Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007231.1 Hibiscus syriacus cultivar Beakdansim tig00019141_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: 157327
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:3315 original size:15 final size:16
Alignment explanation
Indices: 3288--3324 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3278 CTTTATTATC
3288 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
3304 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
3319 TTATTT
1 TTATTT
3325 TATTCTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:13464 original size:25 final size:23
Alignment explanation
Indices: 13437--13499 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
13427 TAAATCTCCT
13437 AAAGAAATAAAGAAAATGAAAAAATA
1 AAAGAAA-AAAG-AAA-GAAAAAATA
*
13463 AAAGAAAAAAGAAAGAAAAAAGAA
1 AAAGAAAAAAGAAAGAAAAAA-TA
*
13487 AAAGAAAAGAGAA
1 AAAGAAAAAAGAA
13500 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.21
24 16 0.47
25 4 0.12
26 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAGAAAAAAGAAAGAAAAAATA
Found at i:13465 original size:7 final size:7
Alignment explanation
Indices: 13437--13509 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
13427 TAAATCTCCT
13437 AAAGAAA
1 AAAGAAA
13444 TAAAG-AA
1 -AAAGAAA
*
13451 AATGAAA
1 AAAGAAA
*
13458 AAATAAA
1 AAAGAAA
*
13465 AGAAAAAA
1 A-AAGAAA
13473 GAAAGAAA
1 -AAAGAAA
13481 AAAG-AA
1 AAAGAAA
13487 AAAGAAA
1 AAAGAAA
* *
13494 AGAGAAT
1 AAAGAAA
*
13501 AAATAAA
1 AAAGAAA
13508 AA
1 AA
13510 TGGGGTTCAA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
6 9 0.18
7 27 0.53
8 14 0.27
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (7 bp):
AAAGAAA
Found at i:13468 original size:18 final size:18
Alignment explanation
Indices: 13441--13494 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
13431 TCTCCTAAAG
*
13441 AAAT-AAAGAAAATGAAA
1 AAATAAAAGAAAAAGAAA
13458 AAATAAAAGAAAAAAGAAA
1 AAATAAAAG-AAAAAGAAA
*
13477 GAA-AAAAGAAAAAGAAA
1 AAATAAAAGAAAAAGAAA
13494 A
1 A
13495 GAGAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 13 0.41
18 9 0.28
19 10 0.31
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (18 bp):
AAATAAAAGAAAAAGAAA
Found at i:13477 original size:11 final size:11
Alignment explanation
Indices: 13437--13496 Score: 59
Period size: 11 Copynumber: 5.1 Consensus size: 11
13427 TAAATCTCCT
13437 AAAGAAATAAAG
1 AAAGAAA-AAAG
*
13449 AAAATGAAAAAATA
1 -AAA-GAAAAAA-G
13463 AAAGAAAAAAG
1 AAAGAAAAAAG
13474 AAAGAAAAAAG
1 AAAGAAAAAAG
13485 AAA-AAGAAAAG
1 AAAGAA-AAAAG
13496 A
1 A
13497 GAATAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 2 0.05
11 20 0.48
12 7 0.17
13 9 0.21
14 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:13495 original size:18 final size:18
Alignment explanation
Indices: 13437--13496 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
13427 TAAATCTCCT
*
13437 AAAGAAATAAAGAAAATGA
1 AAAGAAA-AAAGAAAAAGA
13456 AAA-AATAAAAGAAAAA-A
1 AAAGAA-AAAAGAAAAAGA
13473 GAAAGAAAAAAGAAAAAGA
1 -AAAGAAAAAAGAAAAAGA
13492 AAAGA
1 AAAGA
13497 GAATAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 28 0.78
19 7 0.19
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAAGA
Found at i:15164 original size:135 final size:134
Alignment explanation
Indices: 14751--15322 Score: 516
Period size: 135 Copynumber: 4.2 Consensus size: 134
14741 ATCAAACTCA
* *
14751 ATTCAATCTTCCCTGAAAAACAGTGGAATGAATCAACA-TCCCTAGATCTGATTTTCCCTGAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTCCC-AGATCTGATTTTCCCTCAAGA
** * * * * *
14815 AATAACGGAACATATCCCCTCTCTTTCCAAATTTGATCTTCCCTAAGTAACAGTGGAACAAGTCC
65 AGCAACAGAACAAATCCCCTCTTTTTCC-AATTTGATCTTCCCTGAGTAACAGTAGAACAAGT-C
*
14880 T-CCTTG
128 TGCCTAG
* * *
14886 ATTCAATCTTCCCTGAAGAACAGTGGAATAAATC-A-ATGTCCTCAAATCTGATTTT-CCTTAAG
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACAT-TCC-CAGATCTGATTTTCCCTCAAG
* * * * *
14948 AAGTAGC-GAAACAAAT-CCCTCTTTTTCTAGATTTGATTTTCCCTGAGTAGA-AATAGAACAAG
64 AAGCAACAG-AACAAATCCCCTCTTTTTCCA-ATTTGATCTTCCCTGAGTA-ACAGTAGAACAAG
*
15010 TTTGCCTCA-
126 TCTGCCT-AG
* * *
15019 ATTCAATCTTCCGTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCAAGAA
* * * *
15084 GCAACATAACAAATCCCCTCTTTTTCCATATTTGATCTTTCCTGAGTAGCAGTATAACAAGTCTG
66 GCAACAGAACAAATCCCCTCTTTTTCCA-ATTTGATCTTCCCTGAGTAACAGTAGAACAAGTCTG
*
15149 CGTAG
130 CCTAG
* * * ** * ** * * *
15154 ATTTAGTCTTCCCTAAAGAACAGTATAATGAAT-AAGTATTTTCAGATCTAAATTTCCCACAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA-CATTCCCAGATCTGATTTTCCCTCAAGA
* * * * * * *
15218 AGCAGCGGAACATATCCCTCTTTCTTTTCGAATTTGATCTTCCCTGAATAACAGTGGAACAAGTC
65 AGCAACAGAACAAATCCC-CTCT-TTTTCCAATTTGATCTTCCCTGAGTAACAGTAGAACAAGTC
*
15283 TGCCTCG
128 TGCCTAG
* * *
15290 ATTCAATCTTCCCTGATGAATAATGGAATGAAT
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAAT
15323 TAATGTTTAC
Statistics
Matches: 353, Mismatches: 66, Indels: 35
0.78 0.15 0.08
Matches are distributed among these distances:
132 2 0.01
133 85 0.24
134 43 0.12
135 154 0.44
136 63 0.18
137 6 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCAAGAA
GCAACAGAACAAATCCCCTCTTTTTCCAATTTGATCTTCCCTGAGTAACAGTAGAACAAGTCTGC
CTAG
Found at i:15519 original size:3 final size:3
Alignment explanation
Indices: 15505--15578 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
15495 GTCCCGATAA
* ** * *
15505 TAT TAA TAT TAT TAT T-T GCT TTAT TAT TAT TCT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
15550 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15579 ACTTTTTCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 3 0.05
3 54 0.92
4 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16732 original size:62 final size:62
Alignment explanation
Indices: 16612--16736 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
16602 AGGGTCGAGG
* * * **
16612 GTTTACCTATGTTCTTTGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTAGAAACATATGGACT
*
16674 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTAGGTTCTTAGAAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTAGAAA-CATATGGACT
16736 G
1 G
16737 GTCATTCGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTAGAAACATATGGACT
Found at i:16733 original size:31 final size:31
Alignment explanation
Indices: 16612--16720 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
16602 AGGGTCGAGG
*
16612 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16643 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16674 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16705 GTTTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
16721 AGAAATCTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:17458 original size:21 final size:21
Alignment explanation
Indices: 17432--17473 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17422 GTAGCAGTAA
*
17432 TGTAGCAGTGAATCGGTACAC
1 TGTAGCAGTGAATCGCTACAC
*
17453 TGTAGCAGTGCATCGCTACAC
1 TGTAGCAGTGAATCGCTACAC
17474 AATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
TGTAGCAGTGAATCGCTACAC
Found at i:22210 original size:19 final size:19
Alignment explanation
Indices: 22158--22211 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
22148 TTATAATTTT
22158 TAATAATTATTTATTATAAA
1 TAAT-ATTATTTATTATAAA
* *
22178 -AATA--A-ATATAATAAA
1 TAATATTATTTATTATAAA
22193 TAATATTATTTATTATAAA
1 TAATATTATTTATTATAAA
22212 AACTTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 9
0.67 0.10 0.23
Matches are distributed among these distances:
15 8 0.31
16 5 0.19
18 2 0.08
19 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTATTTATTATAAA
Found at i:22479 original size:19 final size:21
Alignment explanation
Indices: 22447--22498 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
22437 TTATTTTTTA
*
22447 AAAATAATACTAAA-ATAT-T
1 AAAATAATATTAAAGATATAT
* *
22466 ATATTAATATTAAAGATATAT
1 AAAATAATATTAAAGATATAT
22487 AAAATAATATTA
1 AAAATAATATTA
22499 TTCATCATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 4 0.15
21 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATAATATTAAAGATATAT
Found at i:24791 original size:14 final size:14
Alignment explanation
Indices: 24772--24813 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
24762 CAAGTTAAAC
24772 ATTAATATTAAATT
1 ATTAATATTAAATT
24786 ATTAATATTAAATT
1 ATTAATATTAAATT
*
24800 ATAAATATTTAAAT
1 ATTAATA-TTAAAT
24814 AAAAATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAATATTAAATT
Found at i:24800 original size:11 final size:13
Alignment explanation
Indices: 24766--24814 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
24756 TTTCAACAAG
*
24766 TTAAACATTAATA
1 TTAAATATTAATA
24779 TTAAATTATTAATA
1 TTAAA-TATTAATA
*
24793 TTAAATTATAAATA
1 TTAAA-TATTAATA
24807 TTTAAATA
1 -TTAAATA
24815 AAAATTCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATTAATA
Found at i:25086 original size:3 final size:3
Alignment explanation
Indices: 25078--25104 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25068 CTTTTTTGTA
25078 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
25105 GTTTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25110 original size:6 final size:6
Alignment explanation
Indices: 25101--25128 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25091 ATTATTATTA
25101 TTATGT TTATGT TTATGT TTATGT TTAT
1 TTATGT TTATGT TTATGT TTATGT TTAT
25129 AATTTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
TTATGT
Found at i:25110 original size:18 final size:18
Alignment explanation
Indices: 25078--25128 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
25068 CTTTTTTGTA
25078 TATTATTAT-TATTAT-TAT
1 TATTATTATGT-TTATGT-T
25096 TATTATTATGTTTATGTT
1 TATTATTATGTTTATGTT
25114 TATGT-TTATGTTTAT
1 TAT-TATTATGTTTAT
25129 AATTTTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTATTATGTTTATGTT
Found at i:26985 original size:24 final size:24
Alignment explanation
Indices: 26937--26986 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
26927 CAGTTCGTAT
* * * *
26937 AAAATGCACCGAAGTGTCGCGTAG
1 AAAATGCACCAAAGTGCCACATAG
26961 AAAATGCACCAAAGTGCCACATAG
1 AAAATGCACCAAAGTGCCACATAG
26985 AA
1 AA
26987 TATCCCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAATGCACCAAAGTGCCACATAG
Found at i:27015 original size:21 final size:22
Alignment explanation
Indices: 26977--27030 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
26967 CACCAAAGTG
*
26977 CCACATAGAATATCCCGAATGA
1 CCACATAGAATATCCCGAAAGA
*
26999 CCACATAG-ATGTCCCGAAAGA
1 CCACATAGAATATCCCGAAAGA
* *
27020 CCGCGTAGAAT
1 CCACATAGAAT
27031 TGTCCCAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (22 bp):
CCACATAGAATATCCCGAAAGA
Found at i:27047 original size:23 final size:23
Alignment explanation
Indices: 27008--27052 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
26998 ACCACATAGA
27008 TGTCCCGAAAGACCGCGTAGAAT
1 TGTCCCGAAAGACCGCGTAGAAT
*
27031 TGTCCC-AAAGGATCGCGTAGAA
1 TGTCCCGAAA-GACCGCGTAGAA
27053 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAAGACCGCGTAGAAT
Found at i:31171 original size:2 final size:2
Alignment explanation
Indices: 31166--31196 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31156 TGTGTGTGTG
31166 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 T
31197 TGATTCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31370 original size:23 final size:23
Alignment explanation
Indices: 31338--31390 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
31328 GAACTAATGA
* * *
31338 AACATGCAGTTACATACTTTTAT
1 AACATACAGTTACATACATTCAT
31361 AACATACAGTTACATACATTCAT
1 AACATACAGTTACATACATTCAT
31384 AACATAC
1 AACATAC
31391 TTGAATCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (23 bp):
AACATACAGTTACATACATTCAT
Found at i:31641 original size:22 final size:21
Alignment explanation
Indices: 31616--31659 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
31606 CATCAAAATG
31616 CACAAAGAATGTCCCGAAGGAC
1 CACAAAG-ATGTCCCGAAGGAC
*
31638 CACATAGATGTCCCGAAGGAC
1 CACAAAGATGTCCCGAAGGAC
31659 C
1 C
31660 GTGTAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.23, T:0.11
Consensus pattern (21 bp):
CACAAAGATGTCCCGAAGGAC
Found at i:31680 original size:23 final size:22
Alignment explanation
Indices: 31621--31690 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
31611 AAATGCACAA
* * *
31621 AGAATGTCCCGAAGGACCACAT
1 AGAATTTCCCGAAGGACCGCGT
* *
31643 AG-ATGTCCCGAAGGACCGTGT
1 AGAATTTCCCGAAGGACCGCGT
31664 AGAATTTCCCTGAAGGACCGCGT
1 AGAATTTCCC-GAAGGACCGCGT
31687 AGAA
1 AGAA
31691 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.44
22 8 0.20
23 15 0.37
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (22 bp):
AGAATTTCCCGAAGGACCGCGT
Found at i:36795 original size:29 final size:29
Alignment explanation
Indices: 36754--36940 Score: 254
Period size: 29 Copynumber: 6.6 Consensus size: 29
36744 CACATTCGAA
*
36754 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
36783 AATTCCCAGAATGTTACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
36812 AATTCCCAGAATGTTACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
36841 AATTTCCAAAATGTCACATTTTTTAAAAA
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
36870 AAATCCC---CTATCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
36896 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
36925 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
36941 TCGGGTCGGG
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
26 21 0.15
29 117 0.85
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:37687 original size:10 final size:10
Alignment explanation
Indices: 37672--37701 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
37662 TTTATTTTAG
37672 TCACCAAATT
1 TCACCAAATT
37682 TCACCAAATT
1 TCACCAAATT
37692 TCACCAAATT
1 TCACCAAATT
37702 ACTTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (10 bp):
TCACCAAATT
Found at i:44145 original size:29 final size:29
Alignment explanation
Indices: 44107--44263 Score: 208
Period size: 29 Copynumber: 5.3 Consensus size: 29
44097 AAAAATTTCC
44107 AAATGTCACCTTTTTCAAAATAATTCCCA
1 AAATGTCACCTTTTTCAAAATAATTCCCA
*
44136 AAATATCACCTTTTTCAAAATAATTCCCA
1 AAATGTCACCTTTTTCAAAATAATTCCCA
** *
44165 AAACATCACCTTTTTTTCAAAA-AAATCCCA
1 AAATGTCACC--TTTTTCAAAATAATTCCCA
*
44195 AAATGTCACATTTTTTCAAAATAATTCCCA
1 AAATGTCAC-CTTTTTCAAAATAATTCCCA
* * *
44225 AAATGTCACATTTTTTAAATTAATTCCCA
1 AAATGTCACCTTTTTCAAAATAATTCCCA
44254 AAATGTCACC
1 AAATGTCACC
44264 GGGTCGGGTC
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
29 73 0.65
30 30 0.27
31 10 0.09
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATGTCACCTTTTTCAAAATAATTCCCA
Found at i:44293 original size:17 final size:17
Alignment explanation
Indices: 44271--44305 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44261 ACCGGGTCGG
44271 GTCAACGGGTCGGGTCA
1 GTCAACGGGTCGGGTCA
44288 GTCAACGGGTCGGGTCA
1 GTCAACGGGTCGGGTCA
44305 G
1 G
44306 ATCAGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCA
Found at i:44304 original size:13 final size:13
Alignment explanation
Indices: 44258--44287 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
44248 TTCCCAAAAT
*
44258 GTCACCGGGTCGG
1 GTCAACGGGTCGG
44271 GTCAACGGGTCGG
1 GTCAACGGGTCGG
44284 GTCA
1 GTCA
44288 GTCAACGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.43, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:55609 original size:14 final size:14
Alignment explanation
Indices: 55590--55642 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
55580 TTATAACTGC
55590 AAAAATTAATAAAA
1 AAAAATTAATAAAA
* *
55604 AAAAATTAGTATAAT
1 AAAAATTAATA-AAA
*
55619 AAAATTTAATAAAA
1 AAAAATTAATAAAA
55633 TAATAAATTA
1 -AA-AAATTA
55643 TTGATTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.40
15 13 0.43
16 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAAATTAATAAAA
Found at i:60765 original size:2 final size:2
Alignment explanation
Indices: 60701--60745 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
60691 TTTTTTTATG
60701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
60742 AT AT
1 AT AT
60746 TAAATTGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64255 original size:21 final size:22
Alignment explanation
Indices: 64222--64270 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
64212 AAAACAATAC
*
64222 AAAAAATCAATATTATAAA-CTT
1 AAAATATCAATATT-TAAATCTT
*
64244 AAAATATC-ATATTTAAATTTT
1 AAAATATCAATATTTAAATCTT
64265 AAAATA
1 AAAATA
64271 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 13 0.54
22 7 0.29
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATATCAATATTTAAATCTT
Found at i:68065 original size:55 final size:55
Alignment explanation
Indices: 67484--68064 Score: 873
Period size: 55 Copynumber: 10.6 Consensus size: 55
67474 ATAGTCCTTT
* *
67484 AGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * *
67539 AGAGAGTATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCCATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
67594 AGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
67647 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * *
67702 AGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * *
67755 AGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
67810 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * * * *
67865 AGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCTCCCTATTTCCTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
67920 AGAGAGTATAAGACTCGAACAATCTTCAATGATCGCGTCTGCCCTCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * ** *
67975 AGAGAGTATAAGACCCGAACAATCTTCAACGATCGTGTCCACCCCCTATTTCTTT
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
68030 AGAGAGTATGAGACTTGAACAATCTTCAACGATCG
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCG
68065 TAGGGAACCT
Statistics
Matches: 475, Mismatches: 47, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
53 97 0.20
54 2 0.00
55 376 0.79
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
Found at i:87007 original size:19 final size:20
Alignment explanation
Indices: 86973--87010 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
86963 ATTAAATAAT
86973 AATTATATATTTACTAAATG
1 AATTATATATTTACTAAATG
*
86993 AATTATTTA-TTACTAAAT
1 AATTATATATTTACTAAAT
87011 TCGGATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTATATATTTACTAAATG
Found at i:88768 original size:135 final size:134
Alignment explanation
Indices: 88519--88970 Score: 601
Period size: 134 Copynumber: 3.4 Consensus size: 134
88509 GAATAAGTTC
* *
88519 TTCTCATTATGAA---CTTCTCCCTCTTTCAGATGAGTTCTTCTCATTATGAAACTCTCAATTGG
1 TTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAACTCTCAA-TGG
*
88581 AAATGTCAA----T---GGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCAAAC
65 AAATGTCAATCCCTCAAGGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAAC
88639 AAGCT
130 AAGCT
88644 ATTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATG-AACTCTCAATGG
1 -TTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAACTCTCAATGG
*
88708 AAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGGCGTGAATCGAGTGATAGGTCGAA
65 AAATGTCAATCCCTCAAG-GAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAA
88773 CAAGC-
129 CAAGCT
** * * *
88778 TTCTCATTATGAACTTCTTCTCGTTCTGTTGGATGAGTTCTTCTCATTATG-AACTTTTCACTGG
1 TTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAAC-TCTCAATGG
** ** *
88842 AAATGTTGATCCCTCAAGCGAGGCATCACTGATTTGAAATGCCGTGAATCGAGTGATAGGTCGAA
65 AAATGTCAATCCCTCAAG-GAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAA
*
88907 CAAACT
129 CAAGCT
*
88913 CTT-TCATTATGAACTTCTTCTCCCTCTGTCGGATAAGTT-TTCTCATTATGAAACTCTC
1 -TTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAACTCTC
88971 CATTGGAATG
Statistics
Matches: 289, Mismatches: 22, Indels: 22
0.87 0.07 0.07
Matches are distributed among these distances:
126 13 0.04
127 12 0.04
128 9 0.03
129 33 0.11
131 1 0.00
133 51 0.18
134 84 0.29
135 84 0.29
136 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (134 bp):
TTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAACTCTCAATGGA
AATGTCAATCCCTCAAGGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACA
AGCT
Found at i:88981 original size:134 final size:133
Alignment explanation
Indices: 88532--88983 Score: 557
Period size: 135 Copynumber: 3.4 Consensus size: 133
88522 TCATTATGAA
* *
88532 CTTCTCCCTCTTTCAGATGAGTTCTTCTCATTATGAAACTCTCAATTGGAAA---TG-----TCA
1 CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATG-AACTCTCAA-TGGAAATGTTGATCCCTCA
** *
88589 ATG-GAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCAAACAAGCTATTCTCATT
64 A-GCGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCT-TT-TCATT
88653 ATGAACTT
126 ATGAACTT
**
88661 CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATGGAAATGTCAATCCCTCAAG
1 CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATGGAAATGTTGATCCCTCAAG
* ** * *
88726 TGAGGTGTCACTGATTCGAAATGGCGTGAATCGAGTGATAGGTCGAACAAGCTTCTCATTATGAA
66 CGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTTTTCATTATGAA
88791 CTT
131 CTT
** * * *
88794 CTTCTCGTTCTGTTGGATGAGTTCTTCTCATTATGAACTTTTCACTGGAAATGTTGATCCCTCAA
1 CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAC-TCTCAATGGAAATGTTGATCCCTCAA
* *
88859 GCGAGGCATCACTGATTTGAAATGCCGTGAATCGAGTGATAGGTCGAACAAACTCTTTCATTATG
65 GCGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCT-TTTCATTATG
88924 AACTT
129 AACTT
* *
88929 CTTCTCCCTCTGTCGGATAAGTT-TTCTCATTATGAAACTCTCCATTGG-AATGTTG
1 CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATG-AACTCT-CAATGGAAATGTTG
88984 GTTCACTCAT
Statistics
Matches: 283, Mismatches: 27, Indels: 21
0.85 0.08 0.06
Matches are distributed among these distances:
127 6 0.02
128 9 0.03
129 33 0.12
133 48 0.17
134 92 0.33
135 95 0.34
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (133 bp):
CTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATGGAAATGTTGATCCCTCAAG
CGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTTTTCATTATGAA
CTT
Found at i:97216 original size:6 final size:6
Alignment explanation
Indices: 97205--97229 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
97195 TTATACAAAG
97205 ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA A
97230 AGGTATCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:103722 original size:146 final size:146
Alignment explanation
Indices: 103487--103855 Score: 578
Period size: 146 Copynumber: 2.5 Consensus size: 146
103477 TCTGCCGTCA
* * * * * *
103487 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-CATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * **
103551 CGTTCGGAATATTGATCGCAGATTCCGATCACCGGCAAGAGGCTAAAAACCGTCCGGATTTATTT
65 CGTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTT
103616 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCACCG
103633 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
* * *
103698 GTTCGGAATATTGATCAAATATTCCGATCACTGGAAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
*
103763 CTCCGATTCGTCACCG
131 CTCCGATCCGTCACCG
*
103779 TCCACCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
103844 GTTCGGAATATT
66 GTTCGGAATATT
103856 TATCGGAGAT
Statistics
Matches: 206, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 203 0.99
147 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (146 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
CTCCGATCCGTCACCG
Found at i:104531 original size:55 final size:54
Alignment explanation
Indices: 104437--104718 Score: 198
Period size: 55 Copynumber: 5.1 Consensus size: 54
104427 TAACTAAATG
* *
104437 AGACTTGAAAAATCTTCGGAAAACGTGTCCGCTCTCTATTCTTTCAGAGAGTAT
1 AGACTTGAACAATCTTCGGAAAACGTGTACGCTCTCTATTCTTTCAGAGAGTAT
* * *
104491 AAGACTTGAACAATCTTC-GACCAACGTGTATGCT-TCCTATTCTTTCAGGGAGTAT
1 -AGACTTGAACAATCTTCGGA-AAACGTGTACGCTCT-CTATTCTTTCAGAGAGTAT
* * * * * * * *
104546 AGAACTCGAACAACCTTCTGAAACCGGGTTCGCTCCCTATTGCTTT-AGGGAGTAT
1 AG-ACTTGAACAATCTTCGGAAAACGTGTACGCTCTCTATT-CTTTCAGAGAGTAT
* * * * *
104601 AGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCATCT-TTCTTTCAGGGAGTAT
1 AG-ACTTGAACAATCTTCGGAAAACGTGTACGCT-C-TCTATTCTTTCAGAGAGTAT
* * * * *
104657 AAAACTCGAACAATCTTC-AAAAATCGTGT-CTACTCTCTATTTCTTGCAGAGAGTAT
1 -AGACTTGAACAATCTTCGGAAAA-CGTGTAC-GCTCTCTA-TTCTTTCAGAGAGTAT
104713 AAGACT
1 -AGACT
104719 CGGACCATCT
Statistics
Matches: 190, Mismatches: 23, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
54 8 0.04
55 121 0.64
56 58 0.31
57 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (54 bp):
AGACTTGAACAATCTTCGGAAAACGTGTACGCTCTCTATTCTTTCAGAGAGTAT
Found at i:104966 original size:54 final size:54
Alignment explanation
Indices: 104537--105486 Score: 1252
Period size: 54 Copynumber: 17.5 Consensus size: 54
104527 CTATTCTTTC
* * * * * * *
104537 AGGGAGTATAGAACTCGAACAACCTTC-TGAAACCGGGTTCGCTCCCTATTGCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTCGCTCCCTCTTTCTCT
* * ** * *
104592 AGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCATCTTTCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
** * ** * * * *
104647 CAGGGAGTATAAAACTCGAACAATCTTC-AAAAATCGTG-TCTACTCTCTATTTCT-T
1 -AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTC-GCTCCCTCTTTCTCT
* * ** * *
104702 GCAGAGAGTAT-AAGACTCGGACCATCTTCAACAAACGGGTTCACTCCCTCTTTCTTT
1 --AGGGAGTATGGA-ACTCGGA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* ** *
104759 CAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGGTTCACTCCCTCTTTCTCT
1 -AGGGAGTATGGAACTCGGACATCTTCTTCAAAC-GGGTTCGCTCCCTCTTTCTCT
* * * * *
104815 AGGGAGTATGGAACTCAGACATC-TCTTCAAATGGGTTCACTCCTTCTTTCTTT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
104868 AAGGAGTATGGAACTCGGATATC-TCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
104921 AGGAAGTATGGAACTCGGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
104975 AGGGAGTATGGAACTCGGATATCTTCTTCAAATGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
105029 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
105083 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCCCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
105137 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
105191 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
105245 AGGGAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
105299 AGGGAGTATGGAACTCGTACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
105353 AGGGAGTATCGAACTCGTACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
105407 AGGGAGTATGGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
105459 AGGGAGTATGGAACTCGAAAATCTTCTT
1 AGGGAGTATGGAACTCGGACATCTTCTT
105487 TTGCTTCACT
Statistics
Matches: 820, Mismatches: 60, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
52 50 0.06
53 85 0.10
54 480 0.59
55 85 0.10
56 111 0.14
57 9 0.01
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:105924 original size:36 final size:36
Alignment explanation
Indices: 105847--106048 Score: 124
Period size: 36 Copynumber: 5.6 Consensus size: 36
105837 GCTCCAACAC
* * * * *
105847 TCTTATGA-GAAGGCTTAAAATGGATTTCCTTCACGAC
1 TCTT-TGATGAAGACTTAAGATGG-TTTGCTTCACTAT
** *
105884 TCTTTGATGAAGACACAAGATGGTTTGCTTCATTAT
1 TCTTTGATGAAGACTTAAGATGGTTTGCTTCACTAT
* * * *
105920 TCTTTGGTGCATG-CTTAAGACGGTTTGCTTCACTAC
1 TCTTTGATG-AAGACTTAAGATGGTTTGCTTCACTAT
*
105956 TCTTT-AGTGAAGGCTTAAGATGG-TTGCTTCACTAT
1 TCTTTGA-TGAAGACTTAAGATGGTTTGCTTCACTAT
* * * * * **
105991 TATTTGGTGAAGACTTCAGATTGATCTGCTTCACTCC
1 TCTTTGATGAAGACTTAAGA-TGGTTTGCTTCACTAT
* * *
106028 TCTTCGGTGAAGGCTTAAGAT
1 TCTTTGATGAAGACTTAAGAT
106049 TGACTTTGCT
Statistics
Matches: 127, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
35 28 0.22
36 57 0.45
37 42 0.33
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (36 bp):
TCTTTGATGAAGACTTAAGATGGTTTGCTTCACTAT
Found at i:107388 original size:125 final size:123
Alignment explanation
Indices: 107169--107528 Score: 436
Period size: 125 Copynumber: 2.9 Consensus size: 123
107159 ATCTTACATT
* * * * *
107169 GGTACGGGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCT-TGCTCTCAATGCCTTCTTGG
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCT-TC-ATGCCTTATTGG
* * *
107233 TCTGAATCTTGTCATCTTC-ACACGATGTGGGTGCAGTCATGCCCCATCAGTGTCTTATACC
64 TCTGAATCTTGTCATC-TCAACATGATGTGGGTTCAGTCGTGCCCCAT-AGTGTCTTATACC
* ** *
107294 GGTATGGGCCTTCAAAAAACCCCATCACCTCAAATTGTAAGGCTCCTTCTTCATGCCTTTTTGGT
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCT-CTTCTTCATGCCTTATTGGT
* * * * * *
107359 TTAAATCTTGTCATCTCAACATGACGTGGGTTCAGTCGTACCCCAATATTGTCTTATACT
65 CTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC-ATAGTGTCTTATACC
* * * *
107419 GGTACGGGCCTTTAAAATGCCTCATCACCTCAAATTCTAAGGCTCATTCTTCATGCCTCATTGGT
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTC-TTCTTCATGCCTTATTGGT
*
107484 CTGAATCTTGTCATCTCAACCTGATGTGGGTTCAGTCGTGCCCCA
65 CTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCA
107529 ACATATCCTA
Statistics
Matches: 200, Mismatches: 30, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
124 4 0.02
125 189 0.94
126 4 0.02
127 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (123 bp):
GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCTTCATGCCTTATTGGTC
TGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCATAGTGTCTTATACC
Found at i:108864 original size:45 final size:46
Alignment explanation
Indices: 108761--108867 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 46
108751 TTTGGGTGAG
*
108761 TTTTCT-TTCATTCTCTTTTTTATATTTTCATTTTTTCATTTACAA
1 TTTTCTCTTCTTTCTCTTTTTTATATTTTCATTTTTTCATTTACAA
* * * *
108806 TTTTTTCTT-TTTCTTTTTTTTATCTTTTC-TTTTTCTCTTTTA-ACA
1 TTTTCTCTTCTTTCTCTTTTTTATATTTTCATTTTT-TCATTTACA-A
108851 -TTTCTCTTCTTTCTCTT
1 TTTTCTCTTCTTTCTCTT
108868 CATGACGTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
44 13 0.25
45 36 0.71
46 2 0.04
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (46 bp):
TTTTCTCTTCTTTCTCTTTTTTATATTTTCATTTTTTCATTTACAA
Found at i:112834 original size:21 final size:23
Alignment explanation
Indices: 112809--112851 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
112799 ATGTTTTGCC
112809 ATTTTAAATAAAA-AA-AAATTA
1 ATTTTAAATAAAACAACAAATTA
*
112830 ATTTTAATTAAAACAACAAATT
1 ATTTTAAATAAAACAACAAATT
112852 TAGGTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTTTAAATAAAACAACAAATTA
Found at i:114503 original size:146 final size:146
Alignment explanation
Indices: 114228--114599 Score: 541
Period size: 146 Copynumber: 2.6 Consensus size: 146
114218 TCTTCCGTCA
* * * * ** *
114228 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-AATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * ** *
114292 CG-TCGGAATATTGATCGCAGATTCCGATCACCGGCAAGAGGCTAAAAACCGTCTGGATTTATTT
65 CGTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTT
114356 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCACCG
*
114373 TCCACCGTCCGATCGTTCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
* * *
114438 GTTCGGAATATTGATCAAATATTTCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
*
114503 CTCCGATTCGTCACCG
131 CTCCGATCCGTCACCG
* *
114519 TCCACCGTCTGATCATCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
114584 GTTCGGAATATTGATC
66 GTTCGGAATATTGATC
114600 GGAGATCCTG
Statistics
Matches: 204, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
145 55 0.27
146 149 0.73
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (146 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
CTCCGATCCGTCACCG
Found at i:116400 original size:3 final size:3
Alignment explanation
Indices: 116392--116441 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
116382 AATATTGTAA
* * *
116392 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT ACT -AT AGT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
116437 AAT AA
1 AAT AA
116442 ATATAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.92
4 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:116447 original size:12 final size:13
Alignment explanation
Indices: 116392--116449 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
116382 AATATTGTAA
116392 AATAATAAT-AAT
1 AATAATAATAAAT
116404 AATAATAAT-AAT
1 AATAATAATAAAT
* * *
116416 AATCATACTATAGT
1 AATAATAATA-AAT
116430 ATATAATAATAAAT
1 A-ATAATAATAAAT
116444 -ATAATA
1 AATAATA
116450 TATATTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 25 0.68
14 5 0.14
15 7 0.19
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:117204 original size:28 final size:27
Alignment explanation
Indices: 117120--117207 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 27
117110 TTTAAAGTTG
* *
117120 TGAACAATCTAATTTCATCCTCAAATTA
1 TGAACATTCTAATTTTATCCT-AAATTA
* * * *
117148 TGATCATCATTCTAAATTTGTCCCGAAATTT
1 TGA--A-CATTCTAATTTTAT-CCTAAATTA
117179 TGAACATTCTAATTTTATCTCTAAATTA
1 TGAACATTCTAATTTTATC-CTAAATTA
117207 T
1 T
117208 CGATATATGC
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
27 1 0.02
28 22 0.49
29 1 0.02
30 1 0.02
31 18 0.40
32 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (27 bp):
TGAACATTCTAATTTTATCCTAAATTA
Found at i:117346 original size:60 final size:60
Alignment explanation
Indices: 117280--117395 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
117270 ATGGTTCTGC
* *
117280 GACTATA-GGATATTGCTTTATTAAGTCTCC-CGATTATTAAAAGTTACAAAATGGTCCCCT
1 GACTATAGGGA-ATTGCTTTATTAAG-CCCCTCGACTATTAAAAGTTACAAAATGGTCCCCT
* * *
117340 GACTATAGGGAGTTGCTTTGTTGAGCCCCTCGACTATTAAAAGTTACAAAATGGTC
1 GACTATAGGGAATTGCTTTATTAAGCCCCTCGACTATTAAAAGTTACAAAATGGTC
117396 ACTCGACTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 43 0.88
61 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (60 bp):
GACTATAGGGAATTGCTTTATTAAGCCCCTCGACTATTAAAAGTTACAAAATGGTCCCCT
Found at i:117712 original size:31 final size:31
Alignment explanation
Indices: 117677--117772 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
117667 ACAATTTTGT
117677 AACTTTTAACAGTCGAGAGACTCAACAAAGC
1 AACTTTTAACAGTCGAGAGACTCAACAAAGC
* *** *
117708 AACTTCCTATA-A-TCG-GAGGA-TCAA-TTTGT
1 AACTT-TTA-ACAGTCGAGA-GACTCAACAAAGC
*
117737 AACTTTTAACAGTCGAAAGACTCAACAAAGC
1 AACTTTTAACAGTCGAGAGACTCAACAAAGC
117768 AACTT
1 AACTT
117773 CGGGTCTATT
Statistics
Matches: 46, Mismatches: 11, Indels: 16
0.63 0.15 0.22
Matches are distributed among these distances:
27 1 0.02
28 3 0.07
29 11 0.24
30 11 0.24
31 16 0.35
32 3 0.07
33 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (31 bp):
AACTTTTAACAGTCGAGAGACTCAACAAAGC
Found at i:117772 original size:60 final size:60
Alignment explanation
Indices: 117610--117773 Score: 242
Period size: 60 Copynumber: 2.7 Consensus size: 60
117600 TTAAGTGACT
* * * * *
117610 ATTTTGTAACTTTTAATAGTC-AAGAGATTCAACAAAGTAACTCCCTATAGTCGGAGGACA
1 ATTTTGTAACTTTTAACAGTCGAA-AGACTCAACAAAGCAACTTCCTATAATCGGAGGACA
*
117670 ATTTTGTAACTTTTAACAGTCGAGAGACTCAACAAAGCAACTTCCTATAATCGGAGGATCA
1 ATTTTGTAACTTTTAACAGTCGAAAGACTCAACAAAGCAACTTCCTATAATCGGAGGA-CA
117731 A-TTTGTAACTTTTAACAGTCGAAAGACTCAACAAAGCAACTTC
1 ATTTTGTAACTTTTAACAGTCGAAAGACTCAACAAAGCAACTTC
117774 GGGTCTATTT
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
60 91 0.96
61 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (60 bp):
ATTTTGTAACTTTTAACAGTCGAAAGACTCAACAAAGCAACTTCCTATAATCGGAGGACA
Found at i:120698 original size:27 final size:27
Alignment explanation
Indices: 120668--120728 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
120658 AAAAATTGGA
120668 TAGAATGATAAATTTAAGAGTTGCATT
1 TAGAATGATAAATTTAAGAGTTGCATT
* *** *
120695 TAGAATGCTTTGTTTATGAGTTGCATT
1 TAGAATGATAAATTTAAGAGTTGCATT
120722 TAGAATG
1 TAGAATG
120729 CTTTGTCTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (27 bp):
TAGAATGATAAATTTAAGAGTTGCATT
Found at i:120729 original size:27 final size:27
Alignment explanation
Indices: 120680--120734 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
120670 GAATGATAAA
120680 TTTAAGAGTTGCATTTAGAATGCTTTG
1 TTTAAGAGTTGCATTTAGAATGCTTTG
*
120707 TTTATGAGTTGCATTTAGAATGCTTTG
1 TTTAAGAGTTGCATTTAGAATGCTTTG
120734 T
1 T
120735 CTAGCCTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
TTTAAGAGTTGCATTTAGAATGCTTTG
Found at i:122818 original size:15 final size:15
Alignment explanation
Indices: 122798--122828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
122788 CAACATATAG
122798 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
122813 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
122828 A
1 A
122829 TTTAAAATTT
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:123008 original size:20 final size:20
Alignment explanation
Indices: 122983--123033 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
122973 ATCCTATTCT
122983 CTGGTAATCTTTTACTCCCA
1 CTGGTAATCTTTTACTCCCA
*
123003 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTACTCCCA
* *
123023 TTAGTAATCTT
1 CTGGTAATCTT
123034 ACATTCCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTACTCCCA
Found at i:132204 original size:2 final size:2
Alignment explanation
Indices: 132197--132227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
132187 GCATACCCAG
132197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
132228 CAATAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141853 original size:83 final size:84
Alignment explanation
Indices: 141682--141854 Score: 186
Period size: 83 Copynumber: 2.1 Consensus size: 84
141672 GATGCTTGTT
* *
141682 TTCATTCTCATCCCCCTTGCAAATCAATGGAGCATTCATCGCAACAGTGGGTAGAATTTCTGAGT
1 TTCATTCTCATCCCCCTTGAAAATCAATGGAGCATTCATCGCAACAGTGGGTAGAATTTCGGAGT
**** * *****
141747 ATTTGTTATTTAAGTGTTT
66 ATTCAAAATCTAAGCAAAA
* * * *
141766 TTCATTCTCATCCCCC-TGAAAATCAATGGAGCATTCATGGGAATAGTGGGTAGAATTTCGGGGT
1 TTCATTCTCATCCCCCTTGAAAATCAATGGAGCATTCATCGCAACAGTGGGTAGAATTTCGGAGT
*
141830 ATTCAAAATCTGAGCAAAA
66 ATTCAAAATCTAAGCAAAA
141849 TTCATT
1 TTCATT
141855 TTGAGTATTT
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
83 56 0.78
84 16 0.22
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (84 bp):
TTCATTCTCATCCCCCTTGAAAATCAATGGAGCATTCATCGCAACAGTGGGTAGAATTTCGGAGT
ATTCAAAATCTAAGCAAAA
Found at i:145267 original size:19 final size:19
Alignment explanation
Indices: 145233--145269 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
145223 ATGACCAACA
* *
145233 AAATCGCAATGTGATCTCT
1 AAATCGCAACGCGATCTCT
145252 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
145270 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:145528 original size:22 final size:21
Alignment explanation
Indices: 145500--145550 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 21
145490 ACTCTCTCGG
145500 CGACATCCGTTCCTATATCCAA
1 CGACATCC-TTCCTATATCCAA
145522 CGACA----TCCTATATCCAA
1 CGACATCCTTCCTATATCCAA
145539 CGACATCCTTCC
1 CGACATCCTTCC
145551 CATCCGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
17 17 0.68
21 3 0.12
22 5 0.20
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.25
Consensus pattern (21 bp):
CGACATCCTTCCTATATCCAA
Found at i:145532 original size:17 final size:17
Alignment explanation
Indices: 145510--145547 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
145500 CGACATCCGT
145510 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
145527 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
145544 TCCT
1 TCCT
145548 TCCCATCCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:146224 original size:24 final size:24
Alignment explanation
Indices: 146197--146250 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
146187 GTATTCGAAA
*
146197 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
146221 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
146245 TTTGAT
1 TTTGAT
146251 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:148728 original size:20 final size:20
Alignment explanation
Indices: 148682--148815 Score: 189
Period size: 20 Copynumber: 6.8 Consensus size: 20
148672 TTACACATTC
* **
148682 ATTTGAATATCGCAGTGCGA
1 ATTTGACTATCGCAACGCGA
* *
148702 A-TTGACTATCACAACACGA
1 ATTTGACTATCGCAACGCGA
148721 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
148741 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
148761 ATTTGATTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
148781 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
148801 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
148816 ATCAGACAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
19 14 0.14
20 88 0.86
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:149589 original size:21 final size:21
Alignment explanation
Indices: 149565--149660 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
149555 GCACCTTTTC
149565 AACGATGACAGGAGCCTCTTG
1 AACGATGACAGGAGCCTCTTG
* ** * *
149586 AACGGTGGGAGGGGACTCTTG
1 AACGATGACAGGAGCCTCTTG
** * *
149607 AGGGATGATAGGGGCCTCTTG
1 AACGATGACAGGAGCCTCTTG
*
149628 AACGAT-A-GGAGAGGCCTCTTG
1 AACGATGACAG-GA-GCCTCTTG
149649 AACGATGACAGG
1 AACGATGACAGG
149661 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 16, Indels: 7
0.71 0.21 0.09
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 49 0.89
22 2 0.04
23 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.19
Consensus pattern (21 bp):
AACGATGACAGGAGCCTCTTG
Found at i:149614 original size:42 final size:42
Alignment explanation
Indices: 149565--149660 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
149555 GCACCTTTTC
* * *
149565 AACGATGACAGGAGCCTCTTGAACGGTGGGAGGGGACTCTTG
1 AACGATGACAGGAGCCTCTTGAACGATAGGAGAGGACTCTTG
** * * *
149607 AGGGATGATAGGGGCCTCTTGAACGATAGGAGAGGCCTCTTG
1 AACGATGACAGGAGCCTCTTGAACGATAGGAGAGGACTCTTG
149649 AACGATGACAGG
1 AACGATGACAGG
149661 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.19
Consensus pattern (42 bp):
AACGATGACAGGAGCCTCTTGAACGATAGGAGAGGACTCTTG
Found at i:150161 original size:20 final size:20
Alignment explanation
Indices: 150136--150173 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
150126 AATAGTTTCT
150136 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
150156 GAAACTTAAAATCGCAAC
1 GAAACTTAAAATCGCAAC
150174 GCAAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.24, G:0.11, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:150192 original size:20 final size:20
Alignment explanation
Indices: 150166--150230 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
150156 GAAACTTAAA
150166 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* **
150186 ATTGCAACGCGGAAATGACT
1 ATCGCAACGCAAAAATGACT
* **
150206 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCAAAAATGACT
150226 ATCGC
1 ATCGC
150231 TACGGGATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:150307 original size:20 final size:20
Alignment explanation
Indices: 150278--150315 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
150268 CGAAATTAAA
*
150278 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
150298 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
150316 CGTTGCGATT
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:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:150338 original size:32 final size:34
Alignment explanation
Indices: 150282--150356 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 34
150272 ATTAAATTCG
*
150282 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
*
150316 CGTTGCGATTTT-A-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
150348 CGTTGCGAT
1 CGTTGCGAT
150357 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
32 26 0.67
33 1 0.03
34 12 0.31
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:150392 original size:20 final size:20
Alignment explanation
Indices: 150369--150416 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
150359 TCAAATTCGT
150369 GTTGCGATAGTCATTTCCAC
1 GTTGCGATAGTCATTTCCAC
* *
150389 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTCCAC
150409 GTTGCGAT
1 GTTGCGAT
150417 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCAC
Found at i:152292 original size:20 final size:20
Alignment explanation
Indices: 152269--152374 Score: 99
Period size: 20 Copynumber: 5.4 Consensus size: 20
152259 TATGAAACTT
*
152269 AAAATCGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
152289 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
152309 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
152329 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
152348 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
152367 AAAATCGC
1 AAAATCGC
152375 GTTGTGATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
19 23 0.31
20 51 0.69
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:153029 original size:21 final size:21
Alignment explanation
Indices: 153005--153051 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
152995 TATTCGCATT
*
153005 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
153026 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
153047 GCGAT
1 GCGAT
153052 AGTAAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:153108 original size:20 final size:19
Alignment explanation
Indices: 153085--153130 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
153075 GGAAACTGAT
* *
153085 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
153105 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
153124 TTGCGAT
1 TTGCGAT
153131 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:153120 original size:19 final size:19
Alignment explanation
Indices: 153096--153132 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
153086 TGCGATACTG
*
153096 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
153115 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
153133 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Done.