Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012039.1 Kokia drynarioides strain JFW-HI SEQ_127037, 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: 51139
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:129 original size:4 final size:4
Alignment explanation
Indices: 105--150 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
95 AACACATTAC
*
105 CTTT CTTT CCTT C-TT CTTTT CTTT CTTT CTTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT C-TTT CTTT CTTT CTTT C
151 CCGTTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 7 0.18
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:136 original size:13 final size:13
Alignment explanation
Indices: 105--149 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
95 AACACATTAC
*
105 CTTTC-TTTCCTT
1 CTTTCTTTTCTTT
117 C-TTCTTTTCTTT
1 CTTTCTTTTCTTT
129 CTTTCTTTTCTTT
1 CTTTCTTTTCTTT
142 CTTTCTTT
1 CTTTCTTT
150 CCCGTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 3 0.10
12 8 0.27
13 19 0.63
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTCTTTTCTTT
Found at i:5262 original size:21 final size:21
Alignment explanation
Indices: 5238--5284 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5228 ATAACATGTC
*
5238 TTATAAATAA-TATAATTTTTT
1 TTATAAATAAGTAT-ATTGTTT
*
5259 TTATGAATAAGTATATTGTTT
1 TTATAAATAAGTATATTGTTT
5280 TTATA
1 TTATA
5285 GTATATAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
TTATAAATAAGTATATTGTTT
Found at i:7944 original size:24 final size:24
Alignment explanation
Indices: 7912--7959 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
7902 AAATATCAAA
*
7912 TTAAAAATAGTATAAATATATATT
1 TTAAAAATAATATAAATATATATT
*
7936 TTAAGAATAATATAAATATATATT
1 TTAAAAATAATATAAATATATATT
7960 ACATGCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAAAAATAATATAAATATATATT
Found at i:9687 original size:20 final size:20
Alignment explanation
Indices: 9662--9708 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9652 TTTTAATATT
*
9662 TTAATTAAA-ATAAAAACAAG
1 TTAATTAAATATAAAAA-AAC
*
9682 TTAATTAAATTTAAAAAAAC
1 TTAATTAAATATAAAAAAAC
9702 TTAATTA
1 TTAATTA
9709 GGTTTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAATTAAATATAAAAAAAC
Found at i:17616 original size:2 final size:2
Alignment explanation
Indices: 17609--17636 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17599 TACAAGTTAT
17609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17637 GCTAAATTAA
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):
TA
Found at i:21595 original size:219 final size:217
Alignment explanation
Indices: 21155--22103 Score: 831
Period size: 219 Copynumber: 4.4 Consensus size: 217
21145 ATGGTGGCAA
* * *
21155 AGTAAGGACCGACACATAAAGCATCA-ATGTCTGACTCTGAACCATGAACCTGATCAATAAAATG
1 AGTAAGGAACAACACATAAAGCAT-AGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATG
* * * * **
21219 TTACAATTCAGTTGGTAAG-TATGC-TTA-TCTATTCTTGCTT-TTTTCCTGGAAATACAATCTG
65 TTAAAATTCAGTTGGCAAGCTATGCTTTATTCTATT-TT-TTTCTTTTCCTGGTAATACAATCCA
* * *
21280 GGTATCATTTTGCCTAAACTTAAAACTTAAT-TCCCTCCCAGGTAATCTTAAGGATTCACTCTCT
128 GGTATCATTTTGCCTAAACTT--AA-TTACTCTCCC-CCCAGGTAATCTTAAGCATGCACTCTCT
* *
21344 CGTATCAACACATAACAGCTGTCAAGTTC
189 CGTATCAACACATAATAGCTGTCAAATTC
*
21373 AGTAAGGAACAACGCATAAAGCATAGATGTCAGACTCTGAACCATGAACCTG-TCAATAAAATGT
1 AGTAAGGAACAACACATAAAGCATAGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATGT
*
21437 TAAAATTCAG-TCGCAAGCTATGTTCATTTATTCTATTTTTTTCTTTTCCTGGTAATACAATCCA
66 TAAAATTCAGTTGGCAAGCTATG--C-TTTATTCTATTTTTTTCTTTTCCTGGTAATACAATCCA
21501 GGTATCATTTTGCCTAAACTTAATT-CTCTCCCCCACCAGGTAATCTTAAGCATGCACTCTCTCG
128 GGTATCATTTTGCCTAAACTTAATTACTCT-CCCC-CCAGGTAATCTTAAGCATGCACTCTCTCG
* * *
21565 CATCAACACATAATAGCTATTAAATTC
191 TATCAACACATAATAGCTGTCAAATTC
* * *
21592 AGTAAGGACCAAC-CAATAAAGCATCGATGT-AGTACTCTGAACCATGAACCTGATCAATAAATT
1 AGTAAGGAACAACAC-ATAAAGCATAGATGTCAG-ACTCTGAACCATGAACCTGATCAATAAAAT
* * * *
21655 G-TAAAATTCAGTTGGCAAGCTATG-TTTATT-TATTCTTCTCTTTTCCCTGTTAATACAACTCG
64 GTTAAAATTCAGTTGGCAAGCTATGCTTTATTCTATTTTTTTCTTTT-CCTGGTAATACAA-TCC
* * *
21717 A-GTACCATTTTGCCTAAACCTT-ATTGC-CT---CCCAGGTAATCTCAA-CAATGCACTCTCTC
127 AGGTATCATTTTGCCTAAA-CTTAATTACTCTCCCCCCAGGTAATCTTAAGC-ATGCACTCTCTC
21775 GTATCAACACATAACT-GCTGTCAAATTC
190 GTATCAACACATAA-TAGCTGTCAAATTC
** * *
21803 AGTAAGGACCAAGATCAACACATAAAGCACCGATGTC-TACTCTGAACCATGAACTTGATCAATA
1 AGTAAGG----A-A-CAACACATAAAGCATAGATGTCAGACTCTGAACCATGAACCTGATCAATA
* * * * * *
21867 AATTGTT-AAATTCAGTTGGCAA-CTA-GGTTTGTT-TATTCTTTTGCTTTCCCTGGTAATGCAA
60 AAATGTTAAAATTCAGTTGGCAAGCTATGCTTTATTCTATT-TTTTTCTTTTCCTGGTAATACAA
* * * * * * * *
21928 TTC-GAGTACCGTTTTGCC-AGAACCT-ATT--TC-CCTCCCACGTAATC-TAGAGCAAGAACTC
124 TCCAG-GTATCATTTTGCCTA-AACTTAATTACTCTCCCCCCAGGTAATCTTA-AGCATGCACTC
** * *
21986 TCTCGTATCAACACATAGCAGATGTCAAAATC
186 TCTCGTATCAACACATAATAGCTGTCAAATTC
** * * *
22018 AGTAA-GAACCAACACATAAAGCATCA-ATGTTGGACTCTAAACCAAGAACCTGATC-ATCAAAT
1 AGTAAGGAA-CAACACATAAAGCAT-AGATGTCAGACTCTGAACCATGAACCTGATCAATAAAAT
*
22080 -TGATAAATTCAGTTGGCAAGCTAT
64 GTTA-AAATTCAGTTGGCAAGCTAT
22104 ATTTATTTAC
Statistics
Matches: 617, Mismatches: 66, Indels: 102
0.79 0.08 0.13
Matches are distributed among these distances:
208 1 0.00
209 24 0.04
210 36 0.06
211 58 0.09
212 2 0.00
213 1 0.00
214 10 0.02
215 99 0.16
216 96 0.16
217 53 0.09
218 54 0.09
219 110 0.18
220 23 0.04
221 44 0.07
222 6 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (217 bp):
AGTAAGGAACAACACATAAAGCATAGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATGT
TAAAATTCAGTTGGCAAGCTATGCTTTATTCTATTTTTTTCTTTTCCTGGTAATACAATCCAGGT
ATCATTTTGCCTAAACTTAATTACTCTCCCCCCAGGTAATCTTAAGCATGCACTCTCTCGTATCA
ACACATAATAGCTGTCAAATTC
Found at i:21872 original size:216 final size:211
Alignment explanation
Indices: 21155--22112 Score: 923
Period size: 215 Copynumber: 4.4 Consensus size: 211
21145 ATGGTGGCAA
* * * *
21155 AGTAAGGACCGACACATAAAGCATCAATGTCTGACTCTGAACCATGAACCTGATCAATAAAATGT
1 AGTAAGGAACAACACATAAAGCATCGATGTCT-ACTCTGAACCATGAACCTGATCAATAAATTG-
* * * * * * *
21220 TACAATTCAGTTGGTAAG-TATGCTTATCTATTCTTGCT-TTTTTCCTGGAAATACAATCTGGGT
64 TAAAATTCAGTTGGCAAGCTATGTTTATTTATTCTT-CTCTTTTCCCTGGTAATACAATC-GAGT
* * *
21283 ATCATTTTGCCTAAACTTAAAACTTAATTCCCTCCCAGGTAATCTTAAG-GATTCACTCTCTCGT
127 ACCATTTTGCCTAAAC------CTTAATTCCCTCCCAGGTAATCTTAAGCAATGCACTCTCTCGT
*
21347 ATCAACACATAACAGCTGTCAAGTTC
186 ATCAACACATAACAGCTGTCAAATTC
* * * *
21373 AGTAAGGAACAACGCATAAAGCATAGATGTCAGACTCTGAACCATGAACCTG-TCAATAAAATGT
1 AGTAAGGAACAACACATAAAGCATCGATGTC-TACTCTGAACCATGAACCTGATCAATAAATTG-
* * * *
21437 TAAAATTCAG-TCGCAAGCTATGTTCATTTATTCTAT-TTTTTTCTTTTCCTGGTAATACAATCC
64 TAAAATTCAGTTGGCAAGCTATGTTTATTTATTCT-TCTCTTTTC----CCTGGTAATACAATCG
* *
21500 AGGTATCATTTTGCCTAAA-CTTAATTCTCTCCCCCACCAGGTAATCTTAAGC-ATGCACTCTCT
124 A-GTACCATTTTGCCTAAACCTTAA---T-TCCCTC-CCAGGTAATCTTAAGCAATGCACTCTCT
* * * *
21563 CGCATCAACACATAATAGCTATTAAATTC
183 CGTATCAACACATAACAGCTGTCAAATTC
* *
21592 AGTAAGGACCAAC-CAATAAAGCATCGATGTAGTACTCTGAACCATGAACCTGATCAATAAATTG
1 AGTAAGGAACAACAC-ATAAAGCATCGATGT-CTACTCTGAACCATGAACCTGATCAATAAATTG
*
21656 TAAAATTCAGTTGGCAAGCTATGTTTATTTATTCTTCTCTTTTCCCTGTTAATACAACTCGAGTA
64 TAAAATTCAGTTGGCAAGCTATGTTTATTTATTCTTCTCTTTTCCCTGGTAATACAA-TCGAGTA
* *
21721 CCATTTTGCCTAAACCTT-ATTGCCTCCCAGGTAATCTCAA-CAATGCACTCTCTCGTATCAACA
128 CCATTTTGCCTAAACCTTAATTCCCTCCCAGGTAATCTTAAGCAATGCACTCTCTCGTATCAACA
*
21784 CATAACTGCTGTCAAATTC
193 CATAACAGCTGTCAAATTC
* *
21803 AGTAAGGACCAAGATCAACACATAAAGCACCGATGTCTACTCTGAACCATGAACTTGATCAATAA
1 AGTAAGG----A-A-CAACACATAAAGCATCGATGTCTACTCTGAACCATGAACCTGATCAATAA
* * * * *
21868 ATTGTTAAATTCAGTTGGCAA-CTAGGTTTGTTTATTCTTTTGC-TTTCCCTGGTAATGCAATTC
60 ATTGTAAAATTCAGTTGGCAAGCTATGTTTATTTATTCTTCT-CTTTTCCCTGGTAATACAA-TC
* * * *
21931 GAGTACCGTTTTGCC-AGAACC-TATTTCCCTCCCACGTAATC-TAGAGCAA-GAACTCTCTCGT
123 GAGTACCATTTTGCCTA-AACCTTAATTCCCTCCCAGGTAATCTTA-AGCAATGCACTCTCTCGT
* * *
21992 ATCAACACATAGCAGATGTCAAAATC
186 ATCAACACATAACAGCTGTCAAATTC
* * *
22018 AGTAA-GAACCAACACATAAAGCATCAATGT-TGGACTCTAAACCAAGAACCTGATC-ATCAAAT
1 AGTAAGGAA-CAACACATAAAGCATCGATGTCT--ACTCTGAACCATGAACCTGATCAAT-AAAT
*
22080 TG-ATAAATTCAGTTGGCAAGCTATATTTATTTA
62 TGTA-AAATTCAGTTGGCAAGCTATGTTTATTTA
22113 CCCTTTTCTC
Statistics
Matches: 627, Mismatches: 73, Indels: 87
0.80 0.09 0.11
Matches are distributed among these distances:
208 1 0.00
209 22 0.04
210 42 0.07
211 65 0.10
212 4 0.01
213 1 0.00
214 9 0.01
215 107 0.17
216 86 0.14
217 63 0.10
218 53 0.08
219 105 0.17
220 38 0.06
221 31 0.05
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (211 bp):
AGTAAGGAACAACACATAAAGCATCGATGTCTACTCTGAACCATGAACCTGATCAATAAATTGTA
AAATTCAGTTGGCAAGCTATGTTTATTTATTCTTCTCTTTTCCCTGGTAATACAATCGAGTACCA
TTTTGCCTAAACCTTAATTCCCTCCCAGGTAATCTTAAGCAATGCACTCTCTCGTATCAACACAT
AACAGCTGTCAAATTC
Found at i:22090 original size:426 final size:427
Alignment explanation
Indices: 21155--22112 Score: 1056
Period size: 426 Copynumber: 2.2 Consensus size: 427
21145 ATGGTGGCAA
* *
21155 AGTAAGGACCGACACATAAAGCATCAATGTCT-GACTCTGAACCATGAACCTGATCAATAAAATG
1 AGTAAGGACCAACACATAAAGCATCAATGT-TGGACTCTGAACCATGAACCTGATCAATAAATTG
* * * * *
21219 TTACAATTCAGTTGGTAAG-TATGCTTATCTATTCTTGCTTTTTTCCTGGAAATACAATCTGGGT
65 -TA-AATTCAGTTGGCAAGCTATGTTTATTTATTCTTGCTTTTTCCCTGGAAATACAATCTGAGT
* * ** *
21283 ATCATTTTGCCTAAACTTAAAACTTAATTCCCTCCCAGGTAATCTTAAGGATTCACTCTCTCGTA
128 ACCATTTTGCCTAAAC-----ACTTAATTCCCTCCCAGGTAATCTCAACAATGCACTCTCTCGTA
* * *
21348 TCAACACATAACAGCTGTCAAGTTCAGTAAGGAACAACGCATAAAGCATAGATGTCAGACTCTGA
188 TCAACACATAACAGCTGTCAAATTCAGTAAGGAACAACACATAAAGCACAGATGTCAGACTCTGA
*
21413 ACCATGAACCTGTCAATAAAATGTTAAAATTCAGTCGCAAGCTATGTTCATTTATTCTATTTTTT
253 ACCATGAACCTGTCAATAAAATGTTAAAATTCAGTCGCAAGCTAGGTTCATTTATTC---TTTTT
* * * *
21478 TCTTTTCCTGGTAATACAATCCAGGTATCATTTTGCCTAAACTTAATTCTCTCCCCCACCAGGTA
315 GCTTTCCCTGGTAATACAATCCAGGTACCATTTTGCCTAAACCTAATTCTCTCCCCCACCA-GTA
* * * * * *
21543 ATCTTAAGCATGCACTCTCTCGCATCAACACATAATAGCTATTAAATTC
379 ATCTTAAGCAAGAACTCTCTCGCATCAACACATAACAGATATCAAAATC
* * *
21592 AGTAAGGACCAAC-CAATAAAGCATCGATGTAGTACTCTGAACCATGAACCTGATCAATAAATTG
1 AGTAAGGACCAACAC-ATAAAGCATCAATGTTGGACTCTGAACCATGAACCTGATCAATAAATTG
**
21656 TAAAATTCAGTTGGCAAGCTATGTTTATTTATTCTT-CTCTTTTCCCTGTTAATACAA-CTCGAG
65 T-AAATTCAGTTGGCAAGCTATGTTTATTTATTCTTGCT-TTTTCCCTGGAAATACAATCT-GAG
*
21719 TACCATTTTGCCTAAAC-CTT-ATTGCCTCCCAGGTAATCTCAACAATGCACTCTCTCGTATCAA
127 TACCATTTTGCCTAAACACTTAATTCCCTCCCAGGTAATCTCAACAATGCACTCTCTCGTATCAA
* * *
21782 CACATAACTGCTGTCAAATTCAGTAAGGACCAAGATCAACACATAAAGCACCGATGTC-TACTCT
192 CACATAACAGCTGTCAAATTCAGTAAGG----A-A-CAACACATAAAGCACAGATGTCAGACTCT
* * * **
21846 GAACCATGAACTTGATCAATAAATTGTT-AAATTCAGTTGGCAA-CTAGGTTTGTTTATTC-TTT
251 GAACCATGAACCTG-TCAATAAAATGTTAAAATTCAG-TCGCAAGCTAGGTTCATTTATTCTTTT
* * *
21908 TGCTTTCCCTGGTAATGCAATTC-GAGTACCGTTTTGCC-AGAACCT-ATT-TC-CCTCCCA-C-
314 TGCTTTCCCTGGTAATACAATCCAG-GTACCATTTTGCCTA-AACCTAATTCTCTCC-CCCACCA
* * *
21966 GTAATC-TAGAGCAAGAACTCTCTCGTATCAACACATAGCAGATGTCAAAATC
376 GTAATCTTA-AGCAAGAACTCTCTCGCATCAACACATAACAGATATCAAAATC
* * *
22018 AGTAAGAACCAACACATAAAGCATCAATGTTGGACTCTAAACCAAGAACCTGATC-ATCAAATTG
1 AGTAAGGACCAACACATAAAGCATCAATGTTGGACTCTGAACCATGAACCTGATCAAT-AAATTG
*
22082 ATAAATTCAGTTGGCAAGCTATATTTATTTA
65 -TAAATTCAGTTGGCAAGCTATGTTTATTTA
22113 CCCTTTTCTC
Statistics
Matches: 447, Mismatches: 53, Indels: 53
0.81 0.10 0.10
Matches are distributed among these distances:
425 4 0.01
426 121 0.27
427 2 0.00
428 3 0.01
429 6 0.01
430 69 0.15
431 40 0.09
434 1 0.00
435 40 0.09
436 56 0.13
437 105 0.23
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (427 bp):
AGTAAGGACCAACACATAAAGCATCAATGTTGGACTCTGAACCATGAACCTGATCAATAAATTGT
AAATTCAGTTGGCAAGCTATGTTTATTTATTCTTGCTTTTTCCCTGGAAATACAATCTGAGTACC
ATTTTGCCTAAACACTTAATTCCCTCCCAGGTAATCTCAACAATGCACTCTCTCGTATCAACACA
TAACAGCTGTCAAATTCAGTAAGGAACAACACATAAAGCACAGATGTCAGACTCTGAACCATGAA
CCTGTCAATAAAATGTTAAAATTCAGTCGCAAGCTAGGTTCATTTATTCTTTTTGCTTTCCCTGG
TAATACAATCCAGGTACCATTTTGCCTAAACCTAATTCTCTCCCCCACCAGTAATCTTAAGCAAG
AACTCTCTCGCATCAACACATAACAGATATCAAAATC
Found at i:24444 original size:10 final size:9
Alignment explanation
Indices: 24424--24544 Score: 57
Period size: 10 Copynumber: 12.6 Consensus size: 9
24414 TCACGGACCA
24424 AAAAATTTT
1 AAAAATTTT
24433 AAAAATTGTT
1 AAAAATT-TT
*
24443 AAAAATCATT
1 AAAAAT-TTT
24453 AAAAATATCTAT
1 AAAAAT-T-T-T
24465 AAAAATATTT
1 AAAAAT-TTT
*
24475 -AAAATTAT
1 AAAAATTTT
24483 AAAAA-TTT
1 AAAAATTTT
* **
24491 AAATAACTAA
1 AAA-AATTTT
*
24501 AAAAATTTAA
1 AAAAATTT-T
* *
24511 AAAAATGTA
1 AAAAATTTT
24520 AACAAATATTT
1 AA-AAAT-TTT
*
24531 AAAAATTAT
1 AAAAATTTT
24540 AAAAA
1 AAAAA
24545 AAATTCAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
8 7 0.08
9 31 0.35
10 37 0.42
11 5 0.06
12 9 0.10
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTTT
Found at i:24485 original size:18 final size:19
Alignment explanation
Indices: 24424--24544 Score: 85
Period size: 20 Copynumber: 6.3 Consensus size: 19
24414 TCACGGACCA
*
24424 AAAAAT-TTTAAAAATTGTT
1 AAAAATATTTAAAAATT-AT
*
24443 AAAAATCATTAAAAATATCTAT
1 AAAAAT-ATTTAAAA-AT-TAT
24465 AAAAATATTT-AAAATTAT
1 AAAAATATTTAAAAATTAT
*
24483 -AAAA-ATTTAAATAACTA-
1 AAAAATATTTAAA-AATTAT
24500 AAAAA-ATTTAAAAAAATGTA-
1 AAAAATATTT--AAAAAT-TAT
24520 AACAAATATTTAAAAATTAT
1 AA-AAATATTTAAAAATTAT
24540 AAAAA
1 AAAAA
24545 AAATTCAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
16 4 0.05
17 6 0.07
18 15 0.18
19 15 0.18
20 18 0.21
21 12 0.14
22 13 0.15
23 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATATTTAAAAATTAT
Found at i:24554 original size:20 final size:20
Alignment explanation
Indices: 24498--24554 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
24488 TTTAAATAAC
* *
24498 TAAAAAAATTTAAAAAAATG
1 TAAAAAAAATTAAAAAAATA
* * *
24518 TAAACAAATATTTAAAAATTA
1 TAAA-AAAAATTAAAAAAATA
24539 TAAAAAAAATTCAAAA
1 TAAAAAAAATT-AAAA
24555 TCCAACGTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAAAAATTAAAAAAATA
Found at i:33577 original size:51 final size:51
Alignment explanation
Indices: 33508--33608 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
33498 TCCAACACTT
* *
33508 TTTAATTTCTCTCAATTTTGCAGATCAATTAAAGCATAAAGCCCAACCCAA
1 TTTAATTTATCTCAATTTTGCAGATCAACTAAAGCATAAAGCCCAACCCAA
* * * *
33559 TTTAATTTATTTCTATTTTGTAGATCAACTAAAGCGTAAAGCCCAACCCA
1 TTTAATTTATCTCAATTTTGCAGATCAACTAAAGCATAAAGCCCAACCCA
33609 TTTCAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.34
Consensus pattern (51 bp):
TTTAATTTATCTCAATTTTGCAGATCAACTAAAGCATAAAGCCCAACCCAA
Found at i:43129 original size:4 final size:4
Alignment explanation
Indices: 43120--43157 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
43110 TCCTTTGTTA
* *
43120 TCTT TCTT TCTT TCTT TCTT TCTT TCTT CCTT GCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
43158 CTTTTGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:44706 original size:7 final size:7
Alignment explanation
Indices: 44684--44717 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
44674 AGGAATTCAA
*
44684 GGTTTTG
1 GGTTTAG
44691 GGTTT-G
1 GGTTTAG
44697 GGTTTAG
1 GGTTTAG
44704 GGTTTAG
1 GGTTTAG
44711 GGTTTAG
1 GGTTTAG
44718 AGTTCGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:44706 original size:13 final size:14
Alignment explanation
Indices: 44684--44717 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
44674 AGGAATTCAA
*
44684 GGTTTTGGGTTT-G
1 GGTTTAGGGTTTAG
44697 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAG
44711 GGTTTAG
1 GGTTTAG
44718 AGTTCGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:44750 original size:21 final size:21
Alignment explanation
Indices: 44726--44766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44716 AGAGTTCGAG
44726 TTCAAAATTTA-AGATTTTGGA
1 TTCAAAATTTAGAG-TTTTGGA
*
44747 TTCAAGATTTAGAGTTTTGG
1 TTCAAAATTTAGAGTTTTGG
44767 TTCGAGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (21 bp):
TTCAAAATTTAGAGTTTTGGA
Found at i:49029 original size:17 final size:17
Alignment explanation
Indices: 48999--49036 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
48989 AAGTAATTAC
*
48999 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
*
49016 AAGAAGATGGAAGGTTA
1 AAGAAGATGAAAGGTTA
49033 AAGA
1 AAGA
49037 TCAAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:50228 original size:23 final size:23
Alignment explanation
Indices: 50198--50310 Score: 108
Period size: 23 Copynumber: 5.0 Consensus size: 23
50188 AAAACAATAA
*
50198 GCACACACAGTGC-AATCCAGTAG
1 GCACACAAAGTGCAAAT-CAGTAG
*
50221 GCACACACAGTGC-AATCAGTAG
1 GCACACAAAGTGCAAATCAGTAG
* * * *
50243 GCGCCCATAGCGCAAATCAGTAG
1 GCACACAAAGTGCAAATCAGTAG
*
50266 GCACACAAAGTGCGAAA-CAGTAA
1 GCACACAAAGTGC-AAATCAGTAG
50289 GCACACAAAGTGCGAAA-CAGTA
1 GCACACAAAGTGC-AAATCAGTA
50311 AGCGCGCTAG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 15 0.19
23 61 0.77
24 3 0.04
ACGTcount: A:0.39, C:0.27, G:0.23, T:0.12
Consensus pattern (23 bp):
GCACACAAAGTGCAAATCAGTAG
Found at i:50768 original size:11 final size:11
Alignment explanation
Indices: 50741--50771 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
50731 TAAGTCTCTA
50741 ATGATTTTTCT
1 ATGATTTTTCT
50752 AT-ATTTTTCT
1 ATGATTTTTCT
50762 ATGATTTTTC
1 ATGATTTTTC
50772 AAAGTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (11 bp):
ATGATTTTTCT
Done.