Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009886.1 Kokia drynarioides strain JFW-HI SEQ_124622, whole genome shotgun sequence
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: 212314
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:890 original size:4 final size:4
Alignment explanation
Indices: 871--968 Score: 92
Period size: 4 Copynumber: 24.0 Consensus size: 4
861 ACACATTATT
* * * *
871 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC -TTC TTTC TTTCC TCTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTT-C TTTC
* *
919 CTTC TTCC TTTC TTTC TTTC TTTCC TTTC TTTC TTTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTT-C TTTC TTTC TTTC
969 CCGTTTATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
3 6 0.08
4 58 0.74
5 14 0.18
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:902 original size:20 final size:20
Alignment explanation
Indices: 877--957 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
867 TATTTTTCTT
877 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
897 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
*
917 TCCTTCTTCCTTTCTTT-CTT
1 TCCTTCTT-CTTTCTTTCCTC
*
937 TCTTTCCTTTCTTTCTTTCCT
1 TCCTT-C-TTCTTTCTTTCCT
958 TTCTTTCTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
20 34 0.62
21 17 0.31
22 4 0.07
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:965 original size:13 final size:13
Alignment explanation
Indices: 871--969 Score: 107
Period size: 13 Copynumber: 7.7 Consensus size: 13
861 ACACATTATT
871 TTTCTTTCCTTCTTC
1 TTTCTTTCC-T-TTC
*
886 TTTCTTTCCTCTC
1 TTTCTTTCCTTTC
*
899 CTTC-TT-CTTTC
1 TTTCTTTCCTTTC
*
910 TTTCCTCTCC-TTC
1 TTT-CTTTCCTTTC
*
923 TTCCTTT-CTTTC
1 TTTCTTTCCTTTC
935 TTTCTTTCCTTTC
1 TTTCTTTCCTTTC
948 TTTCTTTCCTTTC
1 TTTCTTTCCTTTC
961 TTTCTTTCC
1 TTTCTTTCC
970 CGTTTATTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
11 7 0.10
12 15 0.21
13 38 0.54
14 2 0.03
15 9 0.13
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTCTTTCCTTTC
Found at i:965 original size:17 final size:17
Alignment explanation
Indices: 871--968 Score: 100
Period size: 17 Copynumber: 6.0 Consensus size: 17
861 ACACATTATT
871 TTTCTTTCC-TTC-TTC
1 TTTCTTTCCTTTCTTTC
* *
886 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCTTTCTTTC
*
903 -TTCTTT-CTTTCCTCTC
1 TTTCTTTCCTTT-CTTTC
*
919 CTTC-TTCCTTTCTTTC
1 TTTCTTTCCTTTCTTTC
935 TTTCTTTCCTTTCTTTC
1 TTTCTTTCCTTTCTTTC
952 TTTCCTTT-CTTTCTTTC
1 TTT-CTTTCCTTTCTTTC
969 CCGTTTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
15 12 0.17
16 20 0.29
17 34 0.49
18 4 0.06
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTTCCTTTCTTTC
Found at i:1712 original size:34 final size:34
Alignment explanation
Indices: 1674--1746 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1664 TTCTTTTTCA
* *
1674 TATTAATTTTGAAAAATACGATAATATCATACTT
1 TATTAATTCTAAAAAATACGATAATATCATACTT
* *
1708 TATTAATTCTAAAAAATATGATAATATCATATTT
1 TATTAATTCTAAAAAATACGATAATATCATACTT
1742 TATTA
1 TATTA
1747 CTGTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (34 bp):
TATTAATTCTAAAAAATACGATAATATCATACTT
Found at i:1775 original size:18 final size:19
Alignment explanation
Indices: 1752--1793 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1742 TATTACTGTT
1752 GATTTTT-TTA-ATTTCTTA
1 GATTTTTCTTATATTT-TTA
1770 -ATTTTTCTTATATTTTTA
1 GATTTTTCTTATATTTTTA
1788 GATTTT
1 GATTTT
1794 ATATAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
GATTTTTCTTATATTTTTA
Found at i:2693 original size:22 final size:22
Alignment explanation
Indices: 2650--2693 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2640 TAAAAAAATT
** *
2650 ATTTAATTAAAATTTTAGTTTA
1 ATTTAATTAAAAAATTAATTTA
2672 ATTTAATTAAAAAATTAATTTA
1 ATTTAATTAAAAAATTAATTTA
2694 TAAATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTAATTAAAAAATTAATTTA
Found at i:3830 original size:31 final size:30
Alignment explanation
Indices: 3795--3873 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
3785 CCCTTCAAAA
3795 TTTAAAAAGTTTTCATTATGTTTTT-TTATTT
1 TTTAAAAAGTTTTCATTAT-TTTTTATT-TTT
** *
3826 TTTAAAAAGAATTAATTATTTTTTAATTTTT
1 TTTAAAAAGTTTTCATTATTTTTT-ATTTTT
*
3857 TTTGAAAA-TTTTCATTA
1 TTTAAAAAGTTTTCATTA
3874 ATCTCAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 11 0.28
31 26 0.67
32 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTAAAAAGTTTTCATTATTTTTTATTTTT
Found at i:4990 original size:20 final size:20
Alignment explanation
Indices: 4945--4991 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4935 GAAGCTAAAC
*
4945 ATTAAAGTTAGTTGTAAAAT
1 ATTAAAGGTAGTTGTAAAAT
*
4965 ACTAAAGGTAGTTGTAAAAT
1 ATTAAAGGTAGTTGTAAAAT
*
4985 TTTAAAG
1 ATTAAAG
4992 AATAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTAAAGGTAGTTGTAAAAT
Found at i:5360 original size:21 final size:20
Alignment explanation
Indices: 5318--5361 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5308 TTATTTATTT
* *
5318 AATATTTGTATAAATCATTA
1 AATATTTGTAAAAATCAATA
*
5338 AATATTTTTAAAATATCAATA
1 AATATTTGTAAAA-ATCAATA
5359 AAT
1 AAT
5362 TCAAAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
AATATTTGTAAAAATCAATA
Found at i:17008 original size:11 final size:11
Alignment explanation
Indices: 16988--17039 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
16978 ATACAGTAAC
16988 AATAAAATAAT
1 AATAAAATAAT
*
16999 AATAATATAAT
1 AATAAAATAAT
*
17010 AATAAAATGAT
1 AATAAAATAAT
*
17021 -AGAAAATAAT
1 AATAAAATAAT
17031 GAA-AAAATA
1 -AATAAAATA
17040 GTAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.24
11 25 0.74
12 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:17574 original size:12 final size:12
Alignment explanation
Indices: 17536--17574 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17526 TTCTACCCAC
*
17536 AAATCCAAATAA
1 AAATCCAAAAAA
* *
17548 AAATCGAAAGAA
1 AAATCCAAAAAA
17560 AAATCCAAAAAA
1 AAATCCAAAAAA
17572 AAA
1 AAA
17575 GATTGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.72, C:0.13, G:0.05, T:0.10
Consensus pattern (12 bp):
AAATCCAAAAAA
Found at i:22566 original size:18 final size:18
Alignment explanation
Indices: 22539--22573 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22529 ATTTATAAAA
*
22539 TAATTATTTTATTATTAG
1 TAATTATTTTATCATTAG
*
22557 TAATTTTTTTATCATTA
1 TAATTATTTTATCATTA
22574 ATTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TAATTATTTTATCATTAG
Found at i:24617 original size:28 final size:28
Alignment explanation
Indices: 24586--24639 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
24576 ATTTTAAAAT
*
24586 TTTAAGAT-ATAAAAATAAATATTTTATA
1 TTTAAAATAATAAAAATAAAT-TTTTATA
24614 TTTAAAATAATAAAAATAAATTTTTA
1 TTTAAAATAATAAAAATAAATTTTTA
24640 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTAAAATAATAAAAATAAATTTTTATA
Found at i:30388 original size:20 final size:21
Alignment explanation
Indices: 30365--30407 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
30355 ACTGATATAC
30365 ATTTACCAATG-CTG-AAACAG
1 ATTTA-CAATGTCTGAAAACAG
*
30385 ATTTAGAATGTCTGAAAACAG
1 ATTTACAATGTCTGAAAACAG
30406 AT
1 AT
30408 GCGTCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (21 bp):
ATTTACAATGTCTGAAAACAG
Found at i:31251 original size:50 final size:50
Alignment explanation
Indices: 31183--31289 Score: 214
Period size: 50 Copynumber: 2.1 Consensus size: 50
31173 ATAAGATACA
31183 TTTTTTGCCCCTTTACTTGTTAATTAGTTTCACTTTGGTACCTATACATT
1 TTTTTTGCCCCTTTACTTGTTAATTAGTTTCACTTTGGTACCTATACATT
31233 TTTTTTGCCCCTTTACTTGTTAATTAGTTTCACTTTGGTACCTATACATT
1 TTTTTTGCCCCTTTACTTGTTAATTAGTTTCACTTTGGTACCTATACATT
31283 TTTTTTG
1 TTTTTTG
31290 TCCATTTTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (50 bp):
TTTTTTGCCCCTTTACTTGTTAATTAGTTTCACTTTGGTACCTATACATT
Found at i:34772 original size:19 final size:20
Alignment explanation
Indices: 34729--34775 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34719 TTGCTATTTG
* *
34729 AAAATTTTTATTAAGCTCCT
1 AAAATTTTAATTAAGCTCCC
34749 AAAATTTTAATTAAGC-CCC
1 AAAATTTTAATTAAGCTCCC
*
34768 CAAATTTT
1 AAAATTTT
34776 TTTGGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATTTTAATTAAGCTCCC
Found at i:34808 original size:31 final size:30
Alignment explanation
Indices: 34749--34822 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
34739 TTAAGCTCCT
34749 AAAATTTTAATTAAGCCCCCAAATTTTTTTG
1 AAAATTTTAATTAAGCCCCCAAA-TTTTTTG
* * * *
34780 GAAATTTTCATTAAGCCTCTAGAA-TTTTTG
1 AAAATTTTAATTAAGCCCCCA-AATTTTTTG
34810 AAAATTTTAATTA
1 AAAATTTTAATTA
34823 CCCCCTACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 17 0.47
31 17 0.47
32 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (30 bp):
AAAATTTTAATTAAGCCCCCAAATTTTTTG
Found at i:35375 original size:40 final size:40
Alignment explanation
Indices: 35320--35401 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
35310 TTCAAATTGA
35320 TAGAATTCATAGTTGTTAAAATGACAACATTGTATTTTCT
1 TAGAATTCATAGTTGTTAAAATGACAACATTGTATTTTCT
35360 TAGAATTCATAGTTGTTAAAATGACAACATTGTATTTTCT
1 TAGAATTCATAGTTGTTAAAATGACAACATTGTATTTTCT
35400 TA
1 TA
35402 ATAGCATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (40 bp):
TAGAATTCATAGTTGTTAAAATGACAACATTGTATTTTCT
Found at i:35441 original size:39 final size:39
Alignment explanation
Indices: 35393--35473 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
35383 ACAACATTGT
35393 ATTTTCTTAATAGCATTAAGCATTCGATTAACATGTAAA
1 ATTTTCTTAATAGCATTAAGCATTCGATTAACATGTAAA
*
35432 ATTTTCTTAATAGCGTTAAGCATTCGATTAACATGTAAA
1 ATTTTCTTAATAGCATTAAGCATTCGATTAACATGTAAA
35471 ATT
1 ATT
35474 ATTATTGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (39 bp):
ATTTTCTTAATAGCATTAAGCATTCGATTAACATGTAAA
Found at i:36078 original size:13 final size:13
Alignment explanation
Indices: 36056--36107 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
36046 TTAAATTAAG
36056 TTTTTCAAAAGTAC
1 TTTTT-AAAAGTAC
36070 TTTTTAAAA-TCAC
1 TTTTTAAAAGT-AC
* *
36083 ATTTGAAAAGTAC
1 TTTTTAAAAGTAC
*
36096 TTTTCAAAAGTA
1 TTTTTAAAAGTA
36108 ATACCAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 25 0.78
14 6 0.19
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:37860 original size:23 final size:23
Alignment explanation
Indices: 37834--37907 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
37824 ACGTCTCGTG
37834 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGATTAGTACTTTGTGTA
* * * * *
37857 CTCTCCGTTTAGCACTGTGTGTG
1 CTCTCTGATTAGTACTTTGTGTA
37880 CTCTCT-ATTAGTACTTTG-GTA
1 CTCTCTGATTAGTACTTTGTGTA
37901 CTCTCTG
1 CTCTCTG
37908 TTTGTTCCGT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.20
22 9 0.22
23 23 0.57
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (23 bp):
CTCTCTGATTAGTACTTTGTGTA
Found at i:37881 original size:46 final size:44
Alignment explanation
Indices: 37811--37910 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 44
37801 CACTAGCGCG
37811 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCT-ATTAGTACTTTG-GTA
* *
37857 CTCTCCGTTTAGCACTGTGT-GTGCTCTCTATTAGTACTTTGGTA
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTATTAGTACTTTGGTA
37901 CTCTCTGTTT
1 CTCTCTGTTT
37911 GTTCCGTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 12 0.24
45 12 0.24
46 23 0.46
47 3 0.06
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (44 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTATTAGTACTTTGGTA
Found at i:49043 original size:31 final size:31
Alignment explanation
Indices: 48973--49043 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
48963 TGATTTGGTG
*
48973 CAATTATATACATGAAACTTGAATTGTGATT
1 CAATTGTATACATGAAACTTGAATTGTGATT
*
49004 -TATATGTATACATGAAACTTTG-ATT-TCGATT
1 CAAT-TGTATACATGAAAC-TTGAATTGT-GATT
49035 CAATTGTAT
1 CAATTGTAT
49044 GCATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
30 3 0.09
31 25 0.76
32 5 0.15
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
CAATTGTATACATGAAACTTGAATTGTGATT
Found at i:53674 original size:178 final size:179
Alignment explanation
Indices: 53373--53727 Score: 520
Period size: 178 Copynumber: 2.0 Consensus size: 179
53363 GTATACCTTT
* *
53373 GTCGGACATAGGTACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGTACAAACTAAGAC
1 GTCGGACATAGGTACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGCACAAACTAAAAC
* *
53438 TAGGTAATGGCAATGATAAAATCTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTC
66 TAGGTAATGGCAATGATAAAATCTTGATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACTC
*
53503 -GACCTTGGGTATAGGTGTCCAATACAGTAGTGT-CAGACACGAGTTTAAA
131 GGA-CTTGGGTATAGGTGTCCAATACAGTAGTGTAC-GACACAAGTTTAAA
* * * **
53552 GTCGGACTTAGGTACTTCAAG-AAAATGAAGAG-TCTGAGCGTCATAGTTTAGCACGGACTAAAA
1 GTCGGACATAGGTACTTCAAGAAAAATGAAGAGTTC-GAGCATCATAGCTTAGCACAAACTAAAA
* *
53615 CTAGGTAATGGCAGTGATAAAATCTTTATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACT
65 CTAGGTAATGGCAATGATAAAATCTTGATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACT
* **
53680 CGGACTTGGGTATAGGTGTCCATTATGGTAGTGTACGACACAAGTTTA
130 CGGACTTGGGTATAGGTGTCCAATACAGTAGTGTACGACACAAGTTTA
53728 GAGGCCATAT
Statistics
Matches: 158, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
177 2 0.01
178 133 0.84
179 23 0.15
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (179 bp):
GTCGGACATAGGTACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGCACAAACTAAAAC
TAGGTAATGGCAATGATAAAATCTTGATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACTC
GGACTTGGGTATAGGTGTCCAATACAGTAGTGTACGACACAAGTTTAAA
Found at i:54146 original size:215 final size:215
Alignment explanation
Indices: 53768--54274 Score: 696
Period size: 215 Copynumber: 2.4 Consensus size: 215
53758 CACATAGGTT
* ** *
53768 CTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCATGAACTAAAACTAGGTAATGGCAGT
1 CTTCAAGAAAAATGAAGAGTCCTAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGTAGT
* * * *
53833 GATAAAATCTTGATCTCTTTGTTGGAATTTTACATAGCACATATGTTACTCAGATTTGGGTGTAG
66 GATAAAATCTTGATCACTTTGTTAGAAATTTACATAGCACACATGTTACTCAGATTTGGGTGTAG
* * * * **
53898 TTGTCTGATACTGGTGGTGTCTGACATGAGTTTAGAGGTTGTATCTCTGTATTTGTGTGTCAGAC
131 TTGTCCGATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCTGTATTTCAGTGTCAGAC
53963 ATGAGGGTCAGACACAGATA
196 ATGAGGGTCAGACACAGATA
* *
53983 CTTCAAGAAAAATGAAGAATCCTAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGTAGT
1 CTTCAAGAAAAATGAAGAGTCCTAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGTAGT
* * * *
54048 GATAAAATCTTG-TCCACTTAT-TTATAAATTTACTTAGCACCCGTGTTACTCAGATTTGGGTGT
66 GATAAAATCTTGAT-CACTT-TGTTAGAAATTTACATAGCACACATGTTACTCAGATTTGGGTGT
*
54111 AGTTGTCCGATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCTGTATTTCAGTGTCGG
129 AGTTGTCCGATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCTGTATTTCAGTGTCAG
* * *
54176 ACATGAGTGTCAGGCGCAGATA
194 ACATGAGGGTCAGACACAGATA
* * * * * *
54198 CTTCAAGAAAAATGAAGAGT-TTGAGTATCATAGCGTAGGACAAACTAAAATTATGTAATGGTAG
1 CTTCAAGAAAAATGAAGAGTCCT-AGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGTAG
54262 TGATAAAATCTTG
65 TGATAAAATCTTG
54275 GAACATTGTT
Statistics
Matches: 257, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
214 2 0.01
215 254 0.99
216 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (215 bp):
CTTCAAGAAAAATGAAGAGTCCTAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGTAGT
GATAAAATCTTGATCACTTTGTTAGAAATTTACATAGCACACATGTTACTCAGATTTGGGTGTAG
TTGTCCGATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCTGTATTTCAGTGTCAGAC
ATGAGGGTCAGACACAGATA
Found at i:63037 original size:21 final size:22
Alignment explanation
Indices: 63013--63055 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
63003 CAACAGAGTC
63013 GACATCTACTATTTAA-AAAAT
1 GACATCTACTATTTAATAAAAT
* *
63034 GACATTTATTATTTAATAAAAT
1 GACATCTACTATTTAATAAAAT
63056 TATATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (22 bp):
GACATCTACTATTTAATAAAAT
Found at i:69580 original size:31 final size:30
Alignment explanation
Indices: 69513--69580 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
69503 GTTAAAAAAT
* *
69513 AGCAACTT-GACTTTTTTGAAAAGTTGATG
1 AGCAAATTCGACTTTTTTAAAAAGTTGATG
*
69542 ATCAAATTCGACTCTTTTTAAAAAGTTGA-G
1 AGCAAATTCGACT-TTTTTAAAAAGTTGATG
69572 AGCGAAATT
1 AGC-AAATT
69581 TAACTGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.19
30 7 0.22
31 19 0.59
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (30 bp):
AGCAAATTCGACTTTTTTAAAAAGTTGATG
Found at i:69969 original size:24 final size:24
Alignment explanation
Indices: 69929--69974 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
69919 TCCCTCCAAA
* *
69929 ATAATTTCAATGAATTACAAATAT
1 ATAATTTCAATAAATTAAAAATAT
69953 ATAATTTC-ATAATATTAAAAAT
1 ATAATTTCAATAA-ATTAAAAAT
69975 TGAAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATTTCAATAAATTAAAAATAT
Found at i:85534 original size:87 final size:88
Alignment explanation
Indices: 85388--85559 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 88
85378 GTGAAAGAGC
*
85388 AATAAATACTTGCAACCATATATTATGGGAACTATTTGAGTAATCCATCAATAAAATAATACCTC
1 AATAAATACTTGCAACCATATATTATGGGAACTATTTAAGTAATCCATCAATAAAATAATACCTC
85453 CAATTGGGGG-TTCCTGGAGGTT
66 CAATTGGGGGTTTCCTGGAGGTT
*
85475 AATAAATACTTGCAACCATATATTATGGGAACTATTTAAGTAGTCCATCAATAAAATAATACCTC
1 AATAAATACTTGCAACCATATATTATGGGAACTATTTAAGTAATCCATCAATAAAATAATACCTC
85540 CAATTGGGGGTTTCCTGGAG
66 CAATTGGGGGTTTCCTGGAG
85560 TAACCTCCAG
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
87 73 0.89
88 9 0.11
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (88 bp):
AATAAATACTTGCAACCATATATTATGGGAACTATTTAAGTAATCCATCAATAAAATAATACCTC
CAATTGGGGGTTTCCTGGAGGTT
Found at i:88617 original size:34 final size:34
Alignment explanation
Indices: 88574--88642 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
88564 AATGAAAAAC
88574 TAAAACATATTGAACCTAACATTATAGTTATCTT
1 TAAAACATATTGAACCTAACATTATAGTTATCTT
88608 TAAAACATATTGAACCTAACATTATAGTTATCTT
1 TAAAACATATTGAACCTAACATTATAGTTATCTT
88642 T
1 T
88643 TTGAAGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (34 bp):
TAAAACATATTGAACCTAACATTATAGTTATCTT
Found at i:91479 original size:3 final size:3
Alignment explanation
Indices: 91471--91495 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
91461 AGAGATTCCC
91471 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
91496 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:96199 original size:10 final size:11
Alignment explanation
Indices: 96178--96219 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
96168 GATTTGAAGA
*
96178 ATAAAATTAAT
1 ATAAAATAAAT
96189 A-AAAATAAAT
1 ATAAAATAAAT
96199 ATAAAATATAAT
1 ATAAAATA-AAT
96211 GATAAAATA
1 -ATAAAATA
96220 TATTATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 3 0.11
13 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
ATAAAATAAAT
Found at i:96215 original size:13 final size:12
Alignment explanation
Indices: 96178--96226 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
96168 GATTTGAAGA
96178 ATAAAAT-TAAT
1 ATAAAATATAAT
96189 A-AAAATA-AAT
1 ATAAAATATAAT
96199 ATAAAATATAAT
1 ATAAAATATAAT
*
96211 GATAAAATATATT
1 -ATAAAATATAAT
96224 ATA
1 ATA
96227 TTTTTAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.27
11 7 0.21
12 6 0.18
13 11 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:104474 original size:21 final size:22
Alignment explanation
Indices: 104450--104503 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 22
104440 TTACGTGTAC
104450 TTTATATTATATTTTTTAAAT-
1 TTTATATTATATTTTTTAAATA
104471 TTTAT-TT-TATTTTTTAAATA
1 TTTATATTATATTTTTTAAATA
*
104491 TTT-TATAATATTT
1 TTTATATTATATTT
104504 AAAGTATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 13 0.45
20 6 0.21
21 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATATTATATTTTTTAAATA
Found at i:111391 original size:22 final size:22
Alignment explanation
Indices: 111363--111406 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
111353 TACTATGTAT
111363 AAAGTTATAGATTTAGCCTATG
1 AAAGTTATAGATTTAGCCTATG
*
111385 AAAGTTATATATTTAGCCTATG
1 AAAGTTATAGATTTAGCCTATG
111407 TTTTCCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
AAAGTTATAGATTTAGCCTATG
Found at i:120988 original size:31 final size:32
Alignment explanation
Indices: 120923--120992 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
120913 CTTAACAACC
*
120923 CAATGACTTAATTAAAAAACTTTCAAATAATT
1 CAATGACTTAAATAAAAAACTTTCAAATAATT
* * **
120955 CAATGATTTAAAT-AAAAACTTTCATATCGTT
1 CAATGACTTAAATAAAAAACTTTCAAATAATT
120986 CAATGAC
1 CAATGAC
120993 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (32 bp):
CAATGACTTAAATAAAAAACTTTCAAATAATT
Found at i:124078 original size:14 final size:15
Alignment explanation
Indices: 124052--124082 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
124042 CTAACACATT
124052 CAAAGCTAAAAAGCA
1 CAAAGCTAAAAAGCA
124067 CAAAGC-AAAAAGCA
1 CAAAGCTAAAAAGCA
124081 CA
1 CA
124083 TTATCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.61, C:0.23, G:0.13, T:0.03
Consensus pattern (15 bp):
CAAAGCTAAAAAGCA
Found at i:124599 original size:31 final size:30
Alignment explanation
Indices: 124527--124601 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
124517 TATTAGGGGT
* *
124527 TTAATTAAATTTTTAAAATTTTTGAGAAGG
1 TTAATTAAATTTTCAAAATTTTTGAGAAGA
124557 TT-ATTGAAAATTTTCAAAATTTTTTG-GAAGA
1 TTAATT--AAATTTTCAAAA-TTTTTGAGAAGA
124588 TCTAATTAAATTTT
1 T-TAATTAAATTTT
124602 AATCCTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 3 0.08
30 2 0.05
31 23 0.61
32 7 0.18
33 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.48
Consensus pattern (30 bp):
TTAATTAAATTTTCAAAATTTTTGAGAAGA
Found at i:129237 original size:3 final size:3
Alignment explanation
Indices: 129229--129254 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
129219 ATATCATTGA
129229 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
129255 CAATTAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:130638 original size:2 final size:2
Alignment explanation
Indices: 130631--130661 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
130621 TGCCCAAACT
130631 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 T
130662 TGGTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:131336 original size:3 final size:3
Alignment explanation
Indices: 131328--131354 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
131318 GGCTAATATA
131328 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
131355 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:131815 original size:52 final size:52
Alignment explanation
Indices: 131758--131961 Score: 208
Period size: 52 Copynumber: 4.0 Consensus size: 52
131748 AAATTTATAC
131758 ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
1 ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
131810 ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
1 ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
* * * ** * *** **
131862 CATTGATGAAT--T---AT-TATTTTGATTCTT-TCTTT-ATGTTTGAATTTATGC
1 -ACTGAGGAATAATGGAATATAATTAAATTATTAT-TTTAAT-TTT-AAAAAATAA
*
131910 AGTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
1 ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
131962 CATTGATGAA
Statistics
Matches: 118, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
46 3 0.03
47 23 0.19
48 6 0.05
49 1 0.01
51 1 0.01
52 58 0.49
53 23 0.19
54 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (52 bp):
ACTGAGGAATAATGGAATATAATTAAATTATTATTTTAATTTTAAAAAATAA
Found at i:143676 original size:134 final size:134
Alignment explanation
Indices: 143433--143715 Score: 381
Period size: 134 Copynumber: 2.1 Consensus size: 134
143423 GGGGTCAGCG
* * * * *
143433 TACATACATACATACATACAGTATTTACAGCATTTAGATGCAATAAAAGTCATATTCTATCATTT
1 TACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATT
* * * * *
143498 CTGAGGCAAATAATAAATAAGCATCTATGGTTCAATAAATCATTCAGTGACATAACTGCACTATA
66 CTAAGGCAAATAATAAATAACCAACTATGGGTCAATAAATCATTCAGTGACATAACTGCAATATA
143563 CATA
131 CATA
* * *
143567 TATATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCGTATTCTATCAATT
1 TACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATT
* * *
143632 CTAAGGCAAATTATAAA-ATACCAACTATGGGTCAACT-AATCATTCATTGACATAGCTGCAATA
66 CTAAGGCAAATAATAAATA-ACCAACTATGGGTCAA-TAAATCATTCAGTGACATAACTGCAATA
143695 TACATA
129 TACATA
*
143701 TACATGCATACATAT
1 TACATACATACATAT
143716 CTACATATCT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
133 1 0.01
134 127 0.98
135 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (134 bp):
TACATACATACATATAAACAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATT
CTAAGGCAAATAATAAATAACCAACTATGGGTCAATAAATCATTCAGTGACATAACTGCAATATA
CATA
Found at i:143851 original size:154 final size:154
Alignment explanation
Indices: 143566--143945 Score: 421
Period size: 154 Copynumber: 2.5 Consensus size: 154
143556 CACTATACAT
* *
143566 ATATATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCGTATTCTATCAAT
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * * *
143631 TCTAAGGCAAATTATAAAATACCAACTATGGGTCAACTAATCATTCATTGACATAGCTGCAATAT
66 TCTAAGGCAAATCATAAAATACCAACTATGGGTAAACTAATCATTCATTAACATAACTGCAATAT
143696 ACATATACATGCATACATATCTAC
131 ACATATACATGCATACATATCTAC
* * * * * * *
143720 ATATCTACATCCATACATATAGTATTTACAGCATTTATATGCAAGAGAACTCATGTTCTGA-CAG
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCT-ATCAA
* * *
143784 TTCTAAGGCAAATCAT-AAATAAGCAA-TAATGGGTAAACTAGTCATTCATTAACATAATTGCAA
65 TTCTAAGGCAAATCATAAAAT-ACCAACT-ATGGGTAAACTAATCATTCATTAACATAACTGCAA
* *
143847 TATACATATAC-T--ACACAT-GCATAC
128 TATACATATACATGCATACATATC-TAC
* *
143871 --A-A-AC--ACAT--ATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTATCAAT
1 ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* *
143928 TCTAAGGCATATTATAAA
66 TCTAAGGCAAATCATAAA
143946 GAAACCAAAC
Statistics
Matches: 193, Mismatches: 27, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
142 1 0.01
143 55 0.28
144 2 0.01
145 3 0.02
147 2 0.01
149 1 0.01
150 1 0.01
151 8 0.04
153 6 0.03
154 113 0.59
155 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (154 bp):
ATATATACATACATACAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
TCTAAGGCAAATCATAAAATACCAACTATGGGTAAACTAATCATTCATTAACATAACTGCAATAT
ACATATACATGCATACATATCTAC
Found at i:144237 original size:21 final size:23
Alignment explanation
Indices: 144185--144233 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
144175 AATAAAACAT
144185 GGGAAATTGAGAACAACAACAAA
1 GGGAAATTGAGAACAACAACAAA
144208 TGGGAAATTGAGAACAACGAA-AAA
1 -GGGAAATTGAGAACAAC-AACAAA
144232 GG
1 GG
144234 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 2 0.08
24 20 0.83
25 2 0.08
ACGTcount: A:0.53, C:0.10, G:0.27, T:0.10
Consensus pattern (23 bp):
GGGAAATTGAGAACAACAACAAA
Found at i:149255 original size:28 final size:28
Alignment explanation
Indices: 149206--149267 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
149196 AAATGAGACT
* *
149206 TTTTGGATACCCGTGGGTAAAATGGTAA
1 TTTTGGATACCCGGGGGCAAAATGGTAA
* *
149234 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGGGGGCAAAATGGTAA
149262 TTTTGG
1 TTTTGG
149268 GAAAATTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (28 bp):
TTTTGGATACCCGGGGGCAAAATGGTAA
Found at i:149414 original size:59 final size:59
Alignment explanation
Indices: 149349--149577 Score: 207
Period size: 59 Copynumber: 3.9 Consensus size: 59
149339 AAAATATAAA
* * ** * *
149349 TTTTGGACATTCGGGGGTAAAATGGT-ATTTTTCGAGAGTTTCGGGGTCAAAAATGGAGT
1 TTTTGGACATTCGGGGGTAAAAT-ATAATTTTTCGAAAGTTTCAAGGTCAAAAATGAAAT
* * * *
149408 TTTTGGACATCCGGGGGTAAAATGATAATTTTT-GAAAGTTTTAGGGTTAAAAATGAAAT
1 TTTTGGACATTCGGGGGTAAAAT-ATAATTTTTCGAAAGTTTCAAGGTCAAAAATGAAAT
** * * * * *
149467 TTTTGGAGGTTCGAGGGTAAAAATGTAATTTTT-GGAAGTTTTAAGGTCAAAAATAAAAT
1 TTTTGGACATTCGGGGGT-AAAATATAATTTTTCGAAAGTTTCAAGGTCAAAAATGAAAT
* * *
149526 TTTT-GAAAGTTCGGGGGTAAAATATAA-TTTTCGAAAGTTTCGAGATCAAAAA
1 TTTTGGACA-TTCGGGGGTAAAATATAATTTTTCGAAAGTTTCAAGGTCAAAAA
149578 CGACGCGACA
Statistics
Matches: 141, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.03
58 26 0.18
59 100 0.71
60 11 0.08
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (59 bp):
TTTTGGACATTCGGGGGTAAAATATAATTTTTCGAAAGTTTCAAGGTCAAAAATGAAAT
Found at i:149439 original size:29 final size:29
Alignment explanation
Indices: 149339--149502 Score: 81
Period size: 29 Copynumber: 5.6 Consensus size: 29
149329 AATCGAGATA
*
149339 AAAAT-ATAAATTTTGGACATTCGGGGGT
1 AAAATGATAATTTTTGGACATTCGGGGGT
* **
149367 AAAATGGT-ATTTTTCGAGAGTTTC-GGGGT
1 AAAATGATAATTTTT-G-GACATTCGGGGGT
* * *
149396 CAAAAATG-GAGTTTTTGGACATCCGGGGGT
1 --AAAATGATAATTTTTGGACATTCGGGGGT
* ** *
149426 AAAATGATAATTTTT-GAAAGTTTTAGGGTT
1 AAAATGATAATTTTTGGACA--TTCGGGGGT
** *
149456 AAAAATGA-AATTTTTGGAGGTTCGAGGGT
1 -AAAATGATAATTTTTGGACATTCGGGGGT
149485 AAAAATG-TAATTTTTGGA
1 -AAAATGATAATTTTTGGA
149503 AGTTTTAAGG
Statistics
Matches: 101, Mismatches: 22, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
28 19 0.19
29 39 0.39
30 23 0.23
31 20 0.20
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGATAATTTTTGGACATTCGGGGGT
Found at i:149468 original size:30 final size:30
Alignment explanation
Indices: 149426--149536 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
149416 ATCCGGGGGT
149426 AAAATGATAATTTTTGAAAGTTTTAGGGTTA
1 AAAATGA-AATTTTTGAAAGTTTTAGGGTTA
* * **
149457 AAAATGAAATTTTTGGAGGTTCGAGGG-TA
1 AAAATGAAATTTTTGAAAGTTTTAGGGTTA
* * * *
149486 AAAATGTAATTTTTGGAAGTTTTAAGGTCA
1 AAAATGAAATTTTTGAAAGTTTTAGGGTTA
*
149516 AAAATAAAATTTTTGAAAGTT
1 AAAATGAAATTTTTGAAAGTT
149537 CGGGGGTAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.36
30 35 0.53
31 7 0.11
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
AAAATGAAATTTTTGAAAGTTTTAGGGTTA
Found at i:149645 original size:21 final size:21
Alignment explanation
Indices: 149619--149687 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
149609 GTTTTCTTTT
149619 TTATTAATATATTAATTATTA
1 TTATTAATATATTAATTATTA
149640 TTATTAAT-TATTTAATAAATATTA
1 TTATTAATATA-TTAAT---TATTA
*
149664 TCATTAATA-A--AATTATTA
1 TTATTAATATATTAATTATTA
149682 TTATTA
1 TTATTA
149688 TCATTAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
18 10 0.24
20 2 0.05
21 16 0.39
24 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTAATATATTAATTATTA
Found at i:149680 original size:18 final size:16
Alignment explanation
Indices: 149651--149684 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
149641 TATTAATTAT
149651 TTAATAAATATTATCA
1 TTAATAAATATTATCA
*
149667 TTAATAAA-ATTATTA
1 TTAATAAATATTATCA
149682 TTA
1 TTA
149685 TTATCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATAAATATTATCA
Found at i:149686 original size:24 final size:24
Alignment explanation
Indices: 149659--149704 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
149649 ATTTAATAAA
149659 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
149683 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
149705 TAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:149687 original size:18 final size:17
Alignment explanation
Indices: 149639--149687 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
149629 ATTAATTATT
149639 ATTATTAATTATTTAATAA
1 ATTATT-ATTA-TTAATAA
*
149658 A-TATTATCATTAATAAA
1 ATTATTATTATTAAT-AA
149675 ATTATTATTATTA
1 ATTATTATTATTA
149688 TCATTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 14 0.54
19 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTATTATTAATAA
Found at i:151731 original size:3 final size:3
Alignment explanation
Indices: 151725--151759 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
151715 AGAAGAAGAA
* *
151725 GAT GAT GAT GAT GAT GAT GGT GAT GGT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
151760 AGAGTTGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:152835 original size:4 final size:4
Alignment explanation
Indices: 152828--152852 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
152818 TTTTAATTTA
152828 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
152853 TCTTTTAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:154643 original size:91 final size:90
Alignment explanation
Indices: 154482--154679 Score: 261
Period size: 91 Copynumber: 2.2 Consensus size: 90
154472 TTGTATTTTT
* **
154482 ATAAAATGTTTAATGTGGTATCTATGTTTGAAAATATCCAATGTGGTATTTAAACTATCAATGTG
1 ATAAAATGTTTAATGTGGTACCTATGAATGAAAATATCCAATGTGGTATTTAAACTATCAATGTG
* *
154547 CGGATTATTCGGTATCTATACTTTC
66 CGGATTATTCAGTACCTATACTTTC
* ** * *
154572 ATAAAATGTTTAATGTGGTACCTATGCAATGAAAATGTTTAATTTGGTATTTAAACTATCAATTT
1 ATAAAATGTTTAATGTGGTACCTATG-AATGAAAATATCCAATGTGGTATTTAAACTATCAATGT
* *
154637 GTGGATTATTCAGTACCTTTACTTTC
65 GCGGATTATTCAGTACCTATACTTTC
* *
154663 ATAAAATATCTAATGTG
1 ATAAAATGTTTAATGTG
154680 ATACTTGAAC
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 25 0.27
91 68 0.73
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (90 bp):
ATAAAATGTTTAATGTGGTACCTATGAATGAAAATATCCAATGTGGTATTTAAACTATCAATGTG
CGGATTATTCAGTACCTATACTTTC
Found at i:156157 original size:21 final size:21
Alignment explanation
Indices: 156115--156164 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
156105 TTTTTTAAAA
156115 TTTC-TAGTATTTTATTTCTT
1 TTTCTTAGTATTTTATTTCTT
156135 TTTCTTAGTA-TTT-TTTCTT
1 TTTCTTAGTATTTTATTTCTT
*
156154 TTT-TTATTATT
1 TTTCTTAGTATT
156165 ATTTGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 10 0.37
20 7 0.26
21 5 0.19
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTCTTAGTATTTTATTTCTT
Found at i:162293 original size:2 final size:2
Alignment explanation
Indices: 162288--162312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
162278 TGTGTGTGTG
162288 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 T
162313 GGCTCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:186535 original size:21 final size:22
Alignment explanation
Indices: 186511--186551 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
186501 AATTAAAGAG
*
186511 AAAA-TTAATCTTTTTTGTTAA
1 AAAATTTAATCATTTTTGTTAA
*
186532 AAAATTTATTCATTTTTGTT
1 AAAATTTAATCATTTTTGTT
186552 GTTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (22 bp):
AAAATTTAATCATTTTTGTTAA
Found at i:188844 original size:181 final size:182
Alignment explanation
Indices: 188452--188888 Score: 560
Period size: 181 Copynumber: 2.4 Consensus size: 182
188442 TAAAGCTAAT
* * * * * *
188452 AGCAATGACATGTTTTGTATTAA-CCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACGG
1 AGCAATGGCATGTTTTGTATTAATCCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
* ** *** * * * *
188516 AAAATACTACTTTTTTTGCATAAAACAACAAGGAGAACAGAGGGTTGAAACTTGAAATCAAGCGA
66 AAGATACTACTACTACCGCATAAAACAAAAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCAA
** *
188581 TGTAAAATACATCCATGAAACACAGTATCGATCCAAATAACAATCCCGTGAC
131 CATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
*
188633 AGAAATGGCATGTTTTGTATTAAT-CCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
1 AGCAATGGCATGTTTTGTATTAATCCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
*
188697 AAGATACTACTACTACCGCATAAAACAAGAAAGG-GAACAAACGGTTGAAACTTGAAATCATGCA
66 AAGATACTACTACTACCGCATAAAACAA-AAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCA
* * * * *
188761 ACAT-AATTACATCCATGAAACACTGTATCGAGCCAAGTAACGATCCTGTGAC
130 ACATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
* * *
188813 GGCAATGGCATGTTTTGTATTAATCCCCC-TTTTCCCTAATACTTATAGGCCAAAAAGTCTACAG
1 AGCAATGGCATGTTTTGTATTAATCCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
*
188877 GAGATACTACTA
66 AAGATACTACTA
188889 ACAAGGGAAA
Statistics
Matches: 222, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
180 108 0.49
181 110 0.50
182 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (182 bp):
AGCAATGGCATGTTTTGTATTAATCCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
AAGATACTACTACTACCGCATAAAACAAAAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCAA
CATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
Found at i:188854 original size:180 final size:181
Alignment explanation
Indices: 188452--188888 Score: 556
Period size: 180 Copynumber: 2.4 Consensus size: 181
188442 TAAAGCTAAT
* * * * * *
188452 AGCAATGACATGTTTTGTATTAA-CCCCCTTTTTCTCTAATAATTATAGGCAAAAACATCCACGG
1 AGCAATGGCATGTTTTGTATTAATCCCCC-TTTTCTCTAATACTTATAGGCCAAAACGTCTACAG
* ** *** * * * *
188516 AAAATACTACTTTTTTTGCATAAAACAACAAGGAGAACAGAGGGTTGAAACTTGAAATCAAGCGA
65 AAGATACTACTACTACCGCATAAAACAAAAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCAA
** *
188581 TGTAAAATACATCCATGAAACACAGTATCGATCCAAATAACAATCCCGTGAC
130 CATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
* *
188633 AGAAATGGCATGTTTTGTATTAATCCCCTTTTTCTCTAATACTTATAGGCCAAAACGTCTACAGA
1 AGCAATGGCATGTTTTGTATTAATCCCCCTTTTCTCTAATACTTATAGGCCAAAACGTCTACAGA
*
188698 AGATACTACTACTACCGCATAAAACAAGAAAGG-GAACAAACGGTTGAAACTTGAAATCATGCAA
66 AGATACTACTACTACCGCATAAAACAA-AAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCAA
* * * * *
188762 CAT-AATTACATCCATGAAACACTGTATCGAGCCAAGTAACGATCCTGTGAC
130 CATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
* * * *
188813 GGCAATGGCATGTTTTGTATTAATCCCCCTTTTCCCTAATACTTATAGGCCAAAAAGTCTACAGG
1 AGCAATGGCATGTTTTGTATTAATCCCCCTTTTCTCTAATACTTATAGGCCAAAACGTCTACAGA
188878 AGATACTACTA
66 AGATACTACTA
188889 ACAAGGGAAA
Statistics
Matches: 221, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
180 112 0.51
181 101 0.46
182 8 0.04
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (181 bp):
AGCAATGGCATGTTTTGTATTAATCCCCCTTTTCTCTAATACTTATAGGCCAAAACGTCTACAGA
AGATACTACTACTACCGCATAAAACAAAAAGGAGAACAAACGGTTGAAACTTGAAATCAAGCAAC
ATAAAATACATCCATGAAACACAGTATCGAGCCAAATAACAATCCCGTGAC
Found at i:190214 original size:16 final size:16
Alignment explanation
Indices: 190204--190234 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
190194 AAATTGAATC
190204 AAATCAAAATTACATA
1 AAATCAAAATTACATA
190220 AAATCAAAATT-CATA
1 AAATCAAAATTACATA
190235 TATGATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATCAAAATTACATA
Found at i:192854 original size:18 final size:18
Alignment explanation
Indices: 192824--192876 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
192814 CAATTAATGT
*
192824 ATATTTAAATTTGATTTTA
1 ATATTT-AATTTGATATTA
192843 ATATTTAATTTGATATTA
1 ATATTTAATTTGATATTA
192861 A-A-TTAATTTG-TATTA
1 ATATTTAATTTGATATTA
192876 A
1 A
192877 AAATGTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 6 0.18
16 8 0.24
17 1 0.03
18 12 0.36
19 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
ATATTTAATTTGATATTA
Found at i:193073 original size:42 final size:44
Alignment explanation
Indices: 193026--193112 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
193016 TTTATTTTAT
193026 TTTCTAAGGTTATTTAATT-TT-AAAAAAATTATGATAAAATAA
1 TTTCTAAGGTTATTTAATTCTTAAAAAAAATTATGATAAAATAA
193068 TTTCTAAGGTTATTTAATTCTTAAAAAAAATTATGATAAAATAA
1 TTTCTAAGGTTATTTAATTCTTAAAAAAAATTATGATAAAATAA
193112 T
1 T
193113 AATTTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 19 0.44
43 2 0.05
44 22 0.51
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (44 bp):
TTTCTAAGGTTATTTAATTCTTAAAAAAAATTATGATAAAATAA
Done.