Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002194.1 Kokia drynarioides strain JFW-HI SEQ_114173, 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: 106508
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2089 original size:7 final size:7
Alignment explanation
Indices: 2077--2119 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
2067 GAGCTCAAAG
2077 GATATAT
1 GATATAT
2084 GATATAT
1 GATATAT
2091 GATATAT
1 GATATAT
2098 GATATAT
1 GATATAT
2105 GATATAT
1 GATATAT
2112 GATA-AT
1 GATATAT
2118 GA
1 GA
2120 AATGATTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.11
7 32 0.89
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (7 bp):
GATATAT
Found at i:4211 original size:58 final size:57
Alignment explanation
Indices: 4123--4330 Score: 229
Period size: 57 Copynumber: 3.6 Consensus size: 57
4113 ATAGAAATGG
* * * *
4123 TGAAAACGTAGAAATGTGAAATATTTGGAAATGAAGGTGGTTTTCTCCAAAAATGAAAA
1 TGAAAATGAAGAAATG-AAAATATTTGGAAATGAATGTGGTTTTCTCC-AAAATGAAAA
* *
4182 TGAAAATGAAGAAATGAAAATATTTGGAAATGACTGTGGTTTTTTCCAAAATGAAAA
1 TGAAAATGAAGAAATGAAAATATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
* * * * * * * *
4239 TAAAAATTAAGAAATGGAAACATTTGAAAATAAATGTGATTTTCTCCAAAATAAAAA
1 TGAAAATGAAGAAATGAAAATATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
* **
4296 TGAAAAT-AAAAAATGAAAATGACCTGGAAATGAAT
1 TGAAAATGAAGAAATGAAAAT-ATTTGGAAATGAAT
4331 TTATATTTTT
Statistics
Matches: 124, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
56 10 0.08
57 73 0.59
58 27 0.22
59 14 0.11
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (57 bp):
TGAAAATGAAGAAATGAAAATATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
Found at i:4303 original size:12 final size:13
Alignment explanation
Indices: 4286--4315 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4276 GATTTTCTCC
4286 AAAAT-AAAAATG
1 AAAATAAAAAATG
4298 AAAATAAAAAATG
1 AAAATAAAAAATG
4311 AAAAT
1 AAAAT
4316 GACCTGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAATAAAAAATG
Found at i:14776 original size:25 final size:27
Alignment explanation
Indices: 14729--14780 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
14719 CCAACGTGGC
14729 ATTTTTCTTTTAATTTTGACTTTCTTTT
1 ATTTTTCTTTTAATTTT-ACTTTCTTTT
*
14757 ATTTTT-TTTTCATTTT-CTTTCTTT
1 ATTTTTCTTTTAATTTTACTTTCTTT
14781 CTTTCTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
27 9 0.39
28 6 0.26
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.75
Consensus pattern (27 bp):
ATTTTTCTTTTAATTTTACTTTCTTTT
Found at i:14801 original size:18 final size:18
Alignment explanation
Indices: 14780--14816 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
14770 TTTCTTTCTT
14780 TCTTT-CTTTCCTATTTCC
1 TCTTTCCTTTCCT-TTTCC
14798 TCTTTCCTTTCCTTTTCC
1 TCTTTCCTTTCCTTTTCC
14816 T
1 T
14817 TTCTTTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTCCTTTCCTTTTCC
Found at i:15701 original size:16 final size:16
Alignment explanation
Indices: 15680--15712 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15670 GTGTGTGTGC
15680 GTTGTTAAAAAGTTAA
1 GTTGTTAAAAAGTTAA
15696 GTTGTTAAAAAGTTAA
1 GTTGTTAAAAAGTTAA
15712 G
1 G
15713 AAAATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (16 bp):
GTTGTTAAAAAGTTAA
Found at i:19037 original size:24 final size:23
Alignment explanation
Indices: 18973--19030 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
18963 AGAAAGGATG
* *
18973 GTATGAAAATTTTATTATACGATT
1 GTATG-AAATTTAATTATAAGATT
*
18997 GTATGAAATTATAATTATAAGGTT
1 GTATGAAATT-TAATTATAAGATT
19021 GTATGAAATT
1 GTATGAAATT
19031 GTGATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.43
Consensus pattern (23 bp):
GTATGAAATTTAATTATAAGATT
Found at i:30855 original size:26 final size:25
Alignment explanation
Indices: 30826--30886 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
30816 TTATGCTTAG
*
30826 TTTTTTATTTAAT-TATTTACTTATTA
1 TTTTATATTTAATATATTT--TTATTA
30852 TTTTATATTTAATAATATTTTTATTA
1 TTTTATATTTAAT-ATATTTTTATTA
*
30878 TTTGATATT
1 TTTTATATT
30887 AACAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 26 0.84
28 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTATATTTAATATATTTTTATTA
Found at i:30898 original size:26 final size:26
Alignment explanation
Indices: 30846--30902 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
30836 AATTATTTAC
* *
30846 TTATTATTTTATATTTAATAATATTT
1 TTATTATTTGATATTTAACAATATTT
30872 TTATTATTTGATA-TTAACAAT-TTT
1 TTATTATTTGATATTTAACAATATTT
*
30896 TTTTTAT
1 TTATTAT
30903 GAAATTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 9 0.32
25 7 0.25
26 12 0.43
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATTATTTGATATTTAACAATATTT
Found at i:33214 original size:70 final size:70
Alignment explanation
Indices: 33110--33274 Score: 246
Period size: 70 Copynumber: 2.4 Consensus size: 70
33100 CTGATTCCAT
* **
33110 AACCTTAAACCC-AAACCA-TGAACCCCAATCTCATAACTCGTAATCTCGAACCCTTGAAACTTA
1 AACCTTAAACCCTAAA-CATTGAACCCCAATCTCATAACTCATAAAATCGAACCCTTGAAACTTA
*
33173 AATTCG
65 AATTCA
*
33179 AACCTTAAACCCTAAACATTGAACCCCAATCTCATAACTCATAAAATCGAACCCTTGAACCTTAA
1 AACCTTAAACCCTAAACATTGAACCCCAATCTCATAACTCATAAAATCGAACCCTTGAAACTTAA
33244 ATTCA
66 ATTCA
33249 AATCC-TAAACCCTAAACATTGAACCC
1 AA-CCTTAAACCCTAAACATTGAACCC
33275 ATAACTTCAA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
69 14 0.16
70 72 0.82
71 2 0.02
ACGTcount: A:0.40, C:0.32, G:0.05, T:0.23
Consensus pattern (70 bp):
AACCTTAAACCCTAAACATTGAACCCCAATCTCATAACTCATAAAATCGAACCCTTGAAACTTAA
ATTCA
Found at i:33767 original size:58 final size:59
Alignment explanation
Indices: 33697--33826 Score: 190
Period size: 58 Copynumber: 2.2 Consensus size: 59
33687 TTAATATAAT
* * *
33697 ATTTGGTACCTGAACTTGATACTTTTTTCTAATTTGGCACCTAAA-TTTTTTAGACTCA
1 ATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGACAACTAAATTTTTTTAGACTCA
* *
33755 ATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGATAACTAAACTTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGACAACTAAA--TTTTTTTAGACTCA
33816 ATTTGGTACCT
1 ATTTGGTACCT
33827 AAATTTATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 41 0.64
61 23 0.36
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGACAACTAAATTTTTTTAGACTCA
Found at i:34010 original size:31 final size:31
Alignment explanation
Indices: 33975--34139 Score: 123
Period size: 31 Copynumber: 5.5 Consensus size: 31
33965 TTAAAAAAGA
* *
33975 TTAGGTACCAAATT-AGAAAAAAGAGTCAAGT
1 TTAGGTACCAAATTAAG-AAAAAGTGACAAGT
*
34006 TTAGGTGCCAAATTAAGAAAAAGTGACAAGT
1 TTAGGTACCAAATTAAGAAAAAGTGACAAGT
***
34037 TT-GAGTACCAAATTAGAGCCCAA---A-AAGT
1 TTAG-GTACCAAATTA-AGAAAAAGTGACAAGT
* * * * *
34065 TTAAGTATCAATTTAA-AAATAGTGTCAAGT
1 TTAGGTACCAAATTAAGAAAAAGTGACAAGT
34095 TTAGGTACCAAATTTAA-AAAAAGTGACAAGT
1 TTAGGTACCAAA-TTAAGAAAAAGTGACAAGT
34126 TT-GAGTACCAAATT
1 TTAG-GTACCAAATT
34140 GGACAAAAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 15 0.14
29 1 0.01
30 17 0.16
31 63 0.61
32 6 0.06
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (31 bp):
TTAGGTACCAAATTAAGAAAAAGTGACAAGT
Found at i:34116 original size:89 final size:87
Alignment explanation
Indices: 33991--34193 Score: 273
Period size: 89 Copynumber: 2.3 Consensus size: 87
33981 ACCAAATTAG
* *
33991 AAAAAAGAGTCAAGTTTAGGTGCCAAATTAAGAAAAAGTGACAAGTTTGAGTACCAAATTAGAGC
1 AAAAAAGTGTCAAGTTTAGGTACCAAATTAAGAAAAAGTGACAAGTTTGAGTACCAAATTAGA-C
** * * *
34056 CCAAAAAGTTTAAGTATCAATTT
65 AAAAAAAATTTAAATATCAAATT
*
34079 AAAAATAGTGTCAAGTTTAGGTACCAAATTTAA-AAAAAGTGACAAGTTTGAGTACCAAATTGGA
1 AAAAA-AGTGTCAAGTTTAGGTACCAAA-TTAAGAAAAAGTGACAAGTTTGAGTACCAAATTAGA
34143 CAAAAAAAATTTAAATATCAAATT
64 CAAAAAAAATTTAAATATCAAATT
* **
34167 AAAAAAATGTCAAGTTTAAATACCAAA
1 AAAAAAGTGTCAAGTTTAGGTACCAAA
34194 CGTTATATTA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
87 19 0.19
88 29 0.28
89 50 0.49
90 4 0.04
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (87 bp):
AAAAAAGTGTCAAGTTTAGGTACCAAATTAAGAAAAAGTGACAAGTTTGAGTACCAAATTAGACA
AAAAAAATTTAAATATCAAATT
Found at i:50607 original size:28 final size:27
Alignment explanation
Indices: 50557--50610 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
50547 GGTAAAACCA
*
50557 TTATATTGTTTAGGTATTTAAATAATG
1 TTATATTGTTTAGGTAGTTAAATAATG
50584 TTATACTTCGTTTA-GTAGTTAAATAAT
1 TTATA-TT-GTTTAGGTAGTTAAATAAT
50611 CAGTCCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 14 0.58
29 5 0.21
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (27 bp):
TTATATTGTTTAGGTAGTTAAATAATG
Found at i:51202 original size:17 final size:17
Alignment explanation
Indices: 51177--51210 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51167 AATGTAAAAA
*
51177 ATATTTTTTTTATTTTT
1 ATATATTTTTTATTTTT
51194 ATATATTTTTTATTTTT
1 ATATATTTTTTATTTTT
51211 TAGTGTTCTC
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATATATTTTTTATTTTT
Found at i:55485 original size:18 final size:19
Alignment explanation
Indices: 55444--55485 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
55434 TTATTTGATA
55444 ATTTTATAACATTTTGTAG
1 ATTTTATAACATTTTGTAG
* * *
55463 TTTTTAT-ACCTTTTTTAG
1 ATTTTATAACATTTTGTAG
55481 ATTTT
1 ATTTT
55486 CTTTTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTTTATAACATTTTGTAG
Found at i:62139 original size:24 final size:24
Alignment explanation
Indices: 62098--62144 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62088 TACAAGAATA
62098 TAAAACGTTAAAGAAGATAGAAAGT
1 TAAAACGTTAAAGAAGAT-GAAAGT
* *
62123 TAAAA-GTTAAGGGAGATGAAAG
1 TAAAACGTTAAAGAAGATGAAAG
62145 GTTGAACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (24 bp):
TAAAACGTTAAAGAAGATGAAAGT
Found at i:70451 original size:92 final size:92
Alignment explanation
Indices: 70330--70510 Score: 326
Period size: 92 Copynumber: 2.0 Consensus size: 92
70320 AAAAATTTAA
* *
70330 GAGATCTCCATCTTACAAAGTTTTCAGAATAAGAAAAAACGACTTTGCCATCGGTGTCAATCTTC
1 GAGATCTCCATCCTACAAAGTTTTCAGAATAAGAAAAAACGACTTTGCCATCGGTGCCAATCTTC
* *
70395 CATTGACACACGCTCTACCAAAGTTAG
66 CATCGACACACACTCTACCAAAGTTAG
70422 GAGATCTCCATCCTACAAAGTTTTCAGAATAAGAAAAAACGACTTTGCCATCGGTGCCAATCTTC
1 GAGATCTCCATCCTACAAAGTTTTCAGAATAAGAAAAAACGACTTTGCCATCGGTGCCAATCTTC
70487 CATCGACACACACTCTACCAAAGT
66 CATCGACACACACTCTACCAAAGT
70511 CGGTGCTTCC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (92 bp):
GAGATCTCCATCCTACAAAGTTTTCAGAATAAGAAAAAACGACTTTGCCATCGGTGCCAATCTTC
CATCGACACACACTCTACCAAAGTTAG
Found at i:75805 original size:181 final size:186
Alignment explanation
Indices: 75475--75818 Score: 492
Period size: 181 Copynumber: 1.9 Consensus size: 186
75465 ACCCAAGATG
**
75475 TTTAAAGTTGCTGTGACACTTGTTGTATCTGTTGGCCTGTAAGCTTTCCTTTCCTTCTGCTCCTG
1 TTTAAAGTTGCTGTGACACTTCCTGTATCTGTTGGCCTGTAAGCTTTCC-TTCCTTCTGCTCCTG
* *
75540 TAATTTTGTCATGGTAACATGAATTGATATACTAATGCCAACTAACAACAAAATGTAGCAAGTAT
65 TAATTTTGTCAGGGAAACATGAATTGATATACTAATGCCAACTAACAACAAAATGTAGCAAGTAT
75605 ATTATGAATTAAACTTTCTTATTAATCAATTCAGCTTAAATTGAACAATAATTACTA
130 ATTATGAATTAAACTTTCTTATTAATCAATTCAGCTTAAATTGAACAATAATTACTA
75662 TTTAAAGTTGCTGTGACACTTCCTGTATCTGTTGGCCTGTAAGCATTT-C-T-C-T-T-CTCCTG
1 TTTAAAGTTGCTGTGACACTTCCTGTATCTGTTGGCCTGTAAGC-TTTCCTTCCTTCTGCTCCTG
* * *
75721 TAATATTT-TCAGGGAAACATGAATTGATATACTAATGGCAACTAAGAACAATATGTAGCGAA-T
65 TAAT-TTTGTCAGGGAAACATGAATTGATATACTAATGCCAACTAACAACAAAATGTAGC-AAGT
*
75784 A-AGTTAT-AATTTAATCTTTCTTATTAATCAATTCA
128 ATA-TTATGAA-TTAAACTTTCTTATTAATCAATTCA
75819 ACATACATCC
Statistics
Matches: 144, Mismatches: 8, Indels: 16
0.86 0.05 0.10
Matches are distributed among these distances:
180 3 0.02
181 86 0.60
182 6 0.04
183 1 0.01
184 1 0.01
185 1 0.01
187 43 0.30
188 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (186 bp):
TTTAAAGTTGCTGTGACACTTCCTGTATCTGTTGGCCTGTAAGCTTTCCTTCCTTCTGCTCCTGT
AATTTTGTCAGGGAAACATGAATTGATATACTAATGCCAACTAACAACAAAATGTAGCAAGTATA
TTATGAATTAAACTTTCTTATTAATCAATTCAGCTTAAATTGAACAATAATTACTA
Found at i:77528 original size:33 final size:36
Alignment explanation
Indices: 77479--77556 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
77469 ACATGAGTTC
*
77479 AGCTTT-AAGTTCTTT-TTCTT-GGGCCAGTTGATG
1 AGCTTTAAATTTCTTTCTTCTTAGGGCCAGTTGATG
* *
77512 AGCTTTAAATTTTTTTTCTTCTTATGGCCAGTTGATG
1 AGCTTTAAA-TTTCTTTCTTCTTAGGGCCAGTTGATG
77549 AGCTTTAA
1 AGCTTTAA
77557 GCTTTAGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 6 0.16
34 2 0.05
35 5 0.13
36 5 0.13
37 20 0.53
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47
Consensus pattern (36 bp):
AGCTTTAAATTTCTTTCTTCTTAGGGCCAGTTGATG
Found at i:84234 original size:70 final size:67
Alignment explanation
Indices: 84108--84240 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
84098 ATAAACAATA
* * *
84108 TAATGGTTTTGTCTTTTAACTTAATGTGTAAACATTTATCAAAATGACATAATTTTATCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGTGTAAACATTTATCAAAACGACATAATTTTATCTTTTAA
84173 CT
66 CT
* * *
84175 TAATGGTTTTGACTTTTAACTTTAGAAAGTGTAAACATTTATCAAAACGACGTAGTTTTATTTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGTGTAAACATTTATCAAAACGACATAATTTTATCTTT
84240 T
63 T
84241 TTATTCGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.04
70 36 0.63
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGTGTAAACATTTATCAAAACGACATAATTTTATCTTTTAA
CT
Found at i:86419 original size:35 final size:34
Alignment explanation
Indices: 86380--86488 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 34
86370 TTTTTTTAAT
86380 ATAAAATATTTTTATCCACCCACATTGTTGATATG
1 ATAAAATATTTTTAT-CACCCACATTGTTGATATG
* * * **
86415 AT-AAA-A-TTTAAT-ACCTAAATAATGTTCTTGAT-
1 ATAAAATATTTTTATCACCCACAT--TGTTGAT-ATG
*
86447 ATAAAATATTTTTATTCACCCACATTATTGATATG
1 ATAAAATATTTTTA-TCACCCACATTGTTGATATG
86482 ATAAAAT
1 ATAAAAT
86489 CTAATACCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
30 6 0.11
32 12 0.22
33 6 0.11
34 6 0.11
35 17 0.31
36 1 0.02
37 6 0.11
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (34 bp):
ATAAAATATTTTTATCACCCACATTGTTGATATG
Found at i:86456 original size:67 final size:67
Alignment explanation
Indices: 86378--86517 Score: 237
Period size: 67 Copynumber: 2.1 Consensus size: 67
86368 TATTTTTTTA
* *
86378 ATATAAAATATTTTTATCCACCCACATTGTTGATATGATAAAATTTAATACCTAAATAATGTTCT
1 ATATAAAATATTTTTATCCACCCACATTATTGATATGATAAAATCTAATACCTAAATAATGTTCT
86443 TG
66 TG
* *
86445 ATATAAAATATTTTTATTCACCCACATTATTGATATGATAAAATCTAATACCTAAATAATGTTGT
1 ATATAAAATATTTTTATCCACCCACATTATTGATATGATAAAATCTAATACCTAAATAATGTTCT
86510 TG
66 TG
86512 AT-TAAA
1 ATATAAA
86518 TTAATATTAC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
66 4 0.06
67 65 0.94
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (67 bp):
ATATAAAATATTTTTATCCACCCACATTATTGATATGATAAAATCTAATACCTAAATAATGTTCT
TG
Found at i:104089 original size:15 final size:15
Alignment explanation
Indices: 104069--104098 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
104059 AAAATTTATA
104069 CATAATTTTTAAGGT
1 CATAATTTTTAAGGT
104084 CATAATTTTTAAGGT
1 CATAATTTTTAAGGT
104099 AAATAACACA
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:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
CATAATTTTTAAGGT
Done.