Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001369.1 Hibiscus syriacus cultivar Beakdansim tig00002678_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: 163235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2260 original size:17 final size:17
Alignment explanation
Indices: 2238--2276 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2228 AGAAGTTCCG
*
2238 TTTTAATATAAAATATA
1 TTTTAATAAAAAATATA
*
2255 TTTTAATAAAAAATATT
1 TTTTAATAAAAAATATA
2272 TTTTA
1 TTTTA
2277 TATCACAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATAAAAAATATA
Found at i:8789 original size:16 final size:17
Alignment explanation
Indices: 8755--8797 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
8745 AGATTTTATT
*
8755 ATTTATTTTA-TTAGAA
1 ATTTATTTTACATAGAA
8771 ATTTATTTTACATAG-A
1 ATTTATTTTACATAGAA
*
8787 ATTTAGTTTAC
1 ATTTATTTTAC
8798 CATTGCTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (17 bp):
ATTTATTTTACATAGAA
Found at i:10668 original size:21 final size:21
Alignment explanation
Indices: 10626--10668 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
10616 TTTCTGGGCT
*
10626 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
10647 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
10668 A
1 A
10669 ACGAACATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:12527 original size:103 final size:103
Alignment explanation
Indices: 12302--12519 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
12292 GTCGAGGGTC
*
12302 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTAGTGAGACACATAG
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
12367 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * *
12405 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
*
12470 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
12508 TATGTGGTCCTT
1 TATGTGGTCCTT
12520 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:12603 original size:23 final size:23
Alignment explanation
Indices: 12526--12602 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
12516 CCTTATGGAC
12526 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATATGGCACTACGGTGCA
* *
12550 ATTCTATATGGCACTCCGGTGCA
1 ATTATATATGGCACTACGGTGCA
* *
12573 ATTATATGTGGCACTTCGGTGCA
1 ATTATATATGGCACTACGGTGCA
12596 ATTATAT
1 ATTATAT
12603 GAGCTATGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 45 0.94
24 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (23 bp):
ATTATATATGGCACTACGGTGCA
Found at i:15363 original size:11 final size:11
Alignment explanation
Indices: 15347--15409 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
15337 AAAATTACAT
15347 TATTAAAAATA
1 TATTAAAAATA
15358 TATTAAAAATA
1 TATTAAAAATA
* * ***
15369 CACTATTGATA
1 TATTAAAAATA
15380 -ATTATAAAAT-
1 TATTA-AAAATA
15390 T-TTAAAAATA
1 TATTAAAAATA
15400 TATTAAAAAT
1 TATTAAAAAT
15410 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:15995 original size:14 final size:14
Alignment explanation
Indices: 15978--16023 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
15968 TCTCGAATCC
15978 CTAATCCATAAATA
1 CTAATCCATAAATA
* *
15992 CTAAACCATAAATT
1 CTAATCCATAAATA
* *
16006 CTAATCCCTAAGTA
1 CTAATCCATAAATA
16020 CTAA
1 CTAA
16024 ACCTTAAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (14 bp):
CTAATCCATAAATA
Found at i:16021 original size:28 final size:28
Alignment explanation
Indices: 15978--16031 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
15968 TCTCGAATCC
15978 CTAATCCATAAATACTAAACCATAAATT
1 CTAATCCATAAATACTAAACCATAAATT
* * *
16006 CTAATCCCTAAGTACTAAACCTTAAA
1 CTAATCCATAAATACTAAACCATAAA
16032 CCATAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (28 bp):
CTAATCCATAAATACTAAACCATAAATT
Found at i:16047 original size:14 final size:14
Alignment explanation
Indices: 15978--16031 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
15968 TCTCGAATCC
*
15978 CTAATCCATAAATA
1 CTAAACCATAAATA
*
15992 CTAAACCATAAATT
1 CTAAACCATAAATA
* * *
16006 CTAATCCCTAAGTA
1 CTAAACCATAAATA
*
16020 CTAAACCTTAAA
1 CTAAACCATAAA
16032 CCATAAATAC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (14 bp):
CTAAACCATAAATA
Found at i:18105 original size:11 final size:11
Alignment explanation
Indices: 18089--18188 Score: 76
Period size: 11 Copynumber: 8.7 Consensus size: 11
18079 CATTAACCCG
18089 TCGAGCTTGAA
1 TCGAGCTTGAA
**
18100 TCGAGCTCCAAA
1 TCGAGCT-TGAA
18112 TCGAGCTTGAA
1 TCGAGCTTGAA
*
18123 TCAAGCTTGAA
1 TCGAGCTTGAA
*
18134 TCG-GTCTCTAAA
1 TCGAG-CT-TGAA
* *
18146 TCAAGCTTCAA
1 TCGAGCTTGAA
*
18157 TCGAGCTTGAGT
1 TCGAGCTTGA-A
*
18169 TCTGAGCTTCAA
1 TC-GAGCTTGAA
18181 TCGAGCTT
1 TCGAGCTT
18189 TTGAATTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
10 1 0.01
11 40 0.58
12 20 0.29
13 8 0.12
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:18131 original size:34 final size:34
Alignment explanation
Indices: 18092--18188 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 34
18082 TAACCCGTCG
*
18092 AGCTTGAATCGAGCTCCAAATCGAGCTTGAATCA
1 AGCTTGAATCGAGCTCCAAATCGAGCTTCAATCA
* * *
18126 AGCTTGAATCG-GTCTCTAAATCAAGCTTCAATCG
1 AGCTTGAATCGAG-CTCCAAATCGAGCTTCAATCA
* *
18160 AGCTTGAGTTCTGAGCTTC-AATCGAGCTT
1 AGCTTGA-ATC-GAGCTCCAAATCGAGCTT
18189 TTGAATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
33 1 0.02
34 35 0.69
35 11 0.22
36 3 0.06
37 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (34 bp):
AGCTTGAATCGAGCTCCAAATCGAGCTTCAATCA
Found at i:21958 original size:18 final size:16
Alignment explanation
Indices: 21933--21977 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
21923 TCTCACTTCT
*
21933 ATTCTCTCTTCTAGAC
1 ATTCTCTCTCCTAGAC
21949 ATTCTCTCTCCTAGAC
1 ATTCTCTCTCCTAGAC
21965 ATTCTCTCTCCTA
1 ATTCTCTCTCCTA
21978 TGTATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTCTCTCTCCTAGAC
Found at i:25855 original size:30 final size:30
Alignment explanation
Indices: 25819--25875 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
25809 CAGCCGATGG
25819 TTGGTGAGATGTAGAAGATGATGAATATGA
1 TTGGTGAGATGTAGAAGATGATGAATATGA
*
25849 TTGGTGAGTTGTAGAAGATGATGAATA
1 TTGGTGAGATGTAGAAGATGATGAATA
25876 GTGAAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (30 bp):
TTGGTGAGATGTAGAAGATGATGAATATGA
Found at i:26358 original size:32 final size:32
Alignment explanation
Indices: 26319--26380 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
26309 AAACAAACGA
26319 ATTACCGAACGTAAACAAACATAAATGAACAG
1 ATTACCGAACGTAAACAAACATAAATGAACAG
* * *
26351 ATTACCGAACGTTAACGAACGTAAATGAAC
1 ATTACCGAACGTAAACAAACATAAATGAAC
26381 GAAAGAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (32 bp):
ATTACCGAACGTAAACAAACATAAATGAACAG
Found at i:34663 original size:18 final size:17
Alignment explanation
Indices: 34619--34669 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
34609 TTATTTAAAA
34619 TAAAAAAAATTAATATATTT
1 TAAAAAAAA-TAA-AT-TTT
*
34639 TAAAAAACATAAATTTT
1 TAAAAAAAATAAATTTT
34656 TAAAAAAAAATAAA
1 T-AAAAAAAATAAA
34670 ATACTCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 13 0.46
19 3 0.11
20 8 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAAAATAAATTTT
Found at i:34941 original size:640 final size:639
Alignment explanation
Indices: 33720--34996 Score: 1935
Period size: 640 Copynumber: 2.0 Consensus size: 639
33710 GTTATATATA
*
33720 TATATATATAGTGTCTTTTTTCCTTCTAAAAGTTTAGGTCAATGGTGAATCCTTCAATCCAGGAT
1 TATATATATAGTGTCTTTTTTCC-TCTAAAAGTTTAGGTCAAGGGTGAATCCTTCAATCCAGGAT
* * * *
33785 CAGGGCATATCTAAGACCGAATTAGAAATTATATAAGAATTTACATATTATCACCAAGAGTAACT
65 CAGGGCATACCTAAAACCGAATTAGAAATTACATAAGAATTTACAGATTATCACCAAGAGTAACT
33850 TTTTGATTAATCTAAGTACATAACATTACATATGTTACTATCTTAAGTGACCTGAATGTAACGAT
130 TTTTGATTAATCTAAGTACATAACATTACATATGTTACTATCTTAAGTGACCTGAATGTAACGAT
* ** * **
33915 AATTAAAAAATTCTATTAAGTGACGTCTGTCACATTTCGAAATTTTTAAAAATTTTATTTAAAAT
195 AACTAAAAAATTCTATTAAGTGACACCTGTCACATTTCGAAAATTTTAAAAAAATTATTTAAAAT
* *
33980 AAAAAATTAAATATATTTTTAAAAAACTCAATTTTAAAAAAATAAAATTACTCCAAAAAATTTGA
260 AAAAAATTAAATATATTTTTAAAAAACTAAATTTTAAAAAAATAAAATTACTCCAAAAAATTTAA
** * * *
34045 AAATCTTAATTTTAATCTTTATATGCACGCCAATCATTTCTGTTACTGTCGAACCTCCACCTATT
325 AAATCTTAATTTTAATCCCTATATGCACACCAATCATTTCTGTTACTGTCGAACCTCCACCGACT
* * * *
34110 AGGACGACGCCAAAACCTCATCTATTGAAACCCCTTACTTTCTGCCCAGTTGTTGCTACCAAAAT
390 AGGACGACCCCAAAACCTCATCCATTGAAACCCCTTACTTGC-GCCCAATTGTTGCTACCAAAAT
* * *
34175 CCCTAAATTTTAATATCCAAATCCCTAACTCAAAACCTTAAATCCTTTAATGTGAAAACTCAAAA
454 CCCTAAATTTTAATAACCAAATCCCTAACTCAAAACCTTAAATCCCTTAATGTCAAAACTCAAAA
34240 TTTGAAATCTCAATCGAATTAAAAAATCTGTTTTCCATACCCATCAAAACTAGGTGTACGACCCA
519 TTTGAAATCTCAATCGAATTAAAAAATCTGTTTTCCATACCCATCAAAACTAGGTGTACGACCCA
*
34305 GGTCGATCCAAATTAGTCAAGAC-AAAGTCTTAAAACTAGATGGCAATAAAAAGTGC
584 GGTCGATCCAAATTAGTCAAGACGAAA-TCTTAAAACTAGATGACAATAAAAAGTGC
* * *
34361 TATATATATAGTGTCTTTTTTTCC-CTTAAAGTTTAGGTCAAGGGTGACTCCTTCAGTCCAGGAT
1 TATATATATAGTGTC-TTTTTTCCTCTAAAAGTTTAGGTCAAGGGTGAATCCTTCAATCCAGGAT
* *
34425 CATGGCATACCTAAAACCGAATTAGAAATTACATAAGAATTTACAGATTGTCACCAAGAGTAACT
65 CAGGGCATACCTAAAACCGAATTAGAAATTACATAAGAATTTACAGATTATCACCAAGAGTAACT
* * *
34490 TTTTGGTTAATCTAAGTGCATAACATTACATATGTTACTATTTTAAGTGACCTGAATGTAACGAT
130 TTTTGATTAATCTAAGTACATAACATTACATATGTTACTATCTTAAGTGACCTGAATGTAACGAT
34555 AACTAAAAAATTCTATTAAGTGACACCTGTCACATTTCGAAAATTTTAAAAAAATTATTTAAAAT
195 AACTAAAAAATTCTATTAAGTGACACCTGTCACATTTCGAAAATTTTAAAAAAATTATTTAAAAT
34620 AAAAAAAATT-AATATA-TTTTAAAAAACATAAATTTTTAAAAAAAAATAAAA-TACTCCAAAAA
260 --AAAAAATTAAATATATTTTTAAAAAAC-TAAA-TTTT--AAAAAAATAAAATTACTCCAAAAA
* * * *
34682 TTTTAAAAATCTTAATTTTAATCCCTATATGCACATCAATCATTTTTGTTATTGTCGAACCTCCA
319 ATTTAAAAATCTTAATTTTAATCCCTATATGCACACCAATCATTTCTGTTACTGTCGAACCTCCA
* *
34747 TCGACTAGGACGACCCCAAAACCTCATCCATTGAAACCCCTT-C-TGC-CCCAATTGTTGCTATC
384 CCGACTAGGACGACCCCAAAACCTCATCCATTGAAACCCCTTACTTGCGCCCAATTGTTGCTACC
* * *
34809 AAAATCCCTAAATTTTAATAACTAAATCCCTAACTCAAAACTTTAAATCCCTTAATGTCAAACCT
449 AAAATCCCTAAATTTTAATAACCAAATCCCTAACTCAAAACCTTAAATCCCTTAATGTCAAAACT
* * * *
34874 CAAAATTTG-AATTTCAATCGGATTAAAAAAAAAT-TGTTTTTCGTACCCATCAAAACTAGGTGT
514 CAAAATTTGAAATCTCAATCGAATT---AAAAAATCTGTTTTCCATACCCATCAAAACTAGGTGT
*
34937 ACGACCCAGGTCGATCCAAATTAGTCAAGACGAAATCTTAAAACTAGATGACAATCAAAA
576 ACGACCCAGGTCGATCCAAATTAGTCAAGACGAAATCTTAAAACTAGATGACAATAAAAA
34997 TAATAATAAT
Statistics
Matches: 577, Mismatches: 48, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
638 13 0.02
639 82 0.14
640 308 0.53
641 36 0.06
642 21 0.04
643 105 0.18
644 12 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (639 bp):
TATATATATAGTGTCTTTTTTCCTCTAAAAGTTTAGGTCAAGGGTGAATCCTTCAATCCAGGATC
AGGGCATACCTAAAACCGAATTAGAAATTACATAAGAATTTACAGATTATCACCAAGAGTAACTT
TTTGATTAATCTAAGTACATAACATTACATATGTTACTATCTTAAGTGACCTGAATGTAACGATA
ACTAAAAAATTCTATTAAGTGACACCTGTCACATTTCGAAAATTTTAAAAAAATTATTTAAAATA
AAAAATTAAATATATTTTTAAAAAACTAAATTTTAAAAAAATAAAATTACTCCAAAAAATTTAAA
AATCTTAATTTTAATCCCTATATGCACACCAATCATTTCTGTTACTGTCGAACCTCCACCGACTA
GGACGACCCCAAAACCTCATCCATTGAAACCCCTTACTTGCGCCCAATTGTTGCTACCAAAATCC
CTAAATTTTAATAACCAAATCCCTAACTCAAAACCTTAAATCCCTTAATGTCAAAACTCAAAATT
TGAAATCTCAATCGAATTAAAAAATCTGTTTTCCATACCCATCAAAACTAGGTGTACGACCCAGG
TCGATCCAAATTAGTCAAGACGAAATCTTAAAACTAGATGACAATAAAAAGTGC
Found at i:37012 original size:104 final size:102
Alignment explanation
Indices: 36832--37129 Score: 359
Period size: 103 Copynumber: 2.9 Consensus size: 102
36822 TTTGTCTCCC
*
36832 TTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCCCTTGAAGC-TCAAA
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCCCTTGAAACAT-AAA
*
36896 TTTCGAAGTTGTTTCACTTGAAACAAGAAATTGATCTCAT
65 TTTCGAAATTGTTTCACTTGAAAC-A-AAATTGATCTCAT
** ** *
36936 TTGAGATTGTTT-TCCTAAAAACAAA-TTTCATCTCAATTGAGACAGTTTTCCCTCGAAACATAA
1 TTGAGATTGTTTCT-CTCGAAACAAAGTTTCATCTCGCTTGAGACAG-TTTCCCTTGAAACATAA
* * *
36999 ATTTTGAAATTGTTTCTCTTGAAACAAAATTGATCTTAT
64 ATTTCGAAATTGTTTCACTTGAAACAAAATTGATCTCAT
* * *
37038 TTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAT
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCCCTTGAAACATAAAT
** * * *
37103 CTAGGAGATTGTTTCTCTCGAAACAAA
66 -TTCGAAATTGTTTCACTTGAAACAAA
37130 GTTTCATCTC
Statistics
Matches: 166, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
102 50 0.30
103 59 0.36
104 56 0.34
105 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (102 bp):
TTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCCCTTGAAACATAAAT
TTCGAAATTGTTTCACTTGAAACAAAATTGATCTCAT
Found at i:37236 original size:67 final size:67
Alignment explanation
Indices: 37036--37251 Score: 328
Period size: 67 Copynumber: 3.2 Consensus size: 67
37026 AATTGATCTT
* *
37036 ATTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAAACAT-A
1 ATTTAAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAATTTCTCTTGAAACATAA
37100 A-
66 AC
* *
37101 ATCTAGGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTGAAACAT
1 ATTTA--AGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAATTTCTCTTGAAACAT
37166 AAAC
64 AAAC
* *
37170 ATTTAAGATTGTTTCTCTCGAAACAAAGATTCATCTCCCTTGAGACAATTTCTCTTGAAACATAA
1 ATTTAAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAATTTCTCTTGAAACATAA
37235 AC
66 AC
* *
37237 TTTTTAGATTGTTTC
1 ATTTAAGATTGTTTC
37252 ATATAACTTC
Statistics
Matches: 137, Mismatches: 10, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
65 3 0.02
67 128 0.93
68 2 0.01
69 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (67 bp):
ATTTAAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAATTTCTCTTGAAACATAA
AC
Found at i:38345 original size:11 final size:11
Alignment explanation
Indices: 38310--38353 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
38300 AATGAAATGC
38310 TTTAGTTTTAG
1 TTTAGTTTTAG
*
38321 TTTAAG-TTTGG
1 TTT-AGTTTTAG
38332 TTTAGTTTTAG
1 TTTAGTTTTAG
*
38343 TTTATTTTTAG
1 TTTAGTTTTAG
38354 ATTTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.07
11 24 0.86
12 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (11 bp):
TTTAGTTTTAG
Found at i:39456 original size:22 final size:21
Alignment explanation
Indices: 39417--39457 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39407 TAAATTCGAG
*
39417 GTTTTCATCAAAAAATTACTC
1 GTTTTCAACAAAAAATTACTC
*
39438 GTTTATCAACAAAACATTAC
1 GTTT-TCAACAAAAAATTAC
39458 GACATAGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
GTTTTCAACAAAAAATTACTC
Found at i:40196 original size:35 final size:35
Alignment explanation
Indices: 40123--40197 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
40113 CGTCACGTCC
** **
40123 AGTAAGGCCCTGAGCACACAGTCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
*
40158 AGTAAGGCCCTGAGCACACAACCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
40193 AGTAA
1 AGTAA
40198 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.28, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
Found at i:40302 original size:24 final size:24
Alignment explanation
Indices: 40275--40365 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
40265 CATAATTCAA
* *
40275 GTCAAGTATTATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
40299 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
40323 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
40346 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
40366 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:40335 original size:23 final size:24
Alignment explanation
Indices: 40287--40349 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 24
40277 CAAGTATTAT
*
40287 ATCAGAATCCAGGTCATGTATCAG
1 ATCAGAATCCAGGTCATATATCAG
*
40311 ATCAGAATCCATGTCA-ATATCAG
1 ATCAGAATCCAGGTCATATATCAG
40334 ATCAGAATCCAGGTCA
1 ATCAGAATCCAGGTCA
40350 GGTATCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAGAATCCAGGTCATATATCAG
Found at i:42693 original size:27 final size:27
Alignment explanation
Indices: 42646--42703 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
42636 TCAAAGTTTT
42646 GGTCAACAGTGGTCAACGTC-GGTCAAC
1 GGTCAACAG-GGTCAACGTCGGGTCAAC
42673 GGTCAACA-GGTCAACGGGTCGGGGTCAAC
1 GGTCAACAGGGTCAAC--GTC-GGGTCAAC
42702 GG
1 GG
42704 GTCGAGTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 7 0.26
27 11 0.41
29 9 0.33
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (27 bp):
GGTCAACAGGGTCAACGTCGGGTCAAC
Found at i:42727 original size:13 final size:13
Alignment explanation
Indices: 42681--42742 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 13
42671 ACGGTCAACA
42681 GGTCAACGGGTCGG
1 GGTCAACGGGTC-G
42695 GGTCAACGGGTCGAGTCG
1 GGTCAAC--G--G-GTCG
*
42713 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
42726 GGTAAACGGGTCG
1 GGTCAACGGGTCG
42739 GGTC
1 GGTC
42743 GGGTTATGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
13 18 0.46
14 8 0.21
16 1 0.03
18 9 0.23
19 3 0.08
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:42737 original size:31 final size:32
Alignment explanation
Indices: 42681--42746 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
42671 ACGGTCAACA
*
42681 GGTCAACGGGTCGGGGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGGGGTAAACGGGTCGAGTCG
* *
42713 GGTCAACTGGTC-GGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGGTAAACGGGTCGAGTCG
42744 GGT
1 GGT
42747 TATGACCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18
Consensus pattern (32 bp):
GGTCAACGGGTCGGGGTAAACGGGTCGAGTCG
Found at i:44396 original size:18 final size:18
Alignment explanation
Indices: 44373--44419 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
44363 TGTTTATGAG
*
44373 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
* *
44391 GGAATTCGAATATGTCAA
1 GGAATTGGAATCTGTCAA
44409 -GAATTGGAATC
1 GGAATTGGAATC
44420 CAATTCCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:47978 original size:39 final size:40
Alignment explanation
Indices: 47924--48001 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
47914 GTTTTTAAAA
* *
47924 AAAAAACCTGA-TTTTTTCGGATAAAAATCCAGTTTTTTT
1 AAAAAACCGGATTTTTTTCGGATAAAAAACCAGTTTTTTT
* *
47963 AAAAAACCGGATTTTTTTTGGATAAAAAACCGGTTTTTT
1 AAAAAACCGGATTTTTTTCGGATAAAAAACCAGTTTTTT
48002 ATCCGGTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 10 0.29
40 24 0.71
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (40 bp):
AAAAAACCGGATTTTTTTCGGATAAAAAACCAGTTTTTTT
Found at i:58939 original size:21 final size:21
Alignment explanation
Indices: 58888--58939 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
58878 AGTACAGAGG
* *
58888 GTATCGATTCTCCTAAAGGGA
1 GTATCGGTACTCCTAAAGGGA
*
58909 GT-TTGGTACTCCTAAAGGGA
1 GTATCGGTACTCCTAAAGGGA
58929 GTATCGGTACT
1 GTATCGGTACT
58940 ACCTTTGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTACTCCTAAAGGGA
Found at i:63049 original size:2 final size:2
Alignment explanation
Indices: 63042--63066 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63032 GAAAGGGGGA
63042 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 A
63067 AGGGTAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65677 original size:29 final size:29
Alignment explanation
Indices: 65634--65716 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
65624 CTCACCTAAC
65634 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
65664 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
65693 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
65717 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:70427 original size:29 final size:29
Alignment explanation
Indices: 70384--70466 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
70374 CTCACCTAAC
70384 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
70414 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
70443 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
70467 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:73991 original size:18 final size:19
Alignment explanation
Indices: 73956--73993 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
73946 CACGGAATGT
73956 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
73976 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
73994 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:74006 original size:15 final size:16
Alignment explanation
Indices: 73955--73999 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
73945 TCACGGAATG
73955 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
73973 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
73991 TAAGATTAC
1 TAAGATTAC
74000 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 7 0.28
20 10 0.40
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:76753 original size:18 final size:18
Alignment explanation
Indices: 76730--76764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76720 AGGGATTATA
*
76730 AGTGGTCCCTCGGGACAT
1 AGTGGTCACTCGGGACAT
*
76748 AGTGGTCATTCGGGACA
1 AGTGGTCACTCGGGACA
76765 AATTTGAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCACTCGGGACAT
Found at i:78058 original size:21 final size:21
Alignment explanation
Indices: 78033--78085 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
78023 TTTATCCGAT
78033 AGATGAAGCAAGATTTTATGA
1 AGATGAAGCAAGATTTTATGA
78054 AGATGAAGCAAGATTTTATGA
1 AGATGAAGCAAGATTTTATGA
78075 AGATGAAGCAA
1 AGATGAAGCAA
78086 TGGAATCGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.25
Consensus pattern (21 bp):
AGATGAAGCAAGATTTTATGA
Found at i:78659 original size:12 final size:12
Alignment explanation
Indices: 78638--78670 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
78628 TACGACTCAG
78638 AGAGGAAGAGGT
1 AGAGGAAGAGGT
*
78650 AGAGGTAGAGGT
1 AGAGGAAGAGGT
78662 AGAGGAAGA
1 AGAGGAAGA
78671 AGTCAGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.48, T:0.09
Consensus pattern (12 bp):
AGAGGAAGAGGT
Found at i:81394 original size:78 final size:78
Alignment explanation
Indices: 81234--81383 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 78
81224 TGGTTTTGGA
*
81234 AGACTTTGCATGAAGCACTAGGAACTCGACTGAACTTTAGCATAATTTTTCATCCTCAGACTGAT
1 AGACTTTGCATGAAGCACTAGGAACTCGACTGAACTTTAGCACAATTTTTCATCCTCAGACTGAT
*
81299 GGACAGTCTAAGC
66 AGACAGTCTAAGC
* * *
81312 AGACTTTGCATGAAGCGCTAGGAACTCGACTGAACTTTAGTACAATGTTTT-ATCCTTAGACTGA
1 AGACTTTGCATGAAGCACTAGGAACTCGACTGAACTTTAGCACAAT-TTTTCATCCTCAGACTGA
81376 TAGACAGT
65 TAGACAGT
81384 TTGAGTAGAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 62 0.94
79 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (78 bp):
AGACTTTGCATGAAGCACTAGGAACTCGACTGAACTTTAGCACAATTTTTCATCCTCAGACTGAT
AGACAGTCTAAGC
Found at i:86014 original size:2 final size:2
Alignment explanation
Indices: 86007--86035 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
85997 TGTTTTATTA
86007 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 A
86036 GGCATGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88642 original size:22 final size:21
Alignment explanation
Indices: 88614--88692 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 21
88604 TGTTTAAGCC
88614 TTCATAGGGTTATTGATACCCA
1 TTCATAGGG-TATTGATACCCA
*
88636 TTCATAGGGGTATCCG-TACCCA
1 TTCATA-GGGTAT-TGATACCCA
88658 TTCATAAGGGTATTGATACCCA
1 TTCAT-AGGGTATTGATACCCA
88680 TTCATAGAGGTAT
1 TTCATAG-GGTAT
88693 CGGTACCTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.06
22 42 0.84
23 5 0.10
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCATAGGGTATTGATACCCA
Found at i:88672 original size:44 final size:44
Alignment explanation
Indices: 88614--88699 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
88604 TGTTTAAGCC
*
88614 TTCATAGGGTTATTGATACCCATTCATAGGGGTATCCGTACCCA
1 TTCATAGGGTTATTGATACCCATTCATAGAGGTATCCGTACCCA
*
88658 TTCATAAGGG-TATTGATACCCATTCATAGAGGTATCGGTACC
1 TTCAT-AGGGTTATTGATACCCATTCATAGAGGTATCCGTACC
88700 TCTTAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
TTCATAGGGTTATTGATACCCATTCATAGAGGTATCCGTACCCA
Found at i:90103 original size:48 final size:47
Alignment explanation
Indices: 89984--90109 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 47
89974 CGGTGCACTA
89984 AGAGTGCATCGATGCAT-G-AAATGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCATAGTAAATGCATTCGATGTTTCAAAATAGCC
*
90029 AGAGTGCATCGATGCATAGCT-GATGCATTCGATGTTTTCATAAA-A-CTC
1 AGAGTGCATCGATGCATAG-TAAATGCATTCGATG-TTTCA-AAATAGC-C
** * *
90077 TTAGTGCATTGATGCATAGTATATGCA-TCGATG
1 AGAGTGCATCGATGCATAGTAAATGCATTCGATG
90110 CATAGTATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
45 17 0.25
46 1 0.01
47 20 0.29
48 28 0.41
49 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (47 bp):
AGAGTGCATCGATGCATAGTAAATGCATTCGATGTTTCAAAATAGCC
Found at i:90109 original size:19 final size:19
Alignment explanation
Indices: 90081--90131 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
90071 AAACTCTTAG
*
90081 TGCATTGATGCATAGTATA
1 TGCATCGATGCATAGTATA
90100 TGCATCGATGCATAGTATA
1 TGCATCGATGCATAGTATA
90119 TGCATCGATGCAT
1 TGCATCGATGCAT
90132 GAAATGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCATAGTATA
Found at i:92793 original size:22 final size:22
Alignment explanation
Indices: 92765--92840 Score: 152
Period size: 22 Copynumber: 3.5 Consensus size: 22
92755 CATGACCTTG
92765 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
92787 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
92809 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
92831 TGCATCGATG
1 TGCATCGATG
92841 AACTGTTAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:95111 original size:61 final size:61
Alignment explanation
Indices: 95016--95141 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
95006 CCAAGATTGT
95016 CTTTACCGTTGTTTAAAACAAAACATTTACATCCAAAAGGATGAAAATAGCTAATGTTAGG
1 CTTTACCGTTGTTTAAAACAAAACATTTACATCCAAAAGGATGAAAATAGCTAATGTTAGG
95077 CTTTACCGTTGTTTAAAACAAAACATTTACATCCAAAAGGATGAAAATAGCTAATGTTAGG
1 CTTTACCGTTGTTTAAAACAAAACATTTACATCCAAAAGGATGAAAATAGCTAATGTTAGG
95138 CTTT
1 CTTT
95142 TTATTTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (61 bp):
CTTTACCGTTGTTTAAAACAAAACATTTACATCCAAAAGGATGAAAATAGCTAATGTTAGG
Found at i:98707 original size:65 final size:65
Alignment explanation
Indices: 98567--98726 Score: 170
Period size: 65 Copynumber: 2.5 Consensus size: 65
98557 TGCACTAAGA
* *
98567 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGGGTGCATCAATGCATGACTG
1 GTGCATCGATGCATGAAATACATTCGATGTTTTCAAAATAGCCAGAGTGCATCAATGCATGACTG
* * * * *
98631 GTGCATTGATGCATCAAATACATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGTATAGT
1 GTGCATCGATGCATGAAATACATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCAATGCAT-G-
98694 A-T-
62 ACTG
98696 GTGCATCGATGCATGAAATTA-ATTCGATGTT
1 GTGCATCGATGCATGAAA-TACATTCGATGTT
98727 CAATTTATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
64 27 0.33
65 46 0.57
66 7 0.09
67 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATACATTCGATGTTTTCAAAATAGCCAGAGTGCATCAATGCATGACTG
Found at i:98765 original size:65 final size:64
Alignment explanation
Indices: 98567--98774 Score: 169
Period size: 65 Copynumber: 3.2 Consensus size: 64
98557 TGCACTAAGA
** * * * *
98567 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGC-CAGGGTGCATCAATGCATGACTG
1 GTGCATCGATGCATGAAATTAATTCGATGTTTCAATATA-CTCATGGTGCATCGATGCATGATTG
* * * *
98631 GTGCATTGATGCATCAAA-TACATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGTAT-A
1 GTGCATCGATGCATGAAATTA-ATTCGATG-TTTCAAT-ATACTCATG-GTGCATCGATGCATGA
98692 GTAT-
62 -T-TG
* *
98696 GTGCATCGATGCATGAAATTAATTCGATG-TTCAATTTATTTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATTAATTCGATGTTTCAATATA-CTCATGGTGCATCGATGCAT-GATT
98760 G
64 G
*
98761 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
98775 CACCTTGAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
63 4 0.04
64 46 0.41
65 59 0.52
66 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATTAATTCGATGTTTCAATATACTCATGGTGCATCGATGCATGATTG
Found at i:101292 original size:13 final size:14
Alignment explanation
Indices: 101269--101298 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
101259 TTCCCATTAC
101269 AGACGTGCATATGA
1 AGACGTGCATATGA
101283 AGAC-TGCATATGA
1 AGACGTGCATATGA
101296 AGA
1 AGA
101299 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:101476 original size:3 final size:3
Alignment explanation
Indices: 101468--101502 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
101458 GAATAGGGTT
101468 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
101503 TTTTGCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:101860 original size:22 final size:22
Alignment explanation
Indices: 101715--101867 Score: 191
Period size: 22 Copynumber: 7.0 Consensus size: 22
101705 GATGTTTGAG
101715 CATTCATAGGGGTATCGGTACC
1 CATTCATAGGGGTATCGGTACC
*
101737 CATTC-TAGGGGTAACGGTACC
1 CATTCATAGGGGTATCGGTACC
* *
101758 CATTCATAAGGGTAACGGTACC
1 CATTCATAGGGGTATCGGTACC
* * *
101780 CATTCATAAGGGTATTGATACC
1 CATTCATAGGGGTATCGGTACC
**
101802 CATTCATAGGGGTATATGTACC
1 CATTCATAGGGGTATCGGTACC
* * *
101824 CATTCATAAGGGTATTGATACC
1 CATTCATAGGGGTATCGGTACC
*
101846 CATTCATAGGGGTATCAGTACC
1 CATTCATAGGGGTATCGGTACC
101868 TCTTAATATT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
21 20 0.18
22 93 0.82
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
CATTCATAGGGGTATCGGTACC
Found at i:101867 original size:44 final size:44
Alignment explanation
Indices: 101715--101867 Score: 211
Period size: 44 Copynumber: 3.5 Consensus size: 44
101705 GATGTTTGAG
* * ** *
101715 CATTCATAGGGGTATCGGTACCCATTC-TAGGGGTAACGGTACC
1 CATTCATAGGGGTATCAGTACCCATTCATAAGGGTATTGATACC
* * *
101758 CATTCATAAGGGTAACGGTACCCATTCATAAGGGTATTGATACC
1 CATTCATAGGGGTATCAGTACCCATTCATAAGGGTATTGATACC
101802 CATTCATAGGGGTAT-ATGTACCCATTCATAAGGGTATTGATACC
1 CATTCATAGGGGTATCA-GTACCCATTCATAAGGGTATTGATACC
101846 CATTCATAGGGGTATCAGTACC
1 CATTCATAGGGGTATCAGTACC
101868 TCTTAATATT
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
43 25 0.26
44 72 0.73
45 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
CATTCATAGGGGTATCAGTACCCATTCATAAGGGTATTGATACC
Found at i:109944 original size:21 final size:21
Alignment explanation
Indices: 109919--109991 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
109909 GTTATTCCTT
109919 TGATGAATTACGTGAGGCTTA
1 TGATGAATTACGTGAGGCTTA
*
109940 TGATGAATTACATGAGGCTTA
1 TGATGAATTACGTGAGGCTTA
109961 TGATGAATTACAG-GAGGCTTA
1 TGATGAATTAC-GTGAGGCTTA
109982 TGATGAATTA
1 TGATGAATTA
109992 TCCTCAGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (21 bp):
TGATGAATTACGTGAGGCTTA
Found at i:125348 original size:21 final size:20
Alignment explanation
Indices: 125315--125353 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
125305 TAATGGATGG
*
125315 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
125335 TTGTTTTTCTTATGATGTT
1 TTGTTTTT-GTATGATGTT
125354 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:125453 original size:23 final size:19
Alignment explanation
Indices: 125399--125443 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
125389 CATTCCTTAG
* *
125399 GAGAATTCTTAGTGTTCGA
1 GAGAATGCTTAGTGTTCAA
125418 GAGAATGCTTAGTGTTCAA
1 GAGAATGCTTAGTGTTCAA
125437 GAGAATG
1 GAGAATG
125444 ACTAAGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (19 bp):
GAGAATGCTTAGTGTTCAA
Found at i:126305 original size:23 final size:22
Alignment explanation
Indices: 126262--126308 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
126252 TGTCATAGCA
126262 TTTTTTATTTTACTTGTTTATT
1 TTTTTTATTTTACTTGTTTATT
126284 TTTTTATAGTTTTACTTG-TTATT
1 TTTTT-TA-TTTTACTTGTTTATT
126307 TT
1 TT
126309 CCTTGTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.22
23 9 0.39
24 9 0.39
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (22 bp):
TTTTTTATTTTACTTGTTTATT
Found at i:134734 original size:20 final size:20
Alignment explanation
Indices: 134705--134743 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
134695 AGAGCTCATA
*
134705 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
134725 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
134744 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:142657 original size:26 final size:27
Alignment explanation
Indices: 142628--142687 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
142618 ATTATATATG
* *
142628 AAATATATCAATTTA-AATTATAATAA
1 AAATATATAAAATTATAATTATAATAA
*
142654 AAAT-TAAAAAATTATAATTATAATAA
1 AAATATATAAAATTATAATTATAATAA
*
142680 AAACATAT
1 AAATATAT
142688 TTTATAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 7 0.26
26 18 0.67
27 2 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATATATAAAATTATAATTATAATAA
Found at i:142682 original size:20 final size:20
Alignment explanation
Indices: 142642--142682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
142632 ATATCAATTT
*
142642 AAATTATAATAAAAATTAAA
1 AAATTATAATAAAAATAAAA
* *
142662 AAATTATAATTATAATAAAA
1 AAATTATAATAAAAATAAAA
142682 A
1 A
142683 CATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTATAATAAAAATAAAA
Found at i:151004 original size:18 final size:17
Alignment explanation
Indices: 150981--151017 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
150971 CTAATTTAAC
150981 TTTTAAAAATAAAAGTTA
1 TTTTAAAAATAAAA-TTA
*
150999 TTTTAAATATAAAATTA
1 TTTTAAAAATAAAATTA
151016 TT
1 TT
151018 CAAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTTAAAAATAAAATTA
Found at i:151065 original size:16 final size:17
Alignment explanation
Indices: 151026--151066 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
151016 TTCAAATATT
151026 TAAAAAAATACAAAAAA
1 TAAAAAAATACAAAAAA
**
151043 T-AAAAAATA-AATTAA
1 TAAAAAAATACAAAAAA
151058 TAAAAAAAT
1 TAAAAAAAT
151067 TGAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 15 0.71
17 1 0.05
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAAAATACAAAAAA
Found at i:158058 original size:6 final size:6
Alignment explanation
Indices: 158049--158074 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
158039 AGAAAAAGAA
158049 AGGGAT AGGGAT AGGGAT AGGGAT AG
1 AGGGAT AGGGAT AGGGAT AGGGAT AG
158075 AGAAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGGGAT
Found at i:158491 original size:15 final size:15
Alignment explanation
Indices: 158462--158506 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
158452 TGATTAAAAT
158462 TTGAATAATATTTAAA
1 TTGAATAA-ATTTAAA
*
158478 TTGAATAAATTTAAT
1 TTGAATAAATTTAAA
158493 TTGAGGATAAATTT
1 TTGA--ATAAATTT
158507 GATTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.38
16 8 0.31
17 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (15 bp):
TTGAATAAATTTAAA
Found at i:160858 original size:20 final size:20
Alignment explanation
Indices: 160833--160884 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
160823 TGAGTGTTGC
* *
160833 ATGAAGGTTTGGAATTTTTG
1 ATGAAGGTCTGGAATTTTCG
160853 ATGAAGGTCTGGAATTTTCG
1 ATGAAGGTCTGGAATTTTCG
160873 ATGAAGGTCTGG
1 ATGAAGGTCTGG
160885 GTTGATTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.37
Consensus pattern (20 bp):
ATGAAGGTCTGGAATTTTCG
Done.