Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021940.1 Corchorus olitorius cultivar O-4 contig21973, 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: 122469
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:705 original size:13 final size:12
Alignment explanation
Indices: 675--730 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
665 CCCGTTGAGG
675 AAATG-TTTTAT
1 AAATGCTTTTAT
*
686 AACTGCTTTATAT
1 AAATGCTTT-TAT
699 AAATGC-TTTAT
1 AAATGCTTTTAT
710 AAATG-TTTTAAT
1 AAATGCTTTT-AT
722 AAATG-TTTT
1 AAATGCTTTT
731 GGGTGCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 15 0.38
12 16 0.41
13 8 0.21
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (12 bp):
AAATGCTTTTAT
Found at i:708 original size:24 final size:23
Alignment explanation
Indices: 675--726 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
665 CCCGTTGAGG
* *
675 AAATGTTTTATAACTGCTTTATAT
1 AAATGCTTTATAAATGCTTTA-AT
*
699 AAATGCTTTATAAATGTTTTAAT
1 AAATGCTTTATAAATGCTTTAAT
722 AAATG
1 AAATG
727 TTTTGGGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (23 bp):
AAATGCTTTATAAATGCTTTAAT
Found at i:5038 original size:11 final size:11
Alignment explanation
Indices: 5022--5046 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5012 AGATAACTTC
5022 TTTTCTTCTAG
1 TTTTCTTCTAG
5033 TTTTCTTCTAG
1 TTTTCTTCTAG
5044 TTT
1 TTT
5047 CTAGGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:5837 original size:15 final size:15
Alignment explanation
Indices: 5807--5848 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5797 TTACTTTGCT
5807 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
5823 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
5838 TTGCTTTCTGT
1 TTGTTTTCTGT
5849 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:6225 original size:21 final size:20
Alignment explanation
Indices: 6192--6232 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6182 AAAAAAATTG
6192 ATTTTTTTTTGCGT-TTTTT
1 ATTTTTTTTTGCGTCTTTTT
6211 ATTTTTGTGTTTGCGTCTTTTT
1 ATTTTT-T-TTTGCGTCTTTTT
6233 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 7 0.37
22 5 0.26
ACGTcount: A:0.05, C:0.07, G:0.15, T:0.73
Consensus pattern (20 bp):
ATTTTTTTTTGCGTCTTTTT
Found at i:6283 original size:23 final size:23
Alignment explanation
Indices: 6254--6297 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
6244 TTGTTTTGTG
6254 TTTTGCGTCGA-AAAAAAAAGAGC
1 TTTTGCGTC-ATAAAAAAAAGAGC
6277 TTTTGCGTCATAAAAAAAAGA
1 TTTTGCGTCATAAAAAAAAGA
6298 AAAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (23 bp):
TTTTGCGTCATAAAAAAAAGAGC
Found at i:6415 original size:17 final size:16
Alignment explanation
Indices: 6389--6423 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6379 CTACTAACAA
6389 TTTTTCTTTTGAGATTT
1 TTTTTCTTTTGAG-TTT
*
6406 TTTTTTTTTTGAGTTT
1 TTTTTCTTTTGAGTTT
6422 TT
1 TT
6424 CTAGGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.09, C:0.03, G:0.11, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTTGAGTTT
Found at i:9413 original size:21 final size:21
Alignment explanation
Indices: 9389--9443 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
9379 CCGCCCATTG
*
9389 CCGTGCCACCACCGGTTATGC
1 CCGTGCCACCACCGGCTATGC
9410 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTATGC
*
9431 CCGTGCCATCACC
1 CCGTGCCACCACC
9444 ATTCAGTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.47, G:0.22, T:0.16
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTATGC
Found at i:13649 original size:171 final size:171
Alignment explanation
Indices: 13364--13705 Score: 666
Period size: 171 Copynumber: 2.0 Consensus size: 171
13354 AGCAGCGTCT
*
13364 TACTCGAGTGTCACTCAAGCTGTAGTTACTCGATTTATCAAGAAGGAAATCATTTGCAGGTACGG
1 TACTCGAGTGTCACTCAAGCTGTAGTTACTCGATTTATCAAGAAGGAAATCATTTGCAGGTACAG
13429 GTTGCCAGAAAGAATCATAACTGATAATGCATCAAACTTAAATCGGGGATTGATAGAAGAGACGT
66 GTTGCCAGAAAGAATCATAACTGATAATGCATCAAACTTAAATCGGGGATTGATAGAAGAGACGT
13494 GCAAATAGTTCAAGATTATTAATAGCAATTCGACTATGTAC
131 GCAAATAGTTCAAGATTATTAATAGCAATTCGACTATGTAC
13535 TACTCGAGTGTCACTCAAGCTGTAGTTACTCGATTTATCAAGAAGGAAATCATTTGCAGGTACAG
1 TACTCGAGTGTCACTCAAGCTGTAGTTACTCGATTTATCAAGAAGGAAATCATTTGCAGGTACAG
*
13600 GTTGCCAGAAAGAATCATAATTGATAATGCATCAAACTTAAATCGGGGATTGATAGAAGAGACGT
66 GTTGCCAGAAAGAATCATAACTGATAATGCATCAAACTTAAATCGGGGATTGATAGAAGAGACGT
13665 GCAAATAGTTCAAGATTATTAATAGCAATTCGACTATGTAC
131 GCAAATAGTTCAAGATTATTAATAGCAATTCGACTATGTAC
13706 CGACCTAAGA
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 169 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (171 bp):
TACTCGAGTGTCACTCAAGCTGTAGTTACTCGATTTATCAAGAAGGAAATCATTTGCAGGTACAG
GTTGCCAGAAAGAATCATAACTGATAATGCATCAAACTTAAATCGGGGATTGATAGAAGAGACGT
GCAAATAGTTCAAGATTATTAATAGCAATTCGACTATGTAC
Found at i:15403 original size:61 final size:61
Alignment explanation
Indices: 15329--16431 Score: 731
Period size: 61 Copynumber: 17.8 Consensus size: 61
15319 GCATCAACTA
* * * *
15329 CAGATAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTAGTCTTATTCCAGTTCAAACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTTCAGACCT
* *
15390 CAGATAGGTCTTTCTCATTTTTAAAGTAGACCACAGACT-GTCTTCTTCCAGTTCAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTTCAGACCT
* * *
15450 CAGATAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTAGTCTTCTTCCAGTTTAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTTCAGACCT
* * * *
15511 CAG--A---------CAGTTTTAAATTAAACCACAGACTGGTCATCTT-CAGTTTCGGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAG-TTCAGACCT
* * *
15561 CAGACAGGTCTTTCTTAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCTAGTTTAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTTCAGACCT
* ** * * * * * * ** *
15622 CAGACAAGTCTCCCTTAATTTTTAAATTCGACTACAGACTGGTCATCTT-TTGTTCCACACCT
1 CAGACAGGTCTTTC-TCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTT-CAGACCT
* * * * * *
15684 CAGACA-ATCTTTCTCAATTTTGAAGTAGACCACAGACTAGTCATCTT-CTGTTTCAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAG-TTCAGACCT
* * * * * *
15744 CAGACAAGTCTTTCTCAATTTCAAAGTCGACCACAGACTGGTCATC-TCCAATAGTC-GACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGT--TCAGACCT
* * * * *
15805 CAGACAAGTCTTTCTCAATTTTAAAGTTGACCACAGACTGATCATCTT-CAGTTTCAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAG-TTCAGACCT
* * * * *
15866 CAGACAGGTCTTTCTCAGTTTTCAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCT
1 CAGACAGGTCTTTCTCAGTTTT-AAAGTAGACCACAGACTGGTC--T-TCTTCCAGTTCAGACCT
* * * * * * *
15931 CATACAGGTCTCTCTTAGTTTTAAAAGTTGACCACAGACTGGTCTCCTTCTTCAAATCCAGACCT
1 CAGACAGGTCTTTCTCAGTTTT-AAAGTAGACCACAGACTGG--T-CTTCTTCCAGTTCAGACCT
** * * * * * * *
15996 CAGACAAATCTCTCTCTTAGTTTTTAAATTCGACCACAGACTGATCTTTATCTTCTATTTTAGAC
1 CAGACAGGTCT-T-TCTCAG-TTTTAAAGTAGACCACAGACTGGTC--T-TCTTCCAGTTCAGAC
16061 CT
60 CT
* ** * * * * *
16063 TAGACAGGTCTCCCTTAGTTTTAAAAGTTGACCACAGACTGGTCTTCTTCTCCAAATCCAGACCC
1 CAGACAGGTCTTTCTCAGTTTT-AAAGTAGACCACAGACTGGTCTTC-T-TCC-AGTTCAGACCT
* * * * * * *
16128 CAGACAGGTCTCTCTCTTAGTTTTTAAACTCGACCACAGACCGGTCTTTATCTTCTAGTTTAGAT
1 CAGACAGGTCT-T-TCTCAG-TTTTAAAGTAGACCACAGACTGGTC--T-TCTTCCAGTTCAGAC
16193 CT
60 CT
* * * * * * **
16195 CAGACAGATCTTTCTTAGTTTTTAAACTTGACCATAGACTGATCTTTATCTTCCAGTTTGGACCT
1 CAGACAGGTCTTTCTCAG-TTTTAAAGTAGACCACAGACTGGTC--T-TCTTCCAGTTCAGACCT
* * * * *
16260 CAGACAGGTCTTTCTTAGTTTTTAAATTTGACCACAGACTGGTCTTTATCTTCTAGTTTAGACCT
1 CAGACAGGTCTTTCTCAG-TTTTAAAGTAGACCACAGACTGGTC--T-TCTTCCAGTTCAGACCT
* * * * * *
16325 CAAACATGTC--TCTTAGTTTTAAAATCGACCACA-ACATGGTCATCTTCC-GTTCCAGACCT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGAC-TGGTCTTCTTCCAGTT-CAGACCT
* * * * *
16384 CAGACGGGTCTCTCTTAGTTTTAAAGTCGACCACAAACTGGTCTTCTT
1 CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTT
16432 TCTTAATAAC
Statistics
Matches: 856, Mismatches: 133, Indels: 106
0.78 0.12 0.10
Matches are distributed among these distances:
49 3 0.00
50 39 0.05
52 1 0.00
58 3 0.00
59 19 0.02
60 102 0.12
61 261 0.30
62 88 0.10
63 8 0.01
64 7 0.01
65 222 0.26
66 5 0.01
67 83 0.10
68 11 0.01
69 2 0.00
70 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (61 bp):
CAGACAGGTCTTTCTCAGTTTTAAAGTAGACCACAGACTGGTCTTCTTCCAGTTCAGACCT
Found at i:15534 original size:50 final size:50
Alignment explanation
Indices: 15465--15567 Score: 145
Period size: 50 Copynumber: 2.1 Consensus size: 50
15455 AGGTCTTTCT
* *
15465 CAGTTTTAAAGTAGACCACAGACTAGTCTTCTTCCAGTTT-AGACCTCAGA
1 CAGTTTTAAAGTAAACCACAGACTAGTCATCTT-CAGTTTCAGACCTCAGA
* * *
15515 CAGTTTTAAATTAAACCACAGACTGGTCATCTTCAGTTTCGGACCTCAGA
1 CAGTTTTAAAGTAAACCACAGACTAGTCATCTTCAGTTTCAGACCTCAGA
15565 CAG
1 CAG
15568 GTCTTTCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 6 0.13
50 41 0.87
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (50 bp):
CAGTTTTAAAGTAAACCACAGACTAGTCATCTTCAGTTTCAGACCTCAGA
Found at i:15823 original size:28 final size:29
Alignment explanation
Indices: 15739--15823 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 29
15729 TTCTGTTTCA
15739 GACCTCAGACAAGTCTTTCTCAATTTCAAAGTC
1 GACCTCAGACAAGTCTTTCTCAA--T--AAGTC
* ** *
15772 GACCACAGACTGGTC-ATCTCCAAT-AGTC
1 GACCTCAGACAAGTCTTTCT-CAATAAGTC
15800 GACCTCAGACAAGTCTTTCTCAAT
1 GACCTCAGACAAGTCTTTCTCAAT
15824 TTTAAAGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
28 20 0.48
29 3 0.07
31 1 0.02
32 3 0.07
33 15 0.36
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27
Consensus pattern (29 bp):
GACCTCAGACAAGTCTTTCTCAATAAGTC
Found at i:15842 original size:33 final size:33
Alignment explanation
Indices: 15739--15842 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 33
15729 TTCTGTTTCA
* *
15739 GACCTCAGACAAGTCTTTCTCAATTTCAAAGTC
1 GACCACAGACAAGTCTTTCTCAATTTTAAAGTC
** *
15772 GACCACAGACTGGTC-ATCTCCAA---T--AGTC
1 GACCACAGACAAGTCTTTCT-CAATTTTAAAGTC
* *
15800 GACCTCAGACAAGTCTTTCTCAATTTTAAAGTT
1 GACCACAGACAAGTCTTTCTCAATTTTAAAGTC
15833 GACCACAGAC
1 GACCACAGAC
15843 TGATCATCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
28 19 0.36
29 3 0.06
31 1 0.02
32 3 0.06
33 27 0.51
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (33 bp):
GACCACAGACAAGTCTTTCTCAATTTTAAAGTC
Found at i:15938 original size:65 final size:63
Alignment explanation
Indices: 15516--16428 Score: 689
Period size: 65 Copynumber: 14.5 Consensus size: 63
15506 GACCTCAGAC
** *
15516 AGTTTTAAATTAAACCACAGACTGGTC--ATCTTC-AGTTTCGGACCTCAGACAGGTCTTTCTT
1 AGTTTTAAATTCGACCACAGACTGGTCTTATCTTCTAGTTT-AGACCTCAGACAGGTCTTTCTT
* * * **
15577 AGTTTTAAAGTAGACCACAGACTGGTC-T-TCTTCTAGTTTAGACCTCAGACAAGTCTCCCTT
1 AGTTTTAAATTCGACCACAGACTGGTCTTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
* * * * * * *
15638 AATTTTTAAATTCGACTACAGACTGGTC--ATCTT-TTGTTCCACACCTCAGACA-ATCTTTCTC
1 -AGTTTTAAATTCGACCACAGACTGGTCTTATCTTCTAGTT-TAGACCTCAGACAGGTCTTTCTT
* * * * * * *
15699 AATTTTGAAGTAGACCACAGACTAGTC--ATCTTCT-GTTTCAGACCTCAGACAAGTCTTTCTC
1 AGTTTTAAATTCGACCACAGACTGGTCTTATCTTCTAGTTT-AGACCTCAGACAGGTCTTTCTT
* * * * * * *
15760 AATTTCAAAGTCGACCACAGACTGGTC--ATCTCCAATAG--TCGACCTCAGACAAGTCTTTCTC
1 AGTTTTAAATTCGACCACAGACTGGTCTTATCTTC--TAGTTTAGACCTCAGACAGGTCTTTCTT
* * *
15821 AATTTTAAAGTT-GACCACAGACTGATC--ATCTTC-AGTTTCAGACCTCAGACAGGTCTTTCTC
1 AGTTTTAAA-TTCGACCACAGACTGGTCTTATCTTCTAGTTT-AGACCTCAGACAGGTCTTTCTT
* * *
15882 AGTTTTCAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCATACAGGTCTCTCTT
1 AGTTTT-AAATTCGACCACAGACTGGTC-TTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
* * ** **
15947 AGTTTTAAAAGTT-GACCACAGACTGGTCTCCT-TCTTCAAATCCAGACCTCAGACAAATCTCTC
1 AGTTTT-AAA-TTCGACCACAGACTGGTCT--TATCTTCTAGTTTAGACCTCAGACAGGTCT-T-
16010 TCTT
60 TCTT
* * * **
16014 AGTTTTTAAATTCGACCACAGACTGATCTTTATCTTCTATTTTAGACCTTAGACAGGTCTCCCTT
1 AG-TTTTAAATTCGACCACAGACTGGTC-TTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
* * * * ** *
16079 AGTTTTAAAAGTT-GACCACAGACTGGTCTTCTTCTCCAAATCCAGACCCCAGACAGGTCTCTCT
1 AGTTTT-AAA-TTCGACCACAGACTGGTCTT-ATCTTCTAGTTTAGACCTCAGACAGGTCT-T-T
16143 CTT
61 CTT
* * * *
16146 AGTTTTTAAACTCGACCACAGACCGGTCTTTATCTTCTAGTTTAGATCTCAGACAGATCTTTCTT
1 AG-TTTTAAATTCGACCACAGACTGGTC-TTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
* * * *
16211 AGTTTTTAAACTT-GACCATAGACTGATCTTTATCTTCCAGTTTGGACCTCAGACAGGTCTTTCT
1 AG-TTTTAAA-TTCGACCACAGACTGGTC-TTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCT
16275 T
63 T
* * *
16276 AGTTTTTAAATTTGACCACAGACTGGTCTTTATCTTCTAGTTTAGACCTCAAACATGTC--TCTT
1 AG-TTTTAAATTCGACCACAGACTGGTC-TTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
* * * * *
16339 AGTTTTAAAATCGACCACA-ACATGGTC--ATCTTC-CGTTCCAGACCTCAGACGGGTCTCTCTT
1 AGTTTTAAATTCGACCACAGAC-TGGTCTTATCTTCTAGTT-TAGACCTCAGACAGGTCTTTCTT
* *
16400 AGTTTTAAAGTCGACCACAAACTGGTCTT
1 AGTTTTAAATTCGACCACAGACTGGTCTT
16429 CTTTCTTAAT
Statistics
Matches: 699, Mismatches: 106, Indels: 92
0.78 0.12 0.10
Matches are distributed among these distances:
58 5 0.01
59 19 0.03
60 41 0.06
61 198 0.28
62 85 0.12
63 7 0.01
64 10 0.01
65 221 0.32
66 16 0.02
67 86 0.12
68 11 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (63 bp):
AGTTTTAAATTCGACCACAGACTGGTCTTATCTTCTAGTTTAGACCTCAGACAGGTCTTTCTT
Found at i:16033 original size:132 final size:129
Alignment explanation
Indices: 15518--16428 Score: 711
Period size: 132 Copynumber: 7.2 Consensus size: 129
15508 CCTCAGACAG
** * * *
15518 TTTTAAATTAAACCACAGACTGGTC---ATCTTC-AGTTTCGGACCTCAGACAGGTCTTTCTTAG
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTT-AGACCTCAGACAGGTCTCTCTTAG
* * * ** * ** *
15579 TTTT-AAAGTAGACCACAGACTGG--TCTTCTTCTAGTTTAGACCTCAGACAAGTCTCCCTTAAT
65 TTTTAAAAGTTGACCACAGACTGGTCTCTTCTTCAAATCCAGACCTCAGACAGGTCTTTCTTAGT
* * * * * * * * *
15641 TTTTAAATTCGACTACAGACTGGTC---ATCTT-TTGTTCCACACCTCAGACA-ATCTTTCTCAA
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTT-TAGACCTCAGACAGGTCTCTCTTAG
* * * * * *
15701 TTTT-GAAGTAGACCACAGACTAGTCATCTTCTGT----TTCAGACCTCAGACAAGTCTTTCTCA
65 TTTTAAAAGTTGACCACAGACTGGTC-TCTTCT-TCAAATCCAGACCTCAGACAGGTCTTTCTTA
*
15761 -A
128 GT
* * * * * * * *
15762 TTTCAAAGTCGACCACAGACTGGTC---ATCTCCAATAG--TCGACCTCAGACAAGTCTTTCTCA
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTC--TAGTTTAGACCTCAGACAGGTCTCTCTTA
* * * ** * *
15822 ATTTT-AAAGTTGACCACAGACT-G-ATCATCTTCAGTTTCAGACCTCAGACAGGTCTTTCTCAG
64 GTTTTAAAAGTTGACCACAGACTGGTCTCTTCTTCAAATCCAGACCTCAGACAGGTCTTTCTTAG
15884 T
129 T
* *
15885 TTTCAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCATACAGGTCTCTCTTAGT
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTTAGT
**
15950 TTTAAAAGTTGACCACAGACTGGTCTCCTTCTTCAAATCCAGACCTCAGACAAATCTCTCTCTTA
66 TTTAAAAGTTGACCACAGACTGGTCT-CTTCTTCAAATCCAGACCTCAGACAGGTCT-T-TCTTA
16015 GT
128 GT
* * *
16017 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTATTTTAGACCTTAGACAGGTCTCCCTTAGT
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTTAGT
* *
16082 TTTAAAAGTTGACCACAGACTGGTCTTCTTCTCCAAATCCAGACCCCAGACAGGTCTCTCTCTTA
66 TTTAAAAGTTGACCACAGACTGGTC-TCTTCTTCAAATCCAGACCTCAGACAGGTCT-T-TCTTA
16147 GT
128 GT
* * * * * *
16149 TTTTAAACTCGACCACAGACCGGTCTTTATCTTCTAGTTTAGATCTCAGACAGATCTTTCTTAGT
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTTAGT
* * * * * * * ***
16214 TTTTAAACTTGACCATAGACTGATCTTTATCTTCCAGTTTGGACCTCAGACAGGTCTTTCTTAGT
66 TTTAAAAGTTGACCACAGACTGGTCTCT-TCTTCAAATCCAGACCTCAGACAGGTCTTTCTTAGT
* * * *
16279 TTTTAAATTTGACCACAGACTGGTCTTTATCTTCTAGTTTAGACCTCAAACA--TGTCTCTTAGT
1 TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTTAGT
* ** * *
16342 TTTAAAA-TCGACCACA-ACATGGTCATCTTC--C-GTTCCAGACCTCAGACGGGTCTCTCTTAG
66 TTTAAAAGTTGACCACAGAC-TGGTC-TCTTCTTCAAATCCAGACCTCAGACAGGTCTTTCTTAG
16402 -
129 T
* * *
16402 TTTTAAAGTCGACCACAAACTGGTCTT
1 TTTTAAATTCGACCACAGACTGATCTT
16429 CTTTCTTAAT
Statistics
Matches: 657, Mismatches: 101, Indels: 60
0.80 0.12 0.07
Matches are distributed among these distances:
118 1 0.00
119 5 0.01
121 37 0.06
122 105 0.16
123 87 0.13
124 27 0.04
125 7 0.01
126 31 0.05
127 30 0.05
128 18 0.03
129 1 0.00
130 78 0.12
131 4 0.01
132 225 0.34
133 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (129 bp):
TTTTAAATTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTTAGT
TTTAAAAGTTGACCACAGACTGGTCTCTTCTTCAAATCCAGACCTCAGACAGGTCTTTCTTAGT
Found at i:16103 original size:197 final size:190
Alignment explanation
Indices: 15515--16371 Score: 667
Period size: 197 Copynumber: 4.5 Consensus size: 190
15505 AGACCTCAGA
* * * *
15515 CAGTTTTAAA-TTAAACCACAGACTGGTC---ATCTTC-AGTTTCGGACCTCAGACAGGTCTTTC
1 CAGTTTTAAAGTT-GACCACAGACTGATCTTTATCTTCTAGTTT-AGACCTCAGACAGGTCTCTC
* * * * * **
15575 TTAGTTTT-AAAGTAGACCACAGACTGG--TCTTCTTCTAGTTTAGACCTCAGACAAGTCTCCCT
64 TTAGTTTTAAAAGTCGACCACAGACTGGTCTCTTCTTCAAATTCAGACCTCAGACAAATCTTTCT
* * * * * * * *
15637 TAATTTTTAAA-TTCGACTACAGACTGGTCATCTTTTGTTCCACACCTCAGACA-ATCTTTCT
129 TAGTTTTTAAACTT-GACCACAGACTGATCATCTTCTATTTCAGACCTCAGACAGGTCTTTCT
* * * * *
15698 CAATTTTGAAGTAGACCACAGACT-AGTC---ATCTTCT-GTTTCAGACCTCAGACAAGTCTTTC
1 CAGTTTTAAAGTTGACCACAGACTGA-TCTTTATCTTCTAGTTT-AGACCTCAGACAGGTCTCTC
* * * * *
15758 TCA-ATTTCAAAGTCGACCACAGACTGGTCATC-TC--CAATAGTC-GACCTCAGACAAGTCTTT
64 TTAGTTTTAAAAGTCGACCACAGACTGGTC-TCTTCTTCAA-ATTCAGACCTCAGACAAATCTTT
* * *
15818 CTCA-ATTTTAAAGTTGACCACAGACTGATCATCTTC-AGTTTCAGACCTCAGACAGGTCTTTCT
127 CTTAGTTTTTAAACTTGACCACAGACTGATCATCTTCTA-TTTCAGACCTCAGACAGGTCTTTCT
*
15881 CAGTTTTCAAA-TTCGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCATACAGGTCTCTC
1 CAGTTTT-AAAGTT-GACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTC
* *
15945 TTAGTTTTAAAAGTTGACCACAGACTGGTCTCCTTCTTCAAATCCAGACCTCAGACAAATCTCTC
64 TTAGTTTTAAAAGTCGACCACAGACTGGTCT-CTTCTTCAAATTCAGACCTCAGACAAATCT-T-
* *
16010 TCTTAGTTTTTAAA-TTCGACCACAGACTGATCTTTATCTTCTATTTTAGACCTTAGACAGGTCT
126 TCTTAGTTTTTAAACTT-GACCACAGACTGATC---ATCTTCTATTTCAGACCTCAGACAGGTCT
**
16074 CCCT
187 TTCT
* * * * * ** *
16078 TAGTTTTAAAAGTTGACCACAGACTGGTCTTCT-TCTCCAAATCCAGACCCCAGACAGGTCTCTC
1 CAGTTTT-AAAGTTGACCACAGACTGATCTT-TATCTTCTAGTTTAGACCTCAGACAGG--TCTC
* * * * * * * * *
16142 TCTTAGTTTTTAAACTCGACCACAGACCGGTCTTTATCTTCTAGTTTAGATCTCAGACAGATCTT
62 TCTTAGTTTTAAAAGTCGACCACAGACTGGTCTCT-TCTTCAAATTCAGACCTCAGACAAATCTT
* * *
16207 TCTTAGTTTTTAAACTTGACCATAGACTGATCTTTATCTTCCAGTTT-GGACCTCAGACAGGTCT
126 TCTTAGTTTTTAAACTTGACCACAGACTGATC---ATCTTCTA-TTTCAGACCTCAGACAGGTCT
16271 TTCT
187 TTCT
* * * * *
16275 TAGTTTTTAAATTTGACCACAGACTGGTCTTTATCTTCTAGTTTAGACCTCAAACA--TGTCTCT
1 CAG-TTTTAAAGTTGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCT
16338 TAGTTTTAAAA-TCGACCACA-ACATGGTCATCTTC
65 TAGTTTTAAAAGTCGACCACAGAC-TGGTC-TCTTC
16372 CGTTCCAGAC
Statistics
Matches: 548, Mismatches: 83, Indels: 77
0.77 0.12 0.11
Matches are distributed among these distances:
182 42 0.08
183 106 0.19
184 17 0.03
185 3 0.01
186 2 0.00
187 27 0.05
188 28 0.05
189 2 0.00
190 2 0.00
191 20 0.04
192 16 0.03
193 24 0.04
194 22 0.04
196 1 0.00
197 166 0.30
198 15 0.03
199 55 0.10
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (190 bp):
CAGTTTTAAAGTTGACCACAGACTGATCTTTATCTTCTAGTTTAGACCTCAGACAGGTCTCTCTT
AGTTTTAAAAGTCGACCACAGACTGGTCTCTTCTTCAAATTCAGACCTCAGACAAATCTTTCTTA
GTTTTTAAACTTGACCACAGACTGATCATCTTCTATTTCAGACCTCAGACAGGTCTTTCT
Found at i:16298 original size:34 final size:34
Alignment explanation
Indices: 16123--16306 Score: 89
Period size: 34 Copynumber: 5.5 Consensus size: 34
16113 TCCAAATCCA
* * *
16123 GACCCCAGACAGGTCTCTCTCTTAGTTTTTAAACTC
1 GACCACAGACAGGTCT-T-TCTTAGTTTTTAAATTT
* * *
16159 GACCACAGACCGGTC--T-TTA-TCTTCT-AGTTT
1 GACCACAGACAGGTCTTTCTTAGT-TTTTAAATTT
* * * *
16189 AGATCTCAGACAGATCTTTCTTAGTTTTTAAACTT
1 -GACCACAGACAGGTCTTTCTTAGTTTTTAAATTT
* * * * ** *
16224 GACCATAGACTGATC--T-TTA-TCTTCCAGTTT
1 GACCACAGACAGGTCTTTCTTAGTTTTTAAATTT
*
16254 GGACCTCAGACAGGTCTTTCTTAGTTTTTAAATTT
1 -GACCACAGACAGGTCTTTCTTAGTTTTTAAATTT
*
16289 GACCACAGACTGGTCTTT
1 GACCACAGACAGGTCTTT
16307 ATCTTCTAGT
Statistics
Matches: 104, Mismatches: 32, Indels: 26
0.64 0.20 0.16
Matches are distributed among these distances:
30 9 0.09
31 31 0.30
32 2 0.02
33 2 0.02
34 36 0.35
35 11 0.11
36 13 0.12
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (34 bp):
GACCACAGACAGGTCTTTCTTAGTTTTTAAATTT
Found at i:20788 original size:17 final size:17
Alignment explanation
Indices: 20755--20788 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20745 AAAAAAGTTT
*
20755 TCAAAAATCCAAAAAAA
1 TCAAAAATCAAAAAAAA
*
20772 TCAAAATTCAAAAAAAA
1 TCAAAAATCAAAAAAAA
20789 AATCAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (17 bp):
TCAAAAATCAAAAAAAA
Found at i:20860 original size:38 final size:37
Alignment explanation
Indices: 20801--20907 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 37
20791 TCAAAAAGCA
*
20801 TTTTCTTCATAGTTTTTAAATTGGGAAAGTTCCCACCAAG
1 TTTT-TTCA-AGTTTTCAAATTGGGAAAGTTCCCACC-AG
*
20841 TTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCATCAG
1 TTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCACCAG
* * *
20878 -GTTTT--AGTCTTCAAATTGGGGAAGTTCCCA
1 TTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCA
20908 TCAGGTTTAG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 23 0.37
36 4 0.06
37 2 0.03
38 25 0.40
39 4 0.06
40 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (37 bp):
TTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCACCAG
Found at i:20924 original size:33 final size:34
Alignment explanation
Indices: 20810--20944 Score: 155
Period size: 34 Copynumber: 3.9 Consensus size: 34
20800 ATTTTCTTCA
* * *
20810 TAGTTTTTAAATTGGGAAAGTTCCCACCAAGTTTTT
1 TAGTTTTCAAATTGGGAAAGTTCCCATC-AG-GTTT
20846 TCAAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
1 T--AGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
* *
20882 TAGTCTTCAAATTGGGGAAGTTCCCATCAGG-TT
1 TAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
* *
20915 TAGTTTTCAATTTAGAGAAAGTTCCCATCA
1 TAGTTTTCAAATT-GGGAAAGTTCCCATCA
20945 AAAGCATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
33 13 0.15
34 42 0.48
36 5 0.06
37 2 0.02
38 25 0.29
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (34 bp):
TAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
Found at i:23443 original size:218 final size:217
Alignment explanation
Indices: 23044--23487 Score: 762
Period size: 218 Copynumber: 2.0 Consensus size: 217
23034 ATAGAATACA
* *
23044 CAAATATTTTAGAGATTGACATTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCAT
1 CAAATTTTTTAGAGATTAACATTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCAT
*
23109 ATTTTCATCTTAATTAATTGAATAAACCCCGTCTATATGAATTTAGTGTCATCTAATAATTAAAC
66 ATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTAGTGTCATCTAATAATTAAAC
* *
23174 AAAATGCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
131 AAAATGCAAAATTCAGTATCCCCAAACTGAAATACTTAATACCCAAATCATTTCTCATCATCCCC
23239 AAATAATCATATGCACCATCCC
196 AAATAATCATATGCACCATCCC
**
23261 CAAATTTTTTAGAGATTAACATTTTTTTATATGGCCAAAATTGGCTTTAAACGTGTTTTAATCCA
1 CAAATTTTTTAGAGATTAACA-TTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCA
** * * *
23326 TATTTTCATCCTAATTAATTGAATAAAGTCTGTCTATATGAATTTTGTGTCATCTAATAATTAGA
65 TATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTAGTGTCATCTAATAATTAAA
*
23391 CAAAATGCAAAATTTAGTATCCCCAAACTGAAATACTTAATACCCAAATCATTTCTCATCATCCC
130 CAAAATGCAAAATTCAGTATCCCCAAACTGAAATACTTAATACCCAAATCATTTCTCATCATCCC
23456 CAAATAATCATATGCACCATCCC
195 CAAATAATCATATGCACCATCCC
23479 CAAATTTTT
1 CAAATTTTT
23488 AATACCCATA
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
217 19 0.09
218 194 0.91
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (217 bp):
CAAATTTTTTAGAGATTAACATTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCAT
ATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTAGTGTCATCTAATAATTAAAC
AAAATGCAAAATTCAGTATCCCCAAACTGAAATACTTAATACCCAAATCATTTCTCATCATCCCC
AAATAATCATATGCACCATCCC
Found at i:24157 original size:21 final size:21
Alignment explanation
Indices: 24131--24178 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
24121 TAGTGTCCTA
*
24131 GCGACGGATCCGGCTGGTGGT
1 GCGACGGATCCGGCTGCTGGT
*
24152 GCGACGGTTCCGGCTGCTGGT
1 GCGACGGATCCGGCTGCTGGT
24173 GCGACG
1 GCGACG
24179 ATTCCAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.27, G:0.46, T:0.19
Consensus pattern (21 bp):
GCGACGGATCCGGCTGCTGGT
Found at i:24302 original size:16 final size:16
Alignment explanation
Indices: 24250--24304 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
24240 GTTAAAAGAA
*
24250 AAAAAAAATAGCATAGT
1 AAAAAAAATATCA-AGT
* *
24267 AAAAAAAATATTAAGG
1 AAAAAAAATATCAAGT
24283 AAAAATAAA-ATCAAGT
1 AAAAA-AAATATCAAGT
24299 AAAAAA
1 AAAAAA
24305 TGTAATATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 17 0.53
17 14 0.44
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (16 bp):
AAAAAAAATATCAAGT
Found at i:24626 original size:17 final size:16
Alignment explanation
Indices: 24572--24622 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
24562 ATCACCCCCC
*
24572 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
24589 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
24606 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
24622 A
1 A
24623 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:25240 original size:49 final size:47
Alignment explanation
Indices: 25139--25280 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 47
25129 GAGCGTGCCA
* * * *
25139 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
*
25186 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAT
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
25235 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
25281 GGATTGCTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.35
49 41 0.51
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:27920 original size:15 final size:15
Alignment explanation
Indices: 27900--27973 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
27890 AACACTTTCA
27900 GTGCCATCATCTTCG
1 GTGCCATCATCTTCG
*
27915 GTGCCATCAGT-TTTG
1 GTGCCATCA-TCTTCG
*
27930 GTGCCATCATTTTCG
1 GTGCCATCATCTTCG
* *
27945 GTGCCGTCGATGTT-G
1 GTGCCATC-ATCTTCG
27960 GTGCCATCATCTTC
1 GTGCCATCATCTTC
27974 TTCCATGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
14 5 0.10
15 39 0.80
16 5 0.10
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.36
Consensus pattern (15 bp):
GTGCCATCATCTTCG
Found at i:27936 original size:30 final size:30
Alignment explanation
Indices: 27900--27973 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
27890 AACACTTTCA
*
27900 GTGCCATCATCTTCGGTGCCATC-AGTTTTG
1 GTGCCATCATCTTCGGTGCCATCGA-TGTTG
* *
27930 GTGCCATCATTTTCGGTGCCGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTG
27960 GTGCCATCATCTTC
1 GTGCCATCATCTTC
27974 TTCCATGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.36
Consensus pattern (30 bp):
GTGCCATCATCTTCGGTGCCATCGATGTTG
Found at i:29213 original size:18 final size:18
Alignment explanation
Indices: 29186--29273 Score: 122
Period size: 18 Copynumber: 4.9 Consensus size: 18
29176 AAGTGTGGCA
29186 ACTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
29204 ACTGGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* *
29222 ACTTGGTGTGGTGAGACC
1 ACTTGGTGCGGTGCGACC
* **
29240 ATTTGGTGCGGTGCGAAT
1 ACTTGGTGCGGTGCGACC
29258 ACTTGGTGCGGTGCGA
1 ACTTGGTGCGGTGCGA
29274 TTTGTTGTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.14, C:0.20, G:0.41, T:0.25
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:29882 original size:48 final size:47
Alignment explanation
Indices: 29806--29948 Score: 146
Period size: 49 Copynumber: 3.0 Consensus size: 47
29796 CGAGCGTGCC
* *
29806 AATCAATTTTGTCA--AAAAATTGATAAAAAGTGCGATGAAAATTAAAA
1 AATCAATTTTGT-AGTAAAAATTGAGAAAAAGTGC-ATGAAAAATAAAA
* ** *
29853 AATGAATTTTGTTTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAA
1 AATCAATTTTGTAGTAAAAATTGAGAAAAAG-TGCATG-AAAAATAAAA
** *
29902 GTTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 AATCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA-TGAAAAATAAA
29949 GGATTGCTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
47 11 0.14
48 29 0.37
49 39 0.49
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (47 bp):
AATCAATTTTGTAGTAAAAATTGAGAAAAAGTGCATGAAAAATAAAA
Found at i:51054 original size:4 final size:4
Alignment explanation
Indices: 51045--51070 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
51035 TTTTCAGAAT
51045 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
51071 CGAAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:53243 original size:122 final size:122
Alignment explanation
Indices: 53026--53268 Score: 459
Period size: 122 Copynumber: 2.0 Consensus size: 122
53016 TATTTCATCG
53026 TTCCTATTTGTCGAAATTACAAAATCACCTATTATAAGTATTCAAATTTGGACACATCTTTCGTC
1 TTCCTATTTGTCGAAATTACAAAATCACCTATTATAAGTATTCAAATTTGGACACATCTTTCGTC
*
53091 TAACACATCTTATCAAAAGCGGTGGCGGGCAGTGCAGCGAACAGCTATTTAAAATCT
66 TAACACATCTTATCAAAAGCGGTGGCGGGCAGTACAGCGAACAGCTATTTAAAATCT
53148 TTCCTATTTGTCGAAATTACAAAATCACCTATTATAAGTATTCAAATTTGGACACATCTTTCGTC
1 TTCCTATTTGTCGAAATTACAAAATCACCTATTATAAGTATTCAAATTTGGACACATCTTTCGTC
* *
53213 TAACACATCTTATCAAAAGCGGTGGCGGGCAGTATAGCGAACGGCTATTTAAAATC
66 TAACACATCTTATCAAAAGCGGTGGCGGGCAGTACAGCGAACAGCTATTTAAAATC
53269 CTGATTGAAA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (122 bp):
TTCCTATTTGTCGAAATTACAAAATCACCTATTATAAGTATTCAAATTTGGACACATCTTTCGTC
TAACACATCTTATCAAAAGCGGTGGCGGGCAGTACAGCGAACAGCTATTTAAAATCT
Found at i:56006 original size:30 final size:30
Alignment explanation
Indices: 55958--56024 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
55948 GGATGGGGTG
**
55958 CGTGTATAACACGCGCTGACATGGATGACA
1 CGTGTATAACAAACGCTGACATGGATGACA
* **
55988 CGTGTATAACAAATGCTGATGTGGATGACA
1 CGTGTATAACAAACGCTGACATGGATGACA
*
56018 TGTGTAT
1 CGTGTAT
56025 GCTCACATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (30 bp):
CGTGTATAACAAACGCTGACATGGATGACA
Found at i:56207 original size:18 final size:18
Alignment explanation
Indices: 56184--56220 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56174 TCAAGAACAC
**
56184 CAAGAACATTCAAAATTG
1 CAAGAACATGAAAAATTG
56202 CAAGAACATGAAAAATTG
1 CAAGAACATGAAAAATTG
56220 C
1 C
56221 CAAAAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (18 bp):
CAAGAACATGAAAAATTG
Found at i:61865 original size:27 final size:27
Alignment explanation
Indices: 61803--61874 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
61793 GTGGCTACGA
* *
61803 CAGTGAAGCATTAATCTGCGATTGCGG
1 CAGTGAAGCATTAATCTGAGACTGCGG
* *
61830 CAGGGAAGCATTAATCTGAGGCTGCGG
1 CAGTGAAGCATTAATCTGAGACTGCGG
* **
61857 CAGTAAAGCGGTAATCTG
1 CAGTGAAGCATTAATCTG
61875 TGGATGTGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (27 bp):
CAGTGAAGCATTAATCTGAGACTGCGG
Found at i:69325 original size:45 final size:45
Alignment explanation
Indices: 69270--69369 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
69260 GGGTCGACAT
* * *
69270 TATTCAGATCGAGAAATTG-GTTATGTAAACCTTCTTCGACACCAA
1 TATTAAGATCGAGAAATTGAG-TATGAAAACCTTCTTCGACAACAA
* *
69315 TATTAAGATCGGGAATTTGAGTATGAAAACCTTCTTCGACAACAA
1 TATTAAGATCGAGAAATTGAGTATGAAAACCTTCTTCGACAACAA
69360 TATTAAGATC
1 TATTAAGATC
69370 TGGACTCATG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (45 bp):
TATTAAGATCGAGAAATTGAGTATGAAAACCTTCTTCGACAACAA
Found at i:73173 original size:64 final size:63
Alignment explanation
Indices: 73094--73225 Score: 203
Period size: 64 Copynumber: 2.1 Consensus size: 63
73084 ACTAGATGTG
* * *
73094 TCAATTGGATAGGTTGGGTGGGTTTCAAATTTGGATCATGTGTGTTCAAATCAATTAGGTTTAC
1 TCAATTGGATAGGTTGGGAGGGTTTCAAATTTGGATCATCTATGTTCAAATCAATTAGG-TTAC
* *
73158 TCAATTGGATGGGTTGGGAGGGTTTCAAATTTGGATTATCTATGTTCAAATCAATTAGGTTAC
1 TCAATTGGATAGGTTGGGAGGGTTTCAAATTTGGATCATCTATGTTCAAATCAATTAGGTTAC
73221 T-AATT
1 TCAATT
73226 TTTCACGGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 4 0.06
63 5 0.08
64 54 0.86
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (63 bp):
TCAATTGGATAGGTTGGGAGGGTTTCAAATTTGGATCATCTATGTTCAAATCAATTAGGTTAC
Found at i:77614 original size:29 final size:29
Alignment explanation
Indices: 77582--77653 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
77572 ACATAGGGAC
77582 ATTTTTCAGTCATTTTT-ACATTCAGGGGT
1 ATTTTT-AGTCATTTTTCACATTCAGGGGT
* *
77611 A-TTTTGGTCATTTTTGCATATTCAGGGGT
1 ATTTTTAGTCATTTTT-CACATTCAGGGGT
*
77640 A-TTTTGGTCATTTT
1 ATTTTTAGTCATTTT
77654 AAGTTCACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 9 0.23
28 4 0.10
29 26 0.67
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.51
Consensus pattern (29 bp):
ATTTTTAGTCATTTTTCACATTCAGGGGT
Found at i:77620 original size:27 final size:28
Alignment explanation
Indices: 77590--77653 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 28
77580 ACATTTTTCA
77590 GTCATTTTT-ACATTCAGGGGTATTTTG
1 GTCATTTTTCACATTCAGGGGTATTTTG
*
77617 GTCATTTTTGCATATTCAGGGGTATTTTG
1 GTCATTTTT-CACATTCAGGGGTATTTTG
77646 GTCATTTT
1 GTCATTTT
77654 AAGTTCACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 9 0.26
29 25 0.74
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (28 bp):
GTCATTTTTCACATTCAGGGGTATTTTG
Found at i:91557 original size:12 final size:12
Alignment explanation
Indices: 91523--91565 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
91513 ATGGAAGTCA
*
91523 TGGTGGTGGTGG
1 TGGTGGTAGTGG
* * *
91535 AGGAGGCAGTGG
1 TGGTGGTAGTGG
91547 TGGTGGTAGTGG
1 TGGTGGTAGTGG
91559 TGGTGGT
1 TGGTGGT
91566 GGAGGTAGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.09, C:0.02, G:0.60, T:0.28
Consensus pattern (12 bp):
TGGTGGTAGTGG
Found at i:91581 original size:18 final size:18
Alignment explanation
Indices: 91527--91582 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
91517 AAGTCATGGT
91527 GGTGGTGGAGG-AG-GCA
1 GGTGGTGGAGGTAGTGCA
* **
91543 -GTGGTGGTGGTAGTGGT
1 GGTGGTGGAGGTAGTGCA
91560 GGTGGTGGAGGTAGTGCA
1 GGTGGTGGAGGTAGTGCA
91578 GGTGG
1 GGTGG
91583 AGCCTCTGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 9 0.29
16 2 0.06
17 1 0.03
18 19 0.61
ACGTcount: A:0.12, C:0.04, G:0.61, T:0.23
Consensus pattern (18 bp):
GGTGGTGGAGGTAGTGCA
Found at i:91790 original size:12 final size:12
Alignment explanation
Indices: 91775--91825 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
91765 GTGGAGCACA
91775 TGGTGGCGGAGG
1 TGGTGGCGGAGG
* *
91787 TGGTGGTGGAAG
1 TGGTGGCGGAGG
91799 TGGT---GGAGG
1 TGGTGGCGGAGG
91808 TGGTGGCGGAGG
1 TGGTGGCGGAGG
91820 TGGTGG
1 TGGTGG
91826 TAGTGGTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.24
12 25 0.76
ACGTcount: A:0.10, C:0.04, G:0.65, T:0.22
Consensus pattern (12 bp):
TGGTGGCGGAGG
Found at i:91823 original size:21 final size:21
Alignment explanation
Indices: 91776--91833 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
91766 TGGAGCACAT
* *
91776 GGTGGCGGAGGTGGTGGTGGA
1 GGTGGTGGAGGTGGTGGCGGA
*
91797 AGTGGTGGAGGTGGTGGCGGA
1 GGTGGTGGAGGTGGTGGCGGA
91818 GGTGGTGGTA-GTGGTG
1 GGTGGTGG-AGGTGGTG
91834 CTGGGGGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.10, C:0.03, G:0.64, T:0.22
Consensus pattern (21 bp):
GGTGGTGGAGGTGGTGGCGGA
Found at i:91863 original size:12 final size:12
Alignment explanation
Indices: 91846--91899 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
91836 GGGGGAGAGC
91846 ATGGTGGTGGTT
1 ATGGTGGTGGTT
*
91858 ATGGTGGTGGTC
1 ATGGTGGTGGTT
* *
91870 AAGGTGCTGGTT
1 ATGGTGGTGGTT
* *
91882 CTGGCGGTGGTT
1 ATGGTGGTGGTT
91894 ATGGTG
1 ATGGTG
91900 CTGGCGGTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.09, C:0.07, G:0.48, T:0.35
Consensus pattern (12 bp):
ATGGTGGTGGTT
Found at i:91890 original size:15 final size:15
Alignment explanation
Indices: 91872--91929 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
91862 TGGTGGTCAA
*
91872 GGTGCTGGTTCTGGC
1 GGTGCTGGTGCTGGC
*
91887 GGTGGTTATGGTGCTGGC
1 GGT-G--CTGGTGCTGGC
*
91905 GGTGCTGGTGCTGGA
1 GGTGCTGGTGCTGGC
*
91920 GGTGGTGGTG
1 GGTGCTGGTG
91930 GTGGTGGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 21 0.60
16 1 0.03
17 1 0.03
18 12 0.34
ACGTcount: A:0.03, C:0.12, G:0.53, T:0.31
Consensus pattern (15 bp):
GGTGCTGGTGCTGGC
Found at i:91899 original size:24 final size:24
Alignment explanation
Indices: 91845--91903 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
91835 TGGGGGAGAG
* *
91845 CATGGTGGTGGTTATGGTGGTGGT
1 CATGGTGCTGGTTATGGCGGTGGT
* *
91869 CAAGGTGCTGGTTCTGGCGGTGGT
1 CATGGTGCTGGTTATGGCGGTGGT
*
91893 TATGGTGCTGG
1 CATGGTGCTGG
91904 CGGTGCTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.08, C:0.10, G:0.47, T:0.34
Consensus pattern (24 bp):
CATGGTGCTGGTTATGGCGGTGGT
Found at i:91935 original size:12 final size:12
Alignment explanation
Indices: 91775--91959 Score: 55
Period size: 12 Copynumber: 15.2 Consensus size: 12
91765 GTGGAGCACA
* *
91775 TGGTGGCGGAGG
1 TGGTGGTGGTGG
**
91787 TGGTGGTGGAAG
1 TGGTGGTGGTGG
*
91799 TGGTGGAGGTGG
1 TGGTGGTGGTGG
* *
91811 TGGCGGAGGTGG
1 TGGTGGTGGTGG
* *
91823 TGGTAGTGGTGC
1 TGGTGGTGGTGG
* *
91835 TGGGGGAGAGCATGG
1 TGGTGGTG-G--TGG
**
91850 TGGTGGTTATGG
1 TGGTGGTGGTGG
***
91862 TGGTGGTCAAGG
1 TGGTGGTGGTGG
* **
91874 TGCTGGTTCTGG
1 TGGTGGTGGTGG
* **
91886 CGGTGGTTATGG
1 TGGTGGTGGTGG
* * *
91898 TGCTGGCGGTGC
1 TGGTGGTGGTGG
* *
91910 TGGTGCTGGAGG
1 TGGTGGTGGTGG
91922 TGGTGGTGGTGG
1 TGGTGGTGGTGG
**
91934 TGGAAGTGGTGG
1 TGGTGGTGGTGG
* * *
91946 AGGCGGAGGTGG
1 TGGTGGTGGTGG
91958 TG
1 TG
91960 TTGGAGGGGC
Statistics
Matches: 123, Mismatches: 47, Indels: 6
0.70 0.27 0.03
Matches are distributed among these distances:
12 115 0.93
13 1 0.01
15 7 0.06
ACGTcount: A:0.10, C:0.07, G:0.57, T:0.26
Consensus pattern (12 bp):
TGGTGGTGGTGG
Found at i:92028 original size:24 final size:24
Alignment explanation
Indices: 91974--92028 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
91964 AGGGGCACAT
*
91974 GGTGGGGGATATGGTGGTGGAGAA
1 GGTGGAGGATATGGTGGTGGAGAA
* * * *
91998 GGAGGAGGATCTGGTGGTGGTGCA
1 GGTGGAGGATATGGTGGTGGAGAA
92022 GGTGGAG
1 GGTGGAG
92029 CAGGTGGAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.04, G:0.58, T:0.20
Consensus pattern (24 bp):
GGTGGAGGATATGGTGGTGGAGAA
Found at i:93861 original size:34 final size:32
Alignment explanation
Indices: 93805--93870 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
93795 GCTCTTACAA
** *
93805 CCAATGAAGTTACGGGGGTTCATCACGCCATT
1 CCAATGAAGTTACGGGCCTTCATCACACCATT
93837 CCAATGAAGTTAAACGGGCCTTCATCACACCATT
1 CCAATGAAGTT--ACGGGCCTTCATCACACCATT
93871 ACAAGTTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 11 0.38
34 18 0.62
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (32 bp):
CCAATGAAGTTACGGGCCTTCATCACACCATT
Found at i:98653 original size:16 final size:16
Alignment explanation
Indices: 98632--98662 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
98622 AGTGATCCAA
98632 CCTGGAACCATTTGAT
1 CCTGGAACCATTTGAT
98648 CCTGGAACCATTTGA
1 CCTGGAACCATTTGA
98663 GATATGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (16 bp):
CCTGGAACCATTTGAT
Found at i:99743 original size:21 final size:19
Alignment explanation
Indices: 99718--99775 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
99708 GCTGCTCTAA
99718 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
99739 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
99758 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
99776 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:104341 original size:15 final size:15
Alignment explanation
Indices: 104311--104353 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
104301 TTACTCTGCT
104311 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
104327 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
104342 TTGCTTTCTGTT
1 TTGTTTTCTGTT
104354 AATCTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.09, G:0.14, T:0.65
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:104561 original size:30 final size:29
Alignment explanation
Indices: 104525--104596 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
104515 TTTGGCGCCA
*
104525 TTGCCGGGGAAGAATAACTTTTTCTGGTAT
1 TTGCCGGGGAAG-AGAACTTTTTCTGGTAT
* *
104555 TTGCCGGGGAAGGGAACTTTTTCTGGTTT
1 TTGCCGGGGAAGAGAACTTTTTCTGGTAT
104584 TTGCCAGGGGAAG
1 TTGCC-GGGGAAG
104597 GAAAATAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.50
30 19 0.50
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (29 bp):
TTGCCGGGGAAGAGAACTTTTTCTGGTAT
Found at i:104599 original size:29 final size:29
Alignment explanation
Indices: 104525--104597 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 29
104515 TTTGGCGCCA
**
104525 TTGCCGGGGAAGAATAACTTTTTCTGGTAT
1 TTGCCGGGGAAG-GGAACTTTTTCTGGTAT
*
104555 TTGCCGGGGAAGGGAACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT
104584 TTGCCAGGGGAAGG
1 TTGCC-GGGGAAGG
104598 AAAATAGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.19, C:0.14, G:0.34, T:0.33
Consensus pattern (29 bp):
TTGCCGGGGAAGGGAACTTTTTCTGGTAT
Found at i:104800 original size:21 final size:21
Alignment explanation
Indices: 104744--104801 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 21
104734 TTTGCATCGA
*
104744 AAAAAAAAAATT-TGCGTCAT
1 AAAAAAAAATTTCTGCGTCAT
*
104764 AAAAAAAATTTGTTTCTGCGTCAT
1 AAAAAAAA---ATTTCTGCGTCAT
104788 AAAAAAAAATTTCT
1 AAAAAAAAATTTCT
104802 TGTTCCTGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
23 2 0.06
24 16 0.52
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAAAAAAATTTCTGCGTCAT
Found at i:106384 original size:28 final size:29
Alignment explanation
Indices: 106353--106410 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
106343 TGTTTCTGCG
*
106353 TCATAAAAAAAAAAGATTT-TTGTGTTTT
1 TCATAAAAAAAAAAGATTTCTTGCGTTTT
*
106381 TCATAAAAAAAAAAGTTTTCTTGCGTTTT
1 TCATAAAAAAAAAAGATTTCTTGCGTTTT
106410 T
1 T
106411 AATTTATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (29 bp):
TCATAAAAAAAAAAGATTTCTTGCGTTTT
Found at i:109586 original size:22 final size:21
Alignment explanation
Indices: 109561--109612 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
109551 CCACTACCAA
* *
109561 GCCATTACCGGCCATTCACCGT
1 GCCATCACCGGCCATGC-CCGT
*
109583 GCCAGCACCGGCCATGCCCGT
1 GCCATCACCGGCCATGCCCGT
109604 GCCATCACC
1 GCCATCACC
109613 ATTCCAAGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.17, C:0.46, G:0.21, T:0.15
Consensus pattern (21 bp):
GCCATCACCGGCCATGCCCGT
Found at i:109605 original size:21 final size:22
Alignment explanation
Indices: 109567--109612 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
109557 CCAAGCCATT
*
109567 ACCGGCCATTCACCGTGCCAGC
1 ACCGGCCATGCACCGTGCCAGC
*
109589 ACCGGCCATGC-CCGTGCCATC
1 ACCGGCCATGCACCGTGCCAGC
109610 ACC
1 ACC
109613 ATTCCAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (22 bp):
ACCGGCCATGCACCGTGCCAGC
Found at i:109984 original size:15 final size:14
Alignment explanation
Indices: 109964--109993 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
109954 ATCTTTTTAA
109964 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
109979 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
109993 T
1 T
109994 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:110327 original size:24 final size:24
Alignment explanation
Indices: 110295--110343 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
110285 AATATTTTCT
*
110295 TTGATTGATTGATTTATAGCATGA
1 TTGATTGATTGATTTATAACATGA
110319 TTGATTGATTGATTTATAACATGA
1 TTGATTGATTGATTTATAACATGA
110343 T
1 T
110344 ATCTGATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (24 bp):
TTGATTGATTGATTTATAACATGA
Found at i:112918 original size:15 final size:15
Alignment explanation
Indices: 112888--112929 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
112878 TTACTTTGCT
*
112888 TTGTTTGCTAGTTTAA
1 TTGTTTTCT-GTTTAA
112904 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
112919 TTGCTTTCTGT
1 TTGTTTTCTGT
112930 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:114222 original size:18 final size:19
Alignment explanation
Indices: 114181--114222 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
114171 CTGATTCTTG
*
114181 ATTTCATATCTATTTCTTT
1 ATTTCATATCTATTTCTCT
* *
114200 CTTTCA-ATCTGTTTCTCT
1 ATTTCATATCTATTTCTCT
114218 ATTTC
1 ATTTC
114223 TCCTACATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTCATATCTATTTCTCT
Found at i:115517 original size:84 final size:84
Alignment explanation
Indices: 115376--115543 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
115366 TGTATACCGT
115376 ATATCCTCCTTGATTTGTGAGGTTCCATTACCTGCCTTGACCTTTATCATGCTCTTTCACCTAAT
1 ATATCCTCCTTGATTTGTGAGGTTCCATTACCTGCCTTGACCTTTATCATGCTCTTTCACCTAAT
115441 TATGCTCTAAAACAAGTAC
66 TATGCTCTAAAACAAGTAC
115460 ATATCCTCCTTGATTTGTGAGGTTCCATTACCTGCCTTGACCTTTATCATGCTCTTTCACCTAAT
1 ATATCCTCCTTGATTTGTGAGGTTCCATTACCTGCCTTGACCTTTATCATGCTCTTTCACCTAAT
115525 TATGCTCTAAAACAAGTAC
66 TATGCTCTAAAACAAGTAC
115544 CTACAGTGAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (84 bp):
ATATCCTCCTTGATTTGTGAGGTTCCATTACCTGCCTTGACCTTTATCATGCTCTTTCACCTAAT
TATGCTCTAAAACAAGTAC
Found at i:118081 original size:29 final size:27
Alignment explanation
Indices: 118027--118084 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
118017 TTTATCTACC
**
118027 AATGAGCAGGTATATCTTTTGTTAAAA
1 AATGAGCAGGTATATCTAATGTTAAAA
*
118054 AATGAGCAGGTGTATCTAATGAATTAAAA
1 AATGAGCAGGTATATCTAATG--TTAAAA
118083 AA
1 AA
118085 AAATAGAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 18 0.69
29 8 0.31
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (27 bp):
AATGAGCAGGTATATCTAATGTTAAAA
Found at i:121189 original size:55 final size:56
Alignment explanation
Indices: 121106--121238 Score: 209
Period size: 55 Copynumber: 2.4 Consensus size: 56
121096 AACATTAAAA
*
121106 AAAATTACAAATCACTTGTTTTACATATTTATTAAGTTGCATATAGAAATG-A-T-AT
1 AAAATTACAAATCACTTGTTTTACATATTGATTAAGTTGCATATA-AAA-GAAGTAAT
*
121161 AAAATTACAAATCACTTGTTTTACATATTGATTAAGTTGCATATAATAGAAGTAAT
1 AAAATTACAAATCACTTGTTTTACATATTGATTAAGTTGCATATAAAAGAAGTAAT
121217 AAAATTACAAATCACTTGTTTT
1 AAAATTACAAATCACTTGTTTT
121239 TTATTTCTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
53 1 0.01
54 3 0.04
55 45 0.62
56 24 0.33
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (56 bp):
AAAATTACAAATCACTTGTTTTACATATTGATTAAGTTGCATATAAAAGAAGTAAT
Found at i:122095 original size:39 final size:40
Alignment explanation
Indices: 122045--122121 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
122035 ATTCCTATGT
122045 AATATATATAATAACTAAAATACTTACATTAATTAAATGC
1 AATATATATAATAACTAAAATACTTACATTAATTAAATGC
*
122085 AATAT-TATAATAACTGAAATACTTACATTAATTAAAT
1 AATATATATAATAACTAAAATACTTACATTAATTAAAT
122122 TTTTAGGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 31 0.86
40 5 0.14
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (40 bp):
AATATATATAATAACTAAAATACTTACATTAATTAAATGC
Found at i:122151 original size:24 final size:23
Alignment explanation
Indices: 122112--122157 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
122102 AATACTTACA
*
122112 TTAATTAAATTTTTAGGTATTTT
1 TTAATTAAATTCTTAGGTATTTT
122135 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
122158 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
TTAATTAAATTCTTAGGTATTTT
Done.