Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014439.1 Kokia drynarioides strain JFW-HI SEQ_129477, 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: 92494
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:8570 original size:6 final size:6
Alignment explanation
Indices: 8559--8603 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
8549 TGATCAAAAT
* * *
8559 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
8604 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:11108 original size:18 final size:18
Alignment explanation
Indices: 11085--11139 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
11075 ACCAAATTAA
11085 GAAAATGTGTCAAGTTAG
1 GAAAATGTGTCAAGTTAG
11103 GAAAATGTGTCAAGTTAG
1 GAAAATGTGTCAAGTTAG
*
11121 GAAAAGGTG-CTAAGTTAG
1 GAAAATGTGTC-AAGTTAG
11139 G
1 G
11140 TACCGAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 1 0.03
18 34 0.97
ACGTcount: A:0.38, C:0.05, G:0.31, T:0.25
Consensus pattern (18 bp):
GAAAATGTGTCAAGTTAG
Found at i:11185 original size:27 final size:27
Alignment explanation
Indices: 11136--11188 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
11126 GGTGCTAAGT
* *
11136 TAGGTACCGAATTGAACCCAAAAAATA
1 TAGGTACCAAATTGAACACAAAAAATA
* *
11163 TAGGTACCAAATTGAGCATAAAAAAT
1 TAGGTACCAAATTGAACACAAAAAAT
11189 GTTTACGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (27 bp):
TAGGTACCAAATTGAACACAAAAAATA
Found at i:11353 original size:17 final size:18
Alignment explanation
Indices: 11331--11372 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11321 CATTTTTTGT
11331 AATATTCTAAAA-TTTTA
1 AATATTCTAAAACTTTTA
*
11348 AATATTTTTAAAACTTTTA
1 AATA-TTCTAAAACTTTTA
*
11367 TATATT
1 AATATT
11373 TTTTTGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTCTAAAACTTTTA
Found at i:11365 original size:19 final size:18
Alignment explanation
Indices: 11338--11375 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
11328 TGTAATATTC
11338 TAAAATTTTAAATATTTT
1 TAAAATTTTAAATATTTT
*
11356 TAAAACTTTTATATATTTT
1 TAAAA-TTTTAAATATTTT
11375 T
1 T
11376 TTGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TAAAATTTTAAATATTTT
Found at i:11447 original size:21 final size:20
Alignment explanation
Indices: 11408--11453 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
11398 AACTTTAGAA
* *
11408 TTTATATATTTATAGTTTTT
1 TTTATATATTTAAAATTTTT
11428 TTTATATATTTTAAAATTTTT
1 TTTATATA-TTTAAAATTTTT
*
11449 GTTAT
1 TTTAT
11454 TTTCCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATATATTTAAAATTTTT
Found at i:11522 original size:18 final size:17
Alignment explanation
Indices: 11496--11535 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11486 TTACATAATT
*
11496 TTTTAATAATGTTTTTA
1 TTTTAATAATATTTTTA
11513 TTTTATATAATATTTTTA
1 TTTTA-ATAATATTTTTA
*
11531 ATTTA
1 TTTTA
11536 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTAATAATATTTTTA
Found at i:16535 original size:23 final size:24
Alignment explanation
Indices: 16483--16539 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
16473 ATTTTATATG
*
16483 ATTTTTATAGTTTCTAATAATTTA
1 ATTTTTATAGTTTCTAATAAATTA
*
16507 ATTTTTTATA-TTT-TAATAAAATTC
1 A-TTTTTATAGTTTCTAAT-AAATTA
16531 ATTTTTATA
1 ATTTTTATA
16540 AATTTCCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 12 0.41
24 9 0.31
25 8 0.28
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTTATAGTTTCTAATAAATTA
Found at i:17613 original size:3 final size:3
Alignment explanation
Indices: 17605--17632 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17595 AATTCAAAAT
17605 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17633 AAGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19166 original size:29 final size:29
Alignment explanation
Indices: 19124--19180 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
19114 AAATTTGACA
19124 TTTTTTTTCTAATTTGGTA-TCTAAACTTT
1 TTTTTTTTCTAATTTGGTACTC-AAACTTT
19153 TTTTTTGTTC-AATTTGGTACTCAAACTT
1 TTTTTT-TTCTAATTTGGTACTCAAACTT
19181 GACACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTTTTTCTAATTTGGTACTCAAACTTT
Found at i:19200 original size:31 final size:31
Alignment explanation
Indices: 19103--19221 Score: 84
Period size: 32 Copynumber: 3.9 Consensus size: 31
19093 TTAATATAAT
* * * *
19103 ATTTGGTATCTAAATTTGACATTTTTTTTCTA
1 ATTTGGTACCTAAACTTGACA-CTTTTTCCTA
* ** **
19135 ATTTGGTATCTAAACTT---TTTTTTTGTTCA
1 ATTTGGTACCTAAACTTGACACTTTTTCCT-A
19164 ATTTGGTA-CTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTCCTA
* *
19195 ATTTGGTACCTAAACTTGCCATTTTTT
1 ATTTGGTACCTAAACTTGACACTTTTT
19222 TTAAGTTGGC
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
28 9 0.13
29 15 0.21
31 23 0.32
32 24 0.34
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:19541 original size:60 final size:58
Alignment explanation
Indices: 19445--19631 Score: 178
Period size: 58 Copynumber: 3.2 Consensus size: 58
19435 TTAAATTTAA
* * * * * *
19445 GTACCAATTTGAATCTATAAAAGCTTAAGTATCAAATTAGGAAAAAATGTCAAGTTCA-
1 GTACCAAATTGGATC-AAAAAAGTTTAAGTACCAAATTAAGAAAAAATGTCAAGTTCAG
* * * *
19503 ATACCAAATTGGATCCAAAAAAAAGTTTAAGTACCAAATTATGAAAAAGTGTCAAGTGCAG
1 GTACCAAATTGGAT-C--AAAAAAGTTTAAGTACCAAATTAAGAAAAAATGTCAAGTTCAG
* * * * * *
19564 GTACCAAATTGGGTCAAAAAATTTTAAATACAAAACTAAGAAAAAATGTCCAAGTTCAT
1 GTACCAAATTGGATCAAAAAAGTTTAAGTACCAAATTAAGAAAAAATGT-CAAGTTCAG
19623 GTACCAAAT
1 GTACCAAAT
19632 ATTATATTAA
Statistics
Matches: 105, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
58 39 0.37
59 17 0.16
60 37 0.35
61 12 0.11
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (58 bp):
GTACCAAATTGGATCAAAAAAGTTTAAGTACCAAATTAAGAAAAAATGTCAAGTTCAG
Found at i:21081 original size:22 final size:22
Alignment explanation
Indices: 21039--21081 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21029 AAAATTTAAA
*
21039 AATAATATCAACCAAATATCAC
1 AATAATATCAACCAAAAATCAC
21061 AATAATATC-ACCTAAAAATCA
1 AATAATATCAACC-AAAAATCA
21082 GATTCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (22 bp):
AATAATATCAACCAAAAATCAC
Found at i:26841 original size:18 final size:19
Alignment explanation
Indices: 26804--26841 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
26794 ATTTTATTGC
* *
26804 AAAATAAATTGAGTGAAAT
1 AAAATAAATAGAGAGAAAT
26823 AAAATAAATAG-GAGAAAT
1 AAAATAAATAGAGAGAAAT
26841 A
1 A
26842 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (19 bp):
AAAATAAATAGAGAGAAAT
Found at i:26846 original size:2 final size:2
Alignment explanation
Indices: 26839--26866 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26829 AATAGGAGAA
26839 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
26867 TAAATCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34108 original size:21 final size:21
Alignment explanation
Indices: 34084--34177 Score: 152
Period size: 21 Copynumber: 4.5 Consensus size: 21
34074 ACAAAGGTGA
34084 CTTCTACCAAAACAATTCATG
1 CTTCTACCAAAACAATTCATG
* *
34105 CTTCTACCGAAATAATTCATG
1 CTTCTACCAAAACAATTCATG
*
34126 CTTCTACTAAAACAATTCATG
1 CTTCTACCAAAACAATTCATG
*
34147 CTTCTACTAAAACAATTCATG
1 CTTCTACCAAAACAATTCATG
34168 CTTCTACCAA
1 CTTCTACCAA
34178 TACTAAAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (21 bp):
CTTCTACCAAAACAATTCATG
Found at i:34930 original size:25 final size:25
Alignment explanation
Indices: 34866--35042 Score: 156
Period size: 25 Copynumber: 6.7 Consensus size: 25
34856 GATAGAATGG
*
34866 CGCTCTTACGAGGCAAAATCCAGAATAT
1 CGCTCTTACGA-GCCAAA--CAGAATAT
* * *
34894 CGCTCTTTCGAGCCAAACGGAACAT
1 CGCTCTTACGAGCCAAACAGAATAT
*
34919 CGCTCTTACGAGCCAGACAGAATATAT
1 CGCTCTTACGAGCCAAACAG-A-ATAT
* * * *
34946 TGCACTTATGAGCCAGACAGAATAT
1 CGCTCTTACGAGCCAAACAGAATAT
* *
34971 TGCTCTTACGAGCCAAAATTCAAAATATAT
1 CGCTCTTACGAGCC-AAA--C-AGA-ATAT
35001 CGCTCTTACGAGCCAAACAGAATAT
1 CGCTCTTACGAGCCAAACAGAATAT
*
35026 CGCTCTTACAAGCCAAA
1 CGCTCTTACGAGCCAAA
35043 ATTCAGAGCG
Statistics
Matches: 124, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
25 59 0.48
26 6 0.05
27 26 0.21
28 11 0.09
29 5 0.04
30 17 0.14
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (25 bp):
CGCTCTTACGAGCCAAACAGAATAT
Found at i:35045 original size:55 final size:55
Alignment explanation
Indices: 34866--35047 Score: 203
Period size: 55 Copynumber: 3.4 Consensus size: 55
34856 GATAGAATGG
* * * * * *
34866 CGCTCTTACGAGGCAAAA-TCCAGA-ATATCGCTCTTTCGAGCCAAACGGAACAT
1 CGCTCTTACGAGCCAAAATTCAAAATATATCGCTCTTACGAGCCAAACAGAATAT
* * * * * *
34919 CGCTCTTACGAGCC-AGA--CAGAATATATTGCACTTATGAGCCAGACAGAATAT
1 CGCTCTTACGAGCCAAAATTCAAAATATATCGCTCTTACGAGCCAAACAGAATAT
*
34971 TGCTCTTACGAGCCAAAATTCAAAATATATCGCTCTTACGAGCCAAACAGAATAT
1 CGCTCTTACGAGCCAAAATTCAAAATATATCGCTCTTACGAGCCAAACAGAATAT
*
35026 CGCTCTTACAAGCCAAAATTCA
1 CGCTCTTACGAGCCAAAATTCA
35048 GAGCGTCTTC
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
51 2 0.02
52 37 0.36
53 15 0.14
55 50 0.48
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (55 bp):
CGCTCTTACGAGCCAAAATTCAAAATATATCGCTCTTACGAGCCAAACAGAATAT
Found at i:39454 original size:17 final size:18
Alignment explanation
Indices: 39404--39465 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
39394 CTCTAAATTA
* *
39404 CAATGACAAATAGAAATG
1 CAATGACAATTACAAATG
* *
39422 CAATGATAA-CACAAATG
1 CAATGACAATTACAAATG
39439 CAATGACAATTA-AAATG
1 CAATGACAATTACAAATG
*
39456 TAATGACAAT
1 CAATGACAAT
39466 GGGAATGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 28 0.76
18 9 0.24
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (18 bp):
CAATGACAATTACAAATG
Found at i:45806 original size:52 final size:52
Alignment explanation
Indices: 45678--45864 Score: 184
Period size: 52 Copynumber: 3.6 Consensus size: 52
45668 TAGCTCTAAT
* ** *
45678 GAGCCTAGACAGAATATCACTCTTACGAGCTAGAATCCAAAATATCT-CTCTTTC
1 GAGCC-AGACAGAATATCACTCTTACGAGCCAG-ATAGAATATAT-TGCTCTTTC
* * *
45732 GAGCTAGACAGAACATCGCTCTTACGAGCCAGATAGAATATATTGCT-TTTAC
1 GAGCCAGACAGAATATCACTCTTACGAGCCAGATAGAATATATTGCTCTTT-C
* * * * *
45784 GAGCCAGACAGTATATCACTCTTAAGAGCTAGATAGAAT-T-TCGCTCTTTT
1 GAGCCAGACAGAATATCACTCTTACGAGCCAGATAGAATATATTGCTCTTTC
* *
45834 GAGCCAGATAGAATATCGCTCTTACGAGCCA
1 GAGCCAGACAGAATATCACTCTTACGAGCCA
45865 AAATTCAGAG
Statistics
Matches: 110, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
50 30 0.27
51 8 0.07
52 44 0.40
53 24 0.22
54 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (52 bp):
GAGCCAGACAGAATATCACTCTTACGAGCCAGATAGAATATATTGCTCTTTC
Found at i:45863 original size:25 final size:25
Alignment explanation
Indices: 45678--45864 Score: 149
Period size: 25 Copynumber: 7.2 Consensus size: 25
45668 TAGCTCTAAT
* *
45678 GAGCCTAGACAGAATATCACTCTTAC
1 GAGCC-AGATAGAATATCGCTCTTAC
* * * *
45704 GAGCTAGAATCCAAAATATCTCTCTTTC
1 GAGCCAG-AT--AGAATATCGCTCTTAC
* * *
45732 GAGCTAGACAGAACATCGCTCTTAC
1 GAGCCAGATAGAATATCGCTCTTAC
* *
45757 GAGCCAGATAGAATATATTGCTTTTAC
1 GAGCCAGATAG-A-ATATCGCTCTTAC
* * * *
45784 GAGCCAGACAGTATATCACTCTTAA
1 GAGCCAGATAGAATATCGCTCTTAC
* * **
45809 GAGCTAGATAGAATTTCGCTCTTTT
1 GAGCCAGATAGAATATCGCTCTTAC
45834 GAGCCAGATAGAATATCGCTCTTAC
1 GAGCCAGATAGAATATCGCTCTTAC
45859 GAGCCA
1 GAGCCA
45865 AAATTCAGAG
Statistics
Matches: 124, Mismatches: 32, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
25 77 0.62
26 6 0.05
27 21 0.17
28 20 0.16
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (25 bp):
GAGCCAGATAGAATATCGCTCTTAC
Found at i:49725 original size:22 final size:22
Alignment explanation
Indices: 49700--49741 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49690 ATTTAAAAAC
*
49700 AATATCAACTAAATATCATAAT
1 AATATCAACTAAAAATCATAAT
*
49722 AATATCACCTAAAAATCATA
1 AATATCAACTAAAAATCATA
49742 TTCAAACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
AATATCAACTAAAAATCATAAT
Found at i:65997 original size:2 final size:2
Alignment explanation
Indices: 65990--66015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65980 TCATGATAAC
65990 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
66016 CAGAGTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67733 original size:158 final size:158
Alignment explanation
Indices: 67440--67760 Score: 428
Period size: 158 Copynumber: 2.0 Consensus size: 158
67430 ATTTTGGGAT
* * * * *
67440 TTACATGTTATTTGGGTACTGGTCTTAGATGTCCTACCGATGGCTAAGATCCAGCATTTGTTGTG
1 TTACAAGTTATATGGGTACTGGTATTAGATGTCCTACCGACGGCTAAGATCCAGCATTGGTTGTG
* ** * *
67505 GATTCTCCACAGCTCGTGTGAGCAGCACTGTGTAGCCTAACATCTCGACCCATAGCTCGTGTAAG
66 GATTCTCCACAGCTCATGTGAGCAGCACTGCATAGCCTAACATCTCAACCCATAGCTCATGTAAG
67570 CAGGCCCACTTTACAACTCGTGTGAGCA
131 CAGGCCCACTTTACAACTCGTGTGAGCA
* * * * * *
67598 TTACAAGTTATATGGGTGCTGGTATTTGATGTCCTACCGACGGTTGAGGTCCTGCATTGGTTGTG
1 TTACAAGTTATATGGGTACTGGTATTAGATGTCCTACCGACGGCTAAGATCCAGCATTGGTTGTG
* *
67663 GATTCTCCATAGCTCATGTGAGCAGCA-TCGCATAGCCTAACATCTCAACCCATAGCTCATGTGA
66 GATTCTCCACAGCTCATGTGAGCAGCACT-GCATAGCCTAACATCTCAACCCATAGCTCATGTAA
* * *
67727 GGAGGCCCATTTTACAACTTGTGTGAGCA
130 GCAGGCCCACTTTACAACTCGTGTGAGCA
*
67756 CTACA
1 TTACA
67761 TGATATAGGA
Statistics
Matches: 140, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
157 1 0.01
158 139 0.99
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (158 bp):
TTACAAGTTATATGGGTACTGGTATTAGATGTCCTACCGACGGCTAAGATCCAGCATTGGTTGTG
GATTCTCCACAGCTCATGTGAGCAGCACTGCATAGCCTAACATCTCAACCCATAGCTCATGTAAG
CAGGCCCACTTTACAACTCGTGTGAGCA
Found at i:79945 original size:42 final size:42
Alignment explanation
Indices: 79886--79982 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
79876 TTAAGATATG
** *
79886 ATTCGCATGTTAAGCATGTTGGCT-ATTTTGAATATAAATTCA
1 ATTCGCATGTTAAGCATG-CCGATGATTTTGAATATAAATTCA
* **
79928 ATTCGCATGTTAAGCATGCCGATGATTTTGATTATAAATTTG
1 ATTCGCATGTTAAGCATGCCGATGATTTTGAATATAAATTCA
79970 ATTCGCATGTTAA
1 ATTCGCATGTTAA
79983 AATGTCCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (42 bp):
ATTCGCATGTTAAGCATGCCGATGATTTTGAATATAAATTCA
Found at i:80092 original size:24 final size:24
Alignment explanation
Indices: 80065--80113 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
80055 TTTACTGCAA
* *
80065 TATTGAGTGGCTTGGCCACAACGT
1 TATTGAGTGCCTTGACCACAACGT
*
80089 TATTGAGTGCCTTGACCATAACGT
1 TATTGAGTGCCTTGACCACAACGT
80113 T
1 T
80114 CAACTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (24 bp):
TATTGAGTGCCTTGACCACAACGT
Found at i:80138 original size:63 final size:63
Alignment explanation
Indices: 80054--80212 Score: 237
Period size: 63 Copynumber: 2.5 Consensus size: 63
80044 ATATTGGCAG
* *
80054 TTTTACTGCAATATTGAGTGGCTTGGCCACAACGTTATTGAGTGCCTTGACCATAACGTTCAAC
1 TTTT-CTGCAATATTGAGTGGCTTGGCCACAACGTTATTGAGTGCCTTGACCACAACGTGCAAC
* ** * *
80118 TTTTTTGCAATATTGAGTGGCTTGGTTAAAACGTTATTGAGTGGCTTGACCACAACGTGCAAC
1 TTTTCTGCAATATTGAGTGGCTTGGCCACAACGTTATTGAGTGCCTTGACCACAACGTGCAAC
*
80181 TTTTCTGCAATATTGAGTGGCTTGGCCGCAAC
1 TTTTCTGCAATATTGAGTGGCTTGGCCACAAC
80213 ATGCTACTTG
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
63 79 0.95
64 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (63 bp):
TTTTCTGCAATATTGAGTGGCTTGGCCACAACGTTATTGAGTGCCTTGACCACAACGTGCAAC
Found at i:80174 original size:24 final size:24
Alignment explanation
Indices: 80128--80175 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
80118 TTTTTTGCAA
***
80128 TATTGAGTGGCTTGGTTAAAACGT
1 TATTGAGTGGCTTGACCAAAACGT
*
80152 TATTGAGTGGCTTGACCACAACGT
1 TATTGAGTGGCTTGACCAAAACGT
80176 GCAACTTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCAAAACGT
Found at i:80233 original size:39 final size:39
Alignment explanation
Indices: 80152--80282 Score: 181
Period size: 39 Copynumber: 3.4 Consensus size: 39
80142 GTTAAAACGT
* *
80152 TATTGAGTGGCTTGACCACAACGTGCAACTTTTCTGCAA
1 TATTGAGTGGCTTGACCACAACGTGCAACTTGTCTACAA
* * * * *
80191 TATTGAGTGGCTTGGCCGCAACATGCTACTTGTCTACTA
1 TATTGAGTGGCTTGACCACAACGTGCAACTTGTCTACAA
*
80230 TATTGAGTGGCTTAACCACAACGTGCAACTTGTCTACAA
1 TATTGAGTGGCTTGACCACAACGTGCAACTTGTCTACAA
*
80269 TATTAAGTGGCTTG
1 TATTGAGTGGCTTG
80283 GCCATAACAT
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (39 bp):
TATTGAGTGGCTTGACCACAACGTGCAACTTGTCTACAA
Found at i:83063 original size:69 final size:68
Alignment explanation
Indices: 82921--83083 Score: 184
Period size: 69 Copynumber: 2.4 Consensus size: 68
82911 TCTTCCTGCC
* * * *
82921 ATGTTGATGGTGCAAAGTTCAGAATAGACCTTCTTTTAGCCATGTTAAGGATGCAAAACTTCTCC
1 ATGTTGATGGTGCAAAGTTCA-AATAGACCCTCCTCTAGCCATGTTAAGGATGCAAAAATTCTCC
*
82986 CACC
65 CACA
* * *
82990 ATGTTAATGGTGCAAAGTTCAAATA-AGCCCTCCTCTAGTCATGTTAAGGGTGCAAAAATTCTTC
1 ATGTTGATGGTGCAAAGTTCAAATAGA-CCCTCCTCTAGCCATGTTAAGGATGCAAAAATTC-TC
* *
83054 TCATA
64 CCACA
*
83059 ATGTTGATGGTGTAAAGTTCGAAAT
1 ATGTTGATGGTGCAAAGTTC-AAAT
83084 GAGCTCTGCT
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
67 1 0.01
68 32 0.41
69 42 0.53
70 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (68 bp):
ATGTTGATGGTGCAAAGTTCAAATAGACCCTCCTCTAGCCATGTTAAGGATGCAAAAATTCTCCC
ACA
Found at i:83316 original size:157 final size:156
Alignment explanation
Indices: 83072--83488 Score: 420
Period size: 157 Copynumber: 2.7 Consensus size: 156
83062 TTGATGGTGT
* * * * *
83072 AAAGTTC-GAAATGAGCTCTGCTCACACCATGTTGAAGTTACAAGTGTTCTTCCTA--TTGTAAT
1 AAAGTTCAG-AATGAGCTCTTCTCACACCATGTTGAAGTTGCAAGGGTTCTTCCCACCATGT--T
* * * *
83134 GATGTTGCAAATTTCAGAATGGGTCCTCCCTAGCCATGTCGAAGTCTCTCATCATGTTGAGGGTT
63 GATGTTGCAAATTTCAGAAT-GGTCCTCCCTAGCCATGTCGAAGTCTCTCACCATGCTGAAGGTG
* * * *
83199 CTAAACTTTTTCCCACCTTATTAATGATGC
127 CAAAACTTCTTCCCACCATATTAATGATAC
*
83229 AAAGTTCAGAATGAGCTCTTCTCACACCATGTTGAAGTTGTAAGGGTTCTTCCCACCATGTTGAT
1 AAAGTTCAGAATGAGCTCTTCTCACACCATGTTGAAGTTGCAAGGGTTCTTCCCACCATGTTGAT
* * * * * *
83294 GTTGCAAATTTCAGAATAGGTCCTCCCCTTGGCATTTTGAAGTTTTTCACCATGCTGAAGGTGCA
66 GTTGCAAATTTCAGAAT-GGTCCT-CCCTAGCCATGTCGAAGTCTCTCACCATGCTGAAGGTGCA
* *
83359 AAACTTCTTCCCTCCATATTGATGATAC
129 AAACTTCTTCCCACCATATTAATGATAC
* * * * *
83387 AAAGTTCAAAATG-GGTCCTT-TCACA--ATTTTGAATTTGCAAAGGTTCTTCCCACCATGTTGA
1 AAAGTTCAGAATGAGCT-CTTCTCACACCATGTTGAAGTTGCAAGGGTTCTTCCCACCATGTTGA
* * * *
83448 TTTTGCAAAGTTCAAAATGGATCCT--CTCGCCATGTCGAAGT
65 TGTTGCAAATTTCAGAATGG-TCCTCCCTAGCCATGTCGAAGT
83489 TACAAAGGTG
Statistics
Matches: 218, Mismatches: 36, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
152 12 0.06
154 2 0.01
155 51 0.23
157 82 0.38
158 68 0.31
159 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (156 bp):
AAAGTTCAGAATGAGCTCTTCTCACACCATGTTGAAGTTGCAAGGGTTCTTCCCACCATGTTGAT
GTTGCAAATTTCAGAATGGTCCTCCCTAGCCATGTCGAAGTCTCTCACCATGCTGAAGGTGCAAA
ACTTCTTCCCACCATATTAATGATAC
Found at i:83448 original size:67 final size:67
Alignment explanation
Indices: 83363--83538 Score: 192
Period size: 67 Copynumber: 2.6 Consensus size: 67
83353 GGTGCAAAAC
* * * * * * * * *
83363 TTCTTCCCTCCATATTGATGATACAAAGTTCAAAATGGGTCCTTTCACAATTTTGAATTTGCAAA
1 TTCTTCCCACCATGTTGATGTTGCAAAGTTCAAAATGGGTCCTCTCACAATGTCGAAGTTACAAA
83428 GG
66 GG
* * * *
83430 TTCTTCCCACCATGTTGATTTTGCAAAGTTCAAAATGGATCCTCTCGCCATGTCGAAGTTACAAA
1 TTCTTCCCACCATGTTGATGTTGCAAAGTTCAAAATGGGTCCTCTCACAATGTCGAAGTTACAAA
83495 GG
66 GG
* * *
83497 TGT-TTCCCGCCATGTTAATGTTGCAAAGTTCAGAATGGGTCC
1 T-TCTTCCCACCATGTTGATGTTGCAAAGTTCAAAATGGGTCC
83539 CCCTTTCACC
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 89 0.99
68 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (67 bp):
TTCTTCCCACCATGTTGATGTTGCAAAGTTCAAAATGGGTCCTCTCACAATGTCGAAGTTACAAA
GG
Found at i:91594 original size:15 final size:16
Alignment explanation
Indices: 91559--91598 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
91549 AAAGGTCTTT
*
91559 TTAAAATTTATAAAAA
1 TTAAAATTAATAAAAA
91575 TTAAAATTAATAAAAA
1 TTAAAATTAATAAAAA
91591 -TAAAATTA
1 TTAAAATTA
91599 TAATTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAATTAATAAAAA
Found at i:92104 original size:4 final size:4
Alignment explanation
Indices: 92091--92160 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
92081 AAAATTGAAG
* * *
92091 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GGAA TAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
92139 G-AA G-AA GGAA GAAA GGAAA GAA
1 GAAA GAAA GAAA GAAA -GAAA GAA
92161 GAAGAAGAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
3 9 0.16
4 39 0.71
5 7 0.13
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:92132 original size:33 final size:35
Alignment explanation
Indices: 92088--92158 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 35
92078 ACGAAAATTG
92088 AAGGAAAAAAGAAAGAAAAAAG-AGAAAGAAA-GA
1 AAGGAAAAAAGAAAGAAAAAAGAAGAAAGAAAGGA
* * *
92121 AAGGAATAAAGAAAGAAAGAAGAAGGAAGAAAGGA
1 AAGGAAAAAAGAAAGAAAAAAGAAGAAAGAAAGGA
92156 AAG
1 AAG
92159 AAGAAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 20 0.61
34 8 0.24
35 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (35 bp):
AAGGAAAAAAGAAAGAAAAAAGAAGAAAGAAAGGA
Found at i:92163 original size:30 final size:32
Alignment explanation
Indices: 92088--92172 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
92078 ACGAAAATTG
92088 AAGGAAAAAAGAAAGAAAAAAGAGAAAGAAAGA
1 AAGG-AAAAAGAAAGAAAAAAGAGAAAGAAAGA
* *
92121 AAGGAATAAAGAAAGAAAGAAGAAGGAAGAAAGGA
1 AAGGAA-AAAGAAAGAAAAAAG-AGAAAGAAA-GA
*
92156 AA-GAAGAAG-AAGAAAAA
1 AAGGAAAAAGAAAGAAAAA
92173 TAAAGTAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
32 9 0.20
33 21 0.47
34 11 0.24
35 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (32 bp):
AAGGAAAAAGAAAGAAAAAAGAGAAAGAAAGA
Found at i:92177 original size:19 final size:19
Alignment explanation
Indices: 92087--92171 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 19
92077 AACGAAAATT
92087 GAAGGAA-AAAAGAAAGAA
1 GAAGGAAGAAAAGAAAGAA
92105 -AA--AAGAGAAAGAAAGAAA
1 GAAGGAAGA-AAAGAAAG-AA
**
92123 GGAATAAAG-AAAGAAAGAA
1 -GAAGGAAGAAAAGAAAGAA
*
92142 GAAGGAAGAAAGGAAAGAA
1 GAAGGAAGAAAAGAAAGAA
92161 GAA-GAAGAAAA
1 GAAGGAAGAAAA
92172 ATAAAGTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
15 2 0.04
16 1 0.02
17 10 0.18
18 15 0.27
19 14 0.25
20 10 0.18
22 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (19 bp):
GAAGGAAGAAAAGAAAGAA
Done.