Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000424.1 Hibiscus syriacus cultivar Beakdansim tig00000775_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: 117920
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:227 original size:19 final size:20
Alignment explanation
Indices: 173--239 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
163 TAGTTTACTT
* *
173 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
193 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
213 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
232 TCGCAACG
1 TCGCAACG
240 ACAAAGCGCA
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:267 original size:31 final size:33
Alignment explanation
Indices: 214--289 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 33
204 AAATGGCTAT
*
214 CGCAATGCGAAATGAAAATCGCAACGAC-AAAG
1 CGCAACGCGAAATGAAAATCGCAACGACAAAAG
*
246 CGCAACGCGAAATG-AAATCGCAACGACAAAAT
1 CGCAACGCGAAATGAAAATCGCAACGACAAAAG
278 CGCAACGCGAAA
1 CGCAACGCGAAA
290 CACAAATCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.08
Consensus pattern (33 bp):
CGCAACGCGAAATGAAAATCGCAACGACAAAAG
Found at i:349 original size:32 final size:33
Alignment explanation
Indices: 301--390 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
291 ACAAATCGCA
*
301 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGAATTTCATTTCGCGTTGCGATTTTGTCG
334 TTGC-AATTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGAATTTCATTTCGCGTTGCGATTTTGTCG
* *
365 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGAATTTCATTTCGCGTTGCGAT
391 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 11 0.21
32 37 0.71
33 4 0.08
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGAATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:355 original size:18 final size:18
Alignment explanation
Indices: 296--431 Score: 92
Period size: 19 Copynumber: 7.8 Consensus size: 18
286 GAAACACAAA
*
296 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
315 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
331 T--CGTTGCAATTTCATT
1 TCGCGTTGCGATTTCATT
*
347 TCGCGTTGCGA-TT--TG
1 TCGCGTTGCGATTTCATT
362 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
* **
379 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
*
398 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGAT-TTCATT
418 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
432 TAAGTTTCGT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.09
14 10 0.11
15 4 0.04
16 4 0.04
17 4 0.04
18 12 0.13
19 33 0.36
20 17 0.18
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:409 original size:20 final size:19
Alignment explanation
Indices: 375--429 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
365 TTGCGATTTT
*
375 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
394 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
414 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
430 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2451 original size:19 final size:19
Alignment explanation
Indices: 2407--2473 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
2397 CTATCGCAAC
2407 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2426 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2444 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2458 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2474 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2905 original size:14 final size:14
Alignment explanation
Indices: 2886--2921 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2876 ATTGTTTAAT
2886 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2900 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2914 TGATTTGT
1 TGATTTGT
2922 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:3059 original size:19 final size:19
Alignment explanation
Indices: 3037--3103 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
3027 TATCGCAACA
3037 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3056 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3074 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3088 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3104 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3308 original size:629 final size:629
Alignment explanation
Indices: 2010--3340 Score: 2580
Period size: 629 Copynumber: 2.1 Consensus size: 629
2000 TGGTAAGTCA
*
2010 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCAAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
2075 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
2140 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
2205 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTAATTGATTGTAAAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTAATTGATTGTAAAA
2270 GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTT
261 GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTT
2335 GATTTGTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTA
326 GATTTGTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTA
2400 TCGCAACGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
391 TCGCAACGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
*
2465 GCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
456 GCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
2530 TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
521 TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
2595 ATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 ATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
2639 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
2704 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
2769 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTC-CAAAGTTG-TGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
2832 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTG-TTAATTGA-TTGTAA
2896 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
259 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
2961 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
324 TTGATTTG-TGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
3026 CTATCGCAACAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
388 CTATCGCAAC-GAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
3091 AATCGCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCG
452 AATCGCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCG
3156 ATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTA
517 ATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTA
3221 ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
582 ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
3269 AATGCAAGTTTTGTTAACATATATACTCCTTTT-GTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
3333 TCAATAAT
66 TCAATAAT
3341 AATGTTAAAA
Statistics
Matches: 696, Mismatches: 2, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
626 10 0.01
627 53 0.08
628 87 0.12
629 282 0.41
630 264 0.38
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (629 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTAATTGATTGTAAAA
GATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTT
GATTTGTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTA
TCGCAACGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
GCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
ATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:4251 original size:24 final size:23
Alignment explanation
Indices: 4196--4253 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
4186 AGTCAGTATT
* *
4196 CGAAATTTGATCTTGGTCATACC
1 CGAAATTTGATATTGGTCATACA
* *
4219 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTC-ATACA
*
4243 CGAATTTTGAT
1 CGAAATTTGAT
4254 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (23 bp):
CGAAATTTGATATTGGTCATACA
Found at i:4445 original size:12 final size:12
Alignment explanation
Indices: 4428--4464 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
4418 ATATAATCCT
4428 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4440 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4452 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4464 G
1 G
4465 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6461 original size:14 final size:14
Alignment explanation
Indices: 6438--6471 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6428 TCAATTAAAC
6438 AATCAACTTTTACA
1 AATCAACTTTTACA
*
6452 AATCACCTTTTACA
1 AATCAACTTTTACA
6466 AATCAA
1 AATCAA
6472 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:7884 original size:21 final size:21
Alignment explanation
Indices: 7818--7884 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
7808 GTGAATCGGG
*
7818 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
7838 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
7860 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
7881 CTCT
1 CTCT
7885 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:7903 original size:42 final size:41
Alignment explanation
Indices: 7818--7940 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
7808 GTGAATCGGG
* * * * *
7818 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
7860 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
7902 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
7941 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:10044 original size:19 final size:19
Alignment explanation
Indices: 9927--10111 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
9917 TCTTTTGGTT
*
9927 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
9946 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
9966 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
9984 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
10000 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
10018 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
10033 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
10053 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
10072 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
10091 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
10110 GA
1 GA
10112 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:10065 original size:39 final size:38
Alignment explanation
Indices: 9927--10111 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
9917 TCTTTTGGTT
* *
9927 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
9966 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
10000 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
10033 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
10072 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
10110 GA
1 GA
10112 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
33 42 0.33
34 16 0.13
35 2 0.02
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:10157 original size:20 final size:20
Alignment explanation
Indices: 10121--10158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10111 ATTTTGGTTT
*
10121 CGCGTTGCGATAGTCATTTC
1 CGCGTTGCGATACTCATTTC
*
10141 CGCGTTGCGATTCTCATT
1 CGCGTTGCGATACTCATT
10159 CTCGAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATACTCATTTC
Found at i:10757 original size:20 final size:20
Alignment explanation
Indices: 10672--10765 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
10662 CGCTAAGTAA
*
10672 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
10692 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
10712 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
10733 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
10753 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
10766 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:10784 original size:41 final size:41
Alignment explanation
Indices: 10754--10849 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
10744 ATAGTCAGTA
* * *
10754 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
10795 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
10836 TCGCATTGCGAATT
1 TCGCATTGCGAATT
10850 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:10798 original size:20 final size:20
Alignment explanation
Indices: 10754--10846 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
10744 ATAGTCAGTA
* **
10754 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
10775 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
10795 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
10816 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
10836 TCGCATTGCGA
1 TCGCATTGCGA
10847 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:14582 original size:27 final size:26
Alignment explanation
Indices: 14528--14595 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
14518 ATATCTTTAA
*
14528 AAATATATTTT-TTATGTTAAGTTATT
1 AAATATATTTTATTA-GTTAACTTATT
14554 AAATATATTTTATTA-TTAACTTAATTT
1 AAATATATTTTATTAGTTAACTT-A-TT
14581 AAGA-ATATTTTATTA
1 AA-ATATATTTTATTA
14596 CTCTTTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 6 0.16
26 12 0.32
27 18 0.49
28 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (26 bp):
AAATATATTTTATTAGTTAACTTATT
Found at i:14611 original size:2 final size:2
Alignment explanation
Indices: 14604--14637 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14594 TACTCTTTTA
14604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14638 TCTTATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14703 original size:17 final size:18
Alignment explanation
Indices: 14671--14707 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
14661 TTGTATGCTT
14671 ATTTTAAATCTTAAAAATA
1 ATTTTAAA-CTTAAAAATA
14690 ATTTTAAA-TTAAAAATA
1 ATTTTAAACTTAAAAATA
14707 A
1 A
14708 AATATTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAACTTAAAAATA
Found at i:14745 original size:35 final size:35
Alignment explanation
Indices: 14679--14790 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
14669 TTATTTTAAA
* * *
14679 TCTTAAAAATA-ATTTTAAATTAAAAATAAAATAT
1 TCTTAAATATATATTTAAAAATAAAAATAAAATAT
14713 TCTTAAATATATATTTAAAAATAAAAATAAAATAT
1 TCTTAAATATATATTTAAAAATAAAAATAAAATAT
* * * * *
14748 ATTTTAAA-AT-TATAATAATAATAATAATAAAACAT
1 -TCTTAAATATATAT-TTAAAAATAAAAATAAAATAT
14783 TCTTAAAT
1 TCTTAAAT
14791 TAAGTTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 19 0.29
35 40 0.62
36 6 0.09
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (35 bp):
TCTTAAATATATATTTAAAAATAAAAATAAAATAT
Found at i:14845 original size:25 final size:24
Alignment explanation
Indices: 14798--14845 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
14788 AATTAAGTTA
* * *
14798 ATAAAAAATATTTAATAACTTAAG
1 ATAAAAAATATTGAAAAAATTAAG
14822 ATAAAAATATATTGAAAAAATTAA
1 ATAAAAA-ATATTGAAAAAATTAA
14846 AAATATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAAAAAATATTGAAAAAATTAAG
Found at i:15388 original size:3 final size:3
Alignment explanation
Indices: 15380--15409 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
15370 TGCTTACTCC
*
15380 AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15410 CACAAACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:22603 original size:13 final size:13
Alignment explanation
Indices: 22585--22615 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
22575 GCTAGATGCT
22585 AGATAAAAGAAAA
1 AGATAAAAGAAAA
*
22598 AGATAAAAGAAAG
1 AGATAAAAGAAAA
22611 AGATA
1 AGATA
22616 TGCAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (13 bp):
AGATAAAAGAAAA
Found at i:39113 original size:23 final size:23
Alignment explanation
Indices: 39081--39132 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
39071 TTAGCTCTAT
39081 CGCCGAGAAAATCTTAAATTCAC
1 CGCCGAGAAAATCTTAAATTCAC
*
39104 CGCCGGGAAAATCTTAAATTCAC
1 CGCCGAGAAAATCTTAAATTCAC
*
39127 CACCGA
1 CGCCGA
39133 TCGTTGCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.19
Consensus pattern (23 bp):
CGCCGAGAAAATCTTAAATTCAC
Found at i:39479 original size:5 final size:5
Alignment explanation
Indices: 39469--39505 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
39459 TGACCGGTCT
*
39469 GACCC GACCC GACCC GA-CC AACCC GA-CC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
39506 GTTGACTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 7 0.25
5 21 0.75
ACGTcount: A:0.24, C:0.57, G:0.19, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:39494 original size:9 final size:9
Alignment explanation
Indices: 39469--39506 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
39459 TGACCGGTCT
39469 GACCCGACCC
1 GACCCGA-CC
39479 GACCCGACC
1 GACCCGACC
*
39488 AACCCGACC
1 GACCCGACC
39497 GACCCGACC
1 GACCCGACC
39506 G
1 G
39507 TTGACTCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.24, C:0.55, G:0.21, T:0.00
Consensus pattern (9 bp):
GACCCGACC
Found at i:39500 original size:18 final size:19
Alignment explanation
Indices: 39470--39505 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
39460 GACCGGTCTG
39470 ACCCGACCCGACCCGACCA
1 ACCCGACCCGACCCGACCA
39489 ACCCGA-CCGACCCGACC
1 ACCCGACCCGACCCGACC
39506 GTTGACTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.58, G:0.17, T:0.00
Consensus pattern (19 bp):
ACCCGACCCGACCCGACCA
Found at i:39518 original size:12 final size:12
Alignment explanation
Indices: 39501--39546 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
39491 CCGACCGACC
39501 CGACCGTTGACT
1 CGACCGTTGACT
39513 CGACCGTTGACT
1 CGACCGTTGACT
* *
39525 CGACC--CGACC
1 CGACCGTTGACT
39535 CGACCGTTGACT
1 CGACCGTTGACT
39547 TCTTTGACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 8 0.29
12 20 0.71
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.20
Consensus pattern (12 bp):
CGACCGTTGACT
Found at i:46794 original size:19 final size:19
Alignment explanation
Indices: 46770--46818 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
46760 GCTGCTGGAA
*
46770 ACCGGTTTG-ACCAGTTTCG
1 ACCGGTTCGAACC-GTTTCG
*
46789 ACCGGTTCGAACCGTTTTG
1 ACCGGTTCGAACCGTTTCG
46808 ACCGGTCTCGA
1 ACCGGT-TCGA
46819 CCGGTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (19 bp):
ACCGGTTCGAACCGTTTCG
Found at i:46818 original size:29 final size:29
Alignment explanation
Indices: 46769--46824 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
46759 TGCTGCTGGA
*
46769 AACCGGTTTGACCAGTTTCGACCGGTTCG
1 AACCGGTTTGACCAGTCTCGACCGGTTCG
* *
46798 AACCGTTTTGACCGGTCTCGACCGGTT
1 AACCGGTTTGACCAGTCTCGACCGGTT
46825 TGATCGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (29 bp):
AACCGGTTTGACCAGTCTCGACCGGTTCG
Found at i:46821 original size:19 final size:19
Alignment explanation
Indices: 46778--46834 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
46768 AAACCGGTTT
*
46778 GACCAGTTTCGACCGGT-TC
1 GACC-GTTTTGACCGGTCTC
46797 GAACCGTTTTGACCGGTCTC
1 G-ACCGTTTTGACCGGTCTC
* *
46817 GACCGGTTTGATCGGTCT
1 GACCGTTTTGACCGGTCT
46835 GACTCGACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.30
Consensus pattern (19 bp):
GACCGTTTTGACCGGTCTC
Found at i:46849 original size:5 final size:5
Alignment explanation
Indices: 46839--46885 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
46829 CGGTCTGACT
* *
46839 CGACC CGACC CGA-C CAACC CGACC CGACC GTTGACC CGACC CGACC C
1 CGACC CGACC CGACC CGACC CGACC CGACC --CGACC CGACC CGACC C
46886 TACCGTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 3 0.09
5 28 0.80
7 4 0.11
ACGTcount: A:0.21, C:0.55, G:0.19, T:0.04
Consensus pattern (5 bp):
CGACC
Found at i:46860 original size:14 final size:14
Alignment explanation
Indices: 46841--46867 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46831 GTCTGACTCG
46841 ACCCGACCCGACCA
1 ACCCGACCCGACCA
46855 ACCCGACCCGACC
1 ACCCGACCCGACC
46868 GTTGACCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.59, G:0.15, T:0.00
Consensus pattern (14 bp):
ACCCGACCCGACCA
Found at i:46883 original size:22 final size:22
Alignment explanation
Indices: 46855--46896 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
46845 GACCCGACCA
46855 ACCCGACCCGACCGTTGACCCG
1 ACCCGACCCGACCGTTGACCCG
*
46877 ACCCGACCCTACCGTTGACC
1 ACCCGACCCGACCGTTGACC
46897 GTTGATCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (22 bp):
ACCCGACCCGACCGTTGACCCG
Found at i:48554 original size:2 final size:2
Alignment explanation
Indices: 48547--48575 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48537 TAAATGTATT
48547 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48576 TATTTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50357 original size:20 final size:20
Alignment explanation
Indices: 50332--50370 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
50322 TTAAATGACT
50332 GGGGGTATCGGTACCATCCA
1 GGGGGTATCGGTACCATCCA
50352 GGGGGTATCGGTACCATCC
1 GGGGGTATCGGTACCATCC
50371 GAGCATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.21
Consensus pattern (20 bp):
GGGGGTATCGGTACCATCCA
Found at i:53023 original size:13 final size:13
Alignment explanation
Indices: 53005--53038 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
52995 ATGGGCATAT
*
53005 TTTGAAAACTATG
1 TTTGAAAACAATG
53018 TTTGAAAACAATG
1 TTTGAAAACAATG
53031 TTTGAAAA
1 TTTGAAAA
53039 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:57191 original size:21 final size:21
Alignment explanation
Indices: 57167--57207 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
57157 GTTTTAAGAT
57167 CATCAATTTTCTTTTGATGAC
1 CATCAATTTTCTTTTGATGAC
57188 CATCAATTTTCTTTTGATGA
1 CATCAATTTTCTTTTGATGA
57208 TCGTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (21 bp):
CATCAATTTTCTTTTGATGAC
Found at i:57376 original size:22 final size:21
Alignment explanation
Indices: 57334--57373 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57324 AAGACTATTT
57334 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
57355 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
57374 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:71220 original size:23 final size:24
Alignment explanation
Indices: 71172--71232 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 24
71162 CCATAATAAC
*
71172 ATTTTATTAAAATAATATTTTCAT
1 ATTTTATTAAAATAATATATTCAT
*
71196 ATTTT-TTAAATTAAGTATATT-AT
1 ATTTTATTAAAATAA-TATATTCAT
*
71219 ATATTA--AAAATAAT
1 ATTTTATTAAAATAAT
71233 TTTATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 14 0.45
24 10 0.32
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTATTAAAATAATATATTCAT
Found at i:71565 original size:17 final size:18
Alignment explanation
Indices: 71516--71565 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
71506 TGATATTTGA
71516 ATTTTATTTATTATTTTATT
1 ATTTTATTTA--ATTTTATT
* *
71536 ATTTTAATAAATTTT-TT
1 ATTTTATTTAATTTTATT
71553 ATTTTATTTAATT
1 ATTTTATTTAATT
71566 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 13 0.50
18 5 0.19
20 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTATTTAATTTTATT
Found at i:71929 original size:18 final size:18
Alignment explanation
Indices: 71906--71942 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
71896 AAATCGTCAG
71906 TCAAGTTATATAATTATA
1 TCAAGTTATATAATTATA
71924 TCAAGTTATATAATTATA
1 TCAAGTTATATAATTATA
71942 T
1 T
71943 GTTTGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TCAAGTTATATAATTATA
Found at i:81187 original size:17 final size:17
Alignment explanation
Indices: 81161--81195 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
81151 TAAGGTGATT
* *
81161 AAAAAGTAATTTTTTTA
1 AAAAAATAATATTTTTA
81178 AAAAAATAATATTTTTA
1 AAAAAATAATATTTTTA
81195 A
1 A
81196 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAAAAATAATATTTTTA
Found at i:85801 original size:17 final size:18
Alignment explanation
Indices: 85779--85834 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
85769 TTGACCGGTT
85779 CCGACCCGACCCGTTGA-
1 CCGACCCGACCCGTTGAC
85796 CCGACCCGACCGACCCGTTGAC
1 CCGA--C--CCGACCCGTTGAC
*
85818 CCGACCTGACCCGTTGA
1 CCGACCCGACCCGTTGA
85835 TCGTTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.12
18 11 0.33
19 1 0.03
20 1 0.03
21 12 0.36
22 4 0.12
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:85810 original size:21 final size:22
Alignment explanation
Indices: 85779--85828 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
85769 TTGACCGGTT
85779 CCGACCCGACCCGTTGA-CCGAC
1 CCGA-CCGACCCGTTGACCCGAC
85801 CCGACCGACCCGTTGACCCGAC
1 CCGACCGACCCGTTGACCCGAC
*
85823 CTGACC
1 CCGACC
85829 CGTTGATCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.18, C:0.50, G:0.22, T:0.10
Consensus pattern (22 bp):
CCGACCGACCCGTTGACCCGAC
Found at i:85830 original size:18 final size:17
Alignment explanation
Indices: 85798--85834 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
85788 CCCGTTGACC
85798 GACCCGACCGACCCGTT
1 GACCCGACCGACCCGTT
85815 GACCCGACCTGACCCGTT
1 GACCCGACC-GACCCGTT
85833 GA
1 GA
85835 TCGTTGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (17 bp):
GACCCGACCGACCCGTT
Found at i:85898 original size:30 final size:28
Alignment explanation
Indices: 85851--86054 Score: 225
Period size: 27 Copynumber: 7.1 Consensus size: 28
85841 ATTAGGTGAC
*
85851 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAA-AGGTGCT
* *
85880 ATTTTAGGAATATAATTCGAAAAAGGTGAT
1 ATTTTGGGAAT-TAATTCG-AAAAGGTGCT
*
85910 ATTTTGGGAATTTAATT--AAAAAGTGCT
1 ATTTTGGGAA-TTAATTCGAAAAGGTGCT
* *
85937 ATTTTGAGAATTTAATTCGAAAAAGGTGAT
1 ATTTTGGGAA-TTAATTCG-AAAAGGTGCT
*
85967 ATTTTGGGAATTAATTCGAAAA-GTGTT
1 ATTTTGGGAATTAATTCGAAAAGGTGCT
85994 ATTTTGGGAATTAATTCGAAAATGGTGCT
1 ATTTTGGGAATTAATTCGAAAA-GGTGCT
* * **
86023 ATTTTGGTAATTATTTTAAAAAGGTGCT
1 ATTTTGGGAATTAATTCGAAAAGGTGCT
86051 ATTT
1 ATTT
86055 CTGTAAAATG
Statistics
Matches: 151, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
27 50 0.33
28 14 0.09
29 40 0.26
30 43 0.28
31 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCGAAAAGGTGCT
Found at i:85939 original size:27 final size:28
Alignment explanation
Indices: 85851--86054 Score: 216
Period size: 30 Copynumber: 7.1 Consensus size: 28
85841 ATTAGGTGAC
**
85851 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTC-AAAAAGGTGCT
* *
85880 ATTTTAGGAATATAATTCGAAAAAGGTGAT
1 ATTTTGGGAAT-TAATTC-AAAAAGGTGCT
85910 ATTTTGGGAATTTAATT-AAAAA-GTGCT
1 ATTTTGGGAA-TTAATTCAAAAAGGTGCT
* *
85937 ATTTTGAGAATTTAATTCGAAAAAGGTGAT
1 ATTTTGGGAA-TTAATTC-AAAAAGGTGCT
* *
85967 ATTTTGGGAATTAATTCGAAAA-GTGTT
1 ATTTTGGGAATTAATTCAAAAAGGTGCT
*
85994 ATTTTGGGAATTAATTCGAAAATGGTGCT
1 ATTTTGGGAATTAATTC-AAAAAGGTGCT
* * *
86023 ATTTTGGTAATTATTTTAAAAAGGTGCT
1 ATTTTGGGAATTAATTCAAAAAGGTGCT
86051 ATTT
1 ATTT
86055 CTGTAAAATG
Statistics
Matches: 150, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
27 41 0.27
28 26 0.17
29 40 0.27
30 42 0.28
31 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCAAAAAGGTGCT
Found at i:85956 original size:57 final size:57
Alignment explanation
Indices: 85844--86054 Score: 248
Period size: 57 Copynumber: 3.7 Consensus size: 57
85834 ATCGTTGATT
* ** *
85844 AGGTGACATTTTGGGAATTAATTCGAAATGGGTGCTATTTT-AGGAATATAATTCGAAAA
1 AGGTGATATTTTGGGAATTAATTC-AAA-AAGTGCTATTTTGA-GAATTTAATTCGAAAA
85903 AGGTGATATTTTGGGAATTTAATT-AAAAAGTGCTATTTTGAGAATTTAATTCGAAAA
1 AGGTGATATTTTGGGAA-TTAATTCAAAAAGTGCTATTTTGAGAATTTAATTCGAAAA
* * *
85960 AGGTGATATTTTGGGAATTAATTCGAAAAGTGTTATTTTGGGAA-TTAATTCGAAAA
1 AGGTGATATTTTGGGAATTAATTCAAAAAGTGCTATTTTGAGAATTTAATTCGAAAA
* * * * *
86016 TGGTGCTATTTTGGTAATTATTTTAAAAAGGTGCTATTT
1 AGGTGATATTTTGGGAATTAATTCAAAAA-GTGCTATTT
86055 CTGTAAAATG
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
56 41 0.31
57 67 0.50
58 4 0.03
59 16 0.12
60 6 0.04
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.39
Consensus pattern (57 bp):
AGGTGATATTTTGGGAATTAATTCAAAAAGTGCTATTTTGAGAATTTAATTCGAAAA
Found at i:91938 original size:3 final size:3
Alignment explanation
Indices: 91930--91994 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
91920 TATATTATAT
* * * *
91930 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
91975 TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
91995 TTACAATATT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:92845 original size:2 final size:2
Alignment explanation
Indices: 92838--92909 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
92828 TTCACCTAAA
92838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92910 CATCAAAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99470 original size:32 final size:32
Alignment explanation
Indices: 99434--99518 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
99424 ATAAGAAGGC
*
99434 CAAACCATTAACTAAAAACAACCTGAGACATT
1 CAAACCATTAACCAAAAACAACCTGAGACATT
* *
99466 CAAACTATTGACCAAAAACAACCTGAGACATT
1 CAAACCATTAACCAAAAACAACCTGAGACATT
* *
99498 CAAACCATTGACCAAACACAA
1 CAAACCATTAACCAAAAACAA
99519 AAACCTGAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.16
Consensus pattern (32 bp):
CAAACCATTAACCAAAAACAACCTGAGACATT
Found at i:99929 original size:32 final size:32
Alignment explanation
Indices: 99881--100112 Score: 320
Period size: 32 Copynumber: 7.2 Consensus size: 32
99871 AAGCAATAGA
* *
99881 GGGCATATTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
99913 GGGCATCTTTGGAGATTCAACATCAAATGTTA
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
99945 GGGCATCTTTGGAGATTTAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * *
99978 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
100010 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
100042 GGGCATCTTTGGAGATTCAACATCAAAATATTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * * *
100075 GGGCATCTTTAGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
100107 TGGCAT
1 GGGCAT
100113 TCAATATCCT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
32 121 0.68
33 58 0.32
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:99990 original size:65 final size:64
Alignment explanation
Indices: 99880--100112 Score: 322
Period size: 65 Copynumber: 3.6 Consensus size: 64
99870 GAAGCAATAG
* * *
99880 AGGGCATATTTGAAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATGTT
1 AGGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATATT
* * *
99944 AGGGCATCTTTGGAGATTTAACATCAAAATGTTGGGGCATCTTTGGAGATTCAATATCGAATATT
1 AGGGCATCTTTGGAGATTCAACATC-AAATGTTGGGGCATCTTTGGAGATTCAACATCAAATATT
* *
100009 GGGGTATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAAATATT
1 AGGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATC-AAATATT
* * * * * *
100074 GGGGCATCTTTAGAGATTCAATATCGAATATTGTGGCAT
1 AGGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCAT
100113 TCAATATCCT
Statistics
Matches: 150, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
64 53 0.35
65 97 0.65
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (64 bp):
AGGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATATT
Found at i:100047 original size:97 final size:97
Alignment explanation
Indices: 99881--100112 Score: 365
Period size: 97 Copynumber: 2.4 Consensus size: 97
99871 AAGCAATAGA
* * * * *
99881 GGGCATATTTGAAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATGTTAG
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTAG
* *
99946 GGCATCTTTGGAGATTTAACATCAAAATGTTG
66 GGCATCTTTGGAGATTCAACATCAAAATATTG
* *
99978 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGTATCTTTGGAGATTCAACATCAAATGTTGG
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTAG
100043 GGCATCTTTGGAGATTCAACATCAAAATATTG
66 GGCATCTTTGGAGATTCAACATCAAAATATTG
* *
100075 GGGCATCTTTAGAGATTCAATATCGAATATTGTGGCAT
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCAT
100113 TCAATATCCT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 123 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (97 bp):
GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTAG
GGCATCTTTGGAGATTCAACATCAAAATATTG
Found at i:100255 original size:34 final size:34
Alignment explanation
Indices: 100214--100338 Score: 133
Period size: 34 Copynumber: 3.7 Consensus size: 34
100204 CTCTTAATTT
* * *
100214 TTTTGTCTAACTCGAGACAATTTATCAAAATAAA
1 TTTTGTCTAACTTGAGACAATTTCTCAAAACAAA
* *
100248 TTTTGTCTTAGTTGAGACAATTTCTCAAAACAAA
1 TTTTGTCTAACTTGAGACAATTTCTCAAAACAAA
* ** *
100282 TTTGGTCTCGCTTGAGACCATTTCTCAAAACAAA
1 TTTTGTCTAACTTGAGACAATTTCTCAAAACAAA
* ** *
100316 TTTCGTCTTGCTTGAGATAATTT
1 TTTTGTCTAACTTGAGACAATTT
100339 TTCTCTGAGA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 77 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (34 bp):
TTTTGTCTAACTTGAGACAATTTCTCAAAACAAA
Found at i:100708 original size:36 final size:36
Alignment explanation
Indices: 100661--100952 Score: 264
Period size: 36 Copynumber: 8.0 Consensus size: 36
100651 CGAAACAGAA
100661 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
*
100697 AAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * * *
100733 AAATTTTTTCTCCCTTCAGACAATCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * ***** * ** *
100769 --AGTTTCTCTCGAAACAAATTTTGTCTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGA--CAGTTTCCCTTGAAAC
* *
100805 ACATTTTGTCTCCCTTGAGACAGTTTCCATTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * *
100841 AAATTTTGTCTCTCTTGAGACGGTTTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
100877 AAATTTTGTCTCCCTTGAGACAATTTCACTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * * *
100913 AAAAGATTTTATCTCGCTTGAGATAGTTTCGCTCGAAAC
1 --AA-ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
100952 A
1 A
100953 TAATATTTTT
Statistics
Matches: 205, Mismatches: 44, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
34 11 0.05
36 153 0.75
37 1 0.00
38 12 0.06
39 28 0.14
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:100712 original size:21 final size:20
Alignment explanation
Indices: 100686--100822 Score: 70
Period size: 21 Copynumber: 7.4 Consensus size: 20
100676 TGAGACAGTT
100686 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTT-TC
*
100707 TCCCTTGAGAC-AA---TT-
1 TCCCTTGAAACAAATTTTTC
100722 TCCCTTGAAACAAATTTTTTC
1 TCCCTTGAAACAAA-TTTTTC
* *
100743 TCCCTTCAGAC-AA----TC
1 TCCCTTGAAACAAATTTTTC
* *
100758 TCCCTTGAGAC--A-GTTTC
1 TCCCTTGAAACAAATTTTTC
*
100775 T--CTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTT-TC
*
100794 TCCCTTGAAACACATTTTGTC
1 TCCCTTGAAACAAATTTT-TC
100815 TCCCTTGA
1 TCCCTTGA
100823 GACAGTTTCC
Statistics
Matches: 91, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
14 1 0.01
15 28 0.31
16 3 0.03
17 5 0.05
18 2 0.02
19 3 0.03
20 6 0.07
21 43 0.47
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (20 bp):
TCCCTTGAAACAAATTTTTC
Found at i:100951 original size:39 final size:39
Alignment explanation
Indices: 100879--100961 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
100869 CTTGAAACAA
* *
100879 ATTTTGTCTCCCTTGAGACAATTTCACTTGAAACAAAAG
1 ATTTTATCTCCCTTGAGACAATTTCACTCGAAACAAAAG
* * * * * *
100918 ATTTTATCTCGCTTGAGATAGTTTCGCTCGAAACATAAT
1 ATTTTATCTCCCTTGAGACAATTTCACTCGAAACAAAAG
100957 ATTTT
1 ATTTT
100962 TAGAAACTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (39 bp):
ATTTTATCTCCCTTGAGACAATTTCACTCGAAACAAAAG
Found at i:101222 original size:43 final size:43
Alignment explanation
Indices: 101047--101222 Score: 255
Period size: 43 Copynumber: 4.1 Consensus size: 43
101037 GATGACAAAT
* *
101047 TTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGG-TTC
1 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
* * ** *
101089 TTTGAGGACAAGCTTGAGAAACTATCGTGATATGTAGGGGTTTC
1 -TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
* *
101133 TTGATAAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCC
1 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
101176 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
1 TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
101219 TTGA
1 TTGA
101223 AGACAAATTT
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
43 115 0.97
44 3 0.03
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.30
Consensus pattern (43 bp):
TTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTTC
Found at i:101462 original size:90 final size:90
Alignment explanation
Indices: 101310--101603 Score: 443
Period size: 91 Copynumber: 3.3 Consensus size: 90
101300 ATTTTCAAGA
* *
101310 GTTTCTTGA-TTTTTAAGTCCTTCGGGTCAT-C-TAAAGACCTTCAGTGCATGATGTTTTCAAAT
1 GTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCGTAAA-ACCTTCAGTGCAGGATGTTTTCAAAT
* *
101372 GAGATCTAAGAAGCTGAGCCTTCTGGG
65 GAGATTTAAGAAACTGAGCCTTC-GGG
101399 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCGTAAAACCTTCAGTGCAGGATGTTTTCAAATG
1 GTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCGTAAAACCTTCAGTGCAGGATGTTTTCAAATG
*
101463 AGATTTGAGAAACTGAGCCTTCGGGG
66 AGATTTAAGAAACTGAGCCTTC-GGG
* * *
101489 GTTTCTTGATTTTTTAAGTCCTTCGGGCTATCCGTAAGACCTTTAGTGCAGGATGTTTTCAAATG
1 GTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCGTAAAACCTTCAGTGCAGGATGTTTTCAAATG
*
101554 AGATTTAAGAAACTAAGCCTTCGGG
66 AGATTTAAGAAACTGAGCCTTCGGG
101579 AGTTTCTTGATTTTTTAAGTCCTTC
1 -GTTTCTTGATTTTTTAAGTCCTTC
101604 AGGTAACCAT
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
89 29 0.15
90 61 0.32
91 100 0.53
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (90 bp):
GTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCGTAAAACCTTCAGTGCAGGATGTTTTCAAATG
AGATTTAAGAAACTGAGCCTTCGGG
Found at i:101822 original size:3 final size:3
Alignment explanation
Indices: 101814--101878 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
101804 TATATTATAT
* * * *
101814 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
101859 TTT TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
101879 TTACAATATT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:101823 original size:12 final size:12
Alignment explanation
Indices: 101806--101875 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
101796 AAAATATATA
101806 TATTATATTTAT
1 TATTATATTTAT
*
101818 TATTATATACTA-
1 TATTATAT-TTAT
*
101830 TAGTATGA-TTAT
1 TATTAT-ATTTAT
*
101842 TATTATTTTTAT
1 TATTATATTTAT
*
101854 TATTATTTTTAT
1 TATTATATTTAT
101866 TATTAATATT
1 TATT-ATATT
101876 ATTTTACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
11 2 0.04
12 38 0.81
13 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:102730 original size:2 final size:2
Alignment explanation
Indices: 102723--102777 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
102713 CACCTAAAAT
102723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102765 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
102778 TCATCAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:103691 original size:14 final size:14
Alignment explanation
Indices: 103672--103739 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
103662 TTAAAAATGT
103672 TATATATTTATACG
1 TATATATTTATACG
103686 TATATATTT-TAC-
1 TATATATTTATACG
* * * *
103698 TACAAATTTTAAAAATG
1 TATATA-TTT--ATACG
103715 TTATATATTTATACG
1 -TATATATTTATACG
103730 TATATATTTA
1 TATATATTTA
103740 ATAAATGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 19 0.47
15 3 0.08
16 1 0.03
17 3 0.08
18 4 0.10
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (14 bp):
TATATATTTATACG
Found at i:105635 original size:18 final size:18
Alignment explanation
Indices: 105596--105637 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
105586 ACCCGACCCG
*
105596 TTGACCCGACCCAACTCG
1 TTGACCCGACCCAACTCA
* *
105614 TTGACCCGACCCGACTTA
1 TTGACCCGACCCAACTCA
105632 TTGACC
1 TTGACC
105638 GTTGATCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.21
Consensus pattern (18 bp):
TTGACCCGACCCAACTCA
Found at i:105721 original size:30 final size:30
Alignment explanation
Indices: 105659--105807 Score: 157
Period size: 29 Copynumber: 5.1 Consensus size: 30
105649 ATCGGGTGAC
* *
105659 ATTTTGGGAA-TTAA-TTCAAAATGGGTGCT
1 ATTTTGGGAATTTAATTTGAAAA-AGGTGCT
*
105688 ATTTTGGGAATTTAATTTGAAAAAGGTGTT
1 ATTTTGGGAATTTAATTTGAAAAAGGTGCT
105718 ATTTTGGGAATTTAATTTG-AAAA-GTGCT
1 ATTTTGGGAATTTAATTTGAAAAAGGTGCT
* * *
105746 ATTTTAGGAA-TTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTTAATTTGAAAAAGGTGCT
* * * *
105775 ATTTTGGTAA-TTATTTTAAAAAATGTGCT
1 ATTTTGGGAATTTAATTTGAAAAAGGTGCT
105804 ATTT
1 ATTT
105808 CTGTAAAATG
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
27 7 0.07
28 16 0.16
29 45 0.44
30 28 0.27
31 6 0.06
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTTGAAAAAGGTGCT
Found at i:106424 original size:20 final size:20
Alignment explanation
Indices: 106399--106506 Score: 110
Period size: 20 Copynumber: 5.3 Consensus size: 20
106389 AATTGGGAAA
106399 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
106419 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
106439 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
106460 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
106480 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
106500 TTCGCAA
1 ATCGCAA
106507 CGCAATTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:106445 original size:61 final size:60
Alignment explanation
Indices: 106378--106513 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 60
106368 GAATAAGTAA
** * * * *
106378 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * * *
106439 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGA-ATTACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
*
106500 TTCGCAACGC-AATT
1 ATCGCAACGCGAATT
106514 TACATAGCGC
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 2 0.03
60 1 0.02
61 56 0.92
62 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (60 bp):
ATCGCAACGCGAATTACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:106778 original size:27 final size:27
Alignment explanation
Indices: 106722--106781 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
106712 ATCGCCGGCG
* *
106722 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCAAAATCAA
* *
106749 AAATCCCTCACAATCATTCAGAAATGAA
1 AAATCCCTCACAACCATTCA-AAATCAA
106777 AAATC
1 AAATC
106782 AACCTCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCAAAATCAA
Found at i:107092 original size:19 final size:19
Alignment explanation
Indices: 107070--107254 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
107060 GAAACCAAAA
* *
107070 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
107089 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
107108 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
107127 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
107147 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
107163 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
107180 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
107194 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
107213 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
107233 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
107253 TC
1 TC
107255 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:107147 original size:39 final size:38
Alignment explanation
Indices: 107070--107159 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
107060 GAAACCAAAA
*
107070 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
107108 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
107147 TCGCGTTGCGATT
1 TCGCGTTGCGATT
107160 GTCTGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 22 0.44
39 28 0.56
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:107170 original size:39 final size:39
Alignment explanation
Indices: 107070--107170 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
107060 GAAACCAAAA
* * **
107070 TCGCATTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
* **
107108 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
107147 TCGCGTTGCGATTGTCT-GGTCGCG
1 TCGCGTTGCGATT-TCTAGGTCGCG
107171 ATAGTCATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 22 0.39
39 33 0.58
40 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (39 bp):
TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
Found at i:107179 original size:33 final size:33
Alignment explanation
Indices: 107142--107229 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
107132 GTTGCGATTT
* *
107142 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
107175 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
107208 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
107230 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:107231 original size:20 final size:20
Alignment explanation
Indices: 107197--107254 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
107187 GCGATTCTCT
**
107197 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
107217 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
107237 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
107255 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:109316 original size:42 final size:42
Alignment explanation
Indices: 109256--109378 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
109246 GCCCGACTCG
* * *
109256 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
109298 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
109340 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
109379 TCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:109336 original size:21 final size:21
Alignment explanation
Indices: 109312--109381 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
109302 TCATTCCTCG
109312 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
109333 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
109354 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
109375 AGAGTCC
1 AGAGTCC
109382 GATTCACATG
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:110756 original size:14 final size:14
Alignment explanation
Indices: 110737--110772 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
110727 ATTGTTTAAT
110737 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
110751 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
110765 TGATTTGT
1 TGATTTGT
110773 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:110998 original size:33 final size:32
Alignment explanation
Indices: 110955--111081 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
110945 ATTAAATTCG
*
110955 CGTTGTGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
110988 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
111021 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
111054 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
111082 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:111044 original size:66 final size:66
Alignment explanation
Indices: 110948--111078 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
110938 GCGCGAAATT
* *
110948 AAATTCGCGTTGTGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
111013 A
66 A
*
111014 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
111079 GATAGTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:113384 original size:12 final size:12
Alignment explanation
Indices: 113367--113391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113357 TTCTTCGGGA
113367 CTTTTTCTTCTT
1 CTTTTTCTTCTT
113379 CTTTTTCTTCTT
1 CTTTTTCTTCTT
113391 C
1 C
113392 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:113598 original size:24 final size:24
Alignment explanation
Indices: 113564--113617 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
113554 CTGAAACATC
* *
113564 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
113588 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
113612 ATCAAA
1 ATCAAA
113618 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:114696 original size:20 final size:20
Alignment explanation
Indices: 114671--114726 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
114661 ATTCATTTGA
114671 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
114691 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
114711 TTATCGCAACGAGAAA
1 CTATCGCAACGCGAAA
114727 TCGCAATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:114790 original size:19 final size:19
Alignment explanation
Indices: 114745--114812 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
114735 TGAATGAAAA
114745 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
114761 TCG--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
114778 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
114797 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
114813 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:114929 original size:14 final size:14
Alignment explanation
Indices: 114910--114946 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
114900 CATCAATTAA
114910 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
114924 ACAAATCATCTTTT
1 ACAAATCAACATTT
114938 ACAAATCAA
1 ACAAATCAA
114947 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:116842 original size:20 final size:19
Alignment explanation
Indices: 116806--116857 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
116796 CTTAAAATCG
*
116806 CAACGCGAAATTACTATCA
1 CAACGCGAAATGACTATCA
* *
116825 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCA
*
116845 CAATGCGAAATGA
1 CAACGCGAAATGA
116858 AAATCGCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (19 bp):
CAACGCGAAATGACTATCA
Found at i:116863 original size:19 final size:18
Alignment explanation
Indices: 116841--116898 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
116831 GGAAATGGCT
116841 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
116860 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
116874 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
116892 ATCGCAA
1 ATCGCAA
116899 CGACAAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:116899 original size:32 final size:32
Alignment explanation
Indices: 116841--116918 Score: 131
Period size: 31 Copynumber: 2.4 Consensus size: 32
116831 GGAAATGGCT
*
116841 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAC-AA
116874 ATCGCAACGCGAAATG-AAATCGCAACGACAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAA
116905 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
116919 CACAAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 16 0.36
32 13 0.30
33 15 0.34
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAA
Found at i:116906 original size:18 final size:18
Alignment explanation
Indices: 116852--116906 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
116842 TCGCAATGCG
116852 AAATGAAAATCGCAACGAC
1 AAATG-AAATCGCAACGAC
116871 --A--AAATCGCAACG-C
1 AAATGAAATCGCAACGAC
116884 GAAATGAAATCGCAACGAC
1 -AAATGAAATCGCAACGAC
116903 AAAT
1 AAAT
116907 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
16 1 0.03
17 1 0.03
18 15 0.50
19 1 0.03
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (18 bp):
AAATGAAATCGCAACGAC
Found at i:116926 original size:32 final size:31
Alignment explanation
Indices: 116841--116929 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 31
116831 GGAAATGGCT
*
116841 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAA--AAAATCGCAACGACAAA
*
116874 ATCGCAACGCGAAATGAAATCGCAACGAC-AA
1 ATCGCAACGCGAAA-AAAATCGCAACGACAAA
116905 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAACGCGAAA-A-AAATCGCA
116930 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 16 0.32
32 21 0.42
33 13 0.26
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (31 bp):
ATCGCAACGCGAAAAAAATCGCAACGACAAA
Found at i:116966 original size:14 final size:14
Alignment explanation
Indices: 116947--117004 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
116937 TTTCATTTCG
116947 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
116961 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
116977 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
116993 CGTTGCGATTTT
1 CGTTGCGATTTT
117005 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:117011 original size:33 final size:33
Alignment explanation
Indices: 116930--117020 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
116920 ACAAATCGCA
*
116930 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
116963 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
116995 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
117021 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:117563 original size:18 final size:18
Alignment explanation
Indices: 117537--117581 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
117527 GTCGATCAGA
*
117537 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
117555 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
117573 TGATGGCTC
1 TGATGGCTC
117582 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Done.