Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003155.1 Hibiscus syriacus cultivar Beakdansim tig00006635_pilon, 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: 74685
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:902 original size:37 final size:36
Alignment explanation
Indices: 844--960 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
834 CCCATTATCA
* * *
844 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
*
880 TTTTCAAAGAAATATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
915 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-T
952 TTTTCAAAG
1 TTTTCAAAG
961 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.47
36 11 0.15
37 28 0.38
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:917 original size:21 final size:21
Alignment explanation
Indices: 893--952 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
883 TCAAAGAAAT
893 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
914 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
928 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
949 ATTT
1 ATTT
953 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:958 original size:72 final size:68
Alignment explanation
Indices: 842--987 Score: 186
Period size: 72 Copynumber: 2.1 Consensus size: 68
832 ATCCCATTAT
*
842 CATTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTT
1 CATTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ATAGTTACCAAAC-TT
907 GAAAAC
63 GAAAAC
* * * * *
913 CATTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTGGTTACCAAACTTG
1 CATTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGATAGTTACCAAACTTG
977 AAAAC
64 AAAAC
982 CATTTT
1 CATTTT
988 TAATACTTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
69 14 0.21
70 10 0.15
71 13 0.19
72 30 0.45
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
CATTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGATAGTTACCAAACTTGAA
AAC
Found at i:969 original size:35 final size:36
Alignment explanation
Indices: 859--988 Score: 153
Period size: 35 Copynumber: 3.7 Consensus size: 36
849 AACAAACATC
*
859 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAATATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AATATT
*
896 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AATATT
* **
931 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAATATT
966 TACCAAAC-TTGAAAACCATTTTT
1 TACCAAACTTTGAAAACCATTTTT
989 AATACTTTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
34 15 0.18
35 43 0.51
37 26 0.31
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAATATT
Found at i:4489 original size:264 final size:265
Alignment explanation
Indices: 3383--4546 Score: 1574
Period size: 265 Copynumber: 4.4 Consensus size: 265
3373 TTCTCTATCC
* * * * * * * *
3383 CGTGTTATATGTCTACAAA-AACAATCATTTAAGTTGAATAAATAAAACAAATAAGATCATTATA
1 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * * * * * *
3447 ATTTG-TTTGGTGATAACATGATCTAACATTTTCACTCAGTAACAAAGAGAACTTTCT-AA-AGC
66 GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGC
* * * * *
3509 --GAACTCCGGTTATTACAATAGATCCATTTATTTTTAGAACTCTTTCGATTGATAGATTAAATT
131 GTGAACTCCAGTTATTACAATAGATCCAATCA-TTTTAGAATTCTTTCGATTGATAAATTAAATT
* * * * *
3572 ATTGATGTTACAGTAAACAACAACAATATTTATCAGTACAATTTCACATGTACATTTTAATTTTC
195 ATTGATGTCACAGTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTC
3637 AT-A-A
260 ATAACA
* * ***
3641 CGTGTTAGATATAGGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
1 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* **
3706 GTTTGACTTGATGATAATGTGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGT
66 GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCG-
* * *
3771 AG-GAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATCAAATC
130 CGTGAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATTAAATT
* * * *
3835 ATTGACGTCACAATAAACGACAACAATATTTATCAGTATAGTTTTACATATACATTTCAATTTTC
195 ATTGATGTCACAGTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTC
3900 ATAACA
260 ATAACA
* * * **
3906 AGTGTTTCATGTCTATAAATAACAATCATTGAGGTCGAATAAATACAATAAATATTATCGTTATA
1 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * **
3971 GTTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAAAATAACTTTGTCAAGTAC
66 GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGC
* *
4036 GTGAACTCCATTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAGATTAAATTA
131 GTGAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATTAAATTA
**
4101 TTGATGTCACTTTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTCA
196 TTGATGTCACAGTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTCA
4166 TAACA
261 TAACA
* * * *
4171 CGTGATAGATGTATGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
1 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * *
4236 GTTTGATTTGATAATAACATGATCTAACATTTTCACTCAATAACAAAAATAACTTTTTCAAGCGC
66 GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGC
* * *
4301 GTGAACTCCATTTATTACAACAGATCCAATCATTTTAGAATT-TTTTGATTGATAAATTAAATTA
131 GTGAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATTAAATTA
* * * *
4365 TTGATGTCATAGTAAACGGCAACAATATTTATTAGTATAGTTTCTCATGTACATTTCAATTTTCA
196 TTGATGTCACAGTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTCA
4430 TAACA
261 TAACA
4435 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
1 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * * * * * *
4500 ATTTGACTAGATAGTGATATGATCTAACGTTTTCACACAGTAACAAA
66 GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAA
4547 GAGAGTTTTT
Statistics
Matches: 796, Mismatches: 101, Indels: 12
0.88 0.11 0.01
Matches are distributed among these distances:
258 13 0.02
259 43 0.05
260 46 0.06
261 2 0.00
262 1 0.00
263 86 0.11
264 212 0.27
265 393 0.49
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (265 bp):
CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
GTTTGACTTGATAATAACATGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGC
GTGAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATTAAATTA
TTGATGTCACAGTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTCA
TAACA
Found at i:4507 original size:529 final size:524
Alignment explanation
Indices: 3383--4546 Score: 1672
Period size: 529 Copynumber: 2.2 Consensus size: 524
3373 TTCTCTATCC
* * * * * * * *
3383 CGTGTTATATGTCTACAAAAACAATCATTTAAGTTGAATAAATAAAACAAATAAGATCATTATAA
1 CGTGTTACATGTCTATAAAAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATAA
* * * * *
3448 TTTG-TTTGGTGATAACATGATCTAACATTTTCACTCAGTAACAAAGAGAACTTTCTAAAGCGAA
66 TTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAAAAGAACTTTCTAAAGCGAA
* * *
3512 CTCCGGTTATTACAATAGATCCATTTATTTTTAGAACTCTTTCGATTGATAGATTAAATTATTGA
131 CTCCAGTTATTACAATAGATCCAATCATTTTTAGAACTCTTTCGATTGATAGATTAAATTATTGA
* *
3577 TGTTACAGTAAACAACAACAATATTTATCAGTACAATTTCACATGTACATTTTAATTTTCATAAC
196 TGTCACAGTAAACAACAACAATATTTATCAGTACAATTTCACATGTACATTTCAATTTTCATAAC
*
3642 GTGTTAGATATAGGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATAG
261 GTGATAGATATAGGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATAG
* ** *
3707 TTTGACTTGATGATAATGTGATCTAACATTTTCACTCAGTAACAAAAATAACTTTCTCAAGCGTA
326 TTTGACTTGATAATAACATGATCTAACATTTTCACTCAATAACAAAAATAACTTTCTCAAGCGTA
*
3772 GGAACTCCAGTTATTACAATAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATCAAATCAT
391 GGAACTCCAGTTATTACAACAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATCAAATCAT
3837 TGACGTCACAATAAACGACAACAATATTTATCAGTATAGTTTTACATATACATTTCAATTTTCAT
456 TGACGTCACAATAAACGACAACAATATTTATCAGTATAGTTTTACATATACATTTCAATTTTCAT
3902 AACA
521 AACA
* * **
3906 AGTGTTTCATGTCTATAAATAACAATCATTGAGGTCGAATAAATACAATAAATATTATCGTTATA
1 CGTGTTACATGTCTATAAA-AACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * *
3971 GTTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAAAATAACTTTGTCAAGTAC
65 ATTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAAAAGAACTTTCT-AA--A-
* * *
4036 GTGAACTCCATTTATTACAATAGATCCAATCA-TTTTAGAATTCTTTCGATTGATAGATTAAATT
126 GCGAACTCCAGTTATTACAATAGATCCAATCATTTTTAGAACTCTTTCGATTGATAGATTAAATT
** * * *
4100 ATTGATGTCACTTTAAACGACAACAATATTTATCAGTATAGTTTCACATGTACATTTCAATTTTC
191 ATTGATGTCACAGTAAACAACAACAATATTTATCAGTACAATTTCACATGTACATTTCAATTTTC
* *
4165 ATAACACGTGATAGATGTATGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATC
256 AT-A-ACGTGATAGATATAGGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATC
* *
4230 GTTATAGTTTGATTTGATAATAACATGATCTAACATTTTCACTCAATAACAAAAATAACTTTTTC
319 GTTATAGTTTGACTTGATAATAACATGATCTAACATTTTCACTCAATAACAAAAATAACTTTCTC
* * *
4295 AAGCG-CGTGAACTCCATTTATTACAACAGATCCAATCATTTTAGAATT-TTTTGATTGATAAAT
384 AAGCGTAG-GAACTCCAGTTATTACAACAGATCCAATCATTTTAGAATTCTTTCGATTGATAAAT
* * * * * * * *
4358 TAAATTATTGATGTCATAGTAAACGGCAACAATATTTATTAGTATAGTTTCT-CATGTACATTTC
448 CAAATCATTGACGTCACAATAAACGACAACAATATTTATCAGTATAGTTT-TACATATACATTTC
4422 AATTTTCATAACA
512 AATTTTCATAACA
4435 CGTGTTACATGTCTATAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
1 CGTGTTACATGTCTATAAA-AACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATA
* * * * *
4500 ATTTGACTAGATAGTGATATGATCTAACGTTTTCACACAGTAACAAA
65 ATTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAA
4547 GAGAGTTTTT
Statistics
Matches: 566, Mismatches: 65, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
523 15 0.03
524 41 0.07
525 45 0.08
526 2 0.00
528 92 0.16
529 211 0.37
530 160 0.28
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (524 bp):
CGTGTTACATGTCTATAAAAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATAA
TTTGACTTGATAATAACATGATCTAACGTTTTCACTCAGTAACAAAAAGAACTTTCTAAAGCGAA
CTCCAGTTATTACAATAGATCCAATCATTTTTAGAACTCTTTCGATTGATAGATTAAATTATTGA
TGTCACAGTAAACAACAACAATATTTATCAGTACAATTTCACATGTACATTTCAATTTTCATAAC
GTGATAGATATAGGTAAACAACAATCATTGAGGTCGAATAAATACAATAAATAAGATCGTTATAG
TTTGACTTGATAATAACATGATCTAACATTTTCACTCAATAACAAAAATAACTTTCTCAAGCGTA
GGAACTCCAGTTATTACAACAGATCCAATCATTTTAGAATTCTTTCGATTGATAAATCAAATCAT
TGACGTCACAATAAACGACAACAATATTTATCAGTATAGTTTTACATATACATTTCAATTTTCAT
AACA
Found at i:8430 original size:71 final size:71
Alignment explanation
Indices: 8346--8625 Score: 418
Period size: 71 Copynumber: 3.9 Consensus size: 71
8336 GCATTCAATG
* *
8346 AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCATATGTGCTTTTATGACCTTTTAAGAAG
1 AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTTAAGAAG
8411 TGAATT
66 TGAATT
* *
8417 AGGATCATATGATGACCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTTAATAAG
1 AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTTAAGAAG
8482 TGAATT
66 TGAATT
* * * *
8488 AGGATCATATGATGATCTGTTTAAGTTGTCGTAACGTTTGTGTGCTTTAATTGATCTTTTAAGAA
1 AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTA-TGATCTTTTAAGAA
**
8553 GTCTATT
65 GTGAATT
* * *
8560 AGGATCATACGATGAT-TTTTCTAAGTTGTCGTAAAGGTTATGTGCTTTTATGATCTTTTAAGAA
1 AGGATCATATGATGATCTTTT-TAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTTAAGAA
8624 GT
65 GT
8626 TATTCGGTTT
Statistics
Matches: 189, Mismatches: 18, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
71 131 0.69
72 58 0.31
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (71 bp):
AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTTAAGAAG
TGAATT
Found at i:8603 original size:143 final size:142
Alignment explanation
Indices: 8346--8625 Score: 418
Period size: 143 Copynumber: 2.0 Consensus size: 142
8336 GCATTCAATG
* *
8346 AGGATCATATGATGATCTTTTTAAGTTGTCGTAACGCATATGTGCTTTTATGACCTTTTAAGAAG
1 AGGATCATATGATGATCTGTTTAAGTTGTCGTAACGCATATGTGCTTTAATGACCTTTTAAGAAG
* * *
8411 TGAATTAGGATCATATGATGACCTTTTTAAGTTGTCGTAACGCTTATGTGCTTTTATGATCTTTT
66 TCAATTAGGATCATACGATGACCTTTTTAAGTTGTCGTAAAGCTTATGTGCTTTTATGATCTTTT
*
8476 AATAAGTGAATT
131 AAGAAGTGAATT
** * *
8488 AGGATCATATGATGATCTGTTTAAGTTGTCGTAACGTTTGTGTGCTTTAATTGATCTTTTAAGAA
1 AGGATCATATGATGATCTGTTTAAGTTGTCGTAACGCATATGTGCTTTAA-TGACCTTTTAAGAA
* * *
8553 GTCTATTAGGATCATACGATGA-TTTTTCTAAGTTGTCGTAAAGGTTATGTGCTTTTATGATCTT
65 GTCAATTAGGATCATACGATGACCTTTT-TAAGTTGTCGTAAAGCTTATGTGCTTTTATGATCTT
8617 TTAAGAAGT
129 TTAAGAAGT
8626 TATTCGGTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
142 49 0.40
143 74 0.60
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (142 bp):
AGGATCATATGATGATCTGTTTAAGTTGTCGTAACGCATATGTGCTTTAATGACCTTTTAAGAAG
TCAATTAGGATCATACGATGACCTTTTTAAGTTGTCGTAAAGCTTATGTGCTTTTATGATCTTTT
AAGAAGTGAATT
Found at i:11990 original size:21 final size:22
Alignment explanation
Indices: 11966--12025 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
11956 ATTTTAAAGG
* *
11966 ATAAATTTA-AATTTATAAAAA
1 ATAAATTAAGAATATATAAAAA
11987 AT-AATTAAGAATATATAAAAA
1 ATAAATTAAGAATATATAAAAA
*
12008 ATAAAATAA-AATATATAA
1 ATAAATTAAGAATATATAA
12026 TAGTTTCACG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.15
21 24 0.71
22 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
ATAAATTAAGAATATATAAAAA
Found at i:15085 original size:21 final size:21
Alignment explanation
Indices: 15059--15118 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
15049 ACATGATAGA
15059 TGGATTGTCACGTTAGCATCG
1 TGGATTGTCACGTTAGCATCG
15080 TGGATTGTCACGTTAGCATCG
1 TGGATTGTCACGTTAGCATCG
* *
15101 TGGATCGTCACATTAGCA
1 TGGATTGTCACGTTAGCA
15119 CCATGAACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (21 bp):
TGGATTGTCACGTTAGCATCG
Found at i:15297 original size:2 final size:2
Alignment explanation
Indices: 15290--15315 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15280 CTAATGTCTT
15290 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
15316 ATAAACTCCA
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):
TA
Found at i:21558 original size:24 final size:20
Alignment explanation
Indices: 21542--21579 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21532 CACATGCTAA
21542 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
21562 TGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
21580 TCAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:22621 original size:258 final size:244
Alignment explanation
Indices: 22157--22630 Score: 758
Period size: 258 Copynumber: 1.9 Consensus size: 244
22147 AAAGGACATA
22157 AGAAAGAATATGAAATATATAGCATATGAATATGAAATCATGAGGTGACATGAATTATATGAAAA
1 AGAAAGAATATGAAATATATAGCATATGAATATGAAATCATGAGGTGACATGAATTATATGAAAA
22222 AAATAACTACGTGACAATATGAAAATATGCTAGTGTGATGGGACCTAGGAACTAGTATATGAAAT
66 AAATAACTACGTGACAATATGAAAATATGCTAGTGTGATGGGACCTAGGAACTAGTATATGAAAT
22287 ATATATTACATTTATATAAGTTATTGGATGAAAAAAGAACAAGAGATAAAAGAGATGAAGGATAA
131 ATATATTACATTTATATAAGTTATTGGATGAAAAAAGAACAAGAGATAAAAGAGATGAAGGATAA
22352 TACTATAGGAGTATGATAAAAACATAATGATGACATGTATGTAATGGTT
196 TACTATAGGAGTATGATAAAAACATAATGATGACATGTATGTAATGGTT
22401 AGAAAGAATATG-AA-ATATAGCATATG-A-ATGAAATCATATGAGGGGTGACATGAATTATATG
1 AGAAAGAATATGAAATATATAGCATATGAATATGAAATC--ATGA--GGTGACATGAATTATATG
22462 AAAAAAATAACTACGTGATTACAAATATATGAAAATATGCTAGTGTGATGGGACCTAGGAACTAG
62 AAAAAAATAACTACGTG---AC--A-ATATGAAAATATGCTAGTGTGATGGGACCTAGGAACTAG
22527 TATACGTGATATATATATATATATACATTTATATAAGTTATTGGATGAAAAAATGAACAAGAGAT
121 TATA--TG--A-A-ATATATAT-TACATTTATATAAGTTATTGGATGAAAAAA-GAACAAGAGAT
22592 AAAAGAGATGAAGGATAATACTATAGGAGTATGATAAAA
178 AAAAGAGATGAAGGATAATACTATAGGAGTATGATAAAA
22631 GAGATGAGGA
Statistics
Matches: 212, Mismatches: 0, Indels: 22
0.91 0.00 0.09
Matches are distributed among these distances:
240 8 0.04
241 1 0.00
242 16 0.08
243 2 0.01
244 47 0.22
247 2 0.01
249 1 0.00
250 43 0.20
252 2 0.01
254 1 0.00
255 1 0.00
256 8 0.04
257 30 0.14
258 50 0.24
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (244 bp):
AGAAAGAATATGAAATATATAGCATATGAATATGAAATCATGAGGTGACATGAATTATATGAAAA
AAATAACTACGTGACAATATGAAAATATGCTAGTGTGATGGGACCTAGGAACTAGTATATGAAAT
ATATATTACATTTATATAAGTTATTGGATGAAAAAAGAACAAGAGATAAAAGAGATGAAGGATAA
TACTATAGGAGTATGATAAAAACATAATGATGACATGTATGTAATGGTT
Found at i:22646 original size:34 final size:35
Alignment explanation
Indices: 22589--22664 Score: 145
Period size: 34 Copynumber: 2.2 Consensus size: 35
22579 ATGAACAAGA
22589 GATAAAAGAGATGAAGGATAATACTATAGGAGTAT
1 GATAAAAGAGATGAAGGATAATACTATAGGAGTAT
22624 GATAAAAGAGATG-AGGATAATACTATAGGAGTAT
1 GATAAAAGAGATGAAGGATAATACTATAGGAGTAT
22658 GATAAAA
1 GATAAAA
22665 CATAAATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 28 0.68
35 13 0.32
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.22
Consensus pattern (35 bp):
GATAAAAGAGATGAAGGATAATACTATAGGAGTAT
Found at i:23037 original size:30 final size:30
Alignment explanation
Indices: 22949--23055 Score: 157
Period size: 28 Copynumber: 3.6 Consensus size: 30
22939 GGACAGTTAC
*
22949 CTTTATGACCTATGGATAGTTTACCGAGGAT
1 CTTTATGACCTCTGGATAG-TTACCGAGGAT
*
22980 CTTTATGATCTCTGGATAGTT--CGAGGAT
1 CTTTATGACCTCTGGATAGTTACCGAGGAT
*
23008 CTTTATGGCCTCTGGATAGTTACCGAGGAT
1 CTTTATGACCTCTGGATAGTTACCGAGGAT
23038 CTTTATGACCTCT-GATAG
1 CTTTATGACCTCTGGATAG
23056 GTCCTTCGGA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
28 26 0.38
29 5 0.07
30 21 0.30
31 17 0.25
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (30 bp):
CTTTATGACCTCTGGATAGTTACCGAGGAT
Found at i:26549 original size:64 final size:63
Alignment explanation
Indices: 26428--26549 Score: 145
Period size: 64 Copynumber: 1.9 Consensus size: 63
26418 ATGCACAGGA
* * * * *
26428 AGTGCATCGATGCACCTATTAAAATGGAAACTTCGAATGCAATTGGTGCATCAATGCATAAAG
1 AGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTGGTACATCAATGCATAAAG
* ** * *
26491 AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTTGTACATCGATGCA
1 AGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTGGTACATCAATGCA
26550 CGGGTACTGC
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
63 14 0.29
64 34 0.71
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (63 bp):
AGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTGGTACATCAATGCATAAAG
Found at i:26584 original size:24 final size:20
Alignment explanation
Indices: 26557--26614 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
26547 GCACGGGTAC
26557 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
26581 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTAGAA
26601 TGCATCGATGCACT
1 TGCATCGATGCACT
26615 TCAAGAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:27359 original size:2 final size:2
Alignment explanation
Indices: 27352--27386 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
27342 AGTATACGTG
* *
27352 AT AT AT AT AT AT AT AT AT AT AT AT AC AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27387 AGTTATTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27697 original size:31 final size:30
Alignment explanation
Indices: 27662--27739 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
27652 TCTTTCGAGG
*
27662 CATATGGACAGTATACCTATGTTCTAAGGAA
1 CATATGGACAGT-TACCTAGGTTCTAAGGAA
* ** *
27693 CATATGGATAGTTTACCTAGGTTCTTCGGGA
1 CATATGGACAG-TTACCTAGGTTCTAAGGAA
*
27724 CCTATGGACAGTTACC
1 CATATGGACAGTTACC
27740 GAGTCCTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.13
31 33 0.85
32 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (30 bp):
CATATGGACAGTTACCTAGGTTCTAAGGAA
Found at i:27749 original size:20 final size:20
Alignment explanation
Indices: 27724--27762 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27714 TTCTTCGGGA
27724 CCTATGGACAGTTACCGAGT
1 CCTATGGACAGTTACCGAGT
*
27744 CCTATGGATAGTTACCGAG
1 CCTATGGACAGTTACCGAG
27763 GATCTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
CCTATGGACAGTTACCGAGT
Found at i:27784 original size:30 final size:30
Alignment explanation
Indices: 27748--27814 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
27738 CCGAGTCCTA
27748 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
27778 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
27808 TGGATAG
1 TGGATAG
27815 GTCCTTCGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:27787 original size:50 final size:51
Alignment explanation
Indices: 27695--27792 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 51
27685 CTAAGGAACA
* * *
27695 TATGGATAGTTTACCTAGGTTCTTCGGGACCTATGGACAGTTACCGAGTCC
1 TATGGATAGTTTACCGAGGATCTTCAGGACCTATGGACAGTTACCGAGTCC
* * * *
27746 TATGGATAG-TTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAG
1 TATGGATAGTTTACCGAGGATCTTCAGGACCTATGGACAGTTACCGAG
27793 GATCTTTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 31 0.77
51 9 0.22
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (51 bp):
TATGGATAGTTTACCGAGGATCTTCAGGACCTATGGACAGTTACCGAGTCC
Found at i:29050 original size:20 final size:21
Alignment explanation
Indices: 29025--29076 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
29015 TTTTCCCAAT
*
29025 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
29045 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
29066 TCGCAATGCGA
1 TCGCAATGCGA
29077 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:29090 original size:20 final size:20
Alignment explanation
Indices: 29065--29178 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
29055 AATTGGGAAA
*
29065 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
29085 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
29105 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
29126 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
29146 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
29166 TTCGCAACGCGAT
1 ATCGCAACGCGAT
29179 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:29109 original size:61 final size:61
Alignment explanation
Indices: 29062--29178 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
29052 GCGAATTGGG
* * * * *
29062 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
29123 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
29179 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:29754 original size:19 final size:19
Alignment explanation
Indices: 29694--29774 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
29684 TTCGAGAATG
29694 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
29714 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
29730 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
29747 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
29766 AAAATCGCA
1 AAAATCGCA
29775 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:29816 original size:20 final size:19
Alignment explanation
Indices: 29770--29935 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
29760 GAAACCAAAA
*
29770 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
29789 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
29808 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
29828 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
29844 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
29861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
29875 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
29894 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
29914 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
29934 TC
1 TC
29936 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29851 original size:39 final size:39
Alignment explanation
Indices: 29775--29851 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
29765 CAAAATCGCA
* **
29775 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
29814 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
29852 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:29860 original size:33 final size:33
Alignment explanation
Indices: 29823--29910 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
29813 GTTGCGATTT
* *
29823 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
29856 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
29889 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
29911 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:32875 original size:20 final size:20
Alignment explanation
Indices: 32850--32887 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32840 AATAGTTTCT
32850 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
32870 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
32888 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:33176 original size:22 final size:22
Alignment explanation
Indices: 33149--33192 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
33139 GATGGAGATA
33149 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
33171 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
33193 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:33405 original size:20 final size:20
Alignment explanation
Indices: 33380--33473 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
33370 GATTATGTAT
33380 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
33400 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
33420 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
33441 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
33461 TATCGCATTGCGA
1 TATCGCGTTGCGA
33474 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:33474 original size:20 final size:20
Alignment explanation
Indices: 33360--33474 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
33350 CGCTTTGAAA
*
33360 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
33381 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
33401 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
33421 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
33442 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
33462 ATCGCATTGCGAT
1 ATCGCATTGCGAT
33475 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:33492 original size:21 final size:21
Alignment explanation
Indices: 33463--33555 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
33453 ATAGTCAGTA
*
33463 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* ***
33484 TCGCGTTGCGA-TTTAATTAT
1 TCGCATTGCGATTTTACCAAT
*
33504 TCGCATTGCGATTTTTCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
33525 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
33545 TCGCATTGCGA
1 TCGCATTGCGA
33556 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:33493 original size:41 final size:40
Alignment explanation
Indices: 33402--33536 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 40
33392 AAAGTCAGTA
* * * ** *
33402 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
* *
33442 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
* *
33484 TCGCGTTGCGAT-TTAATTATTCGCATTGCGATTTTTCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGA-TTTTCCAAT
33525 TCGCGTTGCGAT
1 TCGCGTTGCGAT
33537 TTACTTATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 69 0.87
42 6 0.08
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:33537 original size:41 final size:41
Alignment explanation
Indices: 33463--33555 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
33453 ATAGTCAGTA
33463 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
* *
33504 TCGCATTGCGATTTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
33545 TCGCATTGCGA
1 TCGCATTGCGA
33556 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAATTAT
Found at i:34233 original size:2 final size:2
Alignment explanation
Indices: 34226--34269 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
34216 TTGCAAATAC
34226 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
34268 AT
1 AT
34270 GGGTGTCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35821 original size:15 final size:15
Alignment explanation
Indices: 35801--35831 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35791 CAACAAATAG
35801 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
35816 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
35831 A
1 A
35832 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:36093 original size:10 final size:10
Alignment explanation
Indices: 36066--36100 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
36056 GGACCGGCTG
*
36066 AAAACCGAAA
1 AAAACCGGAA
36076 AAAACCGGAA
1 AAAACCGGAA
*
36086 AAAACCGGGA
1 AAAACCGGAA
36096 AAAAC
1 AAAAC
36101 AGATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.63, C:0.20, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:36515 original size:269 final size:271
Alignment explanation
Indices: 36034--36577 Score: 975
Period size: 269 Copynumber: 2.0 Consensus size: 271
36024 GAACCGGCCA
*
36034 GAACCGCTGAACCGTTCGAACCGGACCGGCTGAAAACCGAAAAAAACCGGAAAAAACCGGGAAAA
1 GAACCGCTAAACCGTTCGAACCGGACCGGCTGAAAACCGAAAAAAACCGGAAAAAACCGGGAAAA
* * *
36099 ACAGATATTTTTGTTTTTTAAAAAAAAATTAAACTAAACAACGTCGTTTGTTAAACGAGCCAAAT
66 ACAGAGATTTTTGTTTTTAAAAAAAAAATTAAACCAAACAACGTCGTTTGTTAAACGAGCCAAAT
36164 CGAACTCAAGTATTATTGAGCTCGACTCGAATTTGAAAACTTTAAAAGTAAGCTCAACTCAACTC
131 CGAACTCAAGTATTATTGAGCTCGACTCGAATTTGAAAACTTTAAAAGTAAGCTCAACTCAACTC
36229 AAACTCACAAGCTAAAAATTATCAAGTTCAACTCAAACTCGAAATATAATATTGAAACTTGAACT
196 AAACTCACAAGCTAAAAATTATCAAGTTCAACTCAAACTCGAAATATAATATTGAAACTTGAACT
36294 CAAAAAGGCTT
261 CAAAAAGGCTT
* *
36305 GAACCGCTAAACCGTTCGAACCGGACCGGCTGAAAACCGAAAAAAACCGG-GAAAATCGGGAAAA
1 GAACCGCTAAACCGTTCGAACCGGACCGGCTGAAAACCGAAAAAAACCGGAAAAAACCGGGAAAA
* *
36369 ACAGGGATTTTT-TTTTTAAAAAAAAAATTAAACCAAACAACGTCGTTTGTTAAACGAGCCAAGT
66 ACAGAGATTTTTGTTTTTAAAAAAAAAATTAAACCAAACAACGTCGTTTGTTAAACGAGCCAAAT
* * *
36433 CGAACTCGAGTATTGTTGAGCTCGACTCGAATTTGAAAATTTTAAAAGTAAGCTCAACTCAACTC
131 CGAACTCAAGTATTATTGAGCTCGACTCGAATTTGAAAACTTTAAAAGTAAGCTCAACTCAACTC
36498 AAACTCACAAGCTAAAAATTATCAAGTTCAACTCAAACTCGAAATATAATATTGAAACTTGAACT
196 AAACTCACAAGCTAAAAATTATCAAGTTCAACTCAAACTCGAAATATAATATTGAAACTTGAACT
36563 CAAAAAGGCTT
261 CAAAAAGGCTT
36574 GAAC
1 GAAC
36578 TCAAAAAAAA
Statistics
Matches: 262, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
269 191 0.73
270 22 0.08
271 49 0.19
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (271 bp):
GAACCGCTAAACCGTTCGAACCGGACCGGCTGAAAACCGAAAAAAACCGGAAAAAACCGGGAAAA
ACAGAGATTTTTGTTTTTAAAAAAAAAATTAAACCAAACAACGTCGTTTGTTAAACGAGCCAAAT
CGAACTCAAGTATTATTGAGCTCGACTCGAATTTGAAAACTTTAAAAGTAAGCTCAACTCAACTC
AAACTCACAAGCTAAAAATTATCAAGTTCAACTCAAACTCGAAATATAATATTGAAACTTGAACT
CAAAAAGGCTT
Found at i:36656 original size:14 final size:14
Alignment explanation
Indices: 36637--36664 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36627 AAGTGAAAGA
36637 ATAGTTATATAATT
1 ATAGTTATATAATT
36651 ATAGTTATATAATT
1 ATAGTTATATAATT
36665 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:39057 original size:14 final size:14
Alignment explanation
Indices: 39038--39065 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39028 AAGTGAAAGA
39038 ATAGTTATATAATT
1 ATAGTTATATAATT
39052 ATAGTTATATAATT
1 ATAGTTATATAATT
39066 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:61804 original size:3 final size:3
Alignment explanation
Indices: 61796--61828 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
61786 CATATGAATA
61796 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61829 TCTTTCAAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.