Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004070.1 Hibiscus syriacus cultivar Beakdansim tig00008911_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: 64211
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1296 original size:35 final size:35
Alignment explanation
Indices: 1250--1318 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1240 CCTTAGGTCC
1250 ATAAGAAATTACCAG-TTGATCGGTGCTGAACCTAT
1 ATAAGAAATTACCAGCTT-ATCGGTGCTGAACCTAT
* *
1285 ATAAGGAATTACTAGCTTATCGGTGCTGAACCTA
1 ATAAGAAATTACCAGCTTATCGGTGCTGAACCTA
1319 CAAAGACTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 29 0.94
36 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (35 bp):
ATAAGAAATTACCAGCTTATCGGTGCTGAACCTAT
Found at i:3187 original size:38 final size:39
Alignment explanation
Indices: 3145--3221 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
3135 TTAAATGGCT
3145 AAATTCAACCTTGAGAAAAG-AAAGAAGATACATGTTTC
1 AAATTCAACCTTGAGAAAAGAAAAGAAGATACATGTTTC
*
3183 AAATTCAACCTTGAGAAAAGAAAAGAAGATATATGTTTC
1 AAATTCAACCTTGAGAAAAGAAAAGAAGATACATGTTTC
3222 GATAGCAGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 20 0.54
39 17 0.46
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (39 bp):
AAATTCAACCTTGAGAAAAGAAAAGAAGATACATGTTTC
Found at i:3867 original size:2 final size:2
Alignment explanation
Indices: 3860--3894 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3850 TACTTATGAA
3860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3895 GACAGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5423 original size:16 final size:18
Alignment explanation
Indices: 5392--5424 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5382 ATAAATAATA
5392 ATAATTAATAAAATTTAT
1 ATAATTAATAAAATTTAT
5410 ATAA-TAAT-AAATTTA
1 ATAATTAATAAAATTTA
5425 ATACTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAATAAAATTTAT
Found at i:7788 original size:25 final size:25
Alignment explanation
Indices: 7741--7793 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
7731 TAATCACGTG
**
7741 TAAGCATCAATTGTGACTCTGTGCC
1 TAAGCATCAATTACGACTCTGTGCC
7766 TAAGCATCAATTACGACGT-TGTGCC
1 TAAGCATCAATTACGAC-TCTGTGCC
7791 TAA
1 TAA
7794 ATCAATAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (25 bp):
TAAGCATCAATTACGACTCTGTGCC
Found at i:9858 original size:3 final size:3
Alignment explanation
Indices: 9850--9886 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9840 AAACATTTTG
9850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9887 CATCATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10671 original size:31 final size:31
Alignment explanation
Indices: 10621--10681 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
10611 GTTATTTCAA
*
10621 ATTTATTAATATAATATATTAATTTATATAT
1 ATTTATTAATATAAAATATTAATTTATATAT
*
10652 ATTTATATAA-ATAAAATATTTATTTATATA
1 ATTTAT-TAATATAAAATATTAATTTATATA
10682 GAAATATCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTATTAATATAAAATATTAATTTATATAT
Found at i:10672 original size:17 final size:18
Alignment explanation
Indices: 10650--10688 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
10640 TAATTTATAT
10650 ATATTTATATAAATA-AA
1 ATATTTATATAAATAGAA
* *
10667 ATATTTATTTATATAGAA
1 ATATTTATATAAATAGAA
10685 ATAT
1 ATAT
10689 CAGAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTTATATAAATAGAA
Found at i:13257 original size:123 final size:123
Alignment explanation
Indices: 12971--13295 Score: 417
Period size: 124 Copynumber: 2.6 Consensus size: 123
12961 GAATCAATGC
* * *
12971 AAGGTTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * * *
13036 GAAC-TTCACCTGGAAATAGCTTTGCTGCTTTATCTCTTTTTGGAAATGGAGTCAAGAAA
66 GAACTTTC-TCTGGAAATAGCTTTGCTGATCTATCTCCTTCTGG-AATAGAATCAAGAAA
*
13095 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * *
13160 GAACTTTCTCTGGAAA-AG-TTGGTGTTGATCTATCTCCTTCTGTG-ATAGAATCATGCAA
66 GAACTTTCTCTGGAAATAGCTT--TGCTGATCTATCTCCTTCTG-GAATAGAATCAAGAAA
* *
13218 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAA-TTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGAT-AAGTTCTTCTCATTA
13282 TGAACTTTCTCTGG
65 TGAACTTTCTCTGG
13296 CAACGCTGAT
Statistics
Matches: 179, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
122 2 0.01
123 84 0.47
124 89 0.50
125 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATAGCTTTGCTGATCTATCTCCTTCTGGAATAGAATCAAGAAA
Found at i:13636 original size:121 final size:113
Alignment explanation
Indices: 13490--14242 Score: 623
Period size: 113 Copynumber: 6.7 Consensus size: 113
13480 AAATTAAGGC
* *
13490 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCATTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTA
* *
13554 TGAACAC-T-TCTAGAAATGTTGATATTGATCGATCTCCTTCTGTGAT-AGAGTCAAAC-A
65 TGAACACTTCTCTAGAAA-----AT-TTGATCCA--T-C--CAGTGATGA-AGTCAAACAA
* * *
13611 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
13676 GAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAATTCAAACAA
66 GAACACTTCTCTAGAAAATTTGATCCATCCAGTGATGAAGTCAAACAA
13724 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * *** * *
13789 TGAAC-TTTAC-CTGGCAACGCTGATCCAT-CA--AATG-A-T-GAA-AA
65 TGAACACTT-CTCTAGAAAATTTGATCCATCCAGTGATGAAGTCAAACAA
* *
13830 AA-GTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * * *** * * *
13894 TGAACTCTAC-CTGGTAACGCTGATCCATCAAATGATGAATTCAAACAA
65 TGAACACTTCTCTAGAAAATTTGATCCATCCAGTGATGAAGTCAAACAA
* ** * *
13942 AGGGTTGAACAAGCTCTTCTCATTAGGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * * * * *
14007 TGAAC-TTTTTCT-GGAAATGTTGATCCATCGAGTGATGGATTCAAGCAA
65 TGAACACTTCTCTAGAAAAT-TTGATCCATCCAGTGATGAAGTCAAACAA
* *
14055 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* ** * * * * ** *
14120 TGAAC-TTTAC-CT-GGCAATGCTGATCCATCAAGTGATGGATTTGAGCAA
65 TGAACACTT-CTCTAGAAAAT-TTGATCCATCCAGTGATGAAGTCAAACAA
* * *
14168 AAGGTTGAACAAATTCTTCTTATTATGAACTT-TTGCTTCCTCTTCAGATGAGTTCTTATCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-CTTCTTCTTCAGATGAGTTCTTCTCATTA
*
14232 TGAACTCTTCT
65 TGAACACTTCT
14243 GGAAATATTG
Statistics
Matches: 543, Mismatches: 67, Indels: 52
0.82 0.10 0.08
Matches are distributed among these distances:
105 83 0.15
106 6 0.01
107 2 0.00
108 4 0.01
109 2 0.00
110 4 0.01
111 2 0.00
112 51 0.09
113 276 0.51
114 31 0.06
115 1 0.00
117 7 0.01
118 2 0.00
121 62 0.11
122 3 0.01
123 7 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACACTTCTCTAGAAAATTTGATCCATCCAGTGATGAAGTCAAACAA
Found at i:13742 original size:113 final size:111
Alignment explanation
Indices: 13604--14248 Score: 794
Period size: 113 Copynumber: 5.8 Consensus size: 111
13594 TGTGATAGAG
* *
13604 TCAAAC-AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
13667 TCTCATTATGAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACT-TTC-CTGG-AAATCTGATCCATCAAGTGATGAAT
13716 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
**
13781 TCTCATTATGAACTTTACCTGGCAACGCTGATCCATCAA---ATG-A-
66 TCTCATTATGAACTTT-CCTGG-AAATCTGATCCATCAAGTGATGAAT
* * *
13824 T-GAA-AAAA-GTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* ** *
13886 TCTCATTATGAACTCTACCTGGTAACGCTGATCCATCAAATGATGAAT
66 TCTCATTATGAACT-TTCCTGG-AAATCTGATCCATCAAGTGATGAAT
* ** * *
13934 TCAAACAAAGGGTTGAACAAGCTCTTCTCATTAGGAACTTCTTATTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
13999 TCTCATTATGAACTTTTTCTGGAAATGTTGATCCATCGAGTGATGGAT
66 TCTCATTATGAAC-TTTCCTGGAAAT-CTGATCCATCAAGTGATGAAT
* * *
14047 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTAT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
14112 TCTCATTATGAACTTTACCTGGCAATGCTGATCCATCAAGTGATGGAT
66 TCTCATTATGAACTTT-CCTGGAAAT-CTGATCCATCAAGTGATGAAT
** * *
14160 TTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAACTT-TTGCTTCC-TCTTCAGATGAGTTC
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-CTTCCTTCTTCAGATGAGTTC
*
14223 TTATCATTATGAACTCTT-CTGGAAAT
65 TTCTCATTATGAACT-TTCCTGGAAAT
14249 ATTGAAAATA
Statistics
Matches: 469, Mismatches: 47, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
105 87 0.19
106 5 0.01
107 2 0.00
108 4 0.01
109 2 0.00
110 4 0.01
111 9 0.02
112 44 0.09
113 281 0.60
114 31 0.07
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (111 bp):
TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCCTGGAAATCTGATCCATCAAGTGATGAAT
Found at i:13866 original size:516 final size:508
Alignment explanation
Indices: 12845--13827 Score: 1174
Period size: 516 Copynumber: 1.9 Consensus size: 508
12835 GCTGAACAAA
*
12845 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGA
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGA
* * * * *
12910 AAATATTGATCCTCAAATGAGGTTCTTCTTTCATTCAATTCCATAGGAGATGAATCAATGCAAGG
66 AAATACTGATCCTCAAATGAGGTTCGTCATTCATTCAATTCCATAGGAGATAAATCAAGGCAAGG
* *
12975 TTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
131 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * * ** * * *
13040 TTCACCTGGAAATAGCTTTGCTGCTTTATCTCTTTTTGGAAATGGAGTCAAGAAAAAGGTTGAAC
196 TACACCTAGAAATAGCTTTACTGATCGATCTCCTTCTGG-AATAGAGTCAAGAAAAAGGTTGAAC
* *
13105 AAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTTTTCTCATTATGAACTTTCTC
260 AAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
* * ** *
13170 TGGAAAAGTTGGTGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCT
325 TGGAAAA----GTGTTGATCCA-CTCC-TCAGTGATAGAATCAAACAAAAGGTTGAACAAACTCT
13235 TCTCATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGCAAC
384 TCTCATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGCAAC
*** * * * * *
13300 GCTGATCCACCGGGTGATGAATTTGAGCAAAAGGTTGAATAAATTCTTCTTTGGGATTAG
449 GCTGATCCACCAAATGATGAAGTTAAACAAAACGTTCAATAAATTCTTCTTTGGGATTAG
* *
13360 TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTCT
1 TTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTATGAACT-T--TCT
* * * * * * *
13425 ACCTGGAAATGCTGATCCTTGAAA-GAGG-T-GTCATTGATTCAACTT-CATATGTGATAAATTA
62 --CTGAAAATACTGATCC-TCAAATGAGGTTCGTCATTCATTCAA-TTCCATAGGAGATAAATCA
*
13486 AGGCAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTC-TCATTCTTCATATGAGTTCTTCT
123 AGGCAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTC-TTCTTCAGATGAGTTCTTCT
** *
13549 CATTATGAAC-ACTTCTAGAAAT-G-TTGATATTGATCGATCTCCTTCTGTG-ATAGAGTCAA-A
186 CATTATGAACTACACCTAGAAATAGCTT--TACTGATCGATCTCCTTCTG-GAATAGAGTCAAGA
*
13609 CAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
248 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
*
13674 ATGAACTCTTCTCTGGAAAA-T-TTGATCCA-T-C-GAGTGAT-GAATTCAAACAAAAGGTTGAA
313 ATGAACT-TTCTCTGGAAAAGTGTTGATCCACTCCTCAGTGATAGAA-TCAAACAAAAGGTTGAA
* *
13733 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTA
376 CAAACTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAATTCTTCTCATTATGAACTTT-
*
13798 C-CTGGCAACGCTGATCCATCAAATGATGAA
439 CTCTGGCAACGCTGATCCACCAAATGATGAA
13828 AAAAGTTAAA
Statistics
Matches: 406, Mismatches: 45, Indels: 42
0.82 0.09 0.09
Matches are distributed among these distances:
505 3 0.01
506 49 0.12
507 56 0.14
508 2 0.00
509 1 0.00
511 7 0.02
512 1 0.00
515 25 0.06
516 102 0.25
517 23 0.06
518 26 0.06
519 88 0.22
520 3 0.01
521 16 0.04
522 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (508 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGA
AAATACTGATCCTCAAATGAGGTTCGTCATTCATTCAATTCCATAGGAGATAAATCAAGGCAAGG
TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
TACACCTAGAAATAGCTTTACTGATCGATCTCCTTCTGGAATAGAGTCAAGAAAAAGGTTGAACA
AATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCT
GGAAAAGTGTTGATCCACTCCTCAGTGATAGAATCAAACAAAAGGTTGAACAAACTCTTCTCATT
ATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGCAACGCTGATC
CACCAAATGATGAAGTTAAACAAAACGTTCAATAAATTCTTCTTTGGGATTAG
Found at i:13996 original size:218 final size:224
Alignment explanation
Indices: 13610--14237 Score: 842
Period size: 218 Copynumber: 2.8 Consensus size: 224
13600 AGAGTCAAAC
* * * *
13610 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** *
13674 ATGAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAATT
66 ATGAACTCTAC-CTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATT
*
13739 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGC
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGA
*
13804 AACGCTGATCCATC-A-AAT-GA-TGAA-A
195 AACGCTGATCCATCGAGAATGGATTCAACA
*
13829 AAA-GTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * **
13893 ATGAACTCTACCTGGTAACGCTGATCCATCAAATGATGAATTCAAACAAAGGGTTGAACAAGCTC
66 ATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTC
* * **
13958 TTCTCATTAGGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGAA
* * *
14023 ATGTTGATCCATCGAGTGATGGATTCAAGCA
196 ACGCTGATCCATCGAG-AATGGATTCAA-CA
* *
14054 AAAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATT
1 AAAGGTTAAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * ** *
14119 ATGAACTTTACCTGGCAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC
66 ATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTC
* *
14184 TTCTTATTATGAACTT-TTGCTTCC-TCTTCAGATGAGTTCTTATCATTATGAACT
131 TTCTCATTATGAACTTCTT-CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
14238 CTTCTGGAAA
Statistics
Matches: 358, Mismatches: 41, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
218 150 0.42
219 36 0.10
221 2 0.01
222 2 0.01
223 3 0.01
225 35 0.10
226 130 0.36
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (224 bp):
AAAGGTTAAACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGAA
ACGCTGATCCATCGAGAATGGATTCAACA
Found at i:14035 original size:331 final size:333
Alignment explanation
Indices: 13604--14239 Score: 989
Period size: 331 Copynumber: 1.9 Consensus size: 333
13594 TGTGATAGAG
* * * *
13604 TCAAACAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
1 TCAAACAAAGGTTGAACAAACTCTTCTCATTAGGAACTTCTTATTCCTCTTCAGATAAGTTCTTC
13669 TCATTATGAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
66 TCATTATGAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
* *
13734 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC
131 AAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTAC
13799 CTGGCAACGCTGATCCATCAA-AT-GA-TGA-AAAAAGTTAAACAAATTCTTCTCATTATGAA-T
196 CTGGCAACGCTGATCCATCAAGATGGATTGACAAAAAGTTAAACAAATTCTTCTCATTATGAACT
* *
13859 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAACGCTGATCCATCA
261 TT-TGCTTCC-TCTTCAGATGAGTTCTTATCATTATGAACTCTACCTGGTAACGCTGATCCATCA
13924 AATGATGAAT
324 AATGATGAAT
* *
13934 TCAAACAAAGGGTTGAACAAGCTCTTCTCATTAGGAACTTCTTATTCCTTCTTCAGATGAGTTCT
1 TCAAACAAA-GGTTGAACAAACTCTTCTCATTAGGAACTTCTTATTCC-TCTTCAGATAAGTTCT
* * *
13999 TCTCATTATGAACT-TTTTCTGG-AAATGTTGATCCATCGAGTGATGGATTCAAGCAAAAGGTTG
64 TCTCATTATGAACTCTTCTCTGGAAAAT-TTGATCCATCGAGTGATGAATTCAAACAAAAGGTTG
14062 AACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTT
128 AACAAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTT
* * * *
14127 TACCTGGCAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATT
193 TACCTGGCAACGCTGATCCATCAA--GATGGA-TTGA-CAAAAAGTTAAACAAATTCTTCTCATT
14192 ATGAACTTTTGCTTCCTCTTCAGATGAGTTCTTATCATTATGAACTCT
254 ATGAACTTTTGCTTCCTCTTCAGATGAGTTCTTATCATTATGAACTCT
14240 TCTGGAAATA
Statistics
Matches: 277, Mismatches: 17, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
330 13 0.05
331 160 0.58
332 29 0.10
334 2 0.01
335 2 0.01
337 3 0.01
338 31 0.11
339 34 0.12
340 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (333 bp):
TCAAACAAAGGTTGAACAAACTCTTCTCATTAGGAACTTCTTATTCCTCTTCAGATAAGTTCTTC
TCATTATGAACTCTTCTCTGGAAAATTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
AAATTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTAC
CTGGCAACGCTGATCCATCAAGATGGATTGACAAAAAGTTAAACAAATTCTTCTCATTATGAACT
TTTGCTTCCTCTTCAGATGAGTTCTTATCATTATGAACTCTACCTGGTAACGCTGATCCATCAAA
TGATGAAT
Found at i:15085 original size:22 final size:22
Alignment explanation
Indices: 15060--15139 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
15050 AATAAAACTT
*
15060 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
15082 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
15104 TCATCTTTGGAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATCTA
15126 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
15140 TGTAGATGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:22222 original size:36 final size:34
Alignment explanation
Indices: 22158--22230 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 34
22148 ATGCAAATGG
*
22158 AAAAATGAAAATATAAATATAAACGTAAAAATGAA
1 AAAAATGAAAATATAAATACAAACGTAAAAAT-AA
* * * *
22193 AAAAATGTAAAATGTAAATGCAAATGTAAATATAA
1 AAAAATG-AAAATATAAATACAAACGTAAAAATAA
22228 AAA
1 AAA
22231 TGCAAATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 12 0.38
36 20 0.62
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.22
Consensus pattern (34 bp):
AAAAATGAAAATATAAATACAAACGTAAAAATAA
Found at i:22233 original size:20 final size:19
Alignment explanation
Indices: 22195--22299 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
22185 AAAATGAAAA
**
22195 AAATGTAAAATGTAAATGC
1 AAATGTAAAATAAAAATGC
22214 AAATGTAAATATAAAAATGC
1 AAATGTAAA-ATAAAAATGC
**
22234 AAATTGTGCAATACAAAA-GC
1 AAA-TGTAAAATA-AAAATGC
** * *
22254 AAACATAAAAGTATAAATGA
1 AAATGTAAAA-TAAAAATGC
*
22274 AAATGTAAAGATGCAAAATGC
1 AAATGTAAA-AT-AAAAATGC
22295 AAATG
1 AAATG
22300 CATGTATAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
19 15 0.23
20 30 0.47
21 19 0.30
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATGTAAAATAAAAATGC
Found at i:23883 original size:26 final size:28
Alignment explanation
Indices: 23841--23911 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
23831 GAAAAATAAA
23841 ATAAAACATTAAT-AAAATAAT-A-TATAT
1 ATAAAA-ATT-ATGAAAATAATAAGTATAT
*
23868 ATAAATATTATGAAAATAATAAGTATAT
1 ATAAAAATTATGAAAATAATAAGTATAT
*
23896 ATAAAAATTTTGAAAA
1 ATAAAAATTATGAAAA
23912 GAAAGAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 2 0.05
26 11 0.29
27 6 0.16
28 19 0.50
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
ATAAAAATTATGAAAATAATAAGTATAT
Found at i:24436 original size:31 final size:31
Alignment explanation
Indices: 24386--24446 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24376 GTTATTTCAA
*
24386 ATTTATTAATATAATATATTAATTTATATAT
1 ATTTATTAATATAAAATATTAATTTATATAT
*
24417 ATTTATATAA-ATAAAATATTTATTTATATA
1 ATTTAT-TAATATAAAATATTAATTTATATA
24447 GAAATATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTATTAATATAAAATATTAATTTATATAT
Found at i:24437 original size:17 final size:18
Alignment explanation
Indices: 24415--24453 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
24405 TAATTTATAT
24415 ATATTTATATAAATA-AA
1 ATATTTATATAAATAGAA
* *
24432 ATATTTATTTATATAGAA
1 ATATTTATATAAATAGAA
24450 ATAT
1 ATAT
24454 CAAAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTTATATAAATAGAA
Found at i:26111 original size:16 final size:16
Alignment explanation
Indices: 26092--26132 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
26082 GAGATGATAA
26092 CCTAGGGTTATGAAAC
1 CCTAGGGTTATGAAAC
26108 CCTAGGGTTATGAAAC
1 CCTAGGGTTATGAAAC
26124 CCTAGGGTT
1 CCTAGGGTT
26133 TCAAACTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (16 bp):
CCTAGGGTTATGAAAC
Found at i:26371 original size:3 final size:3
Alignment explanation
Indices: 26363--26388 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26353 ATATATATAT
26363 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
26389 TGATGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27330 original size:29 final size:29
Alignment explanation
Indices: 27297--27355 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
27287 ACTCAATTGG
* *
27297 ATATGAGATCAGTTGTGTGTCATAAGTTT
1 ATATGAGATCAGTCGTGTATCATAAGTTT
*
27326 ATATGAGATTAGTCGTGTATCATAAGTTT
1 ATATGAGATCAGTCGTGTATCATAAGTTT
27355 A
1 A
27356 CTCCTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
ATATGAGATCAGTCGTGTATCATAAGTTT
Found at i:28547 original size:4 final size:4
Alignment explanation
Indices: 28538--28609 Score: 144
Period size: 4 Copynumber: 18.0 Consensus size: 4
28528 CGTGTGAACA
28538 ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC
1 ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACTC
28586 ACTC ACTC ACTC ACTC ACTC ACTC
1 ACTC ACTC ACTC ACTC ACTC ACTC
28610 TGCCGGTTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
ACTC
Found at i:33208 original size:13 final size:13
Alignment explanation
Indices: 33181--33213 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33171 ATCTATTCCA
*
33181 AAAAATA-ATATT
1 AAAAATATATAAT
33193 AAAAATATATAAT
1 AAAAATATATAAT
33206 AAAAATAT
1 AAAAATAT
33214 TTTTAGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATATATAAT
Found at i:33324 original size:12 final size:12
Alignment explanation
Indices: 33307--33331 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33297 CTGCTTTTAC
33307 AAATATATATAT
1 AAATATATATAT
33319 AAATATATATAT
1 AAATATATATAT
33331 A
1 A
33332 TATTTTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:38313 original size:2 final size:2
Alignment explanation
Indices: 38306--38351 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
38296 TAAATTAATT
*
38306 TA TA TA TA TA TA TA CA TA TA TA TA TA -A TA -A TA TGA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
38346 TA TA TA
1 TA TA TA
38352 AACAACATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:38326 original size:12 final size:11
Alignment explanation
Indices: 38309--38351 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 11
38299 ATTAATTTAT
38309 ATATATATATA
1 ATATATATATA
38320 CATATATATATA
1 -ATATATATATA
38332 ATAATATGATATA
1 AT-ATAT-ATATA
38345 ATATATA
1 ATATATA
38352 AACAACATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.10
12 19 0.66
13 7 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATATATATATA
Found at i:40970 original size:105 final size:108
Alignment explanation
Indices: 40738--40982 Score: 273
Period size: 105 Copynumber: 2.3 Consensus size: 108
40728 AGCCAAGGTT
* *
40738 GAACAAATTCTTCTCATTATGAACTCCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACT-CTTCTCCCTTA-TGGACGAGTTCTTCTCATTATGAACTC
* * *
40803 TCAACTGGAAATCTTGAACCAAATCCTTTTGCGATGGACTTAGAAG
64 T-AACTGGAAATCTTGAACCAAATCCATCTGCGATGAACTTAGAAG
* *
40849 GAACATGTTTTTCTCATTATGAACT-TTCTCCCTTA-GGACGAGTTCTTCTCATTATGAACTCT-
1 GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
* * *** ** * * *
40911 TCTGGAAATGTTGGTTCACCTCCATCTGTGGTGAA-TTTGAAAG
66 ACTGGAAATCTTGAACCAAATCCATCTGCGATGAACTTAG-AAG
40954 GAACAAGTTCTTCTCATTATGAACTCTTC
1 GAACAAGTTCTTCTCATTATGAACTCTTC
40983 ATTGGAAATG
Statistics
Matches: 113, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
104 3 0.03
105 49 0.43
106 3 0.03
107 26 0.23
109 10 0.09
111 22 0.19
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (108 bp):
GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
ACTGGAAATCTTGAACCAAATCCATCTGCGATGAACTTAGAAG
Found at i:42284 original size:35 final size:34
Alignment explanation
Indices: 42228--42312 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 34
42218 CCTTTTTCTC
42228 TTTTCATTTTTCATTTC-TTTTTTCATTTTTCATTT
1 TTTTCATTTTT-ATTTCTTTTTTTC-TTTTTCATTT
42263 TTTTCATTTTT-TTTCATTTTTTTTCTTTTTCATTT
1 TTTTCATTTTTATTTC--TTTTTTTCTTTTTCATTT
42298 TTTT-ATCTTTTATTT
1 TTTTCAT-TTTTATTT
42313 GTTCCCTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
33 4 0.09
34 2 0.04
35 29 0.64
36 10 0.22
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTCATTTTTATTTCTTTTTTTCTTTTTCATTT
Found at i:42299 original size:7 final size:7
Alignment explanation
Indices: 42228--42264 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
42218 CCTTTTTCTC
42228 TTTTCAT
1 TTTTCAT
42235 TTTTCA-
1 TTTTCAT
*
42241 -TTTCTT
1 TTTTCAT
42247 TTTTCAT
1 TTTTCAT
42254 TTTTCAT
1 TTTTCAT
42261 TTTT
1 TTTT
42265 TTCATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
5 4 0.15
7 22 0.85
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCAT
Found at i:42301 original size:10 final size:10
Alignment explanation
Indices: 42253--42292 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
42243 TCTTTTTTCA
42253 TTTTTCA-TT
1 TTTTTCATTT
42262 TTTTTCATTT
1 TTTTTCATTT
42272 TTTTTCATTT
1 TTTTTCATTT
42282 TTTTTC-TTT
1 TTTTTCATTT
42291 TT
1 TT
42293 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 12 0.40
10 18 0.60
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:42308 original size:16 final size:16
Alignment explanation
Indices: 42241--42312 Score: 62
Period size: 16 Copynumber: 4.5 Consensus size: 16
42231 TCATTTTTCA
*
42241 TTTC-TTTTTTCAT-T
1 TTTCATTTTTTTATCT
*
42255 TTTCATTTTTTTCATTTTT
1 TTTCATTTTTTT-A--TCT
42274 TTTCATTTTTTT-TCTT
1 TTTCATTTTTTTATC-T
42290 TTTCATTTTTTTATCT
1 TTTCATTTTTTTATCT
42306 TTT-ATTT
1 TTTCATTT
42313 GTTCCCTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.08
15 11 0.22
16 18 0.37
17 2 0.04
18 1 0.02
19 13 0.27
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCATTTTTTTATCT
Found at i:42308 original size:26 final size:26
Alignment explanation
Indices: 42228--42301 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 26
42218 CCTTTTTCTC
42228 TTTTCATTTTTCATTTCTTTTTTCATTTT
1 TTTTC-TTTTTCA-TT-TTTTTTCATTTT
*
42257 TCATT-TTTTTCATTTTTTTTCATTTT
1 T-TTTCTTTTTCATTTTTTTTCATTTT
42283 TTTTCTTTTTCATTTTTTT
1 TTTTCTTTTTCATTTTTTT
42302 ATCTTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 2 0.05
26 27 0.66
27 2 0.05
28 7 0.17
29 1 0.02
30 2 0.05
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTTTTCATTTTTTTTCATTTT
Found at i:42312 original size:15 final size:16
Alignment explanation
Indices: 42228--42308 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 16
42218 CCTTTTTCTC
42228 TTTTCATTTTTCATTTCTT
1 TTTTC-TTTTTCA-TT-TT
42247 TTTTCATTTTTCATTTTT
1 TTTTC-TTTTTCA-TTTT
*
42265 TTCATTTTTTTTCATTTT
1 TT--TTCTTTTTCATTTT
42283 TTTTCTTTTTCATTTT
1 TTTTCTTTTTCATTTT
42299 TTTATCTTTT
1 TTT-TCTTTT
42309 ATTTGTTCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
16 16 0.28
17 6 0.11
18 10 0.18
19 23 0.40
20 2 0.04
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCATTTT
Found at i:58226 original size:16 final size:17
Alignment explanation
Indices: 58186--58229 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
58176 CCCTACTTGA
58186 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
58203 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
58219 TTAAATATTTA
1 TTAAATATTTA
58230 TTTTTACATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:59064 original size:24 final size:24
Alignment explanation
Indices: 59037--59084 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
59027 CACAATTAAA
59037 GCACCGAAAAGTAGCTGGAAATTG
1 GCACCGAAAAGTAGCTGGAAATTG
*
59061 GCACCGAAAAGTAGTTGGAAATTG
1 GCACCGAAAAGTAGCTGGAAATTG
59085 TTGAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.19
Consensus pattern (24 bp):
GCACCGAAAAGTAGCTGGAAATTG
Done.