Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001998.1 Kokia drynarioides strain JFW-HI SEQ_113857, 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: 40285
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:4201 original size:80 final size:80
Alignment explanation
Indices: 4105--4255 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 80
4095 CACTAATTTC
* * * * * *
4105 TTTTTAACTTTTGTAGGGAAGCTAATGAGTCATGTCTCTTCATTAAGATCTGATGTAGTTAAAAA
1 TTTTTAACTCTTGTAGGAAAGCCAACGAGTCATGTCTCTTCATTAAGATCAGATGTAGCTAAAAA
4170 GGCATGGCAATTTTG
66 GGCATGGCAATTTTG
* * *
4185 TTTTTAACTCTTGTAGGAAAGCCAACGAGTCATGTCTCTTGATTAGGATCAGATGTAGCTGAAAA
1 TTTTTAACTCTTGTAGGAAAGCCAACGAGTCATGTCTCTTCATTAAGATCAGATGTAGCTAAAAA
4250 GGCATG
66 GGCATG
4256 AAATTTCTCC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (80 bp):
TTTTTAACTCTTGTAGGAAAGCCAACGAGTCATGTCTCTTCATTAAGATCAGATGTAGCTAAAAA
GGCATGGCAATTTTG
Found at i:4894 original size:48 final size:47
Alignment explanation
Indices: 4697--4883 Score: 209
Period size: 48 Copynumber: 3.9 Consensus size: 47
4687 GCAAGGCAGT
* * *
4697 TAAA-AAAGATGTATTTAACAAACAAAACAATTAAT-AATGCATATTAG
1 TAAACAAAGATGCATTTAACAAACAAAACACTTAATGAA-GCA-ATTAA
* *
4744 TAAACAAAGATGCATTTAACAAACAAAACAGTTAAT-AATGCAGATTAC
1 TAAACAAAGATGCATTTAACAAACAAAACACTTAATGAA-GCA-ATTAA
* * *
4792 TAAACAAAGTTGCATTTAACAAACAAAACACTTAATGATGCAGATTAT
1 TAAACAAAGATGCATTTAACAAACAAAACACTTAATGAAGCA-ATTAA
*
4840 TAAACAAAGATGCATTTAACAAAAAAAAAACACTTAATGAAGCA
1 TAAACAAAGATGCATTTAAC--AAACAAAACACTTAATGAAGCA
4884 TAAATGAACA
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
47 4 0.03
48 100 0.80
49 1 0.01
50 20 0.16
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (47 bp):
TAAACAAAGATGCATTTAACAAACAAAACACTTAATGAAGCAATTAA
Found at i:4894 original size:96 final size:95
Alignment explanation
Indices: 4709--4894 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 95
4699 AAAAAGATGT
* *
4709 ATTTAACAAACAAAACAATTAATAATGCATATTAGTAAACAAAGATGCATTTAACAAACAAAACA
1 ATTTAACAAACAAAACAATTAATAATGCAGATTAGTAAACAAAGATGCATTTAACAAAAAAAACA
* * *
4774 GTTAATAATGCAGATTACTAAACAAAGTTGC
66 CTTAATAATGCA-ATAAATAAACAAAGTTGC
* * *
4805 ATTTAACAAACAAAACACTTAATGATGCAGATTATTAAACAAAGATGCATTTAACAAAAAAAAAA
1 ATTTAACAAACAAAACAATTAATAATGCAGATTAGTAAACAAAGATGCATTTAAC--AAAAAAAA
*
4870 CACTTAATGAA-GC-ATAAATGAACAA
64 CACTTAAT-AATGCAATAAATAAACAA
4895 CTTTATTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 60 0.77
98 16 0.21
99 2 0.03
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (95 bp):
ATTTAACAAACAAAACAATTAATAATGCAGATTAGTAAACAAAGATGCATTTAACAAAAAAAACA
CTTAATAATGCAATAAATAAACAAAGTTGC
Found at i:6121 original size:79 final size:79
Alignment explanation
Indices: 5755--6110 Score: 534
Period size: 79 Copynumber: 4.5 Consensus size: 79
5745 TGATTAGGGT
*
5755 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGATGGACATTGCCAGTT
1 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGACATTGCCAGTT
*
5820 TAACTGACTAGGGC
66 TAACTGACTAGAGC
* * * * *
5834 TGAGCTCACTTTCGCAGTTTATCCGCTAGGCACTAGGTACCAAGATTTGACAGG-CATTGTCAGT
1 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGA-TGGACATTGCCAGT
*
5898 TTAATTGACTAGAGC
65 TTAACTGACTAGAGC
* * *
5913 TGGGCTCACTTTTGCGGTTTATCCACTAGGCACTAGGTGCCAAGATTTGATTGACATTGCCAGTT
1 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGACATTGCCAGTT
*
5978 TAACTGATTAGAGC
66 TAACTGACTAGAGC
* * *
5992 TGGGCTCACTTTCGCAGTTTATCAGCTAGGCACTAGGTGCCAAGATTTGATGGACATTGTCAGTT
1 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGACATTGCCAGTT
6057 TAACTGACTAGAGC
66 TAACTGACTAGAGC
***
6071 TGGGCTCACTTTTATGGTTTATCCGCTAGGCACTAGGTGC
1 TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGC
6111 TAGGAATTGA
Statistics
Matches: 245, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
78 1 0.00
79 242 0.99
80 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (79 bp):
TGGGCTCACTTTCGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGACATTGCCAGTT
TAACTGACTAGAGC
Found at i:6983 original size:14 final size:12
Alignment explanation
Indices: 6953--6986 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
6943 TGCAATATAT
6953 AACACACGGGTA
1 AACACACGGGTA
6965 AACACACGGGTA
1 AACACACGGGTA
6977 AACACACGGG
1 AACACACGGG
6987 CTGTTACACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.26, T:0.06
Consensus pattern (12 bp):
AACACACGGGTA
Found at i:12722 original size:79 final size:79
Alignment explanation
Indices: 12591--13044 Score: 454
Period size: 79 Copynumber: 5.7 Consensus size: 79
12581 ATAAATTATG
* * * * *
12591 TTGTCAGTTTAACTGACTAGGGCTGGGCTCACTTTCATGGTTAATCCGCTAGGCACTGGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTTGGCTCACTTTCGTGGTTTATCTGCTAGGCACTGGGTGCCA
12656 AGATTTGACGGACA
66 AGATTTGACGGACA
* * * * *
12670 TTGTCAGTTTAACTGACAAGGGCTTAGCTCATTTTCGTGGTTTATCTGCTAGGCACTAGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTTGGCTCACTTTCGTGGTTTATCTGCTAGGCACTGGGTGCCA
*
12735 AGATTTGACAGACA
66 AGATTTGACGGACA
* * * * * *
12749 TTGTCAGTTTAATTGATTAGAG-TTGGGCTCACTTTCGCGATTTATCCT-TTAGGCATTGGGTGC
1 TTGTCAGTTTAACTGACTAGAGCTT-GGCTCACTTTCGTGGTTTAT-CTGCTAGGCACTGGGTGC
12812 CAAGATTTGACGGACA
64 CAAGATTTGACGGACA
* * * *
12828 CTGTCAGTTTAACTAACTAGAG-TTGGGCTCACTTTCGTGGTTTAT-TCGCTACGTACTGGGTGC
1 TTGTCAGTTTAACTGACTAGAGCTT-GGCTCACTTTCGTGGTTTATCT-GCTAGGCACTGGGTGC
* *
12891 TAAAATTTGACGGACA
64 CAAGATTTGACGGACA
* * *
12907 TTATCAGTTTAACTGACTAGAGC-TGAGCTCACTTTTGCGGTTTATCTGCTAGGCACTGGGTGCC
1 TTGTCAGTTTAACTGACTAGAGCTTG-GCTCACTTTCGTGGTTTATCTGCTAGGCACTGGGTGCC
* *
12971 AGGAATTGACGGA-A
65 AAGATTTGACGGACA
* * ** * * *
12985 TTATCATTGGTTAATCCAACTAGAGCTGGGCTCATATTTTGTGGTTTAT-TCGCTAGGCAC
1 TTGTCA--GTTTAA-CTGACTAGAGCTTGGCTCA-CTTTCGTGGTTTATCT-GCTAGGCAC
13045 CGAGTGCCGT
Statistics
Matches: 312, Mismatches: 50, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 10 0.03
79 256 0.82
80 8 0.03
81 15 0.05
82 22 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (79 bp):
TTGTCAGTTTAACTGACTAGAGCTTGGCTCACTTTCGTGGTTTATCTGCTAGGCACTGGGTGCCA
AGATTTGACGGACA
Found at i:12890 original size:158 final size:158
Alignment explanation
Indices: 12591--13044 Score: 502
Period size: 158 Copynumber: 2.9 Consensus size: 158
12581 ATAAATTATG
* ** * *
12591 TTGTCAGTTTAACTGACTAGGGCTGGGCTCACTTTCATGGTTAATCCGCTAGGCACTGGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACTTTCGCGGTTTATCCTCTAGGCACTGGGTGCCA
* * * * *
12656 AGATTTGACGGACATTGTCAGTTTAACTGACAAGGGCTT-AGCTCATTTTCGTGGTTTA-TCTGC
66 AGATTTGACGGACATTGTCAGTTTAACTAACTAGAG-TTGGGCTCAATTTCGTGGTTTATTC-GC
* *
12719 TAGGCACTAGGTGCCAAGATTTGACAGACA
129 TACGCACTAGGTGCCAAAATTTGACAGACA
* * * * * *
12749 TTGTCAGTTTAATTGATTAGAGTTGGGCTCACTTTCGCGATTTATCCTTTAGGCATTGGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACTTTCGCGGTTTATCCTCTAGGCACTGGGTGCCA
* *
12814 AGATTTGACGGACACTGTCAGTTTAACTAACTAGAGTTGGGCTCACTTTCGTGGTTTATTCGCTA
66 AGATTTGACGGACATTGTCAGTTTAACTAACTAGAGTTGGGCTCAATTTCGTGGTTTATTCGCTA
* * * *
12879 CGTACTGGGTGCTAAAATTTGACGGACA
131 CGCACTAGGTGCCAAAATTTGACAGACA
* * *
12907 TTATCAGTTTAACTGACTAGAGCTGAGCTCACTTTTGCGGTTTAT-CTGCTAGGCACTGGGTGCC
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACTTTCGCGGTTTATCCT-CTAGGCACTGGGTGCC
* * * * * * *
12971 AGGAATTGACGGA-ATTATCATTGGTTAATCCAACTAGAGCTGGGCTCATATTTTGTGGTTTATT
65 AAGATTTGACGGACATTGTCA--GTTTAA-CTAACTAGAGTTGGGCTCA-ATTTCGTGGTTTATT
*
13035 CGCTAGGCAC
126 CGCTACGCAC
13045 CGAGTGCCGT
Statistics
Matches: 246, Mismatches: 43, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
157 9 0.04
158 192 0.78
159 7 0.03
160 17 0.07
161 21 0.09
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (158 bp):
TTGTCAGTTTAACTGACTAGAGCTGGGCTCACTTTCGCGGTTTATCCTCTAGGCACTGGGTGCCA
AGATTTGACGGACATTGTCAGTTTAACTAACTAGAGTTGGGCTCAATTTCGTGGTTTATTCGCTA
CGCACTAGGTGCCAAAATTTGACAGACA
Found at i:13931 original size:19 final size:19
Alignment explanation
Indices: 13909--13992 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
13899 TTTTTGATTC
13909 ATTTTTATAATTTTTTA-T
1 ATTTTTATAATTTTTTACT
* *
13927 GATTTTAATAAATTTTTACT
1 -ATTTTTATAATTTTTTACT
*
13947 ATATTTTAT-A-TTTTTACA
1 AT-TTTTATAATTTTTTACT
** *
13965 ACCTTTATAATTTTGTTTCT
1 ATTTTTATAATTTT-TTACT
13985 AATTTTTA
1 -ATTTTTA
13993 ATAAAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
17 5 0.10
18 9 0.18
19 21 0.43
20 9 0.18
21 5 0.10
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACT
Found at i:14291 original size:90 final size:90
Alignment explanation
Indices: 14138--14305 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 90
14128 TTAATGGTAA
* * **
14138 AAGAGCCTTTTTGATGCATTTGATAGATCAAGTACTCAATTGAGTGCAAAAAAATTCAGGAGCTT
1 AAGAGCCTTTTTGATGCATTTGAAAGATCAAGTACCCAATTGAGTGCAAAAAAAGGCAGGAGCTT
14203 AATTACTTTTTTTGAAAAAAAATTT
66 AATTACTTTTTTTGAAAAAAAATTT
* * **
14228 AAGAGCCTTTTTGATGCATTTTGAAAGTTCACGTACCCAATTGAGTG-TGAAAAAGGCAGGAGCT
1 AAGAGCCTTTTTGATGCA-TTTGAAAGATCAAGTACCCAATTGAGTGCAAAAAAAGGCAGGAGCT
**
14292 TAATTGTTTTTTTT
65 TAATTACTTTTTTT
14306 TTAACTTTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
90 43 0.64
91 24 0.36
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (90 bp):
AAGAGCCTTTTTGATGCATTTGAAAGATCAAGTACCCAATTGAGTGCAAAAAAAGGCAGGAGCTT
AATTACTTTTTTTGAAAAAAAATTT
Found at i:16264 original size:11 final size:11
Alignment explanation
Indices: 16248--16279 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
16238 GGGGGGATTT
16248 GAGAGAAAAGA
1 GAGAGAAAAGA
16259 GAGAGAAAAGA
1 GAGAGAAAAGA
16270 GAGAGAAAAG
1 GAGAGAAAAG
16280 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
GAGAGAAAAGA
Found at i:16695 original size:29 final size:29
Alignment explanation
Indices: 16663--16781 Score: 104
Period size: 29 Copynumber: 4.1 Consensus size: 29
16653 AAAATTACAT
16663 TTTGACCCCCAAAC-TTCCAAAAATTTGAA
1 TTTGACCCCCAAACTTTCCAAAAATTT-AA
* *
16692 TTTGACCCTCAAAC-TTCCCAAAATTTAGA
1 TTTGACCCCCAAACTTTCCAAAAATTTA-A
* *
16721 TTTAACCCTTC-AACTTTCCAAAAATTTAAA
1 TTTGACCC-CCAAACTTTCCAAAAATTT-AA
* *
16751 TTTG-GCCCCAGAACTTTCC-AAAATTTCA
1 TTTGACCCCCA-AACTTTCCAAAAATTTAA
16779 TTT
1 TTT
16782 TGATATCATT
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
28 6 0.08
29 44 0.58
30 25 0.33
31 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTGACCCCCAAACTTTCCAAAAATTTAA
Found at i:16766 original size:30 final size:28
Alignment explanation
Indices: 16663--16773 Score: 107
Period size: 30 Copynumber: 3.8 Consensus size: 28
16653 AAAATTACAT
*
16663 TTTGACCCCCAAACTTCCAAAAATTTGAA
1 TTTGA-CCCCAAACTTCCAAAAATTTAAA
* *
16692 TTTGACCCTCAAACTTCCCAAAATTTAGA
1 TTTGACCC-CAAACTTCCAAAAATTTAAA
*
16721 TTTAACCCTTC-AACTTTCCAAAAATTTAAA
1 TTTGACCC--CAAAC-TTCCAAAAATTTAAA
*
16751 TTTGGCCCCAGAACTTTCCAAAA
1 TTTGACCCCA-AAC-TTCCAAAA
16774 TTTCATTTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
28 4 0.06
29 32 0.46
30 33 0.48
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (28 bp):
TTTGACCCCAAACTTCCAAAAATTTAAA
Found at i:22842 original size:33 final size:33
Alignment explanation
Indices: 22805--22904 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 33
22795 AGGAGAACAG
* *
22805 AATGATGAAGTTG-CCTCGGGAGATGTTCAAATC
1 AATGATGAAGCTGCCCT-GAGAGATGTTCAAATC
* *
22838 AATGATGAAGCTGCCCTGATAGATGTTCCAATC
1 AATGATGAAGCTGCCCTGAGAGATGTTCAAATC
* * * *
22871 ATTGATGAAGCTGCCCTGATAGTTGTTCCAATC
1 AATGATGAAGCTGCCCTGAGAGATGTTCAAATC
22904 A
1 A
22905 TTTATGTTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 57 0.95
34 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (33 bp):
AATGATGAAGCTGCCCTGAGAGATGTTCAAATC
Found at i:22905 original size:33 final size:33
Alignment explanation
Indices: 22825--22906 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
22815 TTGCCTCGGG
* *
22825 AGATGTTCAAATCAATGATGAAGCTGCCCTGAT
1 AGATGTTCCAATCATTGATGAAGCTGCCCTGAT
22858 AGATGTTCCAATCATTGATGAAGCTGCCCTGAT
1 AGATGTTCCAATCATTGATGAAGCTGCCCTGAT
*
22891 AGTTGTTCCAATCATT
1 AGATGTTCCAATCATT
22907 TATGTTGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (33 bp):
AGATGTTCCAATCATTGATGAAGCTGCCCTGAT
Found at i:26726 original size:33 final size:33
Alignment explanation
Indices: 26664--26761 Score: 99
Period size: 33 Copynumber: 3.0 Consensus size: 33
26654 AGGCGAACAG
* * * *
26664 AATGATAAAGCTGCCTCGAGAGATGTTCCAATC
1 AATGATGAAGCCGCCTTGATAGATGTTCCAATC
* **
26697 AATGCTGAAGTTG-CTCTGATAGATGTTCCAATC
1 AATGATGAAGCCGCCT-TGATAGATGTTCCAATC
* *
26730 ATTGATGAAGCCGCCTTGATAGTTGTTCCAAT
1 AATGATGAAGCCGCCTTGATAGATGTTCCAAT
26762 AACTTATGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 2 0.04
33 49 0.92
34 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (33 bp):
AATGATGAAGCCGCCTTGATAGATGTTCCAATC
Found at i:27313 original size:22 final size:22
Alignment explanation
Indices: 27288--27364 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
27278 CATGGTGATG
27288 AATTATGTCTCTTAAGTTCAAA
1 AATTATGTCTCTTAAGTTCAAA
* * *
27310 AATTATATCACTATATTA-TTAACAATG
1 AATTATGTCTCT-TA--AGTT--CAA-A
27337 AATTATGTCTCTTAAGTTCAAA
1 AATTATGTCTCTTAAGTTCAAA
27359 AATTAT
1 AATTAT
27365 ATCACTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 16 0.38
23 5 0.12
24 3 0.07
25 3 0.07
26 5 0.12
27 10 0.24
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (22 bp):
AATTATGTCTCTTAAGTTCAAA
Found at i:27338 original size:49 final size:49
Alignment explanation
Indices: 27285--27393 Score: 209
Period size: 49 Copynumber: 2.2 Consensus size: 49
27275 TTTCATGGTG
27285 ATGAATTATGTCTCTTAAGTTCAAAAATTATATCACTATATTATTAACA
1 ATGAATTATGTCTCTTAAGTTCAAAAATTATATCACTATATTATTAACA
27334 ATGAATTATGTCTCTTAAGTTCAAAAATTATATCACTATATTATTAACA
1 ATGAATTATGTCTCTTAAGTTCAAAAATTATATCACTATATTATTAACA
*
27383 ATGAATCATGT
1 ATGAATTATGT
27394 TTATTGTTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (49 bp):
ATGAATTATGTCTCTTAAGTTCAAAAATTATATCACTATATTATTAACA
Found at i:28366 original size:49 final size:49
Alignment explanation
Indices: 28313--28467 Score: 132
Period size: 49 Copynumber: 3.1 Consensus size: 49
28303 GGATATGGTT
*
28313 TTATTGTGTTTATCTTTTTATCTTGAATTCAATTTTGCTAGGATAAAAA
1 TTATTGTGTTTATCTTTTTATCTTGATTTCAATTTTGCTAGGATAAAAA
* * * * * * * * **** **
28362 TTATTGTATTAATCTCTTTTTTATTTATTTTAATTCTCCTTCTTTATAATT
1 TTATTGTGTTTATCT-TTTTATCTTGATTTCAATTTTGCTAGGATA-AAAA
*
28413 TTATTGTGTTTAT-TTTTTATCTCGATTTCAATTTTGCTAGGATAAAAA
1 TTATTGTGTTTATCTTTTTATCTTGATTTCAATTTTGCTAGGATAAAAA
*
28461 TTGTTGT
1 TTATTGT
28468 ATTAATCTCT
Statistics
Matches: 73, Mismatches: 31, Indels: 5
0.67 0.28 0.05
Matches are distributed among these distances:
48 8 0.11
49 32 0.44
50 20 0.27
51 13 0.18
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.57
Consensus pattern (49 bp):
TTATTGTGTTTATCTTTTTATCTTGATTTCAATTTTGCTAGGATAAAAA
Found at i:28443 original size:99 final size:100
Alignment explanation
Indices: 28311--28529 Score: 350
Period size: 99 Copynumber: 2.2 Consensus size: 100
28301 TTGGATATGG
*
28311 TTTTATTGTGTTTATCTTTTTATCTTGAATTCAATTTTGCTAGGATAAAAATTATTGTATTAATC
1 TTTTATTGTGTTTAT-TTTTTATCTCGAATTCAATTTTGCTAGGATAAAAATTATTGTATTAATC
*
28376 TCTTTTTTATTTATTTTAATTCTCCTTCTTTATAA-
65 TCTTTGTTATTTATTTTAATTCTCCTTCTTTATAAT
* *
28411 TTTTATTGTGTTTATTTTTTATCTCGATTTCAATTTTGCTAGGATAAAAATTGTTGTATTAATCT
1 TTTTATTGTGTTTATTTTTTATCTCGAATTCAATTTTGCTAGGATAAAAATTATTGTATTAATCT
* * *
28476 CTTTGTTATTTCTTTTATTTTTCCTTCTTTATAAT
66 CTTTGTTATTTATTTTAATTCTCCTTCTTTATAAT
*
28511 TTTTATTGTGCTTATTTTT
1 TTTTATTGTGTTTATTTTT
28530 GTTTAAATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
99 77 0.70
100 33 0.30
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (100 bp):
TTTTATTGTGTTTATTTTTTATCTCGAATTCAATTTTGCTAGGATAAAAATTATTGTATTAATCT
CTTTGTTATTTATTTTAATTCTCCTTCTTTATAAT
Found at i:33093 original size:23 final size:25
Alignment explanation
Indices: 33067--33112 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33057 CCAATTAGGG
33067 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
33090 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
33113 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:34190 original size:21 final size:20
Alignment explanation
Indices: 34170--34212 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34160 TTAGCTATTT
34170 TTTTATTA-TTT-ATTTTTA
1 TTTTATTATTTTCATTTTTA
34188 TTTTATTATTTTCATTTTTA
1 TTTTATTATTTTCATTTTTA
*
34208 ATTTA
1 TTTTA
34213 ATTTTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTATTTTCATTTTTA
Found at i:34196 original size:14 final size:14
Alignment explanation
Indices: 34165--34205 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
34155 TTACTTTAGC
*
34165 TATT-TTTTTATTA
1 TATTATTTTTATTT
34178 T-TTATTTTTATTT
1 TATTATTTTTATTT
*
34191 TATTATTTTCATTT
1 TATTATTTTTATTT
34205 T
1 T
34206 TAATTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 12 0.50
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTATTTTTATTT
Found at i:39796 original size:27 final size:27
Alignment explanation
Indices: 39765--39816 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
39755 ATTAGTATAT
39765 TTATTTTCAATTTT-ATTTTATTTTATC
1 TTATTTT-AATTTTAATTTTATTTTATC
39792 TTATTTTAATTTTAATTTTATTTTA
1 TTATTTTAATTTTAATTTTATTTTA
39817 ATTATGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (27 bp):
TTATTTTAATTTTAATTTTATTTTATC
Found at i:39805 original size:6 final size:5
Alignment explanation
Indices: 39764--39816 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
39754 AATTAGTATA
*
39764 TTTAT TTTCAAT TTTAT TTTAT TTTAT CTTAT TTTAAT TTTAAT TTTAT
1 TTTAT TTT--AT TTTAT TTTAT TTTAT TTTAT TTT-AT TTT-AT TTTAT
39813 TTTA
1 TTTA
39817 ATTATGCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 27 0.63
6 11 0.26
7 5 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:39817 original size:17 final size:17
Alignment explanation
Indices: 39767--39819 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
39757 TAGTATATTT
39767 ATTTTCAATTTTATTTT-
1 ATTTT-AATTTTATTTTA
*
39784 ATTTT-ATCTTATTTTA
1 ATTTTAATTTTATTTTA
39800 ATTTTAATTTTATTTTA
1 ATTTTAATTTTATTTTA
39817 ATT
1 ATT
39820 ATGCACTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 9 0.28
16 5 0.16
17 18 0.56
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTTATTTTA
Done.