Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006761.1 Kokia drynarioides strain JFW-HI SEQ_121359, 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: 112341
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:180 original size:60 final size:60
Alignment explanation
Indices: 87--203 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
77 ACACAAACAT
* *
87 TTTATACATACAATTATTTAAACTCGAATCTCTTAAAAAAAATATCATCTTCTTTTTCAC
1 TTTATACATACAACTATTCAAACTCGAATCTCTTAAAAAAAATATCATCTTCTTTTTCAC
* * * * *
147 TTTATACATATAACTATTCAAACTCTAATCTCTTAAAATAAATATTATTTTCTTTTT
1 TTTATACATACAACTATTCAAACTCGAATCTCTTAAAAAAAATATCATCTTCTTTTT
204 TATTAAATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.45
Consensus pattern (60 bp):
TTTATACATACAACTATTCAAACTCGAATCTCTTAAAAAAAATATCATCTTCTTTTTCAC
Found at i:4504 original size:41 final size:42
Alignment explanation
Indices: 4418--4537 Score: 163
Period size: 43 Copynumber: 2.9 Consensus size: 42
4408 ATGTAGGGTA
* * *
4418 TTTTTTTGGGTAATGTGTGATGCGTAAAACATACACGGGTATT
1 TTTTTTTGGGTAATGTGTGATGCGTAAAATATCCACAGGT-TT
*
4461 TTTTTTTGGGTAATGTGTGATGCGTAAAATATCCTCAGGTTT
1 TTTTTTTGGGTAATGTGTGATGCGTAAAATATCCACAGGTTT
*
4503 TTCTTTTTGGGTAA--TGTGATGCGTAAGATATCCAC
1 TT-TTTTTGGGTAATGTGTGATGCGTAAAATATCCAC
4538 TTTTTAAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 19 0.27
42 4 0.06
43 47 0.67
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (42 bp):
TTTTTTTGGGTAATGTGTGATGCGTAAAATATCCACAGGTTT
Found at i:4953 original size:58 final size:58
Alignment explanation
Indices: 4883--4998 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
4873 AGAACTCTTA
4883 ACTATTATGAGTTTAGGTGTGGCAGTTGGGTGGATTGACTTACCTTCTTTAGCTGCAT
1 ACTATTATGAGTTTAGGTGTGGCAGTTGGGTGGATTGACTTACCTTCTTTAGCTGCAT
4941 ACTATTATGAGTTTAGGTGTGGCAGTTGGGTGGATTGACTTACCTTCTTTAGCTGCAT
1 ACTATTATGAGTTTAGGTGTGGCAGTTGGGTGGATTGACTTACCTTCTTTAGCTGCAT
4999 CATGCATTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.40
Consensus pattern (58 bp):
ACTATTATGAGTTTAGGTGTGGCAGTTGGGTGGATTGACTTACCTTCTTTAGCTGCAT
Found at i:12606 original size:17 final size:18
Alignment explanation
Indices: 12569--12606 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12559 TGTCTTTATG
12569 TATATTGAAATTAAAATA
1 TATATTGAAATTAAAATA
12587 TATATT-AAATGTAAAA-A
1 TATATTGAAAT-TAAAATA
12604 TAT
1 TAT
12607 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
TATATTGAAATTAAAATA
Found at i:14380 original size:19 final size:19
Alignment explanation
Indices: 14340--14381 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
14330 ATCCTAAGTT
*
14340 TCTTCAATTATATTTTCAA
1 TCTTCAATTATATGTTCAA
*
14359 TCTT-AATTATTATGTTCTA
1 TCTTCAATTA-TATGTTCAA
14378 TCTT
1 TCTT
14382 TCTATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.57
Consensus pattern (19 bp):
TCTTCAATTATATGTTCAA
Found at i:17610 original size:16 final size:18
Alignment explanation
Indices: 17583--17615 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17573 TATGATTGGG
17583 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
17600 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
17616 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:19393 original size:19 final size:20
Alignment explanation
Indices: 19365--19402 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19355 ATGTTTAAAC
19365 TTAATAAAACT-TAATTAAT
1 TTAATAAAACTATAATTAAT
*
19384 TTAATTAAACTATAATTAA
1 TTAATAAAACTATAATTAA
19403 CAAATACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATAAAACTATAATTAAT
Found at i:37961 original size:13 final size:14
Alignment explanation
Indices: 37943--37972 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37933 ACCTTGCTAC
37943 TTTGTTTTTTT-TT
1 TTTGTTTTTTTGTT
37956 TTTGTTTTTTTGTT
1 TTTGTTTTTTTGTT
37970 TTT
1 TTT
37973 TTGTGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTGTTTTTTTGTT
Found at i:37963 original size:8 final size:8
Alignment explanation
Indices: 37947--37976 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
37937 TGCTACTTTG
37947 TTTTT-TT
1 TTTTTGTT
37954 TTTTTGTT
1 TTTTTGTT
37962 TTTTTGTT
1 TTTTTGTT
37970 TTTTTGT
1 TTTTTGT
37977 GAACTTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTGTT
Found at i:40159 original size:3 final size:3
Alignment explanation
Indices: 40153--40178 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40143 AGGCAATAGT
40153 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
40179 TACATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:43960 original size:23 final size:24
Alignment explanation
Indices: 43926--43973 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
43916 GTTGGATATG
43926 AATGAAAAGTGGCACTTCGGTGCA
1 AATGAAAAGTGGCACTTCGGTGCA
*
43950 AATG-AAAGTGGCACTTTGGTGCA
1 AATGAAAAGTGGCACTTCGGTGCA
43973 A
1 A
43974 CTGACAGCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (24 bp):
AATGAAAAGTGGCACTTCGGTGCA
Found at i:44707 original size:20 final size:21
Alignment explanation
Indices: 44672--44721 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
44662 ATTGGTATGG
*
44672 TTTAATTAAGTGTAAATA-GA
1 TTTAATTAAGTGTAAAAATGA
44692 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
44713 -TTAATTAAG
1 TTTAATTAAG
44722 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:54663 original size:107 final size:107
Alignment explanation
Indices: 54475--54688 Score: 374
Period size: 107 Copynumber: 2.0 Consensus size: 107
54465 TACAGATCTG
*
54475 AAACTTGTGTTCAATGCATTTGTTTCTCATATACACATTGCCAAATAAATTGCAATTATTTTGTG
1 AAACTTGTGTTCAATGCATTTGTTTCTCATATACACATTGCCAAATAAATTGCAATTATTTTATG
*
54540 TCAAATTTGTTTATAGAATTAATTATGTTAGTTTACTTGCTT
66 TCAAATTTGTTGATAGAATTAATTATGTTAGTTTACTTGCTT
* *
54582 AAACTTGTGTTCAATTCATTTGTTTCTCATATCCACATTGCCAAATAAATTGCAATTATTTTATG
1 AAACTTGTGTTCAATGCATTTGTTTCTCATATACACATTGCCAAATAAATTGCAATTATTTTATG
* *
54647 TCTAATTTGTTGATAGAATTAATTATGTTAGTTTATTTGCTT
66 TCAAATTTGTTGATAGAATTAATTATGTTAGTTTACTTGCTT
54689 GATATTGAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (107 bp):
AAACTTGTGTTCAATGCATTTGTTTCTCATATACACATTGCCAAATAAATTGCAATTATTTTATG
TCAAATTTGTTGATAGAATTAATTATGTTAGTTTACTTGCTT
Found at i:58625 original size:40 final size:40
Alignment explanation
Indices: 58581--58658 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
58571 TAATTGAATA
58581 AAACATCTTCTATAGAAATATAAATTTTAAATTAAGCTTC
1 AAACATCTTCTATAGAAATATAAATTTTAAATTAAGCTTC
58621 AAACATCTTCTATAGAAATATAAATTTTAAATTAAGCT
1 AAACATCTTCTATAGAAATATAAATTTTAAATTAAGCT
58659 CCTGTAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (40 bp):
AAACATCTTCTATAGAAATATAAATTTTAAATTAAGCTTC
Found at i:58963 original size:14 final size:15
Alignment explanation
Indices: 58936--58977 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
58926 TGTTTGATAA
*
58936 ATTGAAAAATTAAGT
1 ATTGAAAAAATAAGT
58951 ATT-AAAAAATAAGT
1 ATTGAAAAAATAAGT
*
58965 ATTGAAAATATAA
1 ATTGAAAAAATAA
58978 AAATTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (15 bp):
ATTGAAAAAATAAGT
Found at i:60765 original size:19 final size:19
Alignment explanation
Indices: 60743--60789 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
60733 GTAAAAACTT
60743 TTTAAAATTAAAAAAAAAA
1 TTTAAAATTAAAAAAAAAA
* *
60762 TTTAAAAATATAAAAAAAA
1 TTTAAAATTAAAAAAAAAA
*
60781 TTCAAAATT
1 TTTAAAATT
60790 CAATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTAAAATTAAAAAAAAAA
Found at i:62890 original size:15 final size:15
Alignment explanation
Indices: 62870--62899 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62860 ATAGTTATCA
62870 TTATAATGCCTAAAT
1 TTATAATGCCTAAAT
62885 TTATAATGCCTAAAT
1 TTATAATGCCTAAAT
62900 ACAAAAACAC
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:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TTATAATGCCTAAAT
Found at i:81067 original size:18 final size:19
Alignment explanation
Indices: 81044--81086 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
81034 ATTCAAGGTG
81044 TAATTAATTTAAAATT-TT
1 TAATTAATTTAAAATTATT
*
81062 TAATT-ATTTAAATTTATT
1 TAATTAATTTAAAATTATT
81080 TAATTAA
1 TAATTAA
81087 AAACTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTAATTTAAAATTATT
Found at i:82428 original size:15 final size:14
Alignment explanation
Indices: 82404--82451 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
82394 TAAGAGAATG
82404 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
82418 AAAAAAGAAAGTTAAAA
1 AAAAAA-AAAG--AAAA
* *
82435 AACATAAAAGAAAA
1 AAAAAAAAAGAAAA
82449 AAA
1 AAA
82452 TCAAATTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 4 0.14
17 8 0.29
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAGAAAA
Found at i:84424 original size:24 final size:24
Alignment explanation
Indices: 84397--84444 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
84387 AATAAAACTT
*
84397 TCATGCTAATAAAATCACCTCAAG
1 TCATGCTAATAAAACCACCTCAAG
* *
84421 TCATGCTAATCAAACCACTTCAAG
1 TCATGCTAATAAAACCACCTCAAG
84445 AAGGTCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (24 bp):
TCATGCTAATAAAACCACCTCAAG
Found at i:96415 original size:33 final size:34
Alignment explanation
Indices: 96378--96445 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
96368 ACAATGATGT
* *
96378 AAGAGATAATATTC-TCTAAATTTAGATTTTGTA
1 AAGAGATAAGAGTCTTCTAAATTTAGATTTTGTA
*
96411 AAGAGGTAAGAGTCTTCTAAATTTAGATTTTGTA
1 AAGAGATAAGAGTCTTCTAAATTTAGATTTTGTA
96445 A
1 A
96446 TAAAAGGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (34 bp):
AAGAGATAAGAGTCTTCTAAATTTAGATTTTGTA
Found at i:96651 original size:18 final size:17
Alignment explanation
Indices: 96623--96671 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
96613 AAACTGAATA
96623 TTTTAAAAAAATTAATT
1 TTTTAAAAAAATTAATT
96640 TTTTAAATAAAATTAA-T
1 TTTTAAA-AAAATTAATT
*
96657 TTTTAAAAAATTTAA
1 TTTTAAAAAAATTAA
96672 AAATTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.23
17 15 0.50
18 8 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAAATTAATT
Found at i:97758 original size:35 final size:34
Alignment explanation
Indices: 97718--97795 Score: 120
Period size: 35 Copynumber: 2.3 Consensus size: 34
97708 AGCTCTCGCA
*
97718 GGTGAGCTCGCAGTTTTGTAGAGCTCACAGTGTTT
1 GGTGAGCTCGCAGTTTTATAGAGCTCACAGT-TTT
*
97753 GGTGAGCTCGCAGTTTTATAGAGCTCGCAGTTTT
1 GGTGAGCTCGCAGTTTTATAGAGCTCACAGTTTT
*
97787 GGTAAGCTC
1 GGTGAGCTC
97796 ACATATTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 11 0.28
35 29 0.73
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (34 bp):
GGTGAGCTCGCAGTTTTATAGAGCTCACAGTTTT
Found at i:97795 original size:17 final size:17
Alignment explanation
Indices: 97721--97787 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
97711 TCTCGCAGGT
97721 GAGCTCGCAGTTTTGTA
1 GAGCTCGCAGTTTTGTA
*
97738 GAGCTCACAGTGTTTGGT-
1 GAGCTCGCAGT-TTT-GTA
*
97756 GAGCTCGCAGTTTTATA
1 GAGCTCGCAGTTTTGTA
97773 GAGCTCGCAGTTTTG
1 GAGCTCGCAGTTTTG
97788 GTAAGCTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.02
17 27 0.63
18 13 0.30
19 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (17 bp):
GAGCTCGCAGTTTTGTA
Found at i:99294 original size:17 final size:16
Alignment explanation
Indices: 99275--99369 Score: 61
Period size: 17 Copynumber: 5.7 Consensus size: 16
99265 GGTCTCATGC
99275 TTGGTGAGCTCGCAGT
1 TTGGTGAGCTCGCAGT
99291 CTTGGT--GCTCGCATGT
1 -TTGGTGAGCTCGCA-GT
*
99307 TT-GTGGAGCTCACAATGT
1 TTGGT-GAGCTCGC-A-GT
* * *
99325 TTGGGGAGCTCACAAT
1 TTGGTGAGCTCGCAGT
*
99341 TTTGTAGAGCTCGCAGTT
1 TTGGT-GAGCTCGCAG-T
99359 TTGGTGAGCTC
1 TTGGTGAGCTC
99370 ACATTTTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.03
15 9 0.15
16 6 0.10
17 25 0.40
18 19 0.31
19 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.34
Consensus pattern (16 bp):
TTGGTGAGCTCGCAGT
Found at i:99326 original size:18 final size:18
Alignment explanation
Indices: 99303--99352 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
99293 TGGTGCTCGC
99303 ATGTTTGTGGAGCTCACA
1 ATGTTTGTGGAGCTCACA
*
99321 ATGTTTGGGGAGCTCACA
1 ATGTTTGTGGAGCTCACA
*
99339 AT-TTTGTAGAGCTC
1 ATGTTTGTGGAGCTC
99353 GCAGTTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (18 bp):
ATGTTTGTGGAGCTCACA
Found at i:99377 original size:17 final size:17
Alignment explanation
Indices: 99312--99377 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
99302 CATGTTTGTG
* *
99312 GAGCTCACAATGTTTGGG
1 GAGCTCAC-ATTTTTGGT
*
99330 GAGCTCACAATTTT-GT
1 GAGCTCACATTTTTGGT
* *
99346 AGAGCTCGCAGTTTTGGT
1 -GAGCTCACATTTTTGGT
99364 GAGCTCACATTTTT
1 GAGCTCACATTTTT
99378 ACATTCAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.03
17 28 0.72
18 10 0.26
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (17 bp):
GAGCTCACATTTTTGGT
Found at i:103644 original size:30 final size:30
Alignment explanation
Indices: 103608--103668 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
103598 AATGGAACTT
103608 TTGCAAAACAGGCTCACACGTCCATGTGGG
1 TTGCAAAACAGGCTCACACGTCCATGTGGG
103638 TTGCAAAACAGGCTCACACGTCCATGTGGG
1 TTGCAAAACAGGCTCACACGTCCATGTGGG
103668 T
1 T
103669 GCCTGTGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (30 bp):
TTGCAAAACAGGCTCACACGTCCATGTGGG
Found at i:103892 original size:53 final size:54
Alignment explanation
Indices: 103829--103948 Score: 179
Period size: 53 Copynumber: 2.2 Consensus size: 54
103819 ATTGACACAT
* *
103829 GCCCGTGTGCCTCAAAATAGTATACACACACCTTGACACATGCTCGTGTGTC-A
1 GCCCGTGTGCCTCAAAATAGTATACACACACCTTGACACACGCCCGTGTGTCTA
* * * *
103882 GCCCGTGTGCCTCAAAATAGTATAGACATACCTTGACACACGCCCTTGTGTCTT
1 GCCCGTGTGCCTCAAAATAGTATACACACACCTTGACACACGCCCGTGTGTCTA
103936 GCCCGTGTGCCTC
1 GCCCGTGTGCCTC
103949 TTGGAACTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 47 0.78
54 13 0.22
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (54 bp):
GCCCGTGTGCCTCAAAATAGTATACACACACCTTGACACACGCCCGTGTGTCTA
Found at i:106803 original size:25 final size:25
Alignment explanation
Indices: 106775--106848 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 25
106765 TAAATAAAAT
106775 AAAAGTTATGATAATTATATATTT-
1 AAAAGTTATGATAATTATATATTTA
106799 AAAA---A--ATAATTATA-ATTTA
1 AAAAGTTATGATAATTATATATTTA
* *
106818 ATAGAAGTTGTGATAATTATGTATTTA
1 A-A-AAGTTATGATAATTATATATTTA
106845 AAAA
1 AAAA
106849 TAATTAGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 17
0.67 0.03 0.29
Matches are distributed among these distances:
18 4 0.10
19 10 0.26
20 1 0.03
21 3 0.08
24 4 0.10
25 2 0.05
26 9 0.23
27 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (25 bp):
AAAAGTTATGATAATTATATATTTA
Found at i:106832 original size:45 final size:44
Alignment explanation
Indices: 106772--106862 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
106762 TTTTAAATAA
*
106772 AATAAAAGTTATGATAATTATATATTTAAAAAATAATTATAATTT
1 AATAAAAGTTATGATAATTATATATTT-AAAAATAATTAGAATTT
* * *
106817 AATAGAAGTTGTGATAATTATGTATTTAAAAATAATTAGAATTT
1 AATAAAAGTTATGATAATTATATATTTAAAAATAATTAGAATTT
106861 AA
1 AA
106863 ATTACAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 18 0.43
45 24 0.57
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.41
Consensus pattern (44 bp):
AATAAAAGTTATGATAATTATATATTTAAAAATAATTAGAATTT
Found at i:106862 original size:17 final size:18
Alignment explanation
Indices: 106830--106863 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
106820 AGAAGTTGTG
*
106830 ATAATTATGTATTTAAAA
1 ATAATTATGAATTTAAAA
106848 ATAATTA-GAATTTAAA
1 ATAATTATGAATTTAAA
106864 TTACAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATAATTATGAATTTAAAA
Found at i:110123 original size:20 final size:20
Alignment explanation
Indices: 110098--110159 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
110088 ATTGACCGAC
110098 TGTTGACCGTTGACTTTGAT
1 TGTTGACCGTTGACTTTGAT
*
110118 TGTTGACTGTTGACTTTGAT
1 TGTTGACCGTTGACTTTGAT
*
110138 CGTTGACCGTTGACTGTTGAT
1 TGTTGACCGTTGACT-TTGAT
110159 T
1 T
110160 TTTTCGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 32 0.86
21 5 0.14
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.45
Consensus pattern (20 bp):
TGTTGACCGTTGACTTTGAT
Found at i:110129 original size:27 final size:27
Alignment explanation
Indices: 110095--110157 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
110085 GCCATTGACC
* **
110095 GACTGTTGACCGTTGA-CTTTGATTGTT
1 GACTGTTGA-CGTTGATCGTTGACCGTT
*
110122 GACTGTTGACTTTGATCGTTGACCGTT
1 GACTGTTGACGTTGATCGTTGACCGTT
110149 GACTGTTGA
1 GACTGTTGA
110158 TTTTTTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (27 bp):
GACTGTTGACGTTGATCGTTGACCGTT
Done.