Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 2 of 167
Found at i:287068 original size:420 final size:417
Alignment explanation
Indices: 286281--287500 Score: 1467
Period size: 420 Copynumber: 2.9 Consensus size: 417
286271 CAACGGATAC
* *
286281 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATCGAACTTAAATTAGGACAACATTTTAGAT
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
* * * *
286346 CTAATTCTTTAAGAAAAGTGGAGGTAGATAATCCGTCTCCAATCTTACTTAACTTTTT-GCAATC
66 CTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAA-TTTTTCGCAACC
* * *
286410 GAAAATGC-TAAG-TTTTATAAGAGATGAACATCCTCCGGTAATCGGAAGAACTTCCAA-TTCGC
130 G-AAAT-CTTAAGCTTTT-CAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTC-T
* * * * ** * *
286472 TGCACCATCT-AATTGACAGATTTTGAAGAGACGAAAATCCTTTC-AATTCCGGAATTAAAATCA
191 TGCAGC-TCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATT-TGGAATCGAACTTA
* * * * *
286535 AGTTAGGACAATTAC-ATAGTCGTAATTTTTTGAGACAAGTAGAGGTTGACAGCCCGTCTCCAAT
254 A-TTAGGACAA-TCCGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAAT
*
286599 CTTGCTTAATTTTTCGCAAACGATAATGCTAAGCTCTTCAAGAGATGAACATTCTCCCGTTATCG
317 CTTGCTTAATTTTTCGCAAACGA-AATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTATCG
* * ** *
286664 GAAGAACTTCCAATTTTTTGCACCTCTCAATTGACAG
381 GAAGAACTCCCAAATCCTTGCACCTCTAAATTGACAG
* * * * *
286701 ATTTTGAAGAGAGGAAAATCTTTTCAAGTTAGGAATAGAACTTAAATTAGGACAATATTTTAGAT
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
*
286766 CTAATT-TTCTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTTTCGCAACC
66 CTAATTCTT-TGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACC
* * * *
286830 AGAAATCTTAAGCTTTTGAAGAGATGAACATCCTCCGGTTATTGGAAGAACTCCCAATTTTTTGC
130 -GAAATCTTAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTGC
* * *
286895 AGCTCTCAATTGACAGATATTGAAGAGAGGAAAAGCCTTCCAAATTTGGAATGGAACTTACATTA
194 AGCTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTTA-ATTA
286960 GGACAATCCGATAGACCG-AATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGC
258 GGACAATCCGATAG-CCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGC
* * * *
287024 TTAATTTTTCGCAACCGGAAATCCTAAGCTTTTCAAGGGATGAACATCCT-CCGATTATCGGAAG
322 TTAATTTTTCGCAAAC-GAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCG-TTATCGGAAG
*
287088 AACTCCCAAATCCTTGCACCTGTAAATTGACAG
385 AACTCCCAAATCCTTGCACCTCTAAATTGACAG
* * **
287121 ATTTTGAAGAGACGATAATCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATCA-AATAGA
1 ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAAT-ATTTTAGA
* * * ** *
287185 CCTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTCTCCGATCTTGCTTAATTTTTCGCAACC
65 TCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACC
* *
287250 GGATAT-TCTAAGCTTTTCAAGAGATGAACATCCTCCGATAATCGGAAGAACTCCCAATTTCTTG
130 -GAAATCT-TAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTG
* * *
287314 CAGTTCTCAATTGACAAATTTTGAAGAGAGGAAAATCCTTCTAAATTTGGAATCGAACTTAAATT
193 CAGCTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTT-AATT
* * ** * * ** * *
287379 AGGACAAGCATG-TAGGTGTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTTTCCAATCTTA
257 AGGACAATC-CGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTG
* * * * *
287443 CTTAATTTTTCACAAAATGAAATGCTAAGCTTTTCAAGAGAAGAGCATTGTCCCGTTA
321 CTTAATTTTTCGC-AAACGAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTA
287501 GTGGAACACT
Statistics
Matches: 687, Mismatches: 92, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
419 18 0.03
420 643 0.94
421 26 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (417 bp):
ATTTTGAAGAGACGAAAATCCTTCCAAATTTGGAATAGAACTTAAATTAGGACAATATTTTAGAT
CTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACCG
AAATCTTAAGCTTTTCAAGAGATGAACATCCTCCGGTAATCGGAAGAACTCCCAATTTCTTGCAG
CTCTCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTTAATTAGGA
CAATCCGATAGCCGTAATTCTTTGAGACAAGTGGAGGTTGACAGCCCGTATCCAATCTTGCTTAA
TTTTTCGCAAACGAAATGCTAAGCTTTTCAAGAGATGAACATTCTCCCGTTATCGGAAGAACTCC
CAAATCCTTGCACCTCTAAATTGACAG
Found at i:288302 original size:15 final size:15
Alignment explanation
Indices: 288282--288312 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
288272 AAAACAATAT
288282 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
288297 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
288312 A
1 A
288313 CTTACATGAC
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:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:291684 original size:15 final size:15
Alignment explanation
Indices: 291674--291703 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
291664 TCCCTTCTTG
291674 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
291689 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
291704 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:292471 original size:17 final size:18
Alignment explanation
Indices: 292445--292483 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
292435 CAAATTGTGG
292445 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
292461 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
292479 AAAAT
1 AAAAT
292484 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:292660 original size:15 final size:15
Alignment explanation
Indices: 292640--292670 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
292630 AAAACAATAT
292640 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
292655 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
292670 A
1 A
292671 CTTACATGAC
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:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:295156 original size:20 final size:20
Alignment explanation
Indices: 295133--295170 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
295123 TTATTTTTAC
295133 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
295153 ATATATTAATAAATTTAT
1 ATATATTAATAAATTTAT
295171 TGCAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:297646 original size:6 final size:6
Alignment explanation
Indices: 297632--297686 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
297622 GATGGGTGAG
* *
297632 GGGGAA GGAGAA GGAGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
297680 GGGGAA G
1 GGGGAA G
297687 AAGCTTCAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:298130 original size:17 final size:17
Alignment explanation
Indices: 298110--298165 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
298100 TTTATAATTA
298110 TAAAAAATTTTAAAAAT
1 TAAAAAATTTTAAAAAT
298127 TAAAAAGATTTT-AAAAT
1 TAAAAA-ATTTTAAAAAT
*
298144 TCAAAAAGAATTATAAAAAT
1 T--AAAA-AATTTTAAAAAT
298164 TA
1 TA
298166 TATAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 8 0.24
20 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAT
Found at i:298132 original size:18 final size:18
Alignment explanation
Indices: 298105--298165 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
298095 AATAATTTAT
298105 AATTATAAAAAATTTTAAA
1 AATTA-AAAAAATTTTAAA
*
298124 AATTAAAAAGATTTT-AA
1 AATTAAAAAAATTTTAAA
*
298141 AATTCAAAAAGAATTATAAA
1 AATT-AAAAA-AATTTTAAA
298161 AATTA
1 AATTA
298166 TATAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.17
18 14 0.39
19 10 0.28
20 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTAAAAAAATTTTAAA
Found at i:298502 original size:24 final size:23
Alignment explanation
Indices: 298449--298504 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
298439 GTAAGCGAAT
298449 AAAGGAATAAGAAAGACAAATAG
1 AAAGGAATAAGAAAGACAAATAG
298472 AAA-GAATAATGTAAAAGA-AAATA-
1 AAAGGAATAA-G--AAAGACAAATAG
298495 AAAGGAATAA
1 AAAGGAATAA
298505 AAAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.21
23 7 0.24
24 11 0.38
25 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAGGAATAAGAAAGACAAATAG
Found at i:299032 original size:29 final size:29
Alignment explanation
Indices: 299000--299058 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
298990 CGATTTTGGG
299000 TGATCATTTGATTTTAATAGTGAATTTTA
1 TGATCATTTGATTTTAATAGTGAATTTTA
299029 TGATCATTTGATTTTAATAGTGAATTTTA
1 TGATCATTTGATTTTAATAGTGAATTTTA
299058 T
1 T
299059 ACTCTTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGATCATTTGATTTTAATAGTGAATTTTA
Found at i:303736 original size:11 final size:11
Alignment explanation
Indices: 303720--303755 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
303710 NNAAAAAAAA
303720 GAAGAGAGAGG
1 GAAGAGAGAGG
*
303731 GAAGAGAGAAG
1 GAAGAGAGAGG
303742 GAAGAGAGAAGG
1 GAAGAGAG-AGG
303754 GA
1 GA
303756 GGGGGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:303913 original size:16 final size:17
Alignment explanation
Indices: 303892--303929 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
303882 AGGTAAAAAA
* *
303892 TTTATTTTTTGT-TTTT
1 TTTATTTGTTGTATATT
303908 TTTATTTGTTGTATATT
1 TTTATTTGTTGTATATT
303925 TTTAT
1 TTTAT
303930 GTTAAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTATTTGTTGTATATT
Found at i:304498 original size:21 final size:21
Alignment explanation
Indices: 304473--304528 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
304463 TTGAAAGTTT
304473 ATAATATTT-AAATATTAAAAA
1 ATAATATTTAAAAT-TTAAAAA
304494 ATAATATTTAAAATTTAAAAA
1 ATAATATTTAAAATTTAAAAA
304515 AGTAAT-TTTAAAAT
1 A-TAATATTTAAAAT
304529 ATATATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATATTTAAAATTTAAAAA
Found at i:304594 original size:21 final size:22
Alignment explanation
Indices: 304570--304611 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
304560 TTAAAATTTT
*
304570 TAAAATTAATA-ATAAATAAAA
1 TAAAATAAATAGATAAATAAAA
304591 TAAAATAAATAGATAAATAAA
1 TAAAATAAATAGATAAATAAA
304612 GAGAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
TAAAATAAATAGATAAATAAAA
Found at i:304606 original size:18 final size:18
Alignment explanation
Indices: 304580--304636 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
304570 TAAAATTAAT
*
304580 AATAAATAAAATAAAATA
1 AATAGATAAAATAAAATA
*
304598 AATAGAT-AAATAAAGAGA
1 AATAGATAAAATAAA-ATA
* *
304616 AAAAGATAAAAGAAAAGTA
1 AATAGATAAAATAAAA-TA
304635 AA
1 AA
304637 AAAAAGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.23
18 15 0.48
19 9 0.29
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AATAGATAAAATAAAATA
Found at i:304643 original size:10 final size:10
Alignment explanation
Indices: 304615--304659 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
304605 AAATAAAGAG
304615 AAAAAGATAAA
1 AAAAAG-TAAA
304626 AGAAAAGTAAA
1 A-AAAAGTAAA
304637 AAAAAGT--A
1 AAAAAGTAAA
304645 AAAAAGTAAA
1 AAAAAGTAAA
304655 AAAAA
1 AAAAA
304660 AAGTACTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
10 12 0.39
11 6 0.19
12 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (10 bp):
AAAAAGTAAA
Found at i:310105 original size:51 final size:51
Alignment explanation
Indices: 310034--310153 Score: 213
Period size: 51 Copynumber: 2.4 Consensus size: 51
310024 CTGATCACAT
310034 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
310085 TTATCACTTATTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* *
310136 TTGTCACTTGTCACTGAT
1 TTATCACTTGTTACTGAT
310154 AAACATGTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:310183 original size:24 final size:24
Alignment explanation
Indices: 310155--310202 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
310145 GTCACTGATA
310155 AACATGTCAAATTGCATATTTTTT
1 AACATGTCAAATTGCATATTTTTT
*
310179 AACATGTCAACTTGCATATTTTTT
1 AACATGTCAAATTGCATATTTTTT
310203 GTGCTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (24 bp):
AACATGTCAAATTGCATATTTTTT
Found at i:310725 original size:61 final size:61
Alignment explanation
Indices: 310654--310774 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
310644 TTTTCCTATC
310654 CATTTCCACTACCTTTTTCATATAATTTCTATCATTTCCATAACCTTCAAGCATGATTAAT
1 CATTTCCACTACCTTTTTCATATAATTTCTATCATTTCCATAACCTTCAAGCATGATTAAT
*
310715 CATTTTCACTACCTTTTTCATATAATTTCTATCATTTCCATAACCTTCAAGCATGATTAA
1 CATTTCCACTACCTTTTTCATATAATTTCTATCATTTCCATAACCTTCAAGCATGATTAA
310775 ATTCATGCCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (61 bp):
CATTTCCACTACCTTTTTCATATAATTTCTATCATTTCCATAACCTTCAAGCATGATTAAT
Found at i:310761 original size:32 final size:32
Alignment explanation
Indices: 310649--310754 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
310639 GCAATTTTTC
310649 CTATCCATTTCCACTACCTTTTTCATATAATTT
1 CTAT-CATTTCCACTACCTTTTTCATATAATTT
**
310682 CTATCATTTCCA-TAACC---TTCA-AGCATGATT
1 CTATCATTTCCACT-ACCTTTTTCATATAAT--TT
* *
310712 -AATCATTTTCACTACCTTTTTCATATAATTT
1 CTATCATTTCCACTACCTTTTTCATATAATTT
310743 CTATCATTTCCA
1 CTATCATTTCCA
310755 TAACCTTCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
28 3 0.05
29 16 0.29
30 3 0.05
31 3 0.05
32 24 0.43
33 7 0.12
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (32 bp):
CTATCATTTCCACTACCTTTTTCATATAATTT
Found at i:311628 original size:79 final size:79
Alignment explanation
Indices: 311497--311655 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
311487 TAATTCCAGT
311497 CTCTGTGGGATCGACCCTACTCCCTATACTGCTTTAATTTGCAAACTAGGTGTAGGTTTATATTG
1 CTCTGTGGGATCGACCCTACTCCCTATACTGCTTTAATTTGCAAACTAGGTGTAGGTTTATATTG
*
311562 GTGGAATCGACAGC
66 GTGGAATCAACAGC
311576 CTCTGTGGGATCGACCCTACTCCCTATACTGCTTTAATTTGCAAACTAGGTGTAGGTTTATATTG
1 CTCTGTGGGATCGACCCTACTCCCTATACTGCTTTAATTTGCAAACTAGGTGTAGGTTTATATTG
311641 GTGGAATCAACAGC
66 GTGGAATCAACAGC
311655 C
1 C
311656 ATCAGTCACT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (79 bp):
CTCTGTGGGATCGACCCTACTCCCTATACTGCTTTAATTTGCAAACTAGGTGTAGGTTTATATTG
GTGGAATCAACAGC
Found at i:315671 original size:50 final size:50
Alignment explanation
Indices: 315547--315795 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
315537 GATAATAACA
* * ** * *
315547 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
315598 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
315648 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
315698 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
315753 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
315796 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:315725 original size:100 final size:104
Alignment explanation
Indices: 315546--315795 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
315536 TGATAATAAC
**
315546 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
315611 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
315648 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
315711 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
315753 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
315796 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:315911 original size:13 final size:13
Alignment explanation
Indices: 315890--315921 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
315880 GCTTGGATCA
*
315890 TCATCAAATAAAT
1 TCATAAAATAAAT
315903 TCATAAAATAAAT
1 TCATAAAATAAAT
315916 TCATAA
1 TCATAA
315922 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:316169 original size:30 final size:30
Alignment explanation
Indices: 316133--316190 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
316123 CCTCGACTCT
*
316133 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
316163 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
316191 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:319734 original size:17 final size:17
Alignment explanation
Indices: 319704--319744 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
319694 TTAGGTTGAT
* *
319704 TAATTGAAATTTCTTTC
1 TAATTAAAACTTCTTTC
319721 TAATTAAAACTTCTTTC
1 TAATTAAAACTTCTTTC
319738 TAATTAA
1 TAATTAA
319745 CTCAATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATTAAAACTTCTTTC
Found at i:320534 original size:28 final size:28
Alignment explanation
Indices: 320502--320556 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
320492 AGAAATCAGT
320502 CAGATACAGTCTGGGCCTGAGCCCATTA
1 CAGATACAGTCTGGGCCTGAGCCCATTA
* * *
320530 CAGATTCAGTTTGGGCCTTAGCCCATT
1 CAGATACAGTCTGGGCCTGAGCCCATT
320557 TGGATACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (28 bp):
CAGATACAGTCTGGGCCTGAGCCCATTA
Found at i:322924 original size:19 final size:20
Alignment explanation
Indices: 322872--322931 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
322862 AAAAAAAACC
*
322872 TTAAAAATTGTAAAAAAGAATAT
1 TTAAAAATT-TACAAAA-AA-AT
322895 TTAAAAA-TTACAAAAAAA-
1 TTAAAAATTTACAAAAAAAT
322913 TTAAAAATTTACAAAAAAA
1 TTAAAAATTTACAAAAAAA
322932 ATATAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
20 2 0.06
21 6 0.17
22 1 0.03
23 7 0.20
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (20 bp):
TTAAAAATTTACAAAAAAAT
Found at i:323015 original size:9 final size:8
Alignment explanation
Indices: 322969--323015 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
322959 AATATTTAAA
*
322969 AAAATATT
1 AAAATTTT
322977 AGAAATTTT
1 A-AAATTTT
*
322986 AAATTTTT
1 AAAATTTT
322994 AAAATTTT
1 AAAATTTT
323002 AAAATTTT
1 AAAATTTT
323010 ATAAAT
1 A-AAAT
323016 CACATCTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 23 0.68
9 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
AAAATTTT
Found at i:327790 original size:91 final size:91
Alignment explanation
Indices: 327630--327810 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 91
327620 GTGAAGCTTT
* *
327630 TTGATAGTTTCTTGAACACATCAATCTCTGAAAACAACGAGTATAATTTCGGAGCAACCGCTGTT
1 TTGATAGTTTCTTGAACACATCAATCTCTGAAAACAACGAGTATAATTTCGGAGCAACCGCCGTA
327695 AAAATTTCTGGTAATGATTCCCCATC
66 AAAATTTCTGGTAATGATTCCCCATC
327721 TTGATAGTTTCTTGAACACATCAATCTCTGAAAACAACGAGTATAATTTCGGAGCAACCGCCGTA
1 TTGATAGTTTCTTGAACACATCAATCTCTGAAAACAACGAGTATAATTTCGGAGCAACCGCCGTA
327786 AAAATTTCTGGTAATGATTCCCCAT
66 AAAATTTCTGGTAATGATTCCCCAT
327811 TACACCCAAC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (91 bp):
TTGATAGTTTCTTGAACACATCAATCTCTGAAAACAACGAGTATAATTTCGGAGCAACCGCCGTA
AAAATTTCTGGTAATGATTCCCCATC
Found at i:330403 original size:19 final size:20
Alignment explanation
Indices: 330374--330417 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
330364 ATAGATTGAA
330374 ATTCTCCAAAAATAAAATTT
1 ATTCTCCAAAAATAAAATTT
330394 ATTC-CCAAAAATAAAATTT
1 ATTCTCCAAAAATAAAATTT
330413 ATTCT
1 ATTCT
330418 ATGTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTCTCCAAAAATAAAATTT
Found at i:335657 original size:49 final size:49
Alignment explanation
Indices: 335585--335678 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
335575 TGCTATGCAA
* *
335585 TGCTAAACTTGGTCTTTCACTGTCTACACTCTTATCACTGTTTATACAT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
335634 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
335679 CCCTTCTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.43
Consensus pattern (49 bp):
TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
Found at i:341766 original size:5 final size:6
Alignment explanation
Indices: 341749--341774 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
341739 TTAATCATTA
341749 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
341775 GAAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:343065 original size:23 final size:23
Alignment explanation
Indices: 343039--343084 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
343029 TACAGGTGAG
343039 GAAGTTAGTGCCAAAGACTATAA
1 GAAGTTAGTGCCAAAGACTATAA
343062 GAAGTTAGTGCCAAAGACTATAA
1 GAAGTTAGTGCCAAAGACTATAA
343085 AGTCTACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (23 bp):
GAAGTTAGTGCCAAAGACTATAA
Found at i:343389 original size:192 final size:192
Alignment explanation
Indices: 343062--343496 Score: 735
Period size: 192 Copynumber: 2.3 Consensus size: 192
343052 AAGACTATAA
*
343062 GAAGTTAGTGCCAAAGACTATAAAGTCTACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
* * * *
343127 CATGGTCAACAATGGCGGGTTTTACGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
66 AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
* * *
343192 TCACACTTTCATTTGTAGGTTACGGTGATGGACTTATATTTTTTGAGCAAAATACAGATGAG
131 TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
* *
343254 GAAGTTAGTGCCAAAGACTACAAAGTCCACTCAATTTGGGGCAACTAGTGCTATCTTAAATAAAG
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
*
343319 AATGGTCAACAATGGTAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
66 AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
* * * *
343384 TCACACTTTCATTTGTAGGTGATGGTGATGGACTTACGGTTTTTGAGCAAGATATAGATGAG
131 TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
343446 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGC
1 GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGC
343497 ATTTCACATT
Statistics
Matches: 226, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
192 226 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (192 bp):
GAAGTTAGTGCCAAAGACTATAAAGTCCACTCAATTTGGGGCCACTAGTGCTATCTTAAATAAAG
AATGGTCAACAATGGCAGGTTTCAAGCTTCATTGATTTCACATTAATCCCAAAAGATTCCTTTTA
TCACACTTTCATTTGTAGGTGACGGTGATGGACTTACAGTTTTTGAGCAAAATACAGATGAG
Found at i:344814 original size:22 final size:22
Alignment explanation
Indices: 344786--344847 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
344776 CCTTTGTTGG
344786 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
344808 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
*
344830 CCA-CCACCCTTGGCCACC
1 CCACCCA-CCTTAGCCACC
344848 TAAACCACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 3 0.08
22 35 0.92
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.13
Consensus pattern (22 bp):
CCACCCACCTTAGCCACCAACT
Found at i:344987 original size:21 final size:22
Alignment explanation
Indices: 344952--344993 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
344942 TTGTTCTTTG
344952 TTTTGGAGGAGGTTTTTTTGTT
1 TTTTGGAGGAGGTTTTTTTGTT
*
344974 TTTTGGAGG-TGTTTTTTTGT
1 TTTTGGAGGAGGTTTTTTTGT
344994 AAAAAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.07, C:0.00, G:0.31, T:0.62
Consensus pattern (22 bp):
TTTTGGAGGAGGTTTTTTTGTT
Found at i:345337 original size:3 final size:3
Alignment explanation
Indices: 345323--345405 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
345313 GAGCTTTGTT
* *
345323 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
345367 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
345406 ATATGCCCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 12 0.18
3 45 0.69
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:345644 original size:18 final size:19
Alignment explanation
Indices: 345608--345664 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
345598 ACTATTACTA
*
345608 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
345628 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
345645 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
345663 TT
1 TT
345665 TATTGATCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:359183 original size:44 final size:44
Alignment explanation
Indices: 359091--359319 Score: 174
Period size: 44 Copynumber: 5.1 Consensus size: 44
359081 NNNNNNNNAT
* * * *
359091 GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAA
1 GCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCGAAGATA
* * *
359136 GCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 GCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCGAAGATA
* * * ** * *
359180 GCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGAT-
1 GCAGATCTTGTCTTCCTATATTG-GCGCGAAGTAGATCGAAGATA
* * * * * *
359223 GCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATT
1 GCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCGAAGATA
* * * * *
359268 GCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATG
1 GCAGATCTTGTCTTCCTATA-TTGGC-GCGAAGTAGATCGAAGATA
359314 GCAGAT
1 GCAGAT
359320 TTTACCTCCC
Statistics
Matches: 142, Mismatches: 36, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
43 19 0.13
44 61 0.43
45 39 0.27
46 23 0.16
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
GCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCGAAGATA
Found at i:359283 original size:88 final size:89
Alignment explanation
Indices: 359090--359289 Score: 208
Period size: 88 Copynumber: 2.3 Consensus size: 89
359080 NNNNNNNNNA
* * * **
359090 TGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGT
1 TGCAGATCTTGTCTTCCTATATTGATAGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCACAT
*
359155 ATTGGCGTGAAGTAGATCGAAGAT
66 ACTGGCGTGAAGTAGATCGAAGAT
* * * * * * *
359179 AGCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATC-CA-AGATGCAGATCTTGTCTTCCCA
1 TGCAGATCTTGTCTTCCTATATTGATAGCGAAGTAGATCGCAGA-AAGCAGATCTTGTCTTCACA
* *
359241 TACTGGTGGTGAAGTAGATTGAAGAT
65 TACTGG-CGTGAAGTAGATCGAAGAT
* *
359267 TGCAGATCTTGCCTTCCTGTATT
1 TGCAGATCTTGTCTTCCTATATT
359290 TGGCAGCGAA
Statistics
Matches: 88, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
86 1 0.01
87 23 0.26
88 43 0.49
89 21 0.24
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (89 bp):
TGCAGATCTTGTCTTCCTATATTGATAGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCACAT
ACTGGCGTGAAGTAGATCGAAGAT
Found at i:359401 original size:134 final size:135
Alignment explanation
Indices: 359255--359559 Score: 540
Period size: 136 Copynumber: 2.3 Consensus size: 135
359245 GGTGGTGAAG
*
359255 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
359320 TTTACCTCCC-TGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
66 TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
359384 TGGAA
131 TGGAA
*
359389 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
* *
359454 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCC-GTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
359519 GTGGAA
130 GTGGAA
* *
359525 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
359560 GGTAGGAAGT
Statistics
Matches: 163, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 73 0.45
136 90 0.55
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (135 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
TGGAA
Found at i:359745 original size:43 final size:40
Alignment explanation
Indices: 359698--359868 Score: 137
Period size: 40 Copynumber: 4.2 Consensus size: 40
359688 CTTGGGCAAC
*
359698 AGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCG--CATTA-AATCTTATCTCCCTAAGCAGT
* *
359741 AGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
** *** ** * *
359781 AGTGGAGCAGATAAAACCACAGATCTTATTTCCCTAAGCAAT
1 AGTGGAATAGATCGCATTA-A-ATCTTATCTCCCTAAGCAGT
* * * *
359823 AGT-GAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGT
1 AGTGGAA-TAGATCGCATTAAATCTTATCTCCCTAAGCAGT
359863 AGTGGA
1 AGTGGA
359869 GCAGACTAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
40 52 0.50
41 10 0.10
42 28 0.27
43 13 0.13
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
Found at i:359774 original size:40 final size:40
Alignment explanation
Indices: 359722--359873 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
359712 AAGATTACAA
* *
359722 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*** *
359762 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * *
359803 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
359844 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
359874 CTAAAAACAC
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:359816 original size:82 final size:83
Alignment explanation
Indices: 359720--359889 Score: 261
Period size: 82 Copynumber: 2.1 Consensus size: 83
359710 CGAAGATTAC
* * * *
359720 AATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
*
359785 GAGCAGA-TAAAACCACA
66 GAGCAGACTAAAAACACA
* * *
359802 GATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
359867 GAGCAGACTAAAAACACA
66 GAGCAGACTAAAAACACA
359885 AATCT
1 AATCT
359890 CATCCCCATG
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (83 bp):
AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
GAGCAGACTAAAAACACA
Found at i:359826 original size:42 final size:42
Alignment explanation
Indices: 359721--359889 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 42
359711 GAAGATTACA
* *** **
359721 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTA-AG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
*
359762 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
* * * *** *
359803 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCA-AG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
* *
359844 -TCTTATCTCCCTAAGTAGTAGTGGAGCAGACTAAAAACACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-TAAAAACACAG
359886 ATCT
1 ATCT
359890 CATCCCCATG
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
40 58 0.57
41 8 0.08
42 32 0.32
43 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
Found at i:360440 original size:18 final size:18
Alignment explanation
Indices: 360417--360485 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
360407 GCATTTTTAC
360417 TATTATTTATATTATTAT
1 TATTATTTATATTATTAT
*
360435 TATTATTTCTCATGTATATAT
1 TATTATTTAT-AT-TAT-TAT
*
360456 TATTTTTTATATTATTAT
1 TATTATTTATATTATTAT
360474 TA-TATTATATAT
1 TATTATT-TATAT
360486 GCCCTCTCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.07
18 19 0.44
19 5 0.12
20 5 0.12
21 11 0.26
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTATTTATATTATTAT
Found at i:360723 original size:18 final size:19
Alignment explanation
Indices: 360687--360743 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
360677 ACTATTACTA
*
360687 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
360707 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
360724 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
360742 TT
1 TT
360744 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:360845 original size:12 final size:12
Alignment explanation
Indices: 360828--360857 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
360818 GTATTTCTAT
360828 TATATACATATA
1 TATATACATATA
*
360840 TATATACATTTA
1 TATATACATATA
360852 TATATA
1 TATATA
360858 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:364513 original size:29 final size:28
Alignment explanation
Indices: 364473--364543 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
364463 AAGCCGCTAT
*
364473 TTTACACAAATAATATA-AAAAATTAATTA
1 TTTACAAAAATAAT-TAGAAAAA-TAATTA
* * *
364502 TTTATAAAAATAGGTTAGAGAAATAATTA
1 TTTACAAAAATA-ATTAGAAAAATAATTA
364531 TTTACAAAAATAA
1 TTTACAAAAATAA
364544 GTTGTTTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (28 bp):
TTTACAAAAATAATTAGAAAAATAATTA
Found at i:366033 original size:13 final size:13
Alignment explanation
Indices: 366015--366041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
366005 TAACTAAACA
366015 ACCTTGCTGTTAC
1 ACCTTGCTGTTAC
366028 ACCTTGCTGTTAC
1 ACCTTGCTGTTAC
366041 A
1 A
366042 GCAAGCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.37
Consensus pattern (13 bp):
ACCTTGCTGTTAC
Found at i:387168 original size:15 final size:15
Alignment explanation
Indices: 387150--387179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
387140 TAAATTTCAG
387150 TTAATTCAATTAATC
1 TTAATTCAATTAATC
*
387165 TTAATTGAATTAATC
1 TTAATTCAATTAATC
387180 GAAATATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATTCAATTAATC
Found at i:394333 original size:30 final size:30
Alignment explanation
Indices: 394286--394342 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
394276 CATCAAATTA
394286 AAACTTATATATCAAATTACATATTTAACT
1 AAACTTATATATCAAATTACATATTTAACT
*
394316 AAACTTCATATAT-AAATTTCATATTTA
1 AAACTT-ATATATCAAATTACATATTTA
394343 TCCCTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (30 bp):
AAACTTATATATCAAATTACATATTTAACT
Found at i:394411 original size:12 final size:12
Alignment explanation
Indices: 394394--394418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
394384 GAAATCACCC
394394 ATCATTTAATTA
1 ATCATTTAATTA
394406 ATCATTTAATTA
1 ATCATTTAATTA
394418 A
1 A
394419 AGCTTCTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
ATCATTTAATTA
Found at i:395542 original size:23 final size:24
Alignment explanation
Indices: 395516--395566 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
395506 ATGATTTAGG
395516 AAATTATAATTTTATTTC-ATCAA
1 AAATTATAATTTTATTTCAATCAA
395539 AAA-TATAATTTTATTTCAATCAA
1 AAATTATAATTTTATTTCAATCAA
*
395562 TAATT
1 AAATT
395567 TTAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 10 0.40
24 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTATAATTTTATTTCAATCAA
Found at i:396756 original size:17 final size:16
Alignment explanation
Indices: 396730--396760 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
396720 CAATTAATTT
396730 ATTTTTAAAAATTAAG
1 ATTTTTAAAAATTAAG
396746 ATTTTTAAAAATTAA
1 ATTTTTAAAAATTAA
396761 AAAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTTTAAAAATTAAG
Found at i:398192 original size:17 final size:17
Alignment explanation
Indices: 398165--398205 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
398155 ACTTTTTTAA
398165 TAAAAAT-AATA-AATAT
1 TAAAAATAAATATAA-AT
398181 TAAAAATAAATATAAAT
1 TAAAAATAAATATAAAT
*
398198 TACAAATA
1 TAAAAATA
398206 TACATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 13 0.59
18 2 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATAAATATAAAT
Found at i:408239 original size:23 final size:23
Alignment explanation
Indices: 408210--408256 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
408200 ACAAGCTTGA
408210 TGAGAGATTATTTCCCATACATT
1 TGAGAGATTATTTCCCATACATT
*
408233 TGAGAGATTATTTCCCATATATT
1 TGAGAGATTATTTCCCATACATT
408256 T
1 T
408257 TTACCTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (23 bp):
TGAGAGATTATTTCCCATACATT
Found at i:410227 original size:50 final size:50
Alignment explanation
Indices: 410152--410251 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
410142 AAGCTTGCAA
*
410152 CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAATGATATTTGTCTT
1 CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
410202 CACCATTGATAGATTAA-TCACTTTTGTTTAAAATTAACGATATTTGTCTT
1 CACCATTGATAGA-TAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
410252 ACATTCATAC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 45 0.94
51 3 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (50 bp):
CACCATTGATAGATAAGTCACTTTTGTTTAAAATTAACGATATTTGTCTT
Found at i:415526 original size:23 final size:24
Alignment explanation
Indices: 415472--415520 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
415462 GTAAGAAAAA
415472 AACACTTTAGCCATTTTTATAGAT
1 AACACTTTAGCCATTTTTATAGAT
415496 AACACTTTAGCCATTTTTATAGAT
1 AACACTTTAGCCATTTTTATAGAT
415520 A
1 A
415521 CCCTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (24 bp):
AACACTTTAGCCATTTTTATAGAT
Found at i:426133 original size:132 final size:132
Alignment explanation
Indices: 425997--426248 Score: 294
Period size: 131 Copynumber: 1.9 Consensus size: 132
425987 TTGAACATCA
* * *
425997 CCTTCGTTTTAAAGTGTTTTCTTA-AAAACATGAGTAAAAACCTAAAGGAATATTCGAATGTTTT
1 CCTTCGTTTTAAAG-GATTT-TTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTT
* * *
426061 GACCAAACGAGAAGTCACAACCCAACACGA-TAGGGCATGATTCC-CGAATTGTCAAACACAAAG
64 GACCAAACGAGAAATCACAACCCAACAC-ATTAGGGCACGATTCCGCGAATTGCCAAACACAAAG
426124 TATTG
128 TATTG
* * *** * * *
426129 CCTTCGTTTTAAAGGATTTTTAGAAGACACGAGTGAAATTTTGAAGGGATATTCGATTATTTTGA
1 CCTTCGTTTTAAAGGATTTTTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTTGA
* * **
426194 GCAAACGCGAAATTGCAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAA
66 CCAAACGAGAAATCACAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAA
426249 TATCGAATCT
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.04
131 70 0.71
132 25 0.25
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (132 bp):
CCTTCGTTTTAAAGGATTTTTAGAAAACACGAGTAAAAACCTAAAGGAATATTCGAATATTTTGA
CCAAACGAGAAATCACAACCCAACACATTAGGGCACGATTCCGCGAATTGCCAAACACAAAGTAT
TG
Found at i:426281 original size:131 final size:131
Alignment explanation
Indices: 426041--426281 Score: 290
Period size: 131 Copynumber: 1.8 Consensus size: 131
426031 TAAAAACCTA
* * *
426041 AAGGAATATTCGAATGTTTTGACCAAACGAGAAGTCACAACCCAACACGATAGGGCATGATTCCC
1 AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGATAGGGCACGATTCCC
* * *
426106 GAATTGTCAAACACAAAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAGACACGAGTGAAATTTT
66 GAATTGCCAAACACAAAGTATCGCCTTCGTTTTAAAGGAATTTTAGAAGACACGAGTGAAATTTT
426171 G
131 G
* * * * **
426172 AAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACAC-ATTAGGGCACGATTCC
1 AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGA-TAGGGCACGATTCC
* * * *
426236 GCGAATTGCCAAATATCGAA-TCTCGTCTTCGTTTTAAA-GAATTTTA
65 -CGAATTGCCAAACA-CAAAGTATCGCCTTCGTTTTAAAGGAATTTTA
426282 AAAAATTGTG
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
130 1 0.01
131 60 0.66
132 27 0.30
133 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (131 bp):
AAGGAATATTCGAATATTTTGACCAAACGAGAAATCACAACCCAACACGATAGGGCACGATTCCC
GAATTGCCAAACACAAAGTATCGCCTTCGTTTTAAAGGAATTTTAGAAGACACGAGTGAAATTTT
G
Found at i:427313 original size:28 final size:28
Alignment explanation
Indices: 427273--427328 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
427263 AGAGTACATA
427273 TATACACATATAGAAGAGCACTTTAAAC
1 TATACACATATAGAAGAGCACTTTAAAC
427301 TATACACATATAGAAGAGCACTTTAAAC
1 TATACACATATAGAAGAGCACTTTAAAC
427329 AGACAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (28 bp):
TATACACATATAGAAGAGCACTTTAAAC
Found at i:427345 original size:28 final size:28
Alignment explanation
Indices: 427280--427342 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
427270 ATATATACAC
* * *
427280 ATATAGAAGAGCACTTTAAACTATACAC
1 ATATAAAAGAGCACTTTAAACTAGACAA
*
427308 ATATAGAAGAGCACTTTAAAC-AGACAA
1 ATATAAAAGAGCACTTTAAACTAGACAA
*
427335 ATTTAAAA
1 ATATAAAA
427343 AGAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (28 bp):
ATATAAAAGAGCACTTTAAACTAGACAA
Found at i:429658 original size:13 final size:14
Alignment explanation
Indices: 429637--429668 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
429627 ATAAAAACTA
429637 TAAACAAAAGTTAT
1 TAAACAAAAGTTAT
429651 TAAA-AAAAGTTA-
1 TAAACAAAAGTTAT
429663 TAAACA
1 TAAACA
429669 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 9 0.53
14 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (14 bp):
TAAACAAAAGTTAT
Found at i:429682 original size:17 final size:18
Alignment explanation
Indices: 429655--429690 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
429645 AGTTATTAAA
429655 AAAAGTTATAAACATTTT
1 AAAAGTTATAAACATTTT
*
429673 AAAA-TTATAAATATTTT
1 AAAAGTTATAAACATTTT
429690 A
1 A
429691 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAGTTATAAACATTTT
Found at i:430668 original size:107 final size:107
Alignment explanation
Indices: 430481--430701 Score: 293
Period size: 107 Copynumber: 2.1 Consensus size: 107
430471 ATCCCTACAA
** *
430481 TGCAAAATTTGGAGGGGGTGAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTATACTA
1 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTACACTA
* * *
430546 AAACCCATTTGAAAGCAATTGATGAGGAAAGCTTTGACATTT
66 AAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
** * **
430588 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATTTTG-CTATTTTACACT
1 TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAA-TCCGACCAAATTACACT
* * *
430652 AAAACACATTTAAAAGCATTTGGCGAGGAAAGTTTTGACATTT
65 AAAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
430695 T-CAAAAT
1 TGCAAAAT
430702 AAGATAGCAA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
106 6 0.06
107 91 0.92
108 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (107 bp):
TGCAAAATTTGGAGGGGGAAAAACATAAAACTTTGGACTTATTTGAATCCGACCAAATTACACTA
AAACACATTTAAAAGCAATTGACGAGGAAAGCTTTGACATTT
Found at i:452892 original size:12 final size:13
Alignment explanation
Indices: 452877--452910 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
452867 AATTAACATC
452877 CCACTAAACCA-A
1 CCACTAAACCACA
*
452889 CCACTAAACCACC
1 CCACTAAACCACA
452902 CCACTAAAC
1 CCACTAAAC
452911 TATCCCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.44, C:0.47, G:0.00, T:0.09
Consensus pattern (13 bp):
CCACTAAACCACA
Found at i:452917 original size:13 final size:13
Alignment explanation
Indices: 452873--452917 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
452863 AACTAATTAA
452873 CATCCCACTAAAC
1 CATCCCACTAAAC
*
452886 CA-ACCACTAAAC
1 CATCCCACTAAAC
*
452898 CACCCCACTAAAC
1 CATCCCACTAAAC
*
452911 TATCCCA
1 CATCCCA
452918 TTAACTCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.13
Consensus pattern (13 bp):
CATCCCACTAAAC
Found at i:453445 original size:15 final size:14
Alignment explanation
Indices: 453389--453502 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 14
453379 TTATTATGTT
*
453389 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
453403 T-T-TTGTTATTCTAA
1 TCTATTTTTATT-T-A
*
453417 TACTATTATTATTTA
1 T-CTATTTTTATTTA
453432 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
*
453447 TCTATTTATATTTCA
1 TCTATTTTTATTT-A
* *
453462 ACTATTATTATATT-
1 TCTATTTTTAT-TTA
453476 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
*
453491 TCTATTTCTATT
1 TCTATTTTTATT
453503 AATATACTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.08
13 3 0.04
14 22 0.28
15 38 0.47
16 4 0.05
17 7 0.09
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (14 bp):
TCTATTTTTATTTA
Found at i:453466 original size:44 final size:44
Alignment explanation
Indices: 453418--453502 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 44
453408 TTATTCTAAT
453418 ACTATTATTAT-TTATCTAATTT-TTAT-TTATCTATTTATATTTCA
1 ACTATTATTATATT-TCT-ATTTATTATATT-TCTATTTATATTTCA
*
453462 ACTATTATTATATTTCTATTTATTATATTTCTATTTCTATT
1 ACTATTATTATATTTCTATTTATTATATTTCTATTTATATT
453503 AATATACTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
43 4 0.11
44 29 0.78
45 4 0.11
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (44 bp):
ACTATTATTATATTTCTATTTATTATATTTCTATTTATATTTCA
Found at i:453495 original size:29 final size:29
Alignment explanation
Indices: 453377--453496 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 29
453367 TTATTGCTAT
* *
453377 TATTATTATGTTTCTATTTA-TATTTATTT
1 TATTATTATATTTCTATTTATTATTTA-TC
* * * *
453406 TGTTATTCTAATACTA-TTATTATTTATC
1 TATTATTATATTTCTATTTATTATTTATC
* *
453434 TAATTTTTAT-TTATCTATTTA-TATTTCAAC
1 T-ATTATTATATT-TCTATTTATTATTT-ATC
453464 TATTATTATATTTCTATTTATTATATT-TC
1 TATTATTATATTTCTATTTATTAT-TTATC
453493 TATT
1 TATT
453497 TCTATTAATA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
28 6 0.09
29 50 0.72
30 11 0.16
31 2 0.03
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATTATATTTCTATTTATTATTTATC
Found at i:453584 original size:6 final size:6
Alignment explanation
Indices: 453573--453600 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
453563 TAACATTCTA
453573 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
453601 CGTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:453702 original size:24 final size:23
Alignment explanation
Indices: 453611--453703 Score: 62
Period size: 24 Copynumber: 3.9 Consensus size: 23
453601 CGTTTTTTGT
* *
453611 TATTATCTATTTTAACTTTT-TA
1 TATTATGTATTTTAAATTTTATA
* *
453633 TATAATGTTCATTTCAAATTTTTATA
1 TATTATG-T-ATTTTAAA-TTTTATA
* * * *
453659 CATTGTTTACTTTAATATTTTCATA
1 TATTATGTATTTTAA-ATTTT-ATA
453684 TATTATGTATTTTAAATTTT
1 TATTATGTATTTTAAATTTT
453704 TTTACACATT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
22 5 0.10
23 1 0.02
24 20 0.39
25 20 0.39
26 5 0.10
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (23 bp):
TATTATGTATTTTAAATTTTATA
Found at i:453704 original size:25 final size:24
Alignment explanation
Indices: 453611--453738 Score: 80
Period size: 25 Copynumber: 5.2 Consensus size: 24
453601 CGTTTTTTGT
* *
453611 TATTATCTATTTTAACTTTTTATA
1 TATTATGTATTTTAAATTTTTATA
*
453635 TA--ATGTTCATTTCAAATTTTTATA
1 TATTATG-T-ATTTTAAATTTTTATA
* * * * *
453659 CATTGTTTACTTTAATATTTTCATA
1 TATTATGTATTTTAA-ATTTTTATA
*
453684 TATTATGTATTTTAAATTTTTTTACA
1 TATTATGTATTTTAAA--TTTTTATA
* * *
453710 CATTATATATTTTGAATTGTTTATA
1 TATTATGTATTTTAAATT-TTTATA
453735 TATT
1 TATT
453739 TGAAGAGTTT
Statistics
Matches: 76, Mismatches: 20, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
22 2 0.03
23 1 0.01
24 25 0.33
25 28 0.37
26 20 0.26
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (24 bp):
TATTATGTATTTTAAATTTTTATA
Found at i:455615 original size:15 final size:15
Alignment explanation
Indices: 455595--455646 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
455585 ACTACAAAAC
455595 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
455610 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
455629 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
455644 ATT
1 ATT
455647 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:455749 original size:22 final size:22
Alignment explanation
Indices: 455709--455764 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
455699 AATAAAATTG
*
455709 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
455729 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
455751 TATTAATAATTTAT
1 AAATAATAAATTAT
455765 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:459375 original size:31 final size:32
Alignment explanation
Indices: 459340--459400 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
459330 AAAAAGGCTT
459340 AATAGTCTAATAACTTAAAT-AATTTTTTTTG
1 AATAGTCTAATAACTTAAATGAATTTTTTTTG
* *
459371 AATAGTTTAGTAACTTAAATGAATTTTTTT
1 AATAGTCTAATAACTTAAATGAATTTTTTT
459401 ATGTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (32 bp):
AATAGTCTAATAACTTAAATGAATTTTTTTTG
Found at i:465655 original size:15 final size:15
Alignment explanation
Indices: 465635--465666 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
465625 CTCTGCTAAC
*
465635 TTAAGTTATTGTATA
1 TTAAGTTATCGTATA
465650 TTAAGTTATCGTATA
1 TTAAGTTATCGTATA
465665 TT
1 TT
465667 CTATAGGTTA
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:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (15 bp):
TTAAGTTATCGTATA
Found at i:468671 original size:22 final size:22
Alignment explanation
Indices: 468643--468689 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
468633 AAATGCGTCA
468643 GCTACAATGTTGGCACTCCCCG
1 GCTACAATGTTGGCACTCCCCG
468665 GCTACAATGTTGGCACTCCCCG
1 GCTACAATGTTGGCACTCCCCG
468687 GCT
1 GCT
468690 TGTATTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (22 bp):
GCTACAATGTTGGCACTCCCCG
Found at i:472550 original size:3 final size:3
Alignment explanation
Indices: 472544--472590 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
472534 TTTAGCCACT
*
472544 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
472589 TT
1 TT
472591 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:473933 original size:19 final size:20
Alignment explanation
Indices: 473893--473936 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
473883 GTCTCTTTAG
* *
473893 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
473912 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
473931 GCATTA
1 GCATTA
473937 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:480367 original size:88 final size:88
Alignment explanation
Indices: 480211--480457 Score: 390
Period size: 88 Copynumber: 2.8 Consensus size: 88
480201 NNNNNNNNNN
* *
480211 CCTTGCCTCTCTCGGTTAG-GATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGAC
1 CCTTGCCTCTCTTGGTT-GTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGAC
*
480275 AGCGAAGCAGGTCGAAGACACAAA
65 AGCGAAGCAGATCGAAGACACAAA
* * * *
480299 CCTTTCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAGGATCTTGCATTTCTGCATTGATA
1 CCTTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGACA
480364 GCGAAGCAGATCGAAGACACAAA
66 GCGAAGCAGATCGAAGACACAAA
*
480387 CCTTGCCTCT-TTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGAC
1 CCTTGCCTCTCTT-GGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGAC
480451 AGCGAAG
65 AGCGAAG
480458 NNNNNNNNNN
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
87 3 0.02
88 142 0.98
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (88 bp):
CCTTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGACA
GCGAAGCAGATCGAAGACACAAA
Found at i:480438 original size:44 final size:44
Alignment explanation
Indices: 480212--480438 Score: 110
Period size: 44 Copynumber: 5.2 Consensus size: 44
480202 NNNNNNNNNC
* *
480212 CTTGCCTCTCTCGGTTAG-GATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTT-GTGATAGAGCTGGTTGAAGACAAAAGAT
* * * ** ** * * * *
480256 CTTGCCTTCCTGC-ATTGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
* * *
480300 CTTTCCTCTCTT-GGTTGTGATGGAGCTGGTTGAAGACAAAGGAT
1 CTTGCCTCT-TTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
* ** * * * * *
480344 CTTG-C-ATTTCTGCAT-TGATAGCGAAGCAGATCGAAGACACAA-AC
1 CTTGCCTCTTTC-GGTTGTGATA--G-AGCTGGTTGAAGACAAAAGAT
480388 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
480432 CTTGCCT
1 CTTGCCT
480439 TTCTGCATTG
Statistics
Matches: 125, Mismatches: 43, Indels: 30
0.63 0.22 0.15
Matches are distributed among these distances:
41 2 0.02
42 5 0.04
43 34 0.27
44 41 0.33
45 34 0.27
46 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
Found at i:484590 original size:17 final size:17
Alignment explanation
Indices: 484568--484618 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
484558 ATTGCAAAAT
484568 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
484585 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
484604 CATATCTTCAAAGAT
1 CATATCTTCTAAGAT
484619 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:486372 original size:43 final size:43
Alignment explanation
Indices: 486316--486402 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
486306 TCATATTTCA
* *
486316 TTTCTCATTTCATAATAATTTCTCATATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
* * * *
486359 TTTCTCATCTCATATTCATTTCTCATCTTTCCCATTTCATTAT
1 TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
486402 T
1 T
486403 AATCACATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (43 bp):
TTTCTCATCTCATAATAATTTCTCATATTTCCCATTTCAATAT
Found at i:486373 original size:15 final size:14
Alignment explanation
Indices: 486336--486374 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
486326 CATAATAATT
486336 TCTCATATTTTCCA
1 TCTCATATTTTCCA
*
486350 TTTCAATATTTTCTCA
1 TCTC-ATATTTTC-CA
486366 TCTCATATT
1 TCTCATATT
486375 CATTTCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.62
16 5 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (14 bp):
TCTCATATTTTCCA
Found at i:515914 original size:22 final size:24
Alignment explanation
Indices: 515883--515933 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
515873 TGAGTTTCAC
*
515883 ATGATTTATAAAATGTG-AAATAT
1 ATGATATATAAAATGTGTAAATAT
* *
515906 -TGATATATATATTGTGTAAATAT
1 ATGATATATAAAATGTGTAAATAT
515929 ATGAT
1 ATGAT
515934 CAGCATGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.57
23 6 0.26
24 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (24 bp):
ATGATATATAAAATGTGTAAATAT
Found at i:516171 original size:47 final size:47
Alignment explanation
Indices: 516065--516177 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
516055 AAGAATGAAG
* * *
516065 AAGTGATAGTTTATCTACAAAAGTGGTGGCTTGTCCATAATATTATA
1 AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
* * * *
516112 AAGTGGTGGTTTATTTGCAAAAGTGGTGGCTTATCCACAATATTATT
1 AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
*
516159 AAGTGACAGTTTATCTGCA
1 AAGTGATAGTTTATCTGCA
516178 TTACTGTGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (47 bp):
AAGTGATAGTTTATCTGCAAAAGTGGTGGCTTATCCACAATATTATA
Found at i:533796 original size:5 final size:5
Alignment explanation
Indices: 533786--533839 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
533776 ATCCTAAATT
*
533786 AATAA AATAA AA-ATA AATAA AA-AT AATAA AACT-A AATAA AATAA AATAA
1 AATAA AATAA AATA-A AATAA AATAA AATAA AA-TAA AATAA AATAA AATAA
533835 AATAA
1 AATAA
533840 TATCTTCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 5 0.12
5 35 0.83
6 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:533802 original size:19 final size:19
Alignment explanation
Indices: 533780--533836 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
533770 AGCCTAATCC
533780 TAAATTAATAAAATAAAAA
1 TAAATTAATAAAATAAAAA
* *
533799 TAAA-TAAAAATAATAAAAC
1 TAAATTAATAA-AATAAAAA
*
533818 TAAATAAAATAAAATAAAA
1 TAAAT-TAATAAAATAAAA
533837 TAATATCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 15 0.48
20 7 0.23
21 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAATTAATAAAATAAAAA
Found at i:533812 original size:24 final size:24
Alignment explanation
Indices: 533785--533831 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
533775 AATCCTAAAT
533785 TAATAAAA-TAAAAATAAATAAAAA
1 TAATAAAACTAAAAA-AAATAAAAA
*
533809 TAATAAAACTAAATAAAATAAAA
1 TAATAAAACTAAAAAAAATAAAA
533832 TAAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (24 bp):
TAATAAAACTAAAAAAAATAAAAA
Found at i:538824 original size:3 final size:3
Alignment explanation
Indices: 538798--538869 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
538788 TTCTCATTGC
* * * *
538798 TAT TTT TAT T-T TATT TAC TAT TAT TAT TAT TAT T-T TAC TAG TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
538842 TATT TAT TATT TAT TAT TAT TAC TAT TA
1 TA-T TAT TA-T TAT TAT TAT TAT TAT TA
538870 CTGTCATTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 4 0.07
3 42 0.76
4 9 0.16
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:539251 original size:3 final size:3
Alignment explanation
Indices: 539245--539279 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
539235 ACTTAACTAC
539245 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
539280 CACTCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:539290 original size:235 final size:235
Alignment explanation
Indices: 539030--539514 Score: 961
Period size: 235 Copynumber: 2.1 Consensus size: 235
539020 TTTATTTATC
*
539030 TTATTATTATTATTACTCTCATTATTGTTTATCTTAAAGATTATTTATTTATTTCTTTATATATA
1 TTATTATTATTATTACACTCATTATTGTTTATCTTAAAGATTATTTATTTATTTCTTTATATATA
539095 CATTTCATATGTTTCAAAGTTTAGATTATTATTATTATTATTACCATTATATTTATTACTATTAC
66 CATTTCATATGTTTCAAAGTTTAGATTATTATTATTATTATTACCATTATATTTATTACTATTAC
539160 TAGTATTATTATTTTCTTTAATACTATCACTGCTATTATATTATTTGTCTTGTTAATGTACTATT
131 TAGTATTATTATTTTCTTTAATACTATCACTGCTATTATATTATTTGTCTTGTTAATGTACTATT
539225 ATTATTTCCTACTTAACTACTATTATTATTATTATTATTA
196 ATTATTTCCTACTTAACTACTATTATTATTATTATTATTA
539265 TTATTATTATTATTACACTCATTATTGTTTATCTTAAAGATTATTTATTTATTTCTTTATATATA
1 TTATTATTATTATTACACTCATTATTGTTTATCTTAAAGATTATTTATTTATTTCTTTATATATA
539330 CATTTCATATGTTTCAAAGTTTAGATTATTATTATTATTATTACCATTATATTTATTACTATTAC
66 CATTTCATATGTTTCAAAGTTTAGATTATTATTATTATTATTACCATTATATTTATTACTATTAC
539395 TAGTATTATTATTTTCTTTAATACTATCACTGCTATTATATTATTTGTCTTGTTAATGTACTATT
131 TAGTATTATTATTTTCTTTAATACTATCACTGCTATTATATTATTTGTCTTGTTAATGTACTATT
539460 ATTATTTCCTACTTAACTACTATTATTATTATTATTATTA
196 ATTATTTCCTACTTAACTACTATTATTATTATTATTATTA
539500 TTATTATTATTATTA
1 TTATTATTATTATTA
539515 TTATTTATTC
Statistics
Matches: 249, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 249 1.00
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.56
Consensus pattern (235 bp):
TTATTATTATTATTACACTCATTATTGTTTATCTTAAAGATTATTTATTTATTTCTTTATATATA
CATTTCATATGTTTCAAAGTTTAGATTATTATTATTATTATTACCATTATATTTATTACTATTAC
TAGTATTATTATTTTCTTTAATACTATCACTGCTATTATATTATTTGTCTTGTTAATGTACTATT
ATTATTTCCTACTTAACTACTATTATTATTATTATTATTA
Found at i:539486 original size:3 final size:3
Alignment explanation
Indices: 539480--539519 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
539470 ACTTAACTAC
539480 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
539520 TATTCATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:539678 original size:9 final size:10
Alignment explanation
Indices: 539657--539713 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
539647 TGTGCCCTTC
539657 TATTATCTATT
1 TATTAT-TATT
539668 TATT-TTATT
1 TATTATTATT
539677 TA-T-TTATT
1 TATTATTATT
539685 TATTATTA-T
1 TATTATTATT
539694 TATTATTA-T
1 TATTATTATT
539703 TATTATT-TT
1 TATTATTATT
539712 TA
1 TA
539714 CATATTACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.19
9 27 0.63
10 4 0.09
11 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTATTATT
Found at i:539692 original size:3 final size:3
Alignment explanation
Indices: 539657--539709 Score: 54
Period size: 3 Copynumber: 16.3 Consensus size: 3
539647 TGTGCCCTTC
539657 TAT TAT CTATT TAT T-T TATT TATT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TA-T TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
539703 TAT TAT T
1 TAT TAT T
539710 TTTACATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.04
3 28 0.61
4 15 0.33
5 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:539709 original size:12 final size:13
Alignment explanation
Indices: 539657--539706 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
539647 TGTGCCCTTC
539657 TATTATCTATTTAT
1 TATTAT-TATTTAT
539671 T-TTATTTATTTATT
1 TATTA-TTATTTA-T
539685 TATTATTA-TTAT
1 TATTATTATTTAT
539697 TATTATTATT
1 TATTATTATT
539707 ATTTTTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.28
13 13 0.41
14 7 0.22
15 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:543534 original size:37 final size:37
Alignment explanation
Indices: 543479--543553 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
543469 TACTACGTAC
*
543479 GTAGTACAGAGCCGATGGTCTACTTATCTAAAATAAT
1 GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
*
543516 GTAGTACAGAGCCAATGGTCTACTTTTCTAAAATAAT
1 GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
543553 G
1 G
543554 AAGTTCAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (37 bp):
GTAGTACAGAGCCAATGGTCTACTTATCTAAAATAAT
Found at i:553408 original size:18 final size:18
Alignment explanation
Indices: 553385--553459 Score: 132
Period size: 18 Copynumber: 4.2 Consensus size: 18
553375 CCCAACTACT
*
553385 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
553403 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
553421 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
553439 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
553457 GTA
1 GTA
553460 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:557224 original size:643 final size:643
Alignment explanation
Indices: 555993--557286 Score: 2579
Period size: 643 Copynumber: 2.0 Consensus size: 643
555983 AAAGCATTTA
555993 AAAATAAAATCTCCCACTAAAACCAAATATCCTTTAAATGGCATTACACCTATATGAGCAATGTG
1 AAAA-AAAATCTCCCACTAAAACCAAATATCCTTTAAATGGCATTACACCTATATGAGCAATGTG
556058 CTCTTATAAAACCTTAGGTGTAGTTCCTTAGTAAGCAGATCCGCAATCATGGAGTTTGTCCTAAT
65 CTCTTATAAAACCTTAGGTGTAGTTCCTTAGTAAGCAGATCCGCAATCATGGAGTTTGTCCTAAT
556123 ATGCTTTATAAGCACCTAACCACCCTGGACTTTTACTTTAACAACCGGGAACTTAAAGTCTATGT
130 ATGCTTTATAAGCACCTAACCACCCTGGACTTTTACTTTAACAACCGGGAACTTAAAGTCTATGT
556188 GTTTTTACTTTGATGTGCTCCTGTTGCTATTGGAATAAAAGACTGCAAATTGTGACAAAATCTTG
195 GTTTTTACTTTGATGTGCTCCTGTTGCTATTGGAATAAAAGACTGCAAATTGTGACAAAATCTTG
556253 TATCCATATTCCATCAAAATCGAAGTCTGTATACCTGATTATCTCTAACTGATTAAACCTTTGAT
260 TATCCATATTCCATCAAAATCGAAGTCTGTATACCTGATTATCTCTAACTGATTAAACCTTTGAT
556318 ATGTGAGCATGTAATCTTTTGTTCTCTGAAAATACCTTATAACCCTCTTGGATGCGATCCAATGT
325 ATGTGAGCATGTAATCTTTTGTTCTCTGAAAATACCTTATAACCCTCTTGGATGCGATCCAATGT
556383 CCAAACAAGGTTTGTTTAAAATATCTGCCTAACATCCCAATAGTGTACACAATATTCCAATGTAT
390 CCAAACAAGGTTTGTTTAAAATATCTGCCTAACATCCCAATAGTGTACACAATATTCCAATGTAT
556448 ACAAACTTGAATGTATATTAGATTTTCCATTGCTAAAATGTAAAAAATCTTATGCATTTTTGTAA
455 ACAAACTTGAATGTATATTAGATTTTCCATTGCTAAAATGTAAAAAATCTTATGCATTTTTGTAA
556513 TCTCAAAATCATTCTTAGGGCATTGATTGAGACTATACTTGTTATTGACAAGCAGTATGTCATTA
520 TCTCAAAATCATTCTTAGGGCATTGATTGAGACTATACTTGTTATTGACAAGCAGTATGTCATTA
556578 ACATATAAAACCAAATATAGAACCTTATTCCCACTAAACTTATGGTATATATGATTATC
585 ACATATAAAACCAAATATAGAACCTTATTCCCACTAAACTTATGGTATATATGATTATC
556637 AAAAAAAATCTCCCACTAAAACCAAATATCCTTTAAATGGCATTACACCTATATGAGCAATGTGC
1 AAAAAAAATCTCCCACTAAAACCAAATATCCTTTAAATGGCATTACACCTATATGAGCAATGTGC
556702 TCTTATAAAACCTTAGGTGTAGTTCCTTAGTAAGCAGATCCGCAATCATGGAGTTTGTCCTAATA
66 TCTTATAAAACCTTAGGTGTAGTTCCTTAGTAAGCAGATCCGCAATCATGGAGTTTGTCCTAATA
556767 TGCTTTATAAGCACCTAACCACCCTGGACTTTTACTTTAACAACCGGGAACTTAAAGTCTATGTG
131 TGCTTTATAAGCACCTAACCACCCTGGACTTTTACTTTAACAACCGGGAACTTAAAGTCTATGTG
556832 TTTTTACTTTGATGTGCTCCTGTTGCTATTGGAATAAAAGACTGCAAATTGTGACAAAATCTTGT
196 TTTTTACTTTGATGTGCTCCTGTTGCTATTGGAATAAAAGACTGCAAATTGTGACAAAATCTTGT
556897 ATCCATATTCCATCAAAATCGAAGTCTGTATACCTGATTATCTCTAACTGATTAAACCTTTGATA
261 ATCCATATTCCATCAAAATCGAAGTCTGTATACCTGATTATCTCTAACTGATTAAACCTTTGATA
556962 TGTGAGCATGTAATCTTTTGTTCTCTGAAAATACCTTATAACCCTCTTGGATGCGATCCAATGTC
326 TGTGAGCATGTAATCTTTTGTTCTCTGAAAATACCTTATAACCCTCTTGGATGCGATCCAATGTC
557027 CAAACAAGGTTTGTTTAAAATATCTGCCTAACATCCCAATAGTGTACACAATATTCCAATGTATA
391 CAAACAAGGTTTGTTTAAAATATCTGCCTAACATCCCAATAGTGTACACAATATTCCAATGTATA
557092 CAAACTTGAATGTATATTAGATTTTCCATTGCTAAAATGTAAAAAATCTTATGCATTTTTGTAAT
456 CAAACTTGAATGTATATTAGATTTTCCATTGCTAAAATGTAAAAAATCTTATGCATTTTTGTAAT
557157 CTCAAAATCATTCTTAGGGCATTGATTGAGACTATACTTGTTATTGACAAGCAGTATGTCATTAA
521 CTCAAAATCATTCTTAGGGCATTGATTGAGACTATACTTGTTATTGACAAGCAGTATGTCATTAA
557222 CATATAAAACCAAATATAGAACCTTATTCCCACTAAACTTATGGTATATATGATTATC
586 CATATAAAACCAAATATAGAACCTTATTCCCACTAAACTTATGGTATATATGATTATC
557280 AAAAAAA
1 AAAAAAA
557287 TTCATCTTTA
Statistics
Matches: 650, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
643 646 0.99
644 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (643 bp):
AAAAAAAATCTCCCACTAAAACCAAATATCCTTTAAATGGCATTACACCTATATGAGCAATGTGC
TCTTATAAAACCTTAGGTGTAGTTCCTTAGTAAGCAGATCCGCAATCATGGAGTTTGTCCTAATA
TGCTTTATAAGCACCTAACCACCCTGGACTTTTACTTTAACAACCGGGAACTTAAAGTCTATGTG
TTTTTACTTTGATGTGCTCCTGTTGCTATTGGAATAAAAGACTGCAAATTGTGACAAAATCTTGT
ATCCATATTCCATCAAAATCGAAGTCTGTATACCTGATTATCTCTAACTGATTAAACCTTTGATA
TGTGAGCATGTAATCTTTTGTTCTCTGAAAATACCTTATAACCCTCTTGGATGCGATCCAATGTC
CAAACAAGGTTTGTTTAAAATATCTGCCTAACATCCCAATAGTGTACACAATATTCCAATGTATA
CAAACTTGAATGTATATTAGATTTTCCATTGCTAAAATGTAAAAAATCTTATGCATTTTTGTAAT
CTCAAAATCATTCTTAGGGCATTGATTGAGACTATACTTGTTATTGACAAGCAGTATGTCATTAA
CATATAAAACCAAATATAGAACCTTATTCCCACTAAACTTATGGTATATATGATTATC
Found at i:565905 original size:26 final size:26
Alignment explanation
Indices: 565867--565950 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
565857 CATGAAATTC
*
565867 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
565893 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
565919 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
565945 TTATCA
1 TTATCA
565951 GTTTGTATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:568125 original size:13 final size:13
Alignment explanation
Indices: 568109--568142 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
568099 TGCATATAAT
568109 ATATATACACACA
1 ATATATACACACA
568122 ATATATACACACA
1 ATATATACACACA
568135 ATTATATA
1 A-TATATA
568143 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATATACACACA
Found at i:575323 original size:13 final size:14
Alignment explanation
Indices: 575291--575337 Score: 60
Period size: 13 Copynumber: 3.3 Consensus size: 14
575281 TTTTAATTTC
575291 TTTAAAATATTAATAA
1 TTTAAAA-ATT-ATAA
*
575307 TTTAATAATTA-AA
1 TTTAAAAATTATAA
575320 TTTAAAAATTATAA
1 TTTAAAAATTATAA
575334 TTTA
1 TTTA
575338 TAGCCTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
14 7 0.25
15 3 0.11
16 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAAATTATAA
Found at i:579670 original size:20 final size:22
Alignment explanation
Indices: 579645--579695 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 22
579635 TATCCATAAT
579645 TTAATTTAAATAATAAAA-A-A
1 TTAATTTAAATAATAAAATATA
*
579665 TTAATTT-AATTATAAAATATA
1 TTAATTTAAATAATAAAATATA
579686 TTAATATTAA
1 TTAAT-TTAA
579696 TGCAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 6 0.23
22 2 0.08
23 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTTAAATAATAAAATATA
Found at i:596745 original size:4 final size:4
Alignment explanation
Indices: 596738--596777 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
596728 TATCTATACA
596738 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
596778 AAATGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:596807 original size:15 final size:15
Alignment explanation
Indices: 596784--596813 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
596774 TATGAAATGA
596784 TTTAATCTTCTTCTT
1 TTTAATCTTCTTCTT
*
596799 TTTAGTCTTCTTCTT
1 TTTAATCTTCTTCTT
596814 CCCTCTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATCTTCTTCTT
Found at i:597840 original size:34 final size:34
Alignment explanation
Indices: 597802--597869 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
597792 TGTATTTATT
597802 TTTCAATTATTTGATGACGAGAAGAGATTGTATG
1 TTTCAATTATTTGATGACGAGAAGAGATTGTATG
597836 TTTCAATTATTTGATGACGAGAAGAGATTGTATG
1 TTTCAATTATTTGATGACGAGAAGAGATTGTATG
597870 GAATTGTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (34 bp):
TTTCAATTATTTGATGACGAGAAGAGATTGTATG
Found at i:604548 original size:13 final size:14
Alignment explanation
Indices: 604530--604559 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
604520 TGACACACTC
604530 GTTAGTTAA-TTTA
1 GTTAGTTAATTTTA
604543 GTTAGTTAATTTTA
1 GTTAGTTAATTTTA
604557 GTT
1 GTT
604560 TTAATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTAGTTAATTTTA
Found at i:606758 original size:18 final size:17
Alignment explanation
Indices: 606713--606768 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
606703 TAATGTAAAC
606713 TTATTCTATTTATATT--
1 TTATT-TATTTATATTAA
*
606729 TTATTT-TATATATATAA
1 TTATTTATTTATAT-TAA
606746 TTATTTATTTATATTAA
1 TTATTTATTTATATTAA
*
606763 ATATTT
1 TTATTT
606769 TATTCGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 5 0.15
17 14 0.42
18 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTATTTATATTAA
Found at i:606770 original size:18 final size:20
Alignment explanation
Indices: 606724--606772 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
606714 TATTCTATTT
606724 ATATTTTATTTTATATATATA
1 ATATTTTA-TTTATATATATA
606745 AT-TATTTATTTATAT-TA-A
1 ATAT-TTTATTTATATATATA
606763 ATATTTTATT
1 ATATTTTATT
606773 CGCTAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 9 0.35
19 3 0.12
20 8 0.31
21 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTATTTATATATATA
Found at i:614343 original size:13 final size:13
Alignment explanation
Indices: 614325--614349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614315 CTGTAGTTGT
614325 TTTGATATGTTTC
1 TTTGATATGTTTC
614338 TTTGATATGTTT
1 TTTGATATGTTT
614350 TGGTGTATTT
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTGATATGTTTC
Found at i:620454 original size:31 final size:31
Alignment explanation
Indices: 620409--620474 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
620399 ATACAAATTG
620409 GTCAATGAACTATTCAAAAATTTTCATTTAA
1 GTCAATGAACTATTCAAAAATTTTCATTTAA
* * * *
620440 GTCATTGAATTATTCAAAAGTTTTTATTTAA
1 GTCAATGAACTATTCAAAAATTTTCATTTAA
620471 GTCA
1 GTCA
620475 CTAGACTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (31 bp):
GTCAATGAACTATTCAAAAATTTTCATTTAA
Found at i:623369 original size:28 final size:28
Alignment explanation
Indices: 623308--623374 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
623298 ATTGTTTATG
*
623308 TTTAAAAT-TTTAATAAAAATATATAAT
1 TTTAAAATATTAAATAAAAATATATAAT
*
623335 TTT-AAATATTAAATAAAAAT-TATATT
1 TTTAAAATATTAAATAAAAATATATAAT
623361 TTTAAAA-A-TAAATA
1 TTTAAAATATTAAATA
623375 TGGGAGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 6 0.17
26 13 0.36
27 17 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTTAAAATATTAAATAAAAATATATAAT
Found at i:623372 original size:25 final size:27
Alignment explanation
Indices: 623319--623374 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
623309 TTAAAATTTT
*
623319 AATAAAAATATATAATTTTAAATATTA
1 AATAAAAATATATAATTTTAAATAATA
*
623346 AATAAAAAT-TATATTTTTAAA-AATA
1 AATAAAAATATATAATTTTAAATAATA
623371 AATA
1 AATA
623375 TGGGAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 7 0.26
26 11 0.41
27 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATAAAAATATATAATTTTAAATAATA
Found at i:627699 original size:24 final size:24
Alignment explanation
Indices: 627667--627714 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
627657 TGCAGAATTT
627667 GACCTTGTTTCGAGTATTTGAGTG
1 GACCTTGTTTCGAGTATTTGAGTG
627691 GACCTTGTTTCGAGTATTTGAGTG
1 GACCTTGTTTCGAGTATTTGAGTG
627715 ACATGTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.42
Consensus pattern (24 bp):
GACCTTGTTTCGAGTATTTGAGTG
Found at i:628302 original size:26 final size:28
Alignment explanation
Indices: 628266--628319 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
628256 TGGAAAGGAA
628266 GTTCTATAGC-TATATACACACA-ATAT
1 GTTCTATAGCTTATATACACACATATAT
*
628292 GTTCTATAGCTTATATATACACATATAT
1 GTTCTATAGCTTATATACACACATATAT
628320 ATACGCACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.40
27 11 0.44
28 4 0.16
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (28 bp):
GTTCTATAGCTTATATACACACATATAT
Found at i:630553 original size:53 final size:53
Alignment explanation
Indices: 630490--630607 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 53
630480 TACTTTTTCT
* *
630490 TTAGTAAATTTAGTCAATGCATTTTTATAGCTTTGTATATCTTAATCCAATCA
1 TTAGTAAATTTAATCAATGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
* * * * *
630543 TTAGTGAATTTAATCACTTCATTTTTATAGGTTTGTAAATCTTAATCCACTCA
1 TTAGTAAATTTAATCAATGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
*
630596 TTACTAAATTTA
1 TTAGTAAATTTA
630608 TGTTAAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (53 bp):
TTAGTAAATTTAATCAATGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
Done.