Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011300.1 Kokia drynarioides strain JFW-HI SEQ_126280, 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: 110788
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4759 original size:16 final size:17
Alignment explanation
Indices: 4738--4771 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4728 TAAATCAAGG
*
4738 ATAAAAAATA-AAAATA
1 ATAAAAAACATAAAATA
4754 ATAAAAAACATAAAATA
1 ATAAAAAACATAAAATA
4771 A
1 A
4772 AAATGTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAAAAAACATAAAATA
Found at i:15218 original size:12 final size:12
Alignment explanation
Indices: 15201--15265 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
15191 AAATGGAAGC
*
15201 AGAAGAAGGTAA
1 AGAAGAAGGAAA
15213 AGAAGAA-GACAGA
1 AGAAGAAGGA-A-A
15226 A-AAGAAGGAAA
1 AGAAGAAGGAAA
*
15237 AGAAGAA-GATAG
1 AGAAGAAGGA-AA
15249 AGAAGAAGGAAA
1 AGAAGAAGGAAA
15261 AGAAG
1 AGAAG
15266 TCGAGGTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.11
12 33 0.75
13 6 0.14
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.03
Consensus pattern (12 bp):
AGAAGAAGGAAA
Found at i:15231 original size:24 final size:24
Alignment explanation
Indices: 15203--15265 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
15193 ATGGAAGCAG
*
15203 AAGAAGGTAAAGAAGAAGACAGAA
1 AAGAAGGAAAAGAAGAAGACAGAA
* *
15227 AAGAAGGAAAAGAAGAAGATAGAG
1 AAGAAGGAAAAGAAGAAGACAGAA
15251 AAGAAGGAAAAGAAG
1 AAGAAGGAAAAGAAG
15266 TCGAGGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.03
Consensus pattern (24 bp):
AAGAAGGAAAAGAAGAAGACAGAA
Found at i:15714 original size:17 final size:17
Alignment explanation
Indices: 15694--15741 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
15684 TACATCCCCT
*
15694 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* * *
15711 TTGTCACTACATTTGCA
1 TTGTCATTGCATTTGAA
*
15728 TTGTTATTGCATTT
1 TTGTCATTGCATTT
15742 CCATTTCTCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:15737 original size:34 final size:34
Alignment explanation
Indices: 15672--15741 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
15662 GTAGCTGTAA
*
15672 TTTAATTGTCACTACATCCCCTTTGTCATTGCAT
1 TTTAATTGTCACTACATCCCCATTGTCATTGCAT
*** *
15706 TTTAATTGTCACTACATTTGCATTGTTATTGCAT
1 TTTAATTGTCACTACATCCCCATTGTCATTGCAT
15740 TT
1 TT
15742 CCATTTCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.49
Consensus pattern (34 bp):
TTTAATTGTCACTACATCCCCATTGTCATTGCAT
Found at i:29732 original size:50 final size:49
Alignment explanation
Indices: 29672--30216 Score: 250
Period size: 50 Copynumber: 11.0 Consensus size: 49
29662 GATCACTAAC
* * *
29672 CCACTACAACTTCAGTGGCATAAGAGTTGGTGTTGTAGCTTCATCTTGCT
1 CCACTACAACTTCAG-GGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
* * * * * * *
29722 CCACAACAACTATAAGGAG-ATGAGATTTGCTATTGTGGCTTCAAT-TTGAT
1 CCACTACAACT-TCAGG-GTATAAGATTTGATGTTGTAGCTTC-ATCTTGCT
** * * * * *
29772 CCACTGTAACTTTAGAGGTATAGGATTTGATGTTGTAGCCTCGTCTTTCT
1 CCACTACAACTTCAG-GGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
* * * * *
29822 CCACTACAAC-TCAGGGAGATAAGATTTGCTTTTGTAGCTTCAACCTGAC-
1 CCACTACAACTTCAGGG-TATAAGATTTGATGTTGTAGCTTCATCTTG-CT
29871 CCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
1 CCACTACAACTTC-AGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
* * * * * *
29921 CCACTGCATC-TCAAGGGTGATAAGATTTGCT-TCTATAGCTTGAGT-TCGAC-
1 CCACTACAACTTC-AGGGT-ATAAGATTTGATGT-TGTAGCTTCA-TCTTG-CT
* * * * *
29971 CCACTGCAACTTCAGGCATATAGGATGTGATGTTATAGCTTCATCTTGCT
1 CCACTACAACTTCAGG-GTATAAGATTTGATGTTGTAGCTTCATCTTGCT
* * * *
30021 CCATTAC-A----AGGGATATAAAATTTGCT-TCTATAGCTTCAATC-TGAC-
1 CCACTACAACTTCAGGG-TATAAGATTTGATGT-TGTAGCTTC-ATCTTG-CT
* * * * *
30066 CTATTGCTACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTT-CTT
1 CCACTACAACTTC-AGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC-T
* * * * *
30116 CCATTGCAAC-TCTAGGGAGATAAGATTTGCT-TCTGTAGCCTCAATC-TGAC-
1 CCACTACAACTTC-AGGG-TATAAGATTTGATGT-TGTAGCTTC-ATCTTG-CT
* ** *
30166 CCTCTGTAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCT
1 CCACTACAACTTC-AGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
30216 C
1 C
30217 TACAGCATCT
Statistics
Matches: 373, Mismatches: 79, Indels: 86
0.69 0.15 0.16
Matches are distributed among these distances:
44 1 0.00
45 28 0.08
46 5 0.01
48 3 0.01
49 66 0.18
50 238 0.64
51 31 0.08
52 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (49 bp):
CCACTACAACTTCAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCT
Found at i:29981 original size:100 final size:100
Alignment explanation
Indices: 29670--30441 Score: 641
Period size: 100 Copynumber: 7.8 Consensus size: 100
29660 TTGATCACTA
* * * * * **
29670 ACCCACTACAACTTC-AGTGGCATAAGAGTTGGTGTTGTAGCTTCATCTTGCTCCACAACAACT-
1 ACCCACTGCAACTTCAAG-GGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTC
* * * *
29733 ATAAGGAGATGAGATTTGCTAT-TGTGGCTTCAATTTG
65 A-AGGGAGATAAGATTTGCT-TCTGTAGCTTCAATCTG
* * * * * * *
29770 ATCCACTGTAACTT-TAGAGGTATAGGATTTGATGTTGTAGCCTCGTCTTTCTCCACTACAACTC
1 ACCCACTGCAACTTCAAG-GGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTC
* *
29834 -AGGGAGATAAGATTTGCTTTTGTAGCTTCAACCTG
65 AAGGGAGATAAGATTTGCTTCTGTAGCTTCAATCTG
* * *
29869 ACCCACTACAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTCA
1 ACCCACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCA
* * * *
29934 AGGGTGATAAGATTTGCTTCTATAGCTTGAGT-TCG
66 AGGGAGATAAGATTTGCTTCTGTAGCTTCAATCT-G
* * * *
29969 ACCCACTGCAACTTC-AGGCATATAGGATGTGATGTTATAGCTTCATCTTGCTCCA-T--TA--C
1 ACCCACTGCAACTTCAAGG-GTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTC
* * *
30028 AAGGGATATAAAATTTGCTTCTATAGCTTCAATCTG
65 AAGGGAGATAAGATTTGCTTCTGTAGCTTCAATCTG
* * * *
30064 ACCTATTGCTACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTT-CTTCCATTGCAACTC
1 ACCCACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGC-TCCACTGCAACTC
* *
30128 TAGGGAGATAAGATTTGCTTCTGTAGCCTCAATCTG
65 AAGGGAGATAAGATTTGCTTCTGTAGCTTCAATCTG
* * * * *
30164 ACCCTCTGTAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCTACAGCATCTTC
1 ACCCACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAAC-TC
* * **
30229 -AGAGAGATAAATATTTG-TTACTGTAG-TTCTAATCAC
65 AAGGGAGAT-AAGATTTGCTT-CTGTAGCTTC-AATCTG
** * * * *
30265 ACCCTA-TGCAACTTCGGGGGTATAAGATTTGGTGTGGTAGTTTCATCTTGCTCCACTGCAACTT
1 ACCC-ACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAAC-T
* * * *
30329 CAA-GGAGATAAAGATTTGTCAT-TATAGTTTTAAT-TCG
64 CAAGGGAGAT-AAGATTTG-CTTCTGTAGCTTCAATCT-G
* * * * * * * **
30366 ATCC-CTGTAACTTCAAGGATATAGGATTTGATATTGTAACTTCATCTTGCTCCACTACATCTTT
1 ACCCACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCA
30430 AGGGAGATAAGA
66 AGGGAGATAAGA
30442 CTTACTGTTT
Statistics
Matches: 540, Mismatches: 104, Indels: 57
0.77 0.15 0.08
Matches are distributed among these distances:
94 1 0.00
95 73 0.14
96 5 0.01
98 2 0.00
99 90 0.17
100 269 0.50
101 96 0.18
102 3 0.01
103 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (100 bp):
ACCCACTGCAACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCA
AGGGAGATAAGATTTGCTTCTGTAGCTTCAATCTG
Found at i:30105 original size:195 final size:193
Alignment explanation
Indices: 29678--30424 Score: 645
Period size: 195 Copynumber: 3.8 Consensus size: 193
29668 TAACCCACTA
* * * ** *
29678 CAACTTC-AGTGGCATAAGAGTTGGTGTTGTAGCTTCATCTTGCTCCACAACAACT-ATAAGGAG
1 CAACTTCAAG-GGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCA-AGGGAG
* * * * * *
29741 ATGAGATTTGCTAT-TGTGGCTTCAATTTGATCCACTGTAACTTTAGAGG-TATAGGATTTGATG
64 ATAAGATTTGCT-TCTATAGCTTC-ATTCGA-CCCCTGTAACTTCA-AGGATATAGGATTTGATG
* * * * * * * * *
29804 TTGTAGCCTCGTCTTTCTCCACTACAACTCAGGGAGATAAGATTTGCTTTTGTAGCTTCAACCTG
125 TTGTAGCTTCATCTTGCTCCATTAC-A--GAGGGATATAAAATTTGCTTCTGTAGCTTCAATCTG
* *
29869 ACCCACTA
187 ACCTA-TG
* *
29877 CAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCATCTCAAGGGTGAT
1 CAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCAAGGGAGAT
* * * *
29942 AAGATTTGCTTCTATAGCTTGAGTTCGACCCACTGCAACTTC-AGGCATATAGGATGTGATGTTA
66 AAGATTTGCTTCTATAGCTTCA-TTCGACCC-CTGTAACTTCAAGG-ATATAGGATTTGATGTTG
*
30006 TAGCTTCATCTTGCTCCATTACA-AGGGATATAAAATTTGCTTCTATAGCTTCAATCTGACCTAT
128 TAGCTTCATCTTGCTCCATTACAGAGGGATATAAAATTTGCTTCTGTAGCTTCAATCTGACCTA-
30070 TG
192 TG
* * * *
30072 CTACTTCAAGGGTATAGGATTTGATGTTGTAGCTTCATCTT-CTTCCATTGCAACTCTAGGGAGA
1 CAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGC-TCCACTGCAACTCAAGGGAGA
* * * *
30136 TAAGATTTGCTTCTGTAGCCTCAATCTGACCCTCTGTAACTTCAAGGGTATAGGATTTGATGTTG
65 TAAGATTTGCTTCTATAGCTTCATTC-GACCC-CTGTAACTTCAAGGATATAGGATTTGATGTTG
* * *
30201 TAGCTTCATCTTGCTCTACAGCATCTTCAGAGAGATA-AATATTTG-TTACTGTAG-TTCTAATC
128 TAGCTTCATCTTG--CT-C--CAT-TACAGAGGGATATAAAATTTGCTT-CTGTAGCTTC-AATC
**
30263 ACACCCTATG
185 TGA-CCTATG
** * * *
30273 CAACTTCGGGGGTATAAGATTTGGTGTGGTAGTTTCATCTTGCTCCACTGCAACTTCAA-GGAGA
1 CAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAAC-TCAAGGGAGA
* * * * *
30337 TAAAGATTTGTCAT-TATAGTTTTAATTCGATCCCTGTAACTTCAAGGATATAGGATTTGATATT
65 T-AAGATTTG-CTTCTATAG-CTTCATTCGACCCCTGTAACTTCAAGGATATAGGATTTGATGTT
* *
30401 GTAACTTCATCTTGCTCCACTACA
127 GTAGCTTCATCTTGCTCCATTACA
30425 TCTTTAGGGA
Statistics
Matches: 451, Mismatches: 72, Indels: 54
0.78 0.12 0.09
Matches are distributed among these distances:
194 3 0.01
195 156 0.35
196 5 0.01
197 5 0.01
198 7 0.02
199 114 0.25
200 11 0.02
201 114 0.25
202 30 0.07
203 6 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (193 bp):
CAACTTCAAGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTCAAGGGAGAT
AAGATTTGCTTCTATAGCTTCATTCGACCCCTGTAACTTCAAGGATATAGGATTTGATGTTGTAG
CTTCATCTTGCTCCATTACAGAGGGATATAAAATTTGCTTCTGTAGCTTCAATCTGACCTATG
Found at i:30357 original size:101 final size:101
Alignment explanation
Indices: 30081--30362 Score: 243
Period size: 101 Copynumber: 2.8 Consensus size: 101
30071 GCTACTTCAA
* * ** *
30081 GGGTATAGGATTTGATGTTGTAGCTTCATCTT-CTTCCATTGCAAC-TCTAGGGAGAT-AAGATT
1 GGGTATAAGATTTGATGTGGTAGCTTCATCTTGC-TCCACAGCAACTTC-AGAGAGATAAAGATT
* * * ** * * **
30143 TG-CTTCTGTAG-CCTCAATCTGACCCTCTGTAACTTCAA
64 TGTC-ACTATAGTTCT-AATCACACCCTATGCAACTTCGG
* * * * *
30181 GGGTATAGGATTTGATGTTGTAGCTTCATCTTGCTCTACAGCATCTTCAGAGAGATAAATATTTG
1 GGGTATAAGATTTGATGTGGTAGCTTCATCTTGCTCCACAGCAACTTCAGAGAGATAAAGATTTG
* *
30246 TTACTGTAGTTCTAATCACACCCTATGCAACTTCGG
66 TCACTATAGTTCTAATCACACCCTATGCAACTTCGG
* * *
30282 GGGTATAAGATTTGGTGTGGTAGTTTCATCTTGCTCCACTGCAACTTCA-AGGAGATAAAGATTT
1 GGGTATAAGATTTGATGTGGTAGCTTCATCTTGCTCCACAGCAACTTCAGA-GAGATAAAGATTT
* *
30346 GTCATTATAGTTTTAAT
65 GTCACTATAGTTCTAAT
30363 TCGATCCCTG
Statistics
Matches: 149, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
100 47 0.32
101 100 0.67
102 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (101 bp):
GGGTATAAGATTTGATGTGGTAGCTTCATCTTGCTCCACAGCAACTTCAGAGAGATAAAGATTTG
TCACTATAGTTCTAATCACACCCTATGCAACTTCGG
Found at i:33708 original size:20 final size:21
Alignment explanation
Indices: 33671--33709 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33661 AAACCGAGCA
*
33671 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
33692 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
33710 TAAAAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:34064 original size:5 final size:5
Alignment explanation
Indices: 34054--34092 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
34044 AATATATTTC
34054 CTTTT CTTTT CTTTT CTTTT CTTCTT CTTTT -TTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CTTTT CTTTT
34093 AATGTGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
CTTTT
Found at i:35182 original size:27 final size:27
Alignment explanation
Indices: 35139--35196 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
35129 GACAGTAGGT
*
35139 TCTTCTGTTCTTCCTTCTTTTCCTTCC
1 TCTTCTGTTCTTCCTTCCTTTCCTTCC
*
35166 TCTTCTCGTTCTT-CTTCCTTTCCTTCT
1 TCTTCT-GTTCTTCCTTCCTTTCCTTCC
35193 TCTT
1 TCTT
35197 TCTCTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.60
Consensus pattern (27 bp):
TCTTCTGTTCTTCCTTCCTTTCCTTCC
Found at i:35184 original size:18 final size:16
Alignment explanation
Indices: 35147--35202 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 16
35137 GTTCTTCTGT
35147 TCTTCCTTCTTTTCCTTCC
1 TCTTCCTTC--TT-CTTCC
35166 TCTTCTCGTTCTTCTTCC
1 TCTTC-C-TTCTTCTTCC
*
35184 T-TTCCTTCTTCTTTC
1 TCTTCCTTCTTCTTCC
35199 TCTT
1 TCTT
35203 TATCGGTCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 10 0.30
16 3 0.09
17 3 0.09
18 6 0.18
19 7 0.21
20 1 0.03
21 3 0.09
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.61
Consensus pattern (16 bp):
TCTTCCTTCTTCTTCC
Found at i:74517 original size:34 final size:34
Alignment explanation
Indices: 74474--74541 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
74464 TAACTTAGGT
74474 TTTCTAGAGACTTACAGAGGAATTCAAGAAAGAA
1 TTTCTAGAGACTTACAGAGGAATTCAAGAAAGAA
74508 TTTCTAGAGACTTACAGAGGAATTCAAGAAAGAA
1 TTTCTAGAGACTTACAGAGGAATTCAAGAAAGAA
74542 GAAGAAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (34 bp):
TTTCTAGAGACTTACAGAGGAATTCAAGAAAGAA
Found at i:76575 original size:9 final size:9
Alignment explanation
Indices: 76561--76585 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
76551 GATTACGTAA
76561 AACAATTTT
1 AACAATTTT
76570 AACAATTTT
1 AACAATTTT
76579 AACAATT
1 AACAATT
76586 ATTTTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (9 bp):
AACAATTTT
Found at i:88470 original size:20 final size:21
Alignment explanation
Indices: 88434--88472 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
88424 CATTTGTTTA
*
88434 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
88455 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
88473 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:93390 original size:15 final size:17
Alignment explanation
Indices: 93372--93404 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
93362 ATTTGTTGTG
93372 TTTTCA-AC-AAATTTT
1 TTTTCACACAAAATTTT
93387 TTTTCACACAAAATTTT
1 TTTTCACACAAAATTTT
93404 T
1 T
93405 CTGCTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTCACACAAAATTTT
Found at i:100072 original size:18 final size:18
Alignment explanation
Indices: 100051--100103 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
100041 ATCTTCCCTG
100051 GGATCTTCTTCTTCTTCA
1 GGATCTTCTTCTTCTTCA
*
100069 GGATCATT-TTCTTCCTCA
1 GGATC-TTCTTCTTCTTCA
*
100087 AGATCTTCTTCTTCTTC
1 GGATCTTCTTCTTCTTC
100104 TTTAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.13, C:0.28, G:0.09, T:0.49
Consensus pattern (18 bp):
GGATCTTCTTCTTCTTCA
Found at i:101567 original size:77 final size:78
Alignment explanation
Indices: 101478--101622 Score: 249
Period size: 77 Copynumber: 1.9 Consensus size: 78
101468 CAAAACATTA
* *
101478 AAAACAAATCTTAATTCAAACTTTTGATAATAATT-AATATAAATTATAAAATTTTATTTA-AAT
1 AAAACAAATCTTAATTCAAACTTTTGATAATAATTAAAT-TAAATTATAAAAATTAATTTATAAT
101541 TTAAAATTTGAAAG
65 TTAAAATTTGAAAG
101555 AAAACAAATCTTAATTCAAACTTTTGATAATAATTAAATTAAATTATAAAAATTAATTTATAATT
1 AAAACAAATCTTAATTCAAACTTTTGATAATAATTAAATTAAATTATAAAAATTAATTTATAATT
101620 TAA
66 TAA
101623 TATTAAGAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
77 54 0.84
78 10 0.16
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (78 bp):
AAAACAAATCTTAATTCAAACTTTTGATAATAATTAAATTAAATTATAAAAATTAATTTATAATT
TAAAATTTGAAAG
Found at i:101603 original size:19 final size:20
Alignment explanation
Indices: 101581--101628 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
101571 CAAACTTTTG
101581 ATAATAATTAAATTA-AATT
1 ATAATAATTAAATTATAATT
* *
101600 ATAAAAATTAATTTATAATT
1 ATAATAATTAAATTATAATT
101620 -TAAT-ATTAA
1 ATAATAATTAA
101629 GAATTATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATAATTAAATTATAATT
Found at i:103810 original size:13 final size:13
Alignment explanation
Indices: 103792--103818 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
103782 TCTCATTTTA
103792 TCATTTTTAGCAT
1 TCATTTTTAGCAT
103805 TCATTTTTAGCAT
1 TCATTTTTAGCAT
103818 T
1 T
103819 TTTTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (13 bp):
TCATTTTTAGCAT
Found at i:104247 original size:48 final size:48
Alignment explanation
Indices: 104193--104288 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
104183 CAAGCTTTAT
*
104193 CTTTCAGATTTTTGACGCATAAAATTTTTCTCTTCAACATTTTCTTAA
1 CTTTCAGATTTTTGACGCATAAAAATTTTCTCTTCAACATTTTCTTAA
*
104241 CTTTCAGATTTTTGACGCATAAAAATTTTCTCTTCAATATTTTCTTAA
1 CTTTCAGATTTTTGACGCATAAAAATTTTCTCTTCAACATTTTCTTAA
104289 GCTTGCTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (48 bp):
CTTTCAGATTTTTGACGCATAAAAATTTTCTCTTCAACATTTTCTTAA
Done.