Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011866.1 Kokia drynarioides strain JFW-HI SEQ_126863, 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: 171124
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:101 original size:33 final size:33
Alignment explanation
Indices: 19--103 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 33
9 ACCTAGTCCC
** * *
19 CCACCACCACCACCTCCATACTACTACAAGTCT
1 CCACCACCACCGTCTCCATACTACTACAAATCA
* * *
52 CCTCCTCCACCGTCTCCTTACTACTACAAATCA
1 CCACCACCACCGTCTCCATACTACTACAAATCA
* *
85 CCACCACCTCCTTCTCCAT
1 CCACCACCACCGTCTCCAT
104 CACCCCCGCC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.25, C:0.49, G:0.02, T:0.24
Consensus pattern (33 bp):
CCACCACCACCGTCTCCATACTACTACAAATCA
Found at i:9787 original size:16 final size:16
Alignment explanation
Indices: 9751--9789 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
9741 GACCAAAATT
9751 TAATTTTATTATTTGA
1 TAATTTTATTATTTGA
*
9767 AAATTTTATATATTT-A
1 TAATTTTAT-TATTTGA
9783 TAATTTT
1 TAATTTT
9790 TTTAAAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TAATTTTATTATTTGA
Found at i:10831 original size:16 final size:18
Alignment explanation
Indices: 10810--10844 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
10800 CGATACCTAT
10810 ATATTTT-TTTA-ATACG
1 ATATTTTATTTATATACG
10826 ATATTTTATTTATATACG
1 ATATTTTATTTATATACG
10844 A
1 A
10845 AAATACTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (18 bp):
ATATTTTATTTATATACG
Found at i:11167 original size:60 final size:60
Alignment explanation
Indices: 10989--11302 Score: 242
Period size: 60 Copynumber: 5.2 Consensus size: 60
10979 TGGCTATGTC
* * ** *
10989 ATGGCCAACA-CCTCTATTTATCTGATAAAAAAA-CAAATTTTTTTATGTTGGA-CATGCA
1 ATGGCCGACACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTATT-GATCATGCA
* * * * * *
11047 ATTGCCGACACCCCCT-TTT-TCAGATAAAAAAATTTTAAAAATTTTTAGTATTGATCATGCA
1 ATGGCCGACACCCACTATTTATCTGATAAAAAAA---TCAAATTTTTTGGTATTGATCATGCA
* *
11108 ATGGCCGGCACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTATTGACCATGCA
1 ATGGCCGACACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTATTGATCATGCA
* ** * * * * * * * *
11168 ATGACCGACACCCTTTTTTTGTCAGATAAAAAACTTTCAAAATTTTTTTGTATTGGTTATGTA
1 ATGGCCGACACCCACTATTTATCTGATAAAAAA--ATC-AAATTTTTTGGTATTGATCATGCA
* * * * * * *
11231 ATGGTCGACATCCACTATTTATTTAATAAAAAAATCAAATTTTTTGGTGTTCATCATGTA
1 ATGGCCGACACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTATTGATCATGCA
*
11291 ATGACCGACACC
1 ATGGCCGACACC
11303 AACTTTCTCT
Statistics
Matches: 196, Mismatches: 49, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
57 12 0.06
58 11 0.06
59 4 0.02
60 78 0.40
61 32 0.16
62 5 0.03
63 54 0.28
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (60 bp):
ATGGCCGACACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTATTGATCATGCA
Found at i:11260 original size:123 final size:119
Alignment explanation
Indices: 10891--11302 Score: 404
Period size: 123 Copynumber: 3.4 Consensus size: 119
10881 GCCATGCATT
* * * *** *
10891 TGATAAAAAAATTTAAATTTTTGGGTGTTGACCATACAATGGTTGATACCCCCTTTTTGTCAGAT
1 TGATAAAAAAA-TCAAATTTTTTGGTGTTGACCATGCAATGACCGACA-CCCCTTTTTGTCAGAT
* * * * * *
10956 -AAAAATTT-TAATTTTTTTGGTGTTGGCTATGTCATGGCCAACACCTCTATTTATC
64 AAAAAATTTAAAATTTTTTT-GTATTGGTTATGTAATGGCCGACACCACTATTTATC
** *
11011 TGATAAAAAAA-CAAATTTTTTTATGTTGGA-CATGCAATTG-CCGACACCCCCTTTT-TCAGAT
1 TGATAAAAAAATCAAATTTTTTGGTGTT-GACCATGCAA-TGACCGACACCCCTTTTTGTCAGAT
* * * * * *
11072 AAAAAAATTTTAAAAATTTTTAGTATTGATCATGCAATGGCCGGCACCCACTATTTATC
64 -AAAAAA-TTTAAAATTTTTTTGTATTGGTTATGTAATGGCCGACA-CCACTATTTATC
* *
11131 TGATAAAAAAATCAAATTTTTTGGTATTGACCATGCAATGACCGACACCCTTTTTTTGTCAGATA
1 TGATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGACCGACACCC-CTTTTTGTCAGATA
* *
11196 AAAAACTTTCAAAATTTTTTTGTATTGGTTATGTAATGGTCGACATCCACTATTTATT
65 AAAAA-TTT-AAAATTTTTTTGTATTGGTTATGTAATGGCCGACA-CCACTATTTATC
* * * *
11254 TAATAAAAAAATCAAATTTTTTGGTGTTCATCATGTAATGACCGACACC
1 TGATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGACCGACACC
11303 AACTTTCTCT
Statistics
Matches: 238, Mismatches: 41, Indels: 23
0.79 0.14 0.08
Matches are distributed among these distances:
116 6 0.03
117 8 0.03
118 26 0.11
119 23 0.10
120 44 0.18
121 29 0.12
122 13 0.05
123 89 0.37
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (119 bp):
TGATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGACCGACACCCCTTTTTGTCAGATAA
AAAATTTAAAATTTTTTTGTATTGGTTATGTAATGGCCGACACCACTATTTATC
Found at i:12125 original size:17 final size:17
Alignment explanation
Indices: 12105--12159 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
12095 AAAAAATAAT
12105 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
*
12122 AATTAGAA-AT-TA--A
1 AATTAGAATATACAGGA
*
12135 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
12152 AATTAGAA
1 AATTAGAA
12160 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:12139 original size:30 final size:30
Alignment explanation
Indices: 12105--12202 Score: 133
Period size: 30 Copynumber: 3.3 Consensus size: 30
12095 AAAAAATAAT
*
12105 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
12135 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
* * * * *
12165 ATTTAAAATAAAAATGAAATTACAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
12195 ATTTAAAA
1 AATTAAAA
12203 AGTAAACGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAATTAA
Found at i:12760 original size:36 final size:36
Alignment explanation
Indices: 12720--12804 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
12710 TCTGTCAAGA
* * *
12720 CGTCAGCGGGCTCGTCCGGGGGCTTGTACTCCGGCT
1 CGTCATCGGGCTCGTCCGCGGGCTCGTACTCCGGCT
12756 CGTCATCGGGCTCGTCCGCGGGCTCGTACTCCGGCT
1 CGTCATCGGGCTCGTCCGCGGGCTCGTACTCCGGCT
*
12792 CATCATCGGGCTC
1 CGTCATCGGGCTC
12805 ATCCTCGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.07, C:0.36, G:0.34, T:0.22
Consensus pattern (36 bp):
CGTCATCGGGCTCGTCCGCGGGCTCGTACTCCGGCT
Found at i:12807 original size:12 final size:12
Alignment explanation
Indices: 12752--12804 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
12742 CTTGTACTCC
12752 GGCTCGTCATCG
1 GGCTCGTCATCG
**
12764 GGCTCGTCCGCG
1 GGCTCGTCATCG
*
12776 GGCTCGT-ACTCC
1 GGCTCGTCA-TCG
*
12788 GGCTCATCATCG
1 GGCTCGTCATCG
12800 GGCTC
1 GGCTC
12805 ATCCTCGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.08, C:0.38, G:0.32, T:0.23
Consensus pattern (12 bp):
GGCTCGTCATCG
Found at i:13485 original size:19 final size:19
Alignment explanation
Indices: 13458--13501 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
13448 TTTTATTTTT
*
13458 AAAAAATTT-GAAAATATA
1 AAAAAATTTCGAAAATAGA
13476 AAAAACATTTCGAAAATAGA
1 AAAAA-ATTTCGAAAATAGA
13496 AAAAAA
1 AAAAAA
13502 ATATTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (19 bp):
AAAAAATTTCGAAAATAGA
Found at i:15650 original size:11 final size:12
Alignment explanation
Indices: 15607--15654 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
15597 TTTTTTTCAT
*
15607 TTATTTCTTAAAA
1 TTATTT-TTAATA
*
15620 TTAATTTTAATTA
1 TTATTTTTAA-TA
15633 TTATTTTTAATA
1 TTATTTTTAATA
15645 -TATTTTTAAT
1 TTATTTTTAAT
15655 TTGTCGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 15 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTTTAATA
Found at i:16441 original size:59 final size:59
Alignment explanation
Indices: 16371--16603 Score: 201
Period size: 59 Copynumber: 3.9 Consensus size: 59
16361 AGGAAAAGTT
* * * *
16371 GGTGTCTGTCATTGCATGGCCAACA-CAAAAAAATTGATTTTTTACCAGATAAAAAAGTG
1 GGTGTCAGCCATTGCATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAG-G
* * * **
16430 GGTGTCAGTCA-TGCAATGACCAACACC--AAAAATTCAAATTTTTATTTGAT-AAAAAGG
1 GGTGTCAGCCATTGC-ATGGCCAACACCAAAAAAATT-AATTTTTTATCAGATAAAAAAGG
* * * *
16487 GGTGTAAACCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGA-CAAAAAGG
1 GGTGTCAGCCATTGCATGGCCAACACCAAAAAAA-TT--AA-TTTTTTATCAGATAAAAAAGG
* *
16549 AAGTGTC-GACCATTGCATGGCCAACACCAAAAAATTTAATTTTTTATCAGATAAA
1 -GGTGTCAG-CCATTGCATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAA
16604 TAGCAATGGT
Statistics
Matches: 141, Mismatches: 20, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
57 20 0.14
58 19 0.13
59 45 0.32
60 7 0.05
61 2 0.01
62 19 0.13
63 29 0.21
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (59 bp):
GGTGTCAGCCATTGCATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGG
Found at i:16669 original size:44 final size:44
Alignment explanation
Indices: 16563--16692 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 44
16553 GTCGACCATT
*
16563 GCATGGCCAACACCAAAAAATTT-AATTTTTTATCAGATAAATA
1 GCATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAA
*** *
16606 GCAATGGTTGACACCAAAAAATTTGAAATTTTTTATCTGA-AAAAA
1 GC-ATGGCCAACACCAAAAAATTTG-AATTTTTTATCAGATAAAAA
* * * *
16651 GCATGACCAACACAAAAAAATTTGATTTTTTTATTAGATAAA
1 GCATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAA
16693 TAGGGGTGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 13 0.19
44 38 0.54
45 6 0.09
46 13 0.19
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (44 bp):
GCATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAA
Found at i:25367 original size:21 final size:21
Alignment explanation
Indices: 25341--25398 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
25331 AGTTAAAAAC
25341 TTTAAAAATTATAAAAATTAT
1 TTTAAAAATTATAAAAATTAT
*
25362 TTTAAAAATTAATCATTAAATTAT
1 TTTAAAAATT-AT-A-AAAATTAT
*
25386 TTT-AAGATTATAA
1 TTTAAAAATTATAA
25399 CAATATAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 6 0.19
24 10 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTAAAAATTATAAAAATTAT
Found at i:25851 original size:3 final size:3
Alignment explanation
Indices: 25843--25875 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25833 ATTTAAGCAA
25843 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25876 GGTGGGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27679 original size:30 final size:31
Alignment explanation
Indices: 27618--27681 Score: 112
Period size: 32 Copynumber: 2.1 Consensus size: 31
27608 CACTGTGTTA
27618 TAATAGGGAAGAGCTGGGACTCTAAAATCTAC
1 TAATAGGGAAGAGCTGGGACTCT-AAATCTAC
27650 TAATAGGGAAGAGCTGGGACTCT-AATCTAC
1 TAATAGGGAAGAGCTGGGACTCTAAATCTAC
27680 TA
1 TA
27682 GTCTTGGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 9 0.28
32 23 0.72
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
TAATAGGGAAGAGCTGGGACTCTAAATCTAC
Found at i:34795 original size:20 final size:19
Alignment explanation
Indices: 34770--34827 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
34760 ATAGTTAAAA
34770 TAAATAAATTAATAATAACT
1 TAAATAAATTAATAA-AACT
*
34790 TAAATATATT-ATAAATA-T
1 TAAATAAATTAATAAA-ACT
34808 T-AA-AAATTAATAAAAACT
1 TAAATAAATTAAT-AAAACT
34826 TA
1 TA
34828 TTTTGAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 8 0.26
19 5 0.16
20 9 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATAAATTAATAAAACT
Found at i:35471 original size:3 final size:3
Alignment explanation
Indices: 35463--35488 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35453 TGTATATTTT
35463 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
35489 TCCATTCCAC
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:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:37451 original size:23 final size:23
Alignment explanation
Indices: 37310--37461 Score: 114
Period size: 23 Copynumber: 6.5 Consensus size: 23
37300 CGAAGTATTT
37310 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
37336 AACAGTAAGCACACACAGTG-TA
1 AACAGTAAGCACACAAAGTGCGA
* * *
37358 ATCCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * * * *
37381 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
37403 AATCAGTAGGCACACAAAGTGTGA
1 AA-CAGTAAGCACACAAAGTGCGA
37427 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
37450 AACAGTAAGCAC
1 AACAGTAAGCAC
37462 GTTAGCGTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
22 20 0.19
23 65 0.61
24 3 0.03
26 14 0.13
27 4 0.04
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:44090 original size:3 final size:3
Alignment explanation
Indices: 44082--44112 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
44072 TCTAATATTT
44082 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
44113 AGAAGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:46545 original size:18 final size:16
Alignment explanation
Indices: 46508--46548 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
46498 TCCAAATGGG
46508 ATTAGAATAAATTTTTA
1 ATTA-AATAAATTTTTA
46525 ATTAAATAAATTTAATTA
1 ATTAAATAAATTT--TTA
46543 ATTAAA
1 ATTAAA
46549 AATTTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTAAATAAATTTTTA
Found at i:52169 original size:31 final size:31
Alignment explanation
Indices: 52134--52200 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
52124 AAAAAAAATT
*
52134 AATAACCCAATGGCTTAAAT-AAAATTTTTTA
1 AATAACCCAATGACTTAAATGAAAA-TTTTTA
***
52165 AATAATTTAATGACTTAAATGAAAATTTTTA
1 AATAACCCAATGACTTAAATGAAAATTTTTA
52196 AATAA
1 AATAA
52201 TTCATTGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (31 bp):
AATAACCCAATGACTTAAATGAAAATTTTTA
Found at i:52201 original size:31 final size:31
Alignment explanation
Indices: 52142--52202 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52132 TTAATAACCC
*
52142 AATGGCTTAAATAAAATTTTTTAAATAATTT
1 AATGACTTAAATAAAATTTTTTAAATAATTT
52173 AATGACTTAAATGAAAA-TTTTTAAATAATT
1 AATGACTTAAAT-AAAATTTTTTAAATAATT
52203 CATTGATCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (31 bp):
AATGACTTAAATAAAATTTTTTAAATAATTT
Found at i:71440 original size:83 final size:83
Alignment explanation
Indices: 71301--71466 Score: 323
Period size: 83 Copynumber: 2.0 Consensus size: 83
71291 ATTTTCACCG
*
71301 GATAATTTATTTAAATTTTTTATTAACATTATGTCACACTCATTTGGATTTATAATTTGATCCTT
1 GATAATTTATTTAAATTTTTTATTAACATTATGTCACACTCATTTAGATTTATAATTTGATCCTT
71366 CTATAATTAAAATAAGTA
66 CTATAATTAAAATAAGTA
71384 GATAATTTATTTAAATTTTTTATTAACATTATGTCACACTCATTTAGATTTATAATTTGATCCTT
1 GATAATTTATTTAAATTTTTTATTAACATTATGTCACACTCATTTAGATTTATAATTTGATCCTT
71449 CTATAATTAAAATAAGTA
66 CTATAATTAAAATAAGTA
71467 ATATTATTCG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (83 bp):
GATAATTTATTTAAATTTTTTATTAACATTATGTCACACTCATTTAGATTTATAATTTGATCCTT
CTATAATTAAAATAAGTA
Found at i:82638 original size:52 final size:52
Alignment explanation
Indices: 82576--82679 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
82566 GGCCCATGCC
82576 TAGCTATATATCTGACGCAACCAAGAGAAATATATAAGAAAACGTATTAGGG
1 TAGCTATATATCTGACGCAACCAAGAGAAATATATAAGAAAACGTATTAGGG
82628 TAGCTATATATCTGACGCAACCAAGAGAAATATATAAGAAAACGTATTAGGG
1 TAGCTATATATCTGACGCAACCAAGAGAAATATATAAGAAAACGTATTAGGG
82680 ACAAGCATGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (52 bp):
TAGCTATATATCTGACGCAACCAAGAGAAATATATAAGAAAACGTATTAGGG
Found at i:85095 original size:4 final size:4
Alignment explanation
Indices: 85086--85119 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
85076 AGACTCATCT
85086 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
85120 CATCAGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:95257 original size:57 final size:60
Alignment explanation
Indices: 95154--95316 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 60
95144 CTAATATAAT
* * * * ** *
95154 ATTTGGTATCTGAGCTTGATATTTTTTTTTTTAATTTGGCACCTAAT-TTTTTTTA-A-TCA
1 ATTTGGTACCTGAACTTGACA--TTTTTTTCTAATTTGATACCTAATCTTTTTTTAGACCCA
95213 ATTTGGTACCT-AATCTTGACATTTTTTTCTAATTTGATACCTAATCTTTTTTTAGACCCA
1 ATTTGGTACCTGAA-CTTGACATTTTTTTCTAATTTGATACCTAATCTTTTTTTAGACCCA
* * * *
95273 ATTTGGTTCTTGAACTTGGCATTTTTTCCTAATTTGATACCTAA
1 ATTTGGTACCTGAACTTGACATTTTTTTCTAATTTGATACCTAA
95317 GATTCTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
57 21 0.24
58 9 0.10
59 17 0.19
60 39 0.44
61 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTTCTAATTTGATACCTAATCTTTTTTTAGACCCA
Found at i:95615 original size:30 final size:30
Alignment explanation
Indices: 95570--95663 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 30
95560 CAACTTAAAA
*
95570 AAAAAGTGTTAAGTTTAGATACCAAATTAGG
1 AAAAAGT-ATAAGTTTAGATACCAAATTAGG
*
95601 AAAAAGTATAAGTTT-GAGTATCAAATT-GG
1 AAAAAGTATAAGTTTAGA-TACCAAATTAGG
* * *
95630 ACCAAAA--AAAAGTTTAGGTACTAAATTAGG
1 A--AAAAGTATAAGTTTAGATACCAAATTAGG
95660 AAAA
1 AAAA
95664 TATGTCAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
30 19 0.37
31 11 0.21
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (30 bp):
AAAAAGTATAAGTTTAGATACCAAATTAGG
Found at i:97676 original size:6 final size:6
Alignment explanation
Indices: 97665--97694 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
97655 GAGTTTTTGT
97665 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA
97695 ATAGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGGTGA
Found at i:109013 original size:3 final size:3
Alignment explanation
Indices: 109005--109035 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
108995 GAAAACTAAA
*
109005 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
109036 GTAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:110703 original size:27 final size:27
Alignment explanation
Indices: 110672--110725 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
110662 AAGGTACAGT
110672 TTCAATC-AAATTCATACAAATTTTCAG
1 TTCAATCAAAATT-ATACAAATTTTCAG
* *
110699 TTCAATCAAAATTATGCAACTTTTCAG
1 TTCAATCAAAATTATACAAATTTTCAG
110726 CTGATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (27 bp):
TTCAATCAAAATTATACAAATTTTCAG
Found at i:113297 original size:6 final size:6
Alignment explanation
Indices: 113281--113312 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
113271 TTTACTTGTG
*
113281 TGGCAC GGGCAC TGGCAC TGGCAC TGGCAC TG
1 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TG
113313 ATTCTCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.31, G:0.38, T:0.16
Consensus pattern (6 bp):
TGGCAC
Found at i:114708 original size:30 final size:30
Alignment explanation
Indices: 114667--114742 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
114657 ATTATCATAT
* *
114667 CCATTTCCTATGTTACACGGCCTCTAGTAC
1 CCATGTCCTATGTTACACAGCCTCTAGTAC
*
114697 CCATGTCCTATGTTACACATCCTCTAGTAC
1 CCATGTCCTATGTTACACAGCCTCTAGTAC
114727 CCATGTCCTATGTTAC
1 CCATGTCCTATGTTAC
114743 TGTTTCATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (30 bp):
CCATGTCCTATGTTACACAGCCTCTAGTAC
Found at i:123856 original size:2 final size:2
Alignment explanation
Indices: 123849--123877 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123839 GATGATCATC
123849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
123878 GTTAACAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134504 original size:2 final size:2
Alignment explanation
Indices: 134497--134521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
134487 AATTTTCTTT
134497 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
134522 GTATTAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143470 original size:17 final size:16
Alignment explanation
Indices: 143445--143484 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
143435 ATTAAACCTC
143445 AAAAA-CCCCGAAAATA
1 AAAAACCCCCG-AAATA
143461 AAAAACCCCCGAAATA
1 AAAAACCCCCGAAATA
143477 AAAAACCC
1 AAAAACCC
143485 TCAAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.60, C:0.30, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAAACCCCCGAAATA
Found at i:143682 original size:24 final size:24
Alignment explanation
Indices: 143648--143698 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
143638 AATTTGACTC
* *
143648 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
143672 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
143696 AAA
1 AAA
143699 GATTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:145671 original size:24 final size:24
Alignment explanation
Indices: 145637--145687 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
145627 AATTTGACTC
* *
145637 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
145661 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
145685 AAA
1 AAA
145688 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Done.