Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003896.1 Hibiscus syriacus cultivar Beakdansim tig00008418_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: 91756
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:1895 original size:3 final size:3
Alignment explanation
Indices: 1887--1933 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1877 TATCCAACCT
1887 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1934 TTACAAACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3616 original size:23 final size:23
Alignment explanation
Indices: 3582--3677 Score: 95
Period size: 23 Copynumber: 4.2 Consensus size: 23
3572 GAGTCGAGGG
* *
3582 TTCTACGCGGTCTTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGACAA
* *
3605 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
* **
3628 TTCTACACGGTCCTTTAGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * *
3651 TACTATGTGGTCCTTCGGGAC-A
1 TTCTACGCGGTCCTTCGGGACAA
3673 TTCTA
1 TTCTA
3678 TGTGGCACTT
Statistics
Matches: 57, Mismatches: 16, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
22 5 0.09
23 52 0.91
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:20826 original size:22 final size:22
Alignment explanation
Indices: 20749--20835 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 22
20739 CTTCTAGATA
* *
20749 ATTCTACGTGGTCCTTAGGGAC
1 ATTCTACGTGGTCATTTGGGAC
* * *
20771 ATTTCTGCGCGGTCATTCGGGAC
1 A-TTCTACGTGGTCATTTGGGAC
* *
20794 AATACTATGTGGTCATTTGGGAC
1 -ATTCTACGTGGTCATTTGGGAC
* *
20817 ATTCTATGTGGTAATTTGG
1 ATTCTACGTGGTCATTTGG
20836 TACAATTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 18 0.35
23 33 0.63
24 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.36
Consensus pattern (22 bp):
ATTCTACGTGGTCATTTGGGAC
Found at i:26327 original size:31 final size:31
Alignment explanation
Indices: 26289--26351 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
26279 TTATGTAGAT
*
26289 ATAAAGTCCCTGATTTAAATGAAATGTCTTA
1 ATAAAGTCCCTGATTTAAATGAAATATCTTA
26320 ATAAAGTCCCTGATTTAAATGAAATATCTTA
1 ATAAAGTCCCTGATTTAAATGAAATATCTTA
26351 A
1 A
26352 AAGAAAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (31 bp):
ATAAAGTCCCTGATTTAAATGAAATATCTTA
Found at i:27738 original size:32 final size:32
Alignment explanation
Indices: 27701--27777 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
27691 AAATTTTGAC
*
27701 ACTACCTCTCTTCGAGACAC-CAAATTCATACT
1 ACTACCTCTCTT-GAGACACTCAAATCCATACT
* *
27733 ACTACCTCTCATTGAGGCACTCAAATCCATATT
1 ACTACCTCTC-TTGAGACACTCAAATCCATACT
**
27766 TTTACCTCTCTT
1 ACTACCTCTCTT
27778 TGAGGCAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 18 0.47
33 20 0.53
ACGTcount: A:0.27, C:0.32, G:0.06, T:0.34
Consensus pattern (32 bp):
ACTACCTCTCTTGAGACACTCAAATCCATACT
Found at i:27999 original size:32 final size:34
Alignment explanation
Indices: 27963--28044 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 34
27953 AAATTTTAAC
*
27963 GCTACCTCTCTTTGAGGCA-TCAAATTCATAT-T
1 GCTACCTCTCTTTGAGGCACCCAAATTCATATAT
27995 GCTACCTCTCTTTGAGGCACCCAAATTCATATAT
1 GCTACCTCTCTTTGAGGCACCCAAATTCATATAT
*
28029 -TTACCTCTCTTTGAGG
1 GCTACCTCTCTTTGAGG
28045 AATAAAGTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 19 0.41
33 26 0.57
34 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (34 bp):
GCTACCTCTCTTTGAGGCACCCAAATTCATATAT
Found at i:28051 original size:261 final size:261
Alignment explanation
Indices: 27546--28071 Score: 786
Period size: 261 Copynumber: 2.0 Consensus size: 261
27536 TCTTTGAATA
* *
27546 TCATTTTAATTAAAGATTCTTTTAATTTTTCAAGAATTATAGATTTTTTACATGTAAAAAAATTA
1 TCATTTGAATTAAAGATTCTTTTAATTTTTCAAGAATTATAGATTTTTGACATGTAAAAAAATTA
* * * *
27611 TACCTTTCGTATTTTGTCTGAAGCCAAAATACAATCACTTGATTCTTTACCCTATATAATTTATA
66 TACCTTTCGTATCTTGTCTGAAGCCAAAATACAAGCACTCGATTCTTTACCCTATATAATTCATA
*
27676 ATTACTACCAAAAACAAATTTTGACACTACCTCTCTTCGAGACACCAAATTCATACTACTACCTC
131 ATTACTACCAAAAACAAATTTTAACACTACCTCTCTTCGAGACACCAAATTCATACTACTACCTC
* *
27741 TCATTGAGGCACTCAAATCCATATTTTTACCTCTCTTTGAGGCAATAAAGTCACACCCTCGA-CT
196 TCATTGAGGCACCCAAATCCATATATTTACCTCTCTTTGAGGCAATAAAGTCACACCCTC-ATCT
27805 TC
260 TC
* * ***
27807 TCATTTGAATTAAATATTCTTTTAATTTTTCAAGAATTATAGATTTTTGATATGTGTCAAAATTA
1 TCATTTGAATTAAAGATTCTTTTAATTTTTCAAGAATTATAGATTTTTGACATGTAAAAAAATTA
* * * *
27872 TACCTTTTGTATCTTGTCTGAAGCGAAAATATAAGCACTCGATTCTTTACCCTATATAATTCATG
66 TACCTTTCGTATCTTGTCTGAAGCCAAAATACAAGCACTCGATTCTTTACCCTATATAATTCATA
* * * * * *
27937 ATTACTACCAAAAACTAAATTTTAACGCTACCTCTCTTTGAGGCATCAAATTCATATTGCTACCT
131 ATTACTACCAAAAAC-AAATTTTAACACTACCTCTCTTCGAGACACCAAATTCATACTACTACCT
* *
28002 CTCTTTGAGGCACCCAAATTCATATATTTACCTCTCTTTGAGG-AATAAAGTCACACCCTCATCT
195 CTCATTGAGGCACCCAAATCCATATATTTACCTCTCTTTGAGGCAATAAAGTCACACCCTCATCT
28066 TC
260 TC
28068 TCAT
1 TCAT
28072 ATAGAAAACC
Statistics
Matches: 237, Mismatches: 26, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
260 1 0.00
261 155 0.65
262 81 0.34
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (261 bp):
TCATTTGAATTAAAGATTCTTTTAATTTTTCAAGAATTATAGATTTTTGACATGTAAAAAAATTA
TACCTTTCGTATCTTGTCTGAAGCCAAAATACAAGCACTCGATTCTTTACCCTATATAATTCATA
ATTACTACCAAAAACAAATTTTAACACTACCTCTCTTCGAGACACCAAATTCATACTACTACCTC
TCATTGAGGCACCCAAATCCATATATTTACCTCTCTTTGAGGCAATAAAGTCACACCCTCATCTT
C
Found at i:28700 original size:34 final size:33
Alignment explanation
Indices: 28616--28702 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
28606 AAACAGATTA
* * *
28616 AAAAAGAAAAAGAAAATAAAAAAAGAAAAAAAT
1 AAAAAGAAAGAGAAAAGAAAGAAAGAAAAAAAT
* *
28649 CAAAAGAGAGAGAAAAGAAAGAAAGAAAAAAAT
1 AAAAAGAAAGAGAAAAGAAAGAAAGAAAAAAAT
*
28682 AAATAATAAAGA-ATAAAGAAA
1 AAA-AAGAAAGAGA-AAAGAAA
28703 ACAAATCAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (33 bp):
AAAAAGAAAGAGAAAAGAAAGAAAGAAAAAAAT
Found at i:30489 original size:79 final size:79
Alignment explanation
Indices: 30358--30568 Score: 280
Period size: 79 Copynumber: 2.7 Consensus size: 79
30348 GATGAGGGAG
** *
30358 AAGAACTTGTTCAACCTTTGCTCGATTTTATCA-AAGAATGAGGTGGATCAACATTTCCAGTGAA
1 AAGAACTTGTTCAACCTTTGCTCGATTCCATCACAA-AAGGAGGTGGATCAACATTTCCAGTGAA
*
30422 TAAGTTCATAATGAC
65 GAAGTTCATAATGAC
* * *
30437 AAGAACTTGTTCAACCTTTACTTGATTCCATCACAAAAGGAGGTAGATCAACATTTCCAGTGAAG
1 AAGAACTTGTTCAACCTTTGCTCGATTCCATCACAAAAGGAGGTGGATCAACATTTCCAGTGAAG
** *
30502 AAGTTCATGGTGAG
66 AAGTTCATAATGAC
* * * *
30516 AAGAACTTGTTCAATCTTTGCCCGATTCCATCACAGAAGGAGGTGGATAAACA
1 AAGAACTTGTTCAACCTTTGCTCGATTCCATCACAAAAGGAGGTGGATCAACA
30569 ATTTTAATTG
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
79 112 0.98
80 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (79 bp):
AAGAACTTGTTCAACCTTTGCTCGATTCCATCACAAAAGGAGGTGGATCAACATTTCCAGTGAAG
AAGTTCATAATGAC
Found at i:31009 original size:3 final size:3
Alignment explanation
Indices: 31001--31122 Score: 244
Period size: 3 Copynumber: 40.7 Consensus size: 3
30991 TATCCAACCT
31001 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31049 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31097 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
31123 TTACAAACCA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:36154 original size:85 final size:85
Alignment explanation
Indices: 36065--36370 Score: 451
Period size: 85 Copynumber: 3.6 Consensus size: 85
36055 GCGCAATTGT
* * *
36065 GTCATAAATCTATGACGCGCATGTATGACTTACATTGCGCGTCATTGAAGCACCCGTCATAAATT
1 GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCACCCGTCATAAATT
36130 AAGATGACACACATTTGTGC
66 AAGATGACACACATTTGTGC
36150 GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGC-CCCTGTCATAAAT
1 GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCACCC-GTCATAAAT
36214 TAAGATG--ACACATTTGTGC
65 TAAGATGACACACATTTGTGC
* * *
36233 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATC
1 GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCACCCGTCATAAAT-
* * *
36298 T--GCTTGACATACATTTGTGT
65 TAAG-ATGACACACATTTGTGC
* *
36318 GTCATAAATTTATAACACGCATATATGACTTACATTGCGTGTCATTGAAGCAC
1 GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCAC
36371 ACATCATTTA
Statistics
Matches: 203, Mismatches: 12, Indels: 12
0.89 0.05 0.05
Matches are distributed among these distances:
82 1 0.00
83 72 0.35
84 7 0.03
85 123 0.61
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
GTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCATTGAAGCACCCGTCATAAATT
AAGATGACACACATTTGTGC
Found at i:36343 original size:168 final size:167
Alignment explanation
Indices: 36065--36368 Score: 493
Period size: 168 Copynumber: 1.8 Consensus size: 167
36055 GCGCAATTGT
* *
36065 GTCATAAATCTATGACGCGCATGTATGACTTACATTGCGCGTCATTGAAGCACCCGTCATAAATT
1 GTCATAAATCTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCACCCATCATAAATT
*
36130 AAGATGACACACATTTGTGCGTCATAAATTTATGACACGCATATATGACTTACATTGCGCGTCAT
66 -AGATGACACACATTTGTGCGTCATAAATTTATAACACGCATATATGACTTACATTGCGCGTCAT
36195 TGAAGCCCCTGTCATAAATTAAGATGACACATTTGTGC
130 TGAAGCCCCTGTCATAAATTAAGATGACACATTTGTGC
* *
36233 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATC
1 GTCATAAATCTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCACCCATCATAAAT-
* * * *
36298 T-GCTTGACATACATTTGTGTGTCATAAATTTATAACACGCATATATGACTTACATTGCGTGTCA
65 TAG-ATGACACACATTTGTGCGTCATAAATTTATAACACGCATATATGACTTACATTGCGCGTCA
36362 TTGAAGC
129 TTGAAGC
36369 ACACATCATT
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
167 1 0.01
168 123 0.98
169 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (167 bp):
GTCATAAATCTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCACCCATCATAAATT
AGATGACACACATTTGTGCGTCATAAATTTATAACACGCATATATGACTTACATTGCGCGTCATT
GAAGCCCCTGTCATAAATTAAGATGACACATTTGTGC
Found at i:36432 original size:2 final size:2
Alignment explanation
Indices: 36425--36459 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36415 TTTCGAAAAT
36425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36460 TGTAGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44653 original size:39 final size:39
Alignment explanation
Indices: 44564--44658 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 39
44554 AAACGTTAAT
* * **
44564 GTGAAATAGTTTAAGAAAATAAGAATTTAGAATTCTATG
1 GTGAAATAATTTAAGAAAATAAGAATTTAGAATGCTAAA
* *
44603 GTGGCAA-AATTTAAG-AAATTAGAGATTTAGAATGCTAAA
1 GT-GAAATAATTTAAGAAAATAAGA-ATTTAGAATGCTAAA
*
44642 GTGAAATAATTTGAGAA
1 GTGAAATAATTTAAGAA
44659 TTATGAATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
38 10 0.23
39 30 0.68
40 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (39 bp):
GTGAAATAATTTAAGAAAATAAGAATTTAGAATGCTAAA
Found at i:51700 original size:18 final size:17
Alignment explanation
Indices: 51680--51762 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
51670 AATTATGAAT
*
51680 ATTTAAATTATTTTTAAT
1 ATTTAAATTA-TTTTAAA
*
51698 ATTT-AATTAGTTTAAA
1 ATTTAAATTATTTTAAA
* * *
51714 AATAAAAATATTTTAAA
1 ATTTAAATTATTTTAAA
*
51731 AATTAAATTATTTTTAAA
1 ATTTAAATTA-TTTTAAA
*
51749 ATTTATA-TATTTTA
1 ATTTAAATTATTTTA
51763 TTATAAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
16 12 0.23
17 25 0.47
18 16 0.30
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (17 bp):
ATTTAAATTATTTTAAA
Found at i:51751 original size:17 final size:17
Alignment explanation
Indices: 51682--51751 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
51672 TTATGAATAT
* *
51682 TTAAATTATTTTTAATA
1 TTAAATTATTTTAAAAA
* *
51699 TTTAATTAGTTTAAAAA
1 TTAAATTATTTTAAAAA
* *
51716 TAAAAATATTTTAAAAA
1 TTAAATTATTTTAAAAA
*
51733 TTAAATTATTTTTAAAA
1 TTAAATTATTTTAAAAA
51750 TT
1 TT
51752 TATATATTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (17 bp):
TTAAATTATTTTAAAAA
Found at i:55203 original size:8 final size:7
Alignment explanation
Indices: 55185--55270 Score: 50
Period size: 7 Copynumber: 11.6 Consensus size: 7
55175 AATTTAATCC
55185 TTTTATT
1 TTTTATT
*
55192 TTTTACT
1 TTTTATT
55199 TTTT-TT
1 TTTTATT
*
55205 TATTATT
1 TTTTATT
55212 TTTATCATT
1 TTT-T-ATT
55221 TTTTATTT
1 TTTTA-TT
*
55229 TATTTGTT
1 T-TTTATT
55237 CATTTTA-T
1 --TTTTATT
55245 TTTTATT
1 TTTTATT
*
55252 TTATTACT
1 TT-TTATT
*
55260 TATTATT
1 TTTTATT
55267 TTTT
1 TTTT
55271 TAATACTTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
6 9 0.15
7 25 0.42
8 13 0.22
9 12 0.20
10 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTATT
Found at i:55210 original size:20 final size:20
Alignment explanation
Indices: 55185--55272 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 20
55175 AATTTAATCC
55185 TTTTATTTTTTAC-TTTTTT
1 TTTTATTTTTTACATTTTTT
55204 TTATTA-TTTTTATCATTTTTT
1 TT-TTATTTTTTA-CATTTTTT
* *
55225 ATTTTATTTGTT-CATTTTAT
1 -TTTTATTTTTTACATTTTTT
*
55245 TTTTATTTTATTACTTATTATTT
1 TTTTATTTT-TTAC--ATTTTTT
55268 TTTTA
1 TTTTA
55273 ATACTTTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
19 16 0.29
20 13 0.24
21 10 0.18
22 6 0.11
23 10 0.18
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTTACATTTTTT
Found at i:55262 original size:18 final size:18
Alignment explanation
Indices: 55241--55278 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
55231 TTTGTTCATT
*
55241 TTATT-TTTATTTTATTAC
1 TTATTATTT-TTTTAATAC
55259 TTATTATTTTTTTAATAC
1 TTATTATTTTTTTAATAC
55277 TT
1 TT
55279 TGTTTATACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTTTTTTAATAC
Found at i:55271 original size:24 final size:23
Alignment explanation
Indices: 55198--55271 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
55188 TATTTTTTAC
* *
55198 TTTT-TTTTATTATTTTTATCATT
1 TTTTATTTTATTATTATTAT-TTT
* *
55221 TTTTATTTTATTTGTTCATT-TTAT
1 TTTTATTTTA-TTATT-ATTATTTT
55245 TTTTATTTTATTACTTATTATTTT
1 TTTTATTTTATTA-TTATTATTTT
55269 TTT
1 TTT
55272 AATACTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 9 0.22
24 24 0.60
25 5 0.12
26 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (23 bp):
TTTTATTTTATTATTATTATTTT
Found at i:55342 original size:56 final size:57
Alignment explanation
Indices: 55248--55368 Score: 138
Period size: 60 Copynumber: 2.1 Consensus size: 57
55238 ATTTTATTTT
* *
55248 TATTTTATTACTTATTATTTTTTTAATACTTTGTTTATACGT-TAT-TATATATATA
1 TATTTTATTACTTATTATTTTATTAATACTTTGTTTATACATATATATATATATATA
* * * * *
55303 TATTTTATTTACTTTTTATTATTATTATTATTTTCTTATATATATATATATATATATATA
1 TATTTTA-TTACTTATTATT-TTATTAATACTTTGTT-TATACATATATATATATATATA
55363 TATTTT
1 TATTTT
55369 TGCTTTCACA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
55 7 0.13
56 11 0.20
57 12 0.22
58 5 0.09
59 3 0.06
60 16 0.30
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (57 bp):
TATTTTATTACTTATTATTTTATTAATACTTTGTTTATACATATATATATATATATA
Found at i:55346 original size:2 final size:2
Alignment explanation
Indices: 55339--55365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55329 ATTATTTTCT
55339 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55366 TTTTGCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55430 original size:16 final size:15
Alignment explanation
Indices: 55406--55451 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
55396 TATATATTAA
*
55406 TTTTATTTTTTTATCT
1 TTTTCTTTTTTT-TCT
55422 TTTTCTTTTATTTTCT
1 TTTTCTTTT-TTTTCT
55438 TTTTCTTTCTTTTT
1 TTTTCTTT-TTTTT
55452 ATTCTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:60549 original size:182 final size:182
Alignment explanation
Indices: 60327--60973 Score: 893
Period size: 182 Copynumber: 3.6 Consensus size: 182
60317 TACAAATGAA
* * * * * *
60327 AAATGTATCGATCCATAGCAATATAATAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATGA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGA-AATGATAA
** * * *
60391 AACCGGTAAACCGCTACCAGATATATTGAAAGTGTCGATAAATTAATATAAGTATTGACACTTTT
65 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATAGACACTTTC
*
60456 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATATTTTATAC
130 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * *
60509 AAATGTATCGATCCATAGTAATATAACATGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* * *
60574 ACCTGTAAAAAGCTACCGGATATATTAAAAGTGTCGATACATTAATATAAGTATAGACACTTTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATAGACACTTTCG
* *
60639 TAATTTAAAAGAGAAGAAGTAATAGCACCTAAAAAGTGTCGATACTTTATAC
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * *
60691 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGATAAAATAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* * * * *
60756 ACCGGTAAAAAGATGCTGGATATATTGAAAGTGTTGATAAATTAATATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATAGACACTTTCG
*
60821 TAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTATGA-
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-AC
** * * * * *
60873 AAACATATCGATCCATAACAATATAATAGATAAAAATATGACAAAACCGGTATCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* ** * *
60938 ACCGATAAAGCGCTACCGGTTATGTTGAAAGTGTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
60974 GTACTTTAAT
Statistics
Matches: 409, Mismatches: 54, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
182 407 1.00
183 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATAGACACTTTCG
TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:61127 original size:56 final size:56
Alignment explanation
Indices: 61061--61168 Score: 207
Period size: 56 Copynumber: 1.9 Consensus size: 56
61051 TTTAACATAA
61061 AAAGTATCGACACTTATGTAATTGTATCGATTAAATATAAATAACATATCCGGTAT
1 AAAGTATCGACACTTATGTAATTGTATCGATTAAATATAAATAACATATCCGGTAT
*
61117 AAAGTATCGACACTTATGTAATTGTATCGATTAAATGTAAATAACATATCCG
1 AAAGTATCGACACTTATGTAATTGTATCGATTAAATATAAATAACATATCCG
61169 ACCTCTTTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (56 bp):
AAAGTATCGACACTTATGTAATTGTATCGATTAAATATAAATAACATATCCGGTAT
Found at i:62404 original size:198 final size:198
Alignment explanation
Indices: 61999--62479 Score: 487
Period size: 198 Copynumber: 2.4 Consensus size: 198
61989 ATTAGATTTT
* * * ** * *
61999 GTGTCGATGCATTTATAACAAGTATCGATCC-CAAAATCAAAGAGACCGATAATTATAATGTAAT
1 GTGTCGATACATTT-TAAAAAGTATCGATCCTCGAAA-CATCGAAACCGATAATTATAATGTAAC
* *
62063 AGGTAAATTTCTAATGTAACCGGTAGAAATATACCGGGTTCATGAGAGAATAGGTCAACATAAAA
64 AGGTAAATTTCTAATGTAACCGGTAGAAATATACCGGATTAATGAGAGAATAGGTCAACATAAAA
* * ** * * * *
62128 TATCGACACTTTTTTAATTTGTGTCGATACATTTTTTCAAAATGAATGGCAAACGAGGTGTACGC
129 TATCGACACTCTTTAAATACGTGTCGATACATTTTTTCAAAATGAAAGACAAACGAAGTGCACGC
62193 ATAAA
194 ATAAA
* * *
62198 GTGTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCGAAATCGATAATTATTATTTAACA
1 GTGTCGATACATTT-TAAAAAGTATCGATCCTCGAAACATCGAAACCGATAATTATAATGTAACA
* * * *
62263 GGTAAATTTAC-AATGTAACTGGTTA-AAATATACC-GATTAATTAGCA-AATAGGTCTACATTA
65 GGTAAATTT-CTAATGTAACCGG-TAGAAATATACCGGATTAATGAG-AGAATAGGTCAACATAA
** * *
62324 TGTATCGACACTCTTTAAATACGTGTCGATA-TTTTTTTCCAAAAT-AAAGCACAAACGAATTGC
127 AATATCGACACTCTTTAAATACGTGTCGATACATTTTTT-CAAAATGAAAG-ACAAACGAAGTGC
62387 ACGCATAAA
190 ACGCATAAA
* * *
62396 GTGTCGATACA-TTTAAAATTGTATCG-TTCTCGAAAACATCGAAACCGAT-ATACATAATGTAA
1 GTGTCGATACATTTTAAAA-AGTATCGATCCTCG-AAACATCGAAACCGATAAT-TATAATGTAA
* * *
62458 TAGGTCAATTTATAATGTAACC
63 CAGGTAAATTTCTAATGTAACC
62480 AGTTTAAATT
Statistics
Matches: 233, Mismatches: 39, Indels: 22
0.79 0.13 0.07
Matches are distributed among these distances:
196 12 0.05
197 56 0.24
198 80 0.34
199 78 0.33
200 7 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTTAAAAAGTATCGATCCTCGAAACATCGAAACCGATAATTATAATGTAACAG
GTAAATTTCTAATGTAACCGGTAGAAATATACCGGATTAATGAGAGAATAGGTCAACATAAAATA
TCGACACTCTTTAAATACGTGTCGATACATTTTTTCAAAATGAAAGACAAACGAAGTGCACGCAT
AAA
Found at i:62627 original size:23 final size:23
Alignment explanation
Indices: 62577--62621 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
62567 TACATATTTT
*
62577 ATTATATAAGCGCGACCTATTAC
1 ATTATATAAGCGCGACCTAATAC
*
62600 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCGACCTAATA
62622 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (23 bp):
ATTATATAAGCGCGACCTAATAC
Found at i:65851 original size:18 final size:18
Alignment explanation
Indices: 65828--65862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65818 TTAGGATTAT
*
65828 CTTTAGATGTTTTATTTC
1 CTTTAGATATTTTATTTC
*
65846 CTTTAGCTATTTTATTT
1 CTTTAGATATTTTATTT
65863 TCTAGGTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (18 bp):
CTTTAGATATTTTATTTC
Found at i:66883 original size:14 final size:14
Alignment explanation
Indices: 66864--66895 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
66854 TCCTATCAAC
66864 TTTCTAACTTAAAA
1 TTTCTAACTTAAAA
66878 TTTCTAACTTAAAA
1 TTTCTAACTTAAAA
66892 TTTC
1 TTTC
66896 AGTATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTCTAACTTAAAA
Found at i:67624 original size:32 final size:31
Alignment explanation
Indices: 67588--67664 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
67578 CGGGGCCGTG
*
67588 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
67620 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
67651 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
67665 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:67647 original size:63 final size:63
Alignment explanation
Indices: 67541--67664 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
67531 CCCTAAGGGA
* * ** *
67541 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
67604 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
67665 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:68579 original size:21 final size:21
Alignment explanation
Indices: 68553--68626 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
68543 CAACGGTCAA
* *
68553 CGGTCGAGTCTGGTCAACGGT
1 CGGTCGGGTCGGGTCAACGGT
68574 CGGTCGGGTCGGGTCAACGGT
1 CGGTCGGGTCGGGTCAACGGT
68595 CGGTCGGGTCGGGTCAACGGT
1 CGGTCGGGTCGGGTCAACGGT
68616 CGGGTCGGGTC
1 C-GGTCGGGTC
68627 AGACCGGTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 41 0.82
22 9 0.18
ACGTcount: A:0.09, C:0.24, G:0.46, T:0.20
Consensus pattern (21 bp):
CGGTCGGGTCGGGTCAACGGT
Found at i:68692 original size:9 final size:10
Alignment explanation
Indices: 68629--68692 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
68619 GTCGGGTCAG
68629 ACCGG-TCAA
1 ACCGGTTCAA
* *
68638 ACCGATTCAG
1 ACCGGTTCAA
*
68648 ACTGG-TCAA
1 ACCGGTTCAA
*
68657 ACCGGTTCGA
1 ACCGGTTCAA
*
68667 ACCGGTTGAA
1 ACCGGTTCAA
68677 ACCGGTT-AA
1 ACCGGTTCAA
68686 ACCGGTT
1 ACCGGTT
68693 TCCAGCAGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 20 0.45
10 24 0.55
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:74967 original size:32 final size:31
Alignment explanation
Indices: 74931--75007 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
74921 CGGGGCCGTG
*
74931 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
74963 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
74994 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
75008 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:74990 original size:63 final size:63
Alignment explanation
Indices: 74884--75007 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
74874 CCCTAAGGGA
* * ** *
74884 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
74947 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
75008 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:75907 original size:5 final size:5
Alignment explanation
Indices: 75897--75953 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
75887 AACGGTCAAC
* *
75897 GGTCG GGTCG GGTCG GGTCAAC GGTC- GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
75945 GGTCG GGTC
1 GGTCG GGTC
75954 AGACCGGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 32 0.73
7 8 0.18
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:75922 original size:17 final size:18
Alignment explanation
Indices: 75902--75954 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 18
75892 TCAACGGTCG
75902 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA--G-C
75923 GGTCGGGTCGGGTCAA-C
1 GGTCGGGTCGGGTCAAGC
75940 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
75955 GACCGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.50
21 16 0.50
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAAGC
Found at i:75964 original size:26 final size:22
Alignment explanation
Indices: 75890--75953 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 22
75880 AACGGTCAAC
75890 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
75912 GGTCAACGGTC-GGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
75933 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
75954 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 21 0.51
22 20 0.49
ACGTcount: A:0.09, C:0.23, G:0.48, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:75974 original size:19 final size:18
Alignment explanation
Indices: 75950--76028 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 18
75940 GGTCGGGTCG
75950 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
75968 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
* *
75987 GATTC-GAACCGGTTGAAACC
1 G-GTCAG-ACCGG-TCAAACC
*
76007 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
76026 GGT
1 GGT
76029 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
18 5 0.10
19 38 0.76
20 7 0.14
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:76006 original size:10 final size:10
Alignment explanation
Indices: 75956--76049 Score: 81
Period size: 9 Copynumber: 9.7 Consensus size: 10
75946 GTCGGGTCAG
75956 ACCGG-TCAA
1 ACCGGTTCAA
* *
75965 ACCGGCTCAG
1 ACCGGTTCAA
75975 ACCGG-TCAA
1 ACCGGTTCAA
* *
75984 ACCGATTCGA
1 ACCGGTTCAA
*
75994 ACCGGTTGAA
1 ACCGGTTCAA
76004 ACCGG-TCAA
1 ACCGGTTCAA
76013 ACCGG-TCAGA
1 ACCGGTTCA-A
*
76023 ACCGGTTGAAA
1 ACCGGTT-CAA
76034 ACCGGTT-AA
1 ACCGGTTCAA
76043 ACCGGTT
1 ACCGGTT
76050 TCCAGCAGCC
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
9 32 0.45
10 29 0.41
11 9 0.13
12 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:76009 original size:29 final size:30
Alignment explanation
Indices: 75992--76048 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
75982 AAACCGATTC
75992 GAACCGGTTGAAA-CCGGTCAAACCGGTCA
1 GAACCGGTTGAAAACCGGTCAAACCGGTCA
*
76021 GAACCGGTTGAAAACCGGTTAAACCGGT
1 GAACCGGTTGAAAACCGGTCAAACCGGT
76049 TTCCAGCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.16
Consensus pattern (30 bp):
GAACCGGTTGAAAACCGGTCAAACCGGTCA
Found at i:81811 original size:62 final size:62
Alignment explanation
Indices: 81704--81836 Score: 173
Period size: 62 Copynumber: 2.1 Consensus size: 62
81694 ACTGTTACCA
* *
81704 AATGAATTCCATTGGTAGAGATATATTTATGTTTAACTACTACCGACATTTAAACAATCGAC
1 AATGAATTCAATTGGTAGAGATATACTTATGTTTAACTACTACCGACATTTAAACAATCGAC
* *
81766 AATGAATTCAATTGGTA-ATGATA-ACCTTATGTTTCACTA-TCACCGACATTTAAACAATGGAC
1 AATGAATTCAATTGGTAGA-GATATA-CTTATGTTTAACTACT-ACCGACATTTAAACAATCGAC
*
81828 ATTGAATTC
1 AATGAATTC
81837 CATTAACATT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
61 3 0.05
62 60 0.95
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (62 bp):
AATGAATTCAATTGGTAGAGATATACTTATGTTTAACTACTACCGACATTTAAACAATCGAC
Found at i:85234 original size:47 final size:45
Alignment explanation
Indices: 85140--85265 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
85130 GTAACCATGC
* * *
85140 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
85184 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
85231 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
85266 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Done.