Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013033.1 Kokia drynarioides strain JFW-HI SEQ_128051, 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: 111889
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:483 original size:28 final size:25
Alignment explanation
Indices: 436--500 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 25
426 AACCCGTATC
* *
436 AATATTTTTTTAAATTTCATTATTTA
1 AATATTTTTTTAAATATCA-TATTAA
*
462 AATATTTTTTTATTTATATCATATTAA
1 AATATTTTTTTA--AATATCATATTAA
*
489 AAAATTTATTTT
1 AATATTT-TTTT
501 TGTGTCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 12 0.38
27 11 0.34
28 9 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
AATATTTTTTTAAATATCATATTAA
Found at i:1301 original size:31 final size:33
Alignment explanation
Indices: 1238--1317 Score: 128
Period size: 31 Copynumber: 2.5 Consensus size: 33
1228 GGAAAAATGA
*
1238 TGTTAGATGGAAAAATGGTGAGAAGAAGAAGTGG
1 TGTTAGATGGAAAAAAGGT-AGAAGAAGAAGTGG
1272 TGTTAGATGGAAAAAAGGT-GAA-AAGAAGTGG
1 TGTTAGATGGAAAAAAGGTAGAAGAAGAAGTGG
1303 TGTTAGATGGAAAAA
1 TGTTAGATGGAAAAA
1318 TTGGGAAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 24 0.53
32 3 0.07
34 18 0.40
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (33 bp):
TGTTAGATGGAAAAAAGGTAGAAGAAGAAGTGG
Found at i:1337 original size:17 final size:17
Alignment explanation
Indices: 1315--1369 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1305 TTAGATGGAA
1315 AAATTGGGAAGAAGATG
1 AAATTGGGAAGAAGATG
1332 AAATTGTGGAAGAA-AT-
1 AAATTG-GGAAGAAGATG
*
1348 -AATGGGGAAGAAGATG
1 AAATTGGGAAGAAGATG
1364 AAATTG
1 AAATTG
1370 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 7 0.22
15 6 0.19
17 12 0.38
18 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (17 bp):
AAATTGGGAAGAAGATG
Found at i:1444 original size:27 final size:26
Alignment explanation
Indices: 1374--1450 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
1364 AAATTGAAAA
*
1374 TTAAAATTA-TTTAATAATTTTATAT
1 TTAAAAATATTTTAATAATTTTATAT
* * *
1399 TTAAACATATTTAAAAATATTTTATAT
1 TTAAAAATATTTTAATA-ATTTTATAT
1426 TTAAAAAATAATTTTAATAATTTTA
1 TT-AAAAAT-ATTTTAATAATTTTA
1451 AAATCATTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
25 7 0.17
26 5 0.12
27 11 0.27
28 11 0.27
29 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAAAATATTTTAATAATTTTATAT
Found at i:9901 original size:32 final size:33
Alignment explanation
Indices: 9865--9947 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 33
9855 AGTTTTGATC
9865 ATTTAATTAAAAAAATTATAAATTAA-TCACTA
1 ATTTAATTAAAAAAATTATAAATTAAGTCACTA
* * * *
9897 ATTT-ACTCAAAAAATT-TTATTTAAGTCACTA
1 ATTTAATTAAAAAAATTATAAATTAAGTCACTA
* *
9928 AATTATTTAAAAAAAATTAT
1 ATTTAATT-AAAAAAATTAT
9948 TTAAATCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
30 6 0.15
31 19 0.49
32 5 0.13
33 8 0.21
34 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (33 bp):
ATTTAATTAAAAAAATTATAAATTAAGTCACTA
Found at i:9926 original size:31 final size:30
Alignment explanation
Indices: 9887--9987 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
9877 AAATTATAAA
*
9887 TTAA-TCACTAATTTACTCAAAAAATTTTAT
1 TTAAGTCACTAA-TTATTCAAAAAATTTTAT
* **
9917 TTAAGTCACTAAATTATTTAAAAAAAATTAT
1 TTAAGTCACT-AATTATTCAAAAAATTTTAT
* * * **
9948 TTAAATCAATGAACTATTCAAAAGTTTTTAT
1 TTAAGTCACT-AATTATTCAAAAAATTTTAT
9979 TTAAGTCAC
1 TTAAGTCAC
9988 CGAATTTTTA
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
30 4 0.07
31 48 0.89
32 2 0.04
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (30 bp):
TTAAGTCACTAATTATTCAAAAAATTTTAT
Found at i:15490 original size:18 final size:17
Alignment explanation
Indices: 15433--15497 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 17
15423 GATATTTTTT
15433 TTAATTTGTTTTTTTGAA
1 TTAATTT-TTTTTTTGAA
*
15451 CTAATTTTTTTTTGGTGAA
1 TTAATTTTTTTTT--TGAA
*
15470 TTAATTTTTTTTTTCATA
1 TTAATTTTTTTTTTGA-A
15488 TTAATCTTTT
1 TTAAT-TTTT
15498 AATTTGGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 8 0.20
18 12 0.30
19 20 0.50
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTTTTTGAA
Found at i:15620 original size:23 final size:25
Alignment explanation
Indices: 15594--15640 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
15584 AAAATTCTAA
*
15594 AAATTA-AAAAG-ATGTATAAATAG
1 AAATTATAAAAGAATATATAAATAG
15617 AAATTATAAAAGAATATATAAATA
1 AAATTATAAAAGAATATATAAATA
15641 TATAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (25 bp):
AAATTATAAAAGAATATATAAATAG
Found at i:16229 original size:3 final size:3
Alignment explanation
Indices: 16221--16264 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
16211 GATTCAAGAA
16221 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16265 ACTAAAGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:26751 original size:83 final size:83
Alignment explanation
Indices: 26612--26780 Score: 320
Period size: 83 Copynumber: 2.0 Consensus size: 83
26602 GTAAGAAAAC
26612 AAACTCCAAAATCACTACTTTTGCAGTGTAAGAAATTCTAACATGTGGACGGTAGAAGTTTTCAA
1 AAACTCCAAAATCACTACTTTTGCAGTGTAAGAAATTCTAACATGTGGACGGTAGAAGTTTTCAA
*
26677 CTTTTAACTGACACTTTA
66 CTTTTAACTGACACCTTA
*
26695 AAACTCCAAAATCACTACTTTTGCAGTGTAAGAAATTGTAACATGTGGACGGTAGAAGTTTTCAA
1 AAACTCCAAAATCACTACTTTTGCAGTGTAAGAAATTCTAACATGTGGACGGTAGAAGTTTTCAA
26760 CTTTTAACTGACACCTTA
66 CTTTTAACTGACACCTTA
26778 AAA
1 AAA
26781 GAAAAAAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (83 bp):
AAACTCCAAAATCACTACTTTTGCAGTGTAAGAAATTCTAACATGTGGACGGTAGAAGTTTTCAA
CTTTTAACTGACACCTTA
Found at i:28154 original size:2 final size:2
Alignment explanation
Indices: 28147--28189 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28137 TCAGCCATGA
28147 AT AT AT AT AT 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 AT AT AT AT AT
28189 A
1 A
28190 AGCATTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35257 original size:15 final size:15
Alignment explanation
Indices: 35210--35259 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
35200 TTAAAAAATT
35210 ATTTATATA-TTTTA
1 ATTTATATATTTTTA
*
35224 ATTTA-ATATTTAATA
1 ATTTATATATTT-TTA
*
35239 ATTTATATATTTTTT
1 ATTTATATATTTTTA
35254 ATTTAT
1 ATTTAT
35260 TTAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 14 0.47
16 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATATTTTTA
Found at i:35267 original size:29 final size:29
Alignment explanation
Indices: 35186--35272 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
35176 CCACCCATAT
* *
35186 TATTTTTAATTTTTTTAAAA-AATTATTTA
1 TATTTTTAATTTATTTAAAATAATT-TATA
*
35215 TATATTTTAATTTAATATT-TAATAATTTATA
1 TAT-TTTTAATTT-AT-TTAAAATAATTTATA
*
35246 TATTTTTTATTTATTTAAAAT-ATTTAT
1 TATTTTTAATTTATTTAAAATAATTTAT
35273 GATCTATCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
28 8 0.17
29 8 0.17
30 17 0.35
31 9 0.19
32 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTTTAATTTATTTAAAATAATTTATA
Found at i:39659 original size:17 final size:19
Alignment explanation
Indices: 39620--39666 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
39610 AATAAATTAA
*
39620 AAATAGTTTGAACTAGATTT
1 AAATA-TTTAAACTAGATTT
39640 AAAT-TTTAAACTAG-TTT
1 AAATATTTAAACTAGATTT
39657 AAATATTTAA
1 AAATATTTAA
39667 TTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 7 0.28
18 14 0.56
20 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (19 bp):
AAATATTTAAACTAGATTT
Found at i:47980 original size:62 final size:62
Alignment explanation
Indices: 47883--48009 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 62
47873 TTCTTCTACA
* *
47883 TTATGTAAACTGATCATACTTATGAATCCTGTATAATACCCTTGTTATCATCTTACCTATGT
1 TTATGCAAACTGATCATACTTATGAATCCTGTATAATAACCTTGTTATCATCTTACCTATGT
* *
47945 TTATGCAAACTGATCATACTTATGAATCCTGTATAATAACTTTGTTGTCATCTTACCTATGT
1 TTATGCAAACTGATCATACTTATGAATCCTGTATAATAACCTTGTTATCATCTTACCTATGT
48007 TTA
1 TTA
48010 CTTCTCTGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (62 bp):
TTATGCAAACTGATCATACTTATGAATCCTGTATAATAACCTTGTTATCATCTTACCTATGT
Found at i:58574 original size:21 final size:22
Alignment explanation
Indices: 58545--58586 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
58535 TTACATTTTC
*
58545 TAAAGTTAAAAGTCAAAACTAT
1 TAAAGTTAAAAGGCAAAACTAT
58567 TAAA-TTAAAAGGCAAAACTA
1 TAAAGTTAAAAGGCAAAACTA
58587 CTCTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAAGTTAAAAGGCAAAACTAT
Found at i:62540 original size:41 final size:41
Alignment explanation
Indices: 62446--62872 Score: 406
Period size: 41 Copynumber: 10.4 Consensus size: 41
62436 AAAAAAGTAA
* * * * * *
62446 AGCAATAGCGGCGTTTATAGGAAAAACGCCACTAACGATCAG
1 AGCATTAGCGGCGTTTAT-GGGAAAGCGCCGCTAAAGGTCAG
* * *
62488 AGCATTAGCGGCGTTTACGGGGAAGCGCTGCTAAAGGTC-G
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* **
62528 TAGCATTAGCGGCGTTTATGGGGAAGCGTTGCTAAAGGTCAG
1 -AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* * * * ***
62570 AGTATTAACGGCGTTTATGGGAAAGCGTCACTAAAGGTTTT
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* * * ** *
62611 AGCAATAGTGGCTTTTATGATAAAGCACCGCTAAAGGTCAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* *** * *
62652 AGCAATAGCGGCGTTTATAATAAAGAGCCGCTAAAAGTCAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* *
62693 AGTATTAGTGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* * * *
62734 TGCATTAGCGGCGTTTATGGAAAAGTGCCGCTAAAGGTTAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
* * * **
62775 AGCATTAACGGCGTTTATTGAAAAGCGCCGCTAAAATTCAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
** ** *
62816 AGCATTAGTAGCGTTTATGCAAAAGCGCCGTTAAAGGTCAG
1 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
62857 AGCATTAGCGGCGTTT
1 AGCATTAGCGGCGTTT
62873 TCCCATAAAC
Statistics
Matches: 314, Mismatches: 69, Indels: 5
0.81 0.18 0.01
Matches are distributed among these distances:
40 1 0.00
41 296 0.94
42 17 0.05
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
Found at i:63445 original size:19 final size:18
Alignment explanation
Indices: 63411--63447 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
63401 GTTAAATTAC
*
63411 ATATTTAATTTTTAGATT
1 ATATTTAATATTTAGATT
63429 ATATTTGAATATTTAGATT
1 ATATTT-AATATTTAGATT
63448 TGCATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (18 bp):
ATATTTAATATTTAGATT
Found at i:64948 original size:43 final size:43
Alignment explanation
Indices: 64870--65001 Score: 160
Period size: 43 Copynumber: 3.1 Consensus size: 43
64860 CCGCTAAAGG
* * * *
64870 CGTTTATGAGAAAAATGTCGCTAAAGGT-CA-AGCAATAGCGT
1 CGTTTATGAGAAAAAAGCCGCAAAAGGTCCAGAGCAATAGCGA
* * *
64911 CGTTTATGAGAAAAAAACCGCAAAAGGTCCAGAGCAATAACGG
1 CGTTTATGAGAAAAAAGCCGCAAAAGGTCCAGAGCAATAGCGA
* * *
64954 CGTTTATGAGAAAAACGCCGCAAAAGGTCCAGAACATTAGCGA
1 CGTTTATGAGAAAAAAGCCGCAAAAGGTCCAGAGCAATAGCGA
64997 CGTTT
1 CGTTT
65002 TTCCCATAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 24 0.31
42 2 0.03
43 51 0.66
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (43 bp):
CGTTTATGAGAAAAAAGCCGCAAAAGGTCCAGAGCAATAGCGA
Found at i:68660 original size:23 final size:23
Alignment explanation
Indices: 68573--68718 Score: 129
Period size: 23 Copynumber: 6.3 Consensus size: 23
68563 ACACTAGCGC
* *
68573 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
* *
68596 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
68619 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
68644 ACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
68667 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
68690 ACTATCTGTTTAGCAC--TGTGT
1 GCTCTCTGATTAGCACTGTGTGT
68711 GCTCTCTG
1 GCTCTCTG
68719 TTTCCCAGCA
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.10
23 78 0.72
25 16 0.15
26 3 0.03
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:68703 original size:46 final size:46
Alignment explanation
Indices: 68573--68719 Score: 149
Period size: 46 Copynumber: 3.2 Consensus size: 46
68563 ACACTAGCGC
* * * * *
68573 GCTCTCTGT-TTAGCAC-GTCTCGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GTACTATCTGTTTAGCACTTGT-GT
* *
68619 GCTCTCTGTTATTAGCACTGTGTGTACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGTACTATCTGTTTAGCAC-TTGTGT
* *
68667 GCTCTCTG-ATTAGTACTTTGTGTACTATCTGTTTAGCAC-TGTGT
1 GCTCTCTGTATTAGCACTGTGTGTACTATCTGTTTAGCACTTGTGT
68711 GCTCTCTGT
1 GCTCTCTGT
68720 TTCCCAGCAC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
44 13 0.15
46 35 0.40
47 1 0.01
48 33 0.38
49 5 0.06
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (46 bp):
GCTCTCTGTATTAGCACTGTGTGTACTATCTGTTTAGCACTTGTGT
Found at i:68744 original size:46 final size:43
Alignment explanation
Indices: 68573--68745 Score: 141
Period size: 48 Copynumber: 3.7 Consensus size: 43
68563 ACACTAGCGC
* * *
68573 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCAC-T-TTGTGCTCTCTGTTTAGCACTTGT-GT
* *
68619 GCTCTCTGTTATTAGCACTGTGTGTACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG-T-TTAGCACT-T-TGTGCTCTCTGTTTAGCAC-TTGTGT
* * *
68667 GCTCTCTGATTAGTACTTTGTGTACTATCTGTTTAGCAC-TGTGT
1 GCTCTCTGTTTAGCACTTTGTG--CTCTCTGTTTAGCACTTGTGT
68711 GCTCTCTGTTTCCCAGCACTTATGTGCTCTCTGTT
1 GCTCTCTGTTT---AGCACTT-TGTGCTCTCTGTT
68746 AGTACTTTGG
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
44 18 0.17
45 1 0.01
46 36 0.35
47 9 0.09
48 37 0.36
49 2 0.02
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (43 bp):
GCTCTCTGTTTAGCACTTTGTGCTCTCTGTTTAGCACTTGTGT
Found at i:70064 original size:14 final size:13
Alignment explanation
Indices: 70039--70115 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 13
70029 ATAGTATTAG
70039 TTAATT-AAATAT
1 TTAATTAAAATAT
70051 TTAATTCAAAATAT
1 TTAATT-AAAATAT
70065 TTAATTATTTAATTATAT
1 TTAATTA---AA--ATAT
70083 TTAATT-AAATAT
1 TTAATTAAAATAT
* *
70095 TTAATTCAAGATAG
1 TTAATT-AAAATAT
70109 TTAATTA
1 TTAATTA
70116 TTTAATTAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
12 16 0.30
13 2 0.04
14 24 0.44
16 2 0.04
18 10 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (13 bp):
TTAATTAAAATAT
Found at i:70068 original size:22 final size:22
Alignment explanation
Indices: 70040--70122 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
70030 TAGTATTAGT
70040 TAATTAAATATTTAATTCAAAA
1 TAATTAAATATTTAATTCAAAA
* * **
70062 TATTTAATTATTTAATT-ATATT
1 TAATTAAATATTTAATTCA-AAA
*
70084 TAATTAAATATTTAATTCAAGA
1 TAATTAAATATTTAATTCAAAA
* *
70106 TAGTTAATTATTTAATT
1 TAATTAAATATTTAATT
70123 AGTTAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.02
22 47 0.96
23 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTAAATATTTAATTCAAAA
Found at i:70102 original size:44 final size:44
Alignment explanation
Indices: 70039--70123 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
70029 ATAGTATTAG
*
70039 TTAATTAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
1 TTAATTAAATATTTAATTCAAAATAGTTAATTATTTAATTATAT
*
70083 TTAATTAAATATTTAATTCAAGATAGTTAATTATTTAATTA
1 TTAATTAAATATTTAATTCAAAATAGTTAATTATTTAATTA
70124 GTTAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (44 bp):
TTAATTAAATATTTAATTCAAAATAGTTAATTATTTAATTATAT
Found at i:70154 original size:56 final size:56
Alignment explanation
Indices: 70088--70319 Score: 298
Period size: 56 Copynumber: 4.2 Consensus size: 56
70078 TATATTTAAT
* *
70088 TAAATATTTAATTCAAGATAGTTAATTATTTAATTAGTTAATTATTAAAAACAACC
1 TAAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACC
* * *
70144 TAAATATTTAATTCAAAATATTTAATTATTTAATTAGCTATTTATTAAAAACAATC
1 TAAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACC
*
70200 TAAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATTAAAAATAA-C
1 TAAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACC
* * * *
70255 TCAGATATTTAA-T-----TATTTAATTATTCAATTAGTTATTTATTAAAAAAAAACC
1 T-AAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATT-AAAAACAACC
*
70307 CAAATATTTAATT
1 TAAATATTTAATT
70320 ATTTGGTTGT
Statistics
Matches: 158, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
50 26 0.16
51 16 0.10
52 2 0.01
55 3 0.02
56 111 0.70
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (56 bp):
TAAATATTTAATTCAAAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACC
Found at i:70231 original size:8 final size:8
Alignment explanation
Indices: 70218--70295 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
70208 TAATTCAAAA
70218 TATTTAAT
1 TATTTAAT
70226 TATTTAAT
1 TATTTAAT
*
70234 TAGTTAAT
1 TATTTAAT
*
70242 TATTAAAAAT
1 TATT--TAAT
* * *
70252 AACTCAGA-
1 TATTTA-AT
70260 TATTTAAT
1 TATTTAAT
70268 TATTTAAT
1 TATTTAAT
*
70276 TATTCAAT
1 TATTTAAT
* *
70284 TAGTTATT
1 TATTTAAT
70292 TATT
1 TATT
70296 AAAAAAAAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
7 1 0.02
8 45 0.87
9 1 0.02
10 5 0.10
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (8 bp):
TATTTAAT
Found at i:74882 original size:9 final size:9
Alignment explanation
Indices: 74870--74904 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
74860 ATTAAATTCA
74870 GTTAATTTG
1 GTTAATTTG
74879 GTTAATTTG
1 GTTAATTTG
**
74888 GTTAATTCA
1 GTTAATTTG
74897 GTTAATTT
1 GTTAATTT
74905 TTTATTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (9 bp):
GTTAATTTG
Found at i:75061 original size:13 final size:13
Alignment explanation
Indices: 75043--75067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75033 TCCAAAAAAA
75043 AAGTGTCAAATTT
1 AAGTGTCAAATTT
75056 AAGTGTCAAATT
1 AAGTGTCAAATT
75068 AGGAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AAGTGTCAAATTT
Found at i:75135 original size:18 final size:17
Alignment explanation
Indices: 75095--75131 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
75085 TTAGATATCG
75095 AATTAA-AAAAATATTA
1 AATTAAGAAAAATATTA
*
75111 AATTAAGAAAAATGTTA
1 AATTAAGAAAAATATTA
75128 AATT
1 AATT
75132 TAAGTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AATTAAGAAAAATATTA
Found at i:77768 original size:24 final size:27
Alignment explanation
Indices: 77718--77772 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
77708 GATCACCATC
77718 ACCACCACCACCATGAACACTTGCATG
1 ACCACCACCACCATGAACACTTGCATG
77745 ACCACCACCACCATGAA-A-TT-CATG
1 ACCACCACCACCATGAACACTTGCATG
77769 ACCA
1 ACCA
77773 TGAGGGCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.29
25 2 0.07
26 1 0.04
27 17 0.61
ACGTcount: A:0.36, C:0.40, G:0.09, T:0.15
Consensus pattern (27 bp):
ACCACCACCACCATGAACACTTGCATG
Found at i:80030 original size:15 final size:15
Alignment explanation
Indices: 80012--80041 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
80002 AAAGATGACT
80012 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
80027 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
80042 GGCTTGCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:80034 original size:6 final size:7
Alignment explanation
Indices: 80012--80041 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
80002 AAAGATGACT
80012 AAAGAAA
1 AAAGAAA
80019 AAAGAAAA
1 AAAG-AAA
80027 AAAGAAA
1 AAAGAAA
80034 AAAGAAA
1 AAAGAAA
80041 A
1 A
80042 GGCTTGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:83891 original size:21 final size:22
Alignment explanation
Indices: 83867--83908 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
83857 ATAAAATTGA
83867 ATTTTAT-CAAAATTAATATCT
1 ATTTTATACAAAATTAATATCT
*
83888 ATTTTATAACAGAATTAATAT
1 ATTTTAT-ACAAAATTAATAT
83909 TTTTAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTTATACAAAATTAATATCT
Found at i:85442 original size:17 final size:17
Alignment explanation
Indices: 85420--85453 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
85410 AGCTATGGAA
*
85420 AATGGGGTTCTCAATGT
1 AATGGGGTTCACAATGT
85437 AATGGGGTTCACAATGT
1 AATGGGGTTCACAATGT
85454 TATTGGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (17 bp):
AATGGGGTTCACAATGT
Found at i:85595 original size:18 final size:18
Alignment explanation
Indices: 85574--85618 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
85564 TAATTGAATG
*
85574 TTTTATTTTAATTTATTA
1 TTTTATTTTAAATTATTA
* *
85592 TTTTATATAAAATTATTA
1 TTTTATTTTAAATTATTA
85610 TTTTATTTT
1 TTTTATTTT
85619 TATATATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTTTAAATTATTA
Found at i:85624 original size:26 final size:27
Alignment explanation
Indices: 85585--85636 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
85575 TTTATTTTAA
85585 TTTATTATTTTATATA-AAATTATTAT
1 TTTATTATTTTATATATAAATTATTAT
85611 TTTATT-TTTATATATATAAATTATTA
1 TTTATTATTT-TATATATAAATTATTA
85637 AAATGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.12
26 12 0.50
27 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTATTATTTTATATATAAATTATTAT
Found at i:105866 original size:20 final size:20
Alignment explanation
Indices: 105841--105878 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
105831 AATTAAATTT
*
105841 TAAAATATTGAAATATTTTA
1 TAAAATATTAAAATATTTTA
105861 TAAAATATTAAAATATTT
1 TAAAATATTAAAATATTT
105879 CAGAACCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAATATTAAAATATTTTA
Found at i:106331 original size:18 final size:19
Alignment explanation
Indices: 106293--106333 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
106283 TTTAAATTTT
*
106293 AAAAGTTTAAAATTATCAA
1 AAAAATTTAAAATTATCAA
106312 AAAAATTTAAAATTAT-AA
1 AAAAATTTAAAATTATCAA
106330 AAAA
1 AAAA
106334 TATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATTTAAAATTATCAA
Found at i:110876 original size:96 final size:96
Alignment explanation
Indices: 110704--110895 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
110694 TTTTGGGAAA
** * *
110704 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTTA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTTA
*
110769 GAATCGAAGAT-AAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAGAAA-ATTGCCTCGATT
* * * * *
110800 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTGAGTTAAAGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTTA
110864 GAAACTCG-AGATAAAAGAAAATTGCCTCGATT
66 G-AA-TCGAAGATAAAAGAAAATTGCCTCGATT
110896 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 6 0.07
96 68 0.82
97 9 0.11
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTTA
GAATCGAAGATAAAAGAAAATTGCCTCGATT
Found at i:111225 original size:59 final size:59
Alignment explanation
Indices: 111161--111618 Score: 534
Period size: 59 Copynumber: 7.8 Consensus size: 59
111151 ATTCGAGGTT
* * * *
111161 AAAAATGGGAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGATTTAGGGTC
1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
* * * * **
111220 GAAAATGAGATTTTTGGAA-TGTCGGGGGTAAAAATGGAATTATAAGG-AGTTTTGGGGTC
1 AAAAATGGGATTTTTGAAAGT-TCGAGGGTAAAAATGGAATT-TTTGGAAGTTTTGGGGTC
* * *
111279 AAAAATGAGATTTTTGAAAGTTCGGGGGTAAAAAT-GAATTTTTTGGAAGTTTTTGGGTC
1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTGGGGTC
* *
111338 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTCTTGGGAGTTTTGGGGTC
1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
* * * *
111397 -AAAATGGGATTTTTAAAAGTTCGGGGGTAAAAATAGAATTTTTGGGAG-TTTGGGGT-
1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
* * * * * * *
111453 TAAAATGGGATTTTTGGAAGTTTGGGGGGTAAAAATGGAATTCTTGGGAGTTTTAGGGTC
1 AAAAATGGGATTTTTGAAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
* * *
111513 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTTGGGGTT
1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
* **
111572 AAAAATGAGATTTTTGAAAGTTCCG-GGGTAAAAACAGAATTTTTGGA
1 AAAAATGGGATTTTTGAAAGTT-CGAGGGTAAAAATGGAATTTTTGGA
111619 CAATTTAGGG
Statistics
Matches: 349, Mismatches: 39, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
57 25 0.07
58 77 0.22
59 219 0.63
60 28 0.08
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.33
Consensus pattern (59 bp):
AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC
Found at i:111613 original size:29 final size:29
Alignment explanation
Indices: 111160--111618 Score: 346
Period size: 29 Copynumber: 15.7 Consensus size: 29
111150 AATTCGAGGT
*
111160 TAAAAATGGGAA-TTTTGGAAG-TTCGAGGG
1 TAAAAAT-GGAATTTTTGGAAGTTTTG-GGG
* *
111189 TAAAAATGGAATTTTTGGAAGATTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* **
111218 TCGAAAAT-GAGATTTTTGGAA-TGTCGGGGG
1 T-AAAAATGGA-ATTTTTGGAAGT-TTTGGGG
**
111248 TAAAAATGGAATTATAAGG-AGTTTTGGGG
1 TAAAAATGGAATT-TTTGGAAGTTTTGGGG
* **
111277 TCAAAAAT-GAGATTTTTGAAAGTTCGGGGG
1 T-AAAAATGGA-ATTTTTGGAAGTTTTGGGG
*
111307 TAAAAAT-GAATTTTTTGGAAGTTTTTGGG
1 TAAAAATGGAA-TTTTTGGAAGTTTTGGGG
* * *
111336 TCAAAAATGGGATTTTTGAAAG-TTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTTG-GGG
* *
111366 TAAAAATGGAATTCTTGGGAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* * ** **
111395 TCAAAATGGGATTTTTAAAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* *
111424 TAAAAATAGAATTTTTGGGAG-TTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* * *
111452 TTAAAATGGGATTTTTGGAAGTTTGGGGGG
1 TAAAAATGGAATTTTTGGAAGTTT-TGGGG
* * *
111482 TAAAAATGGAATTCTTGGGAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* *
111511 TCAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTTG-GGG
*
111541 TAAAAATGGAATTTTTGGGAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
* **
111570 TTAAAAAT-GAGATTTTTGAAAGTTCCGGGG
1 -TAAAAATGGA-ATTTTTGGAAGTTTTGGGG
**
111600 TAAAAACAGAATTTTTGGA
1 TAAAAATGGAATTTTTGGA
111619 CAATTTAGGG
Statistics
Matches: 335, Mismatches: 71, Indels: 48
0.74 0.16 0.11
Matches are distributed among these distances:
28 27 0.08
29 166 0.50
30 140 0.42
31 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTTGGGG
Done.