Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014629.1 Kokia drynarioides strain JFW-HI SEQ_129668, 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: 93069
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:353 original size:29 final size:29
Alignment explanation
Indices: 315--471 Score: 94
Period size: 31 Copynumber: 5.3 Consensus size: 29
305 AAAAAAGCTT
315 AGGTACCAAATTAGGAAAAATGCCAAGTTC
1 AGGTACCAAATTAGGAAAAATG-CAAGTTC
* * *
345 AGGTACAAAATT-GGATCCAAAA--AAAGTTT
1 AGGTACCAAATTAGGA---AAAATGCAAGTTC
374 AGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAA-TG-CAAGTTC
* * * *
405 AGGTA-AAAACTGGGTCAAAAA-G--AGTTT
1 AGGTACCAAATTAGG--AAAAATGCAAGTTC
* *
432 AAGTACCAAATTAGGAAAAAGTGTCGAGTTC
1 AGGTACCAAATTAGGAAAAA-TG-CAAGTTC
463 AGGTACCAA
1 AGGTACCAA
472 GTGTTATATT
Statistics
Matches: 95, Mismatches: 16, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
26 5 0.05
27 12 0.13
28 7 0.07
29 19 0.20
30 21 0.22
31 22 0.23
32 9 0.09
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (29 bp):
AGGTACCAAATTAGGAAAAATGCAAGTTC
Found at i:378 original size:59 final size:60
Alignment explanation
Indices: 286--468 Score: 255
Period size: 59 Copynumber: 3.1 Consensus size: 60
276 TAATAATTTT
* * * * *
286 AGGTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAA-TGCCAAGTTC
1 AGGTACAAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
345 AGGTACAAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACAAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
* * * * *
405 AGGTA-AAAACTGGGT-CAAAAAGAGTTTAAGTACCAAATTAGGAAAAAGTGTCGAGTTC
1 AGGTACAAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
463 AGGTAC
1 AGGTAC
469 CAAGTGTTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 45 0.40
59 53 0.47
60 14 0.12
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (60 bp):
AGGTACAAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
Found at i:4855 original size:43 final size:43
Alignment explanation
Indices: 4804--4891 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
4794 TGCACTGTCT
4804 TGGCAAAATTTTGAAACAAATCTTCATTTGCTAGTTGAGCTAA
1 TGGCAAAATTTTGAAACAAATCTTCATTTGCTAGTTGAGCTAA
*
4847 TGGCAAAATTTTGAAACAAATCTTTATTTGCTAGTTGAGCTAA
1 TGGCAAAATTTTGAAACAAATCTTCATTTGCTAGTTGAGCTAA
4890 TG
1 TG
4892 ACTTATAGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (43 bp):
TGGCAAAATTTTGAAACAAATCTTCATTTGCTAGTTGAGCTAA
Found at i:22687 original size:30 final size:28
Alignment explanation
Indices: 22627--22695 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
22617 TATTTATATC
22627 TTTATCATTTTTAAATAATTAAATCAAATT
1 TTTATCA-TTTTAAATAATTAAATCAAA-T
22657 TTTATCATTTTAGAAT-ATTAAAGTGC-AAT
1 TTTATCATTTTA-AATAATTAAA-T-CAAAT
22686 TTTA-CATTTT
1 TTTATCATTTT
22696 TTAATTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 6 0.17
29 16 0.44
30 13 0.36
31 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTATCATTTTAAATAATTAAATCAAAT
Found at i:29886 original size:27 final size:27
Alignment explanation
Indices: 29856--29911 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29846 ATTAAAAAAA
*
29856 CAAAAAAAGCAAAAGA-AAAACCAGCAG
1 CAAAAAAAG-AAAAAATAAAACCAGCAG
*
29883 CAAAACAAGAAAAAATAAAACCAGCAG
1 CAAAAAAAGAAAAAATAAAACCAGCAG
29910 CA
1 CA
29912 TAAACATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.66, C:0.20, G:0.12, T:0.02
Consensus pattern (27 bp):
CAAAAAAAGAAAAAATAAAACCAGCAG
Found at i:42803 original size:28 final size:27
Alignment explanation
Indices: 42779--42830 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
42769 GGCTTTTGAT
* *
42779 TTTTG-CATTTGAGTTTTGTGTTTTTA
1 TTTTGACAATTGAGTTTTGAGTTTTTA
42805 TTTTGAACAATTGAGTTTTGAGTTTT
1 TTTTG-ACAATTGAGTTTTGAGTTTT
42831 GAATTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
28 17 0.77
ACGTcount: A:0.17, C:0.04, G:0.19, T:0.60
Consensus pattern (27 bp):
TTTTGACAATTGAGTTTTGAGTTTTTA
Found at i:43554 original size:18 final size:18
Alignment explanation
Indices: 43531--43570 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43521 ATAATGACAA
*
43531 AATAAAA-AAATTTACATG
1 AATAAAATAAA-TTAAATG
43549 AATAAAATAAATTAAATG
1 AATAAAATAAATTAAATG
43567 AATA
1 AATA
43571 CAGTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
AATAAAATAAATTAAATG
Found at i:43934 original size:15 final size:15
Alignment explanation
Indices: 43889--43939 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
43879 AACGAGAATG
43889 TAAATAACAAA-AAA
1 TAAATAACAAATAAA
* * *
43903 TGAATAACCAATTAA
1 TAAATAACAAATAAA
*
43918 TAAATAATAAATAAA
1 TAAATAACAAATAAA
43933 TAAATAA
1 TAAATAA
43940 ATATATGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (15 bp):
TAAATAACAAATAAA
Found at i:44159 original size:15 final size:16
Alignment explanation
Indices: 44141--44174 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
44131 GAAGAACTAG
*
44141 ATAAATAAACA-AAAA
1 ATAAATAAAAATAAAA
44156 ATAAATAAAAATAAAA
1 ATAAATAAAAATAAAA
44172 ATA
1 ATA
44175 TAGAAGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
ATAAATAAAAATAAAA
Found at i:47809 original size:19 final size:20
Alignment explanation
Indices: 47771--47809 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
47761 TAATTTCATC
* *
47771 TTATTTTTACTTTAACCATT
1 TTATTCTTAATTTAACCATT
47791 TTATTCTTAATTT-ACCATT
1 TTATTCTTAATTTAACCATT
47810 CTACCCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTCTTAATTTAACCATT
Found at i:51842 original size:37 final size:37
Alignment explanation
Indices: 51796--51968 Score: 247
Period size: 37 Copynumber: 4.7 Consensus size: 37
51786 ATCACATAGT
*
51796 ATTATGCTCTAACCAAGACATAAGCCTTCCATATAAC
1 ATTATGCTCTAACCAAGACGTAAGCCTTCCATATAAC
* * *
51833 ATTACGCTCTAACCAAGACGTATGCCTTTCATATAAC
1 ATTATGCTCTAACCAAGACGTAAGCCTTCCATATAAC
* * *
51870 ATTATGCTCTAACCGAGATGTAAACCTTCCATATAAC
1 ATTATGCTCTAACCAAGACGTAAGCCTTCCATATAAC
* *
51907 ATTATGCTCTAACCGAGATGTAAGCCTTCCATATAAC
1 ATTATGCTCTAACCAAGACGTAAGCCTTCCATATAAC
* *
51944 ATTATGCTCTAACCGAGATGTAAGC
1 ATTATGCTCTAACCAAGACGTAAGC
51969 AACATAGTAG
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 125 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (37 bp):
ATTATGCTCTAACCAAGACGTAAGCCTTCCATATAAC
Found at i:51993 original size:36 final size:36
Alignment explanation
Indices: 51798--52033 Score: 179
Period size: 37 Copynumber: 6.4 Consensus size: 36
51788 CACATAGTAT
* ** ** *
51798 TATGCTCTAACCAAGACATAAGCCTTCCATATAACAT
1 TATGCTCTAACCGAGATGTAAG-CTAACATATAACAA
* * * * ** *
51835 TACGCTCTAACCAAGACGTATGCCTTTCATATAACAT
1 TATGCTCTAACCGAGATGTAAG-CTAACATATAACAA
* ** *
51872 TATGCTCTAACCGAGATGTAAACCTTCCATATAACAT
1 TATGCTCTAACCGAGATGT-AAGCTAACATATAACAA
** *
51909 TATGCTCTAACCGAGATGTAAGCCTTCCATATAACAT
1 TATGCTCTAACCGAGATGTAAG-CTAACATATAACAA
*
51946 TATGCTCTAACCGAGATGTAAGC-AACATAGTAGCAA
1 TATGCTCTAACCGAGATGTAAGCTAACATA-TAACAA
** * *
51982 TATGCTCTAACCGAGACATATGC-AACATTATAGCAA
1 TATGCTCTAACCGAGATGTAAGCTAACA-TATAACAA
52018 TATGCTCTAACCGAGA
1 TATGCTCTAACCGAGA
52034 CATATGAAAA
Statistics
Matches: 177, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
35 4 0.02
36 53 0.30
37 119 0.67
38 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (36 bp):
TATGCTCTAACCGAGATGTAAGCTAACATATAACAA
Found at i:52034 original size:36 final size:36
Alignment explanation
Indices: 51946--52149 Score: 257
Period size: 36 Copynumber: 5.6 Consensus size: 36
51936 CATATAACAT
** * *
51946 TATGCTCTAACCGAGATGTAAGCAACAT-AGTAGCAA
1 TATGCTCTAACCGAGACATATGCAACATCA-TAGCTA
* *
51982 TATGCTCTAACCGAGACATATGCAACATTATAGCAA
1 TATGCTCTAACCGAGACATATGCAACATCATAGCTA
* *
52018 TATGCTCTAACCGAGACATATGAAAACATCATAGTTA
1 TATGCTCTAACCGAGACATATG-CAACATCATAGCTA
* *
52055 TATGCTCTAACTGAGACATATGCATCATCATAGCTA
1 TATGCTCTAACCGAGACATATGCAACATCATAGCTA
* * *
52091 TATGCTCTAATCGAGACATAAGCATCATCATAGCTA
1 TATGCTCTAACCGAGACATATGCAACATCATAGCTA
*
52127 TATGCTCTAATCGAGACATATGC
1 TATGCTCTAACCGAGACATATGC
52150 CTTCCTTTGA
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
36 119 0.79
37 32 0.21
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (36 bp):
TATGCTCTAACCGAGACATATGCAACATCATAGCTA
Found at i:52046 original size:73 final size:72
Alignment explanation
Indices: 51946--52149 Score: 266
Period size: 73 Copynumber: 2.8 Consensus size: 72
51936 CATATAACAT
** *
51946 TATGCTCTAACCGAGATGTAAGCAACAT-AGTAGCAATATGCTCTAACCGAGACATATGCAACAT
1 TATGCTCTAACCGAGACATAAGCAACATCA-TAGCTATATGCTCTAACCGAGACATATGCAACAT
*
52010 TATAGCAA
65 CATAGCAA
* * * * *
52018 TATGCTCTAACCGAGACATATGAAAACATCATAGTTATATGCTCTAACTGAGACATATGCATCAT
1 TATGCTCTAACCGAGACATAAG-CAACATCATAGCTATATGCTCTAACCGAGACATATGCAACAT
*
52083 CATAGCTA
65 CATAGCAA
* * *
52091 TATGCTCTAATCGAGACATAAGCATCATCATAGCTATATGCTCTAATCGAGACATATGC
1 TATGCTCTAACCGAGACATAAGCAACATCATAGCTATATGCTCTAACCGAGACATATGC
52150 CTTCCTTTGA
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
72 51 0.45
73 61 0.54
74 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (72 bp):
TATGCTCTAACCGAGACATAAGCAACATCATAGCTATATGCTCTAACCGAGACATATGCAACATC
ATAGCAA
Found at i:52059 original size:109 final size:109
Alignment explanation
Indices: 51946--52148 Score: 282
Period size: 109 Copynumber: 1.9 Consensus size: 109
51936 CATATAACAT
** *
51946 TATGCTCTAACCGAGATGTAAGCAACAT-AGTAGCAATATGCTCTAACCGAGACATATGCAACAT
1 TATGCTCTAACCGAGACATAAGCAACATCA-TAGCAATATGCTCTAACCGAGACATAAGCAACAT
*
52010 TATAGCAATATGCTCTAACCGAGACATATGAAAACATCATAGTTA
65 CATAGCAATATGCTCTAACCGAGACATATGAAAACATCATAGTTA
* * * * * *
52055 TATGCTCTAACTGAGACATATGCATCATCATAGCTATATGCTCTAATCGAGACATAAGCATCATC
1 TATGCTCTAACCGAGACATAAGCAACATCATAGCAATATGCTCTAACCGAGACATAAGCAACATC
* *
52120 ATAGCTATATGCTCTAATCGAGACATATG
66 ATAGCAATATGCTCTAACCGAGACATATG
52149 CCTTCCTTTG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 80 0.99
110 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (109 bp):
TATGCTCTAACCGAGACATAAGCAACATCATAGCAATATGCTCTAACCGAGACATAAGCAACATC
ATAGCAATATGCTCTAACCGAGACATATGAAAACATCATAGTTA
Found at i:52093 original size:18 final size:18
Alignment explanation
Indices: 52072--52131 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
52062 TAACTGAGAC
52072 ATATGCATCATCATAGCT
1 ATATGCATCATCATAGCT
*
52090 ATATGC-TCTAATC-GAGAC-
1 ATATGCATC--ATCATAG-CT
*
52108 ATAAGCATCATCATAGCT
1 ATATGCATCATCATAGCT
52126 ATATGC
1 ATATGC
52132 TCTAATCGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 6 0.19
18 20 0.62
19 6 0.19
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (18 bp):
ATATGCATCATCATAGCT
Found at i:52149 original size:18 final size:18
Alignment explanation
Indices: 52090--52149 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
52080 CATCATAGCT
52090 ATATGCTCTAATCGAGAC
1 ATATGCTCTAATCGAGAC
* *
52108 ATAAGCATC--ATC-ATAGC
1 ATATGC-TCTAATCGAGA-C
52125 TATATGCTCTAATCGAGAC
1 -ATATGCTCTAATCGAGAC
52144 ATATGC
1 ATATGC
52150 CTTCCTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
18 16 0.50
19 6 0.19
20 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (18 bp):
ATATGCTCTAATCGAGAC
Found at i:55300 original size:35 final size:35
Alignment explanation
Indices: 55261--55328 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
55251 TATTCCCTGC
* *
55261 TGACCTGAAGGTCATGATGCTTATTTTACTCCCGT
1 TGACCCGAAGGTCATGATGCTCATTTTACTCCCGT
55296 TGACCCGAAGGTCATGATGCTCATTTTACTCCC
1 TGACCCGAAGGTCATGATGCTCATTTTACTCCC
55329 TATTGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (35 bp):
TGACCCGAAGGTCATGATGCTCATTTTACTCCCGT
Found at i:65498 original size:21 final size:20
Alignment explanation
Indices: 65453--65505 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
65443 TTGTGCTAGT
*
65453 TCTACCGATACAAGTATAATT
1 TCTACCGATACAAG-ATAATA
65474 TCTACCGATACAAG-TAATGCA
1 TCTACCGATACAAGATAAT--A
*
65495 TCTACCTATAC
1 TCTACCGATAC
65506 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.14
21 24 0.86
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (20 bp):
TCTACCGATACAAGATAATA
Found at i:68386 original size:25 final size:26
Alignment explanation
Indices: 68337--68386 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
68327 AAAATTTTAG
*
68337 CTCTAACGAGCCCAGACAGAATATCA
1 CTCTAACGAGCCCAAACAGAATATCA
*
68363 CTCTTACGAG-CCAAACAGAATATC
1 CTCTAACGAGCCCAAACAGAATATC
68387 TTCATCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (26 bp):
CTCTAACGAGCCCAAACAGAATATCA
Found at i:70793 original size:22 final size:22
Alignment explanation
Indices: 70768--70818 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
70758 AATAACTCTC
*
70768 AAATTTAAGATTTTAAGTTTAA
1 AAATTTAAGATTTAAAGTTTAA
* *
70790 AAATTTAAGGTTTAAAGTTTTA
1 AAATTTAAGATTTAAAGTTTAA
*
70812 ACATTTA
1 AAATTTA
70819 TTTGTAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
AAATTTAAGATTTAAAGTTTAA
Found at i:76690 original size:21 final size:22
Alignment explanation
Indices: 76643--76702 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
76633 AATTGTGCAG
***
76643 ATTTCTACCGATACTTTTACTA
1 ATTTCTACCGATACAAGTACTA
76665 A-TTCTACCGATACAAGTA-TA
1 ATTTCTACCGATACAAGTACTA
*
76685 ATTTCTACAGATACAAGT
1 ATTTCTACCGATACAAGT
76703 CATGCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.88
22 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (22 bp):
ATTTCTACCGATACAAGTACTA
Found at i:77536 original size:51 final size:51
Alignment explanation
Indices: 77457--77649 Score: 298
Period size: 51 Copynumber: 3.8 Consensus size: 51
77447 CCATATAGGA
* * * *
77457 ATTCATATACTCACGATGACA-TTGAGTCATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGTAAAGG
* *
77508 ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGA
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
77559 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
77610 ATTCATTTACTCACGATAACACTTAGTCATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
77650 CGTTTATAGC
Statistics
Matches: 131, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
51 125 0.95
52 6 0.05
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:83545 original size:14 final size:16
Alignment explanation
Indices: 83512--83543 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
83502 TAATATATTC
83512 TAAATTACATGATATA
1 TAAATTACATGATATA
*
83528 TAAATTACATAATATA
1 TAAATTACATGATATA
83544 AAGTATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATTACATGATATA
Found at i:83604 original size:21 final size:21
Alignment explanation
Indices: 83578--83622 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
83568 TCAGGTTCGG
83578 GCCTTGAATATTCAAGTCCGA
1 GCCTTGAATATTCAAGTCCGA
83599 GCCTTGAATATTCAAGTCCGA
1 GCCTTGAATATTCAAGTCCGA
83620 GCC
1 GCC
83623 CAATCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
GCCTTGAATATTCAAGTCCGA
Found at i:83807 original size:14 final size:14
Alignment explanation
Indices: 83788--83833 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
83778 TGAAAAGAAT
83788 AATTAAATATATAA
1 AATTAAATATATAA
* *
83802 AATTAAATTTATAT
1 AATTAAATATATAA
*
83816 AATTAAAATATTTAA
1 AATT-AAATATATAA
83831 AAT
1 AAT
83834 AGATTATGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAAATATATAA
Found at i:84779 original size:29 final size:29
Alignment explanation
Indices: 84746--84804 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
84736 CATAAGGATC
84746 AATCATTATTAACAATTTACCTTAATTAT
1 AATCATTATTAACAATTTACCTTAATTAT
84775 AATCATTATTAACAATTTACCTTAATTAT
1 AATCATTATTAACAATTTACCTTAATTAT
84804 A
1 A
84805 GAACCATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (29 bp):
AATCATTATTAACAATTTACCTTAATTAT
Found at i:86334 original size:39 final size:37
Alignment explanation
Indices: 86291--86397 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 37
86281 TTTAACAAAA
* * *
86291 TACTATATTTTAAAATGCTAGACCGAAAAATATAATAAG
1 TACTATATTTTAAAATGTTAGGCCGAAAAATAT-AT-AC
* *
86330 TACTATATTTTAAAATGTTAGGCCGAAAAGTATGTAC
1 TACTATATTTTAAAATGTTAGGCCGAAAAATATATAC
*
86367 TA-TATGTTTTAAAATGTTAGGCCGAAAAATA
1 TACTATATTTTAAAATGTTAGGCCGAAAAATA
86398 AGTAATATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 27 0.44
37 3 0.05
38 1 0.02
39 30 0.49
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (37 bp):
TACTATATTTTAAAATGTTAGGCCGAAAAATATATAC
Found at i:86367 original size:34 final size:34
Alignment explanation
Indices: 86291--86416 Score: 135
Period size: 36 Copynumber: 3.5 Consensus size: 34
86281 TTTAACAAAA
* *
86291 TACTATATTTTAAAATGCTAGACCGAAAAATATAATAAG
1 TACTATATTTTAAAATGTTAGGCCG-AAAA-AT-AT--G
*
86330 TACTATATTTTAAAATGTTAGGCCGAAAAGTATG
1 TACTATATTTTAAAATGTTAGGCCGAAAAATATG
*
86364 TACTATATGTTTTAAAATGTTAGGCCGAAAAATAAG
1 TACTATA--TTTTAAAATGTTAGGCCGAAAAATATG
* *
86400 TAATATGTTTTAAAATG
1 TACTATATTTTAAAATG
86417 CTAATAATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
34 18 0.23
36 32 0.41
37 1 0.01
38 4 0.05
39 23 0.29
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (34 bp):
TACTATATTTTAAAATGTTAGGCCGAAAAATATG
Found at i:86384 original size:36 final size:36
Alignment explanation
Indices: 86324--86416 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
86314 CGAAAAATAT
86324 AATAAGTACTATA--TTTTAAAATGTTAGGCCGAAA
1 AATAAGTACTATATGTTTTAAAATGTTAGGCCGAAA
* *
86358 AGTATGTACTATATGTTTTAAAATGTTAGGCCGAAA
1 AATAAGTACTATATGTTTTAAAATGTTAGGCCGAAA
86394 AATAAGTA--ATATGTTTTAAAATG
1 AATAAGTACTATATGTTTTAAAATG
86417 CTAATAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
34 26 0.49
36 27 0.51
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (36 bp):
AATAAGTACTATATGTTTTAAAATGTTAGGCCGAAA
Found at i:86433 original size:55 final size:55
Alignment explanation
Indices: 86368--86471 Score: 181
Period size: 55 Copynumber: 1.9 Consensus size: 55
86358 AGTATGTACT
*
86368 ATATGTTTTAAAATGTTAGGCCGAAAAATAAGTAATATGTTTTAAAATGCTAATA
1 ATATGCTTTAAAATGTTAGGCCGAAAAATAAGTAATATGTTTTAAAATGCTAATA
* *
86423 ATATGCTTTAAAATGTTAGGCCGAAAAGTAAGTACTATGTTTTAAAATG
1 ATATGCTTTAAAATGTTAGGCCGAAAAATAAGTAATATGTTTTAAAATG
86472 TTAGGCCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (55 bp):
ATATGCTTTAAAATGTTAGGCCGAAAAATAAGTAATATGTTTTAAAATGCTAATA
Found at i:86438 original size:91 final size:90
Alignment explanation
Indices: 86338--86506 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 90
86328 AGTACTATAT
*
86338 TTTAAAATGTTAGGCCGAAAAGTATGTACTATATGTTTTAAAATGTTAGGCCGAAAAA-TAAGTA
1 TTTAAAATGTTAGGCCGAAAAGTAAGTAC--TATGTTTTAAAATGTTAGGCCGAAAAAGTAAGTA
*
86402 ATATGTTTTAAAATGCTAATAATATGC
64 ATATATTTTAAAATGCTAATAATATGC
86429 TTTAAAATGTTAGGCCGAAAAGTAAGTACTATGTTTTAAAATGTTAGGCCGAAAAAGTAAGTAAT
1 TTTAAAATGTTAGGCCGAAAAGTAAGTACTATGTTTTAAAATGTTAGGCCGAAAAAGTAAGTAAT
86494 ATATTTTAAAATG
66 ATATTTTAAAATG
86507 TTAGACCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
89 27 0.36
90 20 0.27
91 28 0.37
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (90 bp):
TTTAAAATGTTAGGCCGAAAAGTAAGTACTATGTTTTAAAATGTTAGGCCGAAAAAGTAAGTAAT
ATATTTTAAAATGCTAATAATATGC
Found at i:86550 original size:34 final size:34
Alignment explanation
Indices: 86421--86552 Score: 174
Period size: 34 Copynumber: 3.9 Consensus size: 34
86411 AAAATGCTAA
* *
86421 TAATATGCTTTAAAATGTTAGGCCGAAAAGTAAG
1 TAATATGTTTTAAAATGTTAGGCCAAAAAGTAAG
*
86455 TACTATGTTTTAAAATGTTAGGCCGAAAAAGTAAG
1 TAATATGTTTTAAAATGTTAGGCC-AAAAAGTAAG
* * *
86490 TAATATATTTTAAAATGTTAGACCAAAAAGCAAG
1 TAATATGTTTTAAAATGTTAGGCCAAAAAGTAAG
* * *
86524 TATTATGTTTTAAAATATTACGCCAAAAA
1 TAATATGTTTTAAAATGTTAGGCCAAAAA
86553 ATATGTGCCC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 55 0.65
35 30 0.35
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (34 bp):
TAATATGTTTTAAAATGTTAGGCCAAAAAGTAAG
Found at i:87047 original size:16 final size:17
Alignment explanation
Indices: 87016--87061 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
87006 GTGATCTGGG
87016 GAAAATCAAAAATAAAA
1 GAAAATCAAAAATAAAA
*
87033 GAAAA-CAAAATTAAAA
1 GAAAATCAAAAATAAAA
*
87049 G-AAATAAAAAATA
1 GAAAATCAAAAATA
87062 GGAGTGTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 5 0.20
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (17 bp):
GAAAATCAAAAATAAAA
Found at i:88351 original size:17 final size:17
Alignment explanation
Indices: 88329--88369 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
88319 GCGTTGGTCA
88329 ATCGCACGCTACCACGT
1 ATCGCACGCTACCACGT
88346 ATCGCACGCTACCACGT
1 ATCGCACGCTACCACGT
88363 ATCGCAC
1 ATCGCAC
88370 TCCCAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.41, G:0.17, T:0.17
Consensus pattern (17 bp):
ATCGCACGCTACCACGT
Found at i:89090 original size:40 final size:40
Alignment explanation
Indices: 89037--89141 Score: 174
Period size: 40 Copynumber: 2.6 Consensus size: 40
89027 TTTGGACAAA
*
89037 AAACGCCGTAAAAGGTAAAGCAATAGCAGCGTTTTTCCAC
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAC
* * *
89077 AAACACCGCAAAAGGTAAATCAATAGCAGCGTTTTTCCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAC
89117 AAACGCCGCAAAAGGTAAAGCAATA
1 AAACGCCGCAAAAGGTAAAGCAATA
89142 ACGACATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAC
Found at i:89207 original size:38 final size:40
Alignment explanation
Indices: 89157--89249 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 40
89147 ATTTATAGGA
* *
89157 AAAGTGCCGCTAAAGGTCAGAGCATTA-A-CGGTTATGAG
1 AAAGCGCCGCTAAAGGTCAAAGCATTACAGCGGTTATGAG
* *
89195 AAAGCGTCGCTAAAGGTCAAAGCATTAGCAGCGTTTATGAG
1 AAAGCGCCGCTAAAGGTCAAAGCATTA-CAGCGGTTATGAG
89236 AAAGCGCCGCTAAA
1 AAAGCGCCGCTAAA
89250 AGTTAAGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 24 0.51
40 1 0.02
41 22 0.47
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.19
Consensus pattern (40 bp):
AAAGCGCCGCTAAAGGTCAAAGCATTACAGCGGTTATGAG
Done.