Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002190.1 Hibiscus syriacus cultivar Beakdansim tig00004459_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: 87044
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:236 original size:13 final size:13
Alignment explanation
Indices: 218--242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208 ATTAATGTGT
218 TTAATTGTTAATG
1 TTAATTGTTAATG
231 TTAATTGTTAAT
1 TTAATTGTTAAT
243 TTGTAAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTAATTGTTAATG
Found at i:4642 original size:22 final size:21
Alignment explanation
Indices: 4592--4643 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
4582 AAATTTTATT
* *
4592 TAAAA-TTTAAAAAATAAAAT
1 TAAAATTTTAAAAAAGAAAAA
*
4612 TATATATTTTAAAAAAGAAAACA
1 TA-AAATTTTAAAAAAGAAAA-A
4635 TAAAATTTT
1 TAAAATTTT
4644 GAAATAACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 19 0.76
23 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAATTTTAAAAAAGAAAAA
Found at i:16942 original size:30 final size:30
Alignment explanation
Indices: 16908--16977 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
16898 ATAATAATTC
*
16908 ATTTGATCCCGCAATTGTATAATT-AAAG-TT
1 ATTTGATCCCG-AAGT-TATAATTAAAAGTTT
* *
16938 ATTTGATCTCGTAGTTATAATTAAAAGTTT
1 ATTTGATCCCGAAGTTATAATTAAAAGTTT
16968 ATTTGATCCC
1 ATTTGATCCC
16978 ACAGTTCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 21 0.62
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
ATTTGATCCCGAAGTTATAATTAAAAGTTT
Found at i:16989 original size:30 final size:28
Alignment explanation
Indices: 16925--16989 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
16915 CCCGCAATTG
* **
16925 TATAATTAAAGTTATTTGATCTCGTAGT
1 TATAATTAAAGTTATTTGATCCCACAGT
16953 TATAATTAAAAGTTTATTTGATCCCACAGT
1 TATAATT-AAAG-TTATTTGATCCCACAGT
*
16983 TCTAATT
1 TATAATT
16990 TTATTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 4 0.13
30 20 0.65
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (28 bp):
TATAATTAAAGTTATTTGATCCCACAGT
Found at i:17247 original size:19 final size:19
Alignment explanation
Indices: 17223--17264 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
17213 GAAATACTAG
17223 TTATAAAACTTTAATAAAA
1 TTATAAAACTTTAATAAAA
*
17242 TTATAAAACTTTTATAAAA
1 TTATAAAACTTTAATAAAA
17261 TTAT
1 TTAT
17265 TCATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATAAAACTTTAATAAAA
Found at i:17447 original size:21 final size:20
Alignment explanation
Indices: 17361--17518 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
17351 AAATGACCAA
**
17361 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
17380 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
17400 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
17420 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
17441 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
17462 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
17482 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
17503 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
17519 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:17547 original size:20 final size:20
Alignment explanation
Indices: 17485--17769 Score: 283
Period size: 20 Copynumber: 14.2 Consensus size: 20
17475 CGATTTTCCA
* ** *
17485 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
17505 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
17525 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
17545 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
17565 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
17585 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
17605 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
17625 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
17645 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
17665 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
17685 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
17705 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
17725 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
17745 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
17765 AAATC
1 AAATC
17770 ACAATACTGA
Statistics
Matches: 226, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 222 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:17571 original size:60 final size:60
Alignment explanation
Indices: 17505--17769 Score: 322
Period size: 60 Copynumber: 4.4 Consensus size: 60
17495 GCGAATATGA
* * *
17505 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGAT-AATCCGT
* * * * * *
17565 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGT
* * * *
17625 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
* *
17685 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGATAATCCGT
*
17745 AAATCGCAACGAGAATCTGTAAATC
1 AAATCGCAACGAGAATCCGTAAATC
17770 ACAATACTGA
Statistics
Matches: 180, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 177 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
Found at i:18491 original size:24 final size:24
Alignment explanation
Indices: 18452--18498 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18442 AAATTTGGTC
18452 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
18476 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
18499 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:21054 original size:19 final size:19
Alignment explanation
Indices: 20985--21276 Score: 321
Period size: 19 Copynumber: 16.7 Consensus size: 19
20975 GCAACGAGAG
20985 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21004 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
21018 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
21038 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21057 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21076 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21090 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21109 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21128 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
21142 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
21161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21180 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
21194 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21213 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21232 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
21246 AATCGCAATGCGAAAT-TA
1 AATCGCAATGCGAAATGAA
*
21264 AATCGCATTGCGA
1 AATCGCAATGCGA
21277 TTCTCCCGTT
Statistics
Matches: 233, Mismatches: 14, Indels: 53
0.78 0.05 0.18
Matches are distributed among these distances:
14 50 0.21
15 3 0.01
16 13 0.06
17 12 0.05
18 15 0.06
19 124 0.53
20 16 0.07
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:21112 original size:52 final size:52
Alignment explanation
Indices: 20971--21276 Score: 453
Period size: 52 Copynumber: 5.9 Consensus size: 52
20961 CGGAAATTAC
*
20971 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
21018 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
21076 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
21128 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
21180 AATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
21232 AATCGCAACGAGAGAATCGCAATGCGAAAT-TAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
21277 TTCTCCCGTT
Statistics
Matches: 237, Mismatches: 11, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
47 8 0.03
49 1 0.00
50 1 0.00
51 13 0.05
52 169 0.71
53 29 0.12
55 2 0.01
56 1 0.00
58 13 0.05
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:21165 original size:71 final size:69
Alignment explanation
Indices: 20985--21217 Score: 235
Period size: 71 Copynumber: 3.3 Consensus size: 69
20975 GCAACGAGAG
* * * *
20985 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAACGAGAAATGAAAAT-CGAA-ACGAAAATCGCAATGC-GAAATGAAAATCGCAATGCG
21050 AAATGAA
63 AAATGAA
* * * *
21057 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGTGA
1 AATCGCAACGAGAAATGAAAATCGAAACGA-A-AATCGCAATGCGAAATGAAAATCGCAATGCGA
21122 AATGAA
64 AATGAA
* **
21128 AATCGCAACGAGAGAATCG-CAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CG
1 AATCGCAACGAGA-AAT-GAAAAT-CGAAACGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
21190 AAA-G--
63 AAATGAA
* *
21194 AATCGCAATGCGAAATGAAAATCG
1 AATCGCAACGAGAAATGAAAATCG
21218 CAATGCGAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
64 3 0.02
65 6 0.04
66 11 0.08
68 1 0.01
69 4 0.03
70 3 0.02
71 67 0.48
72 40 0.28
73 6 0.04
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (69 bp):
AATCGCAACGAGAAATGAAAATCGAAACGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
TGAA
Found at i:21217 original size:33 final size:33
Alignment explanation
Indices: 20971--21220 Score: 235
Period size: 33 Copynumber: 7.2 Consensus size: 33
20961 CGGAAATTAC
*
20971 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
21004 AATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAA
1 AATCGCAACGA--AAGAATCGCAATGC-GAAATGAA
21038 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
21076 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
21109 AATCGCAATGTGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
21142 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG-AA--AGAATCGCAATGCGAAATGAA
21180 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
21213 AATCGCAA
1 AATCGCAA
21221 TGCGAAATGA
Statistics
Matches: 183, Mismatches: 11, Indels: 46
0.76 0.05 0.19
Matches are distributed among these distances:
32 1 0.01
33 95 0.52
34 19 0.10
35 10 0.05
36 11 0.06
37 2 0.01
38 34 0.19
39 11 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:21250 original size:33 final size:36
Alignment explanation
Indices: 21013--21270 Score: 244
Period size: 33 Copynumber: 7.3 Consensus size: 36
21003 AAATCCCAAC
21013 ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GC-G-AATGAAAATCGCAATGCGAA
21052 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
* *
21086 A-GAGAATCGCAATGCGAAATGAAAATCGCAATGTGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
21123 ATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
*
21156 ATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
21192 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
21227 ATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
*
21260 AT-TAAATCGCA
1 ATGAAAATCGCA
21271 TTGCGATTCT
Statistics
Matches: 194, Mismatches: 10, Indels: 37
0.80 0.04 0.15
Matches are distributed among these distances:
32 8 0.04
33 101 0.52
34 3 0.02
35 8 0.04
36 12 0.06
37 2 0.01
38 44 0.23
39 16 0.08
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:21325 original size:19 final size:19
Alignment explanation
Indices: 21285--21382 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
21275 GATTCTCCCG
21285 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
21305 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
21324 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
21338 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21357 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21376 TTGCGAT
1 TTGCGAT
21383 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:21379 original size:52 final size:53
Alignment explanation
Indices: 21266--21382 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
21256 CGAAATTAAA
21266 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
21319 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
21371 TCGCATTGCGAT
1 TCGCATTGCGAT
21383 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:21508 original size:14 final size:14
Alignment explanation
Indices: 21489--21525 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
21479 CATCAATTAC
21489 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
21503 ACAAATCATCTTTT
1 ACAAATCAACTTTT
21517 ACAAATCAA
1 ACAAATCAA
21526 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:23463 original size:20 final size:20
Alignment explanation
Indices: 23438--23503 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
23428 TAGTTTACTT
* *
23438 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
23458 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
23477 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
23496 TCGCAACG
1 TCGCAACG
23504 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:23513 original size:14 final size:14
Alignment explanation
Indices: 23494--23549 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
23484 GCGAAATGAA
*
23494 AATCGCAACGACAG
1 AATCGCAACGAAAG
23508 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
23525 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
23540 AATCGCAACG
1 AATCGCAACG
23550 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:23534 original size:32 final size:32
Alignment explanation
Indices: 23475--23565 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
23465 GCGAAACCAA
*
23475 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATG-AAATCGCAACGAAAG
*
23508 AATCGCAATGCGAAATGAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAATCGCAACGAAAG
23540 AATCGCAACGCGAAATGAAATCGCAA
1 AATCGCAACGCGAAATGAAATCGCAA
23566 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 39 0.71
33 16 0.29
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGAAAG
Found at i:23588 original size:19 final size:18
Alignment explanation
Indices: 23566--23693 Score: 110
Period size: 19 Copynumber: 7.3 Consensus size: 18
23556 GAAATCGCAA
23566 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
23585 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
23599 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
23618 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
**
23632 TGCGATTTTCATTCGCGT
1 TGCGATTTTGTTTCGCGT
23650 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
23669 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
23689 TGCGA
1 TGCGA
23694 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 3 0.03
17 1 0.01
18 14 0.16
19 35 0.39
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:23608 original size:33 final size:33
Alignment explanation
Indices: 23566--23656 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
23556 GAAATCGCAA
23566 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
23599 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
23632 TGCGATTTT-CATTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
23657 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 14 0.25
33 39 0.71
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:23876 original size:92 final size:93
Alignment explanation
Indices: 23741--24663 Score: 1735
Period size: 92 Copynumber: 10.1 Consensus size: 93
23731 ATGGATTGCA
23741 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
23805 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
23833 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
23897 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
23925 TTACTTTCAA-CAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC-GTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
23988 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24016 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
24081 TAGCAGAATTGGCAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
24109 TTACTTTCAACC-AAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
24173 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24201 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
24265 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24292 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
24357 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24385 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
24449 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24477 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAAT--ACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
24539 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24566 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
24631 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
24659 TTACT
1 TTACT
24664 AAGCAATCTA
Statistics
Matches: 814, Mismatches: 5, Indels: 23
0.97 0.01 0.03
Matches are distributed among these distances:
89 33 0.04
90 56 0.07
91 71 0.09
92 553 0.68
93 101 0.12
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:26379 original size:14 final size:14
Alignment explanation
Indices: 26360--26416 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
26350 TTGAAATGAA
26360 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
26374 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
26393 AATCGCAACTAGAG
1 AATCGCAACGAGAG
26407 AATCGCAACG
1 AATCGCAACG
26417 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:26391 original size:33 final size:33
Alignment explanation
Indices: 26352--26435 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
26342 GTCTTTTGTT
26352 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
26385 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
26418 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
26436 CGAAATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:26398 original size:19 final size:19
Alignment explanation
Indices: 26374--26457 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
26364 GCAACGAGAG
26374 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
26393 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
26407 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
26426 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
26445 AATCGCAATGCGA
1 AATCGCAACGCGA
26458 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 41 0.75
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:26488 original size:14 final size:14
Alignment explanation
Indices: 26469--26525 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
26459 TTTGGTTTCG
26469 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26483 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
26502 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26516 CGTTGCGATT
1 CGTTGCGATT
26526 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26501 original size:33 final size:33
Alignment explanation
Indices: 26453--26533 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
26443 AAAATCGCAA
**
26453 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
26486 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
26519 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
26534 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:26536 original size:21 final size:21
Alignment explanation
Indices: 26510--26585 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
26500 CGCGTTGCGA
26510 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
26531 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
26551 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
26572 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
26586 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:26566 original size:41 final size:41
Alignment explanation
Indices: 26509--26586 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
26499 TCGCGTTGCG
*
26509 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
26550 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
26587 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:26705 original size:33 final size:33
Alignment explanation
Indices: 26663--26733 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
26653 AATACTAACT
*
26663 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
26696 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
26729 TGAAA
1 TGAAA
26734 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:26967 original size:21 final size:22
Alignment explanation
Indices: 26916--26969 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
26906 TGGTTGTGAG
**
26916 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
26938 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
26959 GGATTTCTTCG
1 GGATTTCTTCG
26970 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:27141 original size:20 final size:20
Alignment explanation
Indices: 27116--27249 Score: 164
Period size: 20 Copynumber: 6.7 Consensus size: 20
27106 CTTTAAATAT
27116 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27136 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
27158 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
27177 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
27197 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27217 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
27237 CGCGTTGCGATTT
1 CGCGTTGCGATTT
27250 TTCATATTCG
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 79 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:27243 original size:40 final size:40
Alignment explanation
Indices: 27115--27249 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
27105 GCTTTAAATA
*
27115 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
27156 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
27196 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
27236 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
27250 TTCATATTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
40 50 0.62
41 30 0.38
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:27261 original size:21 final size:20
Alignment explanation
Indices: 27217--27271 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
27207 TTTACGGATA
* * *
27217 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTTTATATT
27237 CGCGTTGCGATTTTTCATATT
1 CGCGTTGCGATTTTT-ATATT
27258 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
27272 GGAAAATCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (20 bp):
CGCGTTGCGATTTTTATATT
Found at i:27262 original size:81 final size:81
Alignment explanation
Indices: 27118--27268 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
27108 TTAAATATCG
* *
27118 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTAGCGTTGCGATTTACAGATACGCGTT
27183 GCGATATACGGATACA
66 GCGATATACGGATACA
* * * * *
27199 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGTTCGCGTTGCGATTTTTCATATTCGCGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTAGCGTTGCGA-TTTACAGATACGCGT
27263 TGCGAT
65 TGCGAT
27269 TTTGGAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 17 0.27
81 45 0.73
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (81 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTAGCGTTGCGATTTACAGATACGCGTT
GCGATATACGGATACA
Found at i:27281 original size:21 final size:21
Alignment explanation
Indices: 27236--27374 Score: 86
Period size: 21 Copynumber: 6.7 Consensus size: 21
27226 ATTTATGTGT
** * *
27236 TCGCGTTGCGATTTTTCATAT
1 TCGCGTTGCGATTTTGGAAAA
27257 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGGAAAA
** * * **
27278 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTGGAAAA
* *
27299 TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGGAA-AA
*
27320 TCGCGTTGCGATTTTGGAAAC
1 TCGCGTTGCGATTTTGGAAAA
** * **
27341 T-GATTTGCGATTCTGG-GGA
1 TCGCGTTGCGATTTTGGAAAA
27360 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
27375 TATTTCACGT
Statistics
Matches: 88, Mismatches: 27, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
19 1 0.01
20 23 0.26
21 62 0.70
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATTTTGGAAAA
Found at i:27330 original size:42 final size:44
Alignment explanation
Indices: 27236--27335 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 44
27226 ATTTATGTGT
* * *
27236 TCGCGTTGCG-ATTT-TTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTTTGCAAAA
**
27278 TCGCAATGCGAATTTGTAC-TA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTTTGCAA-AA
*
27320 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
27336 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 37 0.79
43 6 0.13
44 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (44 bp):
TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTTTGCAAAA
Found at i:37075 original size:33 final size:37
Alignment explanation
Indices: 37033--37099 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
37023 AAAAACAGCA
37033 GTTCGGAAAAAAAAG-G-A-AAAAAAGAGAAGAAGCT
1 GTTCGGAAAAAAAAGAGAAGAAAAAAGAGAAGAAGCT
37067 GTTC-GAAAAAAAAGAGAAGAAAAAAGAGAAGAA
1 GTTCGGAAAAAAAAGAGAAGAAAAAAGAGAAGAA
37100 AAAAATGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 10 0.33
34 5 0.17
35 1 0.03
36 14 0.47
ACGTcount: A:0.63, C:0.04, G:0.25, T:0.07
Consensus pattern (37 bp):
GTTCGGAAAAAAAAGAGAAGAAAAAAGAGAAGAAGCT
Found at i:37090 original size:14 final size:14
Alignment explanation
Indices: 37071--37104 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
37061 GAAGCTGTTC
37071 GAAAAAAAAGAGAA
1 GAAAAAAAAGAGAA
37085 G--AAAAAAGAGAA
1 GAAAAAAAAGAGAA
37097 GAAAAAAA
1 GAAAAAAA
37105 TGGAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.67
14 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAGAA
Found at i:37101 original size:11 final size:12
Alignment explanation
Indices: 37074--37103 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
37064 GCTGTTCGAA
37074 AAAAAAGAGAAG
1 AAAAAAGAGAAG
37086 AAAAAAGAGAAG
1 AAAAAAGAGAAG
37098 AAAAAA
1 AAAAAA
37104 ATGGAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAG
Found at i:42733 original size:47 final size:45
Alignment explanation
Indices: 42682--42774 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
42672 AGACGTTTTC
*
42682 GTAAAAGGTAAGGGTGACTCAGCGAAAAAGGATTTGTGTAGTTTTAA
1 GTAAAAGGTAAGGGTGA-TCAG-GAAAAAGGATTTGTGCAGTTTTAA
* * **
42729 GTAAAAGTTAAGGGTGATTAGGTGAAAGGATTTGTGCAGTTTTAA
1 GTAAAAGGTAAGGGTGATCAGGAAAAAGGATTTGTGCAGTTTTAA
42774 G
1 G
42775 GCTGTTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
45 22 0.54
46 3 0.07
47 16 0.39
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.30
Consensus pattern (45 bp):
GTAAAAGGTAAGGGTGATCAGGAAAAAGGATTTGTGCAGTTTTAA
Found at i:44211 original size:3 final size:3
Alignment explanation
Indices: 44203--44316 Score: 183
Period size: 3 Copynumber: 37.7 Consensus size: 3
44193 TTTTTATCCA
* *
44203 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44251 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
44297 CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
44317 AATATATTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 99 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44831 original size:22 final size:22
Alignment explanation
Indices: 44788--44831 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44778 AAAAAGAGAG
* * * *
44788 AGACAGAGAACGGAGAAGAAAA
1 AGACAGAGAAAGAAAAAAAAAA
44810 AGACAGAGAAAGAAAAAAAAAA
1 AGACAGAGAAAGAAAAAAAAAA
44832 CAAACTAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
AGACAGAGAAAGAAAAAAAAAA
Found at i:45743 original size:20 final size:21
Alignment explanation
Indices: 45697--45743 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
45687 CTGCTTTTAA
*
45697 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
45718 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
45737 ATATATT
1 ATATATT
45744 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:45821 original size:23 final size:24
Alignment explanation
Indices: 45787--45832 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
45777 TATATATGAT
45787 AAATAATAA-TTT-ATATTTTTTA
1 AAATAATAATTTTAATATTTTTTA
*
45809 AAATAAATTATTTTAATATTTTTT
1 AAAT-AATAATTTTAATATTTTTT
45833 CAATATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 3 0.15
25 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATAATAATTTTAATATTTTTTA
Found at i:57124 original size:7 final size:7
Alignment explanation
Indices: 57112--57166 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
57102 ATTATGCTTG
57112 AAGAAAA
1 AAGAAAA
57119 AAGAAAA
1 AAGAAAA
57126 GAA-AAAGA
1 -AAGAAA-A
*
57134 AAAAAAA
1 AAGAAAA
57141 AAGAAAA
1 AAGAAAA
57148 AAG--AA
1 AAGAAAA
57153 AAGAAAA
1 AAGAAAA
57160 AAGAAAA
1 AAGAAAA
57167 TGAAAAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
5 5 0.12
7 31 0.74
8 6 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:57129 original size:12 final size:12
Alignment explanation
Indices: 57112--57185 Score: 89
Period size: 12 Copynumber: 6.0 Consensus size: 12
57102 ATTATGCTTG
57112 AAGAAAA-AAGAA
1 AAGAAAAGAA-AA
57124 AAGAAAAAGAAAA
1 AAG-AAAAGAAAA
57137 AA-AAAAGAAAA
1 AAGAAAAGAAAA
57148 AAGAAAAGAAAA
1 AAGAAAAGAAAA
57160 AAGAAAATGAAAAA
1 AAGAAAA-G-AAAA
*
57174 AAGAGAAGAAAA
1 AAGAAAAGAAAA
57186 TAAAGGGGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
11 11 0.20
12 23 0.41
13 10 0.18
14 12 0.21
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:57153 original size:36 final size:38
Alignment explanation
Indices: 57112--57185 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 38
57102 ATTATGCTTG
57112 AAGAAAA-AAGAAAAGAAAAAGAAAAAAA-A-AAGAAAA
1 AAGAAAAGAA-AAAAGAAAAAGAAAAAAAGAGAAGAAAA
*
57148 AAGAAAAGAAAAAAGAAAATGAAAAAAAGAGAAGAAAA
1 AAGAAAAGAAAAAAGAAAAAGAAAAAAAGAGAAGAAAA
57186 TAAAGGGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 24 0.71
37 3 0.09
38 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (38 bp):
AAGAAAAGAAAAAAGAAAAAGAAAAAAAGAGAAGAAAA
Found at i:57173 original size:7 final size:6
Alignment explanation
Indices: 57116--57173 Score: 68
Period size: 6 Copynumber: 9.8 Consensus size: 6
57106 TGCTTGAAGA
57116 AAAAAG -AAAAG AAAAAG AAAAA- AAAAAG AAAAA- AGAAAAG AAAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG -AAAAAG
*
57163 AAAATG AAAAA
1 AAAAAG AAAAA
57174 AAGAGAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
5 11 0.24
6 28 0.62
7 5 0.11
8 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:57186 original size:19 final size:17
Alignment explanation
Indices: 57112--57185 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 17
57102 ATTATGCTTG
57112 AAGAAAAAAGAAAAGAAA
1 AAGAAAAAA-AAAAGAAA
57130 AAGAAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAG-AAA
57148 AAGAAAAGAAAAAAGAAA
1 AAGAAAA-AAAAAAGAAA
*
57166 ATGAAAAAAAGAGAAGAAA
1 AAGAAAAAAA-A-AAGAAA
57185 A
1 A
57186 TAAAGGGGTC
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
17 8 0.16
18 29 0.57
19 14 0.27
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:58412 original size:165 final size:165
Alignment explanation
Indices: 58221--58688 Score: 803
Period size: 165 Copynumber: 2.8 Consensus size: 165
58211 CATTAACTGA
*
58221 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
58286 A-CAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
58350 CTGATCTGGTCGGACAGAACCAATCATTGAATTTGG
131 CTGATCTGGTCGGACAGAA-CAATCATTGAATTTGG
* *
58386 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
*
58451 ACCAATCATTGAATTTAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
58516 CTGATCTGGTTGGACAGAACAATCATTGAATTTGG
131 CTGATCTGGTCGGACAGAACAATCATTGAATTTGG
* * * * *
58551 AAGATGAATTTGTTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGATAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
* * *
58616 ATCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
58681 CTGATCTG
131 CTGATCTG
58689 TTTTGGTAAG
Statistics
Matches: 286, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
165 206 0.72
166 80 0.28
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (165 bp):
AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTCGGACAGAACAATCATTGAATTTGG
Found at i:58426 original size:83 final size:82
Alignment explanation
Indices: 58221--58688 Score: 792
Period size: 83 Copynumber: 5.7 Consensus size: 82
58211 CATTAACTGA
* *
58221 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
58286 ACAATCATTGAATTTGG
66 ACAATCATTGAATTTGG
*
58303 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
58368 ACCAATCATTGAATTTGG
66 A-CAATCATTGAATTTGG
*
58386 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
*
58451 ACCAATCATTGAATTTAG
66 A-CAATCATTGAATTTGG
58469 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
58534 ACAATCATTGAATTTGG
66 ACAATCATTGAATTTGG
* * * * * *
58551 AAGATGAATTTGTTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGATAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
58616 ATCAATCATTGAATTTGG
66 A-CAATCATTGAATTTGG
* *
58634 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
58689 TTTTGGTAAG
Statistics
Matches: 370, Mismatches: 14, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
82 140 0.38
83 230 0.62
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (82 bp):
AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACAATCATTGAATTTGG
Found at i:58659 original size:248 final size:248
Alignment explanation
Indices: 58221--58688 Score: 819
Period size: 248 Copynumber: 1.9 Consensus size: 248
58211 CATTAACTGA
*
58221 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
* *
58286 ACAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACAATCATTGAATTTGGAAGATGAATGTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
58351 TGATCTGGTCGGACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGA
131 TGATCTGGTCAGACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGA
58416 AGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
196 AGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
*
58469 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
* *
58534 ACAATCATTGAATTTGGAAGATGAATTTGTTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACAATCATTGAATTTGGAAGATGAATGTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
* * * *
58599 TGATCTGGTTAGATAGAATCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGA
131 TGATCTGGTCAGACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGA
*
58664 AGTGTTCTTTGAGTTATCTGATCTG
196 AGTATTCTTTGAGTTATCTGATCTG
58689 TTTTGGTAAG
Statistics
Matches: 207, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
248 207 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (248 bp):
AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
ACAATCATTGAATTTGGAAGATGAATGTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTCAGACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTAATAGCATCTTCTGGA
AGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
Found at i:59538 original size:113 final size:113
Alignment explanation
Indices: 59329--60004 Score: 1088
Period size: 113 Copynumber: 6.0 Consensus size: 113
59319 CAAAGATTCA
* * *
59329 AATTTATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCAATTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
59394 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
59442 AATTCATCAAATTGATGGATTAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-AATTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
59506 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
59555 AATTCATCACTTGATGGATCATTTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCGTCTGAAG
1 AATTCATCAATTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
59620 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
59669 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCAATTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
59734 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
59782 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAATTCGTCATCTG
1 AATTCATCAATTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
59846 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
59898 AATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCAATTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
59962 AGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
60005 GAATGACTCT
Statistics
Matches: 526, Mismatches: 29, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
112 64 0.12
113 237 0.45
114 120 0.23
115 19 0.04
116 85 0.16
117 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (113 bp):
AATTCATCAATTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:59733 original size:227 final size:225
Alignment explanation
Indices: 59329--60004 Score: 1127
Period size: 227 Copynumber: 3.0 Consensus size: 225
59319 CAAAGATTCA
* * *
59329 AATTTATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
59394 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTGATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATG
*
59459 GATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
130 GATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
59524 AATAAGAAGAATTTGTTCAACCTTTTACCTG
195 AATAAGAAGAATTTGTTCAACCTTTTACCTG
* * *
59555 AATTCATCACTTGATGGATCATTTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCGTCTGAAG
1 AATTCATCATTTGATGGATCA-TCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
59620 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATG
*
59685 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
130 GATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
59750 TAATGAGAAGAATTTGTTCAACCTTTTACCTG
194 TAATAAGAAGAATTTGTTCAACCTTTTACCTG
* * * ** *
59782 AATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTCATCTGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAAAAAGTTCATAATGAGAAGAA--C-TCATCTGA
59847 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGA
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGA
*
59912 TGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTC
128 TGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
59977 ATAATAAGAAGAATTTGTTCAACCTTTT
193 ATAATAAGAAGAATTTGTTCAACCTTTT
60005 GAATGACTCT
Statistics
Matches: 420, Mismatches: 25, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
226 65 0.15
227 193 0.46
228 73 0.17
229 89 0.21
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (225 bp):
AATTCATCATTTGATGGATCATCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGG
ATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATAAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:60329 original size:3 final size:3
Alignment explanation
Indices: 60321--60438 Score: 184
Period size: 3 Copynumber: 39.7 Consensus size: 3
60311 TTTTTATCCA
* *
60321 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
60369 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
60417 TAT TAT CAT TA- TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
60439 AATATATTAA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 103 0.98
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:60919 original size:22 final size:22
Alignment explanation
Indices: 60894--60953 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
60884 CCATCTGCGA
* *
60894 AGAAAAAAAAAGAGAGAGACAG
1 AGAAAAAAAAAGAAAAAGACAG
* *
60916 AGAACAAAGAAGAAAAAGACAG
1 AGAAAAAAAAAGAAAAAGACAG
*
60938 AGAAAGAAAAA-AAAAA
1 AGAAAAAAAAAGAAAAA
60954 CAAACTAGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAGAAAAAGACAG
Found at i:61871 original size:20 final size:21
Alignment explanation
Indices: 61825--61871 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
61815 CTGCTTTTAA
*
61825 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
61846 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
61865 ATATATT
1 ATATATT
61872 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:61949 original size:23 final size:24
Alignment explanation
Indices: 61915--61960 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
61905 TATATATGAT
61915 AAATAATAA-TTT-ATATTTTTTA
1 AAATAATAATTTTAATATTTTTTA
*
61937 AAATAAATTATTTTAATATTTTTT
1 AAAT-AATAATTTTAATATTTTTT
61961 CAATATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 3 0.15
25 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATAATAATTTTAATATTTTTTA
Found at i:62812 original size:37 final size:37
Alignment explanation
Indices: 62771--62893 Score: 178
Period size: 37 Copynumber: 3.4 Consensus size: 37
62761 GTAACTATGC
62771 TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTTGT
1 TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTTGT
62808 TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTTGT
1 TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTTGT
* * * * *
62845 TTAGGGACTGCAATCTGGTTTAAAAT-TTTGTTTTATT
1 TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTT-GT
62882 TTA-GGGCTGGAA
1 TTAGGGGCTGGAA
62894 GAATTGGTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.19
37 63 0.81
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (37 bp):
TTAGGGGCTGGAATATTGTTTAAAATCTTTGTTTTGT
Found at i:64023 original size:20 final size:21
Alignment explanation
Indices: 63983--64022 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63973 AGTACGCTCG
63983 GAGGGAACCGATTCCCCCCCA
1 GAGGGAACCGATTCCCCCCCA
*
64004 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
64023 ACTGTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCA
Found at i:69812 original size:20 final size:21
Alignment explanation
Indices: 69789--69868 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
69779 TTGATGTAGA
69789 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* * *
69809 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-ATG-AG
* *
69832 GGGAATCGATTCCCCCCA-CAG
1 GGGAATCGA-TACCCCCATGAG
69853 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
69869 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 20 0.42
21 13 0.27
22 1 0.02
23 8 0.17
24 6 0.12
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:71521 original size:12 final size:12
Alignment explanation
Indices: 71504--71529 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
71494 TGAGCCTGAA
71504 CAGCCCGAGGAG
1 CAGCCCGAGGAG
71516 CAGCCCGAGGAG
1 CAGCCCGAGGAG
71528 CA
1 CA
71530 AGCACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CAGCCCGAGGAG
Found at i:73732 original size:40 final size:40
Alignment explanation
Indices: 73680--73848 Score: 126
Period size: 38 Copynumber: 4.5 Consensus size: 40
73670 TCTCAAGACT
*
73680 CAAACCATAATATTAAATCTAGAACAATAAAATCAATAAA
1 CAAACCATAATATTAAATCTAAAACAATAAAATCAATAAA
* * * *
73720 CAAACCACAATATTAAAATGT-CAAC--TCAAGAT---T---
1 CAAACCATAATATT-AAATCTAAAACAAT-AAAATCAATAAA
* * * *
73753 CAAACCACAATATTAACTCTAAAATAATAAAATCCAT-AA
1 CAAACCATAATATTAAATCTAAAACAATAAAATCAATAAA
* * * *
73792 -AAACAATAATACTAAGTCTAAAACAATAAAATCCATAAA
1 CAAACCATAATATTAAATCTAAAACAATAAAATCAATAAA
73831 CAAACCATAATATTAAAT
1 CAAACCATAATATTAAAT
73849 TGTCAAATCT
Statistics
Matches: 100, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
32 4 0.04
33 16 0.16
34 4 0.04
35 1 0.01
36 1 0.01
37 1 0.01
38 32 0.32
39 6 0.06
40 30 0.30
41 5 0.05
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.23
Consensus pattern (40 bp):
CAAACCATAATATTAAATCTAAAACAATAAAATCAATAAA
Found at i:73824 original size:111 final size:113
Alignment explanation
Indices: 73681--73886 Score: 308
Period size: 111 Copynumber: 1.8 Consensus size: 113
73671 CTCAAGACTC
* * *
73681 AAACCATAATATTAAATCTAGAACAATAAAATCAATAAACAAACCACAATATTAAAATGTC-AA-
1 AAACAATAATACTAAATCTAAAACAATAAAATCAATAAACAAACCACAATATTAAAATGTCAAAT
*
73744 CTCAAGATTCAAACCACAATATTAACTCTAAAATAATAAAATCCATAA
66 CTCAAGACTCAAACCACAATATTAACTCTAAAATAATAAAATCCATAA
* * * *
73792 AAACAATAATACTAAGTCTAAAACAATAAAATCCATAAACAAACCATAATATTAAATTGTCAAAT
1 AAACAATAATACTAAATCTAAAACAATAAAATCAATAAACAAACCACAATATTAAAATGTCAAAT
* *
73857 CTCAAGACTCAAACCATAATATTAAGTCTA
66 CTCAAGACTCAAACCACAATATTAACTCTA
73887 GAACAATATT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 54 0.65
112 2 0.02
113 27 0.33
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.24
Consensus pattern (113 bp):
AAACAATAATACTAAATCTAAAACAATAAAATCAATAAACAAACCACAATATTAAAATGTCAAAT
CTCAAGACTCAAACCACAATATTAACTCTAAAATAATAAAATCCATAA
Found at i:79435 original size:12 final size:12
Alignment explanation
Indices: 79420--79452 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
79410 GTTTTCCTTT
79420 TCTTTTTTTAAA
1 TCTTTTTTTAAA
79432 TC-TTTTTTAAA
1 TCTTTTTTTAAA
79443 TCTCTTTTTT
1 TCT-TTTTTT
79453 CGTGGAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 2 0.11
13 6 0.32
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTTTTTTAAA
Done.