Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold868
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: 88443
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:4874 original size:5 final size:5
Alignment explanation
Indices: 4861--4899 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
4851 GTTACACCCA
* * *
4861 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAA AAAAG AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
4900 AAATAGCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:6162 original size:29 final size:29
Alignment explanation
Indices: 6122--7047 Score: 1352
Period size: 28 Copynumber: 32.3 Consensus size: 29
6112 CTGTCTAGAA
*
6122 TCAGTGGCACTCCTTTCAAAGCCCACAAA
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6151 TCAGTGGCACT-CTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6179 TCAGTGGCACT-CTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6207 TGCAGTGGCAC-CCTTTCAAAGCCCACAAG
1 T-CAGTGGCACTCCTTTCAAAGCCCACAAG
6236 TCAGTGGCACT-CTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6264 TCAGTGGCAC-CCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6292 TCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6321 TTAGTGGCAC-CCTTTCAAATCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6349 TCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6378 TCAGTGGCACTCCTTTCAAAGCCCACAAA
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6407 TCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6436 TCAGTGGCAC-CCTTTCAAAGCCCACAAC
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6464 TCAGTGGCAC-CCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6492 TCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6521 TCAGTGGCACTCTTTTCAAAGCCCACAAA
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6550 TCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6579 TTAGTGGCAC-CCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6607 TCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6636 TCAGTGGCACTCTTTTCAAAGCCCACAAA
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6665 TCAGTGGCACTCTTTTAAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6694 TCAGTGGCAC-CCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6722 TTAGTGGCAC-CCTTTCAGAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6750 TCAGTGGCAC-CCTTTCGAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* * * *
6778 TCAGTGGCAC-CATTGCGAAGCCCACAAT
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6806 TCAGTGGCACT-CTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6834 TCAGTGGCAC-CCTTTTAAAGCTCACACAAG
1 TCAGTGGCACTCCTTTCAAAGC-C-CACAAG
* *
6864 TCAGTGGCACTCCTTTTAAAGCTCACGCAAG
1 TCAGTGGCACTCCTTTCAAAGC-C-CACAAG
* *
6895 TCAGTGGTAC-CTTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
6923 TCAGTGGCACT-CTTTCAAAGCCCACAAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
*
6951 TCAGTGGCA-TCCTTTCAAAGCCCACGAG
1 TCAGTGGCACTCCTTTCAAAGCCCACAAG
* *
6979 TTAGTGGCA-TTCTTTCAAAGCCCACGCAAG
1 TCAGTGGCACTCCTTTCAAAGCCCA--CAAG
*
7009 TCAGTGGCAC-CCTTTTAAAGCCCATGCAAG
1 TCAGTGGCACTCCTTTCAAAGCCCA--CAAG
*
7039 TCAATGGCA
1 TCAGTGGCA
7048 ACCCTTTTCA
Statistics
Matches: 827, Mismatches: 52, Indels: 35
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.00
28 424 0.51
29 313 0.38
30 61 0.07
31 28 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
TCAGTGGCACTCCTTTCAAAGCCCACAAG
Found at i:6213 original size:57 final size:56
Alignment explanation
Indices: 6122--7047 Score: 1357
Period size: 57 Copynumber: 16.2 Consensus size: 56
6112 CTGTCTAGAA
* *
6122 TCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCAAAGCCCACAAG
1 TCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
6179 TCAGTGGCACTCTTTCAAAGCCCACAAGTGCAGTGGCACCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGT-CAGTGGCACCCTTTCAAAGCCCACAAG
6236 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* *
6292 TCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAATCCCACAAG
1 TCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
6349 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAA
1 TCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
*
6407 TCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAC
1 TCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
6464 TCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
* *
6521 TCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
* *
6579 TTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
* * *
6636 TCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTAAAAGCCCACAAG
1 TCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
* * *
6694 TCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* * * * * *
6750 TCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAAT
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
6806 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCTCACACAAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC-C-CACAAG
* * * *
6864 TCAGTGGCACTCCTTTTAAAGCTCACGCAAGTCAGTGGTACCTTTTCAAAGCCCACAAG
1 TCAGTGGCACT-CTTTCAAAGC-C-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* *
6923 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAG
1 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* * *
6979 TTAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCATGCAAG
1 TCAGTGGCACTCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAG
*
7039 TCAATGGCA
1 TCAGTGGCA
7048 ACCCTTTTCA
Statistics
Matches: 793, Mismatches: 60, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
56 239 0.30
57 283 0.36
58 210 0.26
59 26 0.03
60 12 0.02
61 23 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (56 bp):
TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
Found at i:7601 original size:20 final size:20
Alignment explanation
Indices: 7573--7647 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
7563 TCATACCCTG
7573 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
7593 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
7613 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
7633 ATGTATCGATACATT
1 ATGTATCGATACATT
7648 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:7640 original size:40 final size:39
Alignment explanation
Indices: 7573--7650 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
7563 TCATACCCTG
* *
7573 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
7613 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
7651 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:11352 original size:14 final size:15
Alignment explanation
Indices: 11320--11354 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
11310 GGCTTCATTT
11320 ATTTTATGAAAATTA
1 ATTTTATGAAAATTA
11335 ATTTTATGAAAA-TA
1 ATTTTATGAAAATTA
11349 ATTTTA
1 ATTTTA
11355 AAATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
ATTTTATGAAAATTA
Found at i:12197 original size:11 final size:12
Alignment explanation
Indices: 12174--12200 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12164 AATATTACCA
12174 TTTTCTAATTTT
1 TTTTCTAATTTT
12186 TTTTCTAATTTT
1 TTTTCTAATTTT
12198 TTT
1 TTT
12201 AATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTAATTTT
Found at i:12295 original size:16 final size:16
Alignment explanation
Indices: 12274--12304 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12264 CTAGTAATAT
*
12274 AATTTAAATTCATTAA
1 AATTTAAATTAATTAA
12290 AATTTAAATTAATTA
1 AATTTAAATTAATTA
12305 CCTTTAAGGG
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATTAATTAA
Found at i:12908 original size:2 final size:2
Alignment explanation
Indices: 12901--12939 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12891 AAGCTTCTGG
12901 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12940 TTCTTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17120 original size:22 final size:22
Alignment explanation
Indices: 17083--17133 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17073 TTTAATAAAA
*
17083 AATAATTATTATTTTTAT-ATT
1 AATATTTATTATTTTTATAATT
17104 AATATTTATATATTTTTATAATT
1 AATATTTAT-TATTTTTATAATT
17127 AA-ATTTA
1 AATATTTA
17134 AATAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATATTTATTATTTTTATAATT
Found at i:17313 original size:3 final size:3
Alignment explanation
Indices: 17305--17352 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
17295 GTCCTCACAC
17305 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
17350 ATA
1 ATA
17353 TAAAACCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17647 original size:21 final size:21
Alignment explanation
Indices: 17623--17670 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17613 AGATATCTTA
17623 AATATTAAAACAATA-AAATAC
1 AATATTAAAA-AATATAAATAC
* *
17644 AATATCAAAATATATAAATAC
1 AATATTAAAAAATATAAATAC
*
17665 ATTATT
1 AATATT
17671 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATTAAAAAATATAAATAC
Found at i:17926 original size:34 final size:34
Alignment explanation
Indices: 17883--17954 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
17873 AAAAAAAGGA
17883 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
1 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
*
17917 TTTGGATGTATCCGAAGCTAGTTCCTGGTTTTAC
1 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
17951 TTTG
1 TTTG
17955 AATCATTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (34 bp):
TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
Found at i:19053 original size:43 final size:45
Alignment explanation
Indices: 18999--19103 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 45
18989 TCCTTTTGGT
*
18999 TTTTTGTTGGAATTTCTTTA-TTTTTTGTG-TTTACAGATATTCAA
1 TTTTT-TTGGAATTTCTTTATTTTTTTATGTTTTACAGATATTCAA
**
19043 TTTTTTTGGAATTTCTTTATTTTTTTTATGTTTTATGGATATTCAA
1 TTTTTTTGGAATTTCTTTA-TTTTTTTATGTTTTACAGATATTCAA
*
19089 ATTTTTTGGAATTTC
1 TTTTTTTGGAATTTC
19104 ATCCTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
43 14 0.26
44 5 0.09
45 8 0.15
46 27 0.50
ACGTcount: A:0.20, C:0.06, G:0.12, T:0.62
Consensus pattern (45 bp):
TTTTTTTGGAATTTCTTTATTTTTTTATGTTTTACAGATATTCAA
Found at i:21691 original size:36 final size:34
Alignment explanation
Indices: 21631--21700 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
21621 ATAAAAATAA
**
21631 AAAATATTTTTATATTTTTTATAATTAAATTTAAAT
1 AAAATATTTTTATATTTTAAATAATT--ATTTAAAT
21667 AAAATATTTTT-TATTATTAAATAATTATTTAAAT
1 AAAATATTTTTATATT-TTAAATAATTATTTAAAT
21701 CTGTCTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 8 0.26
35 4 0.13
36 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
AAAATATTTTTATATTTTAAATAATTATTTAAAT
Found at i:21837 original size:3 final size:3
Alignment explanation
Indices: 21829--21856 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21819 GTCCATACAC
21829 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21857 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21861 original size:3 final size:3
Alignment explanation
Indices: 21855--21884 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21845 ATAATAATAA
21855 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21885 GAAACAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:22115 original size:21 final size:22
Alignment explanation
Indices: 22077--22124 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
22067 ATTCATCTAC
* * * *
22077 AAAATTAAAATTATATTTTTTT
1 AAAATTAAAATAAAATTTATAT
22099 AAAATT-AAATAAAATTTATAT
1 AAAATTAAAATAAAATTTATAT
22120 AAAAT
1 AAAAT
22125 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTAAAATAAAATTTATAT
Found at i:34042 original size:20 final size:20
Alignment explanation
Indices: 34004--34042 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33994 TCATAGTTGA
* * *
34004 TAATTGCATTTAACCAATAC
1 TAATTACATTGAACAAATAC
34024 TAATTACATTGAACAAATA
1 TAATTACATTGAACAAATA
34043 AGAAAAGTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
TAATTACATTGAACAAATAC
Found at i:36312 original size:2 final size:2
Alignment explanation
Indices: 36305--36340 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36295 TATTGTTGAT
36305 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
36341 ATGAATGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37398 original size:21 final size:22
Alignment explanation
Indices: 37369--37409 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
37359 AAATAGTATC
37369 TTATATTAAAA-TAATATATATT
1 TTATATTAAAATTAAT-TATATT
37391 TTAT-TTAAAATTAATTATA
1 TTATATTAAAATTAATTATA
37410 AAATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATATTAAAATTAATTATATT
Found at i:37420 original size:21 final size:21
Alignment explanation
Indices: 37396--37435 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
37386 ATATTTTATT
37396 TAAA-ATTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
37417 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
37436 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:37654 original size:21 final size:22
Alignment explanation
Indices: 37630--37670 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37620 TATAATTATA
37630 AATTA-TAAATAAGTTATTTTT
1 AATTAGTAAATAAGTTATTTTT
* *
37651 AATTAGTAATTAATTTATTT
1 AATTAGTAAATAAGTTATTT
37671 ATAGATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
AATTAGTAAATAAGTTATTTTT
Found at i:38223 original size:21 final size:21
Alignment explanation
Indices: 38199--38243 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
38189 GTGCATTTGG
38199 AAGTTTAATCAAGGTATTATT
1 AAGTTTAATCAAGGTATTATT
38220 AAGTTTAATCAAGGTATTATT
1 AAGTTTAATCAAGGTATTATT
38241 AAG
1 AAG
38244 AAAGGTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (21 bp):
AAGTTTAATCAAGGTATTATT
Found at i:41678 original size:20 final size:22
Alignment explanation
Indices: 41627--41678 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
41617 TATATTTTAA
41627 TTTTTATAA-TAGTTTATATCT
1 TTTTTATAATTAGTTTATATCT
* *
41648 TTGTT-TAATTA-TTTTTAT-T
1 TTTTTATAATTAGTTTATATCT
41667 TTTTTATAATTA
1 TTTTTATAATTA
41679 CTATCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTATAATTAGTTTATATCT
Found at i:43257 original size:27 final size:25
Alignment explanation
Indices: 43227--43291 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 25
43217 TATTTTTCGA
* *
43227 TTTTAATTTTTTGGGAATTTCTTGAAT
1 TTTTAATTTTTT-GGAATATATT-AAT
*
43254 TTTT-ATGTTTTATTGAATATATTAAT
1 TTTTAAT-TTTT-TGGAATATATTAAT
43280 TTTTAATTTTTT
1 TTTTAATTTTTT
43292 AAGAATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.03
26 13 0.41
27 17 0.53
28 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.65
Consensus pattern (25 bp):
TTTTAATTTTTTGGAATATATTAAT
Found at i:43297 original size:26 final size:26
Alignment explanation
Indices: 43227--43309 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
43217 TATTTTTCGA
** *
43227 TTTTAATTTTTTGGGAATTTCTTGAAT
1 TTTTAATTTTTTAAGAA-TTATTGAAT
* *
43254 TTTT-ATGTTTTATTGAATATATT-AAT
1 TTTTAATTTTTTA-AGAAT-TATTGAAT
*
43280 TTTTAATTTTTTAAGAATTATTGTAT
1 TTTTAATTTTTTAAGAATTATTGAAT
43306 TTTT
1 TTTT
43310 TTAGATTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.09
26 24 0.53
27 17 0.38
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.63
Consensus pattern (26 bp):
TTTTAATTTTTTAAGAATTATTGAAT
Found at i:43439 original size:19 final size:20
Alignment explanation
Indices: 43414--43459 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
43404 GTTCAAAACC
* *
43414 CAATTAATAATTTGAGATCT
1 CAATTAATAATTTCAAATCT
43434 -AATTAATAATTTCAAATCT
1 CAATTAATAATTTCAAATCT
43453 CAATTAA
1 CAATTAA
43460 CAATGTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (20 bp):
CAATTAATAATTTCAAATCT
Found at i:47136 original size:2 final size:2
Alignment explanation
Indices: 47129--47166 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47119 ATAAACCTTT
47129 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
47167 GAAGAGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47478 original size:18 final size:19
Alignment explanation
Indices: 47438--47478 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
47428 TATGATTTTT
*
47438 TTAAAAAAATTTAAATACA
1 TTAAAAAAATTTAAATAAA
*
47457 -TAAAAAATTTTAAA-AAA
1 TTAAAAAAATTTAAATAAA
47474 TTAAA
1 TTAAA
47479 TATATCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAAAATTTAAATAAA
Found at i:48467 original size:14 final size:14
Alignment explanation
Indices: 48448--48477 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48438 AAAGATAAAA
48448 AAAATAAAAATCAT
1 AAAATAAAAATCAT
*
48462 AAAATAATAATCAT
1 AAAATAAAAATCAT
48476 AA
1 AA
48478 TATTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAAAATCAT
Found at i:49664 original size:2 final size:2
Alignment explanation
Indices: 49657--49701 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
49647 GCATAGTTAG
49657 TC TC TC TC TC TC TC TC TC 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 TC TC TC TC TC
49699 TC T
1 TC T
49702 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:49706 original size:2 final size:2
Alignment explanation
Indices: 49701--49739 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
49691 TCTCTCTCTC
49701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49740 TAGAAAAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52141 original size:13 final size:13
Alignment explanation
Indices: 52125--52153 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52115 GATGCAAAGA
52125 TTAGATAAAATTT
1 TTAGATAAAATTT
52138 TTAGATAAAATTT
1 TTAGATAAAATTT
52151 TTA
1 TTA
52154 AATATTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TTAGATAAAATTT
Found at i:54728 original size:22 final size:21
Alignment explanation
Indices: 54694--54734 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
54684 ATTAAAAAAT
54694 TATTGTTATATTAATATTTATA
1 TATTGTTATATTAA-ATTTATA
54716 TATT-TTATAATTAAATTTA
1 TATTGTTAT-ATTAAATTTA
54735 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTGTTATATTAAATTTATA
Found at i:54762 original size:19 final size:20
Alignment explanation
Indices: 54730--54768 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
54720 TTATAATTAA
54730 ATTTAAATAAAAATA-TATT
1 ATTTAAATAAAAATACTATT
54749 ATTT-AATATAAAATACTATT
1 ATTTAAATA-AAAATACTATT
54769 TTGATCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAATAAAAATACTATT
Found at i:56271 original size:22 final size:23
Alignment explanation
Indices: 56238--56281 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
56228 TGAAAATAAT
56238 TTTTGAAAAAAATATACT-TTTTC
1 TTTTGAAAAAAAT-TACTGTTTTC
56261 TTTT-AAAAAAATTACTGTTTT
1 TTTTGAAAAAAATTACTGTTTT
56282 GTTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTTGAAAAAAATTACTGTTTTC
Found at i:56290 original size:73 final size:70
Alignment explanation
Indices: 56158--56290 Score: 162
Period size: 73 Copynumber: 1.9 Consensus size: 70
56148 ATTGATTTTG
* * * *
56158 TGAAAATAATTTTAAAATATATATTTATTTTTTTAAAAAAAGTTATTATTTTTTGTTATTCAGAT
1 TGAAAATAATTTTAAAAAATATATTTATTCTTTTAAAAAAAGTTACTATTTTTTATTATTCAGAT
56223 TGATA
66 TGATA
*
56228 TGAAAATAATTTTTGAAAAAAATATACTTT-TTCTTTTAAAAAAA-TTACTGTTTTGTTATTATT
1 TGAAAATAA-TTTT--AAAAAATATA-TTTATTCTTTTAAAAAAAGTTACTATTTT-TTATTATT
56291 TGGATGATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
70 9 0.17
71 4 0.08
72 8 0.15
73 29 0.55
74 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (70 bp):
TGAAAATAATTTTAAAAAATATATTTATTCTTTTAAAAAAAGTTACTATTTTTTATTATTCAGAT
TGATA
Found at i:56856 original size:2 final size:2
Alignment explanation
Indices: 56849--56878 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56839 AAAAATAAGA
*
56849 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56879 CTTGGCAAGA
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):
AT
Found at i:57723 original size:2 final size:2
Alignment explanation
Indices: 57716--57760 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
57706 AAGCTTCTGG
57716 TC TC TC TC TC TC TC TC TC 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 TC TC TC TC TC
57758 TC T
1 TC T
57761 TCTTTTCATA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:65142 original size:138 final size:138
Alignment explanation
Indices: 64893--65186 Score: 457
Period size: 138 Copynumber: 2.1 Consensus size: 138
64883 GGTAATAAGA
* * * *
64893 AGATGCAAGCTTTTGTTGTTTTTCTTAATCAAAAGGAGTCACAACCCGGGAATAATTGAACTTTA
1 AGATGCAAGCTTATGTTGTTTTTCTTAAACAAAAGAAGTCACAACCCGGGAATAATTGAACTGTA
* *
64958 GACTCATTGGATGTTATCTTTTAAGGGTGGTGTGGTTGCATGAATGATTGAACAAAATCCGAGTC
66 GACTCATTGGATGTTATCTTTTAAGGGTGGTGTGGTTGAATGAATGATTGAACAAAATCCGAGTA
65023 CTGAATAC
131 CTGAATAC
* * *
65031 GGATGCAAGCTTATGTTGGTTTTT-TTAAACAAAAGAAGTCGCAACCCTGGAATAATTGAACTGT
1 AGATGCAAGCTTATGTT-GTTTTTCTTAAACAAAAGAAGTCACAACCCGGGAATAATTGAACTGT
65095 AGACTCGA-TGGATGTTATCTTTTAAGGGTGGTGTGGTTGAATGAATGATTGAACAAAATCCGAG
65 AGACTC-ATTGGATGTTATCTTTTAAGGGTGGTGTGGTTGAATGAATGATTGAACAAAATCCGAG
*
65159 TACTGAATTC
129 TACTGAATAC
65169 AGATGCAAGCTTTATGTT
1 AGATGCAAGC-TTATGTT
65187 ATGTTTAGTT
Statistics
Matches: 142, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
138 128 0.90
139 14 0.10
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (138 bp):
AGATGCAAGCTTATGTTGTTTTTCTTAAACAAAAGAAGTCACAACCCGGGAATAATTGAACTGTA
GACTCATTGGATGTTATCTTTTAAGGGTGGTGTGGTTGAATGAATGATTGAACAAAATCCGAGTA
CTGAATAC
Found at i:70248 original size:15 final size:16
Alignment explanation
Indices: 70216--70252 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
70206 GCAATTGCTG
*
70216 CTTC-TCTTCTATTGT
1 CTTCTTCTTCTAATGT
70231 CTTCTTCTTCTAAT-T
1 CTTCTTCTTCTAATGT
70246 CTTCTTC
1 CTTCTTC
70253 CACCTTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.08, C:0.30, G:0.03, T:0.59
Consensus pattern (16 bp):
CTTCTTCTTCTAATGT
Found at i:71309 original size:17 final size:17
Alignment explanation
Indices: 71280--71330 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
71270 TTTTAATAGT
*
71280 AAATAAATA-TTAATTA
1 AAATATATATTTAATTA
* * *
71296 TAATATGTATTTAATAA
1 AAATATATATTTAATTA
*
71313 AAATATATATTTTATTA
1 AAATATATATTTAATTA
71330 A
1 A
71331 GTGATATGAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATATATATTTAATTA
Found at i:73248 original size:19 final size:19
Alignment explanation
Indices: 73188--73249 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
73178 TTTTAAATTA
* *
73188 TTTAATATTAATAAAATTT
1 TTTAATTTTAATAAAATAT
73207 ATTTAATTTATAAATAAAA-AT
1 -TTTAATTT-T-AATAAAATAT
*
73228 TTTAATTTTATTAAAATAT
1 TTTAATTTTAATAAAATAT
73247 TTT
1 TTT
73250 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 15 0.42
21 2 0.06
22 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTTTAATAAAATAT
Found at i:73261 original size:13 final size:14
Alignment explanation
Indices: 73230--73264 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
73220 ATAAAAATTT
73230 TAATTTTATTAAAA
1 TAATTTTATTAAAA
73244 T-ATTTT-TTAAAA
1 TAATTTTATTAAAA
73256 TAATTTTAT
1 TAATTTTAT
73265 GTAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.37
13 10 0.53
14 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTTTATTAAAA
Found at i:73903 original size:16 final size:16
Alignment explanation
Indices: 73836--73896 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
73826 TGAATTCAGG
73836 TTATTTTAATTTTAAA
1 TTATTTTAATTTTAAA
* *
73852 TCATTTTGATTTTAAA
1 TTATTTTAATTTTAAA
*
73868 TTATTTTAAGTTTAAA
1 TTATTTTAATTTTAAA
73884 TTATTTTAATTTT
1 TTATTTTAATTTT
73897 GAGTTATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (16 bp):
TTATTTTAATTTTAAA
Found at i:74470 original size:16 final size:16
Alignment explanation
Indices: 74403--74463 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
74393 TGAATTCAGG
74403 TTATTTTAATTTTAAA
1 TTATTTTAATTTTAAA
* *
74419 TCATTTTGATTTTAAA
1 TTATTTTAATTTTAAA
*
74435 TTATTTTAAGTTTAAA
1 TTATTTTAATTTTAAA
74451 TTATTTTAATTTT
1 TTATTTTAATTTT
74464 GAGTTATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (16 bp):
TTATTTTAATTTTAAA
Found at i:74761 original size:567 final size:567
Alignment explanation
Indices: 73687--74830 Score: 2279
Period size: 567 Copynumber: 2.0 Consensus size: 567
73677 AATAAGTTGA
*
73687 TTTTTTGAATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATAT
1 TTTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATAT
73752 TTGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTT
66 TTGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTT
73817 TAAAATTTTTGAATTCAGGTTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTA
131 TAAAATTTTTGAATTCAGGTTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTA
73882 AATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATT
196 AATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATT
73947 TAAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAA
261 TAAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAA
74012 CATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAA
326 CATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAA
74077 CTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTT
391 CTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTT
74142 GAATCATTATTCATTATACTAACTTTGATCTATTTGAAAATTTCAACATTGAACTTGATAAGCCA
456 GAATCATTATTCATTATACTAACTTTGATCTATTTGAAAATTTCAACATTGAACTTGATAAGCCA
74207 AGTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTT
521 AGTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTT
74254 TTTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATAT
1 TTTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATAT
74319 TTGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTT
66 TTGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTT
74384 TAAAATTTTTGAATTCAGGTTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTA
131 TAAAATTTTTGAATTCAGGTTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTA
74449 AATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATT
196 AATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATT
74514 TAAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAA
261 TAAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAA
74579 CATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAA
326 CATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAA
74644 CTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTT
391 CTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTT
74709 GAATCATTATTCATTATACTAACTTTGATCTATTTGAAAATTTCAACATTGAACTTGATAAGCCA
456 GAATCATTATTCATTATACTAACTTTGATCTATTTGAAAATTTCAACATTGAACTTGATAAGCCA
74774 AGTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTT
521 AGTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTT
74821 TTTTTTGTAT
1 TTTTTTGTAT
74831 CCACTCGGAT
Statistics
Matches: 576, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
567 576 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (567 bp):
TTTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATAT
TTGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTT
TAAAATTTTTGAATTCAGGTTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTA
AATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATT
TAAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAA
CATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAA
CTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTT
GAATCATTATTCATTATACTAACTTTGATCTATTTGAAAATTTCAACATTGAACTTGATAAGCCA
AGTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTT
Found at i:75109 original size:17 final size:16
Alignment explanation
Indices: 75056--75110 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
75046 TTTTTAAATT
75056 TTTATTTTAAATAAAAAA
1 TTTA-TTTAAAT-AAAAA
* *
75074 TTAATATAAATAAAAA
1 TTTATTTAAATAAAAA
75090 TTTATTTAAATATAAAA
1 TTTATTTAAATA-AAAA
75107 TTTA
1 TTTA
75111 AATAAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 15 0.47
17 14 0.44
18 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTATTTAAATAAAAA
Found at i:75112 original size:567 final size:560
Alignment explanation
Indices: 73786--75116 Score: 1381
Period size: 567 Copynumber: 2.3 Consensus size: 560
73776 GTTTTAGATT
* * *** * ** ***
73786 AAATTATTTTGATTAAGTCATTTTAGGTTTTTAAAATTTTTGAATTCAGGTTATTTTAATTTTAA
1 AAATTATTTTGATCAAGTCATTTTAGGTATTTAAAATTAAAGAATTAAAATTATAAAAATTTTAA
* * * * **
73851 ATCATTTTGATTTTAAATTATTTTAAGTTTAAATTATTTTAATTTTGAGTTATGATTATGTTTTC
66 A-CA-TATAATTTTAAATTATATTAAGTTTAAAATATTTTAATTTTGAGTTATGATTAAATTTTC
* * ** * * * * *
73916 TAATTAAATTGATTTAGATTAAGTTTAAATTTAAATGAATTATTTAATCATTTTAGATTTAAATA
129 TAATT--ATTGATTTAAATAAAAATTAAATATAAATAAATTATTTAA-CATATAAAATTTAAATA
73981 AAAATTAAAAAATATATGAACGTGAAAAGAACATAATTGATAAAGATTTATATTTTGATTGTATA
191 AAAATTAAAAAATATATGAACGTGAAAAGAACATAATTGATAAAGATTTATATTTTGATTGTATA
74046 TTAATCTTCCATATAAAAATTATATTGATAACTACAAAATAGAAATAAATTAAATTGTCGAAGTA
256 TTAATCTTCCATATAAAAATTATATTGATAACTACAAAATAGAAATAAATTAAATTGTCGAAGTA
74111 TTATTTAAGCTCTATTTGGTTAAATTAACTTGAATCATTATTCATTATACTAACTTTGATCTATT
321 TTATTTAAGCTCTATTTGGTTAAATTAACTTGAATCATTATTCATTATACTAACTTTGATCTATT
74176 TGAAAATTTCAACATTGAACTTGATAAGCCAAGTTATGTTAACCAAATCCAAACAAAACATATTT
386 TGAAAATTTCAACATTGAACTTGATAAGCCAAGTTATGTTAACCAAATCCAAACAAAACATATTT
** * ** * * * * *
74241 TTATTCGATTTTTTTTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTT
451 TTATTCGATTTTTTTTTTTGTATACTGAGGA-ATTATAAAATCAAAATATACTTCGAGAGGAATC
** * *** * * * * **
74306 TGGATGAGTATATTTGTAAATTGTATGGGTTAAGTTGGTTTTAGATT
515 TAAATCAG-ATATTTGTAAATTGTATAAATTAAATCGATTATAGAAC
* * *** * ** ***
74353 AAATTATTTTGATTAAGTCATTTTAGGTTTTTAAAATTTTTGAATTCAGGTTATTTTAATTTTAA
1 AAATTATTTTGATCAAGTCATTTTAGGTATTTAAAATTAAAGAATTAAAATTATAAAAATTTTAA
* * * * **
74418 ATCATTTTGATTTTAAATTATTTTAAGTTTAAATTATTTTAATTTTGAGTTATGATTATGTTTTC
66 A-CA-TATAATTTTAAATTATATTAAGTTTAAAATATTTTAATTTTGAGTTATGATTAAATTTTC
* * ** * * * * *
74483 TAATTAAATTGATTTAGATTAAGTTTAAATTTAAATGAATTATTTAATCATTTTAGATTTAAATA
129 TAATT--ATTGATTTAAATAAAAATTAAATATAAATAAATTATTTAA-CATATAAAATTTAAATA
74548 AAAATTAAAAAATATATGAACGTGAAAAGAACATAATTGATAAAGATTTATATTTTGATTGTATA
191 AAAATTAAAAAATATATGAACGTGAAAAGAACATAATTGATAAAGATTTATATTTTGATTGTATA
74613 TTAATCTTCCATATAAAAATTATATTGATAACTACAAAATAGAAATAAATTAAATTGTCGAAGTA
256 TTAATCTTCCATATAAAAATTATATTGATAACTACAAAATAGAAATAAATTAAATTGTCGAAGTA
74678 TTATTTAAGCTCTATTTGGTTAAATTAACTTGAATCATTATTCATTATACTAACTTTGATCTATT
321 TTATTTAAGCTCTATTTGGTTAAATTAACTTGAATCATTATTCATTATACTAACTTTGATCTATT
74743 TGAAAATTTCAACATTGAACTTGATAAGCCAAGTTATGTTAACCAAATCCAAACAAAACATATTT
386 TGAAAATTTCAACATTGAACTTGATAAGCCAAGTTATGTTAACCAAATCCAAACAAAACATATTT
* ****
74808 TTATTCGATTTTTTTTTTTGTATCCACT-CGG-ATTATAAAAT-AAAATATAC-TCGATTTTAAT
451 TTATTCGATTTTTTTTTTTGTAT--ACTGAGGAATTATAAAATCAAAATATACTTCGAGAGGAAT
74869 CTAAATCA-A-ATTT-TAAATT-TATAAATTAAATCGATTATA-AAC
514 CTAAATCAGATATTTGTAAATTGTATAAATTAAATCGATTATAGAAC
* *
74911 AATTTGAGTTTT-ATCATA-TCTATTTCATATAAGG-ATTTAAAGTTAAAG-A-TAAAATATAAT
1 AAATT-A-TTTTGATCA-AGTC-A-TT--T-T-AGGTATTTAAAATTAAAGAATTAAAAT-T-AT
** *
74971 AAAAATATTTTAAA-A-ATAATTTTAAATTATATTACTTTTTAAAATATGTATTATACTTTT-AT
55 -AAAA-ATTTTAAACATATAATTTTAAATTATATTA-AGTTTAAAATAT-T-TTA-A-TTTTGAG
* *
75033 TATATTTATTAAATTTT-TAAATT-TTTATTTTAAATAAAAAATT-AATATAAATAAAAATTTAT
113 T-TA-TGATTAAATTTTCT-AATTATTGA-TTTAAAT-AAAAATTAAATATAAAT--AAA-TTAT
75095 TTAA-ATATAAAATTTAAATAAA
170 TTAACATATAAAATTTAAATAAA
75117 GAGATAAAGT
Statistics
Matches: 676, Mismatches: 60, Indels: 56
0.85 0.08 0.07
Matches are distributed among these distances:
558 5 0.01
559 19 0.03
560 12 0.02
561 6 0.01
562 20 0.03
563 12 0.02
564 23 0.03
565 15 0.02
566 34 0.05
567 504 0.75
568 17 0.03
569 9 0.01
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (560 bp):
AAATTATTTTGATCAAGTCATTTTAGGTATTTAAAATTAAAGAATTAAAATTATAAAAATTTTAA
ACATATAATTTTAAATTATATTAAGTTTAAAATATTTTAATTTTGAGTTATGATTAAATTTTCTA
ATTATTGATTTAAATAAAAATTAAATATAAATAAATTATTTAACATATAAAATTTAAATAAAAAT
TAAAAAATATATGAACGTGAAAAGAACATAATTGATAAAGATTTATATTTTGATTGTATATTAAT
CTTCCATATAAAAATTATATTGATAACTACAAAATAGAAATAAATTAAATTGTCGAAGTATTATT
TAAGCTCTATTTGGTTAAATTAACTTGAATCATTATTCATTATACTAACTTTGATCTATTTGAAA
ATTTCAACATTGAACTTGATAAGCCAAGTTATGTTAACCAAATCCAAACAAAACATATTTTTATT
CGATTTTTTTTTTTGTATACTGAGGAATTATAAAATCAAAATATACTTCGAGAGGAATCTAAATC
AGATATTTGTAAATTGTATAAATTAAATCGATTATAGAAC
Found at i:75116 original size:17 final size:16
Alignment explanation
Indices: 75063--75116 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
75053 ATTTTTATTT
*
75063 TAAATAAAAAATTAATA
1 TAAATAAAAATTTAA-A
**
75080 TAAATAAAAATTTATT
1 TAAATAAAAATTTAAA
75096 TAAATATAAAATTTAAA
1 TAAATA-AAAATTTAAA
75113 TAAA
1 TAAA
75117 GAGATAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAAAAATTTAAA
Found at i:75405 original size:11 final size:11
Alignment explanation
Indices: 75379--75467 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
75369 TTTTAAAAAT
*
75379 ATATAATTTTTA
1 ATATAA-TTATA
75391 ATATAATTATA
1 ATATAATTATA
**
75402 ATATAAAAATA
1 ATATAATTATA
* * *
75413 ATTTAAATAAA
1 ATATAATTATA
75424 ATATAAATATATA
1 ATAT-AAT-TATA
75437 A-ATAATT-TA
1 ATATAATTATA
*
75446 ATTTAATT-TA
1 ATATAATTATA
*
75456 ATTTAATT-TA
1 ATATAATTATA
75466 AT
1 AT
75468 TTTTTAATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.05
10 20 0.31
11 27 0.42
12 10 0.16
13 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAATTATA
Found at i:75468 original size:5 final size:5
Alignment explanation
Indices: 75439--75479 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
75429 AATATATAAA
75439 TAATT TAATT TAATT TAATT TAATT TAATT T--TT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAA
75480 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
5 31 0.91
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:75483 original size:15 final size:13
Alignment explanation
Indices: 75442--75490 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 13
75432 ATATAAATAA
75442 TTTAATTTAATTT
1 TTTAATTTAATTT
75455 AATTTAATTTAATTT
1 --TTTAATTTAATTT
75470 TTTAATTTAAAATTT
1 TTTAATTT--AATTT
75485 TTTAAT
1 TTTAAT
75491 ATTTAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.25
15 24 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATTTAATTT
Found at i:75528 original size:20 final size:20
Alignment explanation
Indices: 75505--75564 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
75495 AATAATTATA
75505 TTAAATAAATTATTTAAAAT
1 TTAAATAAATTATTTAAAAT
*
75525 TTAAATAAA--A-TTAAATT
1 TTAAATAAATTATTTAAAAT
* * *
75542 TTAAATGAATTTTTTAATAT
1 TTAAATAAATTATTTAAAAT
75562 TTA
1 TTA
75565 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 14 0.44
18 1 0.03
20 17 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATAAATTATTTAAAAT
Found at i:75535 original size:25 final size:26
Alignment explanation
Indices: 75490--75541 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
75480 AATTTTTTAA
* *
75490 TATTTAATAATTATATTAAA-TAAAT
1 TATTTAATAATTAAATAAAATTAAAT
75515 TATTTAA-AATTTAAATAAAATTAAAT
1 TATTTAATAA-TTAAATAAAATTAAAT
75541 T
1 T
75542 TTAAATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 15 0.65
26 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTTAATAATTAAATAAAATTAAAT
Found at i:76786 original size:14 final size:14
Alignment explanation
Indices: 76769--76798 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
76759 TTGAATGATC
*
76769 ATATCACGTGCTCA
1 ATATCACATGCTCA
76783 ATATCACATGCTCA
1 ATATCACATGCTCA
76797 AT
1 AT
76799 CCGAATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (14 bp):
ATATCACATGCTCA
Found at i:81570 original size:21 final size:23
Alignment explanation
Indices: 81527--81573 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
81517 ATCATTAAAC
*
81527 ATTTTAAATAATAGTAATTATTTT
1 ATTTTAAATAATAG-AATAATTTT
81551 ATTTTAAATAA-A-AATAATTTT
1 ATTTTAAATAATAGAATAATTTT
81572 AT
1 AT
81574 GAATCAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
23 1 0.05
24 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTTAAATAATAGAATAATTTT
Found at i:81991 original size:21 final size:21
Alignment explanation
Indices: 81967--82008 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
81957 TTTTTGGATA
81967 ATAATAATTTTTAAGAAAATG
1 ATAATAATTTTTAAGAAAATG
** *
81988 ATAATTTTTTTTAAGGAAATG
1 ATAATAATTTTTAAGAAAATG
82009 GTATTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (21 bp):
ATAATAATTTTTAAGAAAATG
Found at i:82016 original size:21 final size:21
Alignment explanation
Indices: 81974--82020 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
81964 ATAATAATAA
81974 TTTTTAAGAAAATGATAATTT
1 TTTTTAAGAAAATGATAATTT
* *
81995 TTTTTAAGGAAATGGT-ATTT
1 TTTTTAAGAAAATGATAATTT
82015 TTTTTA
1 TTTTTA
82021 TTTTGTAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (21 bp):
TTTTTAAGAAAATGATAATTT
Done.