Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:494950 original size:11 final size:12
Alignment explanation
Indices: 494922--494950 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
494912 TGCTACTCCT
494922 ATTTTTGATTTA
1 ATTTTTGATTTA
494934 ATTTTTGATTTA
1 ATTTTTGATTTA
494946 ATTTT
1 ATTTT
494951 AGGGTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
ATTTTTGATTTA
Found at i:503505 original size:43 final size:42
Alignment explanation
Indices: 503455--503798 Score: 266
Period size: 43 Copynumber: 8.0 Consensus size: 42
503445 AGACTTGTAC
* * *
503455 CGGCGTTTTTAGCAGAAACGCCGCAAAACATCAATACCTACTG
1 CGGCGTTTTTAG-AAAAACGCCGCTAAACATCAACACCTACTG
* * * * *
503498 CGACGTTTGT-GAAAAAACG-CGCAAAACATCAATACCTACTA
1 CGGCGTTTTTAG-AAAAACGCCGCTAAACATCAACACCTACTG
* *
503539 CGGCG-TTTTAGCGAAAAATGCCGCTAAACATCATA-ACCTATTG
1 CGGCGTTTTTA--GAAAAACGCCGCTAAACATCA-ACACCTACTG
* ** * * *
503582 CGGCATTTGTCT-GAAAAACGTTGCTAAATATTAACACCTATTG
1 CGGCGTTT-T-TAGAAAAACGCCGCTAAACATCAACACCTACTG
* * *
503625 CGACGTTTTTATGACAAACGCCGCTAAATATCAACACCTACTG
1 CGGCGTTTTTA-GAAAAACGCCGCTAAACATCAACACCTACTG
* * * *
503668 CGGTGTTTTTATAACAAACGCCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTAGAA-AAACGCCGCTAAACATCAACACCTACTG
* **** * *
503711 CGGCGTTTTTCTGAAAAACAATACTAAATATCAACACCTATTG
1 CGGCGTTTTT-AGAAAAACGCCGCTAAACATCAACACCTACTG
* *
503754 CGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTA-GAAAAACGCCGCTAAACATCAACACCTACTG
503797 CG
1 CG
503799 ACGCTTATAA
Statistics
Matches: 246, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
40 3 0.01
41 26 0.11
42 16 0.07
43 194 0.79
44 5 0.02
45 1 0.00
46 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
CGGCGTTTTTAGAAAAACGCCGCTAAACATCAACACCTACTG
Found at i:503648 original size:86 final size:86
Alignment explanation
Indices: 503551--503801 Score: 317
Period size: 86 Copynumber: 2.9 Consensus size: 86
503541 GCGTTTTAGC
* * * * * ** *
503551 GAAAAATGCCGCTAAACATCATA-ACCTATTGCGGCATTTGTCTGAAAAACGTTGCTAAATATTA
1 GAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCA
503615 ACACCTATTGCGACGTTTTTAT
65 ACACCTATTGCGACGTTTTTAT
* * *
503637 GACAAACGCCGCTAAATATCAACACCTACTGCGGTGTTTTTAT-AACAAACGCCGCTAAATATCA
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA-AAACGCCGCTAAATATCA
* *
503701 ACACCTATTGCGGCGTTTTTCT
65 ACACCTATTGCGACGTTTTTAT
****
503723 GAAAAACAATACTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAA
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAA
503788 CACCTATTGCGACG
66 CACCTATTGCGACG
503802 CTTATAAACG
Statistics
Matches: 141, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
85 3 0.02
86 136 0.96
87 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (86 bp):
GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAA
CACCTATTGCGACGTTTTTAT
Found at i:503707 original size:129 final size:129
Alignment explanation
Indices: 503558--503798 Score: 376
Period size: 129 Copynumber: 1.9 Consensus size: 129
503548 AGCGAAAAAT
** * *
503558 GCCGCTAAACATCATAACCTATTGCGGCATTTGTCTGAAAAACGTTGCTAAATATTAACACCTAT
1 GCCGCTAAACATCATAACCTATTGCGGCATTTGTCTGAAAAACAATACTAAATATCAACACCTAT
*
503623 TGCGACGTTTTTATGACAAACGCCGCTAAATATCAACACCTACTGCGGTGTTTTTATAACAAAC
66 TGCGACGTTTTTATGAAAAACGCCGCTAAATATCAACACCTACTGCGGTGTTTTTATAACAAAC
* * *
503687 GCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTCTGAAAAACAATACTAAATATCAACACCTA
1 GCCGCTAAACATCATA-ACCTATTGCGGCATTTGTCTGAAAAACAATACTAAATATCAACACCTA
* *
503751 TTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATTGCG
65 TTGCGACGTTTTTATGAAAAACGCCGCTAAATATCAACACCTACTGCG
503799 ACGCTTATAA
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 100 0.99
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (129 bp):
GCCGCTAAACATCATAACCTATTGCGGCATTTGTCTGAAAAACAATACTAAATATCAACACCTAT
TGCGACGTTTTTATGAAAAACGCCGCTAAATATCAACACCTACTGCGGTGTTTTTATAACAAAC
Found at i:507681 original size:20 final size:19
Alignment explanation
Indices: 507632--507683 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
507622 CATCATATAA
* *
507632 AAATAATTTAATTTTTATT
1 AAATAATTTTATTTGTATT
* *
507651 AAATTAGTTTATTTGTATT
1 AAATAATTTTATTTGTATT
507670 GAAATAATTTTATT
1 -AAATAATTTTATT
507684 ATTTAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
AAATAATTTTATTTGTATT
Found at i:508865 original size:3 final size:3
Alignment explanation
Indices: 508859--508898 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
508849 ACTAATTTTT
508859 TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
508899 AATAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:508907 original size:22 final size:22
Alignment explanation
Indices: 508863--508909 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
508853 ATTTTTTTAT
* *
508863 TATTATTATTATTATTATTATA
1 TATTATTATTATTAATATAATA
508885 TATTATTATTATTAA-ATAAATA
1 TATTATTATTATTAATAT-AATA
508907 TAT
1 TAT
508910 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATTATTATTAATATAATA
Found at i:509305 original size:17 final size:18
Alignment explanation
Indices: 509283--509316 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
509273 CACTGAACCT
509283 GAAAAAAAAA-GAAAAAA
1 GAAAAAAAAAGGAAAAAA
509300 GAAAAAAAAAGGAAAAA
1 GAAAAAAAAAGGAAAAA
509317 CAGAGAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAGGAAAAAA
Found at i:509638 original size:13 final size:13
Alignment explanation
Indices: 509620--509645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
509610 GCTACCGTTT
509620 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
509633 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
509646 GCGGATTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.54, T:0.08
Consensus pattern (13 bp):
ACGGTGGCCGGCG
Found at i:510235 original size:12 final size:12
Alignment explanation
Indices: 510205--510246 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
510195 ATTACTTTTA
510205 TATTTTAATTAT
1 TATTTTAATTAT
510217 T-TCTTTAATTAT
1 TAT-TTTAATTAT
510229 TATTTT-ATTAT
1 TATTTTAATTAT
510240 TATTTTA
1 TATTTTA
510247 GTCATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 12 0.44
12 14 0.52
13 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:510263 original size:2 final size:2
Alignment explanation
Indices: 510250--510279 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
510240 TATTTTAGTC
*
510250 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
510280 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:511121 original size:24 final size:25
Alignment explanation
Indices: 511094--511148 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
511084 TTTATAATTC
511094 TTTTATATA-TATATATACATATTA
1 TTTTATATAGTATATATACATATTA
* *
511118 TTTT-TATAGTATTTATATATATTA
1 TTTTATATAGTATATATACATATTA
511142 -TTTATAT
1 TTTTATAT
511149 TGCAAGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTATATAGTATATATACATATTA
Found at i:518183 original size:88 final size:88
Alignment explanation
Indices: 518001--518221 Score: 309
Period size: 88 Copynumber: 2.5 Consensus size: 88
517991 AGGAGACCCA
* *
518001 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC-----TGGTATAAAACCACAAAACCAA
518066 TCATTGAATTTGGAAGATGAATGTGCTC
61 TCATTGAATTTGGAAGATGAATGTGCTC
* *
518094 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTAATCTGGTATAAAACTC-CAAAATCAATCAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTATAAAAC-CACAAAACCAATCAT
518158 TGAATTTGGAAGATGAATGTGCTC
65 TGAATTTGGAAGATGAATGTGCTC
* * * *
518182 ATAGCATCTTCTAGAAGTGTTATTTGAATTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTG
518222 ATTCGATAGG
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
88 80 0.68
89 1 0.01
93 37 0.31
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (88 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTATAAAACCACAAAACCAATCATT
GAATTTGGAAGATGAATGTGCTC
Found at i:519488 original size:54 final size:55
Alignment explanation
Indices: 519382--519494 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 55
519372 CAATGATTGA
* ***
519382 GAACATCTGAGCAGAAGCCACAAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** *
519437 GAACATCTGAGCAGAAACCAC-AGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
519491 GAAC
1 GAAC
519495 CTGCTATTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 31 0.61
55 20 0.39
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (55 bp):
GAACATCTGAGCAGAAACCACAAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:519901 original size:22 final size:22
Alignment explanation
Indices: 519871--519925 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
519861 AGATTCTCAC
* *
519871 TTCAGAGATGACAAATTTTCTT
1 TTCAAAGATGACAAATTCTCTT
* * *
519893 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
519915 TTCAAAGATGA
1 TTCAAAGATGA
519926 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:520923 original size:75 final size:76
Alignment explanation
Indices: 520601--521358 Score: 1288
Period size: 76 Copynumber: 10.0 Consensus size: 76
520591 CTATTTCCCA
*
520601 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTTTGATGTTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG---CTTTTTGATGTTTT
520666 CAAAGCCTTCGGGT
63 CAAAGCCTTCGGGT
**
520680 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAAATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
520745 AGCCTTCGGGT
66 AGCCTTCGGGT
520756 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
520821 AGCCTTCGGGT
66 AGCCTTCGGGT
*
520832 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
520896 AGCCTTCGGGT
66 AGCCTTCGGGT
520907 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
520970 AGCC-TCAGGGT
66 AGCCTTC-GGGT
520981 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
521046 AGCCTTCGGGT
66 AGCCTTCGGGT
*
521057 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAG-C--CGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
521118 AGCCTTCGGGT
66 AGCCTTCGGGT
521129 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
521194 AG-C-TCAGGGT
66 AGCCTTC-GGGT
521204 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
521269 AGCC-TCAGGGT
66 AGCCTTC-GGGT
* * *
521280 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCCAAAAGCCTTCGGAAGCTTTTTGATGTGTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
521345 A-CCCTCAGGGT
66 AGCCTTC-GGGT
521356 CAT
1 CAT
521359 TCATAAGACC
Statistics
Matches: 657, Mismatches: 11, Indels: 25
0.95 0.02 0.04
Matches are distributed among these distances:
72 65 0.10
73 7 0.01
74 75 0.11
75 152 0.23
76 309 0.47
77 2 0.00
79 47 0.07
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:521383 original size:151 final size:152
Alignment explanation
Indices: 520601--521358 Score: 1288
Period size: 151 Copynumber: 5.0 Consensus size: 152
520591 CTATTTCCCA
*
520601 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTTTGATGTTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG---CTTTTTGATGTTTT
**
520666 CAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAAATT
63 CAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
520731 TTTGATGTTTTCAAAGCCTTCGGGT
128 TTTGATGTTTTCAAAGCCTTCGGGT
520756 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
520821 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
520885 GATGTTTTCAAAGCCTTCGGGT
131 GATGTTTTCAAAGCCTTCGGGT
520907 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
520970 AGCC-TCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
521034 TGATGTTTTCAAAGCCTTCGGGT
130 TGATGTTTTCAAAGCCTTCGGGT
*
521057 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAG-C--CGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
521118 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
521183 GATGTTTTCAAAG-C-TCAGGGT
131 GATGTTTTCAAAGCCTTC-GGGT
521204 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
521269 AGCC-TCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCCAAAAGCCTTCGGAAGCTTTT
66 AGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
521333 TGATGTGTTCAAA-CCCTCAGGGT
130 TGATGTTTTCAAAGCCTTC-GGGT
521356 CAT
1 CAT
521359 TCATAAGACC
Statistics
Matches: 581, Mismatches: 10, Indels: 27
0.94 0.02 0.04
Matches are distributed among these distances:
146 2 0.00
147 43 0.07
148 97 0.17
149 75 0.13
150 80 0.14
151 153 0.26
152 83 0.14
155 48 0.08
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGT
Found at i:521511 original size:3 final size:3
Alignment explanation
Indices: 521503--521538 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
521493 AAACACTAAT
521503 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
521539 AATAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:521551 original size:2 final size:2
Alignment explanation
Indices: 521544--521568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
521534 TATTAAATAA
521544 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
521569 CAAAGGCCCA
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:521951 original size:17 final size:18
Alignment explanation
Indices: 521929--521962 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
521919 CACTGAACCT
521929 GAAAAAAAAA-GAAAAAA
1 GAAAAAAAAAGGAAAAAA
521946 GAAAAAAAAAGGAAAAA
1 GAAAAAAAAAGGAAAAA
521963 CAGAGAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAGGAAAAAA
Found at i:534752 original size:10 final size:10
Alignment explanation
Indices: 534737--534789 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
534727 CATGTCATAG
534737 CATTTAGTTT
1 CATTTAGTTT
***
534747 CATTTAGAGG
1 CATTTAGTTT
534757 CATTTAGTTT
1 CATTTAGTTT
*
534767 CATTTA-TAGT
1 CATTTAGT-TT
534777 CATTTAGTTT
1 CATTTAGTTT
534787 CAT
1 CAT
534790 GTTGTAGTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 1 0.03
10 31 0.94
11 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (10 bp):
CATTTAGTTT
Found at i:534761 original size:20 final size:20
Alignment explanation
Indices: 534736--534789 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
534726 CCATGTCATA
534736 GCATTTAGTTTCATTTAGAG
1 GCATTTAGTTTCATTTAGAG
*
534756 GCATTTAGTTTCATTTATAG
1 GCATTTAGTTTCATTTAGAG
*
534776 TCATTTAGTTTCAT
1 GCATTTAGTTTCAT
534790 GTTGTAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (20 bp):
GCATTTAGTTTCATTTAGAG
Found at i:538216 original size:24 final size:22
Alignment explanation
Indices: 538181--538240 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
538171 ACTTCAATGA
538181 ATCAGTTG-TAAGGAAGATTAGTAT
1 ATCAG-TGCTAAGGAA-ATTA-TAT
* *
538205 ATCAGTGCTAAGGTAATTATGT
1 ATCAGTGCTAAGGAAATTATAT
538227 A-CAGTGCTAAGGAA
1 ATCAGTGCTAAGGAA
538241 CTTCAGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 12 0.38
22 3 0.09
23 6 0.19
24 11 0.34
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (22 bp):
ATCAGTGCTAAGGAAATTATAT
Found at i:551451 original size:56 final size:54
Alignment explanation
Indices: 551301--551459 Score: 139
Period size: 56 Copynumber: 3.0 Consensus size: 54
551291 TGTGTTTAAC
* * * * *
551301 TTTAATTAAAATATACCCATTTAATTTGTGATGGAATAATCATTCCGTTGAAA-
1 TTTAATTAAAATATAACAATTTAATTTATGACGGAATAATCATTCCGTCGAAAT
* ** * * *
551354 -ATAA-T-AAATAT-TTAATTTAATTTATGACGGGACAATGATTCCGTCGAAATTT
1 TTTAATTAAAATATAACAATTTAATTTATGACGGAATAATCATTCCGTCGAAA--T
* * *
551406 TTTAATTAAAATATAACAATTTAATTTTTGACGGAATAGTCATTCCGTGGAAAT
1 TTTAATTAAAATATAACAATTTAATTTATGACGGAATAATCATTCCGTCGAAAT
551460 AAAAAATATA
Statistics
Matches: 80, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
49 29 0.36
50 6 0.08
51 1 0.01
52 3 0.04
53 3 0.04
54 2 0.03
55 6 0.08
56 30 0.38
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (54 bp):
TTTAATTAAAATATAACAATTTAATTTATGACGGAATAATCATTCCGTCGAAAT
Found at i:553315 original size:31 final size:31
Alignment explanation
Indices: 553262--553334 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
553252 ATAATTTTTA
* *
553262 AAATTTGTGATGGAATCTGTGGACCCATTAC
1 AAATTTGTGACGGAATCTGTGGACCCATCAC
* *
553293 AAATTTGTGACGGAATAC-GTGGATCCGTCAC
1 AAATTTGTGACGGAAT-CTGTGGACCCATCAC
*
553324 AAATTTCTGAC
1 AAATTTGTGAC
553335 AGATTCACCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (31 bp):
AAATTTGTGACGGAATCTGTGGACCCATCAC
Found at i:553359 original size:31 final size:31
Alignment explanation
Indices: 553319--553388 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
553309 ACGTGGATCC
* *
553319 GTCACAAATTTCTGACAGATTCACCTATTCT
1 GTCACAAATTTCTGACAGATCCACATATTCT
* * *
553350 GTCAGAAATTTCTGACGGGTCCACATATTCT
1 GTCACAAATTTCTGACAGATCCACATATTCT
553381 GTCACAAA
1 GTCACAAA
553389 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (31 bp):
GTCACAAATTTCTGACAGATCCACATATTCT
Found at i:554015 original size:17 final size:17
Alignment explanation
Indices: 553960--554017 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
553950 GACTTGTTAG
*
553960 TATTATTATT-ATTATCT
1 TATTATT-TTAATTATAT
*
553977 AATT-TTTTAATTA-AT
1 TATTATTTTAATTATAT
553992 GTAATTATTTTAATTATAT
1 -T-ATTATTTTAATTATAT
554011 TATTATT
1 TATTATT
554018 AATTTTCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 12 0.36
18 10 0.30
19 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTTTAATTATAT
Found at i:555603 original size:2 final size:2
Alignment explanation
Indices: 555596--555634 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
555586 CTCATAGCAG
555596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
555635 TTGGAATCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:559721 original size:13 final size:13
Alignment explanation
Indices: 559703--559727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559693 ATTTCACATT
559703 TACACTTTGAAAA
1 TACACTTTGAAAA
559716 TACACTTTGAAA
1 TACACTTTGAAA
559728 CACTCATCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TACACTTTGAAAA
Found at i:562563 original size:26 final size:26
Alignment explanation
Indices: 562527--562578 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
562517 TCCTCTAGTT
562527 TATTTTGTTGTTTTGATTTTAAAAAA
1 TATTTTGTTGTTTTGATTTTAAAAAA
562553 TATTTTGTTGTTTTGATTTTAAAAAA
1 TATTTTGTTGTTTTGATTTTAAAAAA
562579 AATATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TATTTTGTTGTTTTGATTTTAAAAAA
Found at i:562850 original size:15 final size:16
Alignment explanation
Indices: 562814--562852 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
562804 AGAGCCTTTG
*
562814 AATCATTCAACATTTA
1 AATCATTCAACACTTA
*
562830 AATCATTCAACGCTT-
1 AATCATTCAACACTTA
562845 AATCATTC
1 AATCATTC
562853 TGAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (16 bp):
AATCATTCAACACTTA
Found at i:563649 original size:27 final size:27
Alignment explanation
Indices: 563595--563671 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
563585 GATAATAGTA
*
563595 ATAATAATAATAATAATGTATTATAAT
1 ATAATAATAATAATAATATATTATAAT
* * *
563622 ATAATAGTTATAATAATATAAT-TAA-
1 ATAATAATAATAATAATATATTATAAT
**
563647 ATAATTTTAAT-ATAATAT-TTATAAT
1 ATAATAATAATAATAATATATTATAAT
563672 CCGAACAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 1 0.03
24 10 0.25
25 8 0.20
26 3 0.08
27 18 0.45
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
ATAATAATAATAATAATATATTATAAT
Found at i:563658 original size:36 final size:36
Alignment explanation
Indices: 563580--563671 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 36
563570 ATATGTAACA
* *
563580 TTAATGATAATAGTAATAATAATAATAATAATGTATT
1 TTAAT-ATAATAGTTATAATAATAATAATAATGAATT
*
563617 ATAATATAATAGTTATAATAAT-ATAATTAAAT-AATT
1 TTAATATAATAGTTATAATAATAATAA-T-AATGAATT
*
563653 TTAATATAATATTTATAAT
1 TTAATATAATAGTTATAAT
563672 CCGAACAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.08
36 37 0.77
37 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (36 bp):
TTAATATAATAGTTATAATAATAATAATAATGAATT
Found at i:569197 original size:293 final size:291
Alignment explanation
Indices: 568674--569258 Score: 1088
Period size: 293 Copynumber: 2.0 Consensus size: 291
568664 CTTATTTTAT
568674 TTCGAATTTCAAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
1 TTCGAATTTCAAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
568739 GATTTTTTGCTATAACAGTCCGGCTTGTGGATGCTTTTTGATAGTTTTGATTTTATAATATTATT
66 GATTTTTTGCTATAACAGTCCGGCTTGTGGATGCTTTTTGATAGTTTTGATTTTATAATATTATT
568804 AAACCCTAGAGACTTTTCTCTGGTTTTTGGCGAATTTTTTTGTGAATCGTCTGTCGGAGCTAACC
131 AAACCCTAGAGACTTTTCTCTGGTTTTTGGCGAATTTTTTTGTGAATCGTCTGTCGGAGCTAACC
568869 TACAGGATAATCACTATTCTGTCTGGCGTCAGTTGGTGTCAGAGC-TCAACATCTTCTTGGGAAA
196 TACAGGATAATCACTATTCTGTCTGGCGTCAGTTGGTGTCAGAGCTTCAACATCTTCTTGGGAAA
568933 TTTCACCAGTTTCAATGGCTGGAGGT-GTGG
261 TTTCACCAGTTTCAATGGCTGGAGGTCGTGG
568963 TTCGAATTTC-AATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
1 TTCGAATTTCAAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
569027 GATTTTTTTGCTATAACAGTCCGGCTTGTGGACTGCTTTTTGATAGTTTTGA-TTTATAATATTT
66 GA-TTTTTTGCTATAACAGTCCGGCTTGTGGA-TGCTTTTTGATAGTTTTGATTTTATAATA-TT
569091 ATTAAACCCTAGAGACTTTTCTCTGGTTTTTGGGCGAATTTTCTCTTGTGAATCGTCTGTCGGAG
128 ATTAAACCCTAGAGACTTTTCTCTGGTTTTT-GGCGAATTTT-T-TTGTGAATCGTCTGTCGGAG
569156 CTAACCTACAGGATAATCACTATTCTGTCTGGCGTCAGTTGGTGTCAGAGCTTCAACATCTTCTT
190 CTAACCTACAGGATAATCACTATTCTGTCTGGCGTCAGTTGGTGTCAGAGCTTCAACATCTTCTT
569221 GGGAAATTTCACCAGTTTCAATGGCTGGAGGTCGTGG
255 GGGAAATTTCACCAGTTTCAATGGCTGGAGGTCGTGG
569258 T
1 T
569259 CGTGGTCGTC
Statistics
Matches: 288, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
288 56 0.19
289 48 0.17
290 52 0.18
291 10 0.03
292 1 0.00
293 71 0.25
294 45 0.16
295 5 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (291 bp):
TTCGAATTTCAAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
GATTTTTTGCTATAACAGTCCGGCTTGTGGATGCTTTTTGATAGTTTTGATTTTATAATATTATT
AAACCCTAGAGACTTTTCTCTGGTTTTTGGCGAATTTTTTTGTGAATCGTCTGTCGGAGCTAACC
TACAGGATAATCACTATTCTGTCTGGCGTCAGTTGGTGTCAGAGCTTCAACATCTTCTTGGGAAA
TTTCACCAGTTTCAATGGCTGGAGGTCGTGG
Found at i:569469 original size:15 final size:15
Alignment explanation
Indices: 569449--569478 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
569439 TATCACAATC
569449 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
569464 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
569479 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:582138 original size:33 final size:34
Alignment explanation
Indices: 582092--582158 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
582082 TTCACATGTT
582092 TAAGTTTGGCCACCAACCAAGATGAAATTTCCAA
1 TAAGTTTGGCCACCAACCAAGATGAAATTTCCAA
582126 TAAG-TTGGCCACCAACCAAGATGAAATTTCCAA
1 TAAGTTTGGCCACCAACCAAGATGAAATTTCCAA
582159 CTTGTCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (34 bp):
TAAGTTTGGCCACCAACCAAGATGAAATTTCCAA
Found at i:583559 original size:105 final size:102
Alignment explanation
Indices: 583369--583643 Score: 360
Period size: 105 Copynumber: 2.7 Consensus size: 102
583359 AATAATATTT
583369 TATTCT-AGAATTTGAGCAATGTTGGTAGTATCGATACTACATTGTGAGTATCGATACTTCCATT
1 TATTCTGA-AATTTGAGCAATGTTGGTAGTATCGATAC--CATTGTGAGTATCGATACTTCCA-T
* * *
583433 AACTTTGGTATCGGTACCCCTTCTGG-TACCGGTACCATTTTTG
62 ACCTTTGGTATCAGTACCCC-T-TGGATAACGGTACCA-TTTTG
*
583476 TATTCTGAAATTTGAGTAATGTTGGTAGTATCGATACCATTGTGAGTATCGATACTTCCGATACC
1 TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACCATTGTGAGTATCGATACTTCC-ATACC
*
583541 TTTGGTATCAGTATCCCTTGGATAACGGTACCATTTTG
65 TTTGGTATCAGTACCCCTTGGATAACGGTACCATTTTG
* * * * *
583579 CATTATGGAATTTGAGCAATGTTGGTAGTATC-CTATC-TTGTGAGTATCGATACTTCCATACCT
1 TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACCATTGTGAGTATCGATACTTCCATACCT
583642 TT
66 TT
583644 AGTCGTAAAT
Statistics
Matches: 154, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
100 8 0.05
101 20 0.13
102 3 0.02
103 36 0.23
104 11 0.07
105 40 0.26
106 1 0.01
107 34 0.22
108 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (102 bp):
TATTCTGAAATTTGAGCAATGTTGGTAGTATCGATACCATTGTGAGTATCGATACTTCCATACCT
TTGGTATCAGTACCCCTTGGATAACGGTACCATTTTG
Found at i:600395 original size:22 final size:22
Alignment explanation
Indices: 600367--600412 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
600357 TTCATGTGAG
600367 AAAGCTAAAGTCCTATTAATTA
1 AAAGCTAAAGTCCTATTAATTA
600389 AAAGCTAAAGTCCTATTAATTA
1 AAAGCTAAAGTCCTATTAATTA
600411 AA
1 AA
600413 TCCAGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAGCTAAAGTCCTATTAATTA
Found at i:604064 original size:183 final size:182
Alignment explanation
Indices: 603717--604310 Score: 917
Period size: 183 Copynumber: 3.3 Consensus size: 182
603707 CATATAAAAA
* * * *
603717 TATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTATCGATTA-GATTGAAATTAGTAT
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGA-TACCATTGAAATAAGTAT
* * * *
603781 --ATA-TTTATGGAATTTAAAATAGAAGCAGTAATAGTGCCAATAAAGTGTCGATACAAATAAAA
65 CGACACTTT-TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAA
* *
603843 ATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACATGTTTCAT
129 ATGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
* * *
603897 TATGACAAAATCGGTAAATCGCTACCGGATATGTTGAATGTGTCGATACCATTGAAATAAGTATC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
* * **
603962 GACACTTTTGGAATTTAAAAGGGAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAA
66 GACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAC-AAATAAAAA
* *
604027 TGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTATCAT
130 TGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
* * *
604080 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTCTTGATTCCATTGAAATAAGTATC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
*
604145 GACACTTTTGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
66 GACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
604210 GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
131 GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
*
604262 TATGACAAAACCGATAAAGCGCTACCGGATATGTTGAAAGTGTCGATAC
1 TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAC
604311 TTTAATAATT
Statistics
Matches: 373, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
179 2 0.01
180 54 0.14
182 147 0.39
183 170 0.46
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
GACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACAAATAAAAAT
GTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCAT
Found at i:604073 original size:20 final size:20
Alignment explanation
Indices: 604048--604097 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
604038 ATAACAATAT
604048 AACAGGTAAAAATATGACAA
1 AACAGGTAAAAATATGACAA
** *
604068 AACAGGTATCATTATGACAA
1 AACAGGTAAAAATATGACAA
*
604088 AACCGGTAAA
1 AACAGGTAAA
604098 GCGCTACCGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (20 bp):
AACAGGTAAAAATATGACAA
Found at i:606320 original size:21 final size:24
Alignment explanation
Indices: 606277--606327 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
606267 TTTTGTTTTT
606277 TTATATAAAATGATAGTATATTT-A
1 TTATATAAAATGATAG-ATATTTAA
606301 TTATATAAAATGATA-A-ATTTAA
1 TTATATAAAATGATAGATATTTAA
606323 TTATA
1 TTATA
606328 AATGCAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
24 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TTATATAAAATGATAGATATTTAA
Found at i:606593 original size:18 final size:18
Alignment explanation
Indices: 606574--606639 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
606564 GGTAGAGGAT
* *
606574 GTAGTGGAAGAAGTGGAT
1 GTAGTGGAAGCAGTGGAG
* * *
606592 GTACTGGAGGCAGAGGAG
1 GTAGTGGAAGCAGTGGAG
* *
606610 GTAGTGGATGCAGTAGAG
1 GTAGTGGAAGCAGTGGAG
606628 GTAGTGGAAGCA
1 GTAGTGGAAGCA
606640 ATGAAGGCAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.45, T:0.18
Consensus pattern (18 bp):
GTAGTGGAAGCAGTGGAG
Found at i:606697 original size:15 final size:15
Alignment explanation
Indices: 606677--606707 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
606667 ATGGTAGTAT
606677 GGGATGAAGGTGAGG
1 GGGATGAAGGTGAGG
606692 GGGATGAAGGTGAGG
1 GGGATGAAGGTGAGG
606707 G
1 G
606708 AATACAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.61, T:0.13
Consensus pattern (15 bp):
GGGATGAAGGTGAGG
Found at i:607000 original size:14 final size:16
Alignment explanation
Indices: 606981--607013 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
606971 AAAAAGTTGG
606981 ATGAAGGG-GAAA-AA
1 ATGAAGGGTGAAATAA
606995 ATGAAGGGTGAAATAA
1 ATGAAGGGTGAAATAA
607011 ATG
1 ATG
607014 TGATGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (16 bp):
ATGAAGGGTGAAATAA
Found at i:612295 original size:199 final size:199
Alignment explanation
Indices: 611947--613087 Score: 1528
Period size: 199 Copynumber: 5.7 Consensus size: 199
611937 ATAATTAAAA
* * **
611947 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAGTGTAAGAG
1 GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * *
612012 GTATAAATATATCGGTTTAATTAAAAAATAGATCAACATAATGTATCGATACATTTTAAATTTGT
66 GTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* * * *
612077 GTCGATATTTTTTGTCCAGAATGAATGCCCAACGAGATGCACACATAAAGTGTCGATACATTTAA
131 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
612142 AATT
196 AATT
* * *
612146 GTATCGATCCTAAAAACATCGCAATCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * ** * *
612211 GTAAAAATATACCAGTTTTGTGAGAAAATAGGTCAATATAATGTATCGACACTTTTTAAATTTGT
66 GTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* * * *
612276 GTCAATACTTTTGGTCCAGAATGAATGCCTAAACAAGGTGCACACATAAAGTGTCGATACATTTT
131 GTCGATACTTTTGGTCCAGAATGAATGCC-CAACGAGGTGCACGCATAAAGTGTCGATACA----
612341 TTTAAAA--
191 TTTAAAATT
* * * *
612348 GTATCGACCCCAAAAACATCGAAACCGATCATTATAATGTAATAGGTAAATTTACAATGTAATCG
1 GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
612413 GTAGAAATATACC-GATTAATTAGAAAATAGGTAAACATAATGTATGGACACTTTTTAAATTTGT
66 GTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
* *
612477 GTCGATACTTGTT-GTCCATAATGAATCCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTT
131 GTCGATACTT-TTGGTCCAGAATGAATGCCC-AACGAGGTGCACGCATAAAGTGTCGATACATTT
*
612541 ATTAAA-A
194 A--AAATT
* *
612548 GTATCGATCCCAAAAACATC-AAAACATATAATTATAATGTAATACGTAAATTTACAATGTAACC
1 GTATCGATCCCAAAAACATCGAAACCA-ATAATTATAATGTAATAGGTAAATTTACAATGTAACC
* *
612612 GGTAGAAATATACCGATTTAATTAGAAAATAGGT-AATCATAATGTATAGACAC--TTTAAATTT
65 GGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAA-CATAATGTATCGACACTTTTTAAATTT
* * * *
612674 GTTTCGATACTTTTTGTCCTA-AATGAATGCCCAAACGAGGTGCACGTATAAAGTATCGATACAT
129 GTGTCGATACTTTTGGTCC-AGAATGAATGCCC-AACGAGGTGCACGCATAAAGTGTCGATACAT
612738 TTAAAATT
192 TTAAAATT
* * * * *
612746 GTATCGATCCTAAAAAACATCGAAACCGATAATTATACTGTAATAAGTAAATTTACAATATAACC
1 GTATCGATCC-CAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACC
** *
612811 GGTAGAAATATATTGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTGTTAAATTTG
65 GGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTG
*
612876 TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATATATTTA
130 TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
612941 AAATT
195 AAATT
* * *
612946 GTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATAAGTAAATTTACAATGTAACCA
1 GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
613011 GTAGAAATATATCGGTTTAATAAAAAAATAGGTCAACATAATGTATCGACACTTGTTAAATTTCT
66 GTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
613076 GTCGATACTTTT
131 GTCGATACTTTT
613088 TTAAAATTAC
Statistics
Matches: 835, Mismatches: 85, Indels: 44
0.87 0.09 0.05
Matches are distributed among these distances:
197 7 0.01
198 12 0.01
199 423 0.51
200 151 0.18
201 163 0.20
202 72 0.09
204 7 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
AATT
Found at i:614692 original size:2 final size:2
Alignment explanation
Indices: 614685--614711 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
614675 AAAATGTATG
614685 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
614712 TCCATACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:615277 original size:37 final size:37
Alignment explanation
Indices: 615233--615353 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
615223 ATTAACCGGT
615233 TATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAA
1 TATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAA
* * ** * *** * ***
615270 TATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGT
1 TATG---TTATCCTTGGTAACATTT-TAGGCGTTTACCTAA
615311 TATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAA
1 TATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAA
615348 TATGTT
1 TATGTT
615354 GTAATAACAA
Statistics
Matches: 56, Mismatches: 24, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
37 17 0.30
38 14 0.25
40 14 0.25
41 11 0.20
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (37 bp):
TATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAA
Found at i:615318 original size:78 final size:75
Alignment explanation
Indices: 615192--615353 Score: 297
Period size: 78 Copynumber: 2.1 Consensus size: 75
615182 AAGCGCTACT
615192 TAATATGTTATTATGCTTGATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTA
1 TAATATGTTATTATGCTTGATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTA
615257 GGCGTTTACC
66 GGCGTTTACC
615267 TAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAACATT
1 TAATATGTTATTATGCTTG---ATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAACATT
615332 TTAGGCGTTTACC
63 TTAGGCGTTTACC
615345 TAATATGTT
1 TAATATGTT
615354 GTAATAACAA
Statistics
Matches: 84, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
75 19 0.23
78 65 0.77
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (75 bp):
TAATATGTTATTATGCTTGATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTA
GGCGTTTACC
Found at i:615537 original size:23 final size:23
Alignment explanation
Indices: 615511--615560 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
615501 TAAGTAATTA
**
615511 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
615534 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
615557 ACCT
1 ACCT
615561 GATATGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:615547 original size:135 final size:135
Alignment explanation
Indices: 615263--615547 Score: 462
Period size: 135 Copynumber: 2.1 Consensus size: 135
615253 TTTAGGCGTT
* ** *
615263 TACCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAA
1 TACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTAACCGGTTATGTTATCATTGGTAA
*
615328 CATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAAATAACCTATTTTATTATATA
66 CATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAAATAACCTATTTTATTATATA
615393 AGCGC
131 AGCGC
* * *
615398 TACCTAAAATGTTATTGTGCTTGATAATATTAACGGTAATTAACCGGTTATGTTATCATTGGTAA
1 TACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTAACCGGTTATGTTATCATTGGTAA
* *
615463 CATTTTATGCATTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATA
66 CATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAAATAACCTATTTTATTATATA
615528 AGCGC
131 AGCGC
* *
615533 TACCTATTACGTTAT
1 TACCTAATATGTTAT
615548 ATAAGCGCTA
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 137 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (135 bp):
TACCTAATATGTTATTATGCTTGATAATATTAACAGTAATTAACCGGTTATGTTATCATTGGTAA
CATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAAATAACCTATTTTATTATATA
AGCGC
Found at i:618646 original size:20 final size:21
Alignment explanation
Indices: 618594--618647 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
618584 ATATCGAAGT
618594 GGGTATCGATACCATAGAAGAG
1 GGGTATCGATACCATAG-AGAG
** *
618616 AAGTATTGATACCATAG-GAG
1 GGGTATCGATACCATAGAGAG
618636 GGGTATCGATAC
1 GGGTATCGATAC
618648 TATTGAGTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 12 0.46
22 14 0.54
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (21 bp):
GGGTATCGATACCATAGAGAG
Found at i:619033 original size:54 final size:53
Alignment explanation
Indices: 618964--619080 Score: 171
Period size: 54 Copynumber: 2.2 Consensus size: 53
618954 CATTTTACAA
* * * *
618964 TATCGACACCATGTGTGCAACCCATAGAATTCATAATGAGTTTATGAATAACCT
1 TATCGGCACTATGTGTGCAACCCATAGAATTCATAATGA-CTTATGAATAACCG
* *
619018 TATCGGCACTATGTGTGCAACCCATGGAATTCATAATGACTTATGAATGACCG
1 TATCGGCACTATGTGTGCAACCCATAGAATTCATAATGACTTATGAATAACCG
619071 TATCGGCACT
1 TATCGGCACT
619081 TAGGTGCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 21 0.37
54 36 0.63
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (53 bp):
TATCGGCACTATGTGTGCAACCCATAGAATTCATAATGACTTATGAATAACCG
Found at i:625111 original size:2 final size:2
Alignment explanation
Indices: 625104--625142 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
625094 AACGTGTTTA
*
625104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
625143 ATTGAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:626143 original size:160 final size:162
Alignment explanation
Indices: 625879--626202 Score: 634
Period size: 160 Copynumber: 2.0 Consensus size: 162
625869 AGGGATATAT
625879 AACCCATGAAAAACAAAAATATACACAGAGGGACAGAAACATTTGGGCAGAAATAACAAAAGAAA
1 AACCCATGAAAAACAAAAATATACACAGAGGGACAGAAACATTTGGGCAGAAATAACAAAAGAAA
625944 TTCCACAAGTTTTCTTAAGTAATTATCTTTAAGGTATTGTAATGTGTGTGTTG-TTTC-TTTCTC
66 TTCCACAAGTTTTCTTAAGTAATTATCTTTAAGGTATTGTAATGTGTGTGTTGTTTTCTTTTCTC
626007 TCCTGTTCTATACTAGTTCTAGGATAAAAACG
131 TCCTGTTCTATACTAGTTCTAGGATAAAAACG
626039 AACCCATGAAAAACAAAAATATACACAGAGGGACAGAAACATTTGGGCAGAAATAACAAAAGAAA
1 AACCCATGAAAAACAAAAATATACACAGAGGGACAGAAACATTTGGGCAGAAATAACAAAAGAAA
626104 TTCCACAAGTTTTCTTAAGTAATTATCTTTAAGGTATTGTAATGTGTGTGTTGTTTTCTTTTCTC
66 TTCCACAAGTTTTCTTAAGTAATTATCTTTAAGGTATTGTAATGTGTGTGTTGTTTTCTTTTCTC
626169 TCCTGTTCTATACTAGTTCTAGGATAAAAACG
131 TCCTGTTCTATACTAGTTCTAGGATAAAAACG
626201 AA
1 AA
626203 AATAAAATAG
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
160 118 0.73
161 4 0.02
162 40 0.25
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (162 bp):
AACCCATGAAAAACAAAAATATACACAGAGGGACAGAAACATTTGGGCAGAAATAACAAAAGAAA
TTCCACAAGTTTTCTTAAGTAATTATCTTTAAGGTATTGTAATGTGTGTGTTGTTTTCTTTTCTC
TCCTGTTCTATACTAGTTCTAGGATAAAAACG
Found at i:629212 original size:72 final size:71
Alignment explanation
Indices: 629131--629270 Score: 271
Period size: 72 Copynumber: 2.0 Consensus size: 71
629121 GGATTGTTAT
629131 TTTAAAAAAAAAGCGTGTTTGGGTACCTATTACTATGGGGTAGGTATTTTTCCAAAATTTTATTA
1 TTTAAAAAAAAAGCGTGTTTGGGTACCTATTACTATGGGGTAGGTATTTTTCCAAAATTTTATTA
629196 CCTTTA
66 CCTTTA
629202 TTTAATAAAAAAAGCGTGTTTGGGTACCTATTACTATGGGGTAGGTATTTTTCCAAAATTTTATT
1 TTTAA-AAAAAAAGCGTGTTTGGGTACCTATTACTATGGGGTAGGTATTTTTCCAAAATTTTATT
629267 ACCT
65 ACCT
629271 ACTAACTCGT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 5 0.07
72 63 0.93
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (71 bp):
TTTAAAAAAAAAGCGTGTTTGGGTACCTATTACTATGGGGTAGGTATTTTTCCAAAATTTTATTA
CCTTTA
Found at i:638863 original size:21 final size:21
Alignment explanation
Indices: 638839--638900 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
638829 AATGAATGAA
638839 TGAATGAAAAAAATGAAAAAG
1 TGAATGAAAAAAATGAAAAAG
* *
638860 TGAA-AAAGAAAAATGAAAATG
1 TGAATGAA-AAAAATGAAAAAG
**
638881 AAAATGAAAAAAGA-GAAAAA
1 TGAATGAAAAAA-ATGAAAAA
638901 AGAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (21 bp):
TGAATGAAAAAAATGAAAAAG
Found at i:638888 original size:33 final size:32
Alignment explanation
Indices: 638848--638923 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
638838 ATGAATGAAA
* *
638848 AAAATGAAAAAGTGAAAAAGAAAAATGAAAATG
1 AAAATGAAAAAGAGAAAAA-AAAAATAAAAATG
*
638881 AAAATGAAAAAAGAGAAAAAAGAAATAAAAATG
1 AAAATG-AAAAAGAGAAAAAAAAAATAAAAATG
638914 AAAA-GAAAAA
1 AAAATGAAAAA
638924 TGAGGGTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 5 0.13
32 1 0.03
33 21 0.54
34 12 0.31
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (32 bp):
AAAATGAAAAAGAGAAAAAAAAAATAAAAATG
Found at i:638891 original size:7 final size:7
Alignment explanation
Indices: 638847--638926 Score: 68
Period size: 6 Copynumber: 12.1 Consensus size: 7
638837 AATGAATGAA
638847 AAAAATG
1 AAAAATG
638854 AAAAAGTG
1 AAAAA-TG
638862 AAAAA-G
1 AAAAATG
638868 AAAAATG
1 AAAAATG
638875 -AAAATG
1 AAAAATG
638881 -AAAATG
1 AAAAATG
*
638887 AAAAAAG
1 AAAAATG
638894 AGAAAA--
1 A-AAAATG
638900 AAGAAAT-
1 AA-AAATG
638907 AAAAATG
1 AAAAATG
638914 -AAAA-G
1 AAAAATG
638919 AAAAATG
1 AAAAATG
638926 A
1 A
638927 GGGTTCGAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
5 2 0.03
6 34 0.54
7 16 0.25
8 11 0.17
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:639995 original size:104 final size:105
Alignment explanation
Indices: 639859--640053 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 105
639849 AACAACTATG
* *
639859 ATCCACCACAGAAGAAGGTGAACCAATATTTCCAAAAGAGTTCATAATTAGAAGAGCTCGTCC-T
1 ATCCACCACAGAAGAAGGTGAAACAATATTTCCAAAAGAGTTCATAATGAGAAGAGCTCG-CCTT
* **
639923 AAAGGATAAAGTTTGTAATGAGAAGAACATGTTCCTTTCAA
65 AAAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAA
* * *
639964 ATCCACC-CAGAAGGAGGTGAAACAACT-TTTCCAGAAGAGTTCATAATGAGAAGATCTCGCCTT
1 ATCCACCACAGAAGAAGGTGAAACAA-TATTTCCAAAAGAGTTCATAATGAGAAGAGCTCGCCTT
*
640027 AAAGGAGGAAGTTCATAATGAGAAGAA
65 AAAGGAGAAAGTTCATAATGAGAAGAA
640054 TTTGCTCAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
103 2 0.03
104 69 0.87
105 8 0.10
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (105 bp):
ATCCACCACAGAAGAAGGTGAAACAATATTTCCAAAAGAGTTCATAATGAGAAGAGCTCGCCTTA
AAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAA
Found at i:642555 original size:251 final size:252
Alignment explanation
Indices: 642112--642614 Score: 967
Period size: 251 Copynumber: 2.0 Consensus size: 252
642102 ACATAATTGG
642112 ATTAAGGGTAGTATTTATGTATTTTAAAATATTAAAAAGGGACAGTTTTATGACAACTAGATGTC
1 ATTAAGGGTAGTATTTATGTATTTTAAAATATTAAAAAGGGACAGTTTTATGACAACTAGATGTC
642177 ATTTTTTGATATTTTAAAATAAATAAACATCTCACTAGAAAACCTAAAAAATTGATTCCATTTAA
66 ATTTTTTGATATTTTAAAATAAATAAACATCTCACTAGAAAACCTAAAAAATTGATTCCATTTAA
642242 AAATTAATTAATTTTGAATGGAAAAGGAAAATTCACTATTTTAAACTTATCGAGACAATTTGCTA
131 AAATTAATTAATTTTGAATGGAAAAGGAAAATTCACTATTTTAAACTTATCGAGACAATTTGCTA
642307 ATTTTATTA-GGATTAAGTCTCGGTATTTTTTAAATAATTGAATAT-CCTTATCTTTT
196 ATTTTATTAGGGATTAAGTCTCGGTA-TTTTTAAATAATTGAATATCCCTTATCTTTT
642363 ATTAAGGGTAGTATTTATGTATTTTAAAATATTAAAAAGGGACAGTTTTATGACAACTAGATGTC
1 ATTAAGGGTAGTATTTATGTATTTTAAAATATTAAAAAGGGACAGTTTTATGACAACTAGATGTC
642428 ATTTTTTGATATTTTAAAATAAATAAACATCTCACTAGAAAACCTAAAAAATTGATTCCATTT-A
66 ATTTTTTGATATTTTAAAATAAATAAACATCTCACTAGAAAACCTAAAAAATTGATTCCATTTAA
642492 AAATTAATTAATTTTGAATGGAAAAGGAAATATTCACTATTTTAAACTTATCGAGACAATTTGCT
131 AAATTAATTAATTTTGAATGGAAAAGGAAA-ATTCACTATTTTAAACTTATCGAGACAATTTGCT
642557 AATTTTATTAGGGATTAAGTCTCGGTATTTTTAAATAATTGAATATCCCTTATCTTTT
195 AATTTTATTAGGGATTAAGTCTCGGTATTTTTAAATAATTGAATATCCCTTATCTTTT
642615 CTAATAATAT
Statistics
Matches: 249, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
250 31 0.12
251 191 0.77
252 27 0.11
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (252 bp):
ATTAAGGGTAGTATTTATGTATTTTAAAATATTAAAAAGGGACAGTTTTATGACAACTAGATGTC
ATTTTTTGATATTTTAAAATAAATAAACATCTCACTAGAAAACCTAAAAAATTGATTCCATTTAA
AAATTAATTAATTTTGAATGGAAAAGGAAAATTCACTATTTTAAACTTATCGAGACAATTTGCTA
ATTTTATTAGGGATTAAGTCTCGGTATTTTTAAATAATTGAATATCCCTTATCTTTT
Found at i:650473 original size:16 final size:16
Alignment explanation
Indices: 650443--650489 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
650433 TAAATGACCA
* *
650443 TCATTATTTTCATTCT
1 TCATTCTTTACATTCT
*
650459 TCATTCTTTATATTCT
1 TCATTCTTTACATTCT
*
650475 TCATTTTTTACATTC
1 TCATTCTTTACATTC
650490 ATTTCATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TCATTCTTTACATTCT
Found at i:657118 original size:2 final size:2
Alignment explanation
Indices: 657111--657144 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
657101 CAACTAAATA
657111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
657145 CGATATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:659384 original size:23 final size:26
Alignment explanation
Indices: 659358--659414 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 26
659348 AATGAAATAA
659358 AATAAGTA-AATA-AATAAAT-ATA-T
1 AATAA-TATAATATAATAAATAATACT
659381 AAT-ATATAATATAATAAATAATACT
1 AATAATATAATATAATAAATAATACT
*
659406 AATACTATA
1 AATAATATA
659415 TTTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.07
22 5 0.18
23 10 0.36
24 3 0.11
25 4 0.14
26 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
AATAATATAATATAATAAATAATACT
Found at i:659402 original size:12 final size:12
Alignment explanation
Indices: 659366--659409 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
659356 AAAATAAGTA
659366 AATA-AATAAAT
1 AATATAATAAAT
*
659377 -ATATAATATAT
1 AATATAATAAAT
659388 AATATAATAAAT
1 AATATAATAAAT
659400 AATACTAATA
1 AATA-TAATA
659410 CTATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 3 0.11
11 6 0.21
12 14 0.50
13 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
AATATAATAAAT
Found at i:659515 original size:14 final size:14
Alignment explanation
Indices: 659496--659523 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
659486 AATTATATAT
659496 TATGTTTTCAAAAA
1 TATGTTTTCAAAAA
659510 TATGTTTTCAAAAA
1 TATGTTTTCAAAAA
659524 ACCATACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TATGTTTTCAAAAA
Found at i:659524 original size:37 final size:38
Alignment explanation
Indices: 659431--659546 Score: 89
Period size: 37 Copynumber: 3.1 Consensus size: 38
659421 TAAAAACTAT
* *
659431 AATATGTTTCCAAAAATTATATATATTATATATGTTTTCAAA
1 AATATGTTTTCAAAAA--AT-TATACTAT-TATGTTTTCAAA
**
659473 AA-ACCATTTT--AAAAATTATA-TATTATGTTTTCAAA
1 AATA-TGTTTTCAAAAAATTATACTATTATGTTTTCAAA
** *
659508 AATATGTTTTCAAAAAACCATACT-TTATATTTTCAAA
1 AATATGTTTTCAAAAAATTATACTATTATGTTTTCAAA
659545 AA
1 AA
659547 CTATATATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
35 18 0.30
36 4 0.07
37 26 0.43
38 3 0.05
40 4 0.07
41 1 0.02
42 5 0.08
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (38 bp):
AATATGTTTTCAAAAAATTATACTATTATGTTTTCAAA
Found at i:659555 original size:2 final size:2
Alignment explanation
Indices: 659548--659614 Score: 61
Period size: 2 Copynumber: 35.0 Consensus size: 2
659538 TTTCAAAAAC
* * *
659548 TA TA TA TA T- TA TA TA TT TT TA AA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
659588 TA TA TA TA T- TGA CA TA TA TA T- TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
659615 ATGTAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:666135 original size:6 final size:6
Alignment explanation
Indices: 666119--666163 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
666109 ATAAGTGAGT
* * * *
666119 AAAATA GAAATA AAAATA AAAATA ATAATG AAAATA AAATTA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
666164 TTCTTACACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:668399 original size:24 final size:24
Alignment explanation
Indices: 668372--668420 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
668362 TGCATGACAT
668372 TGTACATAAATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
*
668396 TGTACATAGATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
668420 T
1 T
668421 CAGGAAGACT
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:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (24 bp):
TGTACATAAATGTTTTATACATCA
Found at i:671641 original size:23 final size:25
Alignment explanation
Indices: 671611--671659 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
671601 AAAATAAGTA
671611 AATAAATAAAT-ATA-TAATA-TAT
1 AATAAATAAATAATACTAATACTAT
671633 AATATAATAAATAATACTAATACTAT
1 AATA-AATAAATAATACTAATACTAT
671659 A
1 A
671660 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.17
23 7 0.30
24 3 0.13
25 5 0.22
26 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AATAAATAAATAATACTAATACTAT
Found at i:671647 original size:12 final size:12
Alignment explanation
Indices: 671611--671654 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
671601 AAAATAAGTA
671611 AATA-AATAAAT
1 AATATAATAAAT
*
671622 -ATATAATATAT
1 AATATAATAAAT
671633 AATATAATAAAT
1 AATATAATAAAT
671645 AATACTAATA
1 AATA-TAATA
671655 CTATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 3 0.11
11 6 0.21
12 14 0.50
13 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
AATATAATAAAT
Found at i:671784 original size:24 final size:24
Alignment explanation
Indices: 671755--671901 Score: 109
Period size: 24 Copynumber: 5.6 Consensus size: 24
671745 ATATTTAAAA
*
671755 ATATGTTTTGAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATATTAT
*
671779 ATATGTTTTCAAAAAACAAT-TTAAAAAACT
1 ATATGTTTTC-AAAAACTATATT-----A-T
*
671809 CTATGTTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATATTAT
*
671833 ATATGTTTTCAAAAAACAAT-TTAAAAAACT
1 ATATGTTTTC-AAAAACTATATT-----A-T
671863 ATATGTTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATATTAT
*
671887 TTATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
671902 ACCATTTTAA
Statistics
Matches: 99, Mismatches: 8, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
24 38 0.38
25 18 0.18
29 18 0.18
30 25 0.25
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (24 bp):
ATATGTTTTCAAAAACTATATTAT
Found at i:671816 original size:30 final size:30
Alignment explanation
Indices: 671778--671877 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
671768 AACTATATTA
671778 TATATGTTTTCAAAAAACAATTTAAAAAAC
1 TATATGTTTTCAAAAAACAATTTAAAAAAC
* *
671808 TCTATGTTTTC-AAAAACTATATT-----A-
1 TATATGTTTTCAAAAAACAAT-TTAAAAAAC
671832 TATATGTTTTCAAAAAACAATTTAAAAAAC
1 TATATGTTTTCAAAAAACAATTTAAAAAAC
671862 TATATGTTTTCAAAAA
1 TATATGTTTTCAAAAA
671878 CTATATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
24 12 0.21
25 9 0.16
29 9 0.16
30 28 0.48
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (30 bp):
TATATGTTTTCAAAAAACAATTTAAAAAAC
Found at i:671825 original size:54 final size:54
Alignment explanation
Indices: 671755--671920 Score: 287
Period size: 54 Copynumber: 3.1 Consensus size: 54
671745 ATATTTAAAA
*
671755 ATATGTTTTGAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
*
671809 CTATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
* * *
671863 ATATGTTTTCAAAAACTATATTATTTATGTTTTCAAAAAACCATTTTAAAAACT
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
671917 ATAT
1 ATAT
671921 ATTATAAGTT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (54 bp):
ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACAATTTAAAAAACT
Found at i:671914 original size:37 final size:38
Alignment explanation
Indices: 671868--671943 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 38
671858 AAACTATATG
*
671868 TTTTCAAAAACTATATTATT-TATGTTTTCAAAAAACCA
1 TTTTCAAAAACTATA-TATTATAAGTTTTCAAAAAACCA
*
671906 TTTT-AAAAACTATATATTATAAGTTTTCCAAAAACCA
1 TTTTCAAAAACTATATATTATAAGTTTTCAAAAAACCA
671943 T
1 T
671944 ACTTTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 4 0.11
37 27 0.77
38 4 0.11
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (38 bp):
TTTTCAAAAACTATATATTATAAGTTTTCAAAAAACCA
Found at i:671972 original size:22 final size:22
Alignment explanation
Indices: 671905--671974 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
671895 TCAAAAAACC
671905 ATTTT-AAAAACTATATATTAT
1 ATTTTCAAAAACTATATATTAT
*
671926 AAGTTTTCCAAAAACCATACT-TTAT
1 -A-TTTT-CAAAAACTATA-TATTAT
671951 ATTTTCAAAAACTATATATTAT
1 ATTTTCAAAAACTATATATTAT
671973 AT
1 AT
671975 ATATTTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 1 0.02
22 17 0.41
23 8 0.20
24 1 0.02
25 13 0.32
26 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTTCAAAAACTATATATTAT
Found at i:673313 original size:14 final size:14
Alignment explanation
Indices: 673296--673329 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
673286 AACATACATG
673296 AACATAAATGAACA
1 AACATAAATGAACA
*
673310 AACATAAATGAGCA
1 AACATAAATGAACA
673324 AACATA
1 AACATA
673330 CACAGACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:675941 original size:38 final size:38
Alignment explanation
Indices: 675879--675968 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
675869 ATTATTTCGG
675879 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
*
675916 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
*
675954 GTTGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
675969 ATGGTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 11 0.22
38 30 0.61
39 8 0.16
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:675942 original size:192 final size:181
Alignment explanation
Indices: 675718--676071 Score: 519
Period size: 192 Copynumber: 1.9 Consensus size: 181
675708 ACTTTATTTT
* * *
675718 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTTTGGGTTTAGGGTG
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTTCGGGTTTAGGGTA
*
675783 AAAAAAACCGGACCGACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTT
66 AAAAAAACCGGACCGACCCAAAAATATATATAA-T----TCGGGTCGGATTAAGTCACTATTTTT
675848 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
126 ATTAAAT---AAT--TTTTTT-TTATTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
* * * *
675910 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTTCGGGTTTATGGTA
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTTCGGGTTTAGGGTA
* *
675975 AAAAAAATCGGACCGACCCGAAAATATATATAATTCGGGTCGGATTAAGTCACTATTTTTATTAA
66 AAAAAAACCGGACCGACCCAAAAATATATATAATTCGGGTCGGATTAAGTCACTATTTTTATTAA
676040 ATAATTTTTTTTTATTTCGGGTCGGGTCGGGT
131 ATAATTTTTTTTTATTTCGGGTCGGGTCGGGT
676072 CGGATTTCTA
Statistics
Matches: 152, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
181 21 0.14
182 6 0.04
184 3 0.02
187 32 0.21
191 1 0.01
192 89 0.59
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (181 bp):
GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTTCGGGTTTAGGGTA
AAAAAAACCGGACCGACCCAAAAATATATATAATTCGGGTCGGATTAAGTCACTATTTTTATTAA
ATAATTTTTTTTTATTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
Found at i:676148 original size:38 final size:38
Alignment explanation
Indices: 676096--676169 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
676086 ATATATTCGG
676096 GTCGGGTCGCGTTTTTTTAAGTGTGATATTCAGGTCGA
1 GTCGGGTCGCGTTTTTTTAAGTGTGATATTCAGGTCGA
*
676134 GTCGGGTCAG-GTTTTTTTAAGTGTGATATTCGGGTC
1 GTCGGGTC-GCGTTTTTTTAAGTGTGATATTCAGGTC
676170 AGGTCATGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.15, C:0.12, G:0.32, T:0.41
Consensus pattern (38 bp):
GTCGGGTCGCGTTTTTTTAAGTGTGATATTCAGGTCGA
Found at i:676172 original size:43 final size:37
Alignment explanation
Indices: 676096--676189 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 37
676086 ATATATTCGG
676096 GTCGGGTCGCGTTTTTTTAAGTGTGATATTCAGGTCGA-
1 GTCGGGTCG-GTTTTTTTAAGTGTGATATTCAGGTC-AT
676134 GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCAT
1 GTCGGGTC-GGTTTTTTTAAGTGTGATA-T----TCAGGTCAT
676177 GTCGGGTCGGTTT
1 GTCGGGTCGGTTT
676190 CGGGTTTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
38 26 0.53
39 2 0.04
42 6 0.12
43 15 0.31
ACGTcount: A:0.14, C:0.13, G:0.34, T:0.39
Consensus pattern (37 bp):
GTCGGGTCGGTTTTTTTAAGTGTGATATTCAGGTCAT
Found at i:676786 original size:16 final size:18
Alignment explanation
Indices: 676765--676804 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
676755 GATTGGATTT
676765 CAATTCC-T-ACAAATTC
1 CAATTCCTTCACAAATTC
*
676781 CAATTCCTTCACAGATTC
1 CAATTCCTTCACAAATTC
676799 CAATTC
1 CAATTC
676805 TCTCATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 1 0.05
18 13 0.62
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.33
Consensus pattern (18 bp):
CAATTCCTTCACAAATTC
Found at i:676800 original size:18 final size:16
Alignment explanation
Indices: 676760--676804 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
676750 ATATGGATTG
*
676760 GATTTCAATTCCTACA
1 GATTCCAATTCCTACA
*
676776 AATTCCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
676794 GATTCCAATTC
1 GATTCCAATTC
676805 TCTCATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:676957 original size:3 final size:3
Alignment explanation
Indices: 676949--677103 Score: 87
Period size: 3 Copynumber: 49.7 Consensus size: 3
676939 TATGTAAATC
* * * *
676949 TAA TAA TAA TAAA CAA TAA TAA TAC TAA TAA TAC TAA TAA CAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * *
676995 TGT TAA TAA TAA TAA TAA TAA GAC TTA TGA TAAA TAA TAA TAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A
** * * * *
677042 TGC TAT TAA TAA TAGA TAA T-A TTA TAC TAA TAA CATA TAA TAAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA
*
677089 TAA TTAG TAA TAA TA
1 TAA -TAA TAA TAA TA
677104 TAGAATATAC
Statistics
Matches: 113, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
2 2 0.02
3 95 0.84
4 16 0.14
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:682903 original size:14 final size:14
Alignment explanation
Indices: 682884--682914 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
682874 TCTTGCTTGA
682884 GACGCCTCAACTTT
1 GACGCCTCAACTTT
682898 GACGCCTCAACTTT
1 GACGCCTCAACTTT
682912 GAC
1 GAC
682915 CGCACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (14 bp):
GACGCCTCAACTTT
Found at i:684826 original size:12 final size:12
Alignment explanation
Indices: 684804--684832 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
684794 TGACATTTTT
684804 TATAT-TTATTA
1 TATATATTATTA
684815 TATATATTATTA
1 TATATATTATTA
684827 TATATA
1 TATATA
684833 ATAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATTATTA
Found at i:684840 original size:15 final size:14
Alignment explanation
Indices: 684810--684863 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
684800 TTTTTATATT
684810 TATTATATAT-AT-
1 TATTATATATAATA
684822 TATTATATATAATAA
1 TATTATATATAAT-A
684837 TATTAT-TAATAATA
1 TATTATAT-ATAATA
*
684851 TTATTATTTATAA
1 -TATTATATATAA
684864 AGCCTGAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.28
13 2 0.06
14 2 0.06
15 21 0.58
16 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATATATAATA
Found at i:684846 original size:12 final size:12
Alignment explanation
Indices: 684831--684856 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
684821 TTATTATATA
684831 TAATAATATTAT
1 TAATAATATTAT
684843 TAATAATATTAT
1 TAATAATATTAT
684855 TA
1 TA
684857 TTTATAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:691604 original size:39 final size:40
Alignment explanation
Indices: 691547--691635 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
691537 ACAATCACAT
*
691547 CAATGTTGGAACATTTTTAAAGGCTCATATC-ATAAGAAA
1 CAATGTTGGAACATTTTTAAAGGCTCACATCAATAAGAAA
* *
691586 CAATGTTGAGCACA-TTTTAAAGGCTCACATCAATAAGAAG
1 CAATGTTG-GAACATTTTTAAAGGCTCACATCAATAAGAAA
691626 CAAATGTTGG
1 C-AATGTTGG
691636 GGCATGCTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 24 0.55
40 13 0.30
41 7 0.16
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (40 bp):
CAATGTTGGAACATTTTTAAAGGCTCACATCAATAAGAAA
Found at i:692967 original size:20 final size:20
Alignment explanation
Indices: 692872--692961 Score: 153
Period size: 20 Copynumber: 4.5 Consensus size: 20
692862 TATTTCCCAC
692872 CATTTGTAAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
*
692892 CATTTGTTAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
*
692912 CATTTGTTAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
*
692932 CATTTGTAAAGCCTTCGGGT
1 CATTTGTAAAGCCTCCGGGT
692952 CATTTGTAAA
1 CATTTGTAAA
692962 ATCTTCAAGT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (20 bp):
CATTTGTAAAGCCTCCGGGT
Found at i:692977 original size:60 final size:60
Alignment explanation
Indices: 692872--692985 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
692862 TATTTCCCAC
* * ** *
692872 CATTTGTAAAGCCTCCGGGTCATTTGTTAAGCCTCCGGGTCATTTGTTAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCTCCGGGT
* * * *
692932 CATTTGTAAAGCCTTCGGGTCATTTGTAAAATCTTCAAGTTATTTGTAAAGCCT
1 CATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCT
692986 TTGGGTAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (60 bp):
CATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCTCCGGGT
Found at i:692997 original size:60 final size:60
Alignment explanation
Indices: 692873--692998 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
692863 ATTTCCCACC
* * ** * *
692873 ATTTGTAAAGCCTCCGGGTCATTTGTTAAGCCTCCGGGTCATTTGTTAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCTCCGGGTA
* * * * **
692933 ATTTGTAAAGCCTTCGGGTCATTTGTAAAATCTTCAAGTTATTTGTAAAGCCTTTGGGTA
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCTCCGGGTA
692993 ATTTGT
1 ATTTGT
692999 GAATCCTTTC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (60 bp):
ATTTGTAAAGCCTCCGGGTCATTTGTAAAACCTCCAAGTCATTTGTAAAGCCTCCGGGTA
Found at i:693269 original size:88 final size:90
Alignment explanation
Indices: 693156--693359 Score: 229
Period size: 90 Copynumber: 2.3 Consensus size: 90
693146 AATCATTCCC
**
693156 AGTCTTCACGAAAGAGTAGTGAAGC-AGAAGC-AAATC-ATCCTCATTCTCCACAGAAGAGTAGT
1 AGTCTTCACGAAAGAGTAGTGAAGCAAG-AGCGAAATCAAAACTCATTCTCCACAGAAGAGTAGT
*
693218 GGAA-TGGATTTTTAAGCAAAGTATGA
65 GGAACT-AATTTTTAAGCAAAGTATGA
* * * * * ** *
693244 AGTCTTCAAGCAAGAGTAGTGAAGCAAGAGCGAGATCAAAATTCGTTCTCCATGGAAGAGTATTG
1 AGTCTTCACGAAAGAGTAGTGAAGCAAGAGCGAAATCAAAACTCATTCTCCACAGAAGAGTAGTG
*
693309 GAACTAATTTTTCAGCAAAGTATGA
66 GAACTAATTTTTAAGCAAAGTATGA
* *
693334 A-ACTTCACGGAAGAGTAGTGAAGCAA
1 AGTCTTCACGAAAGAGTAGTGAAGCAA
693360 TTCAATTTCG
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
88 26 0.27
89 28 0.29
90 42 0.43
91 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (90 bp):
AGTCTTCACGAAAGAGTAGTGAAGCAAGAGCGAAATCAAAACTCATTCTCCACAGAAGAGTAGTG
GAACTAATTTTTAAGCAAAGTATGA
Found at i:693485 original size:47 final size:47
Alignment explanation
Indices: 693423--693542 Score: 170
Period size: 47 Copynumber: 2.6 Consensus size: 47
693413 TTCATGCAAA
* * * *
693423 TTCAGCCTTCACAGAAGAGTAGTGAAGCAAGTCATTTGCGAGTCATT
1 TTCAGCCTTCACAGAAGAGTAGTGAAGCAAATCATTTGCAAATCATC
693470 TTCAGCCTTCACAGAAGAGTAGTGAAGCAAATCATTTGCAAATCATC
1 TTCAGCCTTCACAGAAGAGTAGTGAAGCAAATCATTTGCAAATCATC
* *
693517 CTCATCCTTCAC-GAAAGAGTAGTGAA
1 TTCAGCCTTCACAG-AAGAGTAGTGAA
693543 ACAGGAGCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 1 0.02
47 65 0.98
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (47 bp):
TTCAGCCTTCACAGAAGAGTAGTGAAGCAAATCATTTGCAAATCATC
Found at i:701975 original size:88 final size:87
Alignment explanation
Indices: 701843--702106 Score: 402
Period size: 88 Copynumber: 3.0 Consensus size: 87
701833 CATAAAGCTA
* * *
701843 TCCAAAAATGTTATGGATTTGAAACAATTGATATCAATTGTTAGAGATATATCATTTGCAATAAA
1 TCCAAAAATGTTATGCATTT-AAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCAATAAA
* *
701908 TCACATGTATAAACGTTTAAATT
65 TCACATGCATAAACATTTAAATT
*
701931 TCCAAAAATGTTATGCATTTAAAAAATTGATATTCAATTGTTAGAGAGATATCAATTGCAATAAA
1 TCCAAAAATGTTATGCATTTAAAAAATTGATA-TCAATTGTTAGAGAGATATCATTTGCAATAAA
* *
701996 TTAAATGCATAAACATTTAAATT
65 TCACATGCATAAACATTTAAATT
* * *
702019 TCCAAAAATGTTATGCATTAAAAAAATTGATACCATTTGTTAGAGAGATATCATTTGCAATAAAA
1 TCCAAAAATGTTATGCATTTAAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCAAT-AAA
702084 TCACATGCATAAACATTTAAATT
65 TCACATGCATAAACATTTAAATT
702107 AAGGTAAAAA
Statistics
Matches: 160, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
87 37 0.23
88 123 0.77
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (87 bp):
TCCAAAAATGTTATGCATTTAAAAAATTGATATCAATTGTTAGAGAGATATCATTTGCAATAAAT
CACATGCATAAACATTTAAATT
Found at i:719256 original size:22 final size:23
Alignment explanation
Indices: 719229--719283 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
719219 TATTTTTAAT
719229 TTATTA-ATTATAAAAT-ATATTA
1 TTATTAGATTA-AAAATCATATTA
*
719251 TTATTAGTATTAAAAATCATATTT
1 TTATTAG-ATTAAAAATCATATTA
719275 TTAATTAGA
1 TT-ATTAGA
719284 GAAAATAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 5 0.18
24 12 0.43
25 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATTAGATTAAAAATCATATTA
Found at i:719272 original size:24 final size:25
Alignment explanation
Indices: 719235--719282 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
719225 TAATTTATTA
719235 ATTATAAAATATATTATT-ATTAGT
1 ATTATAAAATATATTATTAATTAGT
*
719259 ATTA-AAAATCATATTTTTAATTAG
1 ATTATAAAAT-ATATTATTAATTAG
719283 AGAAAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTATAAAATATATTATTAATTAGT
Found at i:719391 original size:20 final size:21
Alignment explanation
Indices: 719366--719417 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
719356 GACCAACAAA
*
719366 TTCGCAACGCGA-TCTCTAAT
1 TTCGCAACGCGAGTCTCCAAT
* *
719386 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
719406 TTCGCAACGCGA
1 TTCGCAACGCGA
719418 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (21 bp):
TTCGCAACGCGAGTCTCCAAT
Found at i:719451 original size:21 final size:21
Alignment explanation
Indices: 719427--719473 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
719417 AATATGTAAA
*
719427 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
719448 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
719469 TCGCA
1 TCGCA
719474 ACGCGATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:719489 original size:20 final size:20
Alignment explanation
Indices: 719464--719568 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
719454 TGCGATTTTC
719464 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
719484 CAAATTCGTAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
719504 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
*
719524 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
* *
719544 CAAATTTGCAACGCAATAGT
1 CAAATTCGCAACGCGATAGT
719564 CAAAT
1 CAAAT
719569 GTTTTTACGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:719724 original size:22 final size:22
Alignment explanation
Indices: 719699--719746 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
719689 CGGCGACATT
719699 CGTCCCCATCTCCGACGAAATC
1 CGTCCCCATCTCCGACGAAATC
* *
719721 CGTCCCCATTTCTGACGAAATC
1 CGTCCCCATCTCCGACGAAATC
719743 CGTC
1 CGTC
719747 TATCTCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.42, G:0.15, T:0.23
Consensus pattern (22 bp):
CGTCCCCATCTCCGACGAAATC
Found at i:720070 original size:20 final size:20
Alignment explanation
Indices: 720035--720117 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
720025 AAATCGCAAC
*
720035 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
720054 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
***
720074 GCGATTTTCATTTTTTTGTT
1 GCGATTTTCATTTTCGCGTT
*
720094 ACGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
720114 GCGA
1 GCGA
720118 ATTTAAGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 8 0.15
20 46 0.85
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:721260 original size:7 final size:7
Alignment explanation
Indices: 721248--721309 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
721238 GCTATTTTTT
721248 AAAAACA
1 AAAAACA
721255 AAAAACAA
1 AAAAAC-A
721263 AAAAAGGCA
1 AAAAA--CA
*
721272 AAAAAAA
1 AAAAACA
721279 AAAAAC-
1 AAAAACA
721285 AAAAA-A
1 AAAAACA
*
721291 AAACACA
1 AAAAACA
721298 AAAAACA
1 AAAAACA
721305 AAAAA
1 AAAAA
721310 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
6 9 0.20
7 24 0.52
8 6 0.13
9 6 0.13
10 1 0.02
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:721281 original size:24 final size:25
Alignment explanation
Indices: 721248--721309 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
721238 GCTATTTTTT
* **
721248 AAAAACAAAAAACAAAAAAAGGCA-
1 AAAAAAAAAAAACAAAAAAAAACAC
721272 AAAAAAAAAAAACAAAAAAAAACAC
1 AAAAAAAAAAAACAAAAAAAAACAC
721297 AAAAAACAAAAAA
1 AAAAAA-AAAAAA
721310 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 21 0.64
25 6 0.18
26 6 0.18
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAACAAAAAAAAACAC
Found at i:721316 original size:24 final size:22
Alignment explanation
Indices: 721248--721316 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 22
721238 GCTATTTTTT
721248 AAAAACAAAAAACAAAAAAAGGCA
1 AAAAACAAAAAAC-AAAAAA-GCA
*
721272 AAAAAAAAAAAAC-AAAAA--A
1 AAAAACAAAAAACAAAAAAGCA
* *
721291 AAACACAAAAAACAAAAAAGCC
1 AAAAACAAAAAACAAAAAAGCA
721313 AAAA
1 AAAA
721317 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 12 0.32
20 5 0.14
22 8 0.22
24 12 0.32
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAACAAAAAACAAAAAAGCA
Found at i:725113 original size:35 final size:36
Alignment explanation
Indices: 725047--725117 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
725037 ATTAGTTATT
725047 TAGGACCTTTAGAACTCAGCCCCTATATAAAGGAGG
1 TAGGACCTTTAGAACTCAGCCCCTATATAAAGGAGG
725083 TAGGACCTTTAGAACTCAG-CCCTATATAAAGGAGG
1 TAGGACCTTTAGAACTCAGCCCCTATATAAAGGAGG
725118 CTTCATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (36 bp):
TAGGACCTTTAGAACTCAGCCCCTATATAAAGGAGG
Found at i:726881 original size:164 final size:164
Alignment explanation
Indices: 726610--726938 Score: 649
Period size: 164 Copynumber: 2.0 Consensus size: 164
726600 TCAAAAAGTC
*
726610 ATCTCAAGTCTTTTATTGTTCTGGTCTTCTTTTCCAATGCTTGGAAGAGTGGATCATTTGGAAGA
1 ATCTCAAGTCTTTTATTGTTATGGTCTTCTTTTCCAATGCTTGGAAGAGTGGATCATTTGGAAGA
726675 GTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAG
66 GTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAG
726740 ATTCGACCTCGAATCTAAAACATTAAAGGGAGCA
131 ATTCGACCTCGAATCTAAAACATTAAAGGGAGCA
726774 ATCTCAAGTCTTTTATTGTTATGGTCTTCTTTTCCAATGCTTGGAAGAGTGGATCATTTGGAAGA
1 ATCTCAAGTCTTTTATTGTTATGGTCTTCTTTTCCAATGCTTGGAAGAGTGGATCATTTGGAAGA
726839 GTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAG
66 GTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAG
726904 ATTCGACCTCGAATCTAAAACATTAAAGGGAGCA
131 ATTCGACCTCGAATCTAAAACATTAAAGGGAGCA
726938 A
1 A
726939 CATTAGAATT
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (164 bp):
ATCTCAAGTCTTTTATTGTTATGGTCTTCTTTTCCAATGCTTGGAAGAGTGGATCATTTGGAAGA
GTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAG
ATTCGACCTCGAATCTAAAACATTAAAGGGAGCA
Found at i:734390 original size:18 final size:19
Alignment explanation
Indices: 734369--734404 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
734359 AAATTTTGGC
734369 TTTTTTAG-CTTTTTTTTT
1 TTTTTTAGCCTTTTTTTTT
*
734387 TTTTTTTGCCTTTTTTTT
1 TTTTTTAGCCTTTTTTTT
734405 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTTTTAGCCTTTTTTTTT
Found at i:734422 original size:18 final size:18
Alignment explanation
Indices: 734369--734404 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
734359 AAATTTTGGC
*
734369 TTTTTTAGCTTTTTTTTT
1 TTTTTTAGCCTTTTTTTT
*
734387 TTTTTTTGCCTTTTTTTT
1 TTTTTTAGCCTTTTTTTT
734405 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTTTAGCCTTTTTTTT
Found at i:734425 original size:11 final size:11
Alignment explanation
Indices: 734386--734415 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
734376 GCTTTTTTTT
734386 TTTTTTTTGCC
1 TTTTTTTTGCC
734397 TTTTTTTTGCC
1 TTTTTTTTGCC
734408 TTTTTTTT
1 TTTTTTTT
734416 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGCC
Found at i:735618 original size:18 final size:18
Alignment explanation
Indices: 735560--735611 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 18
735550 GCTATTTTTT
735560 AAAAACAAAAAACAAAAAA
1 AAAAACAAAAAAC-AAAAA
735579 AGGCAAAACAAAAAACAAAAA
1 A---AAAACAAAAAACAAAAA
735600 AAAAACAAAAAA
1 AAAAACAAAAAA
735612 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
21 6 0.20
22 12 0.40
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAACAAAAA
Found at i:740277 original size:8 final size:8
Alignment explanation
Indices: 740266--740320 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 8
740256 ATTTTTTTTT
740266 CAAAAAAA
1 CAAAAAAA
740274 CAAAAAAA
1 CAAAAAAA
740282 GGCAAAAAAA
1 --CAAAAAAA
740292 C-AAAAAA
1 CAAAAAAA
740299 -AAAAAAA
1 CAAAAAAA
*
740306 -AAAAAAC
1 CAAAAAAA
740313 CAAAAAAA
1 CAAAAAAA
740321 GCCAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 18 0.44
8 15 0.37
10 8 0.20
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:740280 original size:10 final size:10
Alignment explanation
Indices: 740267--740320 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
740257 TTTTTTTTTC
740267 AAAAAAACAA
1 AAAAAAACAA
**
740277 AAAAAGGCAA
1 AAAAAAACAA
740287 AAAAACAA-AA
1 AAAAA-AACAA
740297 AAAAAAA-AA
1 AAAAAAACAA
*
740306 AAAAAACCAA
1 AAAAAAACAA
740316 AAAAA
1 AAAAA
740321 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 10 0.27
10 27 0.73
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:740306 original size:18 final size:18
Alignment explanation
Indices: 740267--740309 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
740257 TTTTTTTTTC
***
740267 AAAAAAACAAAAAAAGGC
1 AAAAAAACAAAAAAAAAA
740285 AAAAAAACAAAAAAAAAA
1 AAAAAAACAAAAAAAAAA
740303 AAAAAAA
1 AAAAAAA
740310 AACCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAA
Found at i:740327 original size:9 final size:10
Alignment explanation
Indices: 740267--740327 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
740257 TTTTTTTTTC
740267 AAAAAAA-CA
1 AAAAAAACCA
**
740276 AAAAAAGGC-
1 AAAAAAACCA
*
740285 AAAAAAACAA
1 AAAAAAACCA
**
740295 AAAAAAAAAA
1 AAAAAAACCA
740305 AAAAAAACCA
1 AAAAAAACCA
*
740315 AAAAAAGCCA
1 AAAAAAACCA
740325 AAA
1 AAA
740328 TTTCAAAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
9 12 0.29
10 30 0.71
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:744880 original size:25 final size:25
Alignment explanation
Indices: 744833--744880 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
744823 GCTATTTTTT
**
744833 AAAAACAAAAAAAAAAGGCAAAACA
1 AAAAACAAAAAAAAAAGAAAAAACA
744858 AAAAACAAAAAAAAACA-AAAAAA
1 AAAAACAAAAAAAAA-AGAAAAAA
744881 GCCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.00
Consensus pattern (25 bp):
AAAAACAAAAAAAAAAGAAAAAACA
Found at i:744887 original size:10 final size:10
Alignment explanation
Indices: 744833--744880 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 10
744823 GCTATTTTTT
744833 AAAAACAAAAA
1 AAAAAC-AAAA
744844 AAAAAGGCAAAACA
1 AAAAA--C-AAA-A
744858 AAAAACAAAA
1 AAAAACAAAA
744868 AAAAACAAAA
1 AAAAACAAAA
744878 AAA
1 AAA
744881 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 14 0.41
11 8 0.24
12 1 0.03
13 5 0.15
14 6 0.18
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:748490 original size:21 final size:21
Alignment explanation
Indices: 748464--748513 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
748454 GTTAGGAGAA
*
748464 TTACGTGACGAGGTCGGTGCT
1 TTACGTGACGAGGTCGGTACT
* *
748485 TTACGTCATGAGGTCGGTACT
1 TTACGTGACGAGGTCGGTACT
748506 TTACGTGA
1 TTACGTGA
748514 AGATAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGACGAGGTCGGTACT
Found at i:748776 original size:16 final size:16
Alignment explanation
Indices: 748737--748776 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
748727 TTTCAGCATT
*
748737 ATTTATTTATTTATTA
1 ATTTATTTATATATTA
* *
748753 ACTGATTTATATATTA
1 ATTTATTTATATATTA
748769 ATTTATTT
1 ATTTATTT
748777 TCAGCGGCCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTATTTATATATTA
Found at i:748967 original size:21 final size:21
Alignment explanation
Indices: 748916--748981 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
748906 GCCCAATGCA
*
748916 CCTATCATCATTCAAGAGGCG
1 CCTATCATCATTCAAGAGGCC
*
748937 CCT-CCTATCATTCAAGAGGCC
1 CCTATC-ATCATTCAAGAGGCC
*
748958 CCTATCATCA-TCGAAGAAGCC
1 CCTATCATCATTC-AAGAGGCC
748979 CCT
1 CCT
748982 CCCACCGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 3 0.08
21 34 0.89
22 1 0.03
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (21 bp):
CCTATCATCATTCAAGAGGCC
Done.