Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold426
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: 634051
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 3 of 6
Found at i:216000 original size:22 final size:22
Alignment explanation
Indices: 215972--216047 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
215962 TTCAGGGAGG
215972 AAAGAAAGAAAGAAAGAAAAAA
1 AAAGAAAGAAAGAAAGAAAAAA
*
215994 AAAGAAAGAAAGAGAAAGGAGAAAA
1 AAAGAAAG-AA-AGAAA-GAAAAAA
*
216019 AAAG-AA-AAAGAAAAGAAAGAAC
1 AAAGAAAGAAAG-AAAGAAA-AAA
216041 AAAGAAA
1 AAAGAAA
216048 AAAATTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
21 5 0.11
22 19 0.42
23 4 0.09
24 7 0.16
25 10 0.22
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAGAAAGAAAAAA
Found at i:216011 original size:32 final size:34
Alignment explanation
Indices: 215973--216051 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
215963 TCAGGGAGGA
215973 AAGAAAGAAAGAAAGAAAA-AAAAAG-AAAGAAAG
1 AAGAAAGAAAGAAA-AAAAGAAAAAGAAAAGAAAG
*
216006 -AGAAAG-GAGAAAAAAAGAAAAAGAAAAGAAAG
1 AAGAAAGAAAGAAAAAAAGAAAAAGAAAAGAAAG
*
216038 AACAAAGAAA-AAAA
1 AAGAAAGAAAGAAAA
216052 TTTATATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 4 0.10
31 11 0.28
32 14 0.36
33 9 0.23
34 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.00
Consensus pattern (34 bp):
AAGAAAGAAAGAAAAAAAGAAAAAGAAAAGAAAG
Found at i:216018 original size:26 final size:24
Alignment explanation
Indices: 215972--216037 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 24
215962 TTCAGGGAGG
215972 AAAGAAAG-AAAGAAA-GAAAAAA
1 AAAGAAAGAAAAGAAAGGAAAAAA
215994 AAAGAAAGAAAGAGAAAGGAGAAAAA
1 AAAGAAAGAAA-AGAAAGGA-AAAAA
*
216020 AAGAAAAAGAAAAGAAAG
1 AA-AGAAAGAAAAGAAAG
216038 AACAAAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 8 0.21
23 2 0.05
24 5 0.13
25 2 0.05
26 13 0.34
27 8 0.21
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAAGAAAGAAAAGAAAGGAAAAAA
Found at i:216028 original size:27 final size:26
Alignment explanation
Indices: 215971--216037 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
215961 TTTCAGGGAG
*
215971 GAAAG-AAAGAAAGAAAGAAAAAAAAA
1 GAAAGAAAAGAAAG-GAGAAAAAAAAA
215997 GAAAGAAAGAGAAAGGAGAAAAAAAGAA
1 GAAAGAAA-AGAAAGGAGAAAAAAA-AA
216025 -AAAGAAAAGAAAG
1 GAAAGAAAAGAAAG
216038 AACAAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 11 0.30
27 18 0.49
28 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (26 bp):
GAAAGAAAAGAAAGGAGAAAAAAAAA
Found at i:216907 original size:59 final size:59
Alignment explanation
Indices: 216795--216907 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
216785 ATTGTATTTT
**
216795 TATTCATGACATATTTTGTATAATTTGTCAGAATAATTTAATTTAAATTATTATATCTC
1 TATTCATGACATATTTTGTATAATTTGTCAGAATAATTTAATTTAAAAAATTATATCTC
* * * * *
216854 TATTCATGACATTTTTTTTCATAATTTGTTATAGTAATTTAA-TTAAAAAATTAT
1 TATTCATGACATATTTTGT-ATAATTTGTCAGAATAATTTAATTTAAAAAATTAT
216908 GTTTTCTTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 27 0.59
60 19 0.41
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.50
Consensus pattern (59 bp):
TATTCATGACATATTTTGTATAATTTGTCAGAATAATTTAATTTAAAAAATTATATCTC
Found at i:217388 original size:15 final size:15
Alignment explanation
Indices: 217366--217421 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
217356 GGTAAGGTTG
217366 AAAA-AAAAAAGAAA
1 AAAAGAAAAAAGAAA
* *
217380 GAAAGAAAAGAGAAA
1 AAAAGAAAAAAGAAA
217395 AAAAGAAAAAAGAAAA
1 AAAAGAAAAAAG-AAA
217411 AAAAGAAAAAA
1 AAAAGAAAAAA
217422 TTATATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 3 0.08
15 19 0.53
16 14 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:217406 original size:26 final size:24
Alignment explanation
Indices: 217365--217421 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 24
217355 GGGTAAGGTT
217365 GAAAAAAAAAAGAAAGAAAGAAAAGA
1 GAAAAAAAAAAGAAAGAAA-AAAA-A
217391 GAAAAAAAGAAA-AAAGAAAAAAAA
1 GAAAAAAA-AAAGAAAGAAAAAAAA
217415 GAAAAAA
1 GAAAAAA
217422 TTATATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.27
25 4 0.13
26 15 0.50
27 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
GAAAAAAAAAAGAAAGAAAAAAAA
Found at i:217413 original size:8 final size:8
Alignment explanation
Indices: 217369--217421 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
217359 AAGGTTGAAA
217369 AAAAAAAG
1 AAAAAAAG
*
217377 AAAGAAAG
1 AAAAAAAG
*
217385 -AAAAGAG
1 AAAAAAAG
217392 AAAAAAAG
1 AAAAAAAG
217400 -AAAAAAG
1 AAAAAAAG
217407 AAAAAAAAG
1 -AAAAAAAG
217416 AAAAAA
1 AAAAAA
217422 TTATATTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 12 0.32
8 19 0.50
9 7 0.18
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:217421 original size:7 final size:7
Alignment explanation
Indices: 217366--217412 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
217356 GGTAAGGTTG
217366 AAAA-AA
1 AAAAGAA
217372 AAAAGAA
1 AAAAGAA
217379 AGAAAGAA
1 A-AAAGAA
*
217387 AAGAGAAA
1 AAAAG-AA
217395 AAAAGAA
1 AAAAGAA
217402 AAAAGAA
1 AAAAGAA
217409 AAAA
1 AAAA
217413 AAGAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 4 0.11
7 19 0.53
8 13 0.36
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:218176 original size:35 final size:35
Alignment explanation
Indices: 218130--218210 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
218120 GTATTGGCTA
** **
218130 TACATTAGCTGTGTAATGTTATGATGCATTAGTTG
1 TACATTAGCTGTACAATGTTATGACACATTAGTTG
*
218165 TACATTAGCTGTACAATGTTATGACATATTAGTTG
1 TACATTAGCTGTACAATGTTATGACACATTAGTTG
218200 TACATTAGCTG
1 TACATTAGCTG
218211 CAGATATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (35 bp):
TACATTAGCTGTACAATGTTATGACACATTAGTTG
Found at i:220102 original size:35 final size:35
Alignment explanation
Indices: 220054--220147 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
220044 CTTATAATGT
* * *
220054 TGTATTGGCTGTACATTAGCTGTAAAACGTTATGA
1 TGTATTAGTTGTACATTAGCTGTAAAACATTATGA
* *
220089 TGTATTAGTTGTACATTAGCTGTACAATATTATGA
1 TGTATTAGTTGTACATTAGCTGTAAAACATTATGA
** *
220124 CATATTAATTGTACATTAGCTGTA
1 TGTATTAGTTGTACATTAGCTGTA
220148 GATATTGAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TGTATTAGTTGTACATTAGCTGTAAAACATTATGA
Found at i:220551 original size:14 final size:14
Alignment explanation
Indices: 220532--220579 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
220522 TTCTAAATTC
220532 ATATTAATATTTAT
1 ATATTAATATTTAT
220546 ATATTAATAATTTATTTT
1 ATATTAAT-ATTTA---T
*
220564 ATATAAATATTTAT
1 ATATTAATATTTAT
220578 AT
1 AT
220580 GTTTATGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 11 0.38
15 5 0.17
17 5 0.17
18 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTAATATTTAT
Found at i:220767 original size:43 final size:42
Alignment explanation
Indices: 220702--220788 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 42
220692 TTTATATGAT
*
220702 TAAATTTTAAATTTAAATTTATTT-ATTAAATATTTT-TAAA
1 TAAATTTTAAATTTAAATTTATTTAATTAAAAATTTTATAAA
*
220742 TAAATTTTATTAATTATAATTTTATTTAATTAAAAATTTTATAAA
1 TAAATTTTA--AATT-TAAATTTATTTAATTAAAAATTTTATAAA
220787 TA
1 TA
220789 TTAAAATCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 9 0.22
42 4 0.10
43 10 0.25
44 11 0.28
45 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (42 bp):
TAAATTTTAAATTTAAATTTATTTAATTAAAAATTTTATAAA
Found at i:221726 original size:4 final size:4
Alignment explanation
Indices: 221717--221776 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
221707 TGCGTGTGAA
* * *
221717 AAAG AAAG AAAG AAAG ACA- AAAG AAAA AAAG AAAG AAAG -AGG AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
221762 AAA- AAAG AAAA AAAG
1 AAAG AAAG AAAG AAAG
221777 GGAAAAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 10 0.22
4 35 0.78
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:221740 original size:19 final size:19
Alignment explanation
Indices: 221716--221773 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
221706 GTGCGTGTGA
*
221716 AAAAGAAAGAAAGAAAGAC
1 AAAAGAAAAAAAGAAAGAC
221735 AAAAGAAAAAAAGAAAGA-
1 AAAAGAAAAAAAGAAAGAC
* *
221753 AAGAGGAAAAAA-AAAGA-
1 AAAAGAAAAAAAGAAAGAC
221770 AAAA
1 AAAA
221774 AAGGGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 8 0.23
18 10 0.29
19 17 0.49
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAGAAAGAC
Found at i:221765 original size:20 final size:20
Alignment explanation
Indices: 221740--221785 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
221730 AAGACAAAAG
*
221740 AAAAAAAGAAAGAAAGAGGAA
1 AAAAAAAGAAAAAAAG-GGAA
221761 AAAAAAAGAAAAAAAGGGAA
1 AAAAAAAGAAAAAAAGGGAA
221781 AAAAA
1 AAAAA
221786 TTTATGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAGGGAA
Found at i:222588 original size:31 final size:32
Alignment explanation
Indices: 222543--222607 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
222533 AATAAAATAA
*
222543 ATTTATATAAATTTTTACATATTAAT-TATTC
1 ATTTATATAAATTTTGACATATTAATGTATTC
* * *
222574 ATTTATTTATATTTTGACATATTAGTGTATTC
1 ATTTATATAAATTTTGACATATTAATGTATTC
222606 AT
1 AT
222608 ACCGTGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (32 bp):
ATTTATATAAATTTTGACATATTAATGTATTC
Found at i:222919 original size:16 final size:17
Alignment explanation
Indices: 222892--222932 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
222882 ATTTTAAAAT
222892 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
222907 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
222924 AAATTTTAT
1 AAATTTTAT
222933 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:227844 original size:23 final size:21
Alignment explanation
Indices: 227810--227870 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 21
227800 AATATTTAAA
*
227810 TAAATATATAAATAACTATGTAT
1 TAAA-ATATAAATAAATAT-TAT
*
227833 TAAAATTTTAAATTAAATATTAT
1 TAAAA-TATAAA-TAAATATTAT
227856 TAAAATATAAATAAA
1 TAAAATATAAATAAA
227871 AAAATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.12
22 6 0.18
23 17 0.52
24 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAATATAAATAAATATTAT
Found at i:228518 original size:32 final size:31
Alignment explanation
Indices: 228481--228582 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 31
228471 ACTGAAATAT
* * *
228481 TTTAATGATTATCAAATATACAAGTAATTATA
1 TTTAAT-ATTATCAAATTTAAAAATAATTATA
*
228513 TTTAATAATTATCAAATTTAAAAATAATTTTA
1 TTTAAT-ATTATCAAATTTAAAAATAATTATA
* * **
228545 TTCAATATTCATTAAATTTTTAAATAATTATA
1 TTTAATATT-ATCAAATTTAAAAATAATTATA
228577 TTTAAT
1 TTTAAT
228583 CCATTAAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 3 0.05
32 55 0.95
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (31 bp):
TTTAATATTATCAAATTTAAAAATAATTATA
Found at i:230824 original size:9 final size:9
Alignment explanation
Indices: 230810--230842 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
230800 GATGGAAACG
230810 TTTTTTTTC
1 TTTTTTTTC
230819 --TTTTTTC
1 TTTTTTTTC
230826 TTTTTTTTC
1 TTTTTTTTC
230835 TTTTTTTT
1 TTTTTTTT
230843 GAGTATTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:230831 original size:16 final size:16
Alignment explanation
Indices: 230810--230840 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
230800 GATGGAAACG
230810 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTTC
230826 TTTTTTTTCTTTTTT
1 TTTTTTTTCTTTTTT
230841 TTGAGTATTG
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:231563 original size:44 final size:43
Alignment explanation
Indices: 231510--231594 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 43
231500 TGCCAATGAA
*
231510 GAGAGTTTGGGTTGAGATTGAGAACTTGAAACTTGCCATAAAGG
1 GAGAGTTTGGGTTGAGACTGAGAACTT-AAACTTGCCATAAAGG
* *
231554 GAGAGTTTGGGTTGAGGCTGAGAACTTAAGCTTGCCATAAA
1 GAGAGTTTGGGTTGAGACTGAGAACTTAAACTTGCCATAAA
231595 AAAGAGTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 13 0.34
44 25 0.66
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.27
Consensus pattern (43 bp):
GAGAGTTTGGGTTGAGACTGAGAACTTAAACTTGCCATAAAGG
Found at i:231780 original size:19 final size:20
Alignment explanation
Indices: 231743--231781 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
231733 AAAATAAATA
* *
231743 TATAATAATTTAAATATAAT
1 TATAATAATATAAACATAAT
231763 TATAAT-ATATAAACATAAT
1 TATAATAATATAAACATAAT
231782 ACGCTTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAATAATATAAACATAAT
Found at i:232626 original size:16 final size:16
Alignment explanation
Indices: 232605--232635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
232595 ATTTTGCATC
232605 TTAATATAAATTTTAG
1 TTAATATAAATTTTAG
*
232621 TTAATATATATTTTA
1 TTAATATAAATTTTA
232636 TTACTTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAATATAAATTTTAG
Found at i:233088 original size:28 final size:29
Alignment explanation
Indices: 233050--233116 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
233040 AAATATTTAT
233050 TAAAGTTTTAAAAA-AAGTATTA-TTATCTC
1 TAAAG-TTTAAAAATAA-TATTATTTATCTC
*
233079 TTAAA-TTTAAAAATAATTTTATTTATCTC
1 -TAAAGTTTAAAAATAATATTATTTATCTC
233108 TAAAGTTTA
1 TAAAGTTTA
233117 GATAATATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 16 0.48
29 13 0.39
30 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (29 bp):
TAAAGTTTAAAAATAATATTATTTATCTC
Found at i:233547 original size:17 final size:17
Alignment explanation
Indices: 233525--233563 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
233515 CCATTATTTT
233525 AAAATTT-TTAAATATAA
1 AAAATTTATTAAA-ATAA
233542 AAAATTTGATTAAAATAA
1 AAAATTT-ATTAAAATAA
233560 AAAA
1 AAAA
233564 ATAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTTATTAAAATAA
Found at i:233866 original size:16 final size:16
Alignment explanation
Indices: 233845--233876 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
233835 AATTAGAATA
*
233845 TAATTTAATAATAATT
1 TAATTTAACAATAATT
233861 TAATTTAACAATAATT
1 TAATTTAACAATAATT
233877 AAAGATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAACAATAATT
Found at i:234429 original size:18 final size:18
Alignment explanation
Indices: 234372--234436 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
234362 TTATTATTTA
* * *
234372 ATTAATAAAAATTTATTT
1 ATTAATATAAATATATAT
* *
234390 TTTATTATAAATATATAAAT
1 ATTAATATAAATATAT--AT
234410 ATTAATATAAATATATAT
1 ATTAATATAAATATATAT
234428 ATTAA-ATAA
1 ATTAATATAA
234437 TAAAATTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.11
18 19 0.50
20 15 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATATAAATATATAT
Found at i:234440 original size:20 final size:19
Alignment explanation
Indices: 234395--234436 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
234385 TATTTTTTAT
234395 TATAAATATATAAATATTAA
1 TATAAATATAT-AATATTAA
234415 TATAAATATAT-ATATTAA
1 TATAAATATATAATATTAA
234433 -ATAA
1 TATAA
234437 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
20 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAAATATATAATATTAA
Found at i:234775 original size:9 final size:9
Alignment explanation
Indices: 234761--234791 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
234751 TAAGAAAGGG
234761 AAGAAAAGA
1 AAGAAAAGA
*
234770 ACGAAAAGA
1 AAGAAAAGA
234779 AAGAAAAGA
1 AAGAAAAGA
234788 AAGA
1 AAGA
234792 GAGAGAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:234959 original size:13 final size:15
Alignment explanation
Indices: 234938--235010 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 15
234928 TATATTAATA
234938 ATTTATTTATG-TAT
1 ATTTATTTATGTTAT
234952 ATTT-TTTATGTTAT
1 ATTTATTTATGTTAT
* *
234966 A--TAATTATATTAT
1 ATTTATTTATGTTAT
*
234979 TTTTATTTAT-TT-T
1 ATTTATTTATGTTAT
*
234992 ATTT-TTCATGTTAT
1 ATTTATTTATGTTAT
*
235006 TTTTA
1 ATTTA
235011 ATTTGTATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
12 5 0.11
13 20 0.44
14 14 0.31
15 6 0.13
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (15 bp):
ATTTATTTATGTTAT
Found at i:234993 original size:15 final size:17
Alignment explanation
Indices: 234970--235008 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
234960 TGTTATATAA
*
234970 TTATATTATTTTT-AT-
1 TTATTTTATTTTTCATG
234985 TTATTTTATTTTTCATG
1 TTATTTTATTTTTCATG
235002 TTATTTT
1 TTATTTT
235009 TAATTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTTTCATG
Found at i:235929 original size:9 final size:8
Alignment explanation
Indices: 235907--235938 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
235897 AAAAAATCGT
235907 AATTTAAA
1 AATTTAAA
235915 AATTTAAA
1 AATTTAAA
*
235923 AATTTTAA
1 AATTTAAA
235931 AATTTAAA
1 AATTTAAA
235939 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATTTAAA
Found at i:236161 original size:21 final size:21
Alignment explanation
Indices: 236135--236175 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
236125 AATTAAAAAA
*
236135 ATATTTT-TTATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
236156 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
236176 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:238098 original size:15 final size:16
Alignment explanation
Indices: 238068--238109 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
238058 TTACACTGAG
*
238068 TTTAAG-TTTTAAA-T
1 TTTAAGATTTAAAATT
238082 TTTAAGATTTAAAATT
1 TTTAAGATTTAAAATT
238098 TTTAA-ATTTAAA
1 TTTAAGATTTAAA
238110 TAATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
TTTAAGATTTAAAATT
Found at i:238110 original size:14 final size:15
Alignment explanation
Indices: 238068--238110 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
238058 TTACACTGAG
*
238068 TTTAAGTTTTAAA-T
1 TTTAAGATTTAAATT
238082 TTTAAGATTTAAAATT
1 TTTAAGATTT-AAATT
238098 TTTAA-ATTTAAAT
1 TTTAAGATTTAAAT
238111 AATTTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
15 7 0.27
16 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TTTAAGATTTAAATT
Found at i:238116 original size:16 final size:15
Alignment explanation
Indices: 238078--238122 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
238068 TTTAAGTTTT
238078 AAATTTTAAGATTTAA
1 AAATTTTAA-ATTTAA
*
238094 AATTTTTAAATTTAA
1 AAATTTTAAATTTAA
*
238109 ATAATTTTATATTT
1 A-AATTTTAAATTT
238123 TTCGTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AAATTTTAAATTTAA
Found at i:238393 original size:2 final size:2
Alignment explanation
Indices: 238386--238416 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
238376 AAATCATCAA
238386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
238417 AAATGAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239341 original size:24 final size:24
Alignment explanation
Indices: 239310--239355 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
239300 TAAATAAAAT
239310 TTATTAAAATTATACTTATATTTA
1 TTATTAAAATTATACTTATATTTA
*
239334 TTATTAAAATTATATTTATATT
1 TTATTAAAATTATACTTATATT
239356 AAAAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTAAAATTATACTTATATTTA
Found at i:239357 original size:17 final size:18
Alignment explanation
Indices: 239325--239359 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
239315 AAAATTATAC
239325 TTATATTTATTATTAAAA
1 TTATATTTATTATTAAAA
239343 TTATATTTA-TATTAAAA
1 TTATATTTATTATTAAAA
239360 GATAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATTTATTATTAAAA
Found at i:240215 original size:3 final size:3
Alignment explanation
Indices: 240207--240247 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
240197 AGACCCTCCT
240207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
240248 TGGTGGGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:241612 original size:29 final size:28
Alignment explanation
Indices: 241578--241646 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
241568 AAAATTAAAG
241578 ATATTAAAATTTAAAATTTAAATTAT-TAA
1 ATATTAAAATTTAAAA-TT-AATTATATAA
***
241607 ATATTATTTTTTAAAATTAATTATATAA
1 ATATTAAAATTTAAAATTAATTATATAA
241635 ATCGATTAAAAT
1 AT--ATTAAAAT
241647 AAATATATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.19
28 7 0.23
29 13 0.42
30 5 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTAAAATTTAAAATTAATTATATAA
Found at i:242638 original size:26 final size:26
Alignment explanation
Indices: 242602--242652 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
242592 AAATATTTAT
242602 AATAATAATTTAAAAATACAATAAAC
1 AATAATAATTTAAAAATACAATAAAC
*
242628 AATAATAATTTAAAAATATAATAAA
1 AATAATAATTTAAAAATACAATAAA
242653 TAATTGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATAATTTAAAAATACAATAAAC
Found at i:243015 original size:20 final size:19
Alignment explanation
Indices: 242975--243021 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
242965 TATTAAATCC
242975 AAATTTATACTTATTTTTT
1 AAATTTATACTTATTTTTT
242994 AAATTTCATAC-TATTTTATT
1 AAATTT-ATACTTATTTT-TT
243014 AATATTTA
1 AA-ATTTA
243022 ATATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 12 0.48
20 9 0.36
21 4 0.16
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATTTATACTTATTTTTT
Found at i:244927 original size:33 final size:33
Alignment explanation
Indices: 244870--244936 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
244860 ATTTCTTTTT
* * * *
244870 TCTCGTGTTATTTGAATGGATAATCTCTGCTCA
1 TCTCATGTTATTGGAATGGATAATCCCAGCTCA
244903 TCTCATGTTATTGGAAT-GATTAATCCCAGCTCA
1 TCTCATGTTATTGGAATGGA-TAATCCCAGCTCA
244936 T
1 T
244937 ATATCGGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (33 bp):
TCTCATGTTATTGGAATGGATAATCCCAGCTCA
Found at i:245282 original size:25 final size:23
Alignment explanation
Indices: 245230--245301 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
245220 ATTTAAATAC
*
245230 ATATTTTTATTAAATAAATA-TT
1 ATATTTATATTAAATAAATATTT
245252 ATATTTAATATTAAAATCAAATATTT
1 ATATTT-ATATT-AAAT-AAATATTT
*
245278 A-ATTTATTTTTAAATTAAATATTT
1 ATATTTA-TATTAAA-TAAATATTT
245302 TAAATCAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
22 6 0.14
23 4 0.10
24 16 0.38
25 13 0.31
26 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTATATTAAATAAATATTT
Found at i:245297 original size:24 final size:26
Alignment explanation
Indices: 245239--245301 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
245229 CATATTTTTA
245239 TTAAA-TAAATA-TTATATTTAATAT
1 TTAAATTAAATATTTATATTTAATAT
* * *
245263 TAAAATCAAATATTTA-ATTT-ATTT
1 TTAAATTAAATATTTATATTTAATAT
245287 TTAAATTAAATATTT
1 TTAAATTAAATATTT
245302 TAAATCAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 20 0.62
25 9 0.28
26 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAATTAAATATTTATATTTAATAT
Found at i:245395 original size:23 final size:23
Alignment explanation
Indices: 245368--245411 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
245358 AACTTTCAAT
245368 TTTAAAAATT-AATATTTAATAAA
1 TTTAAAAATTAAATA-TTAATAAA
*
245391 TTTAAAATTTAAATATTAATA
1 TTTAAAAATTAAATATTAATA
245412 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAATTAAATATTAATAAA
Found at i:245400 original size:16 final size:14
Alignment explanation
Indices: 245368--245415 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
245358 AACTTTCAAT
*
245368 TTTAAAAATTAATA
1 TTTAAAAATTAAAA
245382 TTTAATAAATTTAAAA
1 TTTAA-AAA-TTAAAA
* *
245398 TTTAAATATTAATA
1 TTTAAAAATTAAAA
245412 TTTA
1 TTTA
245416 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 14 0.48
15 5 0.17
16 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAAAATTAAAA
Found at i:245576 original size:3 final size:3
Alignment explanation
Indices: 245570--245609 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
245560 AAAAAAACAG
245570 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
245610 GAATTATTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:246024 original size:13 final size:13
Alignment explanation
Indices: 245984--246033 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
245974 TATTTTTATA
245984 ATATT-ATAA-TT
1 ATATTAATAATTT
*
245995 ATATTTAAATTATTT
1 ATA-TT-AATAATTT
246010 ATATTAATAATTT
1 ATATTAATAATTT
246023 ATATTATATAA
1 ATATTA-ATAA
246034 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 3 0.09
12 2 0.06
13 13 0.41
14 9 0.28
15 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTAATAATTT
Found at i:246033 original size:14 final size:14
Alignment explanation
Indices: 245978--246033 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
245968 TATTCATATT
*
245978 TTTATAATATTATAA
1 TTTATATTA-TATAA
* *
245993 -TTATATTTAAATTA
1 TTTATA-TTATATAA
246007 TTTATATTA-ATAA
1 TTTATATTATATAA
246020 TTTATATTATATAA
1 TTTATATTATATAA
246034 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 12 0.35
14 15 0.44
15 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATATTATATAA
Found at i:246541 original size:11 final size:11
Alignment explanation
Indices: 246522--246579 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
246512 ATAATAATTT
*
246522 TAAATATAATA
1 TAAAAATAATA
246533 TAAAAATAATAA
1 TAAAAATAAT-A
246545 TTAAAATATAATA
1 -TAAAA-ATAATA
246558 T-AAAAT-ATA
1 TAAAAATAATA
246567 TAAAAATTAATA
1 TAAAAA-TAATA
246579 T
1 T
246580 GATAATATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
9 4 0.10
10 6 0.15
11 13 0.32
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:246550 original size:12 final size:12
Alignment explanation
Indices: 246511--246569 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
246501 TTATATACTT
246511 AATAATAATTTTAA
1 AATAATAA--TTAA
*
246525 ATATAAT-ATAAA
1 A-ATAATAATTAA
246537 AATAATAATTAA
1 AATAATAATTAA
246549 AAT-ATAATATAA
1 AATAATAAT-TAA
246561 AATATATAA
1 AATA-ATAA
246570 AAATTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 10 0.26
12 17 0.45
14 6 0.16
15 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAATTAA
Found at i:246555 original size:14 final size:14
Alignment explanation
Indices: 246512--246586 Score: 59
Period size: 14 Copynumber: 5.4 Consensus size: 14
246502 TATATACTTA
*
246512 ATAATAATTTTAAAT
1 ATAATAA-TTAAAAT
246527 ATAAT-A-TAAAA-
1 ATAATAATTAAAAT
246538 ATAATAATTAAAAT
1 ATAATAATTAAAAT
*
246552 ATAAT-ATAAAATAT
1 ATAATAATTAAA-AT
* *
246566 ATAAAAATTAATAT
1 ATAATAATTAAAAT
246580 GATAATA
1 -ATAATA
246587 TAAATACATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 5 0.10
12 5 0.10
13 10 0.21
14 14 0.29
15 14 0.29
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (14 bp):
ATAATAATTAAAAT
Found at i:246579 original size:12 final size:12
Alignment explanation
Indices: 246523--246579 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
246513 TAATAATTTT
246523 AAATATAATATAA
1 AAAT-TAATATAA
*
246536 AAA-TAATAATTA
1 AAATTAAT-ATAA
246548 AAATATAATAT-A
1 AAAT-TAATATAA
246560 AAA-T-ATATAA
1 AAATTAATATAA
246570 AAATTAATAT
1 AAATTAATAT
246580 GATAATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 5 0.14
12 14 0.38
13 5 0.14
14 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:246591 original size:28 final size:26
Alignment explanation
Indices: 246523--246598 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 26
246513 TAATAATTTT
*
246523 AAATATAATATAAA-AATAATAATTA
1 AAATATAATATAAATAATAAAAATTA
246548 AAATATAATATAAAATATATAAAAATTA
1 AAATATAATAT-AAATA-ATAAAAATTA
*
246576 ATATGATAATATAAATACATAAA
1 AAAT-ATAATATAAATA-ATAAA
246599 TATATCAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
25 11 0.25
26 3 0.07
27 1 0.02
28 22 0.50
29 7 0.16
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
AAATATAATATAAATAATAAAAATTA
Found at i:246592 original size:14 final size:13
Alignment explanation
Indices: 246525--246602 Score: 61
Period size: 14 Copynumber: 5.8 Consensus size: 13
246515 ATAATTTTAA
*
246525 ATATAATATAAAA
1 ATATAATATAAAT
246538 ATAATAAT-TAAA-
1 AT-ATAATATAAAT
246550 ATATAATATAAAAT
1 ATATAATAT-AAAT
* *
246564 ATATAAAAATTAAT
1 ATAT-AATATAAAT
246578 ATGATAATATAAAT
1 AT-ATAATATAAAT
*
246592 ACATAAATATA
1 ATAT-AATATA
246603 TCAAATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
11 5 0.09
12 3 0.06
13 11 0.21
14 28 0.53
15 6 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:246662 original size:30 final size:29
Alignment explanation
Indices: 246595--246662 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
246585 TATAAATACA
*
246595 TAAATATATCAAATTTATATAACATAAAT
1 TAAATATATAAAATTTATATAACATAAAT
*
246624 TATCAATAT-TAAAATTTATATAATATGTAAAT
1 TA--AATATATAAAATTTATATAACA--TAAAT
246656 TAAATAT
1 TAAATAT
246663 GTTCACCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
29 2 0.06
30 19 0.58
31 5 0.15
32 7 0.21
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
TAAATATATAAAATTTATATAACATAAAT
Found at i:247564 original size:2 final size:2
Alignment explanation
Indices: 247557--247601 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
247547 TTATCATTAA
247557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247599 AT A
1 AT A
247602 GAATCCATAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:249113 original size:34 final size:34
Alignment explanation
Indices: 249075--249181 Score: 135
Period size: 34 Copynumber: 3.1 Consensus size: 34
249065 TGTTGAAGAA
249075 ATTTGATAGTTTG-CTATTATTGATTAAATGAGTG
1 ATTTGATAGTTTGTC-ATTATTGATTAAATGAGTG
* * ***
249109 ATTTGATGGTTTGTCATTATTGACTAAATGACAA
1 ATTTGATAGTTTGTCATTATTGATTAAATGAGTG
* *
249143 ATTTGATAGTTTGTCATTGTTTATTAAATGAGTG
1 ATTTGATAGTTTGTCATTATTGATTAAATGAGTG
249177 ATTTG
1 ATTTG
249182 GTGATTTTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 59 0.98
35 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.47
Consensus pattern (34 bp):
ATTTGATAGTTTGTCATTATTGATTAAATGAGTG
Found at i:249116 original size:61 final size:66
Alignment explanation
Indices: 249046--249181 Score: 167
Period size: 68 Copynumber: 2.1 Consensus size: 66
249036 TTGTCATTAT
* *
249046 TGATTTGATGGTTTG-A-TATTG-TTGAA-G-AAATTTGATAGTTTG-CTATTATTGATTAAATG
1 TGATTTGATGGTTTGCATTATTGACTAAATGAAAATTTGATAGTTTGTC-ATTATTGATTAAATG
249105 AG
65 AG
* *
249107 TGATTTGATGGTTTGTCATTATTGACTAAATGACAAATTTGATAGTTTGTCATTGTTTATTAAAT
1 TGATTTGATGGTTTG-CATTATTGACTAAATGA-AAATTTGATAGTTTGTCATTATTGATTAAAT
249172 GAG
64 GAG
249175 TGATTTG
1 TGATTTG
249182 GTGATTTTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
61 15 0.24
63 1 0.02
64 5 0.08
65 3 0.05
66 1 0.02
68 37 0.59
69 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (66 bp):
TGATTTGATGGTTTGCATTATTGACTAAATGAAAATTTGATAGTTTGTCATTATTGATTAAATGA
G
Found at i:249396 original size:13 final size:14
Alignment explanation
Indices: 249364--249398 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
249354 TCACGTAATT
249364 TTTTTTATGTCTTA
1 TTTTTTATGTCTTA
*
249378 TATTTTATGT-TTA
1 TTTTTTATGTCTTA
249391 TTTTTTAT
1 TTTTTTAT
249399 TTTCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTATGTCTTA
Found at i:250842 original size:13 final size:13
Alignment explanation
Indices: 250824--250851 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
250814 AATAATTTTT
250824 TAAATTAAAATAA
1 TAAATTAAAATAA
250837 TAAATTAAAATAA
1 TAAATTAAAATAA
250850 TA
1 TA
250852 TATATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATTAAAATAA
Found at i:250865 original size:38 final size:35
Alignment explanation
Indices: 250822--250900 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
250812 GAAATAATTT
*
250822 TTTAAATTAAAATAATAAATTAAA-ATAATATATATTAA
1 TTTAAATT-AAATAATAAA--AAATA-AATAAATATTAA
* *
250860 TTTAAATTTAATTATAAAAAATAAATAAATATTAA
1 TTTAAATTAAATAATAAAAAATAAATAAATATTAA
250895 TTTAAA
1 TTTAAA
250901 AATAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 20 0.54
36 1 0.03
37 8 0.22
38 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TTTAAATTAAATAATAAAAAATAAATAAATATTAA
Found at i:250899 original size:35 final size:35
Alignment explanation
Indices: 250843--250939 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 35
250833 ATAATAAATT
*
250843 AAAAT-AATATATATTAATTTAAATTTAATTATAA
1 AAAATAAATAAATATTAATTTAAATTTAATTATAA
** * **
250877 AAAATAAATAAATATTAATTTAAAAATAATTTTTT
1 AAAATAAATAAATATTAATTTAAATTTAATTATAA
* *
250912 AATA-AAATAAATAATAATTTAAATTTAA
1 AAAATAAATAAATATTAATTTAAATTTAA
250940 ATAAATATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 26 0.50
35 26 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAATAAATAAATATTAATTTAAATTTAATTATAA
Found at i:251055 original size:22 final size:21
Alignment explanation
Indices: 251030--251077 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
251020 CCTATATAAA
*
251030 AAATATAAAAAAAATTGATGCC
1 AAATAGAAAAAAAATT-ATGCC
* *
251052 AAATAGACAAAAAATTATGTC
1 AAATAGAAAAAAAATTATGCC
251073 AAATA
1 AAATA
251078 AAATCATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (21 bp):
AAATAGAAAAAAAATTATGCC
Found at i:253894 original size:12 final size:12
Alignment explanation
Indices: 253877--253958 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
253867 AAATATAATA
253877 CACACACGCACG
1 CACACACGCACG
*
253889 CACACACGCATG
1 CACACACGCACG
**
253901 CACATGCGCACGCG
1 CACACACGCA--CG
* *
253915 CACACACACACA
1 CACACACGCACG
*
253927 CACACATGCA--
1 CACACACGCACG
*
253937 CACACACGCACC
1 CACACACGCACG
253949 CACAC-CGCAC
1 CACACACGCAC
253959 ACATGCCCGC
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 9 0.16
11 5 0.09
12 33 0.60
14 8 0.15
ACGTcount: A:0.34, C:0.49, G:0.13, T:0.04
Consensus pattern (12 bp):
CACACACGCACG
Found at i:253930 original size:10 final size:10
Alignment explanation
Indices: 253913--253961 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
253903 CATGCGCACG
253913 CGCACACACA
1 CGCACACACA
*
253923 CACACACACA
1 CGCACACACA
*
253933 TGCACACACA
1 CGCACACACA
*
253943 CGCACCCACA
1 CGCACACACA
253953 CCGCACACA
1 -CGCACACA
253962 TGCCCGCCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.39, C:0.51, G:0.08, T:0.02
Consensus pattern (10 bp):
CGCACACACA
Found at i:255744 original size:2 final size:2
Alignment explanation
Indices: 255737--255773 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
255727 TCAGTGATGC
255737 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
255774 ATTGTGTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:261097 original size:20 final size:20
Alignment explanation
Indices: 261072--261125 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
261062 TAATTTTTAA
*
261072 ATTATA-ATTATATTTAAATT
1 ATTATATATTA-ATATAAATT
261092 ATTATATATTAATATAAATT
1 ATTATATATTAATATAAATT
261112 -TTAATATATTAATA
1 ATT-ATATATTAATA
261126 ATTTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 25 0.81
21 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATATATTAATATAAATT
Found at i:261158 original size:19 final size:19
Alignment explanation
Indices: 261136--261182 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
261126 ATTTATATAT
261136 TTTTATCATATTCAT-ATTA
1 TTTTATCATA-TCATGATTA
* *
261155 TTTTTTTATATCATGATTA
1 TTTTATCATATCATGATTA
261174 TTGTTATCA
1 TT-TTATCA
261183 ATTTAATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTTATCATATCATGATTA
Found at i:264865 original size:2 final size:2
Alignment explanation
Indices: 264858--264886 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
264848 CAATAATGTT
264858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
264887 TGTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:264928 original size:17 final size:19
Alignment explanation
Indices: 264908--264966 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
264898 TTTTTTAATT
264908 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
*
264925 ATATAAATTATTAAATATG
1 ATATAAATTATTAAATATA
*
264944 TTA-AAATT-TTAAATATTA
1 ATATAAATTATTAAATA-TA
264962 ATATA
1 ATATA
264967 TTAAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 14 0.41
18 10 0.29
19 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:264970 original size:15 final size:15
Alignment explanation
Indices: 264924--264975 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
264914 ATATAAATAT
*
264924 AATATAAAT-TATTA
1 AATATTAATATATTA
* *
264938 AATATGTTAAAATTTTA
1 AATA--TTAATATATTA
264955 AATATTAATATATTA
1 AATATTAATATATTA
264970 AATATT
1 AATATT
264976 TTTGTTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.13
15 15 0.50
16 3 0.10
17 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTAATATATTA
Found at i:268059 original size:20 final size:20
Alignment explanation
Indices: 268029--268170 Score: 61
Period size: 20 Copynumber: 7.3 Consensus size: 20
268019 TGTCACATAA
268029 AAAATAATTAAAATAAAATAT
1 AAAATAATTAAAAT-AAATAT
*
268050 AAAA-AATTAAGATAAATAT
1 AAAATAATTAAAATAAATAT
* *
268069 --AAT-A-TAAAA-ATATGT
1 AAAATAATTAAAATAAATAT
* * *
268084 -ACAT-ATCAAAATTAATAT
1 AAAATAATTAAAATAAATAT
* **
268102 AATATAATTAAAA-ATTTTAT
1 AAAATAATTAAAATA-AATAT
*
268122 ATAAATATTTAATAATAAATA-
1 A-AAATAATTAA-AATAAATAT
*
268143 AAAATAAAATAAAATAAAATAT
1 AAAAT-AATTAAAAT-AAATAT
268165 AAAATA
1 AAAATA
268171 TATAAATCAT
Statistics
Matches: 88, Mismatches: 20, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
15 4 0.05
16 7 0.08
17 7 0.08
18 3 0.03
19 9 0.10
20 25 0.28
21 23 0.26
22 9 0.10
23 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (20 bp):
AAAATAATTAAAATAAATAT
Found at i:268068 original size:19 final size:21
Alignment explanation
Indices: 268029--268075 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
268019 TGTCACATAA
268029 AAAATAATTAAAATAAAATAT
1 AAAATAATTAAAATAAAATAT
*
268050 AAAA-AATTAAGAT-AAATAT
1 AAAATAATTAAAATAAAATAT
*
268069 AATATAA
1 AAAATAA
268076 AAATATGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATAATTAAAATAAAATAT
Found at i:268168 original size:17 final size:16
Alignment explanation
Indices: 268138--268170 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
268128 ATTTAATAAT
268138 AAATAAAAATAAAATA
1 AAATAAAAATAAAATA
268154 AAATAAAATATAAAATA
1 AAATAAAA-ATAAAATA
268171 TATAAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAATA
Found at i:270979 original size:20 final size:19
Alignment explanation
Indices: 270937--270992 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
270927 TTTTTGTAAT
* * *
270937 TTTGGTGTGTTTGTTTATT
1 TTTGGTGTATTTATTTATG
270956 TTTGGTGTATTTATATTATG
1 TTTGGTGTATTTAT-TTATG
270976 TTTGAGT-TATTT-TTTAT
1 TTTG-GTGTATTTATTTAT
270993 TATTATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.12
19 13 0.41
20 13 0.41
21 2 0.06
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (19 bp):
TTTGGTGTATTTATTTATG
Found at i:271713 original size:14 final size:14
Alignment explanation
Indices: 271694--271721 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
271684 TAATTAAAAA
271694 AATATTTATATATT
1 AATATTTATATATT
271708 AATATTTATATATT
1 AATATTTATATATT
271722 TATAACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:272425 original size:23 final size:20
Alignment explanation
Indices: 272375--272433 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
272365 AGTCAATACC
*
272375 AATAAAA-ATAAATAATAAAA
1 AATAAAATATTAA-AATAAAA
*
272395 AATAAAATTTTAAAATAAAA
1 AATAAAATATTAAAATAAAA
272415 ATATTATAAATATTAAAAT
1 A-A-TA-AAATATTAAAAT
272434 TCGATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 15 0.47
21 4 0.12
22 2 0.06
23 11 0.34
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATATTAAAATAAAA
Found at i:273588 original size:97 final size:100
Alignment explanation
Indices: 273463--273649 Score: 283
Period size: 97 Copynumber: 1.9 Consensus size: 100
273453 TATAATTAAC
273463 ATTTCCTAAGAAAATGGAAAAATCCAAATATTTTGGTCTTTCTCCAAACTTGAG-TAAATTTGTC
1 ATTTCCTAAGAAAATGGAAAAATCCAAATATTTTGGTC-TTCTCCAAACTTGAGTTAAATTTGTC
*
273527 TTCTTGCATGTT-TCCTACAGTTCCTAGCAAATAAT
65 TCCTTGCATGTTGTCCTACAGTTCCTAGCAAATAAT
* * *
273562 ATTTCCTCA-AAAATGG-AAAATCCAAATATTTTGGTCTTCTCTAAACTTGAGTTAATTTTGTCT
1 ATTTCCTAAGAAAATGGAAAAATCCAAATATTTTGGTCTTCTCCAAACTTGAGTTAAATTTGTCT
* *
273625 CCTTGCGTGTTGTGCTACAGTTCCT
66 CCTTGCATGTTGTCCTACAGTTCCT
273650 TGATCTGCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
96 14 0.17
97 39 0.49
98 19 0.24
99 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (100 bp):
ATTTCCTAAGAAAATGGAAAAATCCAAATATTTTGGTCTTCTCCAAACTTGAGTTAAATTTGTCT
CCTTGCATGTTGTCCTACAGTTCCTAGCAAATAAT
Found at i:274418 original size:18 final size:18
Alignment explanation
Indices: 274397--274436 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
274387 ATAATTTTTT
* *
274397 TATATATTTATATTTAAA
1 TATATATTTAAATATAAA
*
274415 TATATTTTTAAATATAAA
1 TATATATTTAAATATAAA
274433 TATA
1 TATA
274437 AAAAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATATTTAAATATAAA
Found at i:274435 original size:26 final size:25
Alignment explanation
Indices: 274369--274435 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
274359 AATATGAATA
274369 TTAAATATTAAATATTTTATAATTTTT
1 TTAAATA-TAAATA-TTTATAATTTTT
* **
274396 TTATATATTTATATTTA-AATATATTT
1 TTAAATATAAATATTTATAAT-T-TTT
274422 TTAAATATAAATAT
1 TTAAATATAAATAT
274436 AAAAAATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 3 0.09
25 5 0.16
26 18 0.56
27 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAAATATAAATATTTATAATTTTT
Found at i:275288 original size:16 final size:16
Alignment explanation
Indices: 275262--275315 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
275252 AATATTATTT
275262 TTTAAATTAATTAAAAA
1 TTTAAA-TAATTAAAAA
*
275279 TTTAAATAATAAATAAA
1 TTTAAATAATTAA-AAA
* *
275296 TTTAAATATTTATAAA
1 TTTAAATAATTAAAAA
275312 TTTA
1 TTTA
275316 TAAATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAATAATTAAAAA
Found at i:276167 original size:21 final size:22
Alignment explanation
Indices: 276142--276189 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
276132 GTAATGTTTG
276142 TATATTTT-AATATGTTATAA-T
1 TATATTTTAAATATGTTA-AATT
*
276163 TATATTTTAAATATTTTAAATT
1 TATATTTTAAATATGTTAAATT
276185 TATAT
1 TATAT
276190 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATATTTTAAATATGTTAAATT
Found at i:276197 original size:17 final size:17
Alignment explanation
Indices: 276175--276248 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
276165 TATTTTAAAT
276175 ATTTTAAATTTATATAA
1 ATTTTAAATTTATATAA
276192 ATTTTAATATTT-TA-ATA
1 ATTTTAA-ATTTATATA-A
*
276209 GTTTT--A-TTATATAA
1 ATTTTAAATTTATATAA
* *
276223 ATTTTTAAATATATATCAT
1 A-TTTTAAATTTATAT-AA
276242 ATTTTAA
1 ATTTTAA
276249 TTAATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
13 2 0.05
14 4 0.09
15 5 0.11
16 1 0.02
17 15 0.34
18 15 0.34
19 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTATATAA
Found at i:276205 original size:8 final size:8
Alignment explanation
Indices: 276143--276214 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 8
276133 TAATGTTTGT
276143 ATATTTTA
1 ATATTTTA
*
276151 ATATGTT-
1 ATATTTTA
*
276158 ATA-ATT-
1 ATATTTTA
276164 ATATTTTAA
1 ATATTTT-A
276173 ATATTTTA
1 ATATTTTA
276181 A-ATTTATA
1 ATATTT-TA
*
276189 TAAATTTTA
1 -ATATTTTA
276198 ATATTTTA
1 ATATTTTA
276206 ATAGTTTTA
1 ATA-TTTTA
276215 TTATATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
6 5 0.09
7 9 0.17
8 20 0.38
9 15 0.28
10 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (8 bp):
ATATTTTA
Found at i:276290 original size:26 final size:23
Alignment explanation
Indices: 276230--276294 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 23
276220 TAAATTTTTA
276230 AATATAT-ATCATA-TTTTAATT
1 AATATATAATCATATTTTTAATT
* *
276251 AATTTATTATTCATATTATATTAATAT
1 AATATA-TAATCATATT-T-TTAAT-T
276278 AATATATAATCATATTT
1 AATATATAATCATATTT
276295 ACTTTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.15
22 1 0.03
23 5 0.15
24 1 0.03
25 2 0.06
26 14 0.41
27 6 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATATAATCATATTTTTAATT
Found at i:276450 original size:17 final size:17
Alignment explanation
Indices: 276425--276464 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
276415 TTTAAATTTA
* *
276425 ATAATTTAAGATATGAT
1 ATAAATTAAAATATGAT
276442 ATAAATTAAAATATGAT
1 ATAAATTAAAATATGAT
*
276459 AAAAAT
1 ATAAAT
276465 AATATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (17 bp):
ATAAATTAAAATATGAT
Found at i:276538 original size:37 final size:38
Alignment explanation
Indices: 276496--276578 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 38
276486 TGAAATTTAT
* **
276496 ATATAATAAAATTATT-AATTTATCTA-AATATATATAA
1 ATATAATAAAATT-TTAAATATAAATATAATATATATAA
*
276533 ATATAA-AATATTTTAAATATAAATATAATATATATAA
1 ATATAATAAAATTTTAAATATAAATATAATATATATAA
276570 ATAT-ATAAA
1 ATATAATAAA
276579 TATCATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 2 0.05
36 13 0.34
37 23 0.61
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (38 bp):
ATATAATAAAATTTTAAATATAAATATAATATATATAA
Found at i:276556 original size:15 final size:15
Alignment explanation
Indices: 276520--276581 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
276510 TTAATTTATC
276520 TAAATATATATAAATA
1 TAAATAT-TATAAATA
*
276536 TAAAATATTTTAAATA
1 T-AAATATTATAAATA
* *
276552 TAAATATAATATATA
1 TAAATATTATAAATA
276567 TAAATA-TATAAATA
1 TAAATATTATAAATA
276581 T
1 T
276582 CATATAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 7 0.18
15 17 0.44
16 9 0.23
17 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATATTATAAATA
Found at i:276894 original size:5 final size:5
Alignment explanation
Indices: 276884--276913 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
276874 TAATTTTTTT
276884 AATTA AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA
276914 TTATTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:276947 original size:45 final size:45
Alignment explanation
Indices: 276896--276981 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 45
276886 TTAAATTAAA
276896 TTAAATTAAATTA-AAT-TATTATTTAATAATAAAAAT-ATTTTATAT
1 TTAAATTAAATTATAATATA-TA-TTAAT-ATAAAAATAATTTTATAT
*
276941 TTAAATTTAATTATAATATATATTAATATAAAAATAATTTT
1 TTAAATTAAATTATAATATATATTAATATAAAAATAATTTT
276982 TTTTATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
44 8 0.22
45 22 0.59
46 5 0.14
47 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (45 bp):
TTAAATTAAATTATAATATATATTAATATAAAAATAATTTTATAT
Found at i:277752 original size:31 final size:31
Alignment explanation
Indices: 277717--277775 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
277707 TTTAAAAGAA
*
277717 TATTAATAAA-AATTTAATAAAA-ATATTTTAT
1 TATTAA-AAATAAATTAA-AAAATATATTTTAT
277748 TATTAAAAATAAATTAAAAAATATATTT
1 TATTAAAAATAAATTAAAAAATATATTT
277776 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TATTAAAAATAAATTAAAAAATATATTTTAT
Found at i:277765 original size:28 final size:30
Alignment explanation
Indices: 277717--277776 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
277707 TTTAAAAGAA
*
277717 TATTAATAAAAATTTAAT-AAAAATAT-TT
1 TATTAATAAAAATTAAATAAAAAATATATT
*
277745 TATTATTAAAAA-TAAATTAAAAAATATATT
1 TATTAATAAAAATTAAA-TAAAAAATATATT
277775 TA
1 TA
277777 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 12 0.44
29 8 0.30
30 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATTAATAAAAATTAAATAAAAAATATATT
Found at i:277777 original size:13 final size:12
Alignment explanation
Indices: 277752--277785 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
277742 TTTTATTATT
277752 AAAAATAAATTA
1 AAAAATAAATTA
*
277764 AAAAATATATTTA
1 AAAAATA-AATTA
277777 AAAAATAAA
1 AAAAATAAA
277786 AAAATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAAATTA
Found at i:278535 original size:15 final size:16
Alignment explanation
Indices: 278510--278541 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
278500 AAAATATTTT
278510 TTAATTATAAAAATAA
1 TTAATTATAAAAATAA
278526 TTAA-TATAAAAATAA
1 TTAATTATAAAAATAA
278541 T
1 T
278542 ATTTTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAATTATAAAAATAA
Found at i:278550 original size:19 final size:18
Alignment explanation
Indices: 278498--278552 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
278488 ATTTATTTAT
*
278498 TAAAAATATTTTTTAATTA
1 TAAAAATATATTTTAA-TA
278517 TAAAAATA-A--TTAATA
1 TAAAAATATATTTTAATA
278532 TAAAAATAATATTTTAATA
1 TAAAAAT-ATATTTTAATA
278551 TA
1 TA
278553 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 1 0.03
19 16 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAATATATTTTAATA
Found at i:278739 original size:25 final size:27
Alignment explanation
Indices: 278700--278793 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 27
278690 TTTTTTATTT
*
278700 TATATATTATATATTTTA-ACATATTAA
1 TATAT-TTATATATTTTATAAATATTAA
*
278727 TA-ATTTATATATTTTATAAATTTTAA
1 TATATTTATATATTTTATAAATATTAA
*
278753 TATGTTTATATA-TTTATATAATATTATA
1 TATATTTATATATTTTATA-AATATTA-A
*
278781 TTATTTTTATATA
1 -TATATTTATATA
278794 ATATTTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
25 12 0.21
26 17 0.30
27 16 0.28
28 1 0.02
29 11 0.19
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TATATTTATATATTTTATAAATATTAA
Found at i:278740 original size:8 final size:8
Alignment explanation
Indices: 278698--278792 Score: 59
Period size: 9 Copynumber: 11.1 Consensus size: 8
278688 TATTTTTTAT
278698 TTTATATA
1 TTTATATA
278706 -TTATATA
1 TTTATATA
*
278713 TTTTAACATA
1 -TTT-ATATA
*
278723 TTAATA-A
1 TTTATATA
278730 TTTATATA
1 TTTATATA
*
278738 TTTTATAAA
1 -TTTATATA
*
278747 TTTTAATATG
1 -TTT-ATATA
278757 TTTATATA
1 TTTATATA
278765 TTTATATAA
1 TTTATAT-A
278774 TATTATATTA
1 T-TTATA-TA
*
278784 TTTTTATA
1 TTTATATA
278792 T
1 T
278793 AATATTTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
7 13 0.19
8 17 0.25
9 24 0.35
10 14 0.20
11 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:278744 original size:34 final size:35
Alignment explanation
Indices: 278695--278787 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
278685 AATTATTTTT
278695 TATTT-TATATATTATATATTTTAACATATTAATA
1 TATTTATATATATTATATATTTTAACATATTAATA
* * * * *
278729 -ATTTATATATTTTATAAATTTTAATATGTTTATA
1 TATTTATATATATTATATATTTTAACATATTAATA
278763 TATTTATATAATATTATATTATTTT
1 TATTTATAT-ATATTATA-TATTTT
278788 TATATAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 4 0.08
34 24 0.50
35 8 0.17
36 7 0.15
37 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
TATTTATATATATTATATATTTTAACATATTAATA
Found at i:278745 original size:16 final size:16
Alignment explanation
Indices: 278688--278772 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
278678 GCATTTAAAT
* *
278688 TATTTTTTATTTTATA
1 TATTTTATAATTTATA
* *
278704 TATTATATATTTTA-A
1 TATTTTATAATTTATA
* *
278719 CATATTAATAATTTATA
1 TAT-TTTATAATTTATA
278736 TATTTTATAAATTT-TAA
1 TATTTTAT-AATTTAT-A
278753 TATGTTTATATATTTATA
1 TAT-TTTATA-ATTTATA
278771 TA
1 TA
278773 ATATTATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.06
16 25 0.46
17 13 0.24
18 12 0.22
19 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (16 bp):
TATTTTATAATTTATA
Found at i:278760 original size:27 final size:27
Alignment explanation
Indices: 278696--278793 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 27
278686 ATTATTTTTT
*
278696 ATTTT-ATATA-TTATATATTTTA-AC
1 ATTTTAATATATTTATATATTTTATAA
*
278720 ATATTAATA-ATTTATATATTTTATAA
1 ATTTTAATATATTTATATATTTTATAA
*
278746 ATTTTAATATGTTTATATATTTATATAA
1 ATTTTAATATATTTATATATTT-TATAA
* * *
278774 TATTATATTATTTTTATATA
1 -ATTTTAATATATTTATATA
278794 ATATTTTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
24 5 0.08
25 15 0.25
26 9 0.15
27 11 0.18
28 5 0.08
29 16 0.26
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTTAATATATTTATATATTTTATAA
Found at i:278803 original size:21 final size:21
Alignment explanation
Indices: 278750--278805 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
278740 TTATAAATTT
278750 TAATATGTTTA-TATATTTATA
1 TAATAT-TTTATTATATTTATA
* *
278771 TAATATTATATTATTTTTATA
1 TAATATTTTATTATATTTATA
278792 TAATATTTTATTAT
1 TAATATTTTATTAT
278806 GTGTCTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAATATTTTATTATATTTATA
Found at i:282508 original size:33 final size:32
Alignment explanation
Indices: 282453--282515 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
282443 GTTAATTACC
* *
282453 ATTAATAAAAAAATTAATAATG-AAGAAATTG
1 ATTAATAAAAAAATGAAAAATGAAAGAAATTG
282484 ATTAATGAAAAAAATGGAAAAATGAAAGAAAT
1 ATTAAT-AAAAAAAT-GAAAAATGAAAGAAAT
282516 AAAGGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 8 0.30
33 6 0.22
34 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (32 bp):
ATTAATAAAAAAATGAAAAATGAAAGAAATTG
Found at i:285234 original size:18 final size:19
Alignment explanation
Indices: 285206--285242 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
285196 GCATAATCAT
285206 AATTGATTAAAAATGAACA
1 AATTGATTAAAAATGAACA
*
285225 AATT-ATTAAAATTGAACA
1 AATTGATTAAAAATGAACA
285243 CCAATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (19 bp):
AATTGATTAAAAATGAACA
Found at i:286665 original size:24 final size:24
Alignment explanation
Indices: 286638--286685 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
286628 AGGGTGATGG
*
286638 AGAGGCTGAGGGTGAAGATGAAGA
1 AGAGGATGAGGGTGAAGATGAAGA
* *
286662 AGAGGATGATGGTGATGATGAAGA
1 AGAGGATGAGGGTGAAGATGAAGA
286686 GGGTGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.44, T:0.17
Consensus pattern (24 bp):
AGAGGATGAGGGTGAAGATGAAGA
Found at i:289871 original size:2 final size:2
Alignment explanation
Indices: 289864--289898 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
289854 CTTGTGACAA
289864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
289899 ACCATGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293865 original size:19 final size:18
Alignment explanation
Indices: 293843--293878 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
293833 TTTATACAAA
*
293843 AAAATTTATATTATTTAAT
1 AAAATATATATT-TTTAAT
293862 AAAATATATATTTTTAA
1 AAAATATATATTTTTAA
293879 GTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATATATATTTTTAAT
Found at i:294592 original size:19 final size:20
Alignment explanation
Indices: 294568--294605 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
294558 AAAATTATAT
294568 TTTATTATAA-TTTTAAAAG
1 TTTATTATAATTTTTAAAAG
*
294587 TTTATTTTAATTTTTAAAA
1 TTTATTATAATTTTTAAAA
294606 TTATGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTATTATAATTTTTAAAAG
Found at i:294905 original size:36 final size:33
Alignment explanation
Indices: 294847--294924 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 33
294837 CTCTACCTTA
* *
294847 AATTTAATAGTCTTTGAAACGAATATCA-TCGTT
1 AATTTAATAATCTTTGAAACGAATATCATTC-CT
*
294880 AATTTAATAATACTCTTGAAGACGAATGTCATTCCT
1 AATTTAATAAT-CT-TTGAA-ACGAATATCATTCCT
294916 AATTTAATA
1 AATTTAATA
294925 GTTTTGGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 10 0.26
34 2 0.05
35 5 0.13
36 19 0.50
37 2 0.05
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (33 bp):
AATTTAATAATCTTTGAAACGAATATCATTCCT
Found at i:296260 original size:19 final size:20
Alignment explanation
Indices: 296222--296262 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
296212 CCAGATTAGA
*
296222 TTTTTTATCAAATTTCTTTT
1 TTTTTTATCAAATTTATTTT
*
296242 TTTTTTAT-AAGTTTATTTT
1 TTTTTTATCAAATTTATTTT
296261 TT
1 TT
296263 AAATCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTATCAAATTTATTTT
Found at i:296921 original size:2 final size:2
Alignment explanation
Indices: 296914--296938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
296904 TCATAGAACA
296914 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
296939 ACATCTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:297226 original size:15 final size:16
Alignment explanation
Indices: 297196--297227 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
297186 TATGAGAGAC
297196 TTTTAAAATATTTAAA
1 TTTTAAAATATTTAAA
297212 TTTTAAAAT-TTTAAA
1 TTTTAAAATATTTAAA
297227 T
1 T
297228 GTACATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATATTTAAA
Found at i:299382 original size:18 final size:18
Alignment explanation
Indices: 299361--299408 Score: 89
Period size: 17 Copynumber: 2.7 Consensus size: 18
299351 AATTGAATTT
299361 GGATTTTATTAATAAATA
1 GGATTTTATTAATAAATA
299379 GGATTTTATT-ATAAATA
1 GGATTTTATTAATAAATA
299396 GGATTTTATTAAT
1 GGATTTTATTAAT
299409 GAATGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (18 bp):
GGATTTTATTAATAAATA
Found at i:302066 original size:3 final size:3
Alignment explanation
Indices: 302058--302084 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
302048 ATTCATGTAA
302058 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
302085 GAAAAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:302791 original size:2 final size:2
Alignment explanation
Indices: 302786--302825 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
302776 TTAATGTGTG
302786 TA TA TA TA 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 TA TA TA TA
302826 ATAGTCCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:303113 original size:10 final size:10
Alignment explanation
Indices: 303088--303149 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
303078 AACATGTCAT
303088 AAATATATAA
1 AAATATATAA
*
303098 ATATATCA-AA
1 AAATAT-ATAA
303108 AAATATATAA
1 AAATATATAA
303118 AAATATGAGTAA
1 AAATAT-A-TAA
* *
303130 AAATTTATAT
1 AAATATATAA
*
303140 AAATTTATAA
1 AAATATATAA
303150 TATTTTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 1 0.02
10 31 0.72
11 3 0.07
12 8 0.19
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (10 bp):
AAATATATAA
Done.