Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold417
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: 511691
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 4 of 6
Found at i:296051 original size:27 final size:27
Alignment explanation
Indices: 296021--296082 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
296011 TTTTCTCTTT
* *
296021 CTTCTTCTCCTTATCTTTCTTTTTGTC
1 CTTCTTCTCCCTATCTTTCTTTTTCTC
* *
296048 CTTCTCCTCCCTGTCTTTCTTTTTCTC
1 CTTCTTCTCCCTATCTTTCTTTTTCTC
*
296075 TTTCTTCT
1 CTTCTTCT
296083 TCTTCTCGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.02, C:0.34, G:0.03, T:0.61
Consensus pattern (27 bp):
CTTCTTCTCCCTATCTTTCTTTTTCTC
Found at i:296198 original size:27 final size:30
Alignment explanation
Indices: 296146--296234 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 30
296136 TTTAGCTTTA
*
296146 TTTCTTTCTTCTTC-TCTGTCTCCTCTCTG-TC
1 TTTCTTT-TTCTTCTTCT-TCTCTTCT-TGTTC
296177 TTTCTTTTTCTTCTTCTTCTCTTTCTTGTTC
1 TTTCTTTTTCTTCTTCTTCTC-TTCTTGTTC
*
296208 TCTTCTTTTTCTTCATCTTCATCTTCT
1 T-TTCTTTTTCTTCTTCTTC-TCTTCT
296235 AACTCTGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
30 12 0.24
31 16 0.31
32 21 0.41
33 2 0.04
ACGTcount: A:0.02, C:0.30, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTCTTTTTCTTCTTCTTCTCTTCTTGTTC
Found at i:296220 original size:21 final size:21
Alignment explanation
Indices: 296175--296214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
296165 CTCCTCTCTG
296175 TCTTTCTTTTTCTTCTTCTTC
1 TCTTTCTTTTTCTTCTTCTTC
*
296196 TCTTTCTTGTTC-TCTTCTT
1 TCTTTCTTTTTCTTCTTCTT
296215 TTTCTTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.70
Consensus pattern (21 bp):
TCTTTCTTTTTCTTCTTCTTC
Found at i:296344 original size:33 final size:34
Alignment explanation
Indices: 296302--296367 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
296292 CCCTCTCCCT
*
296302 CTTCATCCTTCAGCTT-TTTTTCTTTCTTTTTCTC
1 CTTCATCCTTCACCTTGTTTTTC-TTCTTTTTCTC
*
296336 CTTC-TCCTTCTCCTTGTTTTTCTTCTTTTTCT
1 CTTCATCCTTCACCTTGTTTTTCTTCTTTTTCT
296368 TCTCCTCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.03, C:0.30, G:0.03, T:0.64
Consensus pattern (34 bp):
CTTCATCCTTCACCTTGTTTTTCTTCTTTTTCTC
Found at i:296357 original size:24 final size:24
Alignment explanation
Indices: 296328--296373 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
296318 TTTTTCTTTC
296328 TTTTTCTCCTTCTCCTTCTCCTTG
1 TTTTTCTCCTTCTCCTTCTCCTTG
* * *
296352 TTTTTCTTCTTTTTCTTCTCCT
1 TTTTTCTCCTTCTCCTTCTCCT
296374 CTCCCATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTCTCCTTCTCCTTCTCCTTG
Found at i:296481 original size:18 final size:18
Alignment explanation
Indices: 296460--296499 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
296450 CCCCTCCCTT
*
296460 TCTTTCTTCTTCCTC-TCA
1 TCTTTC-TCTTCATCTTCA
296478 TCTTTCTCTTCATCTTCA
1 TCTTTCTCTTCATCTTCA
296496 TCTT
1 TCTT
296500 CATCTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTTCTCTTCATCTTCA
Found at i:296492 original size:12 final size:12
Alignment explanation
Indices: 296457--296505 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
296447 CTTCCCCTCC
*
296457 CTTTCT-TTCTT
1 CTTTCTCTTCAT
*
296468 CTTCCTC-TCAT
1 CTTTCTCTTCAT
296479 CTTTCTCTTCAT
1 CTTTCTCTTCAT
296491 C-TTCATCTTCAT
1 CTTTC-TCTTCAT
296503 CTT
1 CTT
296506 CTTTTACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 17 0.55
12 13 0.42
13 1 0.03
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.57
Consensus pattern (12 bp):
CTTTCTCTTCAT
Found at i:300850 original size:22 final size:23
Alignment explanation
Indices: 300820--300864 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
300810 ATTACGATTA
*
300820 AAATTCAAA-TTCTAAACATACT
1 AAATACAAACTTCTAAACATACT
* *
300842 AAATACAAACTTTTAAAGATACT
1 AAATACAAACTTCTAAACATACT
300865 TTCGTGAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATACAAACTTCTAAACATACT
Found at i:301682 original size:2 final size:2
Alignment explanation
Indices: 301669--301698 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
301659 AAGAAGCATT
*
301669 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
301699 CACGCCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:305955 original size:1 final size:1
Alignment explanation
Indices: 305949--305978 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
305939 TTTTGAAAGC
*
305949 TTTTTTTTTTTTTGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305979 GCAGTTAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:312514 original size:14 final size:15
Alignment explanation
Indices: 312486--312528 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
312476 TAAATTTAGT
*
312486 AATATATAA-AATTA
1 AATATAAAATAATTA
312500 AA-ATAAAATAATTA
1 AATATAAAATAATTA
312514 AATATAAAAT-ATTA
1 AATATAAAATAATTA
312528 A
1 A
312529 TATTCGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
14 14 0.54
15 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAAATAATTA
Found at i:313102 original size:2 final size:2
Alignment explanation
Indices: 313095--313126 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
313085 TGAATGAGTT
313095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
313127 GCTTTAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:313668 original size:16 final size:16
Alignment explanation
Indices: 313615--313674 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
313605 TGGTGTTTTG
*
313615 TTGA-ATTTATGTATT
1 TTGATATTTATATATT
* *
313630 TTCATATTTAAGATATT
1 TTGATATTT-ATATATT
*
313647 AT-ATATTTATATATT
1 TTGATATTTATATATT
313662 TTGATATATTATA
1 TTGATAT-TTATA
313675 ATTCGTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.29
16 14 0.40
17 11 0.31
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (16 bp):
TTGATATTTATATATT
Found at i:314256 original size:25 final size:26
Alignment explanation
Indices: 314212--314275 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
314202 TTTATATTTA
*
314212 ATTTTAACTTTTAAAATTTTT-AAAAT
1 ATTTTAA-TTTTTAAATTTTTAAAAAT
*
314238 ATTTTAATTTTTAATTTTTTAAAAAT
1 ATTTTAATTTTTAAATTTTTAAAAAT
*
314264 ATTTAAATTTTT
1 ATTTTAATTTTT
314276 TTATTCAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 11 0.32
26 23 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTTTAATTTTTAAATTTTTAAAAAT
Found at i:314443 original size:37 final size:38
Alignment explanation
Indices: 314396--314475 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
314386 AATTAGATTT
* *
314396 TATTTGAATTAT-TATTTAAATAATAAAAATTTTATTTAA
1 TATTTGAATTATAAATTTAAAT-ATAAAAATATT-TTTAA
*
314435 -ATTT-AATTATAAATTTTAATATAAAAATATTTTTAA
1 TATTTGAATTATAAATTTAAATATAAAAATATTTTTAA
314471 TATTT
1 TATTT
314476 TTTAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 5 0.14
37 20 0.56
38 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
TATTTGAATTATAAATTTAAATATAAAAATATTTTTAA
Found at i:314737 original size:14 final size:14
Alignment explanation
Indices: 314720--314748 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
314710 TTTTTTTCAT
314720 TTATTATTTGAATA
1 TTATTATTTGAATA
314734 TTATTATTTGAATA
1 TTATTATTTGAATA
314748 T
1 T
314749 GTGTAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATTATTTGAATA
Found at i:314840 original size:18 final size:18
Alignment explanation
Indices: 314817--314875 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
314807 TATTTTTTAA
314817 AAATAAAAATATAAAATT
1 AAATAAAAATATAAAATT
*
314835 AAATAAAAAT-TAAATATG
1 AAATAAAAATATAAA-ATT
* *
314853 AAA-ATAAATATCAAATTT
1 AAATAAAAATAT-AAAATT
314871 AAATA
1 AAATA
314876 TTTAAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 9 0.27
18 20 0.61
19 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAAAAATATAAAATT
Found at i:314856 original size:24 final size:22
Alignment explanation
Indices: 314814--314876 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 22
314804 ATTTATTTTT
*
314814 TAAAAATAAAAATATAAAATTAAA
1 TAAAAAT-TAAATATAAAA-TAAA
314838 TAAAAATTAAATATGAAAATAAA
1 TAAAAATTAAATAT-AAAATAAA
*
314861 TATCAAATTTAAATAT
1 TA--AAAATTAAATAT
314877 TTAAATTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 12 0.35
24 11 0.32
25 11 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAAATTAAATATAAAATAAA
Found at i:314862 original size:12 final size:12
Alignment explanation
Indices: 314823--314876 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
314813 TTAAAAATAA
314823 AAATATAAAATT
1 AAATATAAAATT
314835 AAATA-AAAATT
1 AAATATAAAATT
314846 AAATATGAAAA-T
1 AAATAT-AAAATT
*
314858 AAATATCAAATTT
1 AAATAT-AAAATT
314871 AAATAT
1 AAATAT
314877 TTAAATTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.30
12 15 0.41
13 11 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:315179 original size:2 final size:2
Alignment explanation
Indices: 315166--315201 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
315156 ATCCATTTCA
*
315166 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315202 TATTTTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:316224 original size:2 final size:2
Alignment explanation
Indices: 316219--316255 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
316209 CTTACATATA
*
316219 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
316256 ATGTATTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:321101 original size:18 final size:17
Alignment explanation
Indices: 321062--321104 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
321052 AAAATATTAA
321062 TTTAAAAAATAAATTTG
1 TTTAAAAAATAAATTTG
* *
321079 ATTAAAAAATAAATATTT
1 TTTAAAAAATAAAT-TTG
321097 TTTAAAAA
1 TTTAAAAA
321105 TAAGTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAAAAATAAATTTG
Found at i:321320 original size:21 final size:21
Alignment explanation
Indices: 321296--321346 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
321286 CAAATGTTAG
* *
321296 TAAAAAATAATATT-AAATTAT
1 TAAAAAATAA-ATTAAAAATAA
*
321317 TAAAAATTAAATTAAAAATAA
1 TAAAAAATAAATTAAAAATAA
321338 TAAAAAATA
1 TAAAAAATA
321347 TATAATACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAAATAAATTAAAAATAA
Found at i:323684 original size:26 final size:26
Alignment explanation
Indices: 323655--323704 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
323645 AATATATTCT
323655 CTAAAAAACTAAAGAAAATTAAATAA
1 CTAAAAAACTAAAGAAAATTAAATAA
* * **
323681 CTAACAAATTAATTAAAATTAAAT
1 CTAAAAAACTAAAGAAAATTAAAT
323705 TAAATCCACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (26 bp):
CTAAAAAACTAAAGAAAATTAAATAA
Found at i:323896 original size:17 final size:15
Alignment explanation
Indices: 323876--323915 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
323866 TCTAAATTAT
323876 TATTAAAAAATATTAAA
1 TATTAAAAAAT-TT-AA
*
323893 TATTAAAAAATTTTA
1 TATTAAAAAATTTAA
323908 TATTAAAA
1 TATTAAAA
323916 TTTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 2 0.09
17 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTAAAAAATTTAA
Found at i:323910 original size:15 final size:15
Alignment explanation
Indices: 323876--323924 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 15
323866 TCTAAATTAT
*
323876 TATTAAAAAATATTAAA
1 TATTAAAAAAT-TT-TA
323893 TATTAAAAAATTTTA
1 TATTAAAAAATTTTA
323908 TATT--AAAATTTTA
1 TATTAAAAAATTTTA
323921 TATT
1 TATT
323925 TTATAGTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 13 0.42
15 5 0.16
16 2 0.06
17 11 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAAAAATTTTA
Found at i:328407 original size:50 final size:51
Alignment explanation
Indices: 328299--328416 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 51
328289 CCTCGAAAAT
* * * **
328299 AATGGGGTTGGGGTATCTTTGATGGTGAGAAATTTATATTTTGGAAATAAA
1 AATGGGGTTGGAGTATCTTTGATGATGAAAAATCGATATTTTGGAAATAAA
328350 AATGGGGTTGGAGTAT-TTTCGATGATGAAAAATCGATA-TTTGGAAAT-AA
1 AATGGGGTTGGAGTATCTTT-GATGATGAAAAATCGATATTTTGGAAATAAA
328399 AATCGGGGTTGGAGTATC
1 AAT-GGGGTTGGAGTATC
328417 CCCTCGAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 5 0.08
50 25 0.42
51 29 0.49
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (51 bp):
AATGGGGTTGGAGTATCTTTGATGATGAAAAATCGATATTTTGGAAATAAA
Found at i:328503 original size:51 final size:51
Alignment explanation
Indices: 328448--328547 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
328438 GAATATCCCT
*
328448 GATGGTGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTAAAGTATCCAC
1 GATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTTAAAGTATCCAC
* **
328499 GATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTTAAAGTATCC
328548 TCTTAGAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (51 bp):
GATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTTAAAGTATCCAC
Found at i:328564 original size:79 final size:79
Alignment explanation
Indices: 328483--328924 Score: 414
Period size: 79 Copynumber: 5.6 Consensus size: 79
328473 AATAAAATCG
* *
328483 GGGTTAAAGTATCCACGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
*
328548 TCTTAG-AAATAACG
66 -CTTAGAAAATAACA
* * * ** *
328562 GGGTTAGAGTATCCTCGATGGTGGAAAATCGATGTTTTTGAAATAAAATCGATGTTAGAGTATCT
1 GGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC-
328627 CCTT-GAAAATAACA
65 CCTTAGAAAATAACA
* * * ** * *
328641 GGATTAAAATATCCCTAATGGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTCGGAGTATCC
1 GGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
*
328706 CTTCGAAAATAACA
66 CTTAGAAAATAACA
* * * ** * *
328720 GGGTTTGACTATCCCCGATAGTGAAAAATTAATGTTTTTA-AAATAAAA-CTGGGGTTGAAGCAT
1 GGGTTAGAGTATCCCCGATGGTGAAAAATCGATG-TTTTAGAAATAAAATC-GGGGTTGGAGTAT
*
328783 CCCCTAGAAAATAACA
64 CCCTTAGAAAATAACA
** * * * * * *
328799 AAGTTGGAGTATCCCCGATGGTGAAAAATTGGTATTTTAAAAATAAAA-CTGGGGTTGAAGTATT
1 GGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC-GGGGTTGGAGTA-T
* * *
328863 CCC-TCGAACATAGCA
64 CCCTTAGAAAATAACA
* * *
328878 GGGTTGGAGTATCCCTC-AT-GTGAAAAATCAATATTTTAGAAATAAAA
1 GGGTTAGAGTATCCC-CGATGGTGAAAAATCGATGTTTTAGAAATAAAA
328925 ACATCAATGA
Statistics
Matches: 303, Mismatches: 52, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
78 35 0.12
79 257 0.85
80 11 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (79 bp):
GGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
CTTAGAAAATAACA
Found at i:328584 original size:130 final size:129
Alignment explanation
Indices: 328266--328612 Score: 394
Period size: 129 Copynumber: 2.7 Consensus size: 129
328256 TATTTTGGAG
* * * * * * *
328266 ATAAAAACGGGGTTGAAGTATCCCCTCGAAAATAATGGGGTTGGGGTATCTTTGATGGTGAGAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAA
** * ** *** *
328331 TTTATATTTTGGAAATAAAAAT-GGGGTTGGAGTATTTTCGATGATGAAAAATCGATATTTGGAA
66 TCGATATTTTAGAAAT-AAAATCGGGGTTAAAGTATCCACGATGATGAAAAATCGATATTTAGAA
* *
328395 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGAGTTGGAATATCC-CTGATGGTGAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTC-GATGGTGAAAA
* * *
328459 ATCGGTATTTTAGAAATAAAATCGGGGTTAAAGTATCCACGATGGTGAAAAATCGATGTTTTAGA
65 ATCGATATTTTAGAAATAAAATCGGGGTTAAAGTATCCACGATGATGAAAAATCGAT-ATTTAGA
328524 A
129 A
* * * *
328525 ATAAAATCGGGGTTGGAGTATCCTCT-TAGAAATAACGGGGTTAGAGTATCCTCGATGGTGGAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCTCGATGGTGAAAA
* *
328589 ATCGATGTTTTTGAAATAAAATCG
65 ATCGATATTTTAGAAATAAAATCG
328613 ATGTTAGAGT
Statistics
Matches: 183, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
128 5 0.03
129 96 0.52
130 81 0.44
131 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (129 bp):
ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAA
TCGATATTTTAGAAATAAAATCGGGGTTAAAGTATCCACGATGATGAAAAATCGATATTTAGAA
Found at i:331352 original size:51 final size:51
Alignment explanation
Indices: 331265--331393 Score: 186
Period size: 51 Copynumber: 2.5 Consensus size: 51
331255 CAAAAGTATT
* * *
331265 GATACATTAAGAAATGTATCGATACATCTAGGTTAAAATCCAGAATATATC
1 GATACAATAAAAAATGTATCGATACATCTAGGTTAAAACCCAGAATATATC
* * *
331316 GATATAATGAAAAATGTATCGATACATCTGGGTTAAAACCCAGAATATATC
1 GATACAATAAAAAATGTATCGATACATCTAGGTTAAAACCCAGAATATATC
*
331367 GATACAATAAAAAATTATATCGATACA
1 GATACAATAAAAAA-TGTATCGATACA
331394 AACAGTAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 57 0.84
52 11 0.16
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (51 bp):
GATACAATAAAAAATGTATCGATACATCTAGGTTAAAACCCAGAATATATC
Found at i:333465 original size:2 final size:2
Alignment explanation
Indices: 333458--333489 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
333448 GCAATAATTC
333458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
333490 GTAACTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334659 original size:15 final size:15
Alignment explanation
Indices: 334639--334674 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
334629 TTAAAATTCG
334639 AATCTCAGTATCTGA
1 AATCTCAGTATCTGA
*
334654 AATCTCAGTATCTGT
1 AATCTCAGTATCTGA
334669 AATCTC
1 AATCTC
334675 TTCTCTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (15 bp):
AATCTCAGTATCTGA
Found at i:335181 original size:18 final size:17
Alignment explanation
Indices: 335149--335182 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
335139 CAACATCAAT
*
335149 ATATTTAATATTTATAA
1 ATATTTAAGATTTATAA
335166 ATATTTAAAGATTTATA
1 ATATTT-AAGATTTATA
335183 TTCTCGTTAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATTTAAGATTTATAA
Found at i:335363 original size:19 final size:19
Alignment explanation
Indices: 335328--335369 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
335318 AATATTTATT
335328 TAAATTTAATTAAAAAATA
1 TAAATTTAATTAAAAAATA
335347 TAAATATTAATATAAAATAATA
1 TAAAT-TTAAT-TAAAA-AATA
335369 T
1 T
335370 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 5 0.25
22 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTAAAAAATA
Found at i:337461 original size:13 final size:13
Alignment explanation
Indices: 337434--337467 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
337424 TTATTTGATT
*
337434 TTAATT-TTTTTA
1 TTAATTATTTTAA
337446 TTAATTATTTTAA
1 TTAATTATTTTAA
337459 TTAATTATT
1 TTAATTATT
337468 GATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTAATTATTTTAA
Found at i:337833 original size:6 final size:6
Alignment explanation
Indices: 337824--337855 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
337814 ATATTAAATA
337824 AATTTT AATTTT AATTTT AATTTT AATGTTT A
1 AATTTT AATTTT AATTTT AATTTT AAT-TTT A
337856 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:338027 original size:14 final size:15
Alignment explanation
Indices: 337987--338034 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
337977 ATAAATTTAA
337987 TTATAAAAAAATATT
1 TTATAAAAAAATATT
*
338002 ATTAATATAAAAATATT
1 -TT-ATAAAAAAATATT
338019 TT-TAAAAAAAT-TT
1 TTATAAAAAAATATT
338032 TTA
1 TTA
338035 AATAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
16 4 0.14
17 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAAAAAAATATT
Found at i:338055 original size:20 final size:22
Alignment explanation
Indices: 338020--338067 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
338010 AAAAATATTT
*
338020 TTAAAA-AAATTTTTAAA-TAA
1 TTAAAATAAATTATTAAATTAA
338040 -TAAAATAAATTATTAAATTAA
1 TTAAAATAAATTATTAAATTAA
338061 TTAAAAT
1 TTAAAAT
338068 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 3 0.12
22 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATAAATTATTAAATTAA
Found at i:338278 original size:20 final size:21
Alignment explanation
Indices: 338253--338297 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
338243 TGTAATTTTA
338253 TTAAAATAA-TATATT-AAATT
1 TTAAAA-AATTATATTAAAATT
*
338273 TTAAAAAATTATTTTAAAATT
1 TTAAAAAATTATATTAAAATT
338294 TTAA
1 TTAA
338298 TTAAATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 11 0.50
21 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAAAATTATATTAAAATT
Found at i:338588 original size:13 final size:14
Alignment explanation
Indices: 338572--338609 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
338562 AAATACATAT
338572 AATATAATTA-TAA
1 AATATAATTATTAA
338585 AATATAATTTATTAA
1 AATATAA-TTATTAA
338600 ATATATAATT
1 A-ATATAATT
338610 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 6 0.27
16 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATAATTATTAA
Found at i:338607 original size:16 final size:14
Alignment explanation
Indices: 338572--338610 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
338562 AAATACATAT
338572 AATATAA-TTATAA
1 AATATAATTTATAA
338585 AATATAATTTATTAA
1 AATATAATTTA-TAA
338600 ATATATAATTT
1 A-ATATAATTT
338611 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 4 0.17
16 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATAATTTATAA
Found at i:338624 original size:24 final size:24
Alignment explanation
Indices: 338595--338668 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
338585 AATATAATTT
338595 ATTAAATATATAATTTTTTTAAAA
1 ATTAAATATATAATTTTTTTAAAA
* * *
338619 ATTAAATATAT-ATTTATATCAAA
1 ATTAAATATATAATTTTTTTAAAA
* *
338642 ATTATAT-TATAAAATTTTTTAAAA
1 ATTAAATATAT-AATTTTTTTAAAA
338666 ATT
1 ATT
338669 TTATACTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 3 0.08
23 15 0.38
24 22 0.55
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAAATATATAATTTTTTTAAAA
Found at i:338792 original size:17 final size:19
Alignment explanation
Indices: 338767--338810 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
338757 TTTTTTTTCA
338767 TTATATTTT-TAAAAATAT
1 TTATATTTTATAAAAATAT
*
338785 TT-TATTTTATAATAATAT
1 TTATATTTTATAAAAATAT
338803 TTATATTT
1 TTATATTT
338811 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTTTATAAAAATAT
Found at i:338824 original size:31 final size:32
Alignment explanation
Indices: 338780--338840 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
338770 TATTTTTAAA
338780 AATATTTTATTTTATA-ATAATATT-TATATTT
1 AATATTTTATTTTATACAT-ATATTATATATTT
338811 AATA-TTTATTTTTATACATATATTATATAT
1 AATATTTTA-TTTTATACATATATTATATAT
338841 AAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
AATATTTTATTTTATACATATATTATATATTT
Found at i:338851 original size:31 final size:31
Alignment explanation
Indices: 338789--338852 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
338779 AAATATTTTA
* *
338789 TTTTATAATAATATTTATATTTAATATTTAT
1 TTTTATAATAATATTTATATTAAATAATTAT
338820 TTTTATACAT-ATA-TTATATATAAATAATTAT
1 TTTTATA-ATAATATTTATAT-TAAATAATTAT
338851 TT
1 TT
338853 AATATACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.21
31 21 0.72
32 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTATAATAATATTTATATTAAATAATTAT
Found at i:342170 original size:22 final size:21
Alignment explanation
Indices: 342127--342166 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
342117 TATTTTTATT
342127 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
342148 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
342167 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:342187 original size:12 final size:11
Alignment explanation
Indices: 342142--342192 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
342132 TTAATTATAA
342142 AATATATAAAT
1 AATATATAAAT
*
342153 ATTAATATAAAAT
1 AAT-ATAT-AAAT
*
342166 AATATTTAAAT
1 AATATATAAAT
342177 AATATAATAAAT
1 AATAT-ATAAAT
342189 AATA
1 AATA
342193 AAATGAGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 11 0.33
12 16 0.48
13 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATATAAAT
Found at i:344730 original size:25 final size:25
Alignment explanation
Indices: 344679--344735 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
344669 TTTATATTTT
*** *
344679 ATTTAAGTAAATTATGCATGTCAAA
1 ATTTAAGTAAATTAAAAATGACAAA
*
344704 ATTTAAGTAAATTAAAAATGACTAA
1 ATTTAAGTAAATTAAAAATGACAAA
344729 ATATTAA
1 AT-TTAA
344736 TTTAATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (25 bp):
ATTTAAGTAAATTAAAAATGACAAA
Found at i:345780 original size:24 final size:24
Alignment explanation
Indices: 345753--345798 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
345743 ATAAATTTGA
345753 TTTA-AATTAGATTAAATTTAAATT
1 TTTATAATTAG-TTAAATTTAAATT
*
345777 TTTATATTTAGTTAAATTTAAA
1 TTTATAATTAGTTAAATTTAAA
345799 ATCATTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTATAATTAGTTAAATTTAAATT
Found at i:346277 original size:12 final size:12
Alignment explanation
Indices: 346260--346289 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
346250 TCCATTCATG
346260 TATATAAATGTA
1 TATATAAATGTA
346272 TATATAAATGTA
1 TATATAAATGTA
346284 TATATA
1 TATATA
346290 TATTGATGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
TATATAAATGTA
Found at i:346538 original size:3 final size:3
Alignment explanation
Indices: 346530--346566 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
346520 AACAGTTGGT
346530 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
346567 GGGAAGTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:347125 original size:5 final size:5
Alignment explanation
Indices: 347117--347203 Score: 60
Period size: 5 Copynumber: 18.0 Consensus size: 5
347107 ATGATATGAA
* *
347117 AATAT AATAT AA-AT -ATGAT ACATTT AATA- AATAT AAAAT AATAT AATA-
1 AATAT AATAT AATAT AAT-AT A-ATAT AATAT AATAT AATAT AATAT AATAT
* * *
347165 AATAT GATAT AATA- AATTT CAATAT AAT-T AATAT TATAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
347204 GTTTCATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
3 1 0.02
4 17 0.27
5 38 0.59
6 6 0.09
7 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:347176 original size:19 final size:19
Alignment explanation
Indices: 347102--347178 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
347092 ATCGTTATTT
347102 TAAATATGATATGAAAATATAATA
1 TAAATATGATAT---AATAT-A-A
* *
347126 TAAATATGATA-CATTTAA
1 TAAATATGATATAATATAA
* *
347144 TAAATATAAAATAATATAA
1 TAAATATGATATAATATAA
347163 TAAATATGATATAATA
1 TAAATATGATATAATA
347179 AATTTCAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 10 0.23
19 20 0.45
20 3 0.07
24 11 0.25
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAATATGATATAATATAA
Found at i:347558 original size:27 final size:26
Alignment explanation
Indices: 347528--347593 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 26
347518 GGTTGAATTG
347528 AATTATTATTTAATAATAAAAAATTAT
1 AATTATTATTTAATAATAAAAAA-TAT
*
347555 AATTATTTAAATTTAATAATAAAATATAT
1 AATTA-TT--ATTTAATAATAAAAAATAT
*
347584 AAATATTATT
1 AATTATTATT
347594 ATAAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.09
27 5 0.15
28 4 0.12
29 7 0.21
30 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTATTATTTAATAATAAAAAATAT
Found at i:347602 original size:35 final size:30
Alignment explanation
Indices: 347535--347598 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 30
347525 TTGAATTATT
*
347535 ATTTAATAATAAAAAATTATAATTATTTAA
1 ATTTAATAATAAAAAATTAAAATTATTTAA
*
347565 ATTTAATAATAAAATATATAAATATTATTATAA
1 ATTTAATAATAAAAAAT-TAAA-ATTATT-TAA
347598 A
1 A
347599 AATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.55
31 3 0.10
32 6 0.21
33 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTTAATAATAAAAAATTAAAATTATTTAA
Found at i:347629 original size:15 final size:15
Alignment explanation
Indices: 347581--347631 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
347571 TAATAAAATA
*
347581 TATAAA-TATTATTA
1 TATAAATTATTATTT
*
347595 TAAAAATTATT-TTT
1 TATAAATTATTATTT
*
347609 TAATAATTTATTATTT
1 T-ATAAATTATTATTT
347625 TATAAAT
1 TATAAAT
347632 AGAGATCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 8 0.28
15 17 0.59
16 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAAATTATTATTT
Found at i:347759 original size:17 final size:17
Alignment explanation
Indices: 347737--347772 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
347727 TCTTACGATT
*
347737 AATGATTGGTGTAAAAA
1 AATGATTGATGTAAAAA
347754 AATGATTGATGTAAAAA
1 AATGATTGATGTAAAAA
347771 AA
1 AA
347773 AAAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (17 bp):
AATGATTGATGTAAAAA
Found at i:348580 original size:2 final size:2
Alignment explanation
Indices: 348568--348599 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
348558 TCGCCATTTT
*
348568 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
348600 AAACGTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:348891 original size:21 final size:21
Alignment explanation
Indices: 348858--348911 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
348848 CATTAACTTA
*
348858 ATTA-AAAAATAAAAG-ATAAT
1 ATTATAAAATTAAAAGAAT-AT
*
348878 ATTATAAAATTAAAATAATAT
1 ATTATAAAATTAAAAGAATAT
348899 ATTAATAAAATTA
1 ATT-ATAAAATTA
348912 TATAAGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.14
21 14 0.48
22 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTATAAAATTAAAAGAATAT
Found at i:348897 original size:19 final size:20
Alignment explanation
Indices: 348858--348898 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
348848 CATTAACTTA
348858 ATTAAAAAATAAAAGATAAT
1 ATTAAAAAATAAAAGATAAT
* *
348878 ATTATAAAATTAAA-ATAAT
1 ATTAAAAAATAAAAGATAAT
348897 AT
1 AT
348899 ATTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTAAAAAATAAAAGATAAT
Found at i:348916 original size:21 final size:23
Alignment explanation
Indices: 348876--348924 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
348866 ATAAAAGATA
348876 ATATT-ATAAAATTAAAATAA-T
1 ATATTAATAAAATTAAAATAAGT
*
348897 ATATTAATAAAATT-ATATAAGT
1 ATATTAATAAAATTAAAATAAGT
348919 A-ATTAA
1 ATATTAA
348925 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATTAATAAAATTAAAATAAGT
Found at i:349187 original size:2 final size:2
Alignment explanation
Indices: 349180--349218 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
349170 CCATAAAAAT
349180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
349219 ATAAAGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:349396 original size:14 final size:14
Alignment explanation
Indices: 349347--349397 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
349337 ATTAACAAAA
349347 AAATATAAATT-TAT
1 AAATA-AAATTATAT
349361 AAATAAAAGTAATATAT
1 AAATAAAA-T--TATAT
*
349378 TAATAAAATTATAT
1 AAATAAAATTATAT
349392 AAATAA
1 AAATAA
349398 TTAGATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
16 2 0.06
17 10 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AAATAAAATTATAT
Found at i:350965 original size:26 final size:26
Alignment explanation
Indices: 350902--350965 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
350892 TCATAAATTT
350902 AAATTAT-TATTTATTTTTATTTAAA
1 AAATTATATATTTATTTTTATTTAAA
* *
350927 AAATTAAAAATTTATTTTTATATT-AA
1 AAATTATATATTTATTTTTAT-TTAAA
* *
350953 TATTTATATATTT
1 AAATTATATATTT
350966 TATCAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 6 0.19
26 23 0.74
27 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
AAATTATATATTTATTTTTATTTAAA
Found at i:360047 original size:1 final size:1
Alignment explanation
Indices: 360037--360129 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
360027 TGGCAATTGG
* * * ** * * * **
360037 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAGGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
360102 AGAAAGAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
360130 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:360129 original size:36 final size:32
Alignment explanation
Indices: 360043--360126 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
360033 TTGGAAAAAG
360043 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
1 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
360075 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
1 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
*
360107 GAAAAAA-AAAACAAAAAAAA
1 AAAAAAACAAAACAAAAAAAA
360127 AAAGTGAAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 13 0.25
32 38 0.75
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
Found at i:364124 original size:50 final size:50
Alignment explanation
Indices: 364020--364231 Score: 316
Period size: 50 Copynumber: 4.2 Consensus size: 50
364010 AGGTATTGCC
* * *
364020 ATTGTTGACTATTCTTCACAAAAACCTTTGACAATCGAAAGAGATGACCGTA
1 ATTGTTGACTATTCTTCAC--CAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
364072 ATTGTTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
364122 ATTATTGACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
364172 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
364222 ATTGTTGACT
1 ATTGTTGACT
364232 TAAGCATGGC
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 127 0.87
52 19 0.13
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:364635 original size:29 final size:29
Alignment explanation
Indices: 364598--364653 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
364588 TTTTTTTAGT
364598 ATAAATATAAATTTTAATTATTAATTAAA
1 ATAAATATAAATTTTAATTATTAATTAAA
* *
364627 ATAAATATAATTTTTAATTATTTATTA
1 ATAAATATAAATTTTAATTATTAATTA
364654 TTATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAAATATAAATTTTAATTATTAATTAAA
Found at i:364663 original size:29 final size:29
Alignment explanation
Indices: 364597--364663 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
364587 ATTTTTTTAG
364597 TATAAATATAAATTTTAATTATTAATTAA
1 TATAAATATAAATTTTAATTATTAATTAA
* * * *
364626 AATAAATATAATTTTTAATTATTTATTAT
1 TATAAATATAAATTTTAATTATTAATTAA
*
364655 TATATATAT
1 TATAAATAT
364664 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TATAAATATAAATTTTAATTATTAATTAA
Found at i:365042 original size:22 final size:23
Alignment explanation
Indices: 365000--365046 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
364990 TAATATATTT
365000 TATTTAAAATTAATTATTAAAAA
1 TATTTAAAATTAATTATTAAAAA
365023 TATTTAAATATTAA-TA-TAAAAA
1 TATTTAAA-ATTAATTATTAAAAA
365045 TA
1 TA
365047 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 10 0.43
24 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTAAAATTAATTATTAAAAA
Found at i:365049 original size:17 final size:19
Alignment explanation
Indices: 365029--365068 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
365019 AAAATATTTA
365029 AATA-TTAATATAA-AAAT
1 AATATTTAATATAATAAAT
365046 AATATTTTAATATAATAAAT
1 AATA-TTTAATATAATAAAT
365066 AAT
1 AAT
365069 GAAATGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTTAATATAATAAAT
Found at i:365365 original size:16 final size:15
Alignment explanation
Indices: 365344--365382 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
365334 CATTTTGACC
365344 TTTAAATATATATATA
1 TTTAAATATATA-ATA
*
365360 TTTAAAAATATAATA
1 TTTAAATATATAATA
365375 TATTAAAT
1 T-TTAAAT
365383 TGATACGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAATATATAATA
Found at i:365825 original size:19 final size:19
Alignment explanation
Indices: 365796--365833 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
365786 CTAGATATAA
365796 AATAGTATTTTATATTAAAT
1 AATAGTATTTTAT-TTAAAT
365816 AATA-TATTTTATTTAAAT
1 AATAGTATTTTATTTAAAT
365834 TTAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AATAGTATTTTATTTAAAT
Found at i:367512 original size:10 final size:10
Alignment explanation
Indices: 367497--367521 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
367487 ATGCTCAAAA
367497 TTTTTTAAAT
1 TTTTTTAAAT
367507 TTTTTTAAAT
1 TTTTTTAAAT
367517 TTTTT
1 TTTTT
367522 ATATATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:367596 original size:13 final size:13
Alignment explanation
Indices: 367572--367611 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
367562 TCTTAATGCG
*
367572 TCAAAAATAAATA
1 TCAAACATAAATA
* *
367585 TCGAATATAAATA
1 TCAAACATAAATA
367598 TCAAACATAAATA
1 TCAAACATAAATA
367611 T
1 T
367612 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (13 bp):
TCAAACATAAATA
Found at i:371196 original size:19 final size:19
Alignment explanation
Indices: 371172--371211 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
371162 ATAAAAATAC
371172 TTTTAATAA-TAATATAAAT
1 TTTTAA-AATTAATATAAAT
*
371191 TTTTAAAATTAATTTAAAT
1 TTTTAAAATTAATATAAAT
371210 TT
1 TT
371212 AACTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTAATATAAAT
Found at i:371220 original size:16 final size:16
Alignment explanation
Indices: 371199--371229 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
371189 ATTTTTAAAA
371199 TTAATTTAAATTTAAC
1 TTAATTTAAATTTAAC
371215 TTAATTTAAATTTAA
1 TTAATTTAAATTTAA
371230 AAAATTATAT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATTTAAATTTAAC
Found at i:371720 original size:12 final size:12
Alignment explanation
Indices: 371703--371737 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
371693 CACATTAAAC
371703 TTCATAAATTTT
1 TTCATAAATTTT
371715 TTCATAAAATTTT
1 TTCAT-AAATTTT
*
371728 TTTATAAATT
1 TTCATAAATT
371738 CGATACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCATAAATTTT
Found at i:376703 original size:27 final size:28
Alignment explanation
Indices: 376672--376725 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
376662 GTTACCAAAC
376672 CAACCTAGAGT-AAAACAAGAAATAAAG
1 CAACCTAGAGTAAAAACAAGAAATAAAG
*
376699 CAACCTAGTGTAAAAACAAGAAATAAA
1 CAACCTAGAGTAAAAACAAGAAATAAA
376726 TGAAATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.13
Consensus pattern (28 bp):
CAACCTAGAGTAAAAACAAGAAATAAAG
Found at i:379496 original size:19 final size:19
Alignment explanation
Indices: 379472--379508 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
379462 CATTGTTATC
379472 TAATATAGATAATAGTTAG
1 TAATATAGATAATAGTTAG
379491 TAATATAGATAATAGTTA
1 TAATATAGATAATAGTTA
379509 TATAATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATATAGATAATAGTTAG
Found at i:379622 original size:107 final size:108
Alignment explanation
Indices: 379501--379712 Score: 372
Period size: 107 Copynumber: 2.0 Consensus size: 108
379491 TAATATAGAT
*
379501 AATAGTTATATAATCTATTAGTAGAGTGTTAAATTTCAATTTTAATTATCTGAATTTAAATGTAA
1 AATAGTTATATAATCTATTACTAGAGTGTTAAATTTCAATTTTAATTATCTGAATTTAAATGTAA
379566 AACCTTAATAATAGATTAAGTTGACATTTAAAA-CTTTTTTTC
66 AACCTTAATAATAGATTAAGTTGACATTTAAAATCTTTTTTTC
* *
379608 AATAGTTATATAATCTATTACTAGAGTGTTAAATTTCAATTTTAGTTATCTTAATTTAAATGTAA
1 AATAGTTATATAATCTATTACTAGAGTGTTAAATTTCAATTTTAATTATCTGAATTTAAATGTAA
* *
379673 AACCTTAATAATAGATTGAGTTGATATTTAAAATCTTTTT
66 AACCTTAATAATAGATTAAGTTGACATTTAAAATCTTTTT
379713 CTAAGCCCAA
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 93 0.94
108 6 0.06
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (108 bp):
AATAGTTATATAATCTATTACTAGAGTGTTAAATTTCAATTTTAATTATCTGAATTTAAATGTAA
AACCTTAATAATAGATTAAGTTGACATTTAAAATCTTTTTTTC
Found at i:382011 original size:18 final size:18
Alignment explanation
Indices: 381966--382004 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
381956 AAATTTTTAT
*
381966 TTATATTATATTTATATA
1 TTATATTATATTTAAATA
381984 TTATATTATATTTAAAATA
1 TTATATTATATTT-AAATA
382003 TT
1 TT
382005 TTATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATTATATTTAAATA
Found at i:382960 original size:106 final size:106
Alignment explanation
Indices: 382775--382986 Score: 370
Period size: 106 Copynumber: 2.0 Consensus size: 106
382765 TCATTTTCAC
*
382775 GTGACTCAATTTCATCAAATTTGTTCTCATGGAATTACAACTTTTATCAAAAGGATATTTTCATC
1 GTGACTCAATTTCATCAAATTTGTTCTCATGAAATTACAACTTTTATCAAAAGGATATTTTCATC
382840 AAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAATGG
66 AAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAATGG
* * * * *
382881 GTGACTTAATTTCATCAAATTTGTTCTCATTAAATTCCTACTTTTATCAAAAGGATCTTTTCATC
1 GTGACTCAATTTCATCAAATTTGTTCTCATGAAATTACAACTTTTATCAAAAGGATATTTTCATC
382946 AAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAATGG
66 AAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAATGG
382987 CACCTTACTA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (106 bp):
GTGACTCAATTTCATCAAATTTGTTCTCATGAAATTACAACTTTTATCAAAAGGATATTTTCATC
AAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAATGG
Found at i:383022 original size:106 final size:105
Alignment explanation
Indices: 382814--383022 Score: 251
Period size: 106 Copynumber: 2.0 Consensus size: 105
382804 TGGAATTACA
382814 ACTTTTATCAAAAGGATATTTTCATCAAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAAT
1 ACTTTTATCAAAAGGATATTTTCATCAAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAAT
* *** * ** ***
382879 GGGTGACTTAATTTCATCAAATTTGTTCTCATTAAATTCCT
66 GGCTGACTTAAAGGCACCAAATTCCTAAGCA-TAAATTCCT
*
382920 ACTTTTATCAAAAGGATCTTTTCATCAAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAAT
1 ACTTTTATCAAAAGGATATTTTCATCAAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAAT
* *
382985 GGCACCTTAC-TAAAGGCACCACATTCCTAAGCA-AAATT
66 GG---CTGACTTAAAGGCACCAAATTCCTAAGCATAAATT
383023 ATGCACTTAG
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
106 71 0.82
108 13 0.15
109 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (105 bp):
ACTTTTATCAAAAGGATATTTTCATCAAAAAGAAAACACCTTATTGCTAAGAACTTTATTGTAAT
GGCTGACTTAAAGGCACCAAATTCCTAAGCATAAATTCCT
Found at i:383336 original size:17 final size:18
Alignment explanation
Indices: 383307--383341 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
383297 TATATTTAAT
383307 AAATTATATATTTATAAA
1 AAATTATATATTTATAAA
*
383325 AAATTA-ATATTTTTAAA
1 AAATTATATATTTATAAA
383342 TATTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATATATTTATAAA
Found at i:383361 original size:11 final size:11
Alignment explanation
Indices: 383341--383392 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
383331 ATATTTTTAA
383341 ATATTTATATT
1 ATATTTATATT
*
383352 ATATTAATATT
1 ATATTTATATT
*
383363 ATTTTTTATATT
1 A-TATTTATATT
*
383375 ATATTTATATC
1 ATATTTATATT
383386 ATATTTA
1 ATATTTA
383393 AAATTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTTATATT
Found at i:383398 original size:23 final size:23
Alignment explanation
Indices: 383324--383400 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
383314 ATATTTATAA
*
383324 AAAATTAATATTTTTA-AATATTT
1 AAAATT-ATATTTATATAATATTT
* * * *
383347 -ATATTATATTAATATTATTTTT
1 AAAATTATATTTATATAATATTT
* * *
383369 TATATTATATTTATATCATATTT
1 AAAATTATATTTATATAATATTT
383392 AAAATTATA
1 AAAATTATA
383401 AAATTTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 7 0.17
22 9 0.21
23 26 0.62
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
AAAATTATATTTATATAATATTT
Found at i:383920 original size:18 final size:18
Alignment explanation
Indices: 383867--383920 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
383857 TATTTAAAAA
383867 AATTTATGATT-TAATTTT
1 AATTTAT-ATTATAATTTT
* **
383885 AATTTATATAATTTTTTT
1 AATTTATATTATAATTTT
*
383903 ATTTTATATTATAATTTT
1 AATTTATATTATAATTTT
383921 TTATTCAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTTATATTATAATTTT
Found at i:384211 original size:16 final size:16
Alignment explanation
Indices: 384192--384225 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
384182 ATATTAATAA
*
384192 TATATTAAAATAAATT
1 TATATAAAAATAAATT
384208 TATATAAAAATAAATT
1 TATATAAAAATAAATT
384224 TA
1 TA
384226 ACATATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAAAATAAATT
Found at i:384260 original size:19 final size:19
Alignment explanation
Indices: 384236--384278 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
384226 ACATATAATG
384236 TAATAAAATAATTAAAATA-
1 TAATAAAAT-ATTAAAATAT
*
384255 TAATAAAATATTAATATAT
1 TAATAAAATATTAAAATAT
384274 TAATA
1 TAATA
384279 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAAAATATTAAAATAT
Found at i:384264 original size:24 final size:26
Alignment explanation
Indices: 384214--384264 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
384204 AATTTATATA
* **
384214 AAAATAAATTTAACATATAATGTAAT
1 AAAATAAATTTAAAATATAATAAAAT
384240 AAAAT-AA-TTAAAATATAATAAAAT
1 AAAATAAATTTAAAATATAATAAAAT
384264 A
1 A
384265 TTAATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATAAATTTAAAATATAATAAAAT
Found at i:384306 original size:22 final size:23
Alignment explanation
Indices: 384281--384326 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
384271 TATTAATATT
384281 TTAAAATTTATAT-AATATAAAA
1 TTAAAATTTATATAAATATAAAA
*
384303 TTAATATTTATATAAATATAAAA
1 TTAAAATTTATATAAATATAAAA
384326 T
1 T
384327 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAATTTATATAAATATAAAA
Found at i:384308 original size:49 final size:48
Alignment explanation
Indices: 384243--384339 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 48
384233 ATGTAATAAA
* *
384243 ATAATTAAAATATAATA-AAATATTAATATATTAATATTTTAAAATTTAT
1 ATAATTAAAATATAATATAAATATAAATATA-AAATATTTT-AAATTTAT
**
384292 ATAATATAAAAT-TAATATTTATATAAATATAAAATATTTTAAATTTAT
1 ATAAT-TAAAATATAATATAAATATAAATATAAAATATTTTAAATTTAT
384340 GATTATCTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 8 0.19
49 18 0.43
50 16 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (48 bp):
ATAATTAAAATATAATATAAATATAAATATAAAATATTTTAAATTTAT
Found at i:384328 original size:30 final size:31
Alignment explanation
Indices: 384247--384328 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
384237 AATAAAATAA
384247 TTAAAATATAATAAAATATTAATATATTAATATT
1 TTAAAAT-T-ATAAAATAT-AATATATTAATATT
*
384281 TTAAAATTTATATAATATAA-A-ATTAATATT
1 TTAAAA-TTATAAAATATAATATATTAATATT
384311 TATATAAA-TATAAAATAT
1 T-TA-AAATTATAAAATAT
384329 TTTAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
30 19 0.44
31 3 0.07
32 5 0.12
33 8 0.19
34 7 0.16
35 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAAATTATAAAATATAATATATTAATATT
Found at i:385483 original size:33 final size:32
Alignment explanation
Indices: 385446--385548 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 32
385436 TCGAATTCGA
*
385446 TTAAATTTTAGAGAAAATTTTATTTATCAATTT
1 TTAAATTTTA-AGAAAATTTTATTTATAAATTT
* * *
385479 TTAAAATTTAAAAATAATATT-TTTA-AATATTT
1 TTAAATTTTAAGAA-AATTTTATTTATAA-ATTT
385511 TTATTAATTTTAAAGTAAAATATTTATTTATAAATTT
1 TTA--AATTTT-AAG-AAAAT-TTTATTTATAAATTT
385548 T
1 T
385549 AAAAAATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
31 1 0.02
32 14 0.26
33 14 0.26
34 5 0.09
35 5 0.09
36 4 0.07
37 9 0.17
38 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (32 bp):
TTAAATTTTAAGAAAATTTTATTTATAAATTT
Found at i:386870 original size:17 final size:17
Alignment explanation
Indices: 386848--386882 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
386838 TGGTTAAATG
* *
386848 TGTCAGATATAGGTATA
1 TGTCAGACATAGATATA
386865 TGTCAGACATAGATATA
1 TGTCAGACATAGATATA
386882 T
1 T
386883 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (17 bp):
TGTCAGACATAGATATA
Found at i:387755 original size:30 final size:30
Alignment explanation
Indices: 387719--387778 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
387709 AAAGACCCTT
387719 TAAGTATATGGAAATCTTTGAAAAATTTAA
1 TAAGTATATGGAAATCTTTGAAAAATTTAA
387749 TAAGTATATGGAAATCTTTGAAAAATTTAA
1 TAAGTATATGGAAATCTTTGAAAAATTTAA
387779 CATAACCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (30 bp):
TAAGTATATGGAAATCTTTGAAAAATTTAA
Found at i:389172 original size:17 final size:17
Alignment explanation
Indices: 389152--389250 Score: 67
Period size: 17 Copynumber: 5.5 Consensus size: 17
389142 ATTAATTTAT
389152 TTTTAATATAAATATAA
1 TTTTAATATAAATATAA
*
389169 TTTTAATAAATTTAAAT-TAT
1 TTTTAAT--A--TAAATATAA
*
389189 TATTTAACATAAATATAA
1 T-TTTAATATAAATATAA
* *
389207 TTTTAATATAAATTTTATT
1 TTTTAATATAAA-TATA-A
*
389226 TTTTAATAT-AATCAGAA
1 TTTTAATATAAAT-ATAA
389243 TTTTAATA
1 TTTTAATA
389251 ATTTATTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
17 31 0.48
18 9 0.14
19 11 0.17
20 3 0.05
21 10 0.16
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTTAATATAAATATAA
Found at i:389201 original size:38 final size:37
Alignment explanation
Indices: 389143--389214 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
389133 ATTTTTATTA
* *
389143 TTAATTTATTTTTAATATAAATATAATTTTAATAAAT
1 TTAAATTATTTTTAACATAAATATAATTTTAATAAAT
389180 TTAAATTATTATTTAACATAAATATAATTTTAATA
1 TTAAATTATT-TTTAACATAAATATAATTTTAATA
389215 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 9 0.28
38 23 0.72
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
TTAAATTATTTTTAACATAAATATAATTTTAATAAAT
Found at i:391175 original size:13 final size:13
Alignment explanation
Indices: 391136--391183 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
391126 ATCATACATC
391136 ATATTAAGATACGAA
1 ATATTAA-ATAC-AA
*
391151 TATATATAAATATAA
1 -ATAT-TAAATACAA
391166 ATATTAAATACAA
1 ATATTAAATACAA
391179 ATATT
1 ATATT
391184 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 13 0.45
14 4 0.14
15 2 0.07
16 7 0.24
17 3 0.10
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (13 bp):
ATATTAAATACAA
Found at i:391829 original size:2 final size:2
Alignment explanation
Indices: 391822--391859 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
391812 ATCTATTTGT
391822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
391860 TTAATTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:397020 original size:22 final size:22
Alignment explanation
Indices: 396995--397042 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
396985 TAATTGCTAT
396995 CTGATAATTCATGATCAATTTC
1 CTGATAATTCATGATCAATTTC
*
397017 CTGATAATTCATGATTAATTTC
1 CTGATAATTCATGATCAATTTC
397039 CTGA
1 CTGA
397043 GAAGTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (22 bp):
CTGATAATTCATGATCAATTTC
Found at i:400390 original size:57 final size:56
Alignment explanation
Indices: 400302--400415 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 56
400292 TAATATCTTA
400302 AATCAAATACATCAGACAAGTACAAAATAATCAAACGAAAAATTAGCATAATTGTTC
1 AATCAAATACATCAGACAAGTACAAAATAATCAAAC-AAAAATTAGCATAATTGTTC
* ** * * *
400359 AATCAAATATATCAGACTGGTA-AAATATAATCAAACAAAACTTGGCTTAATTGTTC
1 AATCAAATACATCAGACAAGTACAAA-ATAATCAAACAAAAATTAGCATAATTGTTC
400415 A
1 A
400416 TAACAGCTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 21 0.42
57 29 0.58
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (56 bp):
AATCAAATACATCAGACAAGTACAAAATAATCAAACAAAAATTAGCATAATTGTTC
Found at i:400537 original size:13 final size:13
Alignment explanation
Indices: 400507--400552 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
400497 GCATCATAAT
400507 AATAT-AATA-TA
1 AATATAAATATTA
*
400518 TATATAAATATTA
1 AATATAAATATTA
400531 AATATAAATACTTA
1 AATATAAATA-TTA
400545 AA-ATAAAT
1 AATATAAAT
400553 GAAAAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 4 0.13
12 4 0.13
13 17 0.57
14 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:402298 original size:37 final size:38
Alignment explanation
Indices: 402218--402303 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
402208 GGTATAAGTT
*
402218 AGAACAAAAACTATTATTCTAATCCAGTGGCACGGTTG
1 AGAACAAAAACTACTATTCTAATCCAGTGGCACGGTTG
* * *
402256 AGAACAAAAACTACTATTCTTA-CCGGTGGCATGGGTTG
1 AGAACAAAAACTACTATTCTAATCCAGTGGCA-CGGTTG
402294 -GAACAAAAAC
1 AGAACAAAAAC
402304 CATTCCATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 18 0.42
38 25 0.58
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (38 bp):
AGAACAAAAACTACTATTCTAATCCAGTGGCACGGTTG
Found at i:405126 original size:13 final size:13
Alignment explanation
Indices: 405104--405142 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
405094 TACAAGGATT
*
405104 TGTATTGATACAA
1 TGTATCGATACAA
*
405117 TGTATCGATACAG
1 TGTATCGATACAA
405130 TGTATCGATACAA
1 TGTATCGATACAA
405143 AGGCACTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:407701 original size:19 final size:20
Alignment explanation
Indices: 407657--407727 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
407647 AGATCCAGAA
*
407657 GTATCGATACATATTACTTT
1 GTATCGATACATATTACTTG
407677 GTATCGATACATGA-T-CTTG
1 GTATCGATACAT-ATTACTTG
* * *
407696 GTATCGATATATAGTGAATT-
1 GTATCGATACATA-TTACTTG
407716 GTATCGATACAT
1 GTATCGATACAT
407728 GAAACTGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 24 0.57
21 3 0.07
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (20 bp):
GTATCGATACATATTACTTG
Found at i:409420 original size:84 final size:84
Alignment explanation
Indices: 409202--409426 Score: 236
Period size: 84 Copynumber: 2.7 Consensus size: 84
409192 TTCTACCCGT
* * * * * *
409202 TTCAGAATTCTCTAATTCTGAAGTTGCTGCAAATTGCATATCCTGAAGCATCCGAATGCCTAAAG
1 TTCAGAATTCTCTGATTCAGAACTTACTGCAGATTGCATATCCTGAAGCATACGAATGCCTAAAG
** * *
409267 CTGAACTTGTGCTATCATT
66 CTGAACTTGCACTACCATC
* * * * ** *
409286 TTTAGAATTCTCGGATACAGAACCTACTGCAGATTGTGTATCCTGAAGCATATGAATGCCTAAAG
1 TTCAGAATTCTCTGATTCAGAACTTACTGCAGATTGCATATCCTGAAGCATACGAATGCCTAAAG
* *
409351 CTGAGCTTGCATTACCATC
66 CTGAACTTGCACTACCATC
* * *
409370 TTCAGAATTCTCTGATTCCAGAA-TTACTGCAGATTGCATATCTTGGAGCATCCGAAT
1 TTCAGAATTCTCTGATT-CAGAACTTACTGCAGATTGCATATCCTGAAGCATACGAAT
409427 ACCCGCAGCT
Statistics
Matches: 111, Mismatches: 29, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
84 106 0.95
85 5 0.05
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (84 bp):
TTCAGAATTCTCTGATTCAGAACTTACTGCAGATTGCATATCCTGAAGCATACGAATGCCTAAAG
CTGAACTTGCACTACCATC
Found at i:411882 original size:11 final size:11
Alignment explanation
Indices: 411868--411892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
411858 ATAATATATA
411868 TAAGATACGAT
1 TAAGATACGAT
411879 TAAGATACGAT
1 TAAGATACGAT
411890 TAA
1 TAA
411893 TTAATCTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
TAAGATACGAT
Found at i:412245 original size:13 final size:14
Alignment explanation
Indices: 412229--412277 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
412219 TTTTAACATA
412229 ATTA-ATTAATTAT
1 ATTATATTAATTAT
*
412242 ATTATATTTA-TAT
1 ATTATATTAATTAT
*
412255 ATTA-AATAATTAT
1 ATTATATTAATTAT
412268 ATTATATTAA
1 ATTATATTAA
412278 AAATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.10
13 18 0.62
14 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATATTAATTAT
Found at i:412635 original size:26 final size:26
Alignment explanation
Indices: 412594--412674 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
412584 TTATTTATAT
*
412594 ATATATTAATTTTTTAATAAATTAAAA
1 ATAT-TTAATTATTTAATAAATTAAAA
* **
412621 ATATTTAATTATTTATTTTATATAAAA
1 ATATTTAATTATTTAATAAAT-TAAAA
* *
412648 A-ATTTAATTATTAAATATATTTAAAA
1 ATATTTAATTATTTAATA-AATTAAAA
412674 A
1 A
412675 AATTATTTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
26 32 0.74
27 11 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTTAATTATTTAATAAATTAAAA
Found at i:412675 original size:26 final size:26
Alignment explanation
Indices: 412615--412675 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
412605 TTTTAATAAA
* * *
412615 TTAAAAATATTTAATTATTTATTTTAT
1 TTAAAAA-ATTTAATTATTAAATATAT
*
412642 ATAAAAAATTTAATTATTAAATATAT
1 TTAAAAAATTTAATTATTAAATATAT
412668 TTAAAAAA
1 TTAAAAAA
412676 ATTATTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAAAAAATTTAATTATTAAATATAT
Found at i:412795 original size:9 final size:10
Alignment explanation
Indices: 412769--412807 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
412759 GATTAAATAA
412769 ATATAAAATT
1 ATATAAAATT
*
412779 ATAAAAAATT
1 ATATAAAATT
412789 AT-TAAAA-T
1 ATATAAAATT
412797 ATATAAAATT
1 ATATAAAATT
412807 A
1 A
412808 ATTTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.12
9 9 0.36
10 13 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATATAAAATT
Found at i:413146 original size:27 final size:30
Alignment explanation
Indices: 413107--413181 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 30
413097 AAAATTAATT
*
413107 ATTTA-AT-TTTAATAATTTTAAT-AA-AA
1 ATTTATATATTTAATAATATTAATAAATAA
413133 ATTT-TATATTTAAT-ATATTAATAAATAA
1 ATTTATATATTTAATAATATTAATAAATAA
413161 ATTTATATATTATAATAATAT
1 ATTTATATATT-TAATAATAT
413182 CATCTAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
26 13 0.32
27 8 0.20
28 6 0.15
29 6 0.15
30 4 0.10
31 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTATATATTTAATAATATTAATAAATAA
Found at i:413180 original size:25 final size:26
Alignment explanation
Indices: 413114--413168 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
413104 ATTATTTAAT
* *
413114 TTTAATAATTTTAATAAAAATTTTATA
1 TTTAAT-ATATTAATAAAAAATTTATA
413141 TTTAATATATTAATAAATAAATTTATA
1 TTTAATATATTAATAAA-AAATTTATA
413168 T
1 T
413169 ATTATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAATATATTAATAAAAAATTTATA
Found at i:413403 original size:18 final size:18
Alignment explanation
Indices: 413365--413404 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
413355 TAAATTGTTA
**
413365 TTATATAATTATTTATTT
1 TTATATAATTATTTAAAT
413383 TTATATAATTATTTAAAT
1 TTATATAATTATTTAAAT
413401 TTAT
1 TTAT
413405 TTATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATAATTATTTAAAT
Found at i:413627 original size:34 final size:35
Alignment explanation
Indices: 413567--413686 Score: 233
Period size: 35 Copynumber: 3.5 Consensus size: 35
413557 AATCCAAAGT
413567 TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
1 TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
413602 TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
1 TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
413637 TGATACCTCAAACTTG-TTTTTTTTTTTGGATAAG
1 TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
413671 TGATACCTCAAACTTG
1 TGATACCTCAAACTTG
413687 GCATATGATG
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
34 34 0.40
35 51 0.60
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.48
Consensus pattern (35 bp):
TGATACCTCAAACTTGTTTTTTTTTTTTGGATAAG
Found at i:413846 original size:12 final size:12
Alignment explanation
Indices: 413829--413908 Score: 58
Period size: 12 Copynumber: 6.6 Consensus size: 12
413819 ATAATTATAT
*
413829 TATTAAATTTAA
1 TATTAAATTAAA
413841 TATTAAATTAAA
1 TATTAAATTAAA
*
413853 TA-TATA-TAAA
1 TATTAAATTAAA
413863 TTATATAAA-TAAA
1 -TAT-TAAATTAAA
* *
413876 TTATTAAAATATA
1 -TATTAAATTAAA
*
413889 TATTAATTTAATA
1 TATTAAATTAA-A
413902 TATTAAA
1 TATTAAA
413909 ATATAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
10 4 0.07
11 5 0.09
12 25 0.45
13 21 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATTAAATTAAA
Found at i:413869 original size:48 final size:44
Alignment explanation
Indices: 413816--413916 Score: 114
Period size: 48 Copynumber: 2.2 Consensus size: 44
413806 AATTATTCGT
* *
413816 AATATAATTATATTATT-AAATTTAATATTAAATTAAATATATATAA
1 AATATAATTAAATTATTAAAATAT-ATATT-AATTAAATATAT-TAA
* *
413862 ATTATATAAATAAATTATTAAAATATATATTAATTTAATATATTAA
1 A--ATATAATTAAATTATTAAAATATATATTAATTAAATATATTAA
413908 AATATAATT
1 AATATAATT
413917 TAAGTAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
44 7 0.15
46 5 0.11
47 11 0.23
48 19 0.40
49 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (44 bp):
AATATAATTAAATTATTAAAATATATATTAATTAAATATATTAA
Done.