Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001022.1 Hibiscus syriacus cultivar Beakdansim tig00002035_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: 67531
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2792 original size:12 final size:12
Alignment explanation
Indices: 2775--2803 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2765 TGTTAGCAAC
2775 TTATCTCTTGCA
1 TTATCTCTTGCA
2787 TTATCTCTTGCA
1 TTATCTCTTGCA
2799 TTATC
1 TTATC
2804 ACAGGCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52
Consensus pattern (12 bp):
TTATCTCTTGCA
Found at i:8382 original size:28 final size:28
Alignment explanation
Indices: 8351--8415 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
8341 CATTGTCTTA
8351 ACGACATAAAATTTTAAGCACTAACTTG
1 ACGACATAAAATTTTAAGCACTAACTTG
*
8379 ACGACATAAAATTTTAAGCACTAGCTTG
1 ACGACATAAAATTTTAAGCACTAACTTG
8407 ACGACATAA
1 ACGACATAA
8416 TCTAAACGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (28 bp):
ACGACATAAAATTTTAAGCACTAACTTG
Found at i:14010 original size:272 final size:272
Alignment explanation
Indices: 13524--14063 Score: 1008
Period size: 272 Copynumber: 2.0 Consensus size: 272
13514 ACAACTAAGT
13524 ACTTAACAAATAATCATATTTAATAAAATTCATTAAGCGATTTTAGTGGTAGAAAAGAGTATTAT
1 ACTTAACAAATAATCATATTTAATAAAATTCATTAAGCGATTTTAGTGGTAGAAAAGAGTATTAT
* *
13589 TCTTCATATGAATTCTGAGTTTGAACAATTGTGTCTGCAGGGTGTATAGATGTTAATAACAAATA
66 TCTTCATATGAATTCTGAGTTTGAACAATTGTGTCTGCAGGGTGCATAGATGTTAATAACAAAGA
*
13654 AAGATTTTAAACAATTACTATTTTATAATCACCCCCGTCTATTAAAAAATAATCATACTTAATAT
131 AAGATTTTAAACAATTACTATTTTATAATCACCCCCGACTATTAAAAAATAATCATACTTAATAT
*
13719 TTATCTTAAACACATACCATGTAATTTATTTCATATACTTATCTATCAATTTCACATACATTCAA
196 CTATCTTAAACACATACCATGTAATTTATTTCATATACTTATCTATCAATTTCACATACATTCAA
13784 CTATTGATTTAC
261 CTATTGATTTAC
*
13796 ACTTAACAAATAATCATATTTAATAAAATTCATTAAGCGATTTTAGTGGTAGAAGAGAGTATTAT
1 ACTTAACAAATAATCATATTTAATAAAATTCATTAAGCGATTTTAGTGGTAGAAAAGAGTATTAT
*
13861 TCTTCATATGAATTCTGAGTTTGAACAGTTGTGTCTGCAGGGTGCATAGATGTTAATAACAAAGA
66 TCTTCATATGAATTCTGAGTTTGAACAATTGTGTCTGCAGGGTGCATAGATGTTAATAACAAAGA
*
13926 AAGATTTTAAACAATTACTATTTTATAATCACCTCCGACTATTAAAAAATAATCATACTTAATAT
131 AAGATTTTAAACAATTACTATTTTATAATCACCCCCGACTATTAAAAAATAATCATACTTAATAT
*
13991 CTATCTTAAACACATACCATGTAATTTATTTCATGTACTTATCTATCAATTTCACATACATTCAA
196 CTATCTTAAACACATACCATGTAATTTATTTCATATACTTATCTATCAATTTCACATACATTCAA
14056 CTATTGAT
261 CTATTGAT
14064 ACTTTAGACT
Statistics
Matches: 260, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
272 260 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (272 bp):
ACTTAACAAATAATCATATTTAATAAAATTCATTAAGCGATTTTAGTGGTAGAAAAGAGTATTAT
TCTTCATATGAATTCTGAGTTTGAACAATTGTGTCTGCAGGGTGCATAGATGTTAATAACAAAGA
AAGATTTTAAACAATTACTATTTTATAATCACCCCCGACTATTAAAAAATAATCATACTTAATAT
CTATCTTAAACACATACCATGTAATTTATTTCATATACTTATCTATCAATTTCACATACATTCAA
CTATTGATTTAC
Found at i:14151 original size:39 final size:39
Alignment explanation
Indices: 14097--14175 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
14087 AAAAGGAATA
14097 TTGAGGTTCTTCATTACATGTCTAGCGTAGAATTACCTC
1 TTGAGGTTCTTCATTACATGTCTAGCGTAGAATTACCTC
14136 TTGAGGTTCTTCATTACATGTCTAGCGTAGAATTACCTC
1 TTGAGGTTCTTCATTACATGTCTAGCGTAGAATTACCTC
14175 T
1 T
14176 GTTCCATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (39 bp):
TTGAGGTTCTTCATTACATGTCTAGCGTAGAATTACCTC
Found at i:15727 original size:22 final size:22
Alignment explanation
Indices: 15679--15719 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
15669 TATATACATA
*
15679 AACAATTATGTTTATTTAGTAT
1 AACATTTATGTTTATTTAGTAT
15701 AACATTTAT-TTTATTTAGT
1 AACATTTATGTTTATTTAGT
15720 TTTAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (22 bp):
AACATTTATGTTTATTTAGTAT
Found at i:15755 original size:25 final size:25
Alignment explanation
Indices: 15726--15773 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
15716 TAGTTTTAAC
*
15726 ATATGTATAATTTAATTAAAATTGT
1 ATATGTATAATTGAATTAAAATTGT
15751 ATATGTATAATTGAATTAAAATT
1 ATATGTATAATTGAATTAAAATT
15774 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (25 bp):
ATATGTATAATTGAATTAAAATTGT
Found at i:15784 original size:25 final size:25
Alignment explanation
Indices: 15728--15784 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
15718 GTTTTAACAT
* ** *
15728 ATGTATAATTTAATTAAAATTGTAT
1 ATGTATAATTGAATTAAAATTAAAA
15753 ATGTATAATTGAATTAAAATTAAAA
1 ATGTATAATTGAATTAAAATTAAAA
*
15778 ATTTATA
1 ATGTATA
15785 CAAGTGAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
ATGTATAATTGAATTAAAATTAAAA
Found at i:15822 original size:18 final size:19
Alignment explanation
Indices: 15795--15833 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
15785 CAAGTGAACA
*
15795 AAAATCAAAAT-TATATAT
1 AAAATCAAAATCCATATAT
*
15813 AAAATTAAAATCCATATAT
1 AAAATCAAAATCCATATAT
15832 AA
1 AA
15834 CACTACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATCAAAATCCATATAT
Found at i:16579 original size:31 final size:31
Alignment explanation
Indices: 16538--16615 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
16528 CAGTTACGTC
16538 AGGGATCATATTGCAAATGGACTAAATGTTG
1 AGGGATCATATTGCAAATGGACTAAATGTTG
*
16569 AGGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGATCATATTGCAAATGGACTAAATGTTG
* *
16600 GGGGATTATATTGCAA
1 AGGGATCATATTGCAA
16616 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (31 bp):
AGGGATCATATTGCAAATGGACTAAATGTTG
Found at i:19364 original size:31 final size:31
Alignment explanation
Indices: 19297--19365 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
19287 CGTCGAAGAC
* *
19297 CATATTACAAACATAATAAATGTTGAGGGAT
1 CATATTGCAAACAGAATAAATGTTGAGGGAT
*
19328 CATATTGCAAACAGACTAAATGTTG-GGAGAT
1 CATATTGCAAACAGAATAAATGTTGAGG-GAT
*
19359 TATATTG
1 CATATTG
19366 TAAGTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (31 bp):
CATATTGCAAACAGAATAAATGTTGAGGGAT
Found at i:19616 original size:39 final size:39
Alignment explanation
Indices: 19558--19638 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
19548 ATGATGTTAT
*
19558 AGGTCAAGACATATCTCAATATATTCAATAGATTTAACA
1 AGGTCAAGACACATCTCAATATATTCAATAGATTTAACA
* *
19597 AGGTCAAGACACATGTCAATGTATTCAATAGATTTAACA
1 AGGTCAAGACACATCTCAATATATTCAATAGATTTAACA
19636 AGG
1 AGG
19639 AGCTCGAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (39 bp):
AGGTCAAGACACATCTCAATATATTCAATAGATTTAACA
Found at i:19860 original size:30 final size:29
Alignment explanation
Indices: 19819--19905 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
19809 CGTTTTGATT
* *
19819 TTAAAAGTATATTTTATT-TTATTCTTGAC
1 TTAAAAATATATTTTATTATTATT-TTAAC
* *
19848 TTATTAAATATATTTTATTCTTATTTTAAC
1 TTA-AAAATATATTTTATTATTATTTTAAC
*
19878 TTAAAAATATATTTTATTATTATCTTAA
1 TTAAAAATATATTTTATTATTATTTTAA
19906 ATATATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 25 0.50
30 20 0.40
31 5 0.10
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (29 bp):
TTAAAAATATATTTTATTATTATTTTAAC
Found at i:19904 original size:24 final size:23
Alignment explanation
Indices: 19863--19916 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
19853 AAATATATTT
19863 TATTCTTATTTTAACTTAAAAATA
1 TATT-TTATTTTAACTTAAAAATA
* *
19887 TATTTTATTATTATCTTAAATATA
1 TATTTTATT-TTAACTTAAAAATA
*
19911 TTTTTT
1 TATTTT
19917 CTTGATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTATTTTAACTTAAAAATA
Found at i:20427 original size:21 final size:23
Alignment explanation
Indices: 20403--20445 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20393 TATTTAATAA
*
20403 ATAAG-AGAAAA-ATTACAAAAC
1 ATAAGTAGAAAATATTAAAAAAC
20424 ATAAGTAGAAAATATTAAAAAA
1 ATAAGTAGAAAATATTAAAAAA
20446 AAACTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (23 bp):
ATAAGTAGAAAATATTAAAAAAC
Found at i:33921 original size:15 final size:15
Alignment explanation
Indices: 33901--33950 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
33891 GATTTTCAGG
33901 AGAAGCAAAAGGAGA
1 AGAAGCAAAAGGAGA
33916 AGAAGCATAAGAAGGAGA
1 AGAAGC--AA-AAGGAGA
* *
33934 AGAAGGAAAAAGAGA
1 AGAAGCAAAAGGAGA
33949 AG
1 AG
33951 GGAGAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 14 0.47
16 2 0.07
17 2 0.07
18 12 0.40
ACGTcount: A:0.60, C:0.04, G:0.34, T:0.02
Consensus pattern (15 bp):
AGAAGCAAAAGGAGA
Found at i:34045 original size:21 final size:22
Alignment explanation
Indices: 33996--34045 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
33986 TGGAAAACAC
* *
33996 AAGGATAAGAAAGACAAAAAAG
1 AAGGAAAACAAAGACAAAAAAG
*
34018 AA-AAAAACAAAGAC-AAAAAG
1 AAGGAAAACAAAGACAAAAAAG
34038 AAGGAAAA
1 AAGGAAAA
34046 AGATCGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.35
21 13 0.57
22 2 0.09
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.02
Consensus pattern (22 bp):
AAGGAAAACAAAGACAAAAAAG
Found at i:37184 original size:17 final size:17
Alignment explanation
Indices: 37164--37197 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37154 AGTTATAAAC
37164 ATATAAGAATAAAAATT
1 ATATAAGAATAAAAATT
37181 ATATAAGAATAAAAATT
1 ATATAAGAATAAAAATT
37198 TATTTTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
ATATAAGAATAAAAATT
Found at i:37554 original size:21 final size:21
Alignment explanation
Indices: 37528--37645 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 21
37518 ATCAGTTTCC
*
37528 AAAATCGCAACGCGATTTTTG
1 AAAATCGCAACGCGATATTTG
* * **
37549 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATATTTG
* ** *
37570 AAATTCGCATTGCGAT-TTTCC
1 AAAATCGCAACGCGATATTT-G
* *
37591 AGAATCGCAACGCGA-ATATG
1 AAAATCGCAACGCGATATTTG
*
37611 AAAATCGCAACGCGA-ATATG
1 AAAATCGCAACGCGATATTTG
37631 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
37646 ACACATAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 35 0.44
21 44 0.56
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATATTTG
Found at i:37685 original size:20 final size:20
Alignment explanation
Indices: 37593--37821 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
37583 GATTTTCCAG
* ** *
37593 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* ** *
37613 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
37633 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37653 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37673 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37693 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37713 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37733 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37753 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37773 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37793 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37813 AATCACAAC
1 AATCGCAAC
37822 ACTGAAATTT
Statistics
Matches: 181, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.01
20 177 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38528 original size:24 final size:24
Alignment explanation
Indices: 38492--38546 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
38482 GTGAGTACTA
* * * *
38492 GTCAGTATTCGAAATTTGGTCTTG
1 GTCAATATCCGAAATTTGATATTG
*
38516 GTCAATATCCGAACTTTGATATTG
1 GTCAATATCCGAAATTTGATATTG
38540 GTCAATA
1 GTCAATA
38547 CACGGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
GTCAATATCCGAAATTTGATATTG
Found at i:38750 original size:12 final size:12
Alignment explanation
Indices: 38733--38757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38723 ATATAATCCT
38733 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38745 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38757 G
1 G
38758 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:41092 original size:33 final size:34
Alignment explanation
Indices: 41050--41234 Score: 155
Period size: 33 Copynumber: 5.2 Consensus size: 34
41040 GTAACGAGAG
* *
41050 AATCTCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
41083 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAA--C--AATGAA
* * * *
41122 AATCGCAACGAGAGAATCG-CAAT-GCGGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACAATGAA
* *
41156 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
41189 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
41227 AATCGCAA
1 AATCGCAA
41235 CGAGAGAATC
Statistics
Matches: 121, Mismatches: 14, Indels: 29
0.74 0.09 0.18
Matches are distributed among these distances:
32 1 0.01
33 46 0.38
34 35 0.29
35 1 0.01
36 1 0.01
37 1 0.01
38 14 0.12
39 21 0.17
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:41118 original size:53 final size:52
Alignment explanation
Indices: 41050--41272 Score: 367
Period size: 53 Copynumber: 4.2 Consensus size: 52
41040 GTAACGAGAG
* * *
41050 AATCTCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
41103 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
41156 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
41208 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
41260 AATCGCATTGCGA
1 AATCGCAATGCGA
41273 TTCTCTCGTT
Statistics
Matches: 164, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
52 71 0.43
53 92 0.56
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:41119 original size:19 final size:19
Alignment explanation
Indices: 41050--41272 Score: 225
Period size: 19 Copynumber: 12.7 Consensus size: 19
41040 GTAACGAGAG
*
41050 AATCTCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41069 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
41083 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
41103 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41122 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41136 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
41156 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41175 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41189 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41208 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41227 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
41241 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
41260 AATCGCATTGCGA
1 AATCGCAATGCGA
41273 TTCTCTCGTT
Statistics
Matches: 172, Mismatches: 10, Indels: 44
0.76 0.04 0.19
Matches are distributed among these distances:
14 42 0.24
15 3 0.02
16 6 0.03
17 8 0.05
18 2 0.01
19 82 0.48
20 29 0.17
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:41193 original size:86 final size:84
Alignment explanation
Indices: 41036--41215 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
41026 CGGAAATTAC
* *
41036 AATCGTAACGAGAGAATCTCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
41101 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
41122 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
41185 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
41208 AATCGCAA
1 AATCGCAA
41216 TGCGAAATGA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 52 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:41245 original size:33 final size:33
Alignment explanation
Indices: 41103--41266 Score: 163
Period size: 33 Copynumber: 4.8 Consensus size: 33
41093 CGGAAATGAA
41103 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
41136 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
41169 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
41208 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
41241 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
41267 TTGCGATTCT
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 52 0.49
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:41299 original size:52 final size:52
Alignment explanation
Indices: 41243--41357 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 52
41233 AACGAGAGAA
*
41243 TCGCAATGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** **
41295 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
41347 TCGCATTGCGA
1 TCGCATTGCGA
41358 TTTTCATTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:41358 original size:52 final size:52
Alignment explanation
Indices: 41262--41377 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
41252 GAAATTAAAA
41262 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATT
*
41314 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATT
41366 TCGCATTGCGAT
1 TCGCATTGCGAT
41378 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATT
Found at i:41385 original size:19 final size:19
Alignment explanation
Indices: 41281--41377 Score: 141
Period size: 19 Copynumber: 5.4 Consensus size: 19
41271 GATTCTCTCG
41281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41300 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41319 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41333 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41352 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41371 TTGCGAT
1 TTGCGAT
41378 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 6 0.09
19 50 0.72
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41503 original size:14 final size:14
Alignment explanation
Indices: 41484--41520 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41474 CATCAATTAC
41484 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
41498 ACAAATCATCTTTT
1 ACAAATCAACTTTT
41512 ACAAATCAA
1 ACAAATCAA
41521 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:43475 original size:19 final size:18
Alignment explanation
Indices: 43450--43585 Score: 126
Period size: 19 Copynumber: 7.8 Consensus size: 18
43440 ACGAAACTTA
43450 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
* **
43468 ATAATCGCAACGAGAAACCA
1 A-AATCGCAACGCGAAA-TG
43488 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
43506 AAAATCGCAA--CGACA-G
1 -AAATCGCAACGCGAAATG
*
43522 -AATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
43539 AAATCGCAA--CGAAA-G
1 AAATCGCAACGCGAAATG
43554 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
43571 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
43586 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 9 0.09
19 49 0.51
20 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:43527 original size:14 final size:14
Alignment explanation
Indices: 43508--43563 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
43498 GCGAAATGAA
*
43508 AATCGCAACGACAG
1 AATCGCAACGAAAG
43522 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
43539 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
43554 AATCGCAACG
1 AATCGCAACG
43564 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:43548 original size:32 final size:33
Alignment explanation
Indices: 43451--43580 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 33
43441 CGAAACTTAA
* *
43451 AATCGCAACGCGAAATGATAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
43489 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
43522 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
43554 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
43581 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
32 30 0.35
33 27 0.31
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:43616 original size:14 final size:14
Alignment explanation
Indices: 43597--43623 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43587 TTTGGTTTCG
43597 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
43611 CGTTGCGATTTTG
1 CGTTGCGATTTTG
43624 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:43623 original size:33 final size:33
Alignment explanation
Indices: 43581--43675 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
43571 AAAATCGCAA
43581 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
43614 TGCGATTTTGGTTTCGCGTTGCGATTCTT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
* **
43647 TTCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
43676 GTTTCGCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.04
33 52 0.93
34 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.26, T:0.51
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:43650 original size:21 final size:19
Alignment explanation
Indices: 43581--43709 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
43571 AAAATCGCAA
43581 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
43600 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
43614 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
43633 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
* **
43647 TTCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
43666 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
43685 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
43705 TGCGA
1 TGCGA
43710 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 21 0.23
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 47 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:43890 original size:93 final size:93
Alignment explanation
Indices: 43754--44032 Score: 514
Period size: 93 Copynumber: 3.1 Consensus size: 93
43744 ATGGATTGCA
43754 TTAC-TTCAACCAAAAGAC-AAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
43816 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
43844 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
43909 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
43937 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
44001 TAGCAGAATTGGCAGCAACCGAA-TAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
44028 TTACT
1 TTACT
44033 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
90 4 0.02
91 22 0.12
92 28 0.15
93 131 0.71
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:45761 original size:20 final size:20
Alignment explanation
Indices: 45730--45826 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
45720 TTTTGGTTGA
45730 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*** *
45750 AATGATTGTCGCAACGAGATA
1 AATGAAAATCGCAACGAGA-G
45771 AATGAAAATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
45789 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
45804 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
45824 AAT
1 AAT
45827 CGCAACGCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 2 0.03
19 14 0.23
20 19 0.32
21 12 0.20
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:45796 original size:14 final size:14
Alignment explanation
Indices: 45777--45833 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
45767 GATAAATGAA
45777 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
45791 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
45810 AATCGCAACGAGAG
1 AATCGCAACGAGAG
45824 AATCGCAACG
1 AATCGCAACG
45834 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:45810 original size:33 final size:33
Alignment explanation
Indices: 45728--45850 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
45718 TCTTTTGGTT
*
45728 GAAATGAAAATCGCAACGAGAGAATGATTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
45767 GATAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAATCGCAACGC
45802 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45835 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
45851 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 48 0.59
35 9 0.11
38 1 0.01
39 1 0.01
40 1 0.01
41 21 0.26
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:45890 original size:14 final size:14
Alignment explanation
Indices: 45873--45904 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
45863 TTCGCGTTAG
45873 GATTCTCTCGTTGC
1 GATTCTCTCGTTGC
45887 GATTCTCTCGTTGC
1 GATTCTCTCGTTGC
45901 GATT
1 GATT
45905 TTCATTTCTC
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:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
GATTCTCTCGTTGC
Found at i:45945 original size:41 final size:41
Alignment explanation
Indices: 45888--45965 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
45878 TCTCGTTGCG
*
45888 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
45929 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
45966 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:45950 original size:20 final size:21
Alignment explanation
Indices: 45889--45964 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
45879 CTCGTTGCGA
45889 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
45910 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
45930 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
45951 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
45965 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:46086 original size:33 final size:33
Alignment explanation
Indices: 46044--46114 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
46034 AATACTAACT
46044 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
***
46077 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
46110 TGAAA
1 TGAAA
46115 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAACAACGCGAAA
Found at i:46515 original size:20 final size:20
Alignment explanation
Indices: 46490--46682 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
46480 CTTTAAATAT
46490 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
46510 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
46532 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
46551 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
46571 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
46591 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
46611 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
46631 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
46651 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
46671 CGCGTTGCGATT
1 CGCGTTGCGATT
46683 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.01
20 131 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:47205 original size:21 final size:21
Alignment explanation
Indices: 47179--47225 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
47169 ATTTACATAT
47179 TCGCATTGCGATAGTCAACTA
1 TCGCATTGCGATAGTCAACTA
*
47200 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCAACTA
47221 TCGCA
1 TCGCA
47226 ACGAATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCAACTA
Found at i:47245 original size:42 final size:42
Alignment explanation
Indices: 47213--47310 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
47203 CATTGCGATA
47213 GTCGACTATCGCAACGAA-TTTGGAATAAATCGCAACGCGAAC
1 GTCGACTATCGCAACGAACTTT-GAATAAATCGCAACGCGAAC
* *
47255 TTGGACTATCGCAACGAACTTTGAATAAATCGCAACGCGAAC
1 GTCGACTATCGCAACGAACTTTGAATAAATCGCAACGCGAAC
* *
47297 TTGGACTATCGCAA
1 GTCGACTATCGCAA
47311 TGCGAATATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 50 0.94
43 3 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GTCGACTATCGCAACGAACTTTGAATAAATCGCAACGCGAAC
Found at i:47307 original size:21 final size:20
Alignment explanation
Indices: 47216--47316 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 20
47206 TGCGATAGTC
*
47216 GACTATCGCAA-CGAATTTG
1 GACTATCGCAAGCGAACTTG
*
47235 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAA-GCGAACTTG
*
47258 GACTATCGCAA-CGAACTTT
1 GACTATCGCAAGCGAACTTG
*
47277 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAA-GCGAACTTG
47300 GACTATCGCAATGCGAA
1 GACTATCGCAA-GCGAA
47317 TATGTAAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
19 13 0.20
21 33 0.50
23 20 0.30
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
GACTATCGCAAGCGAACTTG
Found at i:48441 original size:21 final size:21
Alignment explanation
Indices: 48417--48458 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48407 AAAGTTGGAA
*
48417 GAAAGAGAAAAAGAGGGGGAG
1 GAAAGAGAAAAAGAGAGGGAG
*
48438 GAAAGAGAAAAGGAGAGGGAG
1 GAAAGAGAAAAAGAGAGGGAG
48459 AAACTGAGAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (21 bp):
GAAAGAGAAAAAGAGAGGGAG
Found at i:51828 original size:21 final size:21
Alignment explanation
Indices: 51804--51853 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
51794 AAACACGTAC
51804 GACAATATGAGATTCTAAGTT
1 GACAATATGAGATTCTAAGTT
51825 GACAATATGAGATTCTAAGTT
1 GACAATATGAGATTCTAAGTT
*
51846 GATAATAT
1 GACAATAT
51854 AAAAAGTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (21 bp):
GACAATATGAGATTCTAAGTT
Found at i:54317 original size:17 final size:19
Alignment explanation
Indices: 54297--54332 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54287 ATATATTATT
54297 AAAA-AAAATATAA-AGAA
1 AAAATAAAATATAAGAGAA
54314 AAAATAAAATATAAGAGAA
1 AAAATAAAATATAAGAGAA
54333 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAATAAAATATAAGAGAA
Found at i:59554 original size:32 final size:32
Alignment explanation
Indices: 59513--59584 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
59503 TTTTTTCTTC
*
59513 GGGTTTTTGAATTTCTAATGTATTCGAAGCTT
1 GGGTTTTTGAATTTATAATGTATTCGAAGCTT
59545 GGGTTTTTGAATTTATAATGTATTCGAAGCTT
1 GGGTTTTTGAATTTATAATGTATTCGAAGCTT
59577 GGGTTTTT
1 GGGTTTTT
59585 CCTTTCAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.49
Consensus pattern (32 bp):
GGGTTTTTGAATTTATAATGTATTCGAAGCTT
Done.