Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009331.1 Kokia drynarioides strain JFW-HI SEQ_124038, 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: 160581
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1673 original size:19 final size:19
Alignment explanation
Indices: 1640--1696 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1630 ACTCAATTAA
*
1640 TAATT-TTAAAAAAAATAT
1 TAATTATTATAAAAAATAT
1658 TAATTATTATAAAAAATAT
1 TAATTATTATAAAAAATAT
* *
1677 T-AGTATGATAAAATAATAT
1 TAATTATTATAAAA-AATAT
1696 T
1 T
1697 TAAGCAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TAATTATTATAAAAAATAT
Found at i:11112 original size:31 final size:31
Alignment explanation
Indices: 11042--11116 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
11032 AATATGAAAA
*
11042 ATTAGTTTT-TTACTGTTTTCTTGCTTTTTTT
1 ATTA-TTTTGTTATTGTTTTCTTGCTTTTTTT
*
11073 ATTGTTTTGTTATTGTTTTCTTG-TTTTTTT
1 ATTATTTTGTTATTGTTTTCTTGCTTTTTTT
11103 CATTATTTTGTTAT
1 -ATTATTTTGTTAT
11117 CATTTCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.72
Consensus pattern (31 bp):
ATTATTTTGTTATTGTTTTCTTGCTTTTTTT
Found at i:11179 original size:12 final size:11
Alignment explanation
Indices: 11160--11190 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
11150 TGTATAATTC
11160 TTATTTTATTA
1 TTATTTTATTA
11171 TTAATTTTATTA
1 TT-ATTTTATTA
11183 TTATTTTA
1 TTATTTTA
11191 AAAGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:11750 original size:29 final size:30
Alignment explanation
Indices: 11688--11756 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
11678 TAATTAGTTT
* *
11688 AAATATTTAATTTTGTTATTATAATTTATA
1 AAATAATTAATTTTGTTATTATAATTAATA
11718 AAATAATT-ATTTTGTT-TT-TAATTAAATA
1 AAATAATTAATTTTGTTATTATAATT-AATA
*
11746 GAAATATTTAA
1 -AAATAATTAA
11757 AATTAAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
28 5 0.15
29 15 0.45
30 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
AAATAATTAATTTTGTTATTATAATTAATA
Found at i:13779 original size:68 final size:68
Alignment explanation
Indices: 13699--13838 Score: 271
Period size: 68 Copynumber: 2.1 Consensus size: 68
13689 GTTGTGTATT
13699 TAATCTCTATACTTAGTTTGATGAAATTTTGTCTTATGTATTTTTCGAATTGGTTAATTTTAATC
1 TAATCTCTATACTTAGTTTGATGAAATTTTGTCTTATGTATTTTTCGAATTGGTTAATTTTAATC
13764 CTA
66 CTA
*
13767 TAATCTCTATACTTAGTTTGATGAAATTTTGTCTTATGTATTTTTCTAATTGGTTAATTTTAATC
1 TAATCTCTATACTTAGTTTGATGAAATTTTGTCTTATGTATTTTTCGAATTGGTTAATTTTAATC
13832 CTA
66 CTA
13835 TAAT
1 TAAT
13839 TTTAAAATTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (68 bp):
TAATCTCTATACTTAGTTTGATGAAATTTTGTCTTATGTATTTTTCGAATTGGTTAATTTTAATC
CTA
Found at i:19578 original size:72 final size:71
Alignment explanation
Indices: 19462--19595 Score: 232
Period size: 72 Copynumber: 1.9 Consensus size: 71
19452 GCTGTGTATA
**
19462 GATTGCTGGGTTTGTTTAGATGATAGGATATTGGTTGTTCTGATATTGGGTCACAATCTTTGCTG
1 GATTGCTGGGTTTGTTTAGATGATAGGATATTGACTGTTCTGATATTGGGTCACAATCTTTGCTG
19527 TGCGTT
66 TGCGTT
*
19533 GATTGCTGGGTTTGTTTTAGATGATAGGATATTGACTGTTTTGATATTGGGTCACAATCTTTG
1 GATTGCTGGGTTTG-TTTAGATGATAGGATATTGACTGTTCTGATATTGGGTCACAATCTTTG
19596 GTTTCTGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
71 14 0.24
72 45 0.76
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.44
Consensus pattern (71 bp):
GATTGCTGGGTTTGTTTAGATGATAGGATATTGACTGTTCTGATATTGGGTCACAATCTTTGCTG
TGCGTT
Found at i:32560 original size:38 final size:39
Alignment explanation
Indices: 32513--32588 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 39
32503 TAAAATGTAA
***
32513 GGGTGTGTTTAATTTCTTAAAATTTTAAGTATT-AAAAT
1 GGGTGTGTTTAATAAATTAAAATTTTAAGTATTGAAAAT
* *
32551 GGGTTTGTTTAATAAATTGAAATTTTAAGTATTGAAAA
1 GGGTGTGTTTAATAAATTAAAATTTTAAGTATTGAAAA
32589 ATTAAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (39 bp):
GGGTGTGTTTAATAAATTAAAATTTTAAGTATTGAAAAT
Found at i:32586 original size:15 final size:15
Alignment explanation
Indices: 32566--32617 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
32556 TGTTTAATAA
*
32566 ATTGAAATTTTAAGT
1 ATTGAAATTTTAAAT
**
32581 ATTGAAAAATTAAAT
1 ATTGAAATTTTAAAT
32596 ATT-AAATTTTATAAT
1 ATTGAAATTTTA-AAT
32611 CATTGAA
1 -ATTGAA
32618 TTTATGTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.21
15 18 0.62
16 3 0.10
17 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (15 bp):
ATTGAAATTTTAAAT
Found at i:40505 original size:29 final size:30
Alignment explanation
Indices: 40439--40505 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
40429 TTCAAAATTT
*
40439 TATATGAATTTTATTTAACGTGTAATTATA
1 TATATGAATTTTATTTAACGTATAATTATA
*
40469 TATATGAATTTTATTTTA-GTATAATTATA
1 TATATGAATTTTATTTAACGTATAATTATA
*
40498 TATGTGAA
1 TATATGAA
40506 ATTCTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (30 bp):
TATATGAATTTTATTTAACGTATAATTATA
Found at i:40525 original size:18 final size:19
Alignment explanation
Indices: 40488--40540 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
40478 TTTATTTTAG
*
40488 TATAATTATATATGTGAAAT-
1 TATAATTATA-AT-TTAAATA
*
40508 TCTAATTATAATTTAAATA
1 TATAATTATAATTTAAATA
40527 TATAATT-TAATTTA
1 TATAATTATAATTTA
40541 TTTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
19 8 0.28
20 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TATAATTATAATTTAAATA
Found at i:42051 original size:56 final size:56
Alignment explanation
Indices: 41985--42096 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
41975 TTTGCTTTTA
41985 AAGCCTAAAAACTCTAGTAATAGAGTACTATTAATGAA-AACAAAAAAAGAGCTGTT
1 AAGCCTAAAAACTCTAGTAATAGAGTACTATTAATGAACAA-AAAAAAAGAGCTGTT
42041 AAGCCTAAAAACTCTAGTAATAGAGTACTATTAATGAACAAAAAAAAAGAGCTGTT
1 AAGCCTAAAAACTCTAGTAATAGAGTACTATTAATGAACAAAAAAAAAGAGCTGTT
42097 CTATTTATGG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 53 0.96
57 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (56 bp):
AAGCCTAAAAACTCTAGTAATAGAGTACTATTAATGAACAAAAAAAAAGAGCTGTT
Found at i:76142 original size:175 final size:175
Alignment explanation
Indices: 75851--76200 Score: 648
Period size: 175 Copynumber: 2.0 Consensus size: 175
75841 CGTTTTTGAA
*
75851 TCAGAGTTGGAACAGTAATAGTGTCGAGTTAAAAGTTAGAATATGTGGTTAAAATAAGAAGATTA
1 TCAGAGTTGGAACAGTAATAGTGTCGAGATAAAAGTTAGAATATGTGGTTAAAATAAGAAGATTA
75916 GGAAAAAATTAAGGATTAATTAGAAATGGTGAGAAAATAAGAAGGACTAAATAGCAATTTATCCA
66 GGAAAAAATTAAGGATTAATTAGAAATGGTGAGAAAATAAGAAGGACTAAATAGCAATTTATCCA
75981 AATTGAATTATTAGTCAT-ATTGGGAATTAGATTGATTAAGGAGGG
131 AATTGAATTATTAGTCATCA-TGGGAATTAGATTGATTAAGGAGGG
76026 TCAGAGTTGGAACAGTAATAGTGTCGAGATAAAAGTTAGAATATGTGGTTAAAATAAGAAGATTA
1 TCAGAGTTGGAACAGTAATAGTGTCGAGATAAAAGTTAGAATATGTGGTTAAAATAAGAAGATTA
* * *
76091 GGAAAAAATTAAGGATTAATTAGAAATTGTGAGAAAATAGGAAGGACTAAATAGCAATTTATTCA
66 GGAAAAAATTAAGGATTAATTAGAAATGGTGAGAAAATAAGAAGGACTAAATAGCAATTTATCCA
76156 AATTGAATTATTAGTCATCATGGGAATTAGATTGATTAAGGAGGG
131 AATTGAATTATTAGTCATCATGGGAATTAGATTGATTAAGGAGGG
76201 ACAAAAGAGT
Statistics
Matches: 170, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
175 169 0.99
176 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (175 bp):
TCAGAGTTGGAACAGTAATAGTGTCGAGATAAAAGTTAGAATATGTGGTTAAAATAAGAAGATTA
GGAAAAAATTAAGGATTAATTAGAAATGGTGAGAAAATAAGAAGGACTAAATAGCAATTTATCCA
AATTGAATTATTAGTCATCATGGGAATTAGATTGATTAAGGAGGG
Found at i:77774 original size:6 final size:6
Alignment explanation
Indices: 77763--77801 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
77753 TGATCAAAAT
* * *
77763 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
77802 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:81869 original size:25 final size:24
Alignment explanation
Indices: 81817--81873 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
81807 CGATTAGAAT
*
81817 ATTACTTTTTAATTTTATTAATTCAA
1 ATTA-TTTTTAATTTTATTAAAT-AA
*
81843 TTTATTTTTAATTTTATTAAATAA
1 ATTATTTTTAATTTTATTAAATAA
81867 ATTATTT
1 ATTATTT
81874 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.29
25 17 0.61
26 3 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTTTTAATTTTATTAAATAA
Found at i:85586 original size:20 final size:21
Alignment explanation
Indices: 85560--85612 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
85550 AAAAATTTGT
85560 TTTTGAATAATTTT-AC-AAA
1 TTTTGAATAATTTTAACAAAA
85579 TCTTTGAA-AATATTTAACAAAA
1 T-TTTGAATAAT-TTTAACAAAA
*
85601 TTTTCAATAATT
1 TTTTGAATAATT
85613 ATTTTCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 4 0.14
20 9 0.32
21 8 0.29
22 7 0.25
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (21 bp):
TTTTGAATAATTTTAACAAAA
Found at i:99418 original size:17 final size:18
Alignment explanation
Indices: 99393--99432 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
99383 TAATCTAACA
*
99393 AAAAT-TTAAA-ATTCAT
1 AAAATCTTAAAGAATCAT
99409 AAAATCTTAAAGAATCAT
1 AAAATCTTAAAGAATCAT
99427 AAAATC
1 AAAATC
99433 GATTCAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 5 0.24
18 11 0.52
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAATCTTAAAGAATCAT
Found at i:100007 original size:17 final size:17
Alignment explanation
Indices: 99987--100038 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
99977 ATTATTTTTT
99987 AAAAATAAAAATTATTA
1 AAAAATAAAAATTATTA
*
100004 AAAAATGAAAA-TATTTA
1 AAAAATAAAAATTA-TTA
*
100021 AAAAA-ATAAATTA-TA
1 AAAAATAAAAATTATTA
100036 AAA
1 AAA
100039 TTCTATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 20 0.67
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAATAAAAATTATTA
Found at i:102529 original size:96 final size:96
Alignment explanation
Indices: 102342--102533 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
102332 TTTTTGCGAA
* *
102342 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
102407 AAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATCGCCTCGATT
* * * *
102438 AAGGGTATTCGATTATTTCGATTTGGAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* *
102502 GAAACTCGAA-ATAAA-AGAATATCGCCTCGATT
65 -AAAATCGAAGATAAAGA-AACATCGCCTCGATT
102534 TTAAAAGCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 2 0.02
96 73 0.88
97 8 0.10
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATCGCCTCGATT
Found at i:102807 original size:30 final size:30
Alignment explanation
Indices: 102764--103208 Score: 146
Period size: 30 Copynumber: 15.0 Consensus size: 30
102754 TTTCGGATAC
102764 TCGGGGGT-AAAATGATAATTTTTGGAAGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
* * * * *
102793 TCAGGGGGT-GAAATGGTAGTTTTGGGAAAAT
1 TC-GGGGGTAAAAATGATAATTTTTGG-AAGT
* * *
102824 TCGAGGTTAAAAATGA-AATTTTTGGATGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
*
102853 TCGGGGGTAAAAATG-GAATTTTTGGAAGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
**** ** *
102882 TTTACGGTCAAAAATG-GGATTTTTGGGAGT
1 TCGGGGGT-AAAAATGATAATTTTTGGAAGT
* * * *
102912 TCGAGGGTAAAAATG-GAATTTTTGAAATT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
*** ** *
102941 TTTAGGGTCAAAAAT-AGGATTTTTTGAAGT
1 TCGGGGGT-AAAAATGATAATTTTTGGAAGT
*** *
102971 TCAATGGTAAAAATG-GAATTTTTGGAAGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
*** ** *
103000 TTTAGGGTCAAAAATG-GGATTTTGGGAAGT
1 TCGGGGGT-AAAAATGATAATTTTTGGAAGT
** * * **
103030 TTAGGGGTAAAAATG-GAATCTTTAAAAGTT
1 TCGGGGGTAAAAATGATAATTTTTGGAAG-T
* * * * * *
103060 TTGGGGTTAAATATG-GAATTTTTAGAATT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
* ** *
103089 TCGAGGGTAAAAATG-GGATTTTGGGAAGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
* *
103118 TCAGGGGTAAAAAATG-GAATTTTTGGAAGTT
1 TCGGGGGT-AAAAATGATAATTTTTGGAAG-T
* * * *
103149 TCGAGGTTAAAAATG-GAATTTTTAGAAGT
1 TCGGGGGTAAAAATGATAATTTTTGGAAGT
** * *
103178 TCGAAGGTAAAAACGA-AATTTCTGGACAGT
1 TCGGGGGTAAAAATGATAATTTTTGGA-AGT
103208 T
1 T
103209 TAGGGACCTT
Statistics
Matches: 323, Mismatches: 79, Indels: 27
0.75 0.18 0.06
Matches are distributed among these distances:
29 143 0.44
30 164 0.51
31 16 0.05
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
TCGGGGGTAAAAATGATAATTTTTGGAAGT
Found at i:102905 original size:59 final size:59
Alignment explanation
Indices: 102832--103178 Score: 385
Period size: 59 Copynumber: 5.9 Consensus size: 59
102822 ATTCGAGGTT
* * * *
102832 AAAAATGAAATTTTTGGATGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTACGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
* * * *
102891 AAAAATGGGATTTTTGGGAGTTCGAGGGTAAAAATGGAATTTTTGAAATTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
* * *
102950 AAAAATAGG-ATTTTTTGAAGTTCAATGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
1 AAAAAT-GGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
* * * * ** * *
103009 AAAAATGGGATTTTGGGAAGTT-TAGGGGTAAAAATGGAATCTTTAAAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
* * * * * * *
103068 AAATATGGAATTTTTAGAATTTCGAGGGTAAAAATGGGATTTTGGGAAG-TTCAGGGGTA
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTA-GGGTC
* *
103127 AAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAGAAGTT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTT
103179 CGAAGGTAAA
Statistics
Matches: 237, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
58 5 0.02
59 203 0.86
60 28 0.12
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC
Found at i:104234 original size:3 final size:3
Alignment explanation
Indices: 104226--104254 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
104216 GTTGTCGCTC
104226 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
104255 ACTTATGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:104883 original size:17 final size:17
Alignment explanation
Indices: 104863--104909 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
104853 AAATGAGTTT
*
104863 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
104880 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
104897 TAAATTTAAATTT
1 TAAATTTAAATTT
104910 GTTGGGCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:113009 original size:12 final size:12
Alignment explanation
Indices: 112985--113107 Score: 131
Period size: 12 Copynumber: 10.2 Consensus size: 12
112975 AGGACCTGCT
112985 AAAGAAGAGAAG
1 AAAGAAGAGAAG
* *
112997 AAGGAAGAAAAG
1 AAAGAAGAGAAG
* *
113009 AAGGAAGAAAAG
1 AAAGAAGAGAAG
* *
113021 AAAGAGGAAAAG
1 AAAGAAGAGAAG
*
113033 AAAGAGGAGAAG
1 AAAGAAGAGAAG
113045 AAAGAAGAGAAG
1 AAAGAAGAGAAG
113057 AACA-AAGAGAAG
1 AA-AGAAGAGAAG
* *
113069 AAAGAGGAAAAG
1 AAAGAAGAGAAG
*
113081 AAGGAAGAGAAG
1 AAAGAAGAGAAG
*
113093 AAGGAAGAGAAG
1 AAAGAAGAGAAG
113105 AAA
1 AAA
113108 TAAATTTTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
11 1 0.01
12 95 0.98
13 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (12 bp):
AAAGAAGAGAAG
Found at i:113043 original size:48 final size:48
Alignment explanation
Indices: 112985--113106 Score: 181
Period size: 48 Copynumber: 2.5 Consensus size: 48
112975 AGGACCTGCT
* **
112985 AAAGAAGAGAAGAAGGAAGAAAAGAAGGAAGAAAAGAAAGAGGAAAAG
1 AAAGAAGAGAAGAAGGAAGAGAAGAACAAAGAAAAGAAAGAGGAAAAG
* * *
113033 AAAGAGGAGAAGAAAGAAGAGAAGAACAAAGAGAAGAAAGAGGAAAAG
1 AAAGAAGAGAAGAAGGAAGAGAAGAACAAAGAAAAGAAAGAGGAAAAG
*
113081 AAGGAAGAGAAGAAGGAAGAGAAGAA
1 AAAGAAGAGAAGAAGGAAGAGAAGAA
113107 ATAAATTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (48 bp):
AAAGAAGAGAAGAAGGAAGAGAAGAACAAAGAAAAGAAAGAGGAAAAG
Found at i:114698 original size:19 final size:18
Alignment explanation
Indices: 114671--114707 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
114661 AAACCTTTAC
114671 ATAAAATTTTAAAAAAATT
1 ATAAAA-TTTAAAAAAATT
*
114690 ATAACATTTAAAAAAATT
1 ATAAAATTTAAAAAAATT
114708 CAGGTGAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAATTTAAAAAAATT
Found at i:127601 original size:156 final size:154
Alignment explanation
Indices: 127317--127782 Score: 639
Period size: 156 Copynumber: 3.0 Consensus size: 154
127307 TCAAGACTAT
* *
127317 GTCACAATTCAATGATCTTGCTTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAGAAAATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAG-AAATGCTG
* *
127382 GACCTG-AGGCCATGTCTTCCAATCCAAAGGCTGAATTACCCAATGTTTCATCTGGTCGTTCAGT
65 GACCTGCA-GCCATGTCTTTCAA-CCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGT
127446 TGAAGCATGTG-AGTCCACTGGTCTACA
128 TGAAGCATGTGCA-TCCACTGGTCTACA
* * *
127473 GTCACAAGTCAATGGTCCTGATTTTTTCTTAAATCCCCAGAAAAGTAGTGCTAGAGAAGATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAGAA-ATGCTG
* * * * * *
127538 CACCTGCAGCCAGGTCTTTTAACCAAAAGGCTGAATCACCCAATGGTGCATCTGGTCATTCAGTT
65 GACCTGCAGCCATGTCTTTCAACC-AAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
* * * *
127603 GAAGCATGTGTATACACTGGTCCACC
129 GAAGCATGTGCATCCACTGGTCTACA
* *
127629 GTCACAAGTCAATGATCTTGATTTTTTCTTGAGTCCCCAGAAAAGTAGTACTAGAGATAATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAGA-AATGCTG
* * *
127694 GACCTGCCGCCATGTCATTCAACCCAAGGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
65 GACCTGCAGCCATGTCTTTCAA-CCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
*
127759 GAAGCATGTGCATCCACGGGTCTA
129 GAAGCATGTGCATCCACTGGTCTA
127783 TTATTGCGGC
Statistics
Matches: 270, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
155 4 0.01
156 261 0.97
157 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (154 bp):
GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAGAAATGCTGG
ACCTGCAGCCATGTCTTTCAACCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTTGA
AGCATGTGCATCCACTGGTCTACA
Found at i:147424 original size:4 final size:4
Alignment explanation
Indices: 147415--147452 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
147405 TCGTTAGTTC
*
147415 CATA CATA CATA CGTA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
147453 ATTTTGTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:154731 original size:11 final size:11
Alignment explanation
Indices: 154715--154748 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
154705 TTTTTTGTAC
154715 ACGAGAAAAAT
1 ACGAGAAAAAT
154726 ACGAGAAAAAAAT
1 ACGAG--AAAAAT
154739 ACGAGAAAAA
1 ACGAGAAAAA
154749 AATACCTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.68, C:0.09, G:0.18, T:0.06
Consensus pattern (11 bp):
ACGAGAAAAAT
Found at i:154738 original size:13 final size:13
Alignment explanation
Indices: 154720--154753 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
154710 TGTACACGAG
154720 AAAAATACGAGAA
1 AAAAATACGAGAA
154733 AAAAATACGAGAA
1 AAAAATACGAGAA
154746 AAAAATAC
1 AAAAATAC
154754 CTGACACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.71, C:0.09, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAATACGAGAA
Found at i:155939 original size:30 final size:30
Alignment explanation
Indices: 155905--155999 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 30
155895 AAATGGTACA
155905 AAATAAATATTTATTTTATACCATTTTGGT
1 AAATAAATATTTATTTTATACCATTTTGGT
** *** ** *
155935 AAAT-AATGGTGCGTGAATACTATTTTGGT
1 AAATAAATATTTATTTTATACCATTTTGGT
* * * *
155964 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTATACCATTTTGGT
155994 AAATAA
1 AAATAA
156000 CACATTTTGG
Statistics
Matches: 43, Mismatches: 21, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (30 bp):
AAATAAATATTTATTTTATACCATTTTGGT
Found at i:157239 original size:43 final size:42
Alignment explanation
Indices: 157157--157249 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 42
157147 ATTAACATGT
* *
157157 TAAATTATATTACTTGACTCGTGCTAATATATTTGCATGTTA
1 TAAATTATATTACTTGACTCGTACTAATATACTTGCATGTTA
* ** *
157199 CTAAATTATATTACTTTACTTTTATTAATAT-CTTGACATGTTA
1 -TAAATTATATTACTTGACTCGTACTAATATACTTG-CATGTTA
*
157242 TTAATTAT
1 TAAATTAT
157250 GCAGTTCATC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 10 0.24
43 32 0.76
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCGTACTAATATACTTGCATGTTA
Found at i:157873 original size:45 final size:45
Alignment explanation
Indices: 157809--157945 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
157799 GCGTAGCTCA
* * *
157809 TCAAGCCAAGGATATCAGCCTCAGTTTAACGAGCTACTGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
157854 TCAAGCCAATGATATCAGCCTCAATTTGACGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * *
157899 TCAAGGGAAGGATATGAGGCTGAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
157944 TC
1 TC
157946 TATTCCTCCC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:158232 original size:14 final size:14
Alignment explanation
Indices: 158210--158263 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
158200 CATTAACCCT
*
158210 TAAAACCTAAATTA
1 TAAACCCTAAATTA
*
158224 TAAACCCTAAATTG
1 TAAACCCTAAATTA
*
158238 TAAACACTAGAATTA
1 TAAACCCTA-AATTA
*
158253 -AAACTCTAAAT
1 TAAACCCTAAAT
158264 CGTAAACACT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 3 0.09
14 27 0.79
15 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.28
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:158256 original size:28 final size:29
Alignment explanation
Indices: 158212--158276 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
158202 TTAACCCTTA
*
158212 AAAC-CTA-AATTATAAACCCTAAATTGT
1 AAACACTAGAATTATAAACCCTAAATCGT
*
158239 AAACACTAGAATTA-AAACTCTAAATCGT
1 AAACACTAGAATTATAAACCCTAAATCGT
158267 AAACACTAGA
1 AAACACTAGA
158277 TTGATTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 4 0.12
28 25 0.74
29 5 0.15
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.25
Consensus pattern (29 bp):
AAACACTAGAATTATAAACCCTAAATCGT
Done.