Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008751.1 Hibiscus syriacus cultivar Beakdansim tig00111842_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: 806611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:349674 original size:40 final size:40
Alignment explanation
Indices: 349546--349700 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
349536 GCTTTAAATA
*
349546 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
349587 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
349627 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
349667 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
349701 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:349717 original size:21 final size:21
Alignment explanation
Indices: 349687--349769 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
349677 ATTTTCATAT
*
349687 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
349708 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
349729 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
349750 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
349770 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:349760 original size:42 final size:43
Alignment explanation
Indices: 349667--349765 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
349657 ATTTATGTGT
* *
349667 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
349708 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
349750 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
349766 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:356270 original size:44 final size:44
Alignment explanation
Indices: 356217--356301 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
356207 AAAGCAAAAG
* *
356217 AAAACATGTTATAAAGACATAGTCATTAGAAATTAAAAGAAGAA
1 AAAACATGTTATAAAAACAGAGTCATTAGAAATTAAAAGAAGAA
*
356261 AAAACATGTTATAAAAACAGAGTTATTAGAAATTAAAAGAA
1 AAAACATGTTATAAAAACAGAGTCATTAGAAATTAAAAGAA
356302 TAGAAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.24
Consensus pattern (44 bp):
AAAACATGTTATAAAAACAGAGTCATTAGAAATTAAAAGAAGAA
Found at i:358146 original size:2 final size:2
Alignment explanation
Indices: 358139--358167 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
358129 CTAATCACAT
358139 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 T
358168 CATGGGCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:359539 original size:38 final size:39
Alignment explanation
Indices: 359412--359540 Score: 136
Period size: 39 Copynumber: 3.4 Consensus size: 39
359402 AAATTCAATA
* * * *
359412 ATTTATTTCATTTTAAAAAACATGAAAATAAATATAATA
1 ATTTATTTCCTTTTACAAAATATGAAAATAAATATAATG
* * * *
359451 ATTTATTTCCTTTT-CAAAATAAG-AAATAGATCTAGTG
1 ATTTATTTCCTTTTACAAAATATGAAAATAAATATAATG
* * *
359488 ATTTATTTCCTTTTACAAAATATGAAAACAAATGTAACG
1 ATTTATTTCCTTTTACAAAATATGAAAATAAATATAATG
*
359527 ATTTATTTCTTTTT
1 ATTTATTTCCTTTT
359541 TAAATAGAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
37 24 0.33
38 14 0.19
39 35 0.48
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (39 bp):
ATTTATTTCCTTTTACAAAATATGAAAATAAATATAATG
Found at i:359554 original size:76 final size:76
Alignment explanation
Indices: 359412--359554 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 76
359402 AAATTCAATA
* * *
359412 ATTTATTTCATTTTAAAAAACATGAAAATAAATATAATAATTTATTTCCTTTTCAAAATAAGAAA
1 ATTTATTTCATTTTAAAAAACATGAAAACAAATATAACAATTTATTTCCTTTTCAAAATAAAAAA
359477 TAGATCTAGTG
66 TAGATCTAGTG
* * * * * **
359488 ATTTATTTCCTTTTACAAAATATGAAAACAAATGTAACGATTTATTT-CTTTTTTAAATAGAAAA
1 ATTTATTTCATTTTAAAAAACATGAAAACAAATATAACAATTTATTTCCTTTTCAAAATA-AAAA
359552 ATA
65 ATA
359555 AATTTAACGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 10 0.18
76 46 0.82
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (76 bp):
ATTTATTTCATTTTAAAAAACATGAAAACAAATATAACAATTTATTTCCTTTTCAAAATAAAAAA
TAGATCTAGTG
Found at i:359848 original size:58 final size:58
Alignment explanation
Indices: 359777--359905 Score: 204
Period size: 58 Copynumber: 2.2 Consensus size: 58
359767 ATAAATAGAA
* * * * *
359777 AAAGTTATAATCATTTGAGATTTTCAAGGAAATAAATTCAATGATTTATTTTCCTTAC
1 AAAGTTAAAATCATTTAAGATTCTCAAGGAAATAAATTCAACGATTTATTATCCTTAC
*
359835 AAAGTTAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACGATTTATTATCCTTAC
1 AAAGTTAAAATCATTTAAGATTCTCAAGGAAATAAATTCAACGATTTATTATCCTTAC
359893 AAAGTTAAAATCA
1 AAAGTTAAAATCA
359906 ACGCAAGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (58 bp):
AAAGTTAAAATCATTTAAGATTCTCAAGGAAATAAATTCAACGATTTATTATCCTTAC
Found at i:360192 original size:46 final size:45
Alignment explanation
Indices: 360066--360221 Score: 113
Period size: 45 Copynumber: 3.4 Consensus size: 45
360056 AATCCTTTAA
* * *
360066 AATTTCAGCAACCCAATAATC-AGAAGGAATTTATCCTTTGATTTT
1 AATTTCTGCAACCCAATAATCGAGAA-GAAATAATCCTTTGATTTT
* * * * * * *
360111 AATTTTTGCAATCCAATAAACGATATGAAAAAATCCTTTGGTTTTT
1 AATTTCTGCAACCCAATAATCGAGAAGAAATAATCCTTT-GATTTT
* *
360157 AATTTCCT-CAACCCAATAATCGA-AAGCAAATAATCCATTAATTTT
1 AATTT-CTGCAACCCAATAATCGAGAAG-AAATAATCCTTTGATTTT
* *
360202 ACTTT-TGACAACACAATAAT
1 AATTTCTG-CAACCCAATAAT
360222 AAAAGATAAC
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
43 1 0.01
45 48 0.56
46 35 0.41
47 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (45 bp):
AATTTCTGCAACCCAATAATCGAGAAGAAATAATCCTTTGATTTT
Found at i:362843 original size:83 final size:83
Alignment explanation
Indices: 362704--362867 Score: 283
Period size: 83 Copynumber: 2.0 Consensus size: 83
362694 TCTGGGTACG
*
362704 TAGTACCAATACTATTTTTACAATATCGATATTGCATGAACAATACTGACAATGTTCACGTGGTA
1 TAGTACCAATACTATTCTTACAATATCGATATTGCATGAACAATACTGACAATGTTCACGTGGTA
362769 CTGATACCAAAGGTAATA
66 CTGATACCAAAGGTAATA
* * * *
362787 TAGTACCAATACTATTCTTACAATATTGATATTGCATGAACAGTATTGATAATGTTCACGTGGTA
1 TAGTACCAATACTATTCTTACAATATCGATATTGCATGAACAATACTGACAATGTTCACGTGGTA
362852 CTGATACCAAAGGTAA
66 CTGATACCAAAGGTAA
362868 GAGAAGTATC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (83 bp):
TAGTACCAATACTATTCTTACAATATCGATATTGCATGAACAATACTGACAATGTTCACGTGGTA
CTGATACCAAAGGTAATA
Found at i:370491 original size:22 final size:22
Alignment explanation
Indices: 370461--370537 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
370451 GACATTTTTG
370461 GTATTGATACTTAATTAAAGGA
1 GTATTGATACTTAATTAAAGGA
* * *
370483 GTATCGATAC-TACTTTATATAGTA
1 GTATTGATACTTA-ATTA-A-AGGA
370507 GTATTGATACTTAATTAAAGGA
1 GTATTGATACTTAATTAAAGGA
370529 GTATTGATA
1 GTATTGATA
370538 ATACTTTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.04
22 24 0.53
23 2 0.04
24 15 0.33
25 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (22 bp):
GTATTGATACTTAATTAAAGGA
Found at i:370514 original size:46 final size:46
Alignment explanation
Indices: 370461--370563 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
370451 GACATTTTTG
*
370461 GTATTGATACTTAATTAAAGGAGTATCGATACTACTTTATATAGTA
1 GTATTGATACTTAATTAAAGGAGTATCGATAATACTTTATATAGTA
*
370507 GTATTGATACTTAATTAAAGGAGTATTGATAATACTTTATATAGTA
1 GTATTGATACTTAATTAAAGGAGTATCGATAATACTTTATATAGTA
*
370553 CTATTGATACT
1 GTATTGATACT
370564 ATGACCTCAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (46 bp):
GTATTGATACTTAATTAAAGGAGTATCGATAATACTTTATATAGTA
Found at i:370515 original size:24 final size:24
Alignment explanation
Indices: 370482--370564 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
370472 TAATTAAAGG
*
370482 AGTATCGATACTACTTTATATAGT
1 AGTATTGATACTACTTTATATAGT
* *
370506 AGTATTGATACTTA-ATTA-A-AGG
1 AGTATTGATAC-TACTTTATATAGT
*
370528 AGTATTGATAATACTTTATATAGT
1 AGTATTGATACTACTTTATATAGT
*
370552 ACTATTGATACTA
1 AGTATTGATACTA
370565 TGACCTCAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 2 0.04
24 26 0.55
25 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (24 bp):
AGTATTGATACTACTTTATATAGT
Found at i:370517 original size:21 final size:21
Alignment explanation
Indices: 370493--370563 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
370483 GTATCGATAC
370493 TACTTTATATAGTAGTATTGA
1 TACTTTATATAGTAGTATTGA
* * *
370514 TACTTAATTAAAGGAGTATTGATAA
1 TACTTTA-TATAGTAGTATTG---A
*
370539 TACTTTATATAGTACTATTGA
1 TACTTTATATAGTAGTATTGA
370560 TACT
1 TACT
370564 ATGACCTCAG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 11 0.28
22 11 0.28
24 10 0.26
25 7 0.18
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.44
Consensus pattern (21 bp):
TACTTTATATAGTAGTATTGA
Found at i:370541 original size:25 final size:25
Alignment explanation
Indices: 370467--370543 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
370457 TTTGGTATTG
*
370467 ATACTTAATTAAAGGAGTATCGATA
1 ATACTTAATTAAAGGAGTATTGATA
* * * *
370492 CTACTTTA-TATAGTAGTATTG---
1 ATACTTAATTAAAGGAGTATTGATA
370513 ATACTTAATTAAAGGAGTATTGATA
1 ATACTTAATTAAAGGAGTATTGATA
370538 ATACTT
1 ATACTT
370544 TATATAGTAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 6 0.15
22 11 0.28
24 10 0.26
25 12 0.31
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (25 bp):
ATACTTAATTAAAGGAGTATTGATA
Found at i:386402 original size:21 final size:21
Alignment explanation
Indices: 386378--386426 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
386368 ATTGTGAAAT
* *
386378 ATCATATCAATATAATAATTC
1 ATCACATCAACATAATAATTC
386399 ATCACATCAACATAATAATTC
1 ATCACATCAACATAATAATTC
386420 ATCACAT
1 ATCACAT
386427 ATAATTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
ATCACATCAACATAATAATTC
Found at i:389116 original size:292 final size:289
Alignment explanation
Indices: 388595--389173 Score: 1104
Period size: 292 Copynumber: 2.0 Consensus size: 289
388585 TGATCAATTG
388595 GAATTGAGGCAAAGCGAGACCTGAAGCTATTTATTTAATTGATTTTCTTCTCAAATTTCCTTTCG
1 GAATTGAGGCAAAGCGAGACCTGAAGCTATTTATTTAATTGATTTTCTTCTCAAATTTCCTTTCG
*
388660 TTAGTTTTCTATATTCAATTTTTCACAATTACTTTTATTTTTTTACATTTTTTTACTATTTCAAT
66 TTAGTTTTCTATATTCAATTTTTCAAAATTACTTTTATTTTTTTACATTTTTTTACTATTTCAAT
388725 TAAAATCCCCTCATTTATTTGCTTTTTCACTTAAATCAGAATCAAAACCATTCAACATCAAAAAC
131 TAAAATCCCCTCATTTATTTGCTTTTTCACTTAAATCAGAATCAAAACCATTCAACATCAAAAAC
388790 TCCTTAATTCTTACGAATCGACATTTTCTTCTTTATATTACGTTTTTAGCTTACTTATATGAGAA
196 TCCTTAATTCTTACGAATCGACATTTTCTTCTTTATATTACGTTTTTAGCTTACTTATATGAGAA
388855 AATGGCTTATTTATTTGACAATATACGTT
261 AATGGCTTATTTATTTGACAATATACGTT
*
388884 GAATTGAGGCAAAGCGAGACTTGAAGCTATTTATTTAATTGATTTTCTTCTCAAAATTTCCTTTC
1 GAATTGAGGCAAAGCGAGACCTGAAGCTATTTATTTAATTGATTTTCTTCTC-AAATTTCCTTTC
388949 GTTAGTTTTCTATATTCAATTTTTCAAAATTACTTTTATTTTTTTTACATTTTTTTTACTATTTC
65 GTTAGTTTTCTATATTCAATTTTTCAAAATTACTTTTA-TTTTTTTACA-TTTTTTTACTATTTC
*
389014 AATTAAAATCCCCTCATTTTTTTGCTTTTTCACTTAAATCAGAATCAAAACCATTCAACATCAAA
128 AATTAAAATCCCCTCATTTATTTGCTTTTTCACTTAAATCAGAATCAAAACCATTCAACATCAAA
389079 AACTCCTTAATTCTTACGAATCGACATTTTCTTCTTTATATTACGTTTTTAGCTTACTTATATGA
193 AACTCCTTAATTCTTACGAATCGACATTTTCTTCTTTATATTACGTTTTTAGCTTACTTATATGA
389144 GAAAATGGCTTATTTATTTGACAATATACG
258 GAAAATGGCTTATTTATTTGACAATATACG
389174 GTGCTTGTCA
Statistics
Matches: 284, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
289 51 0.18
290 49 0.17
291 10 0.04
292 174 0.61
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (289 bp):
GAATTGAGGCAAAGCGAGACCTGAAGCTATTTATTTAATTGATTTTCTTCTCAAATTTCCTTTCG
TTAGTTTTCTATATTCAATTTTTCAAAATTACTTTTATTTTTTTACATTTTTTTACTATTTCAAT
TAAAATCCCCTCATTTATTTGCTTTTTCACTTAAATCAGAATCAAAACCATTCAACATCAAAAAC
TCCTTAATTCTTACGAATCGACATTTTCTTCTTTATATTACGTTTTTAGCTTACTTATATGAGAA
AATGGCTTATTTATTTGACAATATACGTT
Found at i:393854 original size:18 final size:18
Alignment explanation
Indices: 393831--393897 Score: 98
Period size: 18 Copynumber: 3.6 Consensus size: 18
393821 ATTTAAATAT
393831 TATATTTTTAATTTATAA
1 TATATTTTTAATTTATAA
393849 TATATTTTTAATTTATAATA
1 TATATTTTTAATTTAT-A-A
393869 TTATATTTTTAATTTATAA
1 -TATATTTTTAATTTATAA
*
393888 TATATATTTA
1 TATATTTTTA
393898 TAATAGAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
18 25 0.56
19 2 0.04
20 2 0.04
21 16 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTTTAATTTATAA
Found at i:393872 original size:39 final size:38
Alignment explanation
Indices: 393819--393897 Score: 140
Period size: 39 Copynumber: 2.1 Consensus size: 38
393809 AATGTAAATA
*
393819 TAATTTAAATATTATATTTTTAATTTATAATATATTTT
1 TAATTTAAATATTATATTTTTAATTTATAATATATATT
393857 TAATTTATAATATTATATTTTTAATTTATAATATATATT
1 TAATTTA-AATATTATATTTTTAATTTATAATATATATT
393896 TA
1 TA
393898 TAATAGAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 7 0.18
39 32 0.82
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (38 bp):
TAATTTAAATATTATATTTTTAATTTATAATATATATT
Found at i:393875 original size:21 final size:20
Alignment explanation
Indices: 393819--393901 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
393809 AATGTAAATA
393819 TAATTTA-AATATTATATTTT
1 TAATTTATAATA-TATATTTT
393839 TAATTTAT-A-ATATATTTT
1 TAATTTATAATATATATTTT
393857 TAATTTATAATATTATATTTT
1 TAATTTATAATA-TATATTTT
*
393878 TAATTTATAATATATATTTA
1 TAATTTATAATATATATTTT
393898 TAAT
1 TAAT
393902 AGAGATTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
18 16 0.28
19 2 0.03
20 20 0.34
21 20 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTTATAATATATATTTT
Found at i:394969 original size:7 final size:7
Alignment explanation
Indices: 394959--394987 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
394949 CATTGTAGCT
394959 AGCACCA
1 AGCACCA
394966 AGCACCA
1 AGCACCA
394973 AGCACCA
1 AGCACCA
394980 AGCACCA
1 AGCACCA
394987 A
1 A
394988 ACGTGATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.41, G:0.14, T:0.00
Consensus pattern (7 bp):
AGCACCA
Found at i:407050 original size:21 final size:21
Alignment explanation
Indices: 407026--407068 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
407016 TATTACCTTA
407026 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
407047 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
407068 A
1 A
407069 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:407086 original size:35 final size:35
Alignment explanation
Indices: 407037--407122 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
407027 ATTGAAGTAT
** * *
407037 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
407072 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
407107 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
407123 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:408703 original size:11 final size:12
Alignment explanation
Indices: 408685--408731 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 12
408675 TTTTAATTAT
408685 ATTA-TAATAAA
1 ATTATTAATAAA
408696 A-TATTAATAAA
1 ATTATTAATAAA
* *
408707 ATTTTTCATAAAA
1 ATTATTAAT-AAA
408720 ATTATTAATAAA
1 ATTATTAATAAA
408732 TAAAATAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 2 0.07
11 9 0.31
12 8 0.28
13 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATTAATAAA
Found at i:412621 original size:18 final size:18
Alignment explanation
Indices: 412589--412635 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
412579 GTTAATATTG
* *
412589 GTATTGATACTCATAGGA
1 GTATCGATACCCATAGGA
*
412607 GTTTCGATACCCATAGGA
1 GTATCGATACCCATAGGA
412625 GTATCGATACC
1 GTATCGATACC
412636 AAGGGTAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (18 bp):
GTATCGATACCCATAGGA
Found at i:415247 original size:14 final size:16
Alignment explanation
Indices: 415211--415244 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
415201 TTTAAGTTTT
*
415211 TTAATATTATTTTTAA
1 TTAATATTATTTTAAA
415227 TTAATATT-TTTTAAA
1 TTAATATTATTTTAAA
415242 TTA
1 TTA
415245 TATCCGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATATTATTTTAAA
Found at i:422357 original size:36 final size:36
Alignment explanation
Indices: 422254--422362 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
422244 CCTTAGGTCC
* *
422254 ATAAAGAATTACCAGCTTGATCGGTGTTGAAACTAT
1 ATAAGGAATTACCAGCTTGATCGGTGTTGAACCTAT
422290 ATAAGGAATTACCAGCTTGATCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCGGTGTTGAACCTAT
* ** *
422326 ATAAGGAATTACCAGTTTGATCGAAGCTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCGGTGTTGAACCTAT
422362 A
1 A
422363 AAAACTTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCGGTGTTGAACCTAT
Found at i:423133 original size:22 final size:22
Alignment explanation
Indices: 423107--423168 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
423097 ACTTTGACTT
423107 TTGGTCAAAGTCAACAGTCAAA
1 TTGGTCAAAGTCAACAGTCAAA
**
423129 TTGGTCAAAGTCAATGGTCAAA
1 TTGGTCAAAGTCAACAGTCAAA
423151 --GGTCAAAGTCAACGAGTC
1 TTGGTCAAAGTCAAC-AGTC
423169 TGGTTAACGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.34
21 3 0.09
22 20 0.57
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (22 bp):
TTGGTCAAAGTCAACAGTCAAA
Found at i:424881 original size:30 final size:29
Alignment explanation
Indices: 424783--424870 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 29
424773 ATATATTTAC
* *
424783 ATGATTAAATAATAATAATAATAATTAAATAT
1 ATGACTAAATAATCA-AATAA-AATTAAA-AT
* * *
424815 ATTA-AAAATAATCATATAAAATTAAAAT
1 ATGACTAAATAATCAAATAAAATTAAAAT
*
424843 ATGACTAAATAAT-AAATATAATTAAAAT
1 ATGACTAAATAATCAAATAAAATTAAAAT
424871 TATATACTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 18 0.38
29 14 0.30
30 4 0.09
31 8 0.17
32 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
ATGACTAAATAATCAAATAAAATTAAAAT
Found at i:426591 original size:113 final size:113
Alignment explanation
Indices: 426386--426823 Score: 621
Period size: 113 Copynumber: 4.0 Consensus size: 113
426376 GTAATCTAGC
* * * * * *
426386 AAAAA-GTTGAACAAATTCTTCTTATTATGAATTTCTTC-T-CATTCTTCAGATGAATTCTTCTT
1 AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCA-TCTTCAGATGAGTTCTTCTC
* * * * *
426448 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGGGTGATGAATTAAAG
65 ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTAAAG
426497 AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
*
426562 TTATGAACTTCCTCTGTAAAAGTTAATCCATCGAGTGATGAATTAAAG
66 TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTAAAG
* * *
426610 CAAAAGGTTAAACAAGTTCTTCTCGTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
426675 TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAA-
66 TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATT-AAAG
* *
426723 CAAAAGGTT--A-AA-----TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
426780 TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATT
66 TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATT
426824 CAAATCTTTG
Statistics
Matches: 306, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
105 88 0.29
110 2 0.01
111 6 0.02
112 29 0.09
113 176 0.58
114 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
TTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTAAAG
Found at i:426755 original size:105 final size:105
Alignment explanation
Indices: 426630--426827 Score: 387
Period size: 105 Copynumber: 1.9 Consensus size: 105
426620 AACAAGTTCT
*
426630 TCTCGTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
1 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
426695 AGTTAATCCATCGAGTGATGAATTCAAACAAAAGGTTAAA
66 AGTTAATCCATCGAGTGATGAATTCAAACAAAAGGTTAAA
426735 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
1 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
426800 AGTTAATCCATCGAGTGATGAATTCAAA
66 AGTTAATCCATCGAGTGATGAATTCAAA
426828 TCTTTGCTAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (105 bp):
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
AGTTAATCCATCGAGTGATGAATTCAAACAAAAGGTTAAA
Found at i:426804 original size:218 final size:220
Alignment explanation
Indices: 426383--426823 Score: 638
Period size: 218 Copynumber: 2.0 Consensus size: 220
426373 GATGTAATCT
* * * *
426383 AGCAAAAAGTTGAACAAATTCTTCTTATTATGAATTTCTTCTCATTCTTCAGATGAATTCTTCTT
1 AGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAATTCTTCTC
* * * *
426448 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGGGTGATGAATTAAAGAAAAAGGTTAAACAAG
66 ATTATGAACTTCCTCTGGAAAAGCTAATCCATCGAGTGATGAATTAAAGAAAAAGGTT-AACAA-
426513 TTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTG
129 ---TTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTG
*
426578 TAAAAGTTAATCCATCGAGTGATGAATTAA
191 GAAAAGTTAATCCATCGAGTGATGAATTAA
* * * * *
426608 AGCAAAAGGTTAAACAAGTTCTTCTCGTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATGAATTCTTCT
* *
426673 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAA-CAAAAGGTT-A-AA
65 CATTATGAACTTCCTCTGGAAAAGCTAATCCATCGAGTGATGAATT-AAAGAAAAAGGTTAACAA
*
426735 -TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAA
129 TTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAA
426799 AAGTTAATCCATCGAGTGATGAATT
194 AAGTTAATCCATCGAGTGATGAATT
426824 CAAATCTTTG
Statistics
Matches: 197, Mismatches: 17, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
218 87 0.44
223 2 0.01
224 1 0.01
225 35 0.18
226 69 0.35
227 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (220 bp):
AGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAATTCTTCTC
ATTATGAACTTCCTCTGGAAAAGCTAATCCATCGAGTGATGAATTAAAGAAAAAGGTTAACAATT
CTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAA
GTTAATCCATCGAGTGATGAATTAA
Found at i:428383 original size:10 final size:10
Alignment explanation
Indices: 428364--428403 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
428354 TTTTCTATAT
*
428364 ATTTTGTTTC
1 ATTTTTTTTC
428374 ATTTTTTTTC
1 ATTTTTTTTC
428384 -TTTTCTTTTC
1 ATTTT-TTTTC
428394 ATTTTTTTTC
1 ATTTTTTTTC
428404 TTCATCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 4 0.15
10 19 0.70
11 4 0.15
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:428411 original size:16 final size:16
Alignment explanation
Indices: 428379--428421 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
428369 GTTTCATTTT
*
428379 TTTTCTTTTCTT-TTCA
1 TTTT-TTTTCTTCATCA
428395 TTTTTTTTCTTCATCA
1 TTTTTTTTCTTCATCA
428411 -TTTTTTTCTTC
1 TTTTTTTTCTTC
428422 TTCAAGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTCTTCATCA
Found at i:435295 original size:14 final size:16
Alignment explanation
Indices: 435278--435309 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
435268 ATTATTTTTT
435278 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
435292 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
435308 TG
1 TG
435310 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:439612 original size:28 final size:32
Alignment explanation
Indices: 439551--439612 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
439541 TATTTACATG
439551 ATTAAATAATAATAATAATAACAATTAAATAT
1 ATTAAATAATAATAATAATAACAATTAAATAT
*
439583 ATTAAA-AATAATCAT-ATAA-AATTAAA-AT
1 ATTAAATAATAATAATAATAACAATTAAATAT
439611 AT
1 AT
439613 GACTAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 7 0.24
30 4 0.14
31 8 0.28
32 6 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTAAATAATAATAATAATAACAATTAAATAT
Found at i:440946 original size:3 final size:3
Alignment explanation
Indices: 440938--440986 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
440928 GTAATTATTT
* *
440938 ATA ATA ATA ATA A-A ATAA ATA A-A ATA ATA ATA AT- ATT TTA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
440981 ATA ATA
1 ATA ATA
440987 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:440983 original size:20 final size:19
Alignment explanation
Indices: 440933--440986 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
440923 ATATTGTAAT
440933 TATTTATAATAATAATAAAA
1 TATTT-TAATAATAATAAAA
**
440953 TA-AATAA-AATAATAATAA
1 TATTTTAATAATAATAA-AA
440971 TATTTTAATAATAATA
1 TATTTTAATAATAATA
440987 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 3 0.11
20 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTTTAATAATAATAAAA
Found at i:440987 original size:14 final size:14
Alignment explanation
Indices: 440962--440988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
440952 ATAAATAAAA
440962 TAATAATAATATTT
1 TAATAATAATATTT
440976 TAATAATAATATT
1 TAATAATAATATT
440989 AAAAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATAATAATATTT
Found at i:444315 original size:12 final size:13
Alignment explanation
Indices: 444284--444317 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
444274 AAATTAGATG
*
444284 CACTTAATTAAAT
1 CACTTAAATAAAT
444297 CACTTAAATAAAT
1 CACTTAAATAAAT
444310 -ACTTAAAT
1 CACTTAAAT
444318 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Found at i:446802 original size:26 final size:27
Alignment explanation
Indices: 446773--446831 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
446763 CAGTATTTAG
*
446773 AAACATCCATAAACATATC-CATATTA
1 AAACATCCACAAACATATCACATATTA
** * *
446799 AAACATTTACCAACATATCACATTTTA
1 AAACATCCACAAACATATCACATATTA
446826 AAACAT
1 AAACAT
446832 ACTTGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (27 bp):
AAACATCCACAAACATATCACATATTA
Found at i:449398 original size:16 final size:16
Alignment explanation
Indices: 449373--449403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
449363 ATTCTTGGTG
*
449373 ATTAAGTATTTATTTT
1 ATTAAATATTTATTTT
449389 ATTAAATATTTATTT
1 ATTAAATATTTATTT
449404 AATAAAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTAAATATTTATTTT
Found at i:454758 original size:21 final size:21
Alignment explanation
Indices: 454734--454820 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
454724 GTTTTAAGGT
454734 TAAAATTATAAACCCTAAACC
1 TAAAATTATAAACCCTAAACC
* *
454755 TAAAAAT-TAAA-CCTTAACC
1 TAAAATTATAAACCCTAAACC
* **
454774 CAAAA-TAGTAAACCCTAAAGT
1 TAAAATTA-TAAACCCTAAACC
* * *
454795 TTAAATTTTAAACCCTTAATCC
1 TAAAATTATAAACCC-TAAACC
454817 TAAA
1 TAAA
454821 CACTAAATCT
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
18 1 0.02
19 11 0.23
20 8 0.17
21 21 0.44
22 7 0.15
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (21 bp):
TAAAATTATAAACCCTAAACC
Found at i:454767 original size:20 final size:21
Alignment explanation
Indices: 454742--454792 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
454732 GTTAAAATTA
* *
454742 TAAACCCTAAACCTAAAA-AT
1 TAAACCCTAAACCCAAAATAG
*
454762 TAAA-CCTTAACCCAAAATAG
1 TAAACCCTAAACCCAAAATAG
454782 TAAACCCTAAA
1 TAAACCCTAAA
454793 GTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 11 0.44
20 9 0.36
21 5 0.20
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCAAAATAG
Found at i:455062 original size:15 final size:15
Alignment explanation
Indices: 455022--455083 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
455012 ATGAAGACAA
455022 AAAATACAAT-AC-T
1 AAAATACAATAACAT
*
455035 AGAAACTAAAATAACAT
1 A-AAA-TACAATAACAT
* *
455052 AAATTTCAATAACAT
1 AAAATACAATAACAT
*
455067 AAAATACAATTACAT
1 AAAATACAATAACAT
455082 AA
1 AA
455084 TTATGGTCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 28 0.74
16 4 0.11
17 2 0.05
ACGTcount: A:0.61, C:0.13, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATACAATAACAT
Found at i:457431 original size:102 final size:102
Alignment explanation
Indices: 457202--457416 Score: 274
Period size: 102 Copynumber: 2.1 Consensus size: 102
457192 GCCTACCTCA
* * ** ** * **
457202 TGAAATTGAAGGCATAGTGTCATATGGGTTCAAAATGAACTGATGTGTCGATGTTATTCTAATGT
1 TGAACTTGAAGGCATAGTGTCATATGCGTTTGAAACAAATTTTTGTGTCGATGTTATTCTAATGT
* *
457267 TGAGGTCGAACAAGTTTGTAGATGAATGTCTTCCCCT
66 TGAGGTCGAACAAGTTTGCAAATGAATGTCTTCCCCT
457304 TGAACTTGAAGGCATAGTGTCATATGCGTTTGAAACAAATTTTTGTGTCGATGGTGT-TTC-AAT
1 TGAACTTGAAGGCATAGTGTCATATGCGTTTGAAACAAATTTTTGTGTCGAT-GT-TATTCTAAT
*
457367 GTTGAGGTCGAAGAA-TTTGGCAAATGAATGTCTTCCCCT
64 GTTGAGGTCGAACAAGTTT-GCAAATGAATGTCTTCCCCT
457406 TGAACTTGAAG
1 TGAACTTGAAG
457417 TTATGTTTCC
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
101 3 0.03
102 89 0.91
103 5 0.05
104 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (102 bp):
TGAACTTGAAGGCATAGTGTCATATGCGTTTGAAACAAATTTTTGTGTCGATGTTATTCTAATGT
TGAGGTCGAACAAGTTTGCAAATGAATGTCTTCCCCT
Found at i:458179 original size:156 final size:162
Alignment explanation
Indices: 457814--458193 Score: 368
Period size: 156 Copynumber: 2.3 Consensus size: 162
457804 TTTTCTAGTA
* *
457814 AATTATATGC-ATAGATGATGTTAACCTTCGGGGAACTATTCATCACAATAACTCTCATGCCTAA
1 AATTATATACAATAGATGATGTT-ACCTTC-GGGAACTATTCATCACAATAACTCCCATGCCTAA
* *
457878 TGGGATGACACACTATGACATGGAAGAGATTCCTTGCAAAACGTGAAAGCACTTCTTGTGAAAAA
64 TGGAATGACACACTATGACATGGAAGAGATTCCCTGC-AAA---GAAAG--C-TCTTGTGAAAAA
* *
457943 AAACATTCTTTTTTTCCAAAGATTCTTTGAATTTTCCAATT
122 AAACATTCTCTTTTTCCAAAGATTCTTTGAATTTTCCAATC
* * * ** * * * *
457984 ACTTATATGCAA-ACATGATGTCCCCCTTCAGGGAACTATTCACCACAGTAACTCCCATGTC-GA
1 AATTATATACAATAGATGATGT-TACCTTC-GGGAACTATTCATCACAATAACTCCCATGCCTAA
* **
458047 TGGAATGACACACTATGACATGGCAGAGATTCCCTGC-AA-AAAG-TCTTGTGAAAAAAGTC-TT
64 TGGAATGACACACTATGACATGGAAGAGATTCCCTGCAAAGAAAGCTCTTGTGAAAAAAAACATT
*
458108 C-CTTTTTCC-GAGATTCTTTGAATTTTCCAATC
129 CTCTTTTTCCAAAGATTCTTTGAATTTTCCAATC
* *
458140 AATT-T-TACATATAGATGATGTTTCTCTTCGGGTAACTATTCATCACAACAACTC
1 AATTATATACA-ATAGATGATGTTAC-CTTCGGG-AACTATTCATCACAATAACTC
458194 ACTATATATT
Statistics
Matches: 178, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
154 3 0.02
155 6 0.03
156 54 0.30
157 7 0.04
158 3 0.02
159 14 0.08
163 4 0.02
167 2 0.01
169 35 0.20
170 49 0.28
171 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (162 bp):
AATTATATACAATAGATGATGTTACCTTCGGGAACTATTCATCACAATAACTCCCATGCCTAATG
GAATGACACACTATGACATGGAAGAGATTCCCTGCAAAGAAAGCTCTTGTGAAAAAAAACATTCT
CTTTTTCCAAAGATTCTTTGAATTTTCCAATC
Found at i:459280 original size:21 final size:21
Alignment explanation
Indices: 459226--459273 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
459216 TCAGGGTCTC
459226 CATCATCTATCTTTGTTTCTT
1 CATCATCTATCTTTGTTTCTT
*
459247 CTTCATCTATCTTTGTTTCTT
1 CATCATCTATCTTTGTTTCTT
459268 CATCAT
1 CATCAT
459274 TAATCTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (21 bp):
CATCATCTATCTTTGTTTCTT
Found at i:459825 original size:20 final size:20
Alignment explanation
Indices: 459782--459825 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
459772 TATTCAATTT
*
459782 AAAACATAATATAAAAACAC
1 AAAACATAATATAAAAACAA
*
459802 AAAACTTAATATAAAAACAA
1 AAAACATAATATAAAAACAA
459822 AAAA
1 AAAA
459826 ACTAGATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACATAATATAAAAACAA
Found at i:459870 original size:13 final size:13
Alignment explanation
Indices: 459852--459877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
459842 CATAAATATA
459852 AAAACTTAACATT
1 AAAACTTAACATT
459865 AAAACTTAACATT
1 AAAACTTAACATT
459878 CAATTAAAAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACTTAACATT
Found at i:460393 original size:21 final size:22
Alignment explanation
Indices: 460355--460407 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
460345 TGCCTGGTTT
*
460355 GAAATATAA-CCTTGCAGGCTC
1 GAAATGTAACCCTTGCAGGCTC
*
460376 GAAATGTAACCCTT-CAGGTTC
1 GAAATGTAACCCTTGCAGGCTC
**
460397 GGCATGTAACC
1 GAAATGTAACC
460408 TTGTAGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
GAAATGTAACCCTTGCAGGCTC
Found at i:460716 original size:2 final size:2
Alignment explanation
Indices: 460700--460751 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
460690 CTAGAATTGA
460700 AT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
460742 AT AT AT AT AT
1 AT AT AT AT AT
460752 TTCTAAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:474100 original size:22 final size:22
Alignment explanation
Indices: 474075--474124 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
474065 CATGGAAAAA
474075 GTATTTACCTTTAGCAGAGTTC
1 GTATTTACCTTTAGCAGAGTTC
474097 GTATTTACCTTTAGCAGAGTTC
1 GTATTTACCTTTAGCAGAGTTC
474119 GT-TTTA
1 GTATTTA
474125 ACAATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (22 bp):
GTATTTACCTTTAGCAGAGTTC
Found at i:476236 original size:16 final size:16
Alignment explanation
Indices: 476215--476249 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
476205 TCTAAATTTA
476215 ATCTGTG-TATAGATTG
1 ATCTGTGTTATAGA-TG
476231 ATCTGTGTTATAGATG
1 ATCTGTGTTATAGATG
476247 ATC
1 ATC
476250 CTGACATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (16 bp):
ATCTGTGTTATAGATG
Found at i:479230 original size:75 final size:74
Alignment explanation
Indices: 479099--479293 Score: 218
Period size: 75 Copynumber: 2.7 Consensus size: 74
479089 TTTTTTATAT
* * * **
479099 TTAATATTATGGTTTCAGTCTTAAGATTTGACATTTTAATGTTATGGTTTGATTATGGATTTTAT
1 TTAATATTATGGTTTAAGTCTTGAGATTTGACATTTTAATATTATAATTTGATTATGGATTTTAT
* * * *
479164 TATTTTAGAG
66 T-GTTCAAAC
* * * *
479174 TTAATATTGTGGTTTAAATCTTGAGATTTGACATTTTAATATTGTAATTTGTTTATGGATTTTAT
1 TTAATATTATGGTTTAAGTCTTGAGATTTGACATTTTAATATTATAATTTGATTATGGATTTTAT
479239 TGTTCAAAC
66 TGTTCAAAC
* *
479248 TTAATATTATGGTTTGAGTCTTGATATTTGAC--TTT-AT-TTATAATTT
1 TTAATATTATGGTTTAAGTCTTGAGATTTGACATTTTAATATTATAATTT
479294 TTTACATCCA
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
70 8 0.08
71 2 0.02
72 3 0.03
74 32 0.31
75 57 0.56
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (74 bp):
TTAATATTATGGTTTAAGTCTTGAGATTTGACATTTTAATATTATAATTTGATTATGGATTTTAT
TGTTCAAAC
Found at i:486001 original size:24 final size:23
Alignment explanation
Indices: 485959--486004 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
485949 TTGGATTGCT
* *
485959 GAATTTTTTTTGTTTATTGTTGA
1 GAATTTTTTTTCTTCATTGTTGA
485982 GAATTTTTTTTCTTACATTGTTG
1 GAATTTTTTTTCTT-CATTGTTG
486005 GTTTGATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.63
Consensus pattern (23 bp):
GAATTTTTTTTCTTCATTGTTGA
Found at i:486669 original size:36 final size:36
Alignment explanation
Indices: 486622--486717 Score: 147
Period size: 36 Copynumber: 2.7 Consensus size: 36
486612 CAAGCTTAGG
**
486622 TTGTTTCAAGGGAATTTGTCTCAAAAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAT
**
486658 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAT
*
486694 TTATTTCAAGGGAAACTGTCTCAA
1 TTGTTTCAAGGGAAACTGTCTCAA
486718 GCGAGACTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAAT
Found at i:486726 original size:15 final size:15
Alignment explanation
Indices: 486708--486739 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
486698 TTCAAGGGAA
486708 ACTGTCTCAAGCGAG
1 ACTGTCTCAAGCGAG
*
486723 ACTGTCTCAAGGGAG
1 ACTGTCTCAAGCGAG
486738 AC
1 AC
486740 AAAATTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (15 bp):
ACTGTCTCAAGCGAG
Found at i:486727 original size:51 final size:51
Alignment explanation
Indices: 486663--486917 Score: 336
Period size: 51 Copynumber: 5.1 Consensus size: 51
486653 AAAATTTGTT
* *
486663 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTGTC
1 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
* * *
486714 TCAAGCGAGACTGTCTCAAGGGAGACAAAATTTGCTTCAAGGGAAA-T-TG
1 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
* *
486763 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTC
1 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
* ** ****
486814 TCAAGGGAGACCGTCTCAATAGAGA-AAAAAAAATTTCAAGGGAAACTGTC
1 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
* * *
486864 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTATC
1 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
486915 TCA
1 TCA
486918 GAGGAGATAA
Statistics
Matches: 172, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 43 0.25
50 43 0.25
51 86 0.50
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (51 bp):
TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
Found at i:486780 original size:100 final size:101
Alignment explanation
Indices: 486663--486917 Score: 345
Period size: 100 Copynumber: 2.5 Consensus size: 101
486653 AAAATTTGTT
* * * *
486663 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGCGAGACTGT
1 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGCGAGACCGT
* * ** *
486728 CTCAAGGGAG-ACAAAATTTGCTTCAAGGGAAA-T-TG
66 CTCAAGAGAGAAAAAAAAAT--TTCAAGGGAAACTGTC
* *
486763 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGGGAGACCGT
1 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGCGAGACCGT
*
486828 CTCAATAGAGAAAAAAAAATTTCAAGGGAAACTGTC
66 CTCAAGAGAGAAAAAAAAATTTCAAGGGAAACTGTC
* *
486864 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTATCTCA
1 TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCA
486918 GAGGAGATAA
Statistics
Matches: 137, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
99 11 0.08
100 68 0.50
101 58 0.42
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (101 bp):
TCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGCGAGACCGT
CTCAAGAGAGAAAAAAAAATTTCAAGGGAAACTGTC
Found at i:486887 original size:15 final size:15
Alignment explanation
Indices: 486849--486889 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
486839 AAAAAAAATT
* *
486849 TCAAGGGAAACTGTC
1 TCAAGGGAGACTATC
486864 TCAAGGGAGACTATC
1 TCAAGGGAGACTATC
486879 TCAAGGGAGAC
1 TCAAGGGAGAC
486890 AAAATTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (15 bp):
TCAAGGGAGACTATC
Found at i:486924 original size:36 final size:36
Alignment explanation
Indices: 486877--487053 Score: 236
Period size: 36 Copynumber: 4.9 Consensus size: 36
486867 AGGGAGACTA
*
486877 TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTA
1 TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTG
* *
486913 TCTC-AGAGGAGATAAAATTTGTTTC-AAGGGAACTG
1 TCTCAAG-GGAGACAAAATTTGTTTCAAAGGAAACTG
*
486948 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTG
* *
486984 TCTCAAGGGAGAAAAAATTAT-TTT-TAAGAGAAACTG
1 TCTCAAGGGAGACAAAATT-TGTTTCAAAG-GAAACTG
*
487020 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1 TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAAC
487054 ATATTCAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
35 34 0.28
36 85 0.70
37 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (36 bp):
TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTG
Found at i:487116 original size:67 final size:67
Alignment explanation
Indices: 486877--487247 Score: 353
Period size: 67 Copynumber: 5.4 Consensus size: 67
486867 AGGGAGACTA
* * *
486877 TCTCAAGGGAGACAAAATTTGTTTCAAAGGAAAC-TATCTCAGAGGAGATAAAATT-TGTTTCAA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATAT-TCA-A--AGAT---TTTGTGTTTCAA
*
486940 G-GGAACTG
59 GAGAAACTG
* * ** * *
486948 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC-TGTCTCAAGGGAGAAAAAATTAT-TTTTAA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATAT-TCAA---AG---ATTTTGTGTTTCAA
487011 GAGAAACTG
59 GAGAAACTG
* *
487020 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAATATTTTGTGTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAAAC
487085 TG
66 TG
* *
487087 TCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTG-GTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAAAC
487151 TG
66 TG
* * * *
487153 TCTCAAGAGAGACAAAATTTTGTTTAAAGGGAAACATATTTATAGATTTCGT-TTT-AAGAGAAA
1 TCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAAA
*
487216 CAG
65 CTG
* *
487219 TCTCAAGAGAGAGAAAATTTTGCTTCAAG
1 TCTCAAGAGAGACAAAA-TTTGTTTCAAG
487248 AAAAACTATC
Statistics
Matches: 265, Mismatches: 25, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
66 72 0.27
67 91 0.34
69 1 0.00
70 1 0.00
71 52 0.20
72 45 0.17
73 2 0.01
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.29
Consensus pattern (67 bp):
TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAAAC
TG
Found at i:487340 original size:103 final size:102
Alignment explanation
Indices: 487139--487483 Score: 296
Period size: 103 Copynumber: 3.2 Consensus size: 102
487129 AGATTTTGGT
* * * * *
487139 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTAAAGGGAAACATATTTATAGATTTCG
1 TTCAAGAAAAACTATCTCAAGAGACACAAAATTTTGTTTAAAGGGAAACATATTCAAAGATTTCG
* *
487204 TTTTAAGAGAAACAGTCTCAAGAGAGAGAAAATTTTGC
66 TTTCAAGAGAAACAGTCTCAAAAGAGAGAAAA-TTTGC
* * *
487242 TTCAAGAAAAACTATCTCAAGGGACACAAAATTTTGTTTCAAGGGAAACATATTCAAAGATTTTG
1 TTCAAGAAAAACTATCTCAAGAGACACAAAATTTTGTTTAAAGGGAAACATATTCAAAGATTTCG
* *
487307 TTTCAAGAGAAACTGTCTCAAAAGAGATG-AAATTTGT
66 TTTCAAGAGAAACAGTCTCAAAAGAGA-GAAAATTTGC
* * * *
487344 TTCAAGGGAAACAAATTCAAAGATTTTGGTTTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACA
1 TTCAA--G-AA-AAA--C--------T-ATCTCAAGAGACACAAAATTTTGTTTAAAGGGAAACA
* * * * *
487409 TATTCAAAGATTTTGGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
51 TATTCAAAGA-TTTCGTTTCAAGAGAAACAGTCTCAAAAGAGAGAAAATTTGC
* * *
487462 TTCTAGAGAAAACAATATCAAG
1 TTCAAGA-AAAACTATCTCAAG
487484 TGAGATTAAT
Statistics
Matches: 200, Mismatches: 23, Indels: 37
0.77 0.09 0.14
Matches are distributed among these distances:
102 9 0.05
103 84 0.42
104 8 0.04
105 2 0.01
106 3 0.01
108 1 0.00
113 1 0.00
115 4 0.02
116 3 0.01
117 43 0.22
118 42 0.21
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (102 bp):
TTCAAGAAAAACTATCTCAAGAGACACAAAATTTTGTTTAAAGGGAAACATATTCAAAGATTTCG
TTTCAAGAGAAACAGTCTCAAAAGAGAGAAAATTTGC
Found at i:487363 original size:51 final size:52
Alignment explanation
Indices: 487308--487418 Score: 127
Period size: 52 Copynumber: 2.2 Consensus size: 52
487298 AAGATTTTGT
**
487308 TTCAAGAGAAACT-GTCTCAAAAGAGATGAAA-TTTGTTTCAAGGGAAACAAA
1 TTCAA-AGAAACTGGTCTCAAAAGAGACAAAATTTTGTTTCAAGGGAAACAAA
*** * * *
487359 TTCAAAGATTTTGGTTTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACATA
1 TTCAAAGAAACTGGTCTCAAAAGAGACAAAATTTTGTTTCAAGGGAAACAAA
487411 TTCAAAGA
1 TTCAAAGA
487419 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 4 0.08
51 19 0.38
52 27 0.54
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (52 bp):
TTCAAAGAAACTGGTCTCAAAAGAGACAAAATTTTGTTTCAAGGGAAACAAA
Found at i:487447 original size:29 final size:29
Alignment explanation
Indices: 487339--487437 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 29
487329 AGAGATGAAA
* *
487339 TTTGTTTCAAGGGAAACAAATTCAAAGAT
1 TTTGTTTCAAGAGAAACATATTCAAAGAT
*
487368 TTTGGTTTCAAGAG----AGA--CAAA-AT
1 TTT-GTTTCAAGAGAAACATATTCAAAGAT
*
487391 TTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTTGTTTCAAGAGAAACATATTCAAAGAT
487420 TTTGGTTTCAAGAGAAAC
1 TTT-GTTTCAAGAGAAAC
487438 TGTCTCAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
22 9 0.16
23 5 0.09
24 4 0.07
26 4 0.07
28 4 0.07
29 8 0.14
30 22 0.39
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (29 bp):
TTTGTTTCAAGAGAAACATATTCAAAGAT
Found at i:487740 original size:37 final size:36
Alignment explanation
Indices: 487698--487980 Score: 166
Period size: 37 Copynumber: 8.1 Consensus size: 36
487688 GTTCCAAATG
*
487698 AAAATGTCTCAAGTGAGACGAAATTCGTTTTGAGAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGA-AGA
* *
487735 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGAAGA
* ** * * *
487771 AAAA-----CAACTTTG---AAATTTGTGTTCCGAAGG
1 AAAATGTCTCAAGTGAGACAAAATTCGT-TT-TGAAGA
* * *
487801 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGA-AGA
* *
487838 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGAAGA
* ** * *
487874 AAAA----T-AACTTTG---AAATTTGTGTTTCGAAGG
1 AAAATGTCTCAAGTGAGACAAAATTCGT-TTT-GAAGA
* * * *
487904 AAAATGTTTCAAGTGAGACGAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGA-AGA
* *
487941 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA
1 AAAATGTCTCAAGTGAGACAAAATTCGTTTTGAAGA
487977 AAAA
1 AAAA
487981 CAACTTTGAA
Statistics
Matches: 194, Mismatches: 30, Indels: 45
0.72 0.11 0.17
Matches are distributed among these distances:
28 16 0.08
29 5 0.03
30 14 0.07
31 9 0.05
32 1 0.01
34 1 0.01
35 9 0.05
36 23 0.12
37 100 0.52
38 16 0.08
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (36 bp):
AAAATGTCTCAAGTGAGACAAAATTCGTTTTGAAGA
Found at i:487774 original size:103 final size:103
Alignment explanation
Indices: 487595--488011 Score: 708
Period size: 103 Copynumber: 4.0 Consensus size: 103
487585 AATTTTGGGA
* * * * * *
487595 AAAATGTATCAAGCGAGACGAAGTTTGTTTTGAGAGAGAAATGTCTTAAGTGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
* *
487660 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCAAATG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* *
487698 AAAATGTCTCAAGTGAGACGAAATTCGTTTTGAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
487763 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
487801 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
* *
487866 TTTTAAGAAAAATAACTTTGAAATTTGTGTTTCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
*
487904 AAAATGTTTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
*
487969 TTTTAAGAAAAACAACTTTGAAATTTGTGTTTCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
488007 AAAAT
1 AAAAT
488012 TGAGTGTTCG
Statistics
Matches: 300, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 300 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.32
Consensus pattern (103 bp):
AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
Found at i:487889 original size:65 final size:66
Alignment explanation
Indices: 487820--487945 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
487810 CAAGTGAGAC
*
487820 GAAATTTGT-TTT-AAGAGAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTA-AGAAAAATAAC
1 GAAATTTGTGTTTCAAG-G-AAAATGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAAAATAAC
487882 TTT
64 TTT
* *
487885 GAAATTTGTGTTTCGAAGGAAAATGTTTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAAT
1 GAAATTTGTGTTTC-AAGGAAAATGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAAAAT
487946 GTCTCAAGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
65 9 0.17
66 33 0.61
67 9 0.17
68 3 0.06
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (66 bp):
GAAATTTGTGTTTCAAGGAAAATGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAAAATAACTT
T
Found at i:487932 original size:21 final size:20
Alignment explanation
Indices: 487908--487970 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
487898 CGAAGGAAAA
487908 TGTTTCAAGTGAGACGAAATT
1 TGTTTCAAGTGAGAC-AAATT
* *
487929 TGTTTTAA--GAGA-AAA-A
1 TGTTTCAAGTGAGACAAATT
*
487945 TGTCTCAAGTGAGACAAAATT
1 TGTTTCAAGTGAGAC-AAATT
487966 TGTTT
1 TGTTT
487971 TTAAGAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 4 0.13
19 4 0.13
20 3 0.10
21 11 0.35
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (20 bp):
TGTTTCAAGTGAGACAAATT
Found at i:488480 original size:19 final size:17
Alignment explanation
Indices: 488441--488482 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
488431 TGTATATGTA
488441 TGTGTGAGGGAAATGGT
1 TGTGTGAGGGAAATGGT
* *
488458 TGTGTGAGGGGAATGTT
1 TGTGTGAGGGAAATGGT
488475 TGTGTGAG
1 TGTGTGAG
488483 CAGCCTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.33
Consensus pattern (17 bp):
TGTGTGAGGGAAATGGT
Found at i:489477 original size:2 final size:2
Alignment explanation
Indices: 489470--489508 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
489460 GCTTTATTGT
489470 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
489509 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:490284 original size:151 final size:151
Alignment explanation
Indices: 489990--490307 Score: 588
Period size: 151 Copynumber: 2.1 Consensus size: 151
489980 AAGATTAATA
*
489990 TTTTCTC-ATTGTTCAT-TTCCTAAGAAAGAAACACCTTATTTAAAATATCAATTATTCAAATGA
1 TTTTCTCGATT-TGCATCTTCCTAAGAAAGAAACACCTTATTTAAAATATCAATTATTCAAATGA
490053 CTTACAAACTTTTTAGCGAAATGATAAAGAAAAAATTCAAACAAGACAATATACGAGTGCATAAA
65 CTTACAAACTTTTTAGCGAAATGATAAAGAAAAAATTCAAACAAGACAATATACGAGTGCATAAA
490118 AAGTTTCTAGTGTTGCAATGAT
130 AAGTTTCTAGTGTTGCAATGAT
490140 TTTTCTCGATTTGCATCTTCCTAAGAAAGAAACACCTTATTTAAAATATCAATTATTCAAATGAC
1 TTTTCTCGATTTGCATCTTCCTAAGAAAGAAACACCTTATTTAAAATATCAATTATTCAAATGAC
490205 TTACAAACTTTTTAGCGAAATGATAAAG-AAAAATTCAAACAAGACAATATACGAGTGCATAAAA
66 TTACAAACTTTTTAGCGAAATGATAAAGAAAAAATTCAAACAAGACAATATACGAGTGCATAAAA
490269 AGTTTCTAGTGGTTGCAATGAT
131 AGTTTCTAGT-GTTGCAATGAT
490291 TTTTCTCGATTTGCATC
1 TTTTCTCGATTTGCATC
490308 AGACTGCCCC
Statistics
Matches: 164, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
150 57 0.35
151 107 0.65
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (151 bp):
TTTTCTCGATTTGCATCTTCCTAAGAAAGAAACACCTTATTTAAAATATCAATTATTCAAATGAC
TTACAAACTTTTTAGCGAAATGATAAAGAAAAAATTCAAACAAGACAATATACGAGTGCATAAAA
AGTTTCTAGTGTTGCAATGAT
Found at i:490637 original size:22 final size:22
Alignment explanation
Indices: 490589--490639 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
490579 ATGCTCATGC
* *
490589 AAATACAAAGATGCAAAAATGG
1 AAATGCAAAGATGCAAAAATGA
*
490611 GAATGCAAA-ATGCAAAAATGTA
1 AAATGCAAAGATGCAAAAATG-A
490633 AAATGCA
1 AAATGCA
490640 TCAAAAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.16
Consensus pattern (22 bp):
AAATGCAAAGATGCAAAAATGA
Found at i:492975 original size:38 final size:37
Alignment explanation
Indices: 492916--493284 Score: 182
Period size: 39 Copynumber: 9.5 Consensus size: 37
492906 TTTGTTTTAT
492916 TATATATATATATATATTAGTTTTTGAATGATTTTTGAAA
1 TATATATATA-ATATA-TAGTTTTTGAAT-ATTTTTGAAA
492956 TATATATATAATATATAG-TTTTGAAAATGATTTTTGAAAA
1 TATATATATAATATATAGTTTTTG--AAT-ATTTTTG-AAA
* * * *
492996 TGTATATATATTATATAGTTTTTTGAAAACATTTTGAAA
1 TATATATATAATATATAG-TTTTTGAATA-TTTTTGAAA
* * * * *
493035 -AT-TATATAATACATGGCTTTTTAAAAAACATTTTGAAA
1 TATATATATAATATATAG-TTTTT-GAATA-TTTTTGAAA
*
493073 -ATATATATAATATATAGTTTCTGATATATAGTTTTGAAA
1 TATATATATAATATATAGTTTTTGA-ATAT--TTTTGAAA
* **
493112 TTATTTTGAAAACTTATATAATATATAATTTTAAAATATTTTTGAAA
1 -TA---T----A--TATATAATATATAGTTTTTGAATATTTTTGAAA
* * ** * * *
493159 -ACATATATAATATAT-GGTTTAAAAAACATTCTGAAA
1 TATATATATAATATATAGTTTTTGAATA-TTTTTGAAA
* *
493195 -AT-TATATAATATATAG-TTTTGAAAACTGTTTTAAAA
1 TATATATATAATATATAGTTTTTGAATA-T-TTTTGAAA
* **
493231 AATATATATAATATATAGTTTTAAAATATTTTT-AAA
1 TATATATATAATATATAGTTTTTGAATATTTTTGAAA
493267 TATATATATATATATATA
1 TATATATATA-ATATATA
493285 TTTATTTATT
Statistics
Matches: 264, Mismatches: 36, Indels: 61
0.73 0.10 0.17
Matches are distributed among these distances:
35 28 0.11
36 39 0.15
37 35 0.13
38 42 0.16
39 46 0.17
40 36 0.14
41 1 0.00
42 5 0.02
44 1 0.00
45 1 0.00
47 8 0.03
48 1 0.00
49 4 0.02
50 17 0.06
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (37 bp):
TATATATATAATATATAGTTTTTGAATATTTTTGAAA
Found at i:493118 original size:88 final size:87
Alignment explanation
Indices: 493007--493178 Score: 213
Period size: 86 Copynumber: 2.0 Consensus size: 87
492997 GTATATATAT
**
493007 TATATAGTTTTTTGAAAACATTTTGAAAA-TTATATAATACATGGCTTTTTAAAAAACATTTTGA
1 TATATAG-TTTTTGAAAACATTTTGAAAACTTATATAATACAT--AATTTTAAAAAA-ATTTTGA
*
493071 AAATATATATAATATATAGTTTCTGA
62 AAACATATATAATATATAGTTTCTGA
** * * *
493097 TATATAG-TTTTGAAATTATTTTGAAAACTTATATAATATATAATTTTAAAATATTTTTGAAAAC
1 TATATAGTTTTTGAAAACATTTTGAAAACTTATATAATACATAATTTTAAAAAAATTTTGAAAAC
*
493161 ATATATAATATATGGTTT
66 ATATATAATATATAGTTT
493179 AAAAAACATT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
86 26 0.36
87 9 0.12
88 18 0.25
89 12 0.17
90 7 0.10
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (87 bp):
TATATAGTTTTTGAAAACATTTTGAAAACTTATATAATACATAATTTTAAAAAAATTTTGAAAAC
ATATATAATATATAGTTTCTGA
Found at i:493155 original size:36 final size:35
Alignment explanation
Indices: 493096--493284 Score: 177
Period size: 36 Copynumber: 5.2 Consensus size: 35
493086 ATAGTTTCTG
*
493096 ATATATAGTTTTGAAAT-TATTTTGAAAACTTATATA
1 ATATATAGTTTTAAAATAT-TTTTGAAAA-TTATATA
* *
493132 ATATATAATTTTAAAATATTTTTGAAAACATATATA
1 ATATATAGTTTTAAAATATTTTTGAAAA-TTATATA
* * * *
493168 ATATAT-GGTTTAAAAAACATTCTGAAAATTATATA
1 ATATATAGTTTTAAAATA-TTTTTGAAAATTATATA
* **
493203 ATATATAGTTTTGAAAACTGTTTTAAAAAATATATATA
1 ATATATAGTTTT-AAAA-TATTTTTGAAAAT-TATATA
493241 ATATATAGTTTTAAAATATTTTT-AAATATATATATA
1 ATATATAGTTTTAAAATATTTTTGAAA-AT-TATATA
493277 TATATATA
1 -ATATATA
493285 TTTATTTATT
Statistics
Matches: 127, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
35 23 0.18
36 63 0.50
37 23 0.18
38 18 0.14
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (35 bp):
ATATATAGTTTTAAAATATTTTTGAAAATTATATA
Found at i:493290 original size:4 final size:4
Alignment explanation
Indices: 493283--493340 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
493273 TATATATATA
493283 TATT TATT TATT TA-T T-TT TATT TATCT TATT TCATTT TATT TATTT
1 TATT TATT TATT TATT TATT TATT TAT-T TATT T-A-TT TATT TA-TT
*
493329 TATT TTTT TATT
1 TATT TATT TATT
493341 GTGGTCCAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 4 0.09
4 29 0.63
5 10 0.22
6 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:493302 original size:10 final size:9
Alignment explanation
Indices: 493283--493340 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
493273 TATATATATA
493283 TATTTA-TT
1 TATTTATTT
493291 TATTTATTTT
1 TATTTA-TTT
*
493301 TATTTATCT
1 TATTTATTT
493310 TATTTCATTT
1 TATTT-ATTT
493320 TATTTATTT
1 TATTTATTT
493329 TATTT-TTT
1 TATTTATTT
493337 TATT
1 TATT
493341 GTGGTCCAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 13 0.29
9 16 0.36
10 16 0.36
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTTATTT
Found at i:493302 original size:14 final size:13
Alignment explanation
Indices: 493285--493340 Score: 67
Period size: 14 Copynumber: 4.1 Consensus size: 13
493275 TATATATATA
493285 TTTATTTATTTATT
1 TTTATTTATTTA-T
493299 TTTATTTATCTTAT
1 TTTATTTAT-TTAT
*
493313 TTCATTTTATTTAT
1 TTTA-TTTATTTAT
*
493327 TTTATTTTTTTAT
1 TTTATTTATTTAT
493340 T
1 T
493341 GTGGTCCAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.24
14 20 0.54
15 8 0.22
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:493314 original size:19 final size:18
Alignment explanation
Indices: 493283--493337 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
493273 TATATATATA
493283 TATTTATTTATTTATTTT
1 TATTTATTTATTTATTTT
493301 TATTTATCTTATTTCA-TTT
1 TATTTAT-TTATTT-ATTTT
493320 TATTTATTTTATTT-TTTT
1 TATTTA-TTTATTTATTTT
493338 ATTGTGGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.30
19 21 0.64
20 2 0.06
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTATTTATTTATTTT
Found at i:498169 original size:99 final size:100
Alignment explanation
Indices: 497990--498192 Score: 300
Period size: 99 Copynumber: 2.0 Consensus size: 100
497980 ATTATAATAT
* * * ** * * *
497990 TATTGTATACAATAAAGCTTGAGATGTCTCTCTAGATTAATTGGTTAAACGCCCTGGCTTTATGG
1 TATTGTATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGG
498055 ATAAGATTCAACTAGCCTGATAAAGGTGATTATAA
66 ATAAGATTCAACTAGCCTGATAAAGGTGATTATAA
*
498090 TATT-TATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGG
1 TATTGTATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGG
* *
498154 ATAAGGTTCAGCTAGCCTGATAAAGGTGATTATAA
66 ATAAGATTCAACTAGCCTGATAAAGGTGATTATAA
498189 TATT
1 TATT
498193 AAGATATCCC
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 88 0.96
100 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (100 bp):
TATTGTATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGG
ATAAGATTCAACTAGCCTGATAAAGGTGATTATAA
Found at i:499855 original size:40 final size:40
Alignment explanation
Indices: 499811--500138 Score: 178
Period size: 37 Copynumber: 8.6 Consensus size: 40
499801 TTTTATTATA
* * *
499811 TATATATATATATTATAGTTTGTAAATGATTTTTG-AAATT
1 TATATATATATA-TATAGTTTGAAAACGATTTTTGAAAATG
499851 TATATAT-TATATATAGTTTTGAAAACGATTTTTGAAAATG
1 TATATATATATATATAG-TTTGAAAACGATTTTTGAAAATG
499891 TATATATAT-TATATAGTTTTTTGAAAAC-A-TTTTGAAAAT-
1 TATATATATATATATAG---TTTGAAAACGATTTTTGAAAATG
* * *
499930 TATATA-ATATATGGGT-TTTTAAAAAAC-A-TTTTGAAAA--
1 TATATATATATAT--ATAGTTT-GAAAACGATTTTTGAAAATG
* *
499967 TATATATA-ATATATAGTTTTTGAAAAC--CTTTT-AAAATC
1 TATATATATATATATAG--TTTGAAAACGATTTTTGAAAATG
*
500005 T-TATATA-ATATATAGTTTTAAAAC-ATTTTTGAAAA--
1 TATATATATATATATAGTTTGAAAACGATTTTTGAAAATG
* * *
500040 CATATATA-ATATATGGTTTAAAAAAAC-A-TTTTGAAAA--
1 TATATATATATATATAGTTT--GAAAACGATTTTTGAAAATG
* *
500077 T-TATATA-ATATATAGTTTTGAAAAC--TGTTTT-AATATA
1 TATATATATATATATAG-TTTGAAAACGAT-TTTTGAAAATG
*
500114 TATATATATATATATAGTTTTAAAA
1 TATATATATATATATAGTTTGAAAA
500139 TATTTTTAAA
Statistics
Matches: 241, Mismatches: 19, Indels: 58
0.76 0.06 0.18
Matches are distributed among these distances:
35 17 0.07
36 41 0.17
37 53 0.22
38 46 0.19
39 36 0.15
40 35 0.15
41 3 0.01
42 10 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (40 bp):
TATATATATATATATAGTTTGAAAACGATTTTTGAAAATG
Found at i:499934 original size:37 final size:37
Alignment explanation
Indices: 499841--500134 Score: 250
Period size: 37 Copynumber: 7.8 Consensus size: 37
499831 TGTAAATGAT
*
499841 TTTTGAAATTTATATATTATATATAG--TTTTGAAAACGA
1 TTTTGAAAATTATATA--ATATATAGTTTTTTGAAAAC-A
499879 TTTTTGAAAATGTATATATATTATATAGTTTTTTGAAAACA
1 -TTTTGAAAAT-TATATA-A-TATATAGTTTTTTGAAAACA
* **
499920 TTTTGAAAATTATATAATATATGGGTTTTTAAAAAACA
1 TTTTGAAAATTATATAATATAT-AGTTTTTTGAAAACA
*
499958 TTTTGAAAATATATATAATATATAG-TTTTTGAAAACC
1 TTTTGAAAAT-TATATAATATATAGTTTTTTGAAAACA
499995 TTTT-AAAATCTTATATAATATATAG--TTTT-AAAACA
1 TTTTGAAAA--TTATATAATATATAGTTTTTTGAAAACA
* * ***
500030 TTTTTGAAAACATATATAATATAT-GGTTTAAAAAAACA
1 -TTTTGAAAA-TTATATAATATATAGTTTTTTGAAAACA
500068 TTTTGAAAATTATATAATATATAG--TTTTGAAAAC-
1 TTTTGAAAATTATATAATATATAGTTTTTTGAAAACA
*
500102 TGTTTTAATATATATATATATATATATAGTTTT
1 T-TTTGAA-A-AT-TATATA-ATATATAGTTTT
500135 AAAATATTTT
Statistics
Matches: 217, Mismatches: 17, Indels: 40
0.79 0.06 0.15
Matches are distributed among these distances:
34 1 0.00
35 18 0.08
36 38 0.18
37 50 0.23
38 37 0.17
39 37 0.17
40 23 0.11
41 3 0.01
42 10 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATTATATAATATATAGTTTTTTGAAAACA
Found at i:500146 original size:38 final size:37
Alignment explanation
Indices: 499808--500153 Score: 282
Period size: 38 Copynumber: 9.2 Consensus size: 37
499798 TTGTTTTATT
**
499808 ATATATATATATATATTATAG-TTTGTAAATGATTTTTGAA
1 ATATATATATA-ATA-TATAGTTTTG-AAAACATTTTT-AA
* *
499848 ATTTATATATTATATATAGTTTTGAAAACGATTTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAAC-ATTTTT--AA
* * *
499888 ATGTATATATATTATATAGTTTTTTGAAAACATTTTGAA
1 ATATATATATAATATATAG--TTTTGAAAACATTTTTAA
* * *
499927 A-AT-TATATAATATATGGGTTTTTAAAAAACATTTTGAA
1 ATATATATATAATATAT-AG-TTTT-GAAAACATTTTTAA
* *
499965 A-ATATATATAATATATAGTTTTTGAAAACCTTTTAAA
1 ATATATATATAATATATAG-TTTTGAAAACATTTTTAA
*
500002 ATCT-TATATAATATATAGTTTT-AAAACATTTTTGAA
1 ATATATATATAATATATAGTTTTGAAAACATTTTT-AA
* * ** *
500038 A-ACATATATAATATATGGTTTAAAAAAACATTTTGAA
1 ATATATATATAATATATAGTTT-TGAAAACATTTTTAA
500075 A-AT-TATATAATATATAGTTTTGAAAAC-TGTTTTAA
1 ATATATATATAATATATAGTTTTGAAAACAT-TTTTAA
*
500110 TATATATATATATATATATAGTTTT-AAAATATTTTTAA
1 -ATATATATATA-ATATATAGTTTTGAAAACATTTTTAA
500148 ATATAT
1 ATATAT
500154 TTTTTTTTAT
Statistics
Matches: 256, Mismatches: 31, Indels: 41
0.78 0.09 0.12
Matches are distributed among these distances:
34 1 0.00
35 19 0.07
36 40 0.16
37 54 0.21
38 59 0.23
39 41 0.16
40 27 0.11
41 5 0.02
42 10 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (37 bp):
ATATATATATAATATATAGTTTTGAAAACATTTTTAA
Found at i:500155 original size:12 final size:12
Alignment explanation
Indices: 500125--500157 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
500115 ATATATATAT
*
500125 ATATAGTTTTAA
1 ATATATTTTTAA
500137 A-ATATTTTTAA
1 ATATATTTTTAA
500148 ATATATTTTT
1 ATATATTTTT
500158 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
ATATATTTTTAA
Found at i:500164 original size:10 final size:10
Alignment explanation
Indices: 500151--500207 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
500141 TTTTTAAATA
*
500151 TATTTTTTTT
1 TATTTATTTT
500161 TATTTATTTT
1 TATTTATTTT
*
500171 TATTTA-TCT
1 TATTTATTTT
500180 TATTTCA-TTT
1 TATTT-ATTTT
*
500190 TA-TTAATTT
1 TATTTATTTT
500199 TATTT-TTTT
1 TATTTATTTT
500208 ATTGTGGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 1 0.03
9 17 0.43
10 22 0.55
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (10 bp):
TATTTATTTT
Found at i:500168 original size:14 final size:14
Alignment explanation
Indices: 500151--500210 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
500141 TTTTTAAATA
*
500151 TATTTTTTTTTATT
1 TATTTTATTTTATT
500165 TATTTT-TATTTATCT
1 TATTTTAT-TTTAT-T
*
500180 TATTTCATTTTATT
1 TATTTTATTTTATT
*
500194 AATTTTATTTT-TT
1 TATTTTATTTTATT
500207 TATT
1 TATT
500211 GTGGTCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.15
14 21 0.54
15 11 0.28
16 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:500182 original size:9 final size:9
Alignment explanation
Indices: 500158--500210 Score: 63
Period size: 10 Copynumber: 5.8 Consensus size: 9
500148 ATATATTTTT
500158 TTTTATTTA
1 TTTTATTTA
500167 TTTTTATTTA
1 -TTTTATTTA
*
500177 TCTTATTTCA
1 TTTTATTT-A
*
500187 TTTTATTAA
1 TTTTATTTA
500196 TTTTATTT-
1 TTTTATTTA
500204 TTTTATT
1 TTTTATT
500211 GTGGTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 7 0.18
9 15 0.39
10 16 0.42
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:500184 original size:19 final size:19
Alignment explanation
Indices: 500160--500207 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
500150 ATATTTTTTT
*
500160 TTATTTATTTTTATTTATC
1 TTATTTATTTTTATTAATC
*
500179 TTATTTCA-TTTTATTAATT
1 TTATTT-ATTTTTATTAATC
500198 TTATTT-TTTT
1 TTATTTATTTT
500208 ATTGTGGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 21 0.84
20 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATTTATTTTTATTAATC
Found at i:501201 original size:20 final size:20
Alignment explanation
Indices: 501176--501213 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
501166 CGATAATTAT
501176 ATTTTA-GTCATGTTTTTTAC
1 ATTTTATGT-ATGTTTTTTAC
501196 ATTTTATGTATGTTTTTT
1 ATTTTATGTATGTTTTTT
501214 GTTAATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (20 bp):
ATTTTATGTATGTTTTTTAC
Found at i:509154 original size:13 final size:13
Alignment explanation
Indices: 509136--509160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509126 TACAGACACG
509136 CATATGAAGACTA
1 CATATGAAGACTA
509149 CATATGAAGACT
1 CATATGAAGACT
509161 GTTCAACTAT
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:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:509543 original size:21 final size:21
Alignment explanation
Indices: 509510--509564 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
509500 TTCCAACTTT
*
509510 TTTTATGTCTTAA-AGATATTTA
1 TTTTAT-TTTTAAGAGATA-TTA
*
509532 TGTTT-TTTTTAAGTGATATTA
1 T-TTTATTTTTAAGAGATATTA
509553 TTTTATTTTTAA
1 TTTTATTTTTAA
509565 TGTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 6 0.21
23 3 0.11
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTATTTTTAAGAGATATTA
Found at i:509550 original size:22 final size:21
Alignment explanation
Indices: 509524--509564 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
509514 ATGTCTTAAA
509524 GATATTTATGTTT-TTTTTAAGT
1 GATA-TTAT-TTTATTTTTAAGT
509546 GATATTATTTTATTTTTAA
1 GATATTATTTTATTTTTAA
509565 TGTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (21 bp):
GATATTATTTTATTTTTAAGT
Found at i:513060 original size:26 final size:25
Alignment explanation
Indices: 512978--513060 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
512968 TTATATTTTG
*
512978 TTATAGTTTAAATTGATTTAATTCA
1 TTATAGTTTAAATTGATTTGATTCA
* * * *
513003 TACATAGTAATAAATT-TTTTGAATTTA
1 T-TATAGT-TTAAATTGATTTG-ATTCA
*
513030 TTATAGTTTAAATTGATATGATTCA
1 TTATAGTTTAAATTGATTTGATTCA
513055 TGTATA
1 T-TATA
513061 AAAGTGTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
25 12 0.28
26 20 0.47
27 11 0.26
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TTATAGTTTAAATTGATTTGATTCA
Found at i:516116 original size:15 final size:16
Alignment explanation
Indices: 516098--516135 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
516088 TTTTAATATA
516098 AAATATTATT-TAAAT
1 AAATATTATTATAAAT
*
516113 AAATATTATTATTAAT
1 AAATATTATTATAAAT
516129 -AATATTA
1 AAATATTA
516136 AAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTATTATAAAT
Found at i:516125 original size:18 final size:17
Alignment explanation
Indices: 516089--516122 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
516079 ATTAAATAAT
516089 TTTAATATAAAATATTA
1 TTTAATATAAAATATTA
516106 TTTAA-AT-AAATATTA
1 TTTAATATAAAATATTA
516121 TT
1 TT
516123 ATTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 2 0.12
17 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATATAAAATATTA
Found at i:516237 original size:49 final size:50
Alignment explanation
Indices: 516181--516303 Score: 123
Period size: 49 Copynumber: 2.5 Consensus size: 50
516171 TAATATTTTA
* *
516181 TTAATAAACAATATGTGATTTAAAGT-A-ATATAAAATATTA-TATTATATT
1 TTAATAAACAATATGTGATTTAAA-TCACATATAAAATACTATTAATA-ATT
**
516230 TTAATAAATC-ATAT-T-AAATAAATCACATATAAAATACTATTAATAATT
1 TTAATAAA-CAATATGTGATTTAAATCACATATAAAATACTATTAATAATT
*
516278 TTAAATAAAAAATATGTGATTTAAAT
1 TT-AATAAACAATATGTGATTTAAAT
516304 TATTAGTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
46 1 0.02
47 6 0.10
48 18 0.31
49 26 0.44
50 2 0.03
51 6 0.10
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (50 bp):
TTAATAAACAATATGTGATTTAAATCACATATAAAATACTATTAATAATT
Found at i:517439 original size:30 final size:30
Alignment explanation
Indices: 517405--517468 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
517395 TTAATTTAAA
* * *
517405 AATAGTTTATCGTTGTTATTGATGAAAACC
1 AATAGGTTATAGTTATTATTGATGAAAACC
* *
517435 AATAGGTTGTAGTTATTGTTGATGAAAACC
1 AATAGGTTATAGTTATTATTGATGAAAACC
517465 AATA
1 AATA
517469 AGTTGTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (30 bp):
AATAGGTTATAGTTATTATTGATGAAAACC
Found at i:517449 original size:27 final size:28
Alignment explanation
Indices: 517419--517475 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
517409 GTTTATCGTT
*
517419 GTTA-TTGATGAAAACCAATAGGTTGTA
1 GTTATTTGATGAAAACCAATAAGTTGTA
517446 GTTATTGTTGATGAAAACCAATAAGTTGTA
1 GTTA-T-TTGATGAAAACCAATAAGTTGTA
517476 ATAACTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
30 22 0.85
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (28 bp):
GTTATTTGATGAAAACCAATAAGTTGTA
Found at i:527780 original size:24 final size:24
Alignment explanation
Indices: 527753--527840 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
527743 ATTTCCGACT
*
527753 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATACATGATC
* *
527777 TGAATTCTGTTTTGATTTC-TGATC
1 TGAATTCTGTTCTGA-TACATGATC
* * *
527801 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATACATGATC
*
527825 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
527841 TTCTGATATC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.02
24 49 0.94
25 2 0.04
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATACATGATC
Found at i:527796 original size:12 final size:12
Alignment explanation
Indices: 527781--527845 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
527771 ATGACCTGAA
527781 TTCTGTTTTGAT
1 TTCTGTTTTGAT
* *
527793 TTCTGATCTGGA-
1 TTCTG-TTTTGAT
*
527805 TTCTGTTCTGAT
1 TTCTGTTTTGAT
* * * *
527817 ATATGTTCTGAA
1 TTCTGTTTTGAT
527829 TTCTGTTTTGAT
1 TTCTGTTTTGAT
527841 TTCTG
1 TTCTG
527846 ATATCTCCGT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 3 0.08
12 32 0.82
13 4 0.10
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.55
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:527844 original size:48 final size:49
Alignment explanation
Indices: 527738--527847 Score: 161
Period size: 48 Copynumber: 2.3 Consensus size: 49
527728 TAATATTTTA
*
527738 TTTTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACCTGAATTCTG
1 TTTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTCTG
* * **
527786 TTTTGATTTCTGATC-TGGATTCTGTTCTGATATATGTTCTGAATTCTG
1 TTTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTCTG
527834 TTTTGATTTCTGAT
1 TTTTGATTTCTGAT
527848 ATCTCCGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 55 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (49 bp):
TTTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTCTG
Found at i:528914 original size:19 final size:19
Alignment explanation
Indices: 528890--528929 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
528880 GATATTTTAG
528890 GACATCTTCAGTGTAAATT
1 GACATCTTCAGTGTAAATT
528909 GACATCTTCAGTGTAAATT
1 GACATCTTCAGTGTAAATT
528928 GA
1 GA
528930 AGACACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (19 bp):
GACATCTTCAGTGTAAATT
Found at i:530578 original size:36 final size:36
Alignment explanation
Indices: 530520--530662 Score: 236
Period size: 36 Copynumber: 4.0 Consensus size: 36
530510 ATTACATCCG
530520 CTTTAGC-TTAGGTAAAAGCTTAAACGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
*
530555 CTTTAGCTTTAGGTGAAAA-CTTAAACGGAATATGAA
1 CTTTAGCTTTAGGT-AAAAGCTTAAACGTAATATGAA
*
530591 CTTTAGCTTTAGGTAAAAGCTTAAATGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
*
530627 CTTTAGCTTTATGTAAAAGCTTAAACGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
530663 TAGTTCTTAT
Statistics
Matches: 100, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
35 11 0.11
36 85 0.85
37 4 0.04
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (36 bp):
CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
Found at i:534003 original size:15 final size:16
Alignment explanation
Indices: 533985--534014 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
533975 TTAATTTCAA
533985 AATTTTAT-AAAATAC
1 AATTTTATCAAAATAC
534000 AATTTTATCAAAATA
1 AATTTTATCAAAATA
534015 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTATCAAAATAC
Found at i:539156 original size:35 final size:35
Alignment explanation
Indices: 539116--539248 Score: 176
Period size: 35 Copynumber: 3.8 Consensus size: 35
539106 AGATGAACAT
* *
539116 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
* * * * *
539151 TTGAATCAAAAGTGCCGATGCTTCTTTTCATTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTC-AC
* *
539187 TTGAATCGAAAGTGTTGATGCTTTCTTCCATTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
539222 TTGAATCGAAAGTGTCGATGCTTCCTT
1 TTGAATCGAAAGTGTCGATGCTTCCTT
539249 TCGTCCTTCT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
35 53 0.65
36 28 0.35
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
Found at i:539234 original size:71 final size:71
Alignment explanation
Indices: 539116--539259 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
539106 AGATGAACAT
* *
539116 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCCGATGCTTCTTTTCA
1 TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
*
539181 TTCTTC
66 TCCTTC
* * * *
539187 TTGAATCGAAAGTGTTGATGCTTTCTTCCATTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
539252 TCCTTC
66 TCCTTC
539258 TT
1 TT
539260 ATTCACCTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
TCCTTC
Found at i:543242 original size:18 final size:17
Alignment explanation
Indices: 543211--543244 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
543201 TTTTAACTGC
*
543211 AAAAAAAAAGAAAACAG
1 AAAAAAAAAAAAAACAG
543228 AAAAAAGAAAAAAAACA
1 AAAAAA-AAAAAAAACA
543245 TGTGTTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAACAG
Found at i:543991 original size:14 final size:14
Alignment explanation
Indices: 543972--543999 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
543962 ACTTTGCACT
543972 ATGGTATCGATACC
1 ATGGTATCGATACC
543986 ATGGTATCGATACC
1 ATGGTATCGATACC
544000 CTTTCATGGT
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:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
ATGGTATCGATACC
Found at i:547329 original size:21 final size:21
Alignment explanation
Indices: 547303--547351 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
547293 GGTTACCGCA
547303 ATTGCGGCCATAGCGAGCGCT
1 ATTGCGGCCATAGCGAGCGCT
* * *
547324 ATTGCGACCATAGCGGGCTCT
1 ATTGCGGCCATAGCGAGCGCT
547345 ATTGCGG
1 ATTGCGG
547352 GTATATCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCATAGCGAGCGCT
Found at i:550636 original size:3 final size:3
Alignment explanation
Indices: 550621--550654 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
550611 CTTTTCCCCT
*
550621 TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
550655 CAGCACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:556296 original size:12 final size:12
Alignment explanation
Indices: 556279--556306 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
556269 TTGAAACTCG
556279 ATTTTGAGCTCA
1 ATTTTGAGCTCA
556291 ATTTTGAGCTCA
1 ATTTTGAGCTCA
556303 ATTT
1 ATTT
556307 AGGGCGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (12 bp):
ATTTTGAGCTCA
Found at i:558444 original size:30 final size:30
Alignment explanation
Indices: 558408--558474 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
558398 CAATACAGTC
* *
558408 CCCCAACATTTAGTTCATTTGCAATATGGT
1 CCCCAACATTTAGTTCATTTGCAATAAGAT
*
558438 CCCCAACATTTAGTTCGTTTGCAATAAGAT
1 CCCCAACATTTAGTTCATTTGCAATAAGAT
558468 CCCCAAC
1 CCCCAAC
558475 GTAACTGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (30 bp):
CCCCAACATTTAGTTCATTTGCAATAAGAT
Found at i:560426 original size:50 final size:50
Alignment explanation
Indices: 560348--560450 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
560338 ACAATGTTCA
*
560348 TTTTTCAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
1 TTTTTAAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
*
560398 TTTTTAAAAGAATTGCGAATATG-A-ATTTAGTTTTAATTTTAATTTCACAT
1 TTTTTAAAAGAATTGC-AA-ATGTAGATTTAGTTTTAATTTCAATTTCACAT
560448 TTT
1 TTT
560451 AAAAAAATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 43 0.88
51 3 0.06
52 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.49
Consensus pattern (50 bp):
TTTTTAAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
Found at i:561527 original size:32 final size:32
Alignment explanation
Indices: 561477--561548 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
561467 GTAAGAATTT
* * * * *
561477 TAAATTAAGTTTTTTTTTTCAATTTTCTTGAA
1 TAAATAAAGATTTATTTTTCAAATCTCTTGAA
*
561509 TAAATAAAGATTTATTTTTGAAATCTCTTGAA
1 TAAATAAAGATTTATTTTTCAAATCTCTTGAA
*
561541 TTAATAAA
1 TAAATAAA
561549 TAAATAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (32 bp):
TAAATAAAGATTTATTTTTCAAATCTCTTGAA
Found at i:581966 original size:20 final size:20
Alignment explanation
Indices: 581937--581979 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
581927 ATTCCACCAC
581937 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
581957 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
581977 ATG
1 ATG
581980 AGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:582435 original size:13 final size:13
Alignment explanation
Indices: 582417--582474 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
582407 AACATTGATT
582417 TATATAGATTTTA
1 TATATAGATTTTA
582430 TATATAGA-TTTA
1 TATATAGATTTTA
* *
582442 -ACATTGA--TT-
1 TATATAGATTTTA
582451 TATATAGATTTTA
1 TATATAGATTTTA
582464 TATATAGATTT
1 TATATAGATTT
582475 AACATTGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.19
11 5 0.14
12 6 0.16
13 19 0.51
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (13 bp):
TATATAGATTTTA
Found at i:582448 original size:34 final size:34
Alignment explanation
Indices: 582405--582488 Score: 168
Period size: 34 Copynumber: 2.5 Consensus size: 34
582395 TTAAAAGTCA
582405 TTAACATTGATTTATATAGATTTTATATATAGAT
1 TTAACATTGATTTATATAGATTTTATATATAGAT
582439 TTAACATTGATTTATATAGATTTTATATATAGAT
1 TTAACATTGATTTATATAGATTTTATATATAGAT
582473 TTAACATTGATTTATA
1 TTAACATTGATTTATA
582489 CAATATTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (34 bp):
TTAACATTGATTTATATAGATTTTATATATAGAT
Found at i:582484 original size:11 final size:11
Alignment explanation
Indices: 582413--582486 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
582403 CATTAACATT
582413 GATTT-ATATA
1 GATTTAATATA
582423 GATTTTATATATA
1 GA-TTTA-ATATA
* *
582436 GATTTAACATT
1 GATTTAATATA
582447 GATTT-ATATA
1 GATTTAATATA
582457 GATTTTATATATA
1 GA-TTTA-ATATA
* *
582470 GATTTAACATT
1 GATTTAATATA
582481 GATTTA
1 GATTTA
582487 TACAATATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.13
11 23 0.44
12 8 0.15
13 14 0.27
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (11 bp):
GATTTAATATA
Done.