Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013385.1 Kokia drynarioides strain JFW-HI SEQ_128408, 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: 115927
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:313 original size:4 final size:4
Alignment explanation
Indices: 306--347 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
296 TTCTTCCTTC
*
306 TTCT TTCT TTCT TTCT TTCT TTCT CTT-T TTAT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
348 CTTCATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
3 5 0.15
4 27 0.79
5 2 0.06
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:323 original size:12 final size:11
Alignment explanation
Indices: 303--358 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
293 TCCTTCTTCC
*
303 TTCTTCTTTCT
1 TTCTTTTTTCT
314 TTCTTTCTTTCT
1 TTCTTT-TTTCT
*
326 TTCTCTTTTTAT
1 TTCT-TTTTTCT
*
338 TTCTTTTTTCC
1 TTCTTTTTTCT
*
349 TTCATTTTTC
1 TTCTTTTTTC
359 GTTGGTCCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 19 0.50
12 17 0.45
13 2 0.05
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:3607 original size:41 final size:41
Alignment explanation
Indices: 3562--3652 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
3552 TCAATTAAAT
* *
3562 AAAAAATAACAAAAAAATGAGTATTCATCATAATAGAAACA
1 AAAAAATAACAAAAAAATGAGTATTCATCAAAACAGAAACA
3603 AAAAAATAACAAAAAAATGAGTATTCATCAAAACAGAAACA
1 AAAAAATAACAAAAAAATGAGTATTCATCAAAACAGAAACA
*
3644 AGAAAATAA
1 AAAAAATAA
3653 AAGAGTAGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.66, C:0.10, G:0.08, T:0.16
Consensus pattern (41 bp):
AAAAAATAACAAAAAAATGAGTATTCATCAAAACAGAAACA
Found at i:14219 original size:29 final size:29
Alignment explanation
Indices: 14187--14273 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 29
14177 ATACTTAGAG
14187 AATAAAACCTCACTATTTTCGGGCAAAGT
1 AATAAAACCTCACTATTTTCGGGCAAAGT
* * * * * * *
14216 AATAATATCTTA-TA-ATAC--TCAGAG-
1 AATAAAACCTCACTATTTTCGGGCAAAGT
14240 AATAAAACCTCACTATTTTCGGGCAAAGT
1 AATAAAACCTCACTATTTTCGGGCAAAGT
14269 AATAA
1 AATAA
14274 TATCTTATAA
Statistics
Matches: 39, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
24 9 0.23
25 6 0.15
26 2 0.05
27 2 0.05
28 6 0.15
29 14 0.36
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (29 bp):
AATAAAACCTCACTATTTTCGGGCAAAGT
Found at i:14246 original size:53 final size:53
Alignment explanation
Indices: 14167--14284 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 53
14157 TATTCTGAAA
* *
14167 AATATATT-TAATACTTAGAGAATAAAACCTCACTATTTTCGGGCAAAGTAAT
1 AATATCTTATAATACTCAGAGAATAAAACCTCACTATTTTCGGGCAAAGTAAT
14219 AATATCTTATAATACTCAGAGAATAAAACCTCACTATTTTCGGGCAAAGTAAT
1 AATATCTTATAATACTCAGAGAATAAAACCTCACTATTTTCGGGCAAAGTAAT
14272 AATATCTTATAAT
1 AATATCTTATAAT
14285 TATAATTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 7 0.11
53 56 0.89
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (53 bp):
AATATCTTATAATACTCAGAGAATAAAACCTCACTATTTTCGGGCAAAGTAAT
Found at i:18012 original size:28 final size:28
Alignment explanation
Indices: 17972--18028 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17962 ACTATTAGGC
17972 AGGTTGTTAAATGTTTTAATTTTTTTTT
1 AGGTTGTTAAATGTTTTAATTTTTTTTT
18000 AGGTTGTTAAATGTTTTAATTTTTTTTT
1 AGGTTGTTAAATGTTTTAATTTTTTTTT
18028 A
1 A
18029 CTTTTCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (28 bp):
AGGTTGTTAAATGTTTTAATTTTTTTTT
Found at i:20755 original size:27 final size:27
Alignment explanation
Indices: 20714--20777 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
20704 CGCAACTCTA
20714 ACCTAGGCCACACTTGGGGCTGTGAAC
1 ACCTAGGCCACACTTGGGGCTGTGAAC
*
20741 ACTTAGGCCACACTTGGGGCTGTGAAC
1 ACCTAGGCCACACTTGGGGCTGTGAAC
20768 ACCTAGGCCA
1 ACCTAGGCCA
20778 TTAAACCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (27 bp):
ACCTAGGCCACACTTGGGGCTGTGAAC
Found at i:28916 original size:12 final size:12
Alignment explanation
Indices: 28899--28925 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28889 ATTCTCTCGC
28899 CCTTTATATGGT
1 CCTTTATATGGT
28911 CCTTTATATGGT
1 CCTTTATATGGT
28923 CCT
1 CCT
28926 CATTTAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (12 bp):
CCTTTATATGGT
Found at i:29939 original size:22 final size:23
Alignment explanation
Indices: 29914--29959 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
29904 TACTGAAATC
29914 ATATATGA-AATTATTT-GAAAAA
1 ATAT-TGATAATTATTTGGAAAAA
*
29936 ATATTTATAATTATTTGGAAAAA
1 ATATTGATAATTATTTGGAAAAA
29959 A
1 A
29960 AATTATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 12 0.57
23 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATTGATAATTATTTGGAAAAA
Found at i:29965 original size:22 final size:22
Alignment explanation
Indices: 29922--29965 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29912 TCATATATGA
*
29922 AATTATTTGAAAAAATATTTAT
1 AATTATTTGAAAAAATAATTAT
29944 AATTATTTGGAAAAAA-AATTAT
1 AATTATTT-GAAAAAATAATTAT
29966 TAGTCGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATTATTTGAAAAAATAATTAT
Found at i:30553 original size:2 final size:2
Alignment explanation
Indices: 30546--30577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30536 ATCTATTTTG
30546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30578 TTTAATTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36356 original size:43 final size:41
Alignment explanation
Indices: 36309--36395 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
36299 AATAACATTC
* *
36309 AAACAACCAAAATAACAATC-AAAACAGCAATAAAATAATAGCA
1 AAACAACAAAAATAAC-ATCTAAAACAACAA-AAAA-AATAGCA
* *
36352 AAACAACAAAAATAGCATCTAAAATAACAAAAAAAATAGCA
1 AAACAACAAAAATAACATCTAAAACAACAAAAAAAATAGCA
36393 AAA
1 AAA
36396 AAAATAACAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 10 0.26
42 7 0.18
43 22 0.56
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (41 bp):
AAACAACAAAAATAACATCTAAAACAACAAAAAAAATAGCA
Found at i:36387 original size:12 final size:12
Alignment explanation
Indices: 36372--36404 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
36362 AATAGCATCT
36372 AAAATAACAAAA
1 AAAATAACAAAA
*
36384 AAAATAGCAAAA
1 AAAATAACAAAA
36396 AAAATAACA
1 AAAATAACA
36405 GCATCAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (12 bp):
AAAATAACAAAA
Found at i:36399 original size:24 final size:24
Alignment explanation
Indices: 36353--36404 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
36343 ATAATAGCAA
* ***
36353 AACAACAAAAATAGCATCTAAAAT
1 AACAAAAAAAATAGCAAAAAAAAT
36377 AACAAAAAAAATAGCAAAAAAAAT
1 AACAAAAAAAATAGCAAAAAAAAT
36401 AACA
1 AACA
36405 GCATCAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.71, C:0.13, G:0.04, T:0.12
Consensus pattern (24 bp):
AACAAAAAAAATAGCAAAAAAAAT
Found at i:57269 original size:27 final size:28
Alignment explanation
Indices: 57239--57351 Score: 88
Period size: 28 Copynumber: 4.1 Consensus size: 28
57229 AAAGAAAAGT
57239 CTTTGTGGCAAACTCTGAAA-GAATAAC
1 CTTTGTGGCAAACTCTGAAAGGAATAAC
* * * *
57266 CTTTGTAGCAAGCTTTGAAAGGAATAGC
1 CTTTGTGGCAAACTCTGAAAGGAATAAC
* * * * *
57294 CTTTGTGGAAAACTTTAAAATGAAAAAC
1 CTTTGTGGCAAACTCTGAAAGGAATAAC
* **
57322 CCTTGTGGCTCACTCT-ACAA-GAATAAC
1 CTTTGTGGCAAACTCTGA-AAGGAATAAC
57349 CTT
1 CTT
57352 CATGGTGAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
27 26 0.39
28 40 0.61
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (28 bp):
CTTTGTGGCAAACTCTGAAAGGAATAAC
Found at i:57298 original size:28 final size:27
Alignment explanation
Indices: 57239--57299 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
57229 AAAGAAAAGT
*
57239 CTTTGTGGCAAACTCTGAAAGAATAAC
1 CTTTGTAGCAAACTCTGAAAGAATAAC
* * *
57266 CTTTGTAGCAAGCTTTGAAAGGAATAGC
1 CTTTGTAGCAAACTCTGAAA-GAATAAC
57294 CTTTGT
1 CTTTGT
57300 GGAAAACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (27 bp):
CTTTGTAGCAAACTCTGAAAGAATAAC
Found at i:57309 original size:28 final size:27
Alignment explanation
Indices: 57239--57330 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
57229 AAAGAAAAGT
*
57239 CTTTGTGGCAAACTCTGAAAGAATAAC
1 CTTTGTGGCAAACTTTGAAAGAATAAC
* * *
57266 CTTTGTAGCAAGCTTTGAAAGGAATAGC
1 CTTTGTGGCAAACTTTGAAA-GAATAAC
* * *
57294 CTTTGTGGAAAACTTTAAAATGAAAAAC
1 CTTTGTGGCAAACTTTGAAA-GAATAAC
*
57322 CCTTGTGGC
1 CTTTGTGGC
57331 TCACTCTACA
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 17 0.33
28 34 0.67
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (27 bp):
CTTTGTGGCAAACTTTGAAAGAATAAC
Found at i:59935 original size:11 final size:10
Alignment explanation
Indices: 59905--59938 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
59895 AAGTTATATG
59905 TAATCTAGTT
1 TAATCTAGTT
59915 TAAT-TAGTT
1 TAATCTAGTT
59924 TAATCATAGTT
1 TAATC-TAGTT
59935 TAAT
1 TAAT
59939 TTACATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (10 bp):
TAATCTAGTT
Found at i:59958 original size:21 final size:21
Alignment explanation
Indices: 59934--60004 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
59924 TAATCATAGT
59934 TTAATTTACATTAATGATCTA
1 TTAATTTACATTAATGATCTA
* *
59955 TTAA-TTAAACTTAAT-AGC-A
1 TTAATTTACA-TTAATGATCTA
*
59974 TCT-ATTTATATTAATGATCTA
1 T-TAATTTACATTAATGATCTA
59995 TTAATTTACA
1 TTAATTTACA
60005 ACAAAGAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 8 0.21
20 14 0.36
21 17 0.44
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAATTTACATTAATGATCTA
Found at i:66034 original size:21 final size:21
Alignment explanation
Indices: 65988--66062 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
65978 ATAATGCAAA
* *
65988 CTTCTACCGATACAAGTGACA
1 CTTCTACTGATACAAGTGACT
*
66009 GTTCTACTGATACAAGTGACT
1 CTTCTACTGATACAAGTGACT
* * *
66030 CTTCTATTGAAACAAGT-ATT
1 CTTCTACTGATACAAGTGACT
66050 ACTTCTAC-GATAC
1 -CTTCTACTGATAC
66063 TAAAAACTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 6 0.14
21 38 0.86
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (21 bp):
CTTCTACTGATACAAGTGACT
Found at i:66835 original size:52 final size:53
Alignment explanation
Indices: 66731--66970 Score: 210
Period size: 52 Copynumber: 4.6 Consensus size: 53
66721 TGCATTTTTA
* * ** * *
66731 ATACTCACAATGACACAGAGTCATCAGA-C-CATTAATC-CATATTGGGAATCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCA-TAATCGCATA-AGGGATTCAT
*
66783 ATACTCATGATGACACATAGTCATTGGACCTCATAATC-CATAAGGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCGCATAAGGGATTCAT
* * * *
66835 ATACTCACGATGACATATAATCATTGGACCTCATAATTCGTATAA--GATTAAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAA-TCGCATAAGGGATTCAT
* * * * *
66887 ATACTCATGATGACACAGAGTCATCGGACCT-TTAATCTG-A-AATAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATC-GCATAA-GGGATTCAT
*
66939 ATAACTCACGATGACACAAAGTCATTGGACCT
1 AT-ACTCACGATGACACATAGTCATTGGACCT
66971 TTTTGCATTT
Statistics
Matches: 157, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
49 2 0.01
50 3 0.02
51 4 0.03
52 104 0.66
53 38 0.24
54 6 0.04
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (53 bp):
ATACTCACGATGACACATAGTCATTGGACCTCATAATCGCATAAGGGATTCAT
Found at i:66916 original size:104 final size:105
Alignment explanation
Indices: 66781--66970 Score: 271
Period size: 104 Copynumber: 1.8 Consensus size: 105
66771 ATTGGGAATC
* * *
66781 ATATACTCATGATGACACATAGTCATTGGACCTCATAATC-CATAA-GGGATTCATAT-ACTCAC
1 ATATACTCATGATGACACAGAGTCATCGGACCT-ATAATCTCA-AATAGGATTCATATAACTCAC
*
66843 GATGACATATAA-TCATTGGACCTCATAATTCGTATAAGATTA
64 GATGACACA-AAGTCATTGGACCTCATAATTCGTATAAGATTA
* *
66885 ATATACTCATGATGACACAGAGTCATCGGACCTTTAATCTGAAATAGGATTCATATAACTCACGA
1 ATATACTCATGATGACACAGAGTCATCGGACCTATAATCTCAAATAGGATTCATATAACTCACGA
66950 TGACACAAAGTCATTGGACCT
66 TGACACAAAGTCATTGGACCT
66971 TTTTGCATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
103 7 0.09
104 44 0.58
105 25 0.33
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (105 bp):
ATATACTCATGATGACACAGAGTCATCGGACCTATAATCTCAAATAGGATTCATATAACTCACGA
TGACACAAAGTCATTGGACCTCATAATTCGTATAAGATTA
Found at i:70334 original size:6 final size:6
Alignment explanation
Indices: 70323--70361 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
70313 TGATCAAAAT
* * *
70323 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
70362 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:75238 original size:16 final size:16
Alignment explanation
Indices: 75206--75235 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
75196 AAAATTTTAC
75206 TGTTAAATTTTATAAT
1 TGTTAAATTTTATAAT
75222 TGTTAAA-TTTATAA
1 TGTTAAATTTTATAA
75236 ATTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TGTTAAATTTTATAAT
Found at i:76802 original size:16 final size:16
Alignment explanation
Indices: 76781--76811 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76771 TAATTTACTG
*
76781 ATTACAGTTCTATTCT
1 ATTACAGTCCTATTCT
76797 ATTACAGTCCTATTC
1 ATTACAGTCCTATTC
76812 AATTCCAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTACAGTCCTATTCT
Found at i:78822 original size:29 final size:29
Alignment explanation
Indices: 78778--78999 Score: 218
Period size: 29 Copynumber: 7.6 Consensus size: 29
78768 TCCTAAGCTG
** *
78778 TCCAAAAATTTTATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* *
78807 TCCAAAAATTTCATTTTTAGCCTCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* *
78836 TCCAAAAATTTCATTTTTAGCCTCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* *
78865 TCCAAAAATCCCGTTTTT-GACCCCGAAACT
1 TCCAAAAATTCCATTTTTAG-CCCCG-AACT
* *
78895 TCCCAAAATTCCATTTTTAGCCCCAAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* *
78924 TCCAAAAATTCCATTTTT-GACTCCGAAAAT
1 TCCAAAAATTCCATTTTTAG-CCCCG-AACT
* *
78954 TCCTAAAATTACCA-TTTTACCCCCGAA-T
1 TCCAAAAATT-CCATTTTTAGCCCCGAACT
*
78982 GTCCAAAAACTCCATTTT
1 -TCCAAAAATTCCATTTT
79000 CGACTTTGAA
Statistics
Matches: 164, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
28 6 0.04
29 111 0.68
30 43 0.26
31 4 0.02
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTAGCCCCGAACT
Found at i:78912 original size:59 final size:59
Alignment explanation
Indices: 78778--79058 Score: 259
Period size: 59 Copynumber: 4.8 Consensus size: 59
78768 TCCTAAGCTG
** * * *
78778 TCCAAAAATTTTATTTTTACCCCCGAACTTCCAAAAATTTCATTTTT-AGCCTCG-AACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGA-CCCCGAAACT
* * * *
78836 TCCAAAAATTTCATTTTTAGCCTCGAACTTCCAAAAATCCCGTTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * *
78895 TCCCAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTGACTCCGAAAAT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * * ***
78954 TCCTAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCATTTTCGACTTTGAAACT
1 TCCAAAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAATTCCATTTTTGACCCCGAAACT
* * * *
79013 TCCTAAAATTACCA-TTTTACCCCCGGA-TGTCCAAAAACTCCATTTT
1 TCCAAAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAATTCCATTTT
79059 CGATCTCGAA
Statistics
Matches: 195, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
58 46 0.24
59 146 0.75
60 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
Found at i:78976 original size:88 final size:86
Alignment explanation
Indices: 78792--78999 Score: 224
Period size: 88 Copynumber: 2.4 Consensus size: 86
78782 AAAATTTTAT
* * * * *
78792 TTTTACCCCCGAACTTCCAAAAATTTCATTTTTAGCCTCGAACTTCCAAAAATTTCATTTTTAGC
1 TTTTA-CCCCGAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTAGA
* * *
78857 CTCGAACTTCCAAAAATCCCGT
65 CTCGAAATTCCAAAAATACCGA
*
78879 TTTTGACCCCGAAACTTCCCAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTT-G
1 TTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTAG
*
78943 ACTCCGAAAATTCCTAAAATTACC-A
64 ACT-CG-AAATTCC-AAAAATACCGA
*
78968 TTTTACCCCCGAA-TGTCCAAAAACTCCATTTT
1 TTTTA-CCCCGAACT-TCCAAAAATTCCATTTT
79000 CGACTTTGAA
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
87 13 0.13
88 67 0.66
89 15 0.15
90 7 0.07
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.33
Consensus pattern (86 bp):
TTTTACCCCGAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTAGAC
TCGAAATTCCAAAAATACCGA
Found at i:78980 original size:30 final size:29
Alignment explanation
Indices: 78778--79058 Score: 161
Period size: 29 Copynumber: 9.6 Consensus size: 29
78768 TCCTAAGCTG
**
78778 TCCAAAAATTTTATTTTTACCCCCG-AACT
1 TCCAAAAATTCCA-TTTTACCCCCGAAACT
* * *
78807 TCCAAAAATTTCATTTTTAGCCTCG-AACT
1 TCCAAAAATTCCA-TTTTACCCCCGAAACT
* * *
78836 TCCAAAAATTTCATTTTTAGCCTCG-AACT
1 TCCAAAAATTCCA-TTTTACCCCCGAAACT
* *
78865 TCCAAAAATCCCGTTTTTGA-CCCCGAAACT
1 TCCAAAAATTCC-ATTTT-ACCCCCGAAACT
* *
78895 TCCCAAAATTCCATTTTTAGCCCC-AAACT
1 TCCAAAAATTCCA-TTTTACCCCCGAAACT
* *
78924 TCCAAAAATTCCATTTTTGA-CTCCGAAAAT
1 TCCAAAAATTCCA-TTTT-ACCCCCGAAACT
*
78954 TCCTAAAATTACCATTTTACCCCCG-AA-T
1 TCCAAAAATT-CCATTTTACCCCCGAAACT
* ***
78982 GTCCAAAAACTCCATTTT-CGACTTTGAAACT
1 -TCCAAAAATTCCATTTTAC--CCCCGAAACT
* *
79013 TCCTAAAATTACCATTTTACCCCCG-GA-T
1 TCCAAAAATT-CCATTTTACCCCCGAAACT
*
79041 GTCCAAAAACTCCATTTT
1 -TCCAAAAATTCCATTTT
79059 CGATCTCGAA
Statistics
Matches: 207, Mismatches: 28, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.00
28 16 0.08
29 121 0.58
30 57 0.28
31 11 0.05
32 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTACCCCCGAAACT
Found at i:79107 original size:58 final size:59
Alignment explanation
Indices: 78888--79146 Score: 258
Period size: 59 Copynumber: 4.4 Consensus size: 59
78878 TTTTTGACCC
* * * * * *
78888 CGAAACTTCCCAAAATT-CCATTTTTAGCCCCAAACT-TCCAAAAATTCCATTTTTGACTC
1 CGAAACTTCCTAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCATTTTCGACTT
*
78947 CGAAAATTCCTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACTT
1 CGAAACTTCCTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACTT
* *
79006 TGAAACTTCCTAAAATTACCATTTTACCCCCGGATGTCCAAAAACTCCATTTTCGA-TCT
1 CGAAACTTCCTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACT-T
* ** * * * ** *
79065 CGAAAC-T-CTCAAAATTACCCTTTTACCCCTAAATGTCTAAAAATTCTATTTTTAACCT
1 CGAAACTTCCT-AAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACTT
** *
79123 CGAATTTTCCCAAAATTACCATTT
1 CGAAACTTCCTAAAATTACCATTT
79147 CGCTCTCAAG
Statistics
Matches: 168, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
57 2 0.01
58 44 0.26
59 118 0.70
60 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
CGAAACTTCCTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACTT
Found at i:79138 original size:117 final size:118
Alignment explanation
Indices: 78888--79146 Score: 276
Period size: 117 Copynumber: 2.2 Consensus size: 118
78878 TTTTTGACCC
* * *
78888 CGAAACTTCCCAAAATT-CCATTTTTAGCCCCAAACTTCCAAAAATTCCATTTTTGACTCCGAAA
1 CGAAACTTCCCAAAATTACCA-TTTTACCCCCAAACTTCCAAAAACTCCATTTTCGACTCCGAAA
* * *
78952 ATTCCTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTCGACTT
65 ATTCCTAAAATTACCATTTTACCCCCAAATGTCCAAAAACTCCATTTTCAACCT
* * **
79006 TGAAACTTCCTAAAATTACCATTTTACCCCCGGA-TGTCCAAAAACTCCATTTTCGA-TCTCG-A
1 CGAAACTTCCCAAAATTACCATTTTACCCCCAAACT-TCCAAAAACTCCATTTTCGACTC-CGAA
* * * * * * *
79068 AACT-CTCAAAATTACCCTTTTACCCCTAAATGTCTAAAAATTCTATTTTTAACCT
64 AATTCCT-AAAATTACCATTTTACCCCCAAATGTCCAAAAACTCCATTTTCAACCT
**
79123 CGAATTTTCCCAAAATTACCATTT
1 CGAAACTTCCCAAAATTACCATTT
79147 CGCTCTCAAG
Statistics
Matches: 116, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
116 2 0.02
117 66 0.57
118 45 0.39
119 3 0.03
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (118 bp):
CGAAACTTCCCAAAATTACCATTTTACCCCCAAACTTCCAAAAACTCCATTTTCGACTCCGAAAA
TTCCTAAAATTACCATTTTACCCCCAAATGTCCAAAAACTCCATTTTCAACCT
Found at i:81985 original size:4 final size:4
Alignment explanation
Indices: 81976--82002 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
81966 ATTCTCAAAT
81976 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
82003 TAAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:83652 original size:19 final size:19
Alignment explanation
Indices: 83605--83652 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
83595 GGGCGACATC
*
83605 AATTATAAAAATAATATTTT
1 AATT-TAAAAATAATATTTG
**
83625 AATAAAAAAATAATATTTG
1 AATTTAAAAATAATATTTG
83644 AATTTAAAA
1 AATTTAAAA
83653 GGGTGACGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTTAAAAATAATATTTG
Found at i:85271 original size:4 final size:4
Alignment explanation
Indices: 85262--85304 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
85252 GCGTTTACAT
* *
85262 ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
85305 CCTTCGTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:94072 original size:31 final size:31
Alignment explanation
Indices: 94034--94095 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
94024 TTTAGCAAAA
*
94034 ATTAATATTTTTTGCTTATTTTGAAAGTGTC
1 ATTAATATTTTTCGCTTATTTTGAAAGTGTC
94065 ATTAATATTTTTCGCTTATTTTGAAAGTGTC
1 ATTAATATTTTTCGCTTATTTTGAAAGTGTC
94096 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (31 bp):
ATTAATATTTTTCGCTTATTTTGAAAGTGTC
Found at i:95384 original size:22 final size:22
Alignment explanation
Indices: 95357--95401 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
95347 GTGGTGTGAA
95357 TCGTAGGTTCTATGTCAAAACT
1 TCGTAGGTTCTATGTCAAAACT
95379 TCGTAGGTTCTATGTCAAAACT
1 TCGTAGGTTCTATGTCAAAACT
95401 T
1 T
95402 AATTTCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (22 bp):
TCGTAGGTTCTATGTCAAAACT
Found at i:96932 original size:15 final size:17
Alignment explanation
Indices: 96914--96948 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
96904 ATTATTTTCA
96914 TATTTA-TT-AATTTTT
1 TATTTATTTAAATTTTT
96929 TATTTATTTAAATTTTT
1 TATTTATTTAAATTTTT
96946 TAT
1 TAT
96949 ATAATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTTAAATTTTT
Found at i:98027 original size:19 final size:20
Alignment explanation
Indices: 98003--98043 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
97993 TTAATTAGAA
* *
98003 AATTAATTAAAT-TTATTTT
1 AATTAAATAAATAATATTTT
98022 AATTAAATAAATAATATTTT
1 AATTAAATAAATAATATTTT
98042 AA
1 AA
98044 GAGATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATAAATAATATTTT
Found at i:112772 original size:23 final size:23
Alignment explanation
Indices: 112742--112798 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
112732 CGTCCATTCT
112742 TGCTGACTAGACATTCTAGAAAC
1 TGCTGACTAGACATTCTAGAAAC
* * *
112765 TGCTGACTGGACCTTCTAGAAGC
1 TGCTGACTAGACATTCTAGAAAC
112788 TGCTGACTAGA
1 TGCTGACTAGA
112799 GGTCACGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (23 bp):
TGCTGACTAGACATTCTAGAAAC
Found at i:113544 original size:11 final size:10
Alignment explanation
Indices: 113525--113570 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
113515 AAGCAACCAT
113525 TTTTTTCTTC
1 TTTTTTCTTC
113535 TTTTTCTCTT-
1 TTTTT-TCTTC
113545 TTTTTT-TTC
1 TTTTTTCTTC
*
113554 TTTTTTTTTC
1 TTTTTTCTTC
113564 TATTTTT
1 T-TTTTT
113571 TTGCTATTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 2 0.06
9 7 0.22
10 14 0.44
11 9 0.28
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:113552 original size:22 final size:21
Alignment explanation
Indices: 113524--113572 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
113514 TAAGCAACCA
*
113524 TTTTTTTCTTCTTTTTCTCTTT
1 TTTTTTTCTT-TTTTTCTCTAT
*
113546 TTTTTTTCTTTTTTTTTCTAT
1 TTTTTTTCTTTTTTTCTCTAT
113567 TTTTTT
1 TTTTTT
113573 GCTATTCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTCTCTAT
Found at i:113561 original size:23 final size:22
Alignment explanation
Indices: 113524--113572 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
113514 TAAGCAACCA
*
113524 TTTTTTTCTTCTTTTTCTCTTT
1 TTTTTTTCTTCTTTTTCTATTT
*
113546 TTTTTTTCTTTTTTTTTCTATTT
1 TTTTTTTC-TTCTTTTTCTATTT
113569 TTTT
1 TTTT
113573 GCTATTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTTTCTTCTTTTTCTATTT
Found at i:113571 original size:11 final size:10
Alignment explanation
Indices: 113524--113572 Score: 62
Period size: 11 Copynumber: 4.6 Consensus size: 10
113514 TAAGCAACCA
113524 TTTTTTTCTT
1 TTTTTTTCTT
*
113534 CTTTTTCTCTTT
1 -TTTTTTTC-TT
113546 TTTTTTTCTT
1 TTTTTTTCTT
113556 TTTTTTTCTAT
1 TTTTTTTCT-T
113567 TTTTTT
1 TTTTTT
113573 GCTATTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 11 0.32
11 21 0.62
12 2 0.06
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:113577 original size:11 final size:11
Alignment explanation
Indices: 113524--113578 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
113514 TAAGCAACCA
113524 TTTTTTTCT-T
1 TTTTTTTCTAT
* *
113534 CTTTTTCTCTTT
1 -TTTTTTTCTAT
113546 TTTTTTTCT-T
1 TTTTTTTCTAT
113556 TTTTTTTCTAT
1 TTTTTTTCTAT
*
113567 TTTTTTGCTAT
1 TTTTTTTCTAT
113578 T
1 T
113579 CGTACAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
10 10 0.26
11 28 0.72
12 1 0.03
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTAT
Found at i:113639 original size:25 final size:27
Alignment explanation
Indices: 113590--113640 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
113580 GTACAAACAG
*
113590 TTTTCTCTCTTTTTTTTGCTATTCTTT
1 TTTTCTCTCTTTATTTTGCTATTCTTT
*
113617 TTTTCT-TCTTTATTTT-CTTTTCTT
1 TTTTCTCTCTTTATTTTGCTATTCTT
113641 CTTTATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTCTCTCTTTATTTTGCTATTCTTT
Done.