTATGGGGGTAGCCTGCAAATGATCTCGAGATATGATCACTTTA
96615 TAACCTAT
1 T-ACCTAT
96623 CTCTTAATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 48 0.89
48 6 0.11
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (47 bp):
TACCTATGGGGGTAGCCTGCAAATGATCTCGAGATATGATCACTTTA
Found at i:113403 original size:43 final size:43
Alignment explanation
Indices: 113342--113464 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
113332 CAAACACCGT
* *
113342 TGGTCTTTAGCGGTGCTTTCCTCACAAATGCCGCTAAAGAACA
1 TGGTCTTTAGCGGTGCTTTCCTCACAAACGCAGCTAAAGAACA
*
113385 TGGTCTTTAGC-GTCGCTTTTCTCACAAACGCAGCTAAAGAACA
1 TGGTCTTTAGCGGT-GCTTTCCTCACAAACGCAGCTAAAGAACA
* * *
113428 TGGTCTTTAGTGGCGTTTTTCC-CACAAACGC-GCTAAA
1 TGGTCTTTAGCGGTG-CTTTCCTCACAAACGCAGCTAAA
113465 ATTAACAGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
42 8 0.11
43 57 0.81
44 5 0.07
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (43 bp):
TGGTCTTTAGCGGTGCTTTCCTCACAAACGCAGCTAAAGAACA
Found at i:115432 original size:18 final size:19
Alignment explanation
Indices: 115391--115428 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
115381 AATTAATGAA
115391 TATTTTATATAATTGATAAT
1 TATTTTATAT-ATTGATAAT
115411 TATTTTATAT-TTGA-AAT
1 TATTTTATATATTGATAAT
115428 T
1 T
115429 TATTCAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
20 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATTTTATATATTGATAAT
Found at i:118016 original size:16 final size:17
Alignment explanation
Indices: 117983--118021 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
117973 GACTGAGTCA
117983 ATTAACTATTAAATATTG
1 ATTAACTATT-AATATTG
118001 ATTAACTATT-ATATTG
1 ATTAACTATTAATATTG
118017 ATTAA
1 ATTAA
118022 TATATCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
ATTAACTATTAATATTG
Found at i:118738 original size:6 final size:6
Alignment explanation
Indices: 118727--118770 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
118717 TTGAAATTGT
118727 CACTGC CACTGC CACTGC CACTGC CACTGC CACTGC CACTGC CA
1 CACTGC CACTGC CACTGC CACTGC CACTGC CACTGC CACTGC CA
118771 TTGCTCTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.50, G:0.16, T:0.16
Consensus pattern (6 bp):
CACTGC
Found at i:120985 original size:31 final size:30
Alignment explanation
Indices: 120879--120999 Score: 97
Period size: 31 Copynumber: 4.0 Consensus size: 30
120869 TAAAAAGAAC
*
120879 TTAGGTACCAAATTAGAGAAAAAAAATATCAAG
1 TTAGGTACCAAATTA-AG--AAAAAATGTCAAG
** * *
120912 TTCAGGTACCAAATTGGGTAAAGAA----AAT
1 TT-AGGTACCAAATTAAG-AAAAAATGTCAAG
*
120940 TTAGGTATCAAATTAAGAAAAAATGTCAAG
1 TTAGGTACCAAATTAAGAAAAAATGTCAAG
*
120970 TTAGGTAACCAAATTAAGAAAAAGTGTCAA
1 TTAGGT-ACCAAATTAAGAAAAAATGTCAA
121000 CTCTTATTGG
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.07
27 12 0.17
28 4 0.06
30 8 0.11
31 21 0.30
32 5 0.07
33 3 0.04
34 12 0.17
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (30 bp):
TTAGGTACCAAATTAAGAAAAAATGTCAAG
Found at i:124191 original size:27 final size:28
Alignment explanation
Indices: 124161--124216 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
124151 TAACTTTTTC
124161 AAGCTAGTG-ATGAACTTCATCATAGTA
1 AAGCTAGTGAATGAACTTCATCATAGTA
*
124188 AAGCTAGTGAATGAACTTTATCATAGTA
1 AAGCTAGTGAATGAACTTCATCATAGTA
124216 A
1 A
124217 CAAGACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (28 bp):
AAGCTAGTGAATGAACTTCATCATAGTA
Found at i:126265 original size:25 final size:24
Alignment explanation
Indices: 126237--126312 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
126227 TTACACACAC
*
126237 TTTAACTTTATTTTCACATATATAT
1 TTTAACTTTATATTCACATAT-TAT
* *
126262 TTTAACACTTA-ATTCACATGTTCACT
1 TTTAAC-TTTATATTCACATATT-A-T
*
126288 TTTAACTTTATGTTCACATATTAT
1 TTTAACTTTATATTCACATATTAT
126312 T
1 T
126313 ACATATACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.07
25 19 0.46
26 19 0.46
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (24 bp):
TTTAACTTTATATTCACATATTAT
Found at i:127990 original size:29 final size:30
Alignment explanation
Indices: 127958--128024 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
127948 TCAAGATTTG
*
127958 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
* * *
127987 ATGTATACAATTTCACATTAAACCATAGTTC
1 ATGTATAAAATTGCACA-TAAACCAAAGTTC
128018 ATGTATA
1 ATGTATA
128025 GTTTTGGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAACCAAAGTTC
Done.