Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009346.1 Hibiscus syriacus cultivar Beakdansim tig00113130_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: 78950
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5886 original size:29 final size:29
Alignment explanation
Indices: 5851--5912 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
5841 TTTCAGTACC
* *
5851 TTAAATTCCAGCACTTTCAATTTCCGCCCT
1 TTAATTTCCAGCACTTT-AATTTCAGCCCT
* * *
5881 TTAATTTTCATCACTTTAATTTCAGTCCT
1 TTAATTTCCAGCACTTTAATTTCAGCCCT
5910 TTA
1 TTA
5913 TTTGTGTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (29 bp):
TTAATTTCCAGCACTTTAATTTCAGCCCT
Found at i:7018 original size:17 final size:17
Alignment explanation
Indices: 6986--7051 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
6976 ATATGTTGGA
*
6986 TCATTCAATAAAACTAGT
1 TCATT-AATTAAACTAGT
*
7004 CCATTAATTAAACTAGT
1 TCATTAATTAAACTAGT
* *
7021 TCATTTATTTAAACTGGT
1 TCA-TTAATTAAACTAGT
*
7039 TCATTAATAAAAC
1 TCATTAATTAAAC
7052 AAGCTCCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 21 0.52
18 19 0.47
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
TCATTAATTAAACTAGT
Found at i:11638 original size:35 final size:35
Alignment explanation
Indices: 11585--11670 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
11575 GCTACTTTGT
**
11585 TTAATTATGCTAGATCATTCAATAAAAC-TAGTCCA
1 TTAATTAAACTAGATCATTCAATAAAACAT-GTCCA
* * * *
11620 TTAATTAAACTAGTTCATTCATTTAAACATGTTCA
1 TTAATTAAACTAGATCATTCAATAAAACATGTCCA
*
11655 CTAATTAAACTAGATC
1 TTAATTAAACTAGATC
11671 CTTTAAAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (35 bp):
TTAATTAAACTAGATCATTCAATAAAACATGTCCA
Found at i:11645 original size:18 final size:18
Alignment explanation
Indices: 11594--11667 Score: 73
Period size: 17 Copynumber: 4.2 Consensus size: 18
11584 TTTAATTATG
* *
11594 CTAGATCATTCAATAAAA
1 CTAGTTCATTCAATTAAA
*
11612 CTAGTCCATT-AATTAAA
1 CTAGTTCATTCAATTAAA
*
11629 CTAGTTCATTCATTTAAA
1 CTAGTTCATTCAATTAAA
*
11647 C-ATGTTCACT-AATTAAA
1 CTA-GTTCATTCAATTAAA
11664 CTAG
1 CTAG
11668 ATCCTTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
17 24 0.52
18 22 0.48
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.35
Consensus pattern (18 bp):
CTAGTTCATTCAATTAAA
Found at i:13210 original size:17 final size:17
Alignment explanation
Indices: 13160--13227 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
13150 TTAAAGGAGA
**
13160 TAGTTTAATTAATTAAC
1 TAGTTTAATTAATGGAC
* * *
13177 CAATTTAAATGAATGGAC
1 TAGTTT-AATTAATGGAC
13195 TAGTTTAATTAATGGAC
1 TAGTTTAATTAATGGAC
*
13212 TAGTTTTATTGAATGG
1 TAGTTTAATT-AATGG
13228 TCCAACATAC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 23 0.57
18 17 0.43
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (17 bp):
TAGTTTAATTAATGGAC
Found at i:13226 original size:18 final size:18
Alignment explanation
Indices: 13180--13227 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
13170 AATTAACCAA
*
13180 TTTAAATGAATGGACTAG
1 TTTAATTGAATGGACTAG
13198 TTTAATT-AATGGACTAG
1 TTTAATTGAATGGACTAG
*
13215 TTTTATTGAATGG
1 TTTAATTGAATGG
13228 TCCAACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (18 bp):
TTTAATTGAATGGACTAG
Found at i:13277 original size:18 final size:18
Alignment explanation
Indices: 13237--13284 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
13227 GTCCAACATA
* *
13237 CTTAAATGAAGTAGCTTG
1 CTTAAATGAACTAGCATG
13255 CTTAAATGAACTA-CATG
1 CTTAAATGAACTAGCATG
*
13272 CTTTAATGAACTA
1 CTTAAATGAACTA
13285 AATGTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (18 bp):
CTTAAATGAACTAGCATG
Found at i:16142 original size:87 final size:87
Alignment explanation
Indices: 16050--16221 Score: 222
Period size: 87 Copynumber: 2.0 Consensus size: 87
16040 TCTTTTTGGC
* * * * * *
16050 AAGATCAACTCTGGGAGAGTGATTTACTTCACTACTCTTTAGGAAG-CTTAGAT-TTATAAATCT
1 AAGATCAAATCTGAGAAAGTGATCTACTTCACTACTCTTTAGGAAGAC-CAGATCTT-GAAATCT
16113 TGATTCATTTCACTACTCTTCAAG
64 TGATTCATTTCACTACTCTTCAAG
* *
16137 AAGATCAAATCTGAGAAATTGATCTGCTTCACTACTCTTTAGGAAGACCAGATCTTGAAATCTTG
1 AAGATCAAATCTGAGAAAGTGATCTACTTCACTACTCTTTAGGAAGACCAGATCTTGAAATCTTG
* *
16202 ATTTATTTCACTACTTTTCA
66 ATTCATTTCACTACTCTTCA
16222 GAAAAATTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 70 0.96
88 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (87 bp):
AAGATCAAATCTGAGAAAGTGATCTACTTCACTACTCTTTAGGAAGACCAGATCTTGAAATCTTG
ATTCATTTCACTACTCTTCAAG
Found at i:21378 original size:3 final size:3
Alignment explanation
Indices: 21370--21406 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
21360 AATAGAATGA
21370 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21407 AGAATGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30971 original size:27 final size:27
Alignment explanation
Indices: 30941--31011 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
30931 AAACTCAACA
30941 ACATAT-ATATTAAATATATATACTTAC
1 ACATATAATA-TAAATATATATACTTAC
*
30968 ACATATAATATATATATATATACTTAC
1 ACATATAATATAAATATATATACTTAC
* * *
30995 ATATATAACATATATAT
1 ACATATAATATAAATAT
31012 TTAATAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 37 0.93
28 3 0.08
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (27 bp):
ACATATAATATAAATATATATACTTAC
Found at i:35757 original size:17 final size:17
Alignment explanation
Indices: 35710--35785 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
35700 GAATGATCCA
* *
35710 ACATACTTAAATGAAGT
1 ACATGCTTAAATGAACT
*
35727 AGCTTGCTTAAATGAACT
1 A-CATGCTTAAATGAACT
*
35745 ACATGCTTTAATGAACT
1 ACATGCTTAAATGAACT
* * *
35762 AAATGC-TAAATTAAGT
1 ACATGCTTAAATGAACT
35778 ACATGCTT
1 ACATGCTT
35786 TCAATGATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 12 0.26
17 21 0.45
18 14 0.30
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (17 bp):
ACATGCTTAAATGAACT
Found at i:38621 original size:34 final size:34
Alignment explanation
Indices: 38578--38647 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
38568 TGATGTTCAT
* *
38578 AATCACAACACTTGGTCAAATGTATGAAGTACAC
1 AATCACAACACTTGGTCAAATGTATAAAGTAAAC
*
38612 AATCACAACACTTGGTCGAATGTATAAAGTAAAC
1 AATCACAACACTTGGTCAAATGTATAAAGTAAAC
38646 AA
1 AA
38648 AATAGACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (34 bp):
AATCACAACACTTGGTCAAATGTATAAAGTAAAC
Found at i:40880 original size:20 final size:20
Alignment explanation
Indices: 40786--41194 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
40776 GATTTTCCAT
* ** *
40786 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
40806 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
40826 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40846 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
40866 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
40886 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40906 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
40926 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
40946 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
40966 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40986 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
41006 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41026 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
41046 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41066 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41086 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41106 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41126 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41146 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41166 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41186 AATCACAAC
1 AATCGCAAC
41195 ACTGAAATTT
Statistics
Matches: 337, Mismatches: 42, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 331 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:41906 original size:24 final size:24
Alignment explanation
Indices: 41867--41913 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41857 AAATTTGGTC
41867 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
41891 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
41914 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:42105 original size:12 final size:12
Alignment explanation
Indices: 42088--42112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42078 ATATAATCCT
42088 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42100 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42112 G
1 G
42113 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:44439 original size:19 final size:19
Alignment explanation
Indices: 44417--44742 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
44407 CGGAAAATAC
*
44417 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44436 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
44450 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
44470 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44522 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44536 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44574 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44588 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44607 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
44626 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
44645 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44664 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44683 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
44697 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44716 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44735 AATCGCAA
1 AATCGCAA
44743 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:44504 original size:33 final size:34
Alignment explanation
Indices: 44417--44742 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
44407 CGGAAAATAC
* *
44417 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
44450 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
44484 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44522 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44555 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
44588 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44626 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
44664 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
44696 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
44735 AATCGCAA
1 AATCGCAA
44743 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:44678 original size:161 final size:157
Alignment explanation
Indices: 44445--44764 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
44435 AAATCCCAAC
*
44445 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
44510 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
44575 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
44602 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
44666 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
44731 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
44763 AT
1 AT
44765 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:44780 original size:52 final size:52
Alignment explanation
Indices: 44445--44764 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
44435 AAATCCCAAC
44445 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44498 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44550 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
44602 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
44659 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
44711 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44763 AT
1 AT
44765 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:44880 original size:19 final size:19
Alignment explanation
Indices: 44771--44872 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
44761 AAATTATAAA
44771 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44790 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
44810 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
44826 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44843 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44862 CGCATTGCGAT
1 CGCATTGCGAT
44873 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:44998 original size:14 final size:14
Alignment explanation
Indices: 44979--45015 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44969 CATCAATTAC
44979 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
44993 ACAAATCATCTTTT
1 ACAAATCAACTTTT
45007 ACAAATCAA
1 ACAAATCAA
45016 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:45027 original size:12 final size:12
Alignment explanation
Indices: 45010--45081 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
45000 ATCTTTTACA
45010 AATCAATTAAAC
1 AATCAATTAAAC
*
45022 AATCAA--AAATTG
1 AATCAATTAAA--C
*
45034 AATCAACTT-TAC
1 AATCAA-TTAAAC
45046 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
45059 AATCAA-AAAAC
1 AATCAATTAAAC
45070 AATCAATTAAAC
1 AATCAATTAAAC
45082 TATTGAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 24 0.52
13 8 0.17
14 1 0.02
ACGTcount: A:0.58, C:0.17, G:0.01, T:0.24
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:46920 original size:19 final size:19
Alignment explanation
Indices: 46880--47014 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
46870 TAGTTTACTT
* *
46880 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
46900 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
46919 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
46938 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
46952 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
46971 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
46985 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
47004 TCGCAATGCGA
1 TCGCAACGCGA
47015 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:46955 original size:14 final size:14
Alignment explanation
Indices: 46936--46992 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
46926 GCGAAATGAA
*
46936 AATCGCAACGACAG
1 AATCGCAACGAAAG
46950 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
46967 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
46983 AATCGCAACG
1 AATCGCAACG
46993 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:46959 original size:33 final size:33
Alignment explanation
Indices: 46917--47009 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
46907 GCGAAACCAA
*
46917 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
46950 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
46983 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
47010 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:47006 original size:52 final size:54
Alignment explanation
Indices: 46880--47014 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
46870 TAGTTTACTT
*
46880 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
46938 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
46985 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
47015 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:47032 original size:19 final size:19
Alignment explanation
Indices: 47010--47122 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
47000 AAAATCGCAA
47010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47029 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
47043 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47062 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
47076 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
47095 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
47114 TGCGATTTT
1 TGCGATTTT
47123 AAGTTCGTGT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.62
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:47052 original size:33 final size:33
Alignment explanation
Indices: 47010--47101 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
47000 AAAATCGCAA
47010 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
47043 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
47076 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
47102 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:47129 original size:19 final size:18
Alignment explanation
Indices: 47010--47137 Score: 92
Period size: 19 Copynumber: 7.3 Consensus size: 18
47000 AAAATCGCAA
*
47010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAG-TTCGCGT
*
47029 TGCGATCTT-G-T--CGT
1 TGCGATTTTAGTTCGCGT
*
47043 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAG-TTCGCGT
*
47062 TGCGATTCT-G-T--CGT
1 TGCGATTTTAGTTCGCGT
*
47076 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-AGTTCGCGT
*
47095 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAG-TTCGCGT
*
47114 TGCGATTTTAAGTTCGTGT
1 TGCGATTTT-AGTTCGCGT
47133 TGCGA
1 TGCGA
47138 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 58 0.66
20 1 0.01
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (18 bp):
TGCGATTTTAGTTCGCGT
Found at i:47340 original size:93 final size:93
Alignment explanation
Indices: 47181--47560 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
47171 TTGAATGGAT
47181 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47246 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47274 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47339 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47367 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47431 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47459 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
47524 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47552 AAATTTACT
1 AAATTTACT
47561 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:47494 original size:185 final size:186
Alignment explanation
Indices: 47181--47560 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
47171 TTGAATGGAT
47181 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47246 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
47311 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
47367 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47431 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
47496 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
47552 AAATTTACT
1 AAATTTACT
47561 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:49280 original size:14 final size:14
Alignment explanation
Indices: 49261--49350 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
49251 TTGAAATGAA
49261 AATCGCAACGAGAG
1 AATCGCAACGAGAG
49275 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
49292 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
49308 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
49327 AATCGCAACGAGAG
1 AATCGCAACGAGAG
49341 AATCGCAACG
1 AATCGCAACG
49351 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:49298 original size:33 final size:33
Alignment explanation
Indices: 49253--49367 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
49243 TCTTTTGGTT
49253 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
49286 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
49319 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
49352 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
49368 TGCGATTTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:49299 original size:19 final size:18
Alignment explanation
Indices: 49260--49372 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
49250 GTTGAAATGA
49260 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
49275 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
49292 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
49308 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
49325 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
49341 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
49358 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
49373 TTTTTGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:49403 original size:14 final size:14
Alignment explanation
Indices: 49384--49438 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
49374 TTTTGTTTCG
49384 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
49398 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
49417 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
49431 CGTTGCGA
1 CGTTGCGA
49439 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:49601 original size:33 final size:33
Alignment explanation
Indices: 49559--49629 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
49549 AATACTAACT
*
49559 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
49592 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
49625 TGAAA
1 TGAAA
49630 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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:49863 original size:22 final size:22
Alignment explanation
Indices: 49811--49865 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
49801 TGGTTGTGAG
**
49811 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
49833 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
49855 GGATTTCTTCG
1 GGATTTCTTCG
49866 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:50036 original size:20 final size:20
Alignment explanation
Indices: 50011--50204 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
50001 CTTTAAATAT
50011 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
50031 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
50053 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50072 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
50092 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
50112 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50132 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
50152 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
50172 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
50192 CGCGTTGCGATTT
1 CGCGTTGCGATTT
50205 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:50198 original size:60 final size:60
Alignment explanation
Indices: 50011--50204 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
50001 CTTTAAATAT
**
50011 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
50072 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
50132 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
50192 CGCGTTGCGATTT
1 CGCGTTGCGATTT
50205 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:50221 original size:21 final size:20
Alignment explanation
Indices: 50197--50273 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
50187 ATATTCGCGT
50197 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
50218 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
50238 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
50260 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
50274 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:50284 original size:20 final size:20
Alignment explanation
Indices: 50259--50310 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50249 AAGAATCGCG
*
50259 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
50279 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
50299 TTGCGATTCTGG
1 TTGCGATTCTGG
50311 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:51355 original size:15 final size:15
Alignment explanation
Indices: 51335--51368 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
51325 AATAAAAGTT
51335 GACTCATTAGTACTC
1 GACTCATTAGTACTC
*
51350 GACTCATTAGTACTT
1 GACTCATTAGTACTC
51365 GACT
1 GACT
51369 TTGACGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (15 bp):
GACTCATTAGTACTC
Found at i:57249 original size:14 final size:16
Alignment explanation
Indices: 57213--57249 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
57203 TATTAATGTA
57213 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
57230 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
57245 T-AATA
1 TGAATA
57250 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:57905 original size:130 final size:129
Alignment explanation
Indices: 57701--57947 Score: 386
Period size: 130 Copynumber: 1.9 Consensus size: 129
57691 AATTTTCTTC
* * *
57701 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCTGATCATGCGTTAACACATGTCAGATC
1 TAATTAGGCGGTGACATGTGTCACCAATAACACATATCTGATCATGCGCTAACACATGTCAGATC
** *
57766 CTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGAACCAAATTGATAGCATATATAAA
66 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGAACCAAATTGATAGCATATATAAA
* * * *
57830 TAATTAGGCGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGCGGTGACATGTGTCACCAATAACACATATC-TGATCATGCGCTAACACATGTCAGAT
*
57895 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
65 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGAACCAAATTGAT
57948 TATATAAATA
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 33 0.31
130 73 0.69
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (129 bp):
TAATTAGGCGGTGACATGTGTCACCAATAACACATATCTGATCATGCGCTAACACATGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGAACCAAATTGATAGCATATATAAA
Found at i:58394 original size:35 final size:35
Alignment explanation
Indices: 58344--58419 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
58334 AATTGAATTT
* *
58344 AATTGAATTATTTTGG-AATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGA-GGTTTAGAATGA
58379 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
58414 AATTGA
1 AATTGA
58420 TGACTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
Found at i:62788 original size:20 final size:20
Alignment explanation
Indices: 62763--62800 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
62753 AAGTAAATGT
*
62763 TGGTCAAAGTCAATAGCTAA
1 TGGTCAAAGTCAACAGCTAA
62783 TGGTCAAAGTCAACAGCT
1 TGGTCAAAGTCAACAGCT
62801 CAACTCAGCT
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:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (20 bp):
TGGTCAAAGTCAACAGCTAA
Found at i:70558 original size:20 final size:21
Alignment explanation
Indices: 70519--70562 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
70509 TATTTTGTAG
70519 AGAAAACATCCCCAAACGACT
1 AGAAAACATCCCCAAACGACT
*
70540 AGAAATCATCCCC-AACGACT
1 AGAAAACATCCCCAAACGACT
70560 AGA
1 AGA
70563 CACGACCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.11
Consensus pattern (21 bp):
AGAAAACATCCCCAAACGACT
Found at i:76753 original size:18 final size:18
Alignment explanation
Indices: 76732--76799 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
76722 AAGAGAAAAG
76732 AAAAAGGAAAAAAATGAA
1 AAAAAGGAAAAAAATGAA
*
76750 AAAATAGAAAAAAAATAGAA
1 AAAA-AGGAAAAAAAT-GAA
*
76770 AAGAGAAAG-AAAAAA-GAA
1 AA-A-AAGGAAAAAAATGAA
76788 AAAAAGAGAAAA
1 AAAAAG-GAAAA
76800 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
16 2 0.05
17 2 0.05
18 12 0.30
19 10 0.25
20 11 0.28
21 2 0.05
22 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (18 bp):
AAAAAGGAAAAAAATGAA
Found at i:76805 original size:41 final size:40
Alignment explanation
Indices: 76725--76804 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
76715 ATAAAGAAAG
*
76725 AGAAAAGAAAAAGGAAAAAAATGAAAAAATAGAAAAAAAAT
1 AGAAAAGAAAAAGGAAAAAAA-GAAAAAAGAGAAAAAAAAT
*
76766 AGAAAAGAGAAA-G-AAAAAAGAAAAAAAGAGAAAAGAAAA
1 AGAAAAGAAAAAGGAAAAAAAG-AAAAAAGAGAAAA-AAAA
76805 AAATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.03
39 18 0.51
40 5 0.14
41 11 0.31
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (40 bp):
AGAAAAGAAAAAGGAAAAAAAGAAAAAAGAGAAAAAAAAT
Found at i:76806 original size:7 final size:7
Alignment explanation
Indices: 76721--76806 Score: 57
Period size: 7 Copynumber: 11.4 Consensus size: 7
76711 TCGCATAAAG
*
76721 AAAGAGA
1 AAAGAAA
76728 AAAGAAA
1 AAAGAAA
*
76735 AAGGAAAA
1 AAAG-AAA
76743 AAATGAAAA
1 AAA-G-AAA
76752 AATAGAAA
1 AA-AGAAA
*
76760 AAAAATAGA
1 AAAGA-A-A
*
76769 AAAG-AG
1 AAAGAAA
76775 AAAGAAA
1 AAAGAAA
76782 AAAGAAAA
1 AAAG-AAA
*
76790 AAAGAGA
1 AAAGAAA
76797 AAAGAAA
1 AAAGAAA
76804 AAA
1 AAA
76807 ATAAATAAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
6 4 0.06
7 28 0.44
8 18 0.29
9 12 0.19
10 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:76813 original size:47 final size:48
Alignment explanation
Indices: 76721--76813 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 48
76711 TCGCATAAAG
* * *
76721 AAAGAGAAAAGAAAAAGGAAAAAAATGAAAAAATAGAAAAAAAATAGA
1 AAAGAGAAAAGAAAAAAGAAAAAAATGAAAAAAGAAAAAAAAAATAGA
*
76769 AAAGAG-AAAGAAAAAAGAAAAAAA-GAGAAAAGAAAAAAATAAATA
1 AAAGAGAAAAGAAAAAAGAAAAAAATGAAAAAAGAAAAAAA-AAATA
76814 AAGAGGGTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 12 0.30
47 22 0.55
48 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (48 bp):
AAAGAGAAAAGAAAAAAGAAAAAAATGAAAAAAGAAAAAAAAAATAGA
Found at i:78220 original size:89 final size:89
Alignment explanation
Indices: 78062--78248 Score: 254
Period size: 89 Copynumber: 2.1 Consensus size: 89
78052 CTACCCTAAT
* **
78062 AGTAGTGGAGTGAATCAACGTTTCCAGATCTAATCTACCCTGAAGCAGCGGAGCAGATACCCTTG
1 AGTAGTGGAATGAATCAACGTTTCCAGATCTAATCTACCCTGAAAAAGCGGAGCAGATACCCTTG
*
78127 TTTTATATTTGATCTTCCCTGAAG
66 TTTTATATTTGATCTTCCCTAAAG
* * * *
78151 AGTAGTGGAATGAATCAATGTTTCCAGATCTAATCTCCCCTGAAAAAAGTGGAGCATAT-CCCTC
1 AGTAGTGGAATGAATCAACGTTTCCAGATCTAATCTACCCTG-AAAAAGCGGAGCAGATACCCT-
78215 T-TTTTATATTTGATCTTCCCTAAAG
64 TGTTTTATATTTGATCTTCCCTAAAG
*
78240 -GCAGTGGAA
1 AGTAGTGGAA
78249 CAAATCTACC
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
88 8 0.09
89 66 0.76
90 13 0.15
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (89 bp):
AGTAGTGGAATGAATCAACGTTTCCAGATCTAATCTACCCTGAAAAAGCGGAGCAGATACCCTTG
TTTTATATTTGATCTTCCCTAAAG
Found at i:78290 original size:128 final size:123
Alignment explanation
Indices: 78141--78447 Score: 336
Period size: 123 Copynumber: 2.5 Consensus size: 123
78131 ATATTTGATC
* * *
78141 TTCCCTGAAGAGTAGTGGAATGAATCAATGTTTCCAGATCTAATCT-CCCCTGAAAAAAGTGGAG
1 TTCCCTGAAAAGTAGTGGAATGAATCAATGTTTCCAGATCTAATCTACCTC-G----AAGAGGAG
* * *
78205 CATATCCCTCTTTTT-ATATTTGATCTTCCCTAAAG-GCAGTGGAACAAATCTACCTTGAATCA-
61 CATA-CCC-CTTTTTCAGA-TTGATCTTCCCTAAAGAGCA-TAGAACAAATCTACCTCGAATCAG
78267 TA
122 TA
*
78269 TTCCCTGAAAAGTAGCGGAATGAATCAATGTTTCCAGATCTAATCTACCTCGAAGAGGAGCATAC
1 TTCCCTGAAAAGTAGTGGAATGAATCAATGTTTCCAGATCTAATCTACCTCGAAGAGGAGCATAC
* * * * *
78334 CCCTTTTTCAGATTGATCTTCCCTGAGGAGCATAGAACAAATCTGCCTCGATTCAGTC
66 CCCTTTTTCAGATTGATCTTCCCTAAAGAGCATAGAACAAATCTACCTCGAATCAGTA
* * * * * *
78392 TTCTCTGAAAAGAAATGGAGTGAATCAATGTTTCCAGATCTGATATACCT-GAAGAG
1 TTCCCTGAAAAGTAGTGGAATGAATCAATGTTTCCAGATCTAATCTACCTCGAAGAG
78448 CAGTGAAGCA
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
122 45 0.29
123 52 0.33
124 11 0.07
128 45 0.29
129 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (123 bp):
TTCCCTGAAAAGTAGTGGAATGAATCAATGTTTCCAGATCTAATCTACCTCGAAGAGGAGCATAC
CCCTTTTTCAGATTGATCTTCCCTAAAGAGCATAGAACAAATCTACCTCGAATCAGTA
Done.