Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2298
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: 581295
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 216560 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1335 original size:51 final size:53
Alignment explanation
Indices: 1267--1654 Score: 190
Period size: 49 Copynumber: 7.5 Consensus size: 53
1257 AGTTTCTCAA
* * * *
1267 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
1318 TT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * *** * *
1372 TTCTTCACAATCGGGGATACTCCAAC-CCG--TTGATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * * **
1429 TAT-TTC-CGA--GGGGATACTCCAACCCCGACTTTA-TT-CTAAAATA-TTAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * * * * * *
1476 TT-TTCATAATCGGGGATATTCCAACCCCGGTTTTATTGCCTAACACACTAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * *
1528 TT-TTCCACAATCGGGGATACTCTAACCCCG-GTTTATTTTC---AACACCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-T
* *
1578 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1630 TT-TTCACAGTCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
1655 CTTGTTATTT
Statistics
Matches: 255, Mismatches: 50, Indels: 63
0.69 0.14 0.17
Matches are distributed among these distances:
46 4 0.02
47 3 0.01
49 47 0.18
50 16 0.06
51 44 0.17
52 45 0.18
53 43 0.17
54 35 0.14
55 7 0.03
56 2 0.01
57 8 0.03
58 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1675 original size:28 final size:28
Alignment explanation
Indices: 1643--1714 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1633 TCACAGTCGA
** * **
1643 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1671 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1699 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1715 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:3189 original size:28 final size:31
Alignment explanation
Indices: 3133--3208 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 31
3123 AGAACTTTAC
* *
3133 TTCTTTGTCCTTAAAGAACAGGAAA-TTT-T
1 TTCTTTATCCTCAAAGAACAGGAAATTTTCT
* **
3162 TT-TTTATCCTCAAAGACCAGGATGTTTTCT
1 TTCTTTATCCTCAAAGAACAGGAAATTTTCT
*
3192 TTCTTTGTCCTCAAAGA
1 TTCTTTATCCTCAAAGA
3209 GTAGGGCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 17 0.45
29 5 0.13
30 3 0.08
31 13 0.34
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (31 bp):
TTCTTTATCCTCAAAGAACAGGAAATTTTCT
Found at i:3206 original size:31 final size:29
Alignment explanation
Indices: 3098--3208 Score: 82
Period size: 30 Copynumber: 3.7 Consensus size: 29
3088 AACTTGACCC
** *
3098 TTTTTATCTTTGTCCTCAAAG-AGTGAGAAC
1 TTTTT-TCTTTGTCCTCAAAGAACAG-GAAA
* *
3128 TTTACTTCTTTGTCCTTAAAGAACAGGAAA
1 TTT-TTTCTTTGTCCTCAAAGAACAGGAAA
* * **
3158 TTTTTT-TTTATCCTCAAAGACCAGGATGT
1 TTTTTTCTTTGTCCTCAAAGAACAGGA-AA
3187 TTTCTTTCTTTGTCCTCAAAGA
1 TTT-TTTCTTTGTCCTCAAAGA
3209 GTAGGGCTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 17 0.27
29 5 0.08
30 26 0.41
31 16 0.25
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTTTTCTTTGTCCTCAAAGAACAGGAAA
Found at i:3338 original size:30 final size:30
Alignment explanation
Indices: 3299--3429 Score: 91
Period size: 30 Copynumber: 4.1 Consensus size: 30
3289 TATGACATTT
* *
3299 TTTTCCTTCTTTGTTCTCAAAGAGCAGGATG
1 TTTT-CTTCTTTGTCCTCAAAAAGCAGGATG
*
3330 TTTTCTTCTTTTCTTTGTCCTCAAAAAGCATGATG
1 --TT-TTC--TTCTTTGTCCTCAAAAAGCAGGATG
* * * * * **
3365 TTTTTTTCTTTGACCTCAAAGAGTAGAACA
1 TTTTCTTCTTTGTCCTCAAAAAGCAGGATG
* *
3395 TTTTCTTCTTTTGTCTTCAAAAAACAGGATG
1 TTTTCTTC-TTTGTCCTCAAAAAGCAGGATG
3426 TTTT
1 TTTT
3430 TTTTTCTTTT
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
30 25 0.34
31 18 0.24
32 2 0.03
33 5 0.07
34 2 0.03
35 22 0.30
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTTCTTCTTTGTCCTCAAAAAGCAGGATG
Found at i:3353 original size:35 final size:35
Alignment explanation
Indices: 3305--3662 Score: 146
Period size: 35 Copynumber: 11.1 Consensus size: 35
3295 ATTTTTTTCC
*
3305 TTCTTTGTTCTCAAAGAGCAGGATGTTTTCTTCTT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
3340 TTCTTTGTCCTCAAAAAGCATGATG---T-TT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * * **
3370 TTCTTTGACCTCAAAGAGTAGAACATTTTCTTC--
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * *
3403 -T-TTTGTCTTCAAAAAACAGGATG-TTT-TT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* ** * * * *
3433 TTCTTTTTCCTTTAAGGGCATGATATTTTTTTCTT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
3468 TTCTTTGTCTTC-AA-AGTAGGA-----T-TTC-T
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * ** *
3494 TTC-TTGTCTTCAAAAAGC-GAGACATTTTCTTCAT
1 TTCTTTGTCCTCAAAGAGCAG-GATGTTTTCTTCTT
* * * * *
3528 TTCTTTATCCTCAAGGAGTATGATG-TTT-TTCCT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
3561 TTCTTTGTCCTCAAGGAGCAAGATGTTTTCTTC--
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * ** *
3594 --CTTTGTCCTCTAAGAGCAAGACATTTTCTTCCT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
3627 TTCCTTGTCCTCAAAGAGCATGATGTTTTCTT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
3661 TT
1 TT
3663 ATTCCCAAAA
Statistics
Matches: 237, Mismatches: 56, Indels: 61
0.67 0.16 0.17
Matches are distributed among these distances:
25 8 0.03
26 7 0.03
27 7 0.03
28 1 0.00
29 2 0.01
30 23 0.10
31 44 0.19
32 16 0.07
33 37 0.16
34 19 0.08
35 73 0.31
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (35 bp):
TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
Found at i:3565 original size:33 final size:33
Alignment explanation
Indices: 3527--3655 Score: 113
Period size: 33 Copynumber: 3.9 Consensus size: 33
3517 ATTTTCTTCA
* *
3527 TTTCTTTATCCTCAAGGAGTATGATGTTTTTCC
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
*
3560 TTTCTTTGTCCTCAAGGAGCAAGATG-TTTT-C
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
* *
3591 TTCCTTTGTCCTCTAA-GAGCAAGACAT-TTTCTTCC
1 TTTCTTTATCCTC-AAGGAGCAAG--ATGTTT-TTCC
* * * *
3626 TTTCCTTGTCCTCAAAGAGCATGATGTTTT
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTT
3656 CTTTTTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
31 20 0.25
32 6 0.07
33 30 0.37
34 7 0.09
35 18 0.22
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (33 bp):
TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
Found at i:3601 original size:31 final size:31
Alignment explanation
Indices: 3530--3658 Score: 116
Period size: 31 Copynumber: 4.0 Consensus size: 31
3520 TTCTTCATTT
* * * *
3530 CTTTATCCTCAAGGAGTATGATGTTTTTCCTTT
1 CTTTGTCCTCAAGGAGCAAGATG-TTTT-CTTC
3563 CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
1 CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
**
3594 CTTTGTCCTCTAA-GAGCAAGACATTTTCTTC
1 CTTTGTCCTC-AAGGAGCAAGATGTTTTCTTC
* *
3625 CTTTCCTTGTCCTCAAAGAGCATGATGTTTTCTT
1 C--T--TTGTCCTCAAGGAGCAAGATGTTTTCTT
3659 TTTTATTCCC
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
31 30 0.37
32 6 0.07
33 21 0.26
34 2 0.02
35 22 0.27
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (31 bp):
CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
Found at i:8770 original size:19 final size:19
Alignment explanation
Indices: 8748--8815 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
8738 TTTTTCTTGT
8748 TCTTGTTCTTTTATTCCTC
1 TCTTGTTCTTTTATTCCTC
* * *
8767 TCTTCCTTCTCTCATT-CTC
1 TCTT-GTTCTTTTATTCCTC
*
8786 T-TTGTTCTCTTTGTTCCTC
1 TCTTGTTCT-TTTATTCCTC
*
8805 TTCTTATTCTT
1 -TCTTGTTCTT
8816 CTCATTCTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 11 0.31
20 10 0.28
21 6 0.17
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.62
Consensus pattern (19 bp):
TCTTGTTCTTTTATTCCTC
Found at i:8819 original size:39 final size:37
Alignment explanation
Indices: 8750--8823 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 37
8740 TTTCTTGTTC
*
8750 TTGTTCTTTTATTCCTCTCTTCCTTCTCTCATTCTCT
1 TTGTTCTTTTATTCCTCTCTTCATTCTCTCATTCTCT
*
8787 TTGTTCTCTTTGTTCCTCTTCTT-ATTCTTCTCATTCT
1 TTGTTCT-TTTATTCCTC-TCTTCATTC-TCTCATTCT
8824 TTTCTTTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 7 0.22
38 12 0.38
39 13 0.41
ACGTcount: A:0.05, C:0.30, G:0.04, T:0.61
Consensus pattern (37 bp):
TTGTTCTTTTATTCCTCTCTTCATTCTCTCATTCTCT
Found at i:8841 original size:13 final size:11
Alignment explanation
Indices: 8823--8946 Score: 60
Period size: 11 Copynumber: 10.4 Consensus size: 11
8813 CTTCTCATTC
8823 TTTTCTTTCTCAT
1 TTTTCTTT-TC-T
8836 TTTTCTTTTCT
1 TTTTCTTTTCT
8847 TTTTACTTTTTACT
1 TTTT-C-TTTT-CT
* *
8861 TTTCCTTTTTT
1 TTTTCTTTTCT
8872 TTTTCTCTTT-T
1 TTTTCT-TTTCT
8883 TTTCCCCTCTTTCTCT
1 TTT----TCTTT-TCT
8899 TATTT-TTTTCT
1 T-TTTCTTTTCT
8910 TTTTC--TTCT
1 TTTTCTTTTCT
8919 TTTATACTTCTTCT
1 TTT-T-CTT-TTCT
8933 TTTTCTTTT-T
1 TTTTCTTTTCT
8943 TTTT
1 TTTT
8947 TATTTATTTG
Statistics
Matches: 91, Mismatches: 3, Indels: 37
0.69 0.02 0.28
Matches are distributed among these distances:
9 7 0.08
10 9 0.10
11 22 0.24
12 16 0.18
13 15 0.16
14 14 0.15
15 4 0.04
16 2 0.02
17 2 0.02
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:8870 original size:7 final size:6
Alignment explanation
Indices: 8823--8947 Score: 64
Period size: 6 Copynumber: 20.7 Consensus size: 6
8813 CTTCTCATTC
* *
8823 TTTTCT TTCTCAT TTTTC- TTTTCT TTTTACT TTTTACT TTTCCT TTTT-T
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTT-CT TTTT-CT TTTTCT TTTTCT
* * * *
8872 TTTTCT CTTTT-T TTCCCCTCT TTCTCT TATT-T TTTTCT TTTTCT TCTT-T
1 TTTTCT -TTTTCT TT---TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * *
8921 TATACT TCTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
8948 ATTTATTTGT
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
5 24 0.26
6 45 0.48
7 21 0.22
8 1 0.01
9 3 0.03
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:8914 original size:19 final size:18
Alignment explanation
Indices: 8821--8947 Score: 64
Period size: 19 Copynumber: 6.6 Consensus size: 18
8811 TTCTTCTCAT
*
8821 TCTTTTCTTTCTCATTTTTC
1 TCTTTT-TTTTTC-TTTTTC
*
8841 T-TTTCTTTTTACTTTTTAC
1 TCTTT-TTTTTTCTTTTT-C
*
8860 T-TTTCCTTTTT-TTTTTC
1 TCTTT-TTTTTTCTTTTTC
** *
8877 TCTTTTTTTCCCCTCTTTC
1 TCTTTTTTT-TTCTTTTTC
8896 TCTTATTTTTTTCTTTTTC
1 TCTT-TTTTTTTCTTTTTC
8915 TTCTTTTATACTTCTTCTTTTTC
1 -TCTTTT-T--TT-TTCTTTTTC
8938 T-TTTTTTTTT
1 TCTTTTTTTTT
8948 ATTTATTTGT
Statistics
Matches: 85, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
17 7 0.08
18 15 0.18
19 34 0.40
20 13 0.15
21 4 0.05
22 3 0.04
23 9 0.11
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCTTTTTTTTTCTTTTTC
Found at i:8916 original size:23 final size:24
Alignment explanation
Indices: 8890--8940 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
8880 TTTTTTCCCC
* *
8890 TCTTTCTCTTAT-TTTTTTCTTTT
1 TCTTTCTCTTATACTTCTTCTTTT
*
8913 TC-TTCTTTTATACTTCTTCTTTT
1 TCTTTCTCTTATACTTCTTCTTTT
8936 TCTTT
1 TCTTT
8941 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 13 0.57
24 2 0.09
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
TCTTTCTCTTATACTTCTTCTTTT
Found at i:10966 original size:19 final size:19
Alignment explanation
Indices: 10938--10974 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10928 AAATATTAAA
*
10938 AAATAACTATATTTATATT
1 AAATAACTATATATATATT
*
10957 AAATATCTATATATATAT
1 AAATAACTATATATATAT
10975 CTTTATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATAACTATATATATATT
Found at i:12283 original size:16 final size:16
Alignment explanation
Indices: 12264--12330 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
12254 AGTGTTGTTG
*
12264 TTTTTTATTTAAATTA
1 TTTTATATTTAAATTA
* *
12280 TTTTGA-GTTTAAATCA
1 TTTT-ATATTTAAATTA
*
12296 TTTTATATTTGAATTA
1 TTTTATATTTAAATTA
* *
12312 TTTTAAATTTAAATAA
1 TTTTATATTTAAATTA
12328 TTT
1 TTT
12331 AGATTTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 1 0.03
16 39 0.98
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTATATTTAAATTA
Found at i:12311 original size:32 final size:32
Alignment explanation
Indices: 12264--12338 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
12254 AGTGTTGTTG
* * * *
12264 TTTTTTATTTAAATTATTTTGAGTTTAAATCA
1 TTTTATATTTAAATTATTTTAAATTTAAATAA
*
12296 TTTTATATTTGAATTATTTTAAATTTAAATAA
1 TTTTATATTTAAATTATTTTAAATTTAAATAA
*
12328 -TTTAGATTTAA
1 TTTTATATTTAA
12339 TATTCAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (32 bp):
TTTTATATTTAAATTATTTTAAATTTAAATAA
Found at i:13176 original size:16 final size:16
Alignment explanation
Indices: 13136--13177 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
13126 TAGGTGATTG
*
13136 AATTATTTCAAGTTTA
1 AATTATTTTAAGTTTA
*
13152 AATTATTTTGAGTTTA
1 AATTATTTTAAGTTTA
13168 AATTATTTTA
1 AATTATTTTA
13178 GATTTAAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (16 bp):
AATTATTTTAAGTTTA
Found at i:13608 original size:2 final size:2
Alignment explanation
Indices: 13601--13633 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13591 GCAGTGCAGG
*
13601 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13634 CTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19069 original size:90 final size:89
Alignment explanation
Indices: 18899--19084 Score: 207
Period size: 90 Copynumber: 2.1 Consensus size: 89
18889 TTAAAATTTT
* *
18899 AATTTATTTGATAATAAATAAAAATTAAGATTTACATTAAATTATTTTATTTAAAAATTTTAATT
1 AATTTATTTGATAATAAATAAAAATTAAAACTTACATTAAATTATTTTATTTAAAAATTTTAATT
** **
18964 TTTTATGAATTTTAAAAAGTAA-ATA
66 TTACATGAACATTAAAAA-TAATA-A
* * * * *
18989 AATTTATTTGATAAATAAA-AAAAGTTAAAACTTATATTAAATT-TTTTATCTTCACACTTTTAA
1 AATTTATTTGAT-AATAAATAAAAATTAAAACTTACATTAAATTATTTTAT-TTAAAAATTTTAA
*
19052 TTTTACATTAACATTAAAAATAATAA
64 TTTTACATGAACATTAAAAATAATAA
19078 AATTTAT
1 AATTTAT
19085 ATTAATTTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
89 17 0.21
90 58 0.72
91 6 0.07
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (89 bp):
AATTTATTTGATAATAAATAAAAATTAAAACTTACATTAAATTATTTTATTTAAAAATTTTAATT
TTACATGAACATTAAAAATAATAA
Found at i:20778 original size:21 final size:22
Alignment explanation
Indices: 20749--20795 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
20739 CTAACATTCT
20749 CACCAAATA-CATCACCAAACA
1 CACCAAATAGCATCACCAAACA
* *
20770 CACCTAATATGCTTCACCAAACA
1 CACCAAATA-GCATCACCAAACA
20793 CAC
1 CAC
20796 TTAACAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.15
Consensus pattern (22 bp):
CACCAAATAGCATCACCAAACA
Found at i:30382 original size:21 final size:20
Alignment explanation
Indices: 30353--30395 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30343 GACTAGTGTG
*
30353 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
30374 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
30394 GG
1 GG
30396 TGGTGCTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:30854 original size:13 final size:13
Alignment explanation
Indices: 30836--30873 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
30826 ATAAACCCCC
30836 TGTATCGATACAG
1 TGTATCGATACAG
*
30849 TGTATCGATACAT
1 TGTATCGATACAG
30862 TGTATCGATACA
1 TGTATCGATACA
30874 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:32974 original size:15 final size:15
Alignment explanation
Indices: 32954--32984 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32944 ATTTCGTTTG
*
32954 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
32969 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
32984 G
1 G
32985 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:37003 original size:20 final size:21
Alignment explanation
Indices: 36955--37010 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
36945 AAATCCCAAT
**
36955 AACATGTATCGATACATATTT
1 AACATGTATCGATACATATGC
**
36976 TGCATGTATCGATACAT-TGC
1 AACATGTATCGATACATATGC
36996 AACATGTATCGATAC
1 AACATGTATCGATAC
37011 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
AACATGTATCGATACATATGC
Found at i:37472 original size:16 final size:17
Alignment explanation
Indices: 37447--37479 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
37437 ATGAGACAAA
37447 AAAAATATTAATTAATT
1 AAAAATATTAATTAATT
37464 AAAAA-ATTAATTAATT
1 AAAAATATTAATTAATT
37480 TTACACATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATATTAATTAATT
Found at i:42654 original size:16 final size:17
Alignment explanation
Indices: 42628--42661 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
42618 AAACAAAAAA
42628 TAAAAATATTAATTAAT
1 TAAAAATATTAATTAAT
42645 TAAAAA-ATTAATTAAT
1 TAAAAATATTAATTAAT
42661 T
1 T
42662 TTGTATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATATTAATTAAT
Found at i:46065 original size:3 final size:3
Alignment explanation
Indices: 46057--46102 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
46047 CTTATAATTT
*
46057 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TAA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
46103 ATTCATCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:53610 original size:214 final size:214
Alignment explanation
Indices: 53241--53664 Score: 812
Period size: 214 Copynumber: 2.0 Consensus size: 214
53231 TGCTTGGCAG
*
53241 CCTTGGCATCCATGGCAGCCAATGAGTTTGGACCATGTGGTTTTGGCATTCAATGCCATGCTTTT
1 CCTTGGCATCCATGGCAACCAATGAGTTTGGACCATGTGGTTTTGGCATTCAATGCCATGCTTTT
53306 AGCTTCAAAAGTGATCAAGATGGGTTTTGACATGTGGCAATTGAGATTTGACATGAATCCTGACC
66 AGCTTCAAAAGTGATCAAGATGGGTTTTGACATGTGGCAATTGAGATTTGACATGAATCCTGACC
* *
53371 ACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAGAAAATGTCCCGAAATATGACAATTTGCCTG
131 ACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAAAAAATGTCCCGAAATATGAAAATTTGCCTG
53436 CATGTATCGATACATGCAA
196 CATGTATCGATACATGCAA
53455 CCTTGGCATCCATGGCAACCAATGAGTTTGGACCATGTGGTTTTGGCATTCAATGCCATGCTTTT
1 CCTTGGCATCCATGGCAACCAATGAGTTTGGACCATGTGGTTTTGGCATTCAATGCCATGCTTTT
53520 AGCTTCAAAAGTGATCAAGATGGGTTTTGACATGTGGCAATTGAGATTTGACATGAATCCTGACC
66 AGCTTCAAAAGTGATCAAGATGGGTTTTGACATGTGGCAATTGAGATTTGACATGAATCCTGACC
*
53585 ACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAAAAAATGTCCTGAAATATGAAAATTTGCCTG
131 ACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAAAAAATGTCCCGAAATATGAAAATTTGCCTG
53650 CATGTATCGATACAT
196 CATGTATCGATACAT
53665 TGAATAATGT
Statistics
Matches: 206, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 206 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (214 bp):
CCTTGGCATCCATGGCAACCAATGAGTTTGGACCATGTGGTTTTGGCATTCAATGCCATGCTTTT
AGCTTCAAAAGTGATCAAGATGGGTTTTGACATGTGGCAATTGAGATTTGACATGAATCCTGACC
ACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAAAAAATGTCCCGAAATATGAAAATTTGCCTG
CATGTATCGATACATGCAA
Found at i:54131 original size:13 final size:13
Alignment explanation
Indices: 54113--54139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54103 TACAATAAAC
54113 ATGTATCGATACA
1 ATGTATCGATACA
54126 ATGTATCGATACA
1 ATGTATCGATACA
54139 A
1 A
54140 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:56928 original size:13 final size:13
Alignment explanation
Indices: 56910--56935 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56900 TACAGCAAGT
56910 ATGTATCGATACA
1 ATGTATCGATACA
56923 ATGTATCGATACA
1 ATGTATCGATACA
56936 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:60184 original size:13 final size:13
Alignment explanation
Indices: 60166--60190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60156 CTATTTATAA
60166 TGTATCGATACAC
1 TGTATCGATACAC
60179 TGTATCGATACA
1 TGTATCGATACA
60191 AACAAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:60293 original size:45 final size:46
Alignment explanation
Indices: 60211--60299 Score: 128
Period size: 45 Copynumber: 1.9 Consensus size: 46
60201 TATCGATACA
*
60211 TGAATAGTGATGAACAGTGATTTTTAACGATACATGAATAGTGATATG
1 TGAATAGTGATGAACAGTGA-TTGTAACGATACATGAA-AGTGATATG
*
60259 TGAATAGTG-TGAACAGTGA-TGTATCGATACATGAAAGTGAT
1 TGAATAGTGATGAACAGTGATTGTAACGATACATGAAAGTGAT
60300 GTATCGATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 14 0.36
47 10 0.26
48 9 0.23
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (46 bp):
TGAATAGTGATGAACAGTGATTGTAACGATACATGAAAGTGATATG
Found at i:60322 original size:22 final size:22
Alignment explanation
Indices: 60268--60322 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
60258 GTGAATAGTG
60268 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
60290 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
60311 TGAACAGTGATG
1 TGAACAGTGATG
60323 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:60329 original size:10 final size:10
Alignment explanation
Indices: 60310--60340 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
60300 GTATCGATAC
60310 ATGAACAGTG
1 ATGAACAGTG
*
60320 ATGAATAGTG
1 ATGAACAGTG
60330 ATGAACAGTG
1 ATGAACAGTG
60340 A
1 A
60341 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:60428 original size:53 final size:53
Alignment explanation
Indices: 60364--60500 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
60354 CTACTTCCAA
60364 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
60417 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
60470 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
60501 TATACAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:60513 original size:20 final size:19
Alignment explanation
Indices: 60488--60541 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
60478 TACATATTTG
60488 TGTGTATCGATACTATACAA
1 TGTGTATCGATACTATA-AA
* *
60508 TTTGTATCGATACATTTAAA
1 TGTGTATCGATAC-TATAAA
60528 TGTGTATCGATACT
1 TGTGTATCGATACT
60542 TTTCAGGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 26 0.87
21 3 0.10
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
TGTGTATCGATACTATAAA
Found at i:60605 original size:21 final size:21
Alignment explanation
Indices: 60580--60620 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60570 GTCAACCATG
60580 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
60601 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
60621 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:60949 original size:21 final size:20
Alignment explanation
Indices: 60914--60972 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
60904 ACACGTATAG
60914 GAATGTATC-AGTACAATTCTA
1 GAATGTATCGA-TACAATTC-A
*
60935 GAATGTATCGATAC-ATGCA
1 GAATGTATCGATACAATTCA
*
60954 GAGTTGTATCGATACAATT
1 GA-ATGTATCGATACAATT
60973 AGCCCAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 14 0.44
22 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GAATGTATCGATACAATTCA
Found at i:62500 original size:25 final size:27
Alignment explanation
Indices: 62455--62510 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
62445 ATAGATATAT
*
62455 ATATATAAAGATAAATCAATTA-A-AA
1 ATATATAAAAATAAATCAATTATAGAA
*
62480 ATATA-AAAAATATAATTAATTATAGAA
1 ATATATAAAAATA-AATCAATTATAGAA
62507 ATAT
1 ATAT
62511 TTTAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 6 0.23
25 13 0.50
26 1 0.04
27 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (27 bp):
ATATATAAAAATAAATCAATTATAGAA
Found at i:65000 original size:34 final size:35
Alignment explanation
Indices: 64962--65028 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
64952 CCTTACAACA
64962 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
64996 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
65029 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:65519 original size:13 final size:13
Alignment explanation
Indices: 65501--65536 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
65491 ATTTATAATG
*
65501 TATCGATACACTA
1 TATCGATACAATA
*
65514 TATCGATACAATG
1 TATCGATACAATA
65527 TATCGATACA
1 TATCGATACA
65537 TGAATAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:65597 original size:23 final size:23
Alignment explanation
Indices: 65570--65650 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
65560 TTATCGATAT
65570 ATGAATAGTGATACGTGAACAGT-
1 ATGAATAGTGATAC-TGAACAGTG
65593 ATGAATAGTGACCTA-TGAACAGTG
1 ATGAATAGTGA--TACTGAACAGTG
65617 ATG--TA-TCGATACATGAACAGTG
1 ATGAATAGT-GATAC-TGAACAGTG
65639 ATGAATAGTGAT
1 ATGAATAGTGAT
65651 GAACAGTGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 16 0.33
23 19 0.39
24 8 0.16
25 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (23 bp):
ATGAATAGTGATACTGAACAGTG
Found at i:65648 original size:10 final size:10
Alignment explanation
Indices: 65629--65659 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
65619 GTATCGATAC
65629 ATGAACAGTG
1 ATGAACAGTG
*
65639 ATGAATAGTG
1 ATGAACAGTG
65649 ATGAACAGTG
1 ATGAACAGTG
65659 A
1 A
65660 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:65747 original size:53 final size:53
Alignment explanation
Indices: 65683--65818 Score: 218
Period size: 53 Copynumber: 2.6 Consensus size: 53
65673 CTACTGCCAA
** *
65683 TGTATCGATACATAAAGTGTGTATCGATACAAATTTGGCTACTGCCAATCACT
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATCACC
* **
65736 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCTAATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATCACC
65789 TGTATCGATACATATTGTGTGTATCGATAC
1 TGTATCGATACATATTGTGTGTATCGATAC
65819 TATGCAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATCACC
Found at i:65760 original size:19 final size:19
Alignment explanation
Indices: 65736--65818 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 19
65726 GCCAATCACT
65736 TGTATCGATACATATTGTG
1 TGTATCGATACATATTGTG
*
65755 TGTATCGATACAAATT-TG
1 TGTATCGATACATATTGTG
* * *
65773 -GCTA-C--TGC-TAATGTCC
1 TG-TATCGATACATATTGT-G
65789 TGTATCGATACATATTGTG
1 TGTATCGATACATATTGTG
65808 TGTATCGATAC
1 TGTATCGATAC
65819 TATGCAATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.04
15 3 0.06
16 2 0.04
17 4 0.08
18 4 0.08
19 28 0.58
20 5 0.10
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATATTGTG
Found at i:65851 original size:20 final size:20
Alignment explanation
Indices: 65789--65858 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
65779 GCTAATGTCC
*
65789 TGTATCGATACATATT-GTG
1 TGTATCGATACATATTAATG
* *
65808 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
65828 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
65848 TGTATCGATAC
1 TGTATCGATAC
65859 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 27 0.64
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:66799 original size:13 final size:13
Alignment explanation
Indices: 66781--66811 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
66771 ACTTTTCACT
66781 ATGTATCAATACA
1 ATGTATCAATACA
*
66794 ATGTATCGATACA
1 ATGTATCAATACA
66807 ATGTA
1 ATGTA
66812 CCATGTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:66915 original size:13 final size:13
Alignment explanation
Indices: 66897--66921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66887 ACCAAGAGCA
66897 TGTATCGATACAG
1 TGTATCGATACAG
66910 TGTATCGATACA
1 TGTATCGATACA
66922 AAGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:67692 original size:31 final size:31
Alignment explanation
Indices: 67657--67718 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
67647 ATAATATCTC
* *
67657 TTTTTAGAAAATAATTTCTCCCTCTTTTTCA
1 TTTTTAGAAAACAATTTCTCCCCCTTTTTCA
*
67688 TTTTTAGAAAACAATTTGTCCCCCTTTTTCA
1 TTTTTAGAAAACAATTTCTCCCCCTTTTTCA
67719 AAATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTTTAGAAAACAATTTCTCCCCCTTTTTCA
Found at i:69464 original size:31 final size:31
Alignment explanation
Indices: 69406--69480 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
69396 AAACCGTTTT
69406 TGATGAAGATTTTGATGAAAAATG-AAAAGAAA
1 TGATGAA-A-TTTGATGAAAAATGAAAAAGAAA
* *
69438 TGATGTAAATTTGATG-AAATTCGAAAAAGAAT
1 TGATG-AAATTTGATGAAAAAT-GAAAAAGAAA
69470 TGATGAAATTT
1 TGATGAAATTT
69481 AGGTTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 4 0.11
31 14 0.37
32 18 0.47
33 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (31 bp):
TGATGAAATTTGATGAAAAATGAAAAAGAAA
Found at i:75040 original size:70 final size:70
Alignment explanation
Indices: 74958--75098 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
74948 AAGAGGGGGT
*
74958 GATTTGGTTCTTTTTTAAATTTGAAGATTTTTGAAAGAATTGTTTCAAAAACAACTTAAAGATGA
1 GATTTGGTTCTTTTTGAAATTTGAAGATTTTTGAAAGAATTGTTTCAAAAACAACTTAAAGATGA
75023 AGAGA
66 AGAGA
75028 GATTTGGTTCTTTTTGAAATTTGAAGATTTTTGAAAGAATTGTTTCAAAAACAACTTAAAGATGA
1 GATTTGGTTCTTTTTGAAATTTGAAGATTTTTGAAAGAATTGTTTCAAAAACAACTTAAAGATGA
75093 AGAGA
66 AGAGA
75098 G
1 G
75099 TAGGGAAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (70 bp):
GATTTGGTTCTTTTTGAAATTTGAAGATTTTTGAAAGAATTGTTTCAAAAACAACTTAAAGATGA
AGAGA
Found at i:75875 original size:37 final size:33
Alignment explanation
Indices: 75834--75901 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 33
75824 TAATTCGCTA
*
75834 TGTATCGATACCAAGAGCATGTACTGTATCGATACAG
1 TGTATCGATA-CAA-AGCA-ATA-TGTATCGATACAG
75871 TGTATCGATACAAAGCAATATGTATCGATAC
1 TGTATCGATACAAAGCAATATGTATCGATAC
75902 TTCTGAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 11 0.37
34 2 0.07
35 4 0.13
36 3 0.10
37 10 0.33
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATATGTATCGATACAG
Found at i:75876 original size:13 final size:13
Alignment explanation
Indices: 75858--75882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75848 GAGCATGTAC
75858 TGTATCGATACAG
1 TGTATCGATACAG
75871 TGTATCGATACA
1 TGTATCGATACA
75883 AAGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:79593 original size:58 final size:56
Alignment explanation
Indices: 79503--79614 Score: 188
Period size: 58 Copynumber: 2.0 Consensus size: 56
79493 TAGATGAAGA
79503 AAGATATTACATGAGAAAAGTTCTTTACTCGAGCGCAGTTAAGAGCTTGATGTATGAT
1 AAGATATTACATGAGAAAAGTTCTTTACTCGA--GCAGTTAAGAGCTTGATGTATGAT
* *
79561 AAGATATTACATGAGAAAATTTCTTTACTCGAGCAGTTAAGTGCTTGATGTATG
1 AAGATATTACATGAGAAAAGTTCTTTACTCGAGCAGTTAAGAGCTTGATGTATG
79615 CTATGGTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 21 0.40
58 31 0.60
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (56 bp):
AAGATATTACATGAGAAAAGTTCTTTACTCGAGCAGTTAAGAGCTTGATGTATGAT
Found at i:81407 original size:398 final size:393
Alignment explanation
Indices: 80741--82148 Score: 1194
Period size: 398 Copynumber: 3.5 Consensus size: 393
80731 AATTGCTCCA
* * * *
80741 AATTACCATTTGTAGAAAACTCTTATTTATAGTAGTCTATTGAATAAATTTAATT-TTA-TATTT
1 AATTATCATTTGTAGAAAA-TCTTATTTATAGTAATCTATTAAATAAATTTAATTAATATTATTT
* * * *
80804 T-TAAGATATGAAAA-TAATAGTAAAATTTTATTTGTCTACATATAT-AAAAATTAAGTCAATTA
65 TGT-AGATATGAAAAGGAA-ATTAAAATTTTATTTGTTTACATATATAAAAAAGTAAGTCAATTA
* * *
80866 AAAGTATAAAAGAAAAAAAATATAATTAATTATATAAAATATTTTAATATTAAATTAAATTAAGT
128 AAAGTATAAAAGAAAATAAATATAATTAATTATATAAAATATTTTAATATTAAATTAAATCAAAT
* * * * * * * * *
80931 AAAAAGAATTAACTATGCGACACATGAAGACTTTTTACAG-TTAGCTATATGTGAATAATATAGG
193 CAAAATAATTAAATGTGTGACTCATGAAGACTTTTTA-AGATTACCTACATGTGAATAATATA-A
* *
80995 T-TATTCACATTGGATAATTATCTTTTTTTTGGTAAAAAGTTTTGGCTTTTATATATTTATTATA
256 TCTATTCATATTGGATAATTA-C-TTTTTTT--TAAAAAGTTTTAGCTTTTATATATTTATTATA
81059 TAAGAGTTTTTATTTTTAATTATTGAAATTATTATTGGTTATTGTTTACTATTTAAACTTAATTT
317 TAAGA-TTTTTATTTTTAATTATTGAAATTATTATT-GTTATTGTTTACTATTTAAACTTAATTT
81124 ATTTTT-AAAATTG
380 ATTTTTAAAAATTG
*
81137 AATTATCATTTGTAGAAAACTCTTATTTATAGTAATCTATTAAATAAATTTAATTTACTATTATT
1 AATTATCATTTGTAGAAAA-TCTTATTTATAGTAATCTATTAAATAAATTTAA-TTAATATTATT
81202 TTGT-GATATGAAAAGGAAATTAAAATTTTATTTGTTTACATATATATAAAAAGGTAAGTCAATT
64 TTGTAGATATGAAAAGGAAATTAAAATTTTATTTGTTTACATATATA-AAAAA-GTAAGTCAATT
* *
81266 -AAAGTAT-AAA-AAAATAAATATAATTAATTATATGAAATATTTTAATAATAAATTAAATCAAA
127 AAAAGTATAAAAGAAAATAAATATAATTAATTATATAAAATATTTTAATATTAAATTAAATCAAA
* *
81328 TCAAAATAATTAAATGTGTGACTCATGACGACTTTTTAAGATTACCCACATGTGAATAATATAAT
192 TCAAAATAATTAAATGTGTGACTCATGAAGACTTTTTAAGATTACCTACATGTGAATAATATAAT
* *
81393 CTATCCATATTGG---ATTA-TTTTTTTT--AAGGTTTTAGCTTTTATATATTTATTATATAAGA
257 CTATTCATATTGGATAATTACTTTTTTTTAAAAAGTTTTAGCTTTTATATATTTATTATATAAGA
* * *
81452 TTTTTTTATATTTTTAGTTATTGGAATTA--A----TATTGTTTACTATTTAAACTTTATTT-TT
322 ---TTTT-TATTTTTAATTATTGAAATTATTATTGTTATTGTTTACTATTTAAACTTAATTTATT
*
81510 TTTACAAAAATTTA
383 TTT--AAAAA-TTG
* * * ** * * * ** * *
81524 AATT-TAAATGGCTCCAGATTATC--ATTTCTAGAAAACTCATATT-TATAGTAGCTTAGTAAAT
1 AATTATCATTTG-T--AGAAAATCTTATTTATAG-TAA-TC-TATTAAATA--AATTTAATTAAT
*
81585 ATT-TTTTGTGAGATAT-AGAAAGAAAATTAAAATTTTATTTG-TTACATATATAAAAAAGGTAA
58 ATTATTTTGT-AGATATGA-AAAGGAAATTAAAATTTTATTTGTTTACATATATAAAAAA-GTAA
* * * *
81647 GAT-AATTAAAAGCATAAAAGAAAATAAATATCATAAATTATATGAAATATTTTAATATTAAATT
120 G-TCAATTAAAAGTATAAAAGAAAATAAATATAATTAATTATATAAAATATTTTAATATTAAATT
* * * * ** * *
81711 AAATCAAGTCAAAATAATTAAATGTATAACAT-AT-AATGACTATTTACTATCATCTACATGTGA
184 AAATCAAATCAAAATAATTAAATGTGTGAC-TCATGAA-GACTTTTTAAGATTACCTACATGTGA
* * * * *
81774 ATAATATAAGCTATTCATATTAGATAATTACTTTTTTTAAAAAAAATATTTTATCTTTTATATAT
247 ATAATATAATCTATTCATATTGGATAATTACTTTTTTT--TAAAAA-GTTTTAGCTTTTATATAT
* * * *
81839 TTACTATTTAAGATTTTTAAATTTTTAATTAATTATTAAAATTATTATTAGTTACTGTTTACTAT
309 TTATTATATAAGATTTTT--A--TTT--TTAATTATTGAAATTATTATT-GTTATTGTTTACTAT
*
81904 TTAAA-TTAATTTATTTTAAAATCAAATTTAAATG
367 TTAAACTTAATTTATTTT----T-AAA---AATTG
* * * * *
81938 ACTCTAAATTACTATTTGTATAAAATCTTTATTTATAATAGTCTAATAAATAAATTTAATATAAT
1 AAT-T--A-T-C-ATTTGTAGAAAATC-TTATTTATAGTAATCTATTAAATAAATTTAAT-TAAT
* * * *
82003 -TTAATTTTTTATGAGATATG-AAAGGAAA-AATAAATTTTATTTGTTT--ATACATAAAAAA-A
58 ATT-A--TTTTGT-AGATATGAAAAGGAAATTA-AAATTTTATTTGTTTACATATATAAAAAAGT
* *
82062 AAGTCCATTAAAAATAT-AAA-AAAATAAATATAATTAATTATATAAAATATTTTAATATTAAAT
118 AAGTCAATTAAAAGTATAAAAGAAAATAAATATAATTAATTATATAAAATATTTTAATATTAAAT
82125 TAAATCAAATCAAAATAATTAAAT
183 TAAATCAAATCAAAATAATTAAAT
82149 ATGTAATAAA
Statistics
Matches: 822, Mismatches: 106, Indels: 149
0.76 0.10 0.14
Matches are distributed among these distances:
383 5 0.01
384 25 0.03
386 15 0.02
387 9 0.01
388 60 0.07
389 34 0.04
390 40 0.05
391 129 0.16
392 8 0.01
394 4 0.00
395 11 0.01
396 51 0.06
397 9 0.01
398 145 0.18
399 13 0.02
400 43 0.05
401 10 0.01
402 13 0.02
404 1 0.00
408 6 0.01
409 21 0.03
412 4 0.00
413 1 0.00
414 3 0.00
415 66 0.08
416 4 0.00
417 19 0.02
418 11 0.01
419 18 0.02
420 21 0.03
421 23 0.03
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (393 bp):
AATTATCATTTGTAGAAAATCTTATTTATAGTAATCTATTAAATAAATTTAATTAATATTATTTT
GTAGATATGAAAAGGAAATTAAAATTTTATTTGTTTACATATATAAAAAAGTAAGTCAATTAAAA
GTATAAAAGAAAATAAATATAATTAATTATATAAAATATTTTAATATTAAATTAAATCAAATCAA
AATAATTAAATGTGTGACTCATGAAGACTTTTTAAGATTACCTACATGTGAATAATATAATCTAT
TCATATTGGATAATTACTTTTTTTTAAAAAGTTTTAGCTTTTATATATTTATTATATAAGATTTT
TATTTTTAATTATTGAAATTATTATTGTTATTGTTTACTATTTAAACTTAATTTATTTTTAAAAA
TTG
Found at i:82249 original size:26 final size:27
Alignment explanation
Indices: 82220--82279 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
82210 AAAATTACTT
82220 TATTATAAAAAAATTT-AA-TTTAGATA
1 TATTATAAAAAAATTTAAATTTTA-ATA
* * *
82246 TATTTTTATAAAATTTAAATTTTAATA
1 TATTATAAAAAAATTTAAATTTTAATA
82273 T-TTATAA
1 TATTATAA
82280 TTTTTTTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
26 17 0.63
27 6 0.22
28 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TATTATAAAAAAATTTAAATTTTAATA
Found at i:83625 original size:17 final size:16
Alignment explanation
Indices: 83603--83757 Score: 68
Period size: 16 Copynumber: 9.5 Consensus size: 16
83593 GCTCGGATCA
83603 AATTATCTTTAGATTTG
1 AATTAT-TTTAGATTTG
*
83620 AATTATTTTATATTTAG
1 AATTATTTTAGATTT-G
* *
83637 ATTTATTTTA-AGTTTA
1 AATTATTTTAGA-TTTG
83653 AATTATTTT-GAATTTG
1 AATTATTTTAG-ATTTG
* *
83669 -ATTATTTTTTGAGTTTA
1 AATTA-TTTTAGA-TTTG
* * *
83686 AATTTTTTTTGGCTTTG
1 AA-TTATTTTAGATTTG
*
83703 AATT-TTTTAAGCTTT-
1 AATTATTTT-AGATTTG
* * *
83718 AATAATTTTGGATTCG
1 AATTATTTTAGATTTG
* **
83734 AGTTATTTTAGATTCA
1 AATTATTTTAGATTTG
83750 AATTATTT
1 AATTATTT
83758 CAGGTACAAA
Statistics
Matches: 106, Mismatches: 20, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
15 14 0.13
16 55 0.52
17 29 0.27
18 6 0.06
19 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.57
Consensus pattern (16 bp):
AATTATTTTAGATTTG
Found at i:83634 original size:16 final size:15
Alignment explanation
Indices: 83603--83676 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 15
83593 GCTCGGATCA
83603 AATTATCTTTAGATTTG
1 AATTAT-TTTA-ATTTG
83620 AATTATTTTATATTTAG
1 AATTATTTTA-ATTT-G
* *
83637 ATTTATTTTAAGTTTA
1 AATTATTTTAA-TTTG
83653 AATTATTTTGAATTTG
1 AATTATTTT-AATTTG
83669 -ATTATTTT
1 AATTATTTT
83677 TTGAGTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.16
16 20 0.41
17 21 0.43
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.59
Consensus pattern (15 bp):
AATTATTTTAATTTG
Found at i:83684 original size:33 final size:33
Alignment explanation
Indices: 83620--83694 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
83610 TTTAGATTTG
83620 AATTATTTTATATTTAGATTTATTTTAAGTTTA
1 AATTATTTTATATTTAGATTTATTTTAAGTTTA
* *
83653 AATTATTTTGA-ATTT-GATTATTTTTTGAGTTTA
1 AATTATTTT-ATATTTAGATT-TATTTTAAGTTTA
*
83686 AATTTTTTT
1 AATTATTTT
83695 TGGCTTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.11
33 32 0.86
34 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (33 bp):
AATTATTTTATATTTAGATTTATTTTAAGTTTA
Found at i:83692 original size:16 final size:16
Alignment explanation
Indices: 83632--83694 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
83622 TTATTTTATA
* *
83632 TTTAGATTTATTTTAAG
1 TTTAAATTT-TTTTGAG
* *
83649 TTTAAATTATTTTGAA
1 TTTAAATTTTTTTGAG
* *
83665 TTTGATTATTTTTTGAG
1 TTTAAAT-TTTTTTGAG
83682 TTTAAATTTTTTT
1 TTTAAATTTTTTT
83695 TGGCTTTGAA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
16 16 0.46
17 19 0.54
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TTTAAATTTTTTTGAG
Found at i:83710 original size:33 final size:32
Alignment explanation
Indices: 83620--83727 Score: 80
Period size: 33 Copynumber: 3.3 Consensus size: 32
83610 TTTAGATTTG
83620 AATTATTTT-ATATTT-AGATTTATTTTAAGTTTA
1 AATTATTTTGA-ATTTGA-ATTT-TTTTAAGTTTA
* *
83653 AATTATTTTGAATTTGATTATTTTTTGAGTTTA
1 AATTATTTTGAATTTGAAT-TTTTTTAAGTTTA
* **
83686 AATTTTTTTTGGCTTTGAA-TTTTTTAAGCTTT-
1 AA-TTATTTTGAATTTGAATTTTTTTAAG-TTTA
*
83718 AATAATTTTG
1 AATTATTTTG
83728 GATTCGAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
31 6 0.10
32 10 0.16
33 29 0.48
34 16 0.26
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60
Consensus pattern (32 bp):
AATTATTTTGAATTTGAATTTTTTTAAGTTTA
Found at i:84271 original size:32 final size:33
Alignment explanation
Indices: 84211--84279 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
84201 TTCAACGATT
84211 TGTATCGAAACATAAAGTGTTGTATCGATACAA
1 TGTATCGAAACATAAAGTGTTGTATCGATACAA
** *
84244 TGTATCGATGCAT-AAGTTTTGTATCGATACAA
1 TGTATCGAAACATAAAGTGTTGTATCGATACAA
84276 TGTA
1 TGTA
84280 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGAAACATAAAGTGTTGTATCGATACAA
Found at i:84335 original size:13 final size:13
Alignment explanation
Indices: 84317--84341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84307 ATTACTCTAA
84317 TGTATCGATACAT
1 TGTATCGATACAT
84330 TGTATCGATACA
1 TGTATCGATACA
84342 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:84339 original size:34 final size:33
Alignment explanation
Indices: 84296--84362 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
84286 TGCCAAAAAA
*
84296 TGTATCGATACA-TTACTCTAATGTATCGATACAT
1 TGTATCGATACACTGA-TCT-ATGTATCGATACAT
*
84330 TGTATCGATACACTGATCTTTGTATCGATACAT
1 TGTATCGATACACTGATCTATGTATCGATACAT
84363 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 15 0.50
35 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTGATCTATGTATCGATACAT
Found at i:84391 original size:32 final size:32
Alignment explanation
Indices: 84350--84423 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
84340 CACTGATCTT
*
84350 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAGGCAAATTTACCCAGA
84382 TGTATCGATACATGCAGGCAAATTTACCCAGA
1 TGTATCGATACATGCAGGCAAATTTACCCAGA
*
84414 GGTATCGATA
1 TGTATCGATA
84424 TACTATGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (32 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGA
Found at i:88043 original size:23 final size:22
Alignment explanation
Indices: 88010--88058 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
88000 TTGATACTAG
88010 ATTTTTATAAGTCTTTATATTATA
1 ATTTTTATAAG--TTTATATTATA
*
88034 ATTTTT-TAAGTTTGTATTATA
1 ATTTTTATAAGTTTATATTATA
88055 ATTT
1 ATTT
88059 GATACGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 14 0.58
23 4 0.17
24 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (22 bp):
ATTTTTATAAGTTTATATTATA
Found at i:99576 original size:21 final size:21
Alignment explanation
Indices: 99548--99619 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
99538 AAGCAAAAGC
*
99548 ACAAAA-AATAAAAA-CAACA
1 ACAAAAGAAAAAAAAGCAACA
99567 ACAAAA-AAAAAAAATGCAA-A
1 ACAAAAGAAAAAAAA-GCAACA
* *
99587 AGCAAAATAAAAAAAAGGAACA
1 A-CAAAAGAAAAAAAAGCAACA
99609 ACAAAAGAAAA
1 ACAAAAGAAAA
99620 TGAGGACATG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 13 0.29
20 2 0.04
21 20 0.44
22 10 0.22
ACGTcount: A:0.78, C:0.11, G:0.07, T:0.04
Consensus pattern (21 bp):
ACAAAAGAAAAAAAAGCAACA
Found at i:99586 original size:42 final size:42
Alignment explanation
Indices: 99540--99619 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
99530 AAAGTTGAAA
99540 GCAAAAGCACAAA-AAATAAAAA-CAACAACAAAAAAAAAAAAT
1 GCAAAAGCA-AAATAAA-AAAAAGCAACAACAAAAAAAAAAAAT
* *
99582 GCAAAAGCAAAATAAAAAAAAGGAACAACAAAAGAAAA
1 GCAAAAGCAAAATAAAAAAAAGCAACAACAAAAAAAAA
99620 TGAGGACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 8 0.24
42 26 0.76
ACGTcount: A:0.75, C:0.12, G:0.09, T:0.04
Consensus pattern (42 bp):
GCAAAAGCAAAATAAAAAAAAGCAACAACAAAAAAAAAAAAT
Found at i:102765 original size:17 final size:16
Alignment explanation
Indices: 102743--102783 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
102733 CTTCTTTTCT
102743 AAAAAAAAACAAAAGCA
1 AAAAAAAAACAAAA-CA
*
102760 AAAAAAAAACACAACA
1 AAAAAAAAACAAAACA
102776 AAAAAAAA
1 AAAAAAAA
102784 GAAGAATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAACA
Found at i:103917 original size:55 final size:55
Alignment explanation
Indices: 103782--104107 Score: 431
Period size: 55 Copynumber: 5.8 Consensus size: 55
103772 GATGCCTTTT
* * * *
103782 CCTTTTAAAGCCCACACAAGTTGGTGACAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * *
103842 CTTTTCAAAGCCCACTCAAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
103897 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * * *
103952 CCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * *
104007 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
104062 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAG
104108 TGCAAGATGC
Statistics
Matches: 243, Mismatches: 20, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
54 4 0.02
55 189 0.78
56 3 0.01
59 1 0.00
60 26 0.11
61 20 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:104013 original size:26 final size:26
Alignment explanation
Indices: 103981--104068 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
103971 GTTGGTGGCA
103981 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* * * ** *
104007 CCTTTCAAAGCCCACACAAGTTGGTGG-CA
1 CCTTTC--AGTCCTCA-AAG-AGCAGGACG
*
104036 CCTTTCAGTCCTCAAAGAGTAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
104062 CCTTTCA
1 CCTTTCA
104069 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.38
27 6 0.13
28 6 0.13
29 10 0.22
30 3 0.07
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:104068 original size:165 final size:166
Alignment explanation
Indices: 103782--104107 Score: 487
Period size: 165 Copynumber: 1.9 Consensus size: 166
103772 GATGCCTTTT
*
103782 CCTTTTAAAGCCCACACAAGTTGGTGACACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGACACCTTCAGTCCTCAAAGAGCAGGACGC----TCTTTT
* *
103847 CAAAGCCCACTCAAGTTGGTGGCACTTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCAC
62 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCAC
103912 ACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
127 ACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
103952 CCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-C-TTTCAA
1 CCTTTTAAAGCCCACACAAGTTGGTGACACC-TTCAGTCCTCAAAGAGCAGGACGCTCTTTTCAA
* * * *
104015 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACG
65 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACA
*
104080 AGTTGGTGGCACTTTTTAGTCCTCAAAG
130 AGTTGGTGGCACTTTTCAGTCCTCAAAG
104108 TGCAAGATGC
Statistics
Matches: 144, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
165 87 0.60
166 5 0.03
170 29 0.20
171 23 0.16
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (166 bp):
CCTTTTAAAGCCCACACAAGTTGGTGACACCTTCAGTCCTCAAAGAGCAGGACGCTCTTTTCAAA
GCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
GTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:104303 original size:40 final size:42
Alignment explanation
Indices: 104207--104303 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
104197 AACGTACTCT
* *
104207 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
* * * *
104250 TCTTCCTTGGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTTC
104290 TTTTCCTTTGTCCT
1 TTTTCCTTTGTCCT
104304 TGAAAAGTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
40 14 0.31
41 5 0.11
42 22 0.49
43 4 0.09
ACGTcount: A:0.16, C:0.29, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
Found at i:105521 original size:19 final size:18
Alignment explanation
Indices: 105470--105559 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
105460 TTGAATTCCA
105470 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
105487 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
105508 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
105527 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
105540 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
105559 A
1 A
105560 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:105534 original size:13 final size:13
Alignment explanation
Indices: 105516--105540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105506 ACATAAGTGT
105516 TGTATCGATACAA
1 TGTATCGATACAA
105529 TGTATCGATACA
1 TGTATCGATACA
105541 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:105536 original size:32 final size:32
Alignment explanation
Indices: 105495--105567 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
105485 ACATTCAGTA
105495 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
105527 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
105559 AATGTATCG
1 AATGTATCG
105568 CTAGAAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:105629 original size:13 final size:13
Alignment explanation
Indices: 105611--105636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
105601 CATTTTTCTG
105611 TGTATCGATACAT
1 TGTATCGATACAT
105624 TGTATCGATACAT
1 TGTATCGATACAT
105637 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:105654 original size:34 final size:33
Alignment explanation
Indices: 105591--105657 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
105581 GCCAAGGAAA
*
105591 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
105624 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
105658 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:108065 original size:52 final size:52
Alignment explanation
Indices: 107997--108340 Score: 171
Period size: 52 Copynumber: 6.6 Consensus size: 52
107987 TTAAATTCCT
* *
107997 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * * * *
108048 CAATTTTCCTTTAATCGGGGGTACTCCAACTCCGATTTTATTTCCAAAAACAT
1 CAATTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACAC
* * * * * ** ***** * *
108101 CAATTTTTC-ACAACCGAGGATACTCCAACCTCATTATTTCATCGGGGATACTC
1 CAATTTTCCTATAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCCAAAACAC
* * * * * * * *
108154 CAACCCCGTTACCTCTAA--GGGGATACTCTAACCCCAGCTTTATTTCCAAAATAT
1 CAA----TTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
** * * *
108208 TGA-TTTCC-ACAATCGGGGATACTCCAACCCCGGTTATATTTTCAAAACAC
1 CAATTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * * * * *
108258 TAATTTTCCTTTAATTGGGGATACTCTAACCCCGATTTTATTTCCAAAAACAT
1 CAATTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACAC
* * * *
108311 CAATTTTTC-ACAACCGAGGATACTCCAACC
1 CAATTTTCCTATAATCGGGGATACTCCAACC
108341 TCGTTATTTC
Statistics
Matches: 206, Mismatches: 73, Indels: 27
0.67 0.24 0.09
Matches are distributed among these distances:
48 2 0.01
49 4 0.02
50 31 0.15
51 13 0.06
52 90 0.44
53 36 0.17
54 7 0.03
55 3 0.01
56 15 0.07
57 3 0.01
58 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
CAATTTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
Found at i:108370 original size:210 final size:211
Alignment explanation
Indices: 108008--108454 Score: 720
Period size: 210 Copynumber: 2.1 Consensus size: 211
107998 AATTTTTCAT
* *
108008 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
1 AATCGGGGATACTCCAACCCCGGTTATATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
*
108073 CCAACTCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCATTAT
66 CCAACCCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCATTAT
* * * *
108138 TTCATCGGGGATACTCCAACCCCGTTACCTCTAAGGGGATACTCTAACCCCAGCTTTATTTCCAA
131 TTCATCGAGGATACCCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAA
108203 AATATT-GATTTC-CAC
196 AATATTAG-TTTCTCAC
* *
108218 AATCGGGGATACTCCAACCCCGGTTATATTTTCAAAACACTAATTTTCCTTTAATTGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTATATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* *
108283 CTAACCCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCGTTAT
66 CCAACCCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCATTAT
* * *
108348 TTCATCGAGGATACCCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAA
131 TTCATCGAGGATACCCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAA
*
108413 AATATTAGTTTCTCAT
196 AATATTAGTTTCTCAC
*
108429 AATTGGGGATACTCCAACCCC-GTTAT
1 AATCGGGGATACTCCAACCCCGGTTAT
108455 TTCCGAGGGG
Statistics
Matches: 219, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
210 196 0.89
211 23 0.11
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGGTTATATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
CCAACCCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCATTAT
TTCATCGAGGATACCCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAA
AATATTAGTTTCTCAC
Found at i:108406 original size:108 final size:106
Alignment explanation
Indices: 108064--108414 Score: 315
Period size: 108 Copynumber: 3.3 Consensus size: 106
108054 TCCTTTAATC
* * *
108064 GGGGGTACTCCAACTCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAA
* * *
108129 CCTCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCTAA
66 CCTCGTTATTTCATCGAGGATACACCAACCCCGTTACCTC--A
* * ** * * *
108172 GGGGATACTCTAACCCC-AGCTTTATTTCC-AAAATATTGA-TTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGA-CTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCA
* * * * ** * * *
108234 ACCCCGGTTATATT-TTC-A--AAACACTAATTTTCCTTTA-AT-T
65 ACCTC-GTTAT-TTCATCGAGGATACACCAA--CCCCGTTACCTCA
* *
108274 GGGGATACTCTAACCCCGATTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAA
*
108339 CCTCGTTATTTCATCGAGGATACCCCAACCCCGTTACCTCCGA
66 CCTCGTTATTTCATCGAGGATACACCAACCCCGTTACCT-C-A
* *
108382 GGGGATACTCCAACCCCGGCTTTATTTCTAAAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAA
108415 TATTAGTTTC
Statistics
Matches: 184, Mismatches: 43, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
102 28 0.15
103 15 0.08
104 36 0.20
105 2 0.01
106 35 0.19
107 14 0.08
108 54 0.29
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATCAATTTTTCACAACCGAGGATACTCCAA
CCTCGTTATTTCATCGAGGATACACCAACCCCGTTACCTCA
Found at i:108487 original size:79 final size:78
Alignment explanation
Indices: 108356--108587 Score: 245
Period size: 79 Copynumber: 2.9 Consensus size: 78
108346 ATTTCATCGA
* ** *
108356 GGATACCCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAG
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTCTAAAATATTAG
**
108421 TTTCTCATAATTGG
65 TTTCTCATAACCGG
*
108435 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCCT--AATCATT
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTT-CTAAAAT-ATT
* *
108498 -GATTTTTCACAACCGG
63 AG-TTTCTCATAACCGG
* * * * *
108514 GGATACTCCAACCCCGTTATTTTCAAGGGTATACTCCAACCCCGTTATTATCTCCAAAATATTAA
1 GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTT-TTATTTCTAAAATATT-A
*
108579 ATTTCTCAT
64 GTTTCTCAT
108588 CGGGACATAT
Statistics
Matches: 126, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
78 8 0.06
79 107 0.85
80 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (78 bp):
GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTCTAAAATATTAGT
TTCTCATAACCGG
Found at i:110376 original size:27 final size:27
Alignment explanation
Indices: 110332--110806 Score: 479
Period size: 27 Copynumber: 17.4 Consensus size: 27
110322 GACCTCTTCA
* * *
110332 AAGTCCACGATTCAGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
**
110359 AAGTTTACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
**
110386 AAAGTCCACAACTCTATGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
110414 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * * *
110441 GAGTCCATAACTCTGTGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
110468 AAGTCCACAACTCCGTGGCTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
110495 AAGTCCACAACTCTGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
110522 AAGTCCATAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
110549 AAGGTCCATAACTCCGTGGCACCCTTTT
1 AA-GTCCACAACTCCGTGGCATCCTTTT
*
110577 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
**
110605 AAGTCCACAACTTTGTGGCA-CTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
* * *
110632 AAAGTCCACCACTTCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* ** *
110660 AGGTCCACAACTCTATGGTA-CCTATTT
1 AAGTCCACAACTCCGTGGCATCCT-TTT
* *
110687 AAGTCCACAACTCCGTGGCACCCTTGT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
110714 AAGTCCACAACTCCATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * * *
110741 AAGTCCACAAGTCAGTGGCATCATTTCA
1 AAGTCCACAACTCCGTGGCATCCTTT-T
* * *
110769 AAGCCCACAAATCAGTGGCA-CCATTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
*
110796 AAAGCCCACAA
1 -AAGTCCACAA
110807 GTTAGTGGCG
Statistics
Matches: 382, Mismatches: 55, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.01
27 247 0.65
28 128 0.34
29 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:110399 original size:28 final size:28
Alignment explanation
Indices: 110331--111284 Score: 642
Period size: 28 Copynumber: 34.4 Consensus size: 28
110321 TGACCTCTTC
* *
110331 AAAGTCCACGATTCAGTGGCATCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
** * *
110359 -AAGTTTACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
*
110386 AAAGTCCACAACTCTA-TGGCATCCTTTT
1 AAAGTCCACAAGTC-AGTGGCATCCTTTT
* *
110414 -AAGTCCACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * * *
110441 -GAGTCCATAACTCTGTGGCATTCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * *
110468 -AAGTCCACAACTCCGTGGCTTCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
110495 -AAGTCCACAACTCTGTGGCAT-CTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * *
110521 TAAGTCCATAACTCTGTGGCATCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * * *
110549 AAGGTCCATAACTCCGTGGCACCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * *
110577 AAAGTCCACAACTCCGTGGCACCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* **
110605 -AAGTCCACAACTTTGTGGCA-CTCTTTT
1 AAAGTCCACAAGTCAGTGGCATC-CTTTT
** *
110632 AAAGTCCACCACTTC-GTGGCACCCTTTT
1 AAAGTCCA-CAAGTCAGTGGCATCCTTTT
* * *
110660 -AGGTCCACAACTCTA-TGGTA-CCTATTT
1 AAAGTCCACAAGTC-AGTGGCATCCT-TTT
* * * *
110687 -AAGTCCACAACTCCGTGGCACCCTTGT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
110714 -AAGTCCACAACTCCA-TGGCA-CCCTTT
1 AAAGTCCACAAGT-CAGTGGCATCCTTTT
* *
110740 AAAGTCCACAAGTCAGTGGCATCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
110768 AAAGCCCACAAATCAGTGGCA-CCATTTT
1 AAAGTCCACAAGTCAGTGGCATCC-TTTT
* * * * *
110796 AAAGCCCACAAGTTAGTGGCGTCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
110824 AAAGCCCACAAGTCAGTAGCATCCTTTT
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * *
110852 AAAGCCCATAAGTCAGTGGCATCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * *
110880 AAAGTCCATAAGTCAATGGCA-CCATTTC
1 AAAGTCCACAAGTCAGTGGCATCC-TTTT
* * *
110908 AAAGCCCACAAGTCAGTGGTA-CCATTTC
1 AAAGTCCACAAGTCAGTGGCATCC-TTTT
* * *
110936 AAAGCCCATAAGTCAGTGGCATCCTTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * * *
110964 AAAGCCCATAAGTCCGTGGCATCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
110992 AAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * * * *
111020 AATGCCCACAAGTCCGTGGCATCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * *
111048 AAAG-CTTATAAGTCAGTGGCA-CCATTTC
1 AAAGTC-CACAAGTCAGTGGCATCC-TTTT
* ** *
111076 AAAGCCCACAAGTCAGTGGCATCAATTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
111104 AAAGTCCACAAGTCAATGGCA-CCATTTC
1 AAAGTCCACAAGTCAGTGGCATCC-TTTT
* * **
111132 AAAGCCCACAAGTCAGTGGCATCATTAC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* * *
111160 AAAGCCCACAAGTCAGTGGCATCATTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
* *
111188 AAAGCCCATAAGTCAGTGGCATTCCCTTTT
1 AAAGTCCACAAGTCAGTGGCA-T-CCTTTT
*
111218 AAA-TCCCACAAGTCAGTGGCACTCTTTTT
1 AAAGT-CCACAAGTCAGTGGCA-TCCTTTT
** * *
111247 AAAACCCACAAGTTAGTGGCATCCTTTC
1 AAAGTCCACAAGTCAGTGGCATCCTTTT
*
111275 AAAGCCCACA
1 AAAGTCCACA
111285 CAAGTTAGTG
Statistics
Matches: 782, Mismatches: 112, Indels: 64
0.82 0.12 0.07
Matches are distributed among these distances:
26 19 0.02
27 223 0.29
28 483 0.62
29 34 0.04
30 23 0.03
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
AAAGTCCACAAGTCAGTGGCATCCTTTT
Found at i:110747 original size:219 final size:219
Alignment explanation
Indices: 110328--110806 Score: 563
Period size: 219 Copynumber: 2.2 Consensus size: 219
110318 CTGTGACCTC
* * * * ** *
110328 TTCAAAGTCCACGATTCAGTGGCATCCTTTT-AAGTTTACAACTCCGTGGCATCCTTTTAAAGTC
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* * *
110392 CACAACTCTATGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTGAGTCCATAACTCTGT
66 CACAACTCTATGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTGAGTCCACAACTCTAT
* ** * ** * * *
110457 GGCATTCTTTTAAGTCCACAACTCCGTGGCTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTT
131 GGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTGTAAGTCCACAACTCCATGGCACCCTTTA
* * *
110522 AAGTCCATAACTCTGTGGCATCCT
196 AAGTCCACAACTCAGTGGCATCAT
* * * * * *
110546 TTTAAGGTCCATAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* * * *
110610 CACAACTTTGTGGCA-CTCTTTTAAAGTCCACCACTTCGTGGCACCCTTTT-AGGTCCACAACTC
66 CACAACTCTATGGCATC-CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTGA-GTCCACAACTC
*
110673 TATGGTA-CCTATTTAAGTCCACAACTCCGTGGCACCCTTGTAAGTCCACAACTCCATGGCACCC
128 TATGGCATCCT-TTTAAGTCCACAACTCCGTGGCACCCTTGTAAGTCCACAACTCCATGGCACCC
*
110737 TTTAAAGTCCACAAGTCAGTGGCATCAT
192 TTTAAAGTCCACAACTCAGTGGCATCAT
* *
110765 TTCAAAGCCCACAAATCAGTGGCACCATTTTAAAGCCCACAA
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTAAAGTCCACAA
110807 GTTAGTGGCG
Statistics
Matches: 217, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
217 1 0.00
218 50 0.23
219 166 0.76
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (219 bp):
TTCAAAGCCCACAAATCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
CACAACTCTATGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTGAGTCCACAACTCTAT
GGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTGTAAGTCCACAACTCCATGGCACCCTTTA
AAGTCCACAACTCAGTGGCATCAT
Found at i:110807 original size:56 final size:56
Alignment explanation
Indices: 110729--111316 Score: 707
Period size: 56 Copynumber: 10.4 Consensus size: 56
110719 CACAACTCCA
* * *
110729 TGGCACCCTTT-AAAGTCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAATCAG
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * *
110784 TGGCACCATTTTAAAGCCCACAAGTTAGTGGCGTCATTTCAAAGCCCACAAGTCAG
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * * * * *
110840 TAGCATCC-TTTTAAAGCCCATAAGTCAGTGGCATCATTTCAAAGTCCATAAGTCAA
1 TGGCA-CCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * *
110896 TGGCACCATTTCAAAGCCCACAAGTCAGTGGTACCATTTCAAAGCCCATAAGTCAG
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* *
110952 TGGCATCC-TTTCAAAGCCCATAAGTCCGTGGCATCATTTCAAAGCCCACAAGTCAG
1 TGGCA-CCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * ** *
111008 TGGCATCC-TTTCAATGCCCACAAGTCCGTGGCATCATTTCAAAGCTTATAAGTCAG
1 TGGCA-CCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * *
111064 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCAATTCAAAGTCCACAAGTCAA
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
*
111120 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTACAAAGCCCACAAGTCAG
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
* * * * *
111176 TGGCATCATTTCAAAGCCCATAAGTCAGTGGCATTCCCTTTTAAATCCCACAAGTCAG
1 TGGCACCATTTCAAAGCCCACAAGTCAGTGGCA-T-CATTTCAAAGCCCACAAGTCAG
* * * * * *
111234 TGGCACTCTTTTTAAAACCCACAAGTTAGTGGCATCCTTTCAAAGCCCACACAAGTTAG
1 TGGCAC-CATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAG-CC-CACAAGTCAG
* *
111293 TGGTAACTCTTTTCAAAGCCCACA
1 TGG-CAC-CATTTCAAAGCCCACA
111317 CAAGTTAGTG
Statistics
Matches: 463, Mismatches: 59, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
55 14 0.03
56 359 0.78
57 13 0.03
58 26 0.06
59 34 0.07
60 17 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (56 bp):
TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAG
Found at i:111312 original size:32 final size:31
Alignment explanation
Indices: 110746--111352 Score: 237
Period size: 28 Copynumber: 21.2 Consensus size: 31
110736 CTTTAAAGTC
* *
110746 CACAAGTCAGTGGCA-TCATTTCAAAGCCCA
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
*
110776 CA-AA-TCAGTGGCAC-CATTTT-AAAG-CC-
1 CACAAGTTAGTGGCACTC-TTTTCAAAGCCCA
* *
110802 CACAAGTTAGTGGC-GTCATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* *
110830 CACAAGTCAGTAGCA-TCCTTTT-AAAG-CC-
1 CACAAGTTAGTGGCACT-CTTTTCAAAGCCCA
* * * *
110858 CATAAGTCAGTGGCA-TCATTTCAAAG-TC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * * *
110886 CATAAGTCAATGGCAC-CATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * *
110914 CACAAGTCAGTGGTAC-CATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * *
110942 CATAAGTCAGTGGCA-TCCTTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* ** *
110970 CATAAGTCCGTGGCA-TCATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * *
110998 CACAAGTCAGTGGCA-TCCTTTCAATG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
** * *
111026 CACAAGTCCGTGGCA-TCATTTCAAAG--CT
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * * *
111054 TATAAGTCAGTGGCAC-CATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* ** *
111082 CACAAGTCAGTGGCA-TCAATTCAAAG-TC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * *
111110 CACAAGTCAATGGCAC-CATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * *
111138 CACAAGTCAGTGGCA-TCATTACAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* *
111166 CACAAGTCAGTGGCA-TCATTTCAAAG-CC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
* * * *
111194 CATAAGTCAGTGGCATTCCCTTTT-AAA-TCC-
1 CACAAGTTAGTGGCA--CTCTTTTCAAAGCCCA
* * *
111224 CACAAGTCAGTGGCACTCTTTTTAAA-ACC-
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
*
111253 CACAAGTTAGTGGCA-TCCTTTCAAAGCCCA
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
*
111283 CACAAGTTAGTGGTAACTCTTTTCAAAGCCCA
1 CACAAGTTAGTGG-CACTCTTTTCAAAGCCCA
* *
111315 CACAAGTTAGTGGCACTTTTTTTAAAGCCCA
1 CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
*
111346 CGCAAGT
1 CACAAGT
111353 CGGTGGTAAC
Statistics
Matches: 494, Mismatches: 57, Indels: 51
0.82 0.09 0.08
Matches are distributed among these distances:
26 2 0.00
27 12 0.02
28 362 0.73
29 31 0.06
30 34 0.07
31 26 0.05
32 27 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (31 bp):
CACAAGTTAGTGGCACTCTTTTCAAAGCCCA
Found at i:111484 original size:69 final size:69
Alignment explanation
Indices: 111373--111513 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
111363 CCTTTTCAAA
111373 TCACCACTTTTGTCATCTTAAAGTCCGATATCACTGGCATTGAATCAACATATTGGTACCTTTAT
1 TCACCACTTTTGTCATCTTAAAGTCCGATATCACTGGCATTGAATCAACATATTGGTACCTTTAT
111438 TAGC
66 TAGC
*
111442 TCACCACTTTTGTCATCTTAAAGTCCGATATCGCTGGCATTGAATCAACATATTGGTACCTTTAT
1 TCACCACTTTTGTCATCTTAAAGTCCGATATCACTGGCATTGAATCAACATATTGGTACCTTTAT
111507 TAGC
66 TAGC
111511 TCA
1 TCA
111514 ATGTCGCTGG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (69 bp):
TCACCACTTTTGTCATCTTAAAGTCCGATATCACTGGCATTGAATCAACATATTGGTACCTTTAT
TAGC
Found at i:114839 original size:24 final size:24
Alignment explanation
Indices: 114807--114884 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
114797 ACCTTAGTTG
114807 TTGAAGAATCAATCCACATTGTTT
1 TTGAAGAATCAATCCACATTGTTT
* *
114831 TTGATGAATC--T-C-C-TTAGTTG
1 TTGAAGAATCAATCCACATT-GTTT
114851 TTGAAGAATCAATCCACATTGTTT
1 TTGAAGAATCAATCCACATTGTTT
*
114875 TTGATGAATC
1 TTGAAGAATC
114885 TAACTCTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 1 0.02
22 2 0.05
23 1 0.02
24 22 0.51
25 2 0.05
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (24 bp):
TTGAAGAATCAATCCACATTGTTT
Found at i:114848 original size:44 final size:44
Alignment explanation
Indices: 114798--114885 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
114788 AATAAAAGAA
114798 CCTTAGTTGTTGAAGAATCAATCCACATTGTTTTTGATGAATCT
1 CCTTAGTTGTTGAAGAATCAATCCACATTGTTTTTGATGAATCT
114842 CCTTAGTTGTTGAAGAATCAATCCACATTGTTTTTGATGAATCT
1 CCTTAGTTGTTGAAGAATCAATCCACATTGTTTTTGATGAATCT
114886 AACTCTTCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (44 bp):
CCTTAGTTGTTGAAGAATCAATCCACATTGTTTTTGATGAATCT
Found at i:117049 original size:20 final size:20
Alignment explanation
Indices: 117020--117067 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
117010 AAAACTCAGA
*
117020 TGTATTGATACAATGTTCTT
1 TGTATCGATACAATGTTCTT
117040 TGTATCGATACAATGTTCTT
1 TGTATCGATACAATGTTCTT
117060 TGTATCGA
1 TGTATCGA
117068 AACATTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (20 bp):
TGTATCGATACAATGTTCTT
Found at i:119592 original size:13 final size:13
Alignment explanation
Indices: 119574--119599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
119564 TATATCCAGA
119574 TGTATCGATACAT
1 TGTATCGATACAT
119587 TGTATCGATACAT
1 TGTATCGATACAT
119600 GTTCATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:119608 original size:19 final size:19
Alignment explanation
Indices: 119584--119658 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
119574 TGTATCGATA
119584 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
119603 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
**
119622 CATTGTATCGATACATACT
1 CATTGTATCGATACATGTT
119641 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
119659 AAAGTGGCAG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 37 0.71
20 15 0.29
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:119725 original size:13 final size:13
Alignment explanation
Indices: 119707--119732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
119697 AATGGGACAA
119707 TGTATCGATACAT
1 TGTATCGATACAT
119720 TGTATCGATACAT
1 TGTATCGATACAT
119733 GAAGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:120561 original size:13 final size:13
Alignment explanation
Indices: 120543--120594 Score: 95
Period size: 13 Copynumber: 4.0 Consensus size: 13
120533 ACTCACTTAA
120543 TATCGATACATTG
1 TATCGATACATTG
*
120556 TATCGATACATTT
1 TATCGATACATTG
120569 TATCGATACATTG
1 TATCGATACATTG
120582 TATCGATACATTG
1 TATCGATACATTG
120595 AGCCCAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:127271 original size:13 final size:13
Alignment explanation
Indices: 127253--127278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127243 TACACCAAGT
127253 ATGTATCGATACA
1 ATGTATCGATACA
127266 ATGTATCGATACA
1 ATGTATCGATACA
127279 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:127276 original size:32 final size:33
Alignment explanation
Indices: 127235--127298 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
127225 TAGCCAAACT
* **
127235 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
127267 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
127299 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:132571 original size:13 final size:13
Alignment explanation
Indices: 132553--132578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
132543 TACACCAAGT
132553 ATGTATCGATACA
1 ATGTATCGATACA
132566 ATGTATCGATACA
1 ATGTATCGATACA
132579 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:132576 original size:32 final size:33
Alignment explanation
Indices: 132535--132598 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
132525 TAGCCAAACT
* **
132535 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
132567 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
132599 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:142387 original size:9 final size:9
Alignment explanation
Indices: 142359--142388 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
142349 TTCGAGTCAA
142359 CTTCATCAT
1 CTTCATCAT
*
142368 CATCATCAT
1 CTTCATCAT
142377 CTTCATCAT
1 CTTCATCAT
142386 CTT
1 CTT
142389 AATGGTTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTCATCAT
Found at i:371765 original size:54 final size:52
Alignment explanation
Indices: 371703--371828 Score: 182
Period size: 51 Copynumber: 2.4 Consensus size: 52
371693 GATTAACGGG
* * *
371703 GTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAAATT-AT-TGTTTTGAAAATAAAATCGGA
*
371757 GTTGGAGTATCCCCGATTAT-AAAAAATTATTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAAATTATTGTTTTGAAAATAAAATCGGA
*
371808 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
371829 GAGAATTGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
51 37 0.57
52 1 0.02
53 8 0.12
54 19 0.29
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAAATTATTGTTTTGAAAATAAAATCGGA
Found at i:374208 original size:13 final size:13
Alignment explanation
Indices: 374190--374215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
374180 ACAAAGATCC
374190 ATGTATCGATACA
1 ATGTATCGATACA
374203 ATGTATCGATACA
1 ATGTATCGATACA
374216 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:374211 original size:33 final size:33
Alignment explanation
Indices: 374169--374235 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
374159 AAAATTCCTA
***
374169 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
374202 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
374235 A
1 A
374236 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:374295 original size:13 final size:13
Alignment explanation
Indices: 374277--374301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
374267 ACAATACTTA
374277 TGTATCGATACAT
1 TGTATCGATACAT
374290 TGTATCGATACA
1 TGTATCGATACA
374302 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:374300 original size:32 final size:32
Alignment explanation
Indices: 374258--374320 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
374248 TAGCTAATTA
* *
374258 TGTATTGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
374290 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
374321 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:374314 original size:19 final size:19
Alignment explanation
Indices: 374255--374321 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
374245 CAGTAGCTAA
* *
374255 TTATGTATTGATACAATAC
1 TTATGTATCGATACAACAC
374274 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
374289 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
374306 TTATGTATCGATACAA
1 TTATGTATCGATACAA
374322 ATTGTTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 5 0.12
18 1 0.03
19 24 0.60
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:374975 original size:18 final size:18
Alignment explanation
Indices: 374948--374982 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
374938 TTGTTATAAT
374948 AATTAATTTTATTTTTAA
1 AATTAATTTTATTTTTAA
*
374966 AATTATTTTTATTTTTA
1 AATTAATTTTATTTTTA
374983 CTATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTAATTTTATTTTTAA
Found at i:375463 original size:53 final size:53
Alignment explanation
Indices: 375364--375464 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
375354 TTTGAATCAT
** * * *
375364 TTTTAGGTTTGTTTTAATTAAGTTTGATATTTAAATTATTCAGGTTTAAGTTA
1 TTTTAGGTTTGAATTAATCAAGTTTGATAATCAAATTATTCAGGTTTAAGTTA
*
375417 TTTTAGGTTTGAATTAATCAAGTTTGATAATCAAGTTACTTC-GGTTTA
1 TTTTAGGTTTGAATTAATCAAGTTTGATAATCAAATTA-TTCAGGTTTA
375465 GGCCAATTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 38 0.93
54 3 0.07
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (53 bp):
TTTTAGGTTTGAATTAATCAAGTTTGATAATCAAATTATTCAGGTTTAAGTTA
Found at i:377446 original size:20 final size:20
Alignment explanation
Indices: 377410--377447 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
377400 TAAATCTTAT
377410 TATAAGATTGTCATAATTGA
1 TATAAGATTGTCATAATTGA
*
377430 TATAATATT-TCATTAATT
1 TATAAGATTGTCA-TAATT
377448 TATTGAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
TATAAGATTGTCATAATTGA
Found at i:378800 original size:16 final size:16
Alignment explanation
Indices: 378750--378807 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
378740 ATCGATTCGA
* * *
378750 AACCCGTAATAATTCG
1 AACCCGAAATGATCCG
* *
378766 AACCCAAAATGA-CTTG
1 AACCCGAAATGATC-CG
378782 AACCCGAAATGATCCG
1 AACCCGAAATGATCCG
378798 AACCCGAAAT
1 AACCCGAAAT
378808 AACCTAGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (16 bp):
AACCCGAAATGATCCG
Found at i:379684 original size:16 final size:16
Alignment explanation
Indices: 379639--379716 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
379629 ACCCAAATAT
*
379639 GAAATGACCCAAACTC
1 GAAATGACCCGAACTC
379655 GAAATGACCCGAACTC
1 GAAATGACCCGAACTC
* * *
379671 GAAATGATCTGAACCC
1 GAAATGACCCGAACTC
* *
379687 GAAATAACCCGAACTT
1 GAAATGACCCGAACTC
*
379703 GAAAATGACTCGAA
1 G-AAATGACCCGAA
379717 AATTTTAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
16 40 0.80
17 10 0.20
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (16 bp):
GAAATGACCCGAACTC
Found at i:380170 original size:20 final size:22
Alignment explanation
Indices: 380131--380182 Score: 81
Period size: 20 Copynumber: 2.4 Consensus size: 22
380121 TGGGAACCAC
380131 TCGATACATTGACCTAAAATGTA
1 TCGATACATTGA-CTAAAATGTA
380154 TCGATACATT-A-TAAAATGTA
1 TCGATACATTGACTAAAATGTA
380174 TCGATACAT
1 TCGATACAT
380183 CATGATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.62
22 1 0.03
23 10 0.34
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (22 bp):
TCGATACATTGACTAAAATGTA
Found at i:389423 original size:23 final size:23
Alignment explanation
Indices: 389393--389438 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
389383 TTTTGGCACA
389393 GGTACCTTTGGTCTAAGTAGCTT
1 GGTACCTTTGGTCTAAGTAGCTT
389416 GGTACCTTTGGTCTAAGTAGCTT
1 GGTACCTTTGGTCTAAGTAGCTT
389439 TGACATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (23 bp):
GGTACCTTTGGTCTAAGTAGCTT
Found at i:392897 original size:21 final size:20
Alignment explanation
Indices: 392873--392915 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
392863 GGCTAGTGTG
*
392873 GGGACTACCCGGTTGCGACCT
1 GGGACT-CCCGGTCGCGACCT
* *
392894 GGGAGTGCCGGTCGCGACCT
1 GGGACTCCCGGTCGCGACCT
392914 GG
1 GG
392916 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTCCCGGTCGCGACCT
Found at i:393374 original size:13 final size:13
Alignment explanation
Indices: 393356--393394 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
393346 ATAATCCTCC
*
393356 TGTATCGATACAG
1 TGTATCGATACAA
393369 TGTATCGATACAA
1 TGTATCGATACAA
393382 TGTATCGATACAA
1 TGTATCGATACAA
393395 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:395488 original size:15 final size:15
Alignment explanation
Indices: 395468--395498 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
395458 ATTTCGTTTG
*
395468 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
395483 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
395498 G
1 G
395499 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:397330 original size:21 final size:21
Alignment explanation
Indices: 397301--397345 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
397291 AAGTTTTCAT
*
397301 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
397321 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
397343 TTT
1 TTT
397346 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:397887 original size:1 final size:1
Alignment explanation
Indices: 397881--398015 Score: 108
Period size: 1 Copynumber: 135.0 Consensus size: 1
397871 GGCGTCCTCC
* * ** ** * * *
397881 AAAAAAACAAAAAAAAAACAAAAAAAAAACGAAAAAATGAAAAAACAAAAAAAACAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
397946 AAAAAAACAAAAAAACAAAAAAAAAACAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
398011 AAAAA
1 AAAAA
398016 GGGGGTCCGG
Statistics
Matches: 100, Mismatches: 34, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 100 1.00
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:397897 original size:11 final size:11
Alignment explanation
Indices: 397881--398015 Score: 145
Period size: 11 Copynumber: 12.4 Consensus size: 11
397871 GGCGTCCTCC
397881 AAAAAAACAAA
1 AAAAAAACAAA
397892 AAAAAAACAAA
1 AAAAAAACAAA
397903 AAAAAAACGAAA
1 AAAAAAAC-AAA
**
397915 AAATGAA-AAA
1 AAAAAAACAAA
*
397925 ACAAAAA-AAA
1 AAAAAAACAAA
*
397935 CAAAAAACAAA
1 AAAAAAACAAA
397946 AAAAAAACAAA
1 AAAAAAACAAA
397957 AAAACAAA-AAA
1 AAAA-AAACAAA
397968 AAAACAAA-AAA
1 AAAA-AAACAAA
*
397979 AACAAAAACAAT
1 AA-AAAAACAAA
397991 AAAAAAAC-AA
1 AAAAAAACAAA
*
398001 ACAAAAACAAA
1 AAAAAAACAAA
398012 AAAA
1 AAAA
398016 GGGGGTCCGG
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
10 23 0.22
11 66 0.62
12 17 0.16
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.01
Consensus pattern (11 bp):
AAAAAAACAAA
Done.