Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008806.1 Hibiscus syriacus cultivar Beakdansim tig00111959_pilon, 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: 454619
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:168 original size:19 final size:20
Alignment explanation
Indices: 114--180 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
104 TAGTTTACTT
* *
114 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
134 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
154 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
173 TCGCAACG
1 TCGCAACG
181 ACAAAATTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:211 original size:32 final size:33
Alignment explanation
Indices: 153--243 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
143 GGAAATGGCT
153 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
186 ATTGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
218 ATCGCAACGCGAAAAGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
244 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:232 original size:14 final size:14
Alignment explanation
Indices: 169--226 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
159 ATGCGAAATG
169 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
183 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
199 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
215 AAAATCGCAACG
1 AAAATCGCAACG
227 CGAAAAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:279 original size:14 final size:14
Alignment explanation
Indices: 260--317 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
250 TTGTGTTTCG
260 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
274 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
290 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
306 CGTTGCGATTTT
1 CGTTGCGATTTT
318 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:294 original size:32 final size:33
Alignment explanation
Indices: 255--333 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
245 GCGATTTGTG
255 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
287 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
320 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
334 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:332 original size:19 final size:19
Alignment explanation
Indices: 274--391 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
264 GCGATTTTGT
274 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
292 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
306 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
325 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
345 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
364 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
384 TGTTGCGA
1 CGTTGCGA
392 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2238 original size:14 final size:14
Alignment explanation
Indices: 2219--2254 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2209 ATTGTTTAAT
2219 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2233 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2247 TGATTTGT
1 TGATTTGT
2255 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2393 original size:19 final size:19
Alignment explanation
Indices: 2371--2439 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2361 ATCGCAACGA
2371 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2390 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
* *
2409 GAAAATCACAA-ACG--A-
1 GAAAATCGCAATGCGAAAT
2424 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2440 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.23
16 3 0.07
18 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2483 original size:20 final size:20
Alignment explanation
Indices: 2458--2495 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2448 TCGCATTGCG
*
2458 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2478 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2496 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3557 original size:24 final size:24
Alignment explanation
Indices: 3530--3583 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3520 GTATTCGAAA
* *
3530 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
3554 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
3578 TTTGAT
1 TTTGAT
3584 GATGTTCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:6068 original size:19 final size:19
Alignment explanation
Indices: 6046--6176 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
6036 GGAAATTACT
6046 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6065 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6079 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
6098 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
6112 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
6131 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
6145 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6164 ATCGCAACGCGAA
1 ATCGCAATGCGAA
6177 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6088 original size:33 final size:33
Alignment explanation
Indices: 6046--6172 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
6036 GGAAATTACT
6046 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
6079 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
6111 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
6145 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
6173 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:6153 original size:66 final size:66
Alignment explanation
Indices: 6047--6179 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
6037 GAAATTACTA
*
6047 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
6112 T
66 T
*
6113 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
6178 T
66 T
6179 T
1 T
6180 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:6350 original size:14 final size:14
Alignment explanation
Indices: 6331--6367 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6321 CATCAATTAA
6331 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6345 ACAAATCACCTTTT
1 ACAAATCAACTTTT
6359 ACAAATCAA
1 ACAAATCAA
6368 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:9873 original size:20 final size:19
Alignment explanation
Indices: 9828--9886 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
9818 TCTTTTGGTT
9828 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
9847 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
9868 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
9887 TAGAATCGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:9908 original size:13 final size:13
Alignment explanation
Indices: 9877--9918 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
9867 GGAAATGACT
*
9877 ATCGCAACGATAGA
1 ATCGCAACGAGA-A
9891 ATCGCAACGAGAA
1 ATCGCAACGAGAA
*
9904 ATCGCAACGCGAA
1 ATCGCAACGAGAA
9917 AT
1 AT
9919 GACTATCGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.12
Consensus pattern (13 bp):
ATCGCAACGAGAA
Found at i:9920 original size:46 final size:48
Alignment explanation
Indices: 9854--9967 Score: 151
Period size: 46 Copynumber: 2.4 Consensus size: 48
9844 CGAGATAATG
* * *
9854 AGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGAG-
1 AGAATCGCAACGC-GAAATGACTATCGCAACCAGACAATCGCAACGAGA
* *
9902 A-AATCGCAACGCGAAATGACTATCGCGACCAGACAATCGCAACGCGA
1 AGAATCGCAACGCGAAATGACTATCGCAACCAGACAATCGCAACGAGA
9949 ATGAATCGCAACGCGAAAT
1 A-GAATCGCAACGCGAAAT
9968 AAAAATCGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
46 29 0.50
47 12 0.21
48 1 0.02
49 16 0.28
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (48 bp):
AGAATCGCAACGCGAAATGACTATCGCAACCAGACAATCGCAACGAGA
Found at i:9957 original size:16 final size:17
Alignment explanation
Indices: 9836--9989 Score: 78
Period size: 19 Copynumber: 9.1 Consensus size: 17
9826 TTGAAATGAA
*
9836 AATCGCAACGAGATAATGAG
1 AATCGCAACGCGA-AAT--G
9856 AATCGCAACGCGGAAATG
1 AATCGCAACGC-GAAATG
*
9874 ACTATCGCAA--CGATA-G
1 A--ATCGCAACGCGAAATG
*
9890 AATCGCAA--CGAGA--
1 AATCGCAACGCGAAATG
9903 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
* * *
9920 ACTATCGCGAC-C-AGA-C
1 A--ATCGCAACGCGAAATG
9936 AATCGCAACGCG-AATG
1 AATCGCAACGCGAAATG
*
9952 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAAT--G
9971 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
9988 AA
1 AA
9990 AATCGCAATG
Statistics
Matches: 107, Mismatches: 12, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
13 8 0.07
14 18 0.17
15 6 0.06
16 15 0.14
17 11 0.10
18 4 0.04
19 23 0.21
20 20 0.19
21 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.12
Consensus pattern (17 bp):
AATCGCAACGCGAAATG
Found at i:9976 original size:19 final size:18
Alignment explanation
Indices: 9936--10002 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
9926 GCGACCAGAC
*
9936 AATCGCAACGCG-AAT-G
1 AATCGCAACGCGAAATAA
9952 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAAT-AA
9971 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAAT-AA
*
9990 AATCGCAATGCGA
1 AATCGCAACGCGA
10003 TTTTGTTTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 12 0.27
17 3 0.07
19 30 0.67
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:10030 original size:19 final size:19
Alignment explanation
Indices: 9998--10062 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
9988 AAAATCGCAA
*
9998 TGCGA-TTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
10016 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
10035 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
10055 TGCGATTT
1 TGCGATTT
10063 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 4 0.11
19 23 0.61
20 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:10602 original size:20 final size:20
Alignment explanation
Indices: 10577--10629 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
10567 GCGCTATGTA
10577 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
10597 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
10617 TATCTCGTTGCGA
1 AATCGCGTTGCGA
10630 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:10649 original size:41 final size:40
Alignment explanation
Indices: 10584--10690 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
10574 GTAAATCGCG
* * * * * *
10584 TTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT-CG
1 TTGCGATAGTTAGTATCGCATTGCGAAAGTAAGTAT-TGCA
** * *
10624 TTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATTGCA
1 TTGCGATAGT-TAGTATCGCATTGCGAAAGTAAGTATTGCA
10665 TTGCGATAGTTAGTATCGCATTGCGA
1 TTGCGATAGTTAGTATCGCATTGCGA
10691 TTTTCCCAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
40 23 0.44
41 29 0.56
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (40 bp):
TTGCGATAGTTAGTATCGCATTGCGAAAGTAAGTATTGCA
Found at i:10667 original size:20 final size:20
Alignment explanation
Indices: 10638--10691 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
10628 GATTTTGTAT
10638 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
10658 TATTGCATTGCGATAGTTAG
1 TATCGCATTGCGATAGTAAG
10678 TATCGCATTGCGAT
1 TATCGCATTGCGAT
10692 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:10802 original size:21 final size:21
Alignment explanation
Indices: 10762--10802 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10752 ACTGTATACC
**
10762 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
10783 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
10803 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:15174 original size:16 final size:17
Alignment explanation
Indices: 15153--15187 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
15143 TTCACCAAGG
*
15153 TAATTCTTTTAT-TCCT
1 TAATTCTTCTATGTCCT
15169 TAATTCTTCTATGTCCT
1 TAATTCTTCTATGTCCT
15186 TA
1 TA
15188 GCCAAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (17 bp):
TAATTCTTCTATGTCCT
Found at i:20344 original size:30 final size:31
Alignment explanation
Indices: 20308--20367 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20298 CTTAGCTTTA
**
20308 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
20338 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
20368 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:21288 original size:19 final size:20
Alignment explanation
Indices: 21264--21314 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
21254 CGGCCAAGAG
* *
21264 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
21283 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
21303 CATGTATTTTCA
1 CATGTATTTTCA
21315 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:24515 original size:30 final size:31
Alignment explanation
Indices: 24479--24538 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
24469 CTTAGCTTTA
**
24479 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
24509 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
24539 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:25438 original size:19 final size:20
Alignment explanation
Indices: 25414--25464 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
25404 CGGCCAAGAG
* * *
25414 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAA
25433 CATGTATTTTCATCAAAAAA
1 CATGTATTTTCATCAAAAAA
25453 CATGTATTTTCA
1 CATGTATTTTCA
25465 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAA
Found at i:26115 original size:27 final size:27
Alignment explanation
Indices: 26085--26141 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
26075 ATAAGTATAT
26085 ATTTATTTATTATTAATTATATAAAAA
1 ATTTATTTATTATTAATTATATAAAAA
26112 ATTTATTTATTATTAATTATATAAAAA
1 ATTTATTTATTATTAATTATATAAAAA
26139 ATT
1 ATT
26142 AAATAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTATTTATTATTAATTATATAAAAA
Found at i:26152 original size:27 final size:27
Alignment explanation
Indices: 26095--26152 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
26085 ATTTATTTAT
* * * *
26095 TATTAATTATATAAAAAATTTATTTAT
1 TATTAATTATATAAAAAATTAAATAAA
26122 TATTAATTATATAAAAAATTAAATAAA
1 TATTAATTATATAAAAAATTAAATAAA
26149 TATT
1 TATT
26153 TCTGTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTAATTATATAAAAAATTAAATAAA
Found at i:27154 original size:7 final size:7
Alignment explanation
Indices: 27142--27176 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
27132 ATATATATAT
27142 TTTTTTA
1 TTTTTTA
27149 TTTTTTA
1 TTTTTTA
27156 -TTTTTA
1 TTTTTTA
27162 TTTTTTA
1 TTTTTTA
27169 TTTTTTA
1 TTTTTTA
27176 T
1 T
27177 AAATAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:27161 original size:13 final size:13
Alignment explanation
Indices: 27143--27173 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
27133 TATATATATT
27143 TTTTTATTTTTTA
1 TTTTTATTTTTTA
27156 TTTTTATTTTTTA
1 TTTTTATTTTTTA
27169 TTTTT
1 TTTTT
27174 TATAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:27462 original size:18 final size:18
Alignment explanation
Indices: 27441--27497 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
27431 TTTAAAAAGT
27441 AATTTATATATAAAATTA
1 AATTTATATATAAAATTA
* ** *
27459 AATTTATAAATAGGATTT
1 AATTTATATATAAAATTA
*
27477 AATATATATATAAAATATA
1 AATTTATATATAAAAT-TA
27496 AA
1 AA
27498 ATTAAGTAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 26 0.90
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AATTTATATATAAAATTA
Found at i:27495 original size:43 final size:43
Alignment explanation
Indices: 27448--27530 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
27438 AGTAATTTAT
**
27448 ATATAAAATTAAATTTATAAATAGGATTTAATATATATATAAA
1 ATATAAAATTAAATAAATAAATAGGATTTAATATATATATAAA
* ** *
27491 ATATAAAATTAAGTAAATAAATATTATTTATTATATATAT
1 ATATAAAATTAAATAAATAAATAGGATTTAATATATATAT
27531 TTATATGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (43 bp):
ATATAAAATTAAATAAATAAATAGGATTTAATATATATATAAA
Found at i:29141 original size:9 final size:9
Alignment explanation
Indices: 29127--29192 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
29117 AATATTTATT
29127 TAATAATTA
1 TAATAATTA
*
29136 TAATAAATA
1 TAATAATTA
29145 TAATAA-TA
1 TAATAATTA
*
29153 GTAATAATAA
1 -TAATAATTA
29163 TAATAA-TA
1 TAATAATTA
*
29171 CTAATAATAA
1 -TAATAATTA
*
29181 TAATAATAA
1 TAATAATTA
29190 TAA
1 TAA
29193 AAATAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 3 0.06
9 44 0.90
10 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
TAATAATTA
Found at i:29157 original size:6 final size:6
Alignment explanation
Indices: 29127--29205 Score: 97
Period size: 6 Copynumber: 13.2 Consensus size: 6
29117 AATATTTATT
* * *
29127 TAATAA TTATAA TAA-ATA TAATAA TAGTAA TAATAA TAATAA TACTAA
1 TAATAA TAATAA TAATA-A TAATAA TAATAA TAATAA TAATAA TAATAA
* *
29175 TAATAA TAATAA TAATAA AAATAA AAATAA T
1 TAATAA TAATAA TAATAA TAATAA TAATAA T
29206 GAATGGACAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
5 1 0.02
6 61 0.97
7 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (6 bp):
TAATAA
Found at i:29197 original size:9 final size:9
Alignment explanation
Indices: 29135--29205 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
29125 TTTAATAATT
*
29135 ATAATAAAT
1 ATAATAAAA
29144 ATAATAATAGTA
1 ATAATAA-A--A
*
29156 ATAATAATA
1 ATAATAAAA
**
29165 ATAATACTA
1 ATAATAAAA
*
29174 ATAATAATA
1 ATAATAAAA
29183 ATAATAATAA
1 ATAATAA-AA
29193 A-AATAAAA
1 ATAATAAAA
29201 ATAAT
1 ATAAT
29206 GAATGGACAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
8 3 0.06
9 39 0.75
10 3 0.06
12 7 0.13
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAATAAAA
Found at i:29558 original size:122 final size:121
Alignment explanation
Indices: 29410--29861 Score: 502
Period size: 122 Copynumber: 3.7 Consensus size: 121
29400 TGTAATCTAG
* * *
29410 CAAAAAGTTGAACAAGTTATTCTCATTATGAATTTCTTCTTCGTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
*
29475 CATGAACTCTTCTGGAAATGTTGATGTTGAACTATCTCCTTCTGTGATAGAGTCATT
66 TATGAACTCTTCTGGAAATGTTGATGTTG-ACTATCTCCTTCTGTGATAGAGTCATT
* *
29532 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCCTCTTCAGATAAGTTCT
1 CAAAAGGTTGAACAAGTTATTCTCATTATGAA------CTTCTTCTTCCTCTTCAGATGAGTTCT
* * * *
29597 TCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCTTTCTGTGATAGAGTCATG
60 TCTCATTATGAACTCT-TCTGGAAATGTTGATGTTGA-CTATCTCCTTCTGTGATAGAGTCATT
29661 C-AAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
* * * * *
29725 TATGAAATTCCTCTGGAAA---TGA---TG---A--TCCATCGAGTGAT-GAAT--TT
66 TATG-AACTCTTCTGGAAATGTTGATGTTGACTATCTCCTTC-TGTGATAGAGTCATT
* *
29769 GAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTC
1 ---CAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTC
*
29834 TCATTATGAACTCTTCTGGAAATATTGA
62 TCATTATGAACTCTTCTGGAAATGTTGA
29862 AAACATTCTG
Statistics
Matches: 288, Mismatches: 24, Indels: 43
0.81 0.07 0.12
Matches are distributed among these distances:
108 1 0.00
110 7 0.02
111 6 0.02
112 53 0.18
113 25 0.09
115 3 0.01
116 2 0.01
119 3 0.01
122 74 0.26
123 3 0.01
128 68 0.24
129 43 0.15
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (121 bp):
CAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTTCTGGAAATGTTGATGTTGACTATCTCCTTCTGTGATAGAGTCATT
Found at i:31124 original size:54 final size:54
Alignment explanation
Indices: 31021--31143 Score: 131
Period size: 54 Copynumber: 2.3 Consensus size: 54
31011 TTATTGGTTC
* * ** * * *
31021 GTAAAACACTTGACAACACATTCATCATTTCCTGTGGTTTCTGCCCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCATTTCATGTGGCCTCCGCACAGATGTAT
* * * *
31075 GTAAAACATTTGATAACATATTCATCTTTTCATGTGGCCTCCGTACAGATGTAT
1 GTAAAACATTTGACAACACATTCATCATTTCATGTGGCCTCCGCACAGATGTAT
31129 GTAAAA-ATTTTGACA
1 GTAAAACA-TTTGACA
31144 GTACATTAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATTTCATGTGGCCTCCGCACAGATGTAT
Found at i:32178 original size:75 final size:75
Alignment explanation
Indices: 32048--32213 Score: 217
Period size: 75 Copynumber: 2.2 Consensus size: 75
32038 ATGGATGTTT
* * *
32048 AGCATGCCTCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCTTGATTCTGATTGAA
1 AGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATTGAA
*
32113 AGGGGCTTTC
66 AGGGACTTTC
* * ** *
32123 AGCATGCCCCAACATTGGCTAATACAAATGTTCAAAA-AGTGTCAATATTCCTGATTATGATTGA
1 AGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATA-CATCAACATTCCTGATTATGATTGA
*
32187 AATGGACTTTC
65 AAGGGACTTTC
*
32198 AGCATGCTCCATCATT
1 AGCATGCCCCATCATT
32214 TACTTCTTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 1 0.01
75 77 0.99
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (75 bp):
AGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATTGAA
AGGGACTTTC
Found at i:35949 original size:9 final size:10
Alignment explanation
Indices: 35911--35944 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
35901 TTTGATTCAA
35911 TTTTTTCC--
1 TTTTTTCCTT
35919 TTTTTTCCTT
1 TTTTTTCCTT
35929 TTTTTTCCTT
1 TTTTTTCCTT
35939 TTTTTT
1 TTTTTT
35945 GTTTTGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:42020 original size:17 final size:17
Alignment explanation
Indices: 42000--42050 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
41990 CAAAAATAAT
*
42000 AATAAAATAAT-ATTGTA
1 AATAAAATAATGATT-AA
42017 AAT-AAATAATGATTAA
1 AATAAAATAATGATTAA
42033 AATAAAATAA--ATTAA
1 AATAAAATAATGATTAA
42048 AAT
1 AAT
42051 TATAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 8 0.26
16 11 0.35
17 12 0.39
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
AATAAAATAATGATTAA
Found at i:43507 original size:3 final size:3
Alignment explanation
Indices: 43501--43567 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
43491 AATATTTATT
* *
43501 TAA TAA TTA TAA TAA -ATA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
43546 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
43568 GAATGGACAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:51232 original size:3 final size:3
Alignment explanation
Indices: 51219--51252 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
51209 GTTTGCACAA
*
51219 AAT ATT AAT AAT AATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
51253 TTAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:51243 original size:16 final size:16
Alignment explanation
Indices: 51219--51249 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51209 GTTTGCACAA
*
51219 AATATTAATAATAATT
1 AATAATAATAATAATT
51235 AATAATAATAATAAT
1 AATAATAATAATAAT
51250 AATTTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATAATAATT
Found at i:51246 original size:19 final size:20
Alignment explanation
Indices: 51219--51258 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
51209 GTTTGCACAA
*
51219 AATATTAATAATAA-TTAAT
1 AATAATAATAATAATTTAAT
51238 AATAATAATAATAATTTAAT
1 AATAATAATAATAATTTAAT
51258 A
1 A
51259 TTTTTGGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATAATAATTTAAT
Found at i:51769 original size:91 final size:92
Alignment explanation
Indices: 51659--51833 Score: 246
Period size: 92 Copynumber: 1.9 Consensus size: 92
51649 GTGATAGGTC
* * *
51659 GAACAAGCTCTTCTCATTATGAAC-TTCTTCTCCCTCTTTCGGATGATTTCTTCT-ATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTTCTTCTCCCTCGTT-AGATGAGTTCTTCTCATTATGAAC
51722 TCTCCATTGAAAATATTGATGCAAAGTT
65 TCTCCATTGAAAATATTGATGCAAAGTT
* * * *
51750 GAACAAGTTCTTCTCATTATGAACTTTTTTCTTCCTCGTTAGATGAGTTCTTTTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTTCTTCTCCCTCGTTAGATGAGTTCTTCTCATTATGAACT
* *
51815 CTCCATTGGAAATGTTGAT
66 CTCCATTGAAAATATTGAT
51834 CCATCTCTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
91 34 0.47
92 39 0.53
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTTCTTCTCCCTCGTTAGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATATTGATGCAAAGTT
Found at i:52107 original size:135 final size:134
Alignment explanation
Indices: 51866--52157 Score: 442
Period size: 135 Copynumber: 2.2 Consensus size: 134
51856 TGAAAGGAAC
51866 AAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTAATTCGA
1 AAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTAATTCGA
* * * *
51931 AATGCCGTGAATCGAGTGATAGGTCGAATAAGCTATTCTCATTATGAACTTCTTCTCCCTC-GTT
66 AATGCCATGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATGAACTTCTTCTCCCTCTGTC
51995 GGAT
131 GGAT
* * ** * * *
51999 GAGTTCTTCTCATTATAAACTCTTCACTGAAAATGTTGATTCCTCAAGCGAGGTGTGACTGATTC
1 AAGTTCTTCTCATTATGAACTCTT--CTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTAATTC
* *
52064 GAAATGTCATGAATCGAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
64 GAAATGCCATGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATGAACTTCTTCTCCCTCTG
52129 TCGGAT
129 TCGGAT
52135 AAGTTCTTCTCATTATGAACTCT
1 AAGTTCTTCTCATTATGAACTCT
52158 CCATGGAAAC
Statistics
Matches: 141, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
133 22 0.16
135 92 0.65
136 27 0.19
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (134 bp):
AAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTAATTCGA
AATGCCATGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATGAACTTCTTCTCCCTCTGTC
GGAT
Found at i:52401 original size:225 final size:226
Alignment explanation
Indices: 51966--52379 Score: 573
Period size: 225 Copynumber: 1.8 Consensus size: 226
51956 GAATAAGCTA
* * *
51966 TTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATAAACTCTTCACTGAAA
1 TTCTCATTATAAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATAAACTCTTAACTGAAA
** * * * * * * * *
52031 ATGTTGATTCCTCAAGCGAGGTGTGACTGATTCGAAATGTCATGAATCGAGTGATAGGTCAAACA
66 ATGTCAATCCCTAAAGAGAGGCGTCACTGATTCAAAATGCCATAAATCGAGTGATAGGTCAAACA
* * *
52096 AGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATAAGTTCTTCTCATTATGAACTCTCCA
131 AGCTATTCTCATTATGAACTTCTTCTCCCTCTATCGGATAAGTTATTCTCATTATGAACTCTCCA
52161 TGGAAACACTGATATGAGATCGAACAAGTTC
196 TGGAAACACTGATATGAGATCGAACAAGTTC
* * * *
52192 TTCTTATTATAAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTCATTATGAACTCTTAA-TTAGA
1 TTCTCATTATAAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATAAACTCTTAACTGA-A
* *
52256 AAT-TCAATCCCTAAAGAGAGGCGTCACTGATTCAAAATGCCGTAAATCGAGTGATAGGTCGAAC
65 AATGTCAATCCCTAAAGAGAGGCGTCACTGATTCAAAATGCCATAAATCGAGTGATAGGTCAAAC
* * *
52320 AAGCTATTCTCATTATGAATTTTTTCTCCCTCTATCGGATGAG-TATTCTCATTATGAACT
130 AAGCTATTCTCATTATGAACTTCTTCTCCCTCTATCGGATAAGTTATTCTCATTATGAACT
52380 TTGTACTGGA
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
224 16 0.10
225 89 0.55
226 57 0.35
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (226 bp):
TTCTCATTATAAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATAAACTCTTAACTGAAA
ATGTCAATCCCTAAAGAGAGGCGTCACTGATTCAAAATGCCATAAATCGAGTGATAGGTCAAACA
AGCTATTCTCATTATGAACTTCTTCTCCCTCTATCGGATAAGTTATTCTCATTATGAACTCTCCA
TGGAAACACTGATATGAGATCGAACAAGTTC
Found at i:52928 original size:40 final size:40
Alignment explanation
Indices: 52840--53156 Score: 550
Period size: 40 Copynumber: 8.0 Consensus size: 40
52830 TGTCTCAAGC
* * * * *
52840 GAGATAAAATCTTTTGTTTCGAGG--AAACTATC-TAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
52877 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
52917 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
52957 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
52997 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
53037 GAGATAAAATCTTCTGTTTCAATGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
53077 GAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
53117 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
53157 CAAATGAAAT
Statistics
Matches: 268, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
37 22 0.08
39 7 0.03
40 239 0.89
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:53145 original size:20 final size:20
Alignment explanation
Indices: 53082--53145 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
53072 TGAGTGAGAT
53082 AAAATCTTCTGTTTCAAGGA
1 AAAATCTTCTGTTTCAAGGA
** ** *
53102 AAAATAATCTTGAGT-GA-GA
1 AAAATCTTC-TGTTTCAAGGA
53121 TAAAATCTTCTGTTTCAAGGA
1 -AAAATCTTCTGTTTCAAGGA
53142 AAAA
1 AAAA
53146 CAATCTTGAG
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
AAAATCTTCTGTTTCAAGGA
Found at i:58358 original size:14 final size:13
Alignment explanation
Indices: 58339--58422 Score: 59
Period size: 14 Copynumber: 6.5 Consensus size: 13
58329 AAACATAATT
58339 ATGCAAAGATGAAA
1 ATGCAAA-ATGAAA
*
58353 ATGC-AAATGCAA
1 ATGCAAAATGAAA
58365 ATGCAAAA--AAA
1 ATGCAAAATGAAA
*
58376 ATG-AAAATGTAA
1 ATGCAAAATGAAA
* * *
58388 ATACAAACGTAAAA
1 ATGCAAA-ATGAAA
*
58402 ATGCAAAGATGCAA
1 ATGCAAA-ATGAAA
58416 ATGCAAA
1 ATGCAAA
58423 TGCAAATGGA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
10 4 0.08
11 5 0.09
12 13 0.25
13 8 0.15
14 23 0.43
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGCAAAATGAAA
Found at i:58362 original size:6 final size:6
Alignment explanation
Indices: 58351--58450 Score: 67
Period size: 6 Copynumber: 16.2 Consensus size: 6
58341 GCAAAGATGA
** * * * **
58351 AAATGC AAATGC AAATGC AAA-AA AAATGA AAATGT AAATAC AAACGTAA
1 AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAA--TGC
* * *
58400 AAATGC AAAGATGC AAATGC AAATGC AAATGG AAATGG AAATGG AAATGC
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC
58450 A
1 A
58451 GAAGGTATCG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
5 3 0.04
6 62 0.79
7 4 0.05
8 9 0.12
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:66717 original size:21 final size:20
Alignment explanation
Indices: 66689--66727 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
66679 TTAATTTATT
*
66689 TTTGTATTTTGAATATTTGG
1 TTTGTATTTTGAAAATTTGG
66709 TTTGTTATTTTGAAAATTT
1 TTTG-TATTTTGAAAATTT
66728 TCCTTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
TTTGTATTTTGAAAATTTGG
Found at i:70788 original size:12 final size:12
Alignment explanation
Indices: 70771--70868 Score: 56
Period size: 12 Copynumber: 8.0 Consensus size: 12
70761 TAATATATAG
70771 TTTTGAAAACAT
1 TTTTGAAAACAT
*
70783 TTTTGAAAAGAT
1 TTTTGAAAACAT
* * * *
70795 ATAT-AATATATAG
1 TTTTGAA-A-ACAT
70808 TTTTGAAAACAT
1 TTTTGAAAACAT
*
70820 TTTTGAAAAGAT
1 TTTTGAAAACAT
* * * *
70832 ATAT-AATATATAG
1 TTTTGAA-A-ACAT
70845 TTTTGAAAACAT
1 TTTTGAAAACAT
70857 TTTTGAAAACAT
1 TTTTGAAAACAT
70869 ATATAATATA
Statistics
Matches: 62, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
11 4 0.06
12 44 0.71
13 10 0.16
14 4 0.06
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:70796 original size:37 final size:37
Alignment explanation
Indices: 70720--71013 Score: 434
Period size: 37 Copynumber: 8.0 Consensus size: 37
70710 TACATAATAT
*
70720 ATATATAATATATAGTTTTGAACACA-TTTTGAAAAG
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
70756 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
70793 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
*
70830 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
*
70867 ATATATAATATATAGTTTTGAAAACA-TTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
* * *
70903 ATATATAATATATAATTTTGAAAACATTTTGGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
* * * *
70940 ATATATAATATA-AATTTAGAAAACAATTTTGAAAAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTG-AAAAG
*
70977 ATATATAATATA-AGGTTTTGAAAATATTTTTCGAAAA
1 ATATATAATATATA-GTTTTGAAAACATTTTT-GAAAA
71014 TATAATATTA
Statistics
Matches: 240, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
36 75 0.31
37 147 0.61
38 17 0.07
39 1 0.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
Found at i:70883 original size:147 final size:148
Alignment explanation
Indices: 70720--71013 Score: 459
Period size: 147 Copynumber: 2.0 Consensus size: 148
70710 TACATAATAT
* *
70720 ATATATAATATATAGTTTTGAACACATTTTGAAAAGATATATAATATATAGTTTTGAAAACATTT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATAATATATAATTTTGAAAACATTT
* * * * *
70785 TTGAAAAGATATATAATATATAGTTTTGAAAACATTTTTG-AAAAGATATATAATATATA-GTTT
66 TGGAAAAGATATATAATATA-AATTTAGAAAACAATTTTGAAAAAAATATATAATATA-AGGTTT
70848 TGAAAACATTTTT-GAAAAC
129 TGAAAACATTTTTCGAAAAC
*
70867 ATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAATTTTGAAAACATTT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATAATATATAATTTTGAAAACATTT
*
70932 TGGAAAATATATATAATATAAATTTAGAAAACAATTTTGAAAAAAATATATAATATAAGGTTTTG
66 TGGAAAAGATATATAATATAAATTTAGAAAACAATTTTGAAAAAAATATATAATATAAGGTTTTG
*
70997 AAAATATTTTTCGAAAA
131 AAAACATTTTTCGAAAA
71014 TATAATATTA
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
146 17 0.13
147 112 0.84
148 5 0.04
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (148 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATAATATATAATTTTGAAAACATTT
TGGAAAAGATATATAATATAAATTTAGAAAACAATTTTGAAAAAAATATATAATATAAGGTTTTG
AAAACATTTTTCGAAAAC
Found at i:70913 original size:110 final size:110
Alignment explanation
Indices: 70720--71017 Score: 440
Period size: 110 Copynumber: 2.7 Consensus size: 110
70710 TACATAATAT
* *
70720 ATATATAATATATAGTTTTGAACACATTTTGAAAAGATATATAATATATAGTTTTGAAAACATTT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAAATATATAATATATAGTTTTGAAAACATTT
* * *
70785 TTGAAAAGATATATAATATATAGTTTTGAAAACATTTTTGAAAAG
66 TTGAAAATATATATAATATATAATTTTGAAAACATTTTGGAAAAG
*
70830 ATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTGAAAACA-T
1 ATATATAATATATAGTTTTGAAAACA-TTTTGAAAAAATATATAATATATAGTTTTGAAAACATT
*
70894 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTGGAAAAT
65 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTGGAAAAG
* * *
70940 ATATATAATATA-AATTTAGAAAACAATTTTGAAAAAAATATATAATATA-AGGTTTTGAAAATA
1 ATATATAATATATAGTTTTGAAAAC-ATTTTG-AAAAAATATATAATATATA-GTTTTGAAAACA
71003 TTTTTCGAAAATATA
63 TTTTT-GAAAATATA
71018 ATATTATTTT
Statistics
Matches: 172, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
109 16 0.09
110 108 0.63
111 39 0.23
112 9 0.05
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (110 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAAAATATATAATATATAGTTTTGAAAACATTT
TTGAAAATATATATAATATATAATTTTGAAAACATTTTGGAAAAG
Found at i:80468 original size:195 final size:195
Alignment explanation
Indices: 80237--80619 Score: 581
Period size: 195 Copynumber: 2.0 Consensus size: 195
80227 TACAGCATAG
* ** * *
80237 CTCAAGGTGATAAGGTTTATTTGTCAACGAAAACTTTCGAGTTCGATTCCATTCAGCTCAAAGAC
1 CTCAAGGCGATAAGGGCTATTTGTCAACGAAAACTTTCGAGTTCAATTCCATTAAGCTCAAAGAC
*
80302 ATAACAACCGTTTAGTGGCAGTGA-GGAACTACTTTCCGG-TAGAATTTTCAAACCAAAGTCTTT
66 ATAACAACCGTTTAGTAGCAGT-ATGGAACTACTTTCCGGAT-GAATTTTCAAACCAAAGTCTTT
* * * *
80365 AAGTCAATAAGAATACCAAGGTTGATTACGATTTGGCAGCAAGAAGCCACCTTCAGATTCCATTC
129 AAGTCAATAAGAAGACCAAGGTTGATTACGATTTGGAAACAAGAAGCCACCTTCAAATTCCATTC
80430 AT
194 AT
* * ** *
80432 CTCAAGGCGATAAGGGCTATTTGTCAACGAAAACTTTTGAGTTCAATTCCATTAATCTTGAAGGC
1 CTCAAGGCGATAAGGGCTATTTGTCAACGAAAACTTTCGAGTTCAATTCCATTAAGCTCAAAGAC
**
80497 ATAACAACCGTTTAGTAGCAGTATGGAACTACTTTCCGGATGAATTTTCAAACTGAAGTCTTTAA
66 ATAACAACCGTTTAGTAGCAGTATGGAACTACTTTCCGGATGAATTTTCAAACCAAAGTCTTTAA
80562 GTCAATAAGAAGACCAAGGTTGATTACGATTTGGAAACAAGAAGCCACCTTCAAATTC
131 GTCAATAAGAAGACCAAGGTTGATTACGATTTGGAAACAAGAAGCCACCTTCAAATTC
80620 AAATTTTGAA
Statistics
Matches: 169, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
194 1 0.01
195 167 0.99
196 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (195 bp):
CTCAAGGCGATAAGGGCTATTTGTCAACGAAAACTTTCGAGTTCAATTCCATTAAGCTCAAAGAC
ATAACAACCGTTTAGTAGCAGTATGGAACTACTTTCCGGATGAATTTTCAAACCAAAGTCTTTAA
GTCAATAAGAAGACCAAGGTTGATTACGATTTGGAAACAAGAAGCCACCTTCAAATTCCATTCAT
Found at i:81030 original size:25 final size:25
Alignment explanation
Indices: 81002--81106 Score: 69
Period size: 25 Copynumber: 4.3 Consensus size: 25
80992 AAATATATAT
*
81002 AATATATTTTTGAAAACGTTTTGAA
1 AATATATTTTTGAAAACATTTTGAA
* *
81027 AATATA--TAT-AATATATAGTTTTG-A
1 AATATATTTTTGAA-A-ACA-TTTTGAA
* *
81051 AA-ACATTTTTGAAAACATATAT-AA
1 AATATATTTTTGAAAACAT-TTTGAA
*
81075 TATATATTTTTGAAAACATTTTGAA
1 AATATATTTTTGAAAACATTTTGAA
*
81100 TATATAT
1 AATATAT
81107 ATATATATTG
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
22 2 0.03
23 6 0.10
24 12 0.20
25 38 0.63
26 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (25 bp):
AATATATTTTTGAAAACATTTTGAA
Found at i:81062 original size:12 final size:12
Alignment explanation
Indices: 81045--81096 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
81035 TAATATATAG
81045 TTTTGAAAACAT
1 TTTTGAAAACAT
81057 TTTTGAAAACAT
1 TTTTGAAAACAT
* * *
81069 ATAT-AATATATAT
1 TTTTGAA-A-ACAT
81082 TTTTGAAAACAT
1 TTTTGAAAACAT
81094 TTT
1 TTT
81097 GAATATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
11 2 0.06
12 21 0.68
13 6 0.19
14 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:81071 original size:37 final size:35
Alignment explanation
Indices: 80991--81122 Score: 182
Period size: 37 Copynumber: 3.8 Consensus size: 35
80981 TAATATACAT
*
80991 AAAATATATATAATATAT-TTTTGAAAACGTTTTG
1 AAAATATATATAATATATATTTTGAAAACATTTTG
81025 AAAATATATATAATATATAGTTTTGAAAACATTTTTG
1 AAAATATATATAATATATA-TTTTGAAAACA-TTTTG
*
81062 AAAACATATATAATATATATTTTTGAAAACATTTTG
1 AAAATATATATAATATATA-TTTTGAAAACATTTTG
81098 --AATATATAT-ATATATATTGTTGAAA
1 AAAATATATATAATATATATT-TTGAAA
81123 TATGTTTCGA
Statistics
Matches: 90, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
32 2 0.02
33 13 0.14
34 26 0.29
36 15 0.17
37 34 0.38
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (35 bp):
AAAATATATATAATATATATTTTGAAAACATTTTG
Found at i:81480 original size:21 final size:21
Alignment explanation
Indices: 81447--81486 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
81437 TTTTAGTAGA
*
81447 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
81469 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
81487 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:84492 original size:18 final size:18
Alignment explanation
Indices: 84463--84520 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
84453 CAACAATTGG
*
84463 TAACAATGGATATCTTTT
1 TAACAATTGATATCTTTT
*
84481 TAACAGTTGATATCCTTTTGT
1 TAACAATTGATAT-C-TTT-T
*
84502 TAACAATTGGTATCTTTT
1 TAACAATTGATATCTTTT
84520 T
1 T
84521 CATTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.39
19 4 0.12
20 4 0.12
21 12 0.36
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:84506 original size:21 final size:21
Alignment explanation
Indices: 84463--84520 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
84453 CAACAATTGG
*
84463 TAACAATGGATAT-C-TTT-T
1 TAACAATTGATATCCTTTTGT
*
84481 TAACAGTTGATATCCTTTTGT
1 TAACAATTGATATCCTTTTGT
* *
84502 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCCTTTT
84521 CATTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.34
19 1 0.03
20 3 0.09
21 17 0.53
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (21 bp):
TAACAATTGATATCCTTTTGT
Found at i:85578 original size:38 final size:37
Alignment explanation
Indices: 85507--85624 Score: 137
Period size: 37 Copynumber: 3.1 Consensus size: 37
85497 AAATCCCAAC
* *
85507 ATATATATATATATATAGTTTTGAAAACGTTTTGGAAA
1 ATATATATA-ATATATAGTTTTGAAAACATTTTTGAAA
* *
85545 ATATATATAATATATAATTTAGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * * * *
85582 ACATTTATAATAAATGGTTTTGAAAACATTTATCGAAA
1 ATATATATAATATATAGTTTTGAAAACATTT-TTGAAA
85620 ATATA
1 ATATA
85625 ATATTATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
37 49 0.74
38 17 0.26
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:94148 original size:13 final size:13
Alignment explanation
Indices: 94130--94154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94120 ATGATGATAA
94130 AAAGACTTGAATG
1 AAAGACTTGAATG
94143 AAAGACTTGAAT
1 AAAGACTTGAAT
94155 TGCTTGTCTT
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:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
AAAGACTTGAATG
Found at i:94415 original size:17 final size:17
Alignment explanation
Indices: 94393--94458 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
94383 GCAAACATTA
*
94393 AATGAACTAGTTTGATT
1 AATGAACTAGTTTAATT
* *
94410 AATGAACTAATTTAATG
1 AATGAACTAGTTTAATT
* *
94427 AATAAACTAGTTAAATT
1 AATGAACTAGTTTAATT
*
94444 AGTGAACTAGCTTTA
1 AATGAACTAG-TTTA
94459 TTGAATAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 35 0.92
18 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Found at i:94436 original size:34 final size:35
Alignment explanation
Indices: 94397--94467 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 35
94387 ACATTAAATG
**
94397 AACTAGTTTGATTAATGAACTA-ATTTAATGAATA
1 AACTAGTTAAATTAATGAACTAGATTTAATGAATA
* * *
94431 AACTAGTTAAATTAGTGAACTAGCTTTATTGAATA
1 AACTAGTTAAATTAATGAACTAGATTTAATGAATA
94466 AA
1 AA
94468 AAAACATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 19 0.61
35 12 0.39
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (35 bp):
AACTAGTTAAATTAATGAACTAGATTTAATGAATA
Found at i:101395 original size:15 final size:15
Alignment explanation
Indices: 101375--101450 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
101365 ATGATTATGC
101375 ATAATGTCACCATAT
1 ATAATGTCACCATAT
101390 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
* ** **
101404 ATAGTGGAAAAACTA-
1 ATAATGTCACCA-TAT
*
101419 AAAATTGTCACCATAT
1 ATAA-TGTCACCATAT
101435 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
101449 AT
1 AT
101451 CATTTTGTTC
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
14 13 0.29
15 24 0.53
16 8 0.18
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:106038 original size:20 final size:21
Alignment explanation
Indices: 106013--106051 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
106003 CATTCATACA
106013 TCTAGTTCATT-GAATAAAGT
1 TCTAGTTCATTGGAATAAAGT
106033 TCTAGTTCATTGGAATAAA
1 TCTAGTTCATTGGAATAAA
106052 CTTAGTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
TCTAGTTCATTGGAATAAAGT
Found at i:106076 original size:17 final size:17
Alignment explanation
Indices: 106034--106106 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
106024 GAATAAAGTT
106034 CTAGTTCATTGGAA-TAAA
1 CTAGTTCATT--AATTAAA
106052 CTTAGTTCATTAATTAAA
1 C-TAGTTCATTAATTAAA
* *
106070 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
106087 CTAGTTCTTTTATTAAA
1 CTAGTTCATTAATTAAA
106104 CTA
1 CTA
106107 AATATTAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
17 33 0.69
18 6 0.12
19 9 0.19
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:110623 original size:32 final size:30
Alignment explanation
Indices: 110569--110641 Score: 119
Period size: 32 Copynumber: 2.4 Consensus size: 30
110559 GTTTCGAATA
*
110569 ACATAGGTAACTTTCCATATGTCCCGAAGG
1 ACATAGGTAACTGTCCATATGTCCCGAAGG
110599 ACATAGGTAATCCTGTCCATATGTCCCGAAGG
1 ACATAGGTAA--CTGTCCATATGTCCCGAAGG
110631 ACATAGGTAAC
1 ACATAGGTAAC
110642 CCTCGATTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 11 0.28
32 29 0.73
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
ACATAGGTAACTGTCCATATGTCCCGAAGG
Found at i:111922 original size:22 final size:22
Alignment explanation
Indices: 111875--111930 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
111865 CCTTAAATTG
** *
111875 GTATCGATACCCCTATGCTAGG
1 GTATCGATACCCCTACCCTAGA
111897 GTATCGATACCACCTACCCTA-A
1 GTATCGATACC-CCTACCCTAGA
*
111919 GTATCAATACCC
1 GTATCGATACCC
111931 TTTGAAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 21 0.72
23 7 0.24
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (22 bp):
GTATCGATACCCCTACCCTAGA
Found at i:115015 original size:12 final size:12
Alignment explanation
Indices: 114998--115026 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
114988 GTTGGTATGC
114998 ACACTTTTTAAG
1 ACACTTTTTAAG
115010 ACACTTTTTAAG
1 ACACTTTTTAAG
115022 ACACT
1 ACACT
115027 CATGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (12 bp):
ACACTTTTTAAG
Found at i:117996 original size:17 final size:17
Alignment explanation
Indices: 117959--118026 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
117949 AAAGTTCTCA
* *
117959 TTCATTGAATAAAATTAG
1 TTCATT-AATTAAACTAG
117977 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
117994 TTCGTTCATCAAACTAG
1 TTCATTAATTAAACTAG
* *
118011 TTCTTTTATTAAACTA
1 TTCATTAATTAAACTA
118027 AATCTTAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 36 0.86
18 6 0.14
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:121027 original size:24 final size:23
Alignment explanation
Indices: 120976--121049 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
120966 AAGCATAAAC
*
120976 AATATTATATTGATAATTTTAAT
1 AATATTATATTGATAATTATAAT
* *
120999 AATATTATATTTTATTATTATAAT
1 AATATTATA-TTGATAATTATAAT
*
121023 TATA-T-TATT-ATAATATATAAT
1 AATATTATATTGATAAT-TATAAT
121044 AA-ATTA
1 AATATTA
121050 ATTTTAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.12
21 10 0.24
22 2 0.05
23 10 0.24
24 14 0.34
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
AATATTATATTGATAATTATAAT
Found at i:121030 original size:14 final size:14
Alignment explanation
Indices: 121001--121040 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
120991 ATTTTAATAA
*
121001 TATTAT-ATTTTAT
1 TATTATAATTATAT
121014 TATTATAATTATAT
1 TATTATAATTATAT
121028 TATTATAA-TATAT
1 TATTATAATTATAT
121041 AATAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATAATTATAT
Found at i:121260 original size:17 final size:16
Alignment explanation
Indices: 121238--121271 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
121228 GTATTTGATG
*
121238 TTTATAATAAAGAATTT
1 TTTATAA-AAAAAATTT
121255 TTTATAAAAAAAATTT
1 TTTATAAAAAAAATTT
121271 T
1 T
121272 ATCATCCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTATAAAAAAAATTT
Found at i:121390 original size:14 final size:14
Alignment explanation
Indices: 121352--121390 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
121342 CAGGAAATGT
* *
121352 AATTCATTTTACAG
1 AATTTATTTTCCAG
121366 AATTTATTTTCCAG
1 AATTTATTTTCCAG
*
121380 AATTTGTTTTC
1 AATTTATTTTC
121391 TGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (14 bp):
AATTTATTTTCCAG
Found at i:121609 original size:22 final size:21
Alignment explanation
Indices: 121578--121621 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
121568 TAGTTTTATC
*
121578 ATTTTTGAGAGTTGTCTATAT
1 ATTTTTGAGAGGTGTCTATAT
121599 ATTTTTCGAGAGGTGTCTATAT
1 ATTTTT-GAGAGGTGTCTATAT
121621 A
1 A
121622 GTGTAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (21 bp):
ATTTTTGAGAGGTGTCTATAT
Found at i:126977 original size:15 final size:16
Alignment explanation
Indices: 126947--126983 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
126937 TCCAAAAATC
126947 TGAATATCTAATTTTT
1 TGAATATCTAATTTTT
126963 TGAATATCT-ATTTTT
1 TGAATATCTAATTTTT
126978 TAGAAT
1 T-GAAT
126984 GAATATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (16 bp):
TGAATATCTAATTTTT
Found at i:127287 original size:14 final size:14
Alignment explanation
Indices: 127248--127294 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
127238 TTTAGATTAG
127248 GGTTTAGAGTTTAT
1 GGTTTAGAGTTTAT
**
127262 GACTTAGA-TTTAT
1 GGTTTAGAGTTTAT
*
127275 GGTTTAGAGTTTAG
1 GGTTTAGAGTTTAT
127289 GGTTTA
1 GGTTTA
127295 AGGTTTGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (14 bp):
GGTTTAGAGTTTAT
Found at i:132250 original size:14 final size:15
Alignment explanation
Indices: 132225--132255 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
132215 TGTATACACT
132225 TATTTTTAAAAAAGA
1 TATTTTTAAAAAAGA
132240 TATTTTT-AAAAAGA
1 TATTTTTAAAAAAGA
132254 TA
1 TA
132256 AAATTAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TATTTTTAAAAAAGA
Found at i:132749 original size:27 final size:26
Alignment explanation
Indices: 132693--132750 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
132683 TTTTATGCAT
* *
132693 TTTTTTTACTTTAGTATATATTTTTA
1 TTTTTTTACATTAGTATATATTATTA
*
132719 TTTTTTTAGATTA-TATATATATATTA
1 TTTTTTTACATTAGTATATAT-TATTA
*
132745 GTTTTT
1 TTTTTT
132751 ATTTTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (26 bp):
TTTTTTTACATTAGTATATATTATTA
Found at i:132836 original size:28 final size:26
Alignment explanation
Indices: 132801--132859 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
132791 TTACTATTTT
*
132801 TTATTTTTTATTTTTTTATATATATATA
1 TTATTTTTTACTTTTTTAT-TAT-TATA
*
132829 TTA-TTTTTACTTTTTTATTATTATT
1 TTATTTTTTACTTTTTTATTATTATA
132854 TTATTT
1 TTATTT
132860 ATATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.21
26 5 0.18
27 14 0.50
28 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (26 bp):
TTATTTTTTACTTTTTTATTATTATA
Found at i:132857 original size:8 final size:8
Alignment explanation
Indices: 132740--132869 Score: 54
Period size: 9 Copynumber: 15.1 Consensus size: 8
132730 TATATATATA
*
132740 TATTAGTT
1 TATTATTT
132748 T-TTATTT
1 TATTATTT
132755 TATTAATTT
1 TATT-ATTT
132764 TATTATTAT
1 TATTATT-T
*
132773 ATATATATATA
1 -TAT-TAT-TT
132784 TATATATTT
1 TAT-TATTT
132793 ACTATT-TTT
1 --TATTATTT
132802 TATT-TTT
1 TATTATTT
*
132809 TATTTTTT
1 TATTATTT
*
132817 TATATATATA
1 TAT-TAT-TT
132827 TATTATTTT
1 TATTA-TTT
132836 TACTT-TTT
1 TA-TTATTT
132844 TATTATTAT
1 TATTATT-T
132853 T-TTATTT
1 TATTATTT
*
132860 ATATAATTT
1 -TATTATTT
132869 T
1 T
132870 TTCTTCTTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 34
0.71 0.05 0.24
Matches are distributed among these distances:
7 20 0.20
8 26 0.27
9 27 0.28
10 18 0.18
11 6 0.06
12 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (8 bp):
TATTATTT
Found at i:132863 original size:38 final size:36
Alignment explanation
Indices: 132804--132880 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
132794 CTATTTTTTA
*
132804 TTTTTTATTTTTTTATATATATATATTATTTT-TACTT
1 TTTTTTATTATTTTATATATATA-ATT-TTTTCTACTT
* *
132841 TTTTATTATTATTTTATTTATATAATTTTTTCTTCTT
1 TTTT-TTATTATTTTATATATATAATTTTTTCTACTT
132878 TTT
1 TTT
132881 CTTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.11
37 14 0.40
38 17 0.49
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (36 bp):
TTTTTTATTATTTTATATATATAATTTTTTCTACTT
Found at i:132895 original size:36 final size:33
Alignment explanation
Indices: 132798--132897 Score: 85
Period size: 36 Copynumber: 2.8 Consensus size: 33
132788 TATTTACTAT
* *
132798 TTTTTATTTTTTATTTTTTTATATATATATATTA
1 TTTTTACTTTTT-TTTTTTTATATTTATATATTA
*
132832 TTTTTACTTTTTTATTATTATTTTATTTATATAATT-
1 TTTTTACTTTTTT-TT-TT-TTATATTTATAT-ATTA
*
132868 TTTTCTTCTTTTTCTTTTTCTTATATTTAT
1 TTTT-TACTTTTT-TTTTT-TTATATTTAT
132898 TTTACTTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 1 0.02
34 13 0.24
35 2 0.04
36 25 0.46
37 12 0.22
38 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTACTTTTTTTTTTTTATATTTATATATTA
Found at i:136045 original size:13 final size:13
Alignment explanation
Indices: 136015--136075 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 13
136005 ATTCAATCAT
*
136015 AACAAAAAG-AAA
1 AACAAAGAGAAAA
136027 AA-AAAGAGAAAA
1 AACAAAGAGAAAA
136039 AACAAAGA-AAAA
1 AACAAAGAGAAAA
*
136051 ATATAAAGA-AAAA
1 A-ACAAAGAGAAAA
136064 AACAAAG-GAAAA
1 AACAAAGAGAAAA
136076 TTGAAGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.12
12 21 0.50
13 16 0.38
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.03
Consensus pattern (13 bp):
AACAAAGAGAAAA
Found at i:136051 original size:24 final size:25
Alignment explanation
Indices: 136029--136087 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
136019 AAAAGAAAAA
136029 AAAGAGAAAAAACAAAGAAAAAATAT
1 AAAGA-AAAAAACAAAGAAAAAATAT
*
136055 AAAGAAAAAAACAAAG-GAAAAT-T
1 AAAGAAAAAAACAAAGAAAAAATAT
*
136078 GAAGAAAAAA
1 AAAGAAAAAA
136088 GAAAACAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 10 0.32
24 5 0.16
25 11 0.35
26 5 0.16
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (25 bp):
AAAGAAAAAAACAAAGAAAAAATAT
Found at i:136069 original size:25 final size:23
Alignment explanation
Indices: 136020--136087 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
136010 ATCATAACAA
136020 AAAGAAAAA--AAAGAGAAAAAAC
1 AAAGAAAAATTAAAGA-AAAAAAC
136042 AAAGAAAAAATATAAAGAAAAAAAC
1 AAAG-AAAAAT-TAAAGAAAAAAAC
* *
136067 AAAGGAAAATTGAAGAAAAAA
1 AAAGAAAAATTAAAGAAAAAA
136088 GAAAACAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.10
23 15 0.38
24 5 0.12
25 11 0.28
26 5 0.12
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (23 bp):
AAAGAAAAATTAAAGAAAAAAAC
Found at i:137254 original size:33 final size:33
Alignment explanation
Indices: 137212--137300 Score: 144
Period size: 32 Copynumber: 2.7 Consensus size: 33
137202 ATATTTGAAT
137212 ATTCAACATCAAATGTTGGGGCATTTTTTTTAG
1 ATTCAACATCAAATGTTGGGGCATTTTTTTTAG
*
137245 ATTTAACATCAAATGTTGGGGCA-TTTTTTTAG
1 ATTCAACATCAAATGTTGGGGCATTTTTTTTAG
* *
137277 ATTCAACATCGAATATTGGGGCAT
1 ATTCAACATCAAATGTTGGGGCAT
137301 CTTTGGGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
ATTCAACATCAAATGTTGGGGCATTTTTTTTAG
Found at i:138091 original size:106 final size:105
Alignment explanation
Indices: 137896--138214 Score: 367
Period size: 106 Copynumber: 3.0 Consensus size: 105
137886 ATATCGTGCC
* *
137896 ACTCGAGACAACACATGTT-AACTCCACAACGAAGGGACGACTGGTTATCAACAAACATTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAACAAACATTTCCCA
*
137960 ATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
138000 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAACAAAC-ATTTCCC
*
138065 AATTT-TGAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * ** * * **
138106 ACTCGAGACAGCACAAACTCAACATCACAGCGAAGGGGTG-CT-GCTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAACAAAC-ATTTCCC
* * * * * * *
138169 AGTTCCAGAGCCAATTTTAACTTCACGGAGGAGGATATTAG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
138210 ACTCG
1 ACTCG
138215 GAACAATACA
Statistics
Matches: 186, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
104 72 0.39
105 37 0.20
106 77 0.41
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAACAAACATTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:138655 original size:37 final size:37
Alignment explanation
Indices: 138581--138667 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
138571 ATTGAAAACA
* * *
138581 TTTCCCTTGAAA-TAAATTTTATCTCGCTTAGGGTAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTAGGATAG
*
138617 TTTCCCTTGAAACAAAATTTTGTCTCCCTT-GAGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTAG-GATAG
**
138654 TTTATCTTGAAACA
1 TTTCCCTTGAAACA
138668 TAAACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTAGGATAG
Found at i:138668 original size:87 final size:87
Alignment explanation
Indices: 138470--138648 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 87
138460 GACAGTTTCT
*
138470 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
*
138535 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
* *
138557 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTT-AGGGTAGTTTC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGA-GATAGTTTC
138621 CCTTGAAACAAAATTTTGTCTCC
65 CCTTGAAACAAAATTTTGTCTCC
138644 CTTGA
1 CTTGA
138649 GATAGTTTAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 1 0.01
87 86 0.99
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:138782 original size:37 final size:37
Alignment explanation
Indices: 138732--138834 Score: 172
Period size: 36 Copynumber: 2.8 Consensus size: 37
138722 AAAATGAGTT
*
138732 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
138769 TTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCTT
1 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
138805 TTGAGATAGTTTCCCTTGAAACAAAATCTT
1 TTGAGATAGTTTCCCTTGAAACAAAATCTT
138835 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:138901 original size:102 final size:102
Alignment explanation
Indices: 138745--138931 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
138735 AGACAGTTTC
* * *
138745 CCTTGAAACAAAATCTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAG
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
138810 ATAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
66 ATAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * *
138847 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTT
1 CCTTGAAACAAAATCTT-GTCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTT
**
138909 GAGATAGTTTCTTTTGAAACAAA
63 GAGATAGTTTCCCTTGAAACAAA
138932 TTTTATCCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 6 0.08
101 24 0.32
102 44 0.59
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (102 bp):
CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
ATAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:138910 original size:37 final size:36
Alignment explanation
Indices: 138849--138965 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
138839 TATCTTTTCC
* *
138849 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
138885 TT-AGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
138922 TTGAAACAAATTTTATCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
138958 TTGAAACA
1 TTGAAACA
138966 CAAAAAAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.01
36 37 0.54
37 30 0.43
38 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:138954 original size:36 final size:36
Alignment explanation
Indices: 138732--138965 Score: 141
Period size: 36 Copynumber: 6.6 Consensus size: 36
138722 AAAATGAGTT
** * *
138732 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCCCTC
* ** * *
138769 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTT
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* ** *
138805 TTGAGATAGTTTCCCTTGAAACAAA----AT--CT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* *
138834 TTGA-ATA-TCTT-TTCCTTGAAACAAATTTCGTCTCC-C
1 TTGAGACAGT-TTCTT--TTGAAACAAATTTTGTC-CCTC
* *
138870 TTGAGACAGTTTCTTTT-AGAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCTC
* *
138907 TTGAGATAGTTTCTTTTGAAACAAATTTTATCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
*
138943 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTGAAACA
138966 CAAAAAAAAC
Statistics
Matches: 162, Mismatches: 17, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 14 0.09
30 2 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 80 0.49
37 53 0.33
38 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
Found at i:138993 original size:35 final size:37
Alignment explanation
Indices: 138951--139040 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 37
138941 TCTTGAGACA
*
138951 GTTTCTCTTGAAACACA-A-AAAAAACCCTCGAAATT
1 GTTTCTCTTGAAACACACACAAAAAACCCTCGAAAAT
* *
138986 GTTTCTCTTGAAACACACACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTG-AA-ACACACACAAAAAACCCTCGAAAAT
*
139025 ATTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
139041 CAAACCCTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 10 0.21
36 2 0.04
37 9 0.19
38 3 0.06
39 23 0.49
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (37 bp):
GTTTCTCTTGAAACACACACAAAAAACCCTCGAAAAT
Found at i:140229 original size:2 final size:2
Alignment explanation
Indices: 140222--140265 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
140212 TTTATTAATT
140222 TA TA TA TA TA TA TA T- TA TA -A T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
140261 TA TA T
1 TA TA T
140266 TATTTTTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140293 original size:12 final size:13
Alignment explanation
Indices: 140180--140295 Score: 69
Period size: 14 Copynumber: 8.5 Consensus size: 13
140170 TTTTTTTTAG
140180 ATTATATATATATAT
1 ATTAT-TAT-TATAT
* *
140195 ATTATTTTTTTAT
1 ATTATTATTATAT
140208 CAGTT-TTATTA-AT
1 -A-TTATTATTATAT
140221 -TTATATATATATAT
1 ATTAT-TAT-TATAT
*
140235 ATTATAATTATAT
1 ATTATTATTATAT
140248 ATATATATATATATAT
1 AT-TAT-TAT-TATAT
* *
140264 ATTATTTTTACTTT
1 ATTATTATTA-TAT
140278 ATTATTATTAT-T
1 ATTATTATTATAT
140290 ATTATT
1 ATTATT
140296 TATTTGTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
10 2 0.02
11 1 0.01
12 10 0.12
13 18 0.22
14 27 0.33
15 16 0.20
16 7 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (13 bp):
ATTATTATTATAT
Found at i:145870 original size:64 final size:64
Alignment explanation
Indices: 145760--145906 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 64
145750 CTATATAAGT
* * *
145760 CACAACATAGTTATTATTGCATTCAGATAATCTACAATAGAATTAGTATTG-CATTAAGATAATG
1 CACAACAGAGTTAGTATTGCATTCAGATAATCTACAAGAGAATTAGTA-TGACATTAAGATAATG
* * * * *
145824 CACAACAGAGTTAGTATAT-CATTCAGATAATGTACAGGGGAGTTAGTATGACGTTAAGATAATG
1 CACAACAGAGTTAGTAT-TGCATTCAGATAATCTACAAGAGAATTAGTATGACATTAAGATAATG
* *
145888 TATAACAGAGTTAGTATTG
1 CACAACAGAGTTAGTATTG
145907 TTGGGACTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.04
64 66 0.94
65 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (64 bp):
CACAACAGAGTTAGTATTGCATTCAGATAATCTACAAGAGAATTAGTATGACATTAAGATAATG
Found at i:145899 original size:32 final size:32
Alignment explanation
Indices: 145761--145904 Score: 123
Period size: 32 Copynumber: 4.5 Consensus size: 32
145751 TATATAAGTC
* * * *
145761 ACAACATAGTTATTAT-TGCATTCAGATAATCT
1 ACAACAGAGTTAGTATAT-CATTAAGATAATGT
* * *
145793 ACAATAGAATTAGTAT-TGCATTAAGATAATGC
1 ACAACAGAGTTAGTATAT-CATTAAGATAATGT
*
145825 ACAACAGAGTTAGTATATCATTCAGATAATGT
1 ACAACAGAGTTAGTATATCATTAAGATAATGT
*** *
145857 ACAGGGGAGTTAGTATGA-CGTTAAGATAATGT
1 ACAACAGAGTTAGTAT-ATCATTAAGATAATGT
*
145889 ATAACAGAGTTAGTAT
1 ACAACAGAGTTAGTAT
145905 TGTTGGGACT
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
32 88 0.98
33 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (32 bp):
ACAACAGAGTTAGTATATCATTAAGATAATGT
Found at i:157146 original size:594 final size:605
Alignment explanation
Indices: 155956--157163 Score: 2251
Period size: 594 Copynumber: 2.0 Consensus size: 605
155946 ACCTCTTCTG
*
155956 TGAGGACTTCTGTATATGAAATGTTGAACGACTTTCTTTCTTTATCCCTTCACAAAAGGAGAAAA
1 TGAGGACTTCTGTATATGAAATGTTGAACGA-TTTCTTTCTTTATCCCTTAACAAAAGGAGAAAA
156021 TATATCCCTTGTGTCCCCATTTGAGCCTAAATCATGTTTTCTTGTGATTCAACCCTAACCAAGGA
65 TATATCCCTTGTGTCCCCATTTGAGCCTAAATCATGTTTTCTTGTGATTCAACCCTAACCAAGGA
*
156086 TCGCCCTCCACACTGAGGGGCAAGATGGAGGAAATTTGCTCGCATGAGTGATGACATTGATTCAA
130 TCACCCTCCACACTGAGGGGCAAGATGGAGGAAATTTGCTCGCATGAGTGATGACATTGATTCAA
156151 ATGAGATACCGAAAGGTGAACCAAATTCCAAGTGCAAAGATCCAATCAAAACAAAGAGAGAATAG
195 ATGAGATACCGAAAGGTGAACCAAATTCCAAGTGCAAAGATCCAATCAAAACAAAGAGAGAATAG
*
156216 CAAAGAAAAAGAAGACAATATGCACATGTAAGGAATTACATGTCAAATGACGCATCGAGCTTCAA
260 CAAAGAAAAAGAAG--AATATGCACATGTAAGGAATTACATGTCAAATGACACATCGAGCTTCAA
*
156281 TCCATGAGATTGATCAAACACAATCATTCCAGAATCACTTCACTCAAAGATCATGGAGTATCAAG
323 ACCATGAGATTGATCAAACACAATCATTCCAGAATCACTTCACTCAAAGATCATGGAGTATCAAG
156346 AGAAAGATACATACGAGCAGATTCAAATTGAGCAATACAAGATTGAAGGCACCAGAATGAATTGA
388 AGAAAGATACATACGAGCAGATTCAAATTGAGCAATACAAGATTGAAGGCACCAGAATGAATTGA
156411 TCCTTGGTTCATTACCCGTAAACACTTGTTTGGGCCTTTTATCCTTTATTTATAACCATGAACCA
453 TCCTTGGTTCATTACCCGTAAACACTTGTTTGGGCCTTTTATCCTTTATTTATAACCATGAACCA
156476 TAGCCTACATTACGTACCTTAAAAGTCCCTTCTAATCATACATGGATTTCTAAACAGAAAAGACT
518 TAGCCTACATTACGTACCTTAAAAGTCCCTTCTAATCATACATGGATTTCTAAACAGAAAAGACT
156541 ATCTTCAGA-TTTATCCC-CACA
583 ATCTTCAGATTTTATCCCGCACA
156562 TGAGGAC-TCTGTATATGAAATGTTGAACG-TTT-TTTC-TT-TCCC-TAACAAAA-GAGAAAAT
1 TGAGGACTTCTGTATATGAAATGTTGAACGATTTCTTTCTTTATCCCTTAACAAAAGGAGAAAAT
156620 ATATCCCTTGTGTCCCCATTTGAGCCTAAATCATGTTTTCTTGTGATTCAACCCTAACCAAGGAT
66 ATATCCCTTGTGTCCCCATTTGAGCCTAAATCATGTTTTCTTGTGATTCAACCCTAACCAAGGAT
156685 CACCCTCCACACTGAGGGGCAAGATGGAGGAAATTTGCTCGCATGAGTGATGACATTGATTCAAA
131 CACCCTCCACACTGAGGGGCAAGATGGAGGAAATTTGCTCGCATGAGTGATGACATTGATTCAAA
156750 TGAGATACCGAAAGGTGAACCAAATTCCAAGTGCAAAGATCCAATCAAAACAAAGAGAGAATAGC
196 TGAGATACCGAAAGGTGAACCAAATTCCAAGTGCAAAGATCCAATCAAAACAAAGAGAGAATAGC
156815 AAAG-AAAAGAAG-ATATGCACATGTAAGGAATTACATGTCAAATGACACATCGAGCTTCAAACC
261 AAAGAAAAAGAAGAATATGCACATGTAAGGAATTACATGTCAAATGACACATCGAGCTTCAAACC
156878 ATGAGATTGATCAAACACAATCATTCCAGAATCACTTCACTCAAAGATCATGGAGTATCAAGAGA
326 ATGAGATTGATCAAACACAATCATTCCAGAATCACTTCACTCAAAGATCATGGAGTATCAAGAGA
156943 AAGATACATACGAGCAGATTCAAATTGAGCAATACAAGATTGAAGGCACCAGAATGAATTGATCC
391 AAGATACATACGAGCAGATTCAAATTGAGCAATACAAGATTGAAGGCACCAGAATGAATTGATCC
157008 TTGGTTCAATTACCCGTAAACACTTGTTTGGGCCTTTTATCCTTT-TTTATAACCATGAACCATA
456 TTGGTTC-ATTACCCGTAAACACTTGTTTGGGCCTTTTATCCTTTATTTATAACCATGAACCATA
157072 GCCTACATTACGTACCTTAAAAGTCCCTTCTAATCATACATGGATTTCTAAACAGAAAAGACTAT
520 GCCTACATTACGTACCTTAAAAGTCCCTTCTAATCATACATGGATTTCTAAACAGAAAAGACTAT
157137 CTTCAGATTTTATCCCGCACA
585 CTTCAGATTTTATCCCGCACA
*
157158 TCAGGA
1 TGAGGA
157164 TTAATCTTTA
Statistics
Matches: 594, Mismatches: 5, Indels: 16
0.97 0.01 0.03
Matches are distributed among these distances:
594 277 0.47
595 45 0.08
596 9 0.02
597 8 0.01
598 206 0.35
599 7 0.01
600 4 0.01
601 2 0.00
602 4 0.01
603 3 0.01
605 22 0.04
606 7 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (605 bp):
TGAGGACTTCTGTATATGAAATGTTGAACGATTTCTTTCTTTATCCCTTAACAAAAGGAGAAAAT
ATATCCCTTGTGTCCCCATTTGAGCCTAAATCATGTTTTCTTGTGATTCAACCCTAACCAAGGAT
CACCCTCCACACTGAGGGGCAAGATGGAGGAAATTTGCTCGCATGAGTGATGACATTGATTCAAA
TGAGATACCGAAAGGTGAACCAAATTCCAAGTGCAAAGATCCAATCAAAACAAAGAGAGAATAGC
AAAGAAAAAGAAGAATATGCACATGTAAGGAATTACATGTCAAATGACACATCGAGCTTCAAACC
ATGAGATTGATCAAACACAATCATTCCAGAATCACTTCACTCAAAGATCATGGAGTATCAAGAGA
AAGATACATACGAGCAGATTCAAATTGAGCAATACAAGATTGAAGGCACCAGAATGAATTGATCC
TTGGTTCATTACCCGTAAACACTTGTTTGGGCCTTTTATCCTTTATTTATAACCATGAACCATAG
CCTACATTACGTACCTTAAAAGTCCCTTCTAATCATACATGGATTTCTAAACAGAAAAGACTATC
TTCAGATTTTATCCCGCACA
Found at i:157919 original size:31 final size:32
Alignment explanation
Indices: 157833--157922 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 32
157823 ATAAGGAATA
* * *
157833 ATTG-GGCGTCTTTGAAGATTCAACATTAAAT
1 ATTGAGGCATCTTTGGAGATTCAACATCAAAT
*
157864 GTTGAGGCATCTTTGGAGATTCAACATCAAAT
1 ATTGAGGCATCTTTGGAGATTCAACATCAAAT
* *
157896 ATTGGGGCATC-TTGGGGATTCAACATC
1 ATTGAGGCATCTTTGGAGATTCAACATC
157923 CTGATGCGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 18 0.35
32 33 0.65
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (32 bp):
ATTGAGGCATCTTTGGAGATTCAACATCAAAT
Found at i:158533 original size:124 final size:123
Alignment explanation
Indices: 158313--158577 Score: 413
Period size: 124 Copynumber: 2.1 Consensus size: 123
158303 CCCTGACCAG
* * * *
158313 CACGTAGGAGCCGTGTCAACCCTGGATAACCAAAATTCATTGTATATGAGCATTGTTATCACCCT
1 CACGTAGGAGTCGTGTCAACCCTGGATAACCAAAACTCATCGTATATGAGCAGTGTTATCACCCT
158378 TAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCAT
66 TAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCAT-CCCCGACCAGATCTCCTCAT
* * *
158437 CACGTAGGAGTCGTGTTAACCCTGGATAACCAAACCTCATCGTATATGAGTAGTGTTATCACCCT
1 CACGTAGGAGTCGTGTCAACCCTGGATAACCAAAACTCATCGTATATGAGCAGTGTTATCACCCT
* *
158502 TAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATCCCGGACCATATCTCCTCAT
66 TAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCAT
** *
158560 CATATAGGGGTCGTGTCA
1 CACGTAGGAGTCGTGTCA
158578 CCCATAGATA
Statistics
Matches: 128, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 32 0.25
124 96 0.75
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (123 bp):
CACGTAGGAGTCGTGTCAACCCTGGATAACCAAAACTCATCGTATATGAGCAGTGTTATCACCCT
TAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCAT
Found at i:162751 original size:30 final size:30
Alignment explanation
Indices: 162715--162784 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
162705 CAACTCGTTA
162715 AATATTTTATAACTTTTTAGTAGTTATCTT
1 AATATTTTATAACTTTTTAGTAGTTATCTT
162745 AATATTTTATAACTTTTTAGTAGTTATCTT
1 AATATTTTATAACTTTTTAGTAGTTATCTT
*
162775 AAAATTTTAT
1 AATATTTTAT
162785 TTCATTCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (30 bp):
AATATTTTATAACTTTTTAGTAGTTATCTT
Found at i:164555 original size:24 final size:23
Alignment explanation
Indices: 164500--164556 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
164490 TTCAGAACAA
* *
164500 TCTATGTGATCCTTCGGGATATT
1 TCTATGTGGTCCTTCGGGATAAT
*
164523 TCTACGTGGTCCTTCGGGATAAAT
1 TCTATGTGGTCCTTCGGGAT-AAT
164547 TCTATGTGGT
1 TCTATGTGGT
164557 ATTTCGGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGATAAT
Found at i:164562 original size:24 final size:24
Alignment explanation
Indices: 164512--164587 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
164502 TATGTGATCC
* **
164512 TTCGGGAT-ATTTCTACGTGGTCC
1 TTCGGGATAAATTCTACGTGGTAT
*
164535 TTCGGGATAAATTCTATGTGGTAT
1 TTCGGGATAAATTCTACGTGGTAT
* * * *
164559 TTCGGTACAAATTATACGTGGCAT
1 TTCGGGATAAATTCTACGTGGTAT
164583 TTCGG
1 TTCGG
164588 TACAAATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 8 0.19
24 35 0.81
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (24 bp):
TTCGGGATAAATTCTACGTGGTAT
Found at i:164588 original size:24 final size:24
Alignment explanation
Indices: 164543--164598 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
164533 CCTTCGGGAT
* * *
164543 AAATTCTATGTGGTATTTCGGTAC
1 AAATTATACGTGGCATTTCGGTAC
164567 AAATTATACGTGGCATTTCGGTAC
1 AAATTATACGTGGCATTTCGGTAC
164591 AAATTATA
1 AAATTATA
164599 TGAGTTGTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (24 bp):
AAATTATACGTGGCATTTCGGTAC
Found at i:169651 original size:560 final size:563
Alignment explanation
Indices: 168591--169713 Score: 2207
Period size: 560 Copynumber: 2.0 Consensus size: 563
168581 TATATTTCAG
168591 AGATCGAGTTTGTATTCCTAATGATGAGGAGTTAAGGTGAGATATAATTTCTGAAGCACATTGCA
1 AGATCGAGTTTGTATTCCTAATGATGAGGAGTTAAGGTGAGATATAATTTCTGAAGCACATTGCA
168656 GTCCACTAACTATGCATCCAGGGGGAAACAAGATGTACCAAGATCTGAAAGAGCGTTTTTGGTGG
66 GTCCACTAACTATGCATCCAGGGGGAAACAAGATGTACCAAGATCTGAAAGAGCGTTTTTGGTGG
168721 CCATACATGAAAAGAACCGTGATAGAGTTTGTGTCAAAGTGTCTTACTTATCAATAAGTGAAAAC
131 CCATACATGAAAAGAACCGTGATAGAGTTTGTGTCAAAGTGTCTTACTTATCAATAAGTGAAAAC
168786 TGAGCATCAGGTGCCTTCGGGACTTTTGCAACCGATTTATATTCCTCAATGGAAGTTGGAAAGAG
196 TGAGCATCAGGTGCCTTCGGGACTTTTGCAACCGATTTATATTCCTCAATGGAAGTTGGAAAGAG
*
168851 TTACGATGGATTTGGTAATTGGATTACCTTTGACACCTGGCAAGAAGGATTCAATATGGGTTGTT
261 TTACGATGGATTTGGTAACTGGATTACCTTTGACACCTGGCAAGAAGGATTCAATATGGGTTGTT
*
168916 GTAGATAGATTGACTAAGACCACTCATTTACTTCTGGTTTGAACGGATTATTCGATGGATAAGTA
326 GTAGATAGATTGACTAAGACCACTCATTTACTTCTGGTTCGAACGGATTATTCGATGGATAAGTA
168981 TGCAACTTTATATCTTAAGGAGATAGTTTGATTGCATGGAGTGCCAGTCTCAATAGTATCTAATA
391 TGCAACTTTATATCTTAAGGAGATAGTTTGATTGCATGGAGTGCCAGTCTCAATAGTATCTAATA
169046 GGGATTCAAAATTTACTTCAAGATTTTGGAAATCTTTGCATGGAGCTTTGGGTACTCGA-TGAAC
456 GGGATTCAAAATTTACTTCAAGATTTTGGAAATCTTTGCATGGAGCTTTGGGTACTCGATTGAAC
169110 TTTAGTACTT-CTTTCACCTTCAAAACCAATGGTCAATCAGAA
521 TTTAGTACTTCCTTTCACCTTCAAAACCAATGGTCAATCAGAA
169152 AGATCGAGTTTGTATTCCTAATGATGAGGAGTTAAGGTGAGATATAATTTCTGAAGCACATTGCA
1 AGATCGAGTTTGTATTCCTAATGATGAGGAGTTAAGGTGAGATATAATTTCTGAAGCACATTGCA
169217 GTCCACTAACTATGCATCCAGGGGGAAACAAGATGTACCAAGATCTGAAAGAGCGTTTTTGGTGG
66 GTCCACTAACTATGCATCCAGGGGGAAACAAGATGTACCAAGATCTGAAAGAGCGTTTTTGGTGG
169282 CCATACATGAAAAGAACCGTGATAGAGTTTGTGTCAAAGTGTCTTACTTATCAATAAGTG-AAAC
131 CCATACATGAAAAGAACCGTGATAGAGTTTGTGTCAAAGTGTCTTACTTATCAATAAGTGAAAAC
169346 TGAGCATCAGGTGCCTTCGGGACTTTTGCAACCGATTTATATTCCTCAATGGAAGTTGGAAAGAG
196 TGAGCATCAGGTGCCTTCGGGACTTTTGCAACCGATTTATATTCCTCAATGGAAGTTGGAAAGAG
169411 TTACGATGGATTTGGTAACTGGATTACCTTTGACACCTGGCAAGAAGGATTCAATATGGGTTGTT
261 TTACGATGGATTTGGTAACTGGATTACCTTTGACACCTGGCAAGAAGGATTCAATATGGGTTGTT
169476 GTAGATAGATTGACTAAGACCACTCATTTACTTCTGGTTCGAACGGATTATTCGATGGATAAGTA
326 GTAGATAGATTGACTAAGACCACTCATTTACTTCTGGTTCGAACGGATTATTCGATGGATAAGTA
169541 TGCAACTTTATATCTTAAGGAGATAGTTTGATTGCATGGAGTGCCAGTCTCAATAGTATCTAATA
391 TGCAACTTTATATCTTAAGGAGATAGTTTGATTGCATGGAGTGCCAGTCTCAATAGTATCTAATA
169606 GGGATTCAAAATTTACTTCAAGATTTTGGAAATCTTTGCATGGAGCTTTGGGTACTCGATTGAAC
456 GGGATTCAAAATTTACTTCAAGATTTTGGAAATCTTTGCATGGAGCTTTGGGTACTCGATTGAAC
169671 TTTAGTACTTCCTTTCACCTTCAAAACCAATGGTCAATCAGAA
521 TTTAGTACTTCCTTTCACCTTCAAAACCAATGGTCAATCAGAA
169714 CGACGATTCA
Statistics
Matches: 558, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
560 321 0.58
561 205 0.37
562 32 0.06
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (563 bp):
AGATCGAGTTTGTATTCCTAATGATGAGGAGTTAAGGTGAGATATAATTTCTGAAGCACATTGCA
GTCCACTAACTATGCATCCAGGGGGAAACAAGATGTACCAAGATCTGAAAGAGCGTTTTTGGTGG
CCATACATGAAAAGAACCGTGATAGAGTTTGTGTCAAAGTGTCTTACTTATCAATAAGTGAAAAC
TGAGCATCAGGTGCCTTCGGGACTTTTGCAACCGATTTATATTCCTCAATGGAAGTTGGAAAGAG
TTACGATGGATTTGGTAACTGGATTACCTTTGACACCTGGCAAGAAGGATTCAATATGGGTTGTT
GTAGATAGATTGACTAAGACCACTCATTTACTTCTGGTTCGAACGGATTATTCGATGGATAAGTA
TGCAACTTTATATCTTAAGGAGATAGTTTGATTGCATGGAGTGCCAGTCTCAATAGTATCTAATA
GGGATTCAAAATTTACTTCAAGATTTTGGAAATCTTTGCATGGAGCTTTGGGTACTCGATTGAAC
TTTAGTACTTCCTTTCACCTTCAAAACCAATGGTCAATCAGAA
Found at i:172006 original size:23 final size:22
Alignment explanation
Indices: 171954--172013 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
171944 GGTTCTACAC
* *
171954 GGTCCTTCGGGACAATCTATGT
1 GGTCCTTCGGGATAATCTATAT
* * *
171976 GATACTTCGGGATATTTCTATAT
1 GGTCCTTCGGGATA-ATCTATAT
171999 GGTCCTTCGGGATAA
1 GGTCCTTCGGGATAA
172014 ATTCTACGCG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (22 bp):
GGTCCTTCGGGATAATCTATAT
Found at i:174945 original size:15 final size:15
Alignment explanation
Indices: 174900--174953 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
174890 TTAAATAAGT
174900 AAAAGAATTAAA--A
1 AAAAGAATTAAATTA
* *
174913 GAAA-AATCAAATTA
1 AAAAGAATTAAATTA
* *
174927 AAAAGGATTAAATTG
1 AAAAGAATTAAATTA
174942 AAAAGAATTAAA
1 AAAAGAATTAAA
174954 AGTCAAGGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 6 0.19
13 3 0.10
14 4 0.13
15 18 0.58
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (15 bp):
AAAAGAATTAAATTA
Found at i:176431 original size:23 final size:23
Alignment explanation
Indices: 176405--176486 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
176395 CGTATAAATA
176405 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
* * *
176428 CACCGAAGTGCCGCATAGAAGTG
1 CACCGAAGTGCCACGTAGAATTG
* *
176451 CACCGAAGTGTCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
176474 CACCGTAGTGCCA
1 CACCGAAGTGCCA
176487 TATAAGATTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:177271 original size:67 final size:64
Alignment explanation
Indices: 177170--177292 Score: 156
Period size: 67 Copynumber: 1.9 Consensus size: 64
177160 CATAAATCCA
* * * * *
177170 ATTCGATGTTTGTATTTAAGGGGTGCATCGATGCACTACTTGTGGATCGATACTACACTGATGGC
1 ATTCAATGTTTGTATTTAAGGAGTGCATCAATGCACTACATGTGCATCGATA-TACACTGATGGC
* *
177235 ATTCAATGTTTTTATTTTAAAGGAGTGCATCAATGCACTTCATGTGCATCGATATACA
1 ATTCAATGTTTGTA-TTT-AAGGAGTGCATCAATGCACTACATGTGCATCGATATACA
177293 TTGAACAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 12 0.24
66 7 0.14
67 30 0.61
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (64 bp):
ATTCAATGTTTGTATTTAAGGAGTGCATCAATGCACTACATGTGCATCGATATACACTGATGGC
Found at i:183383 original size:23 final size:23
Alignment explanation
Indices: 183365--183425 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
183355 CTCGTATAAA
183365 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
183388 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
183411 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
183426 TTTACGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:184593 original size:28 final size:28
Alignment explanation
Indices: 184538--184593 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
184528 TAATAAAAAT
* *
184538 TATAAATAAAGATAAAATACAATGCATG
1 TATAAATAAAGAAAAAATACAATACATG
*
184566 TATAAATAAATAAATAAATA-AATACATG
1 TATAAATAAAGAAA-AAATACAATACATG
184594 GTTGAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (28 bp):
TATAAATAAAGAAAAAATACAATACATG
Done.