Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004821.1 Hibiscus syriacus cultivar Beakdansim tig00010865_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: 427682
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--4599 Score: 7757
Period size: 7 Copynumber: 675.3 Consensus size: 7
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4176 CCTAAAC
1 CCTAAAC
4183 CCTAAA-
1 CCTAAAC
4189 CCTAAAC
1 CCTAAAC
4196 CCTAAAC
1 CCTAAAC
4203 CCTAAAC
1 CCTAAAC
4210 CCTAAAC
1 CCTAAAC
4217 CCTAAAC
1 CCTAAAC
4224 CCTAAAC
1 CCTAAAC
4231 CCTAAAC
1 CCTAAAC
4238 CCTAAA-
1 CCTAAAC
4244 CC-AAAC
1 CCTAAAC
4250 CCTAAAC
1 CCTAAAC
4257 CCTAAA-
1 CCTAAAC
4263 CCTAAAC
1 CCTAAAC
4270 CCTAAAC
1 CCTAAAC
4277 CCTAAAC
1 CCTAAAC
4284 CCTAAAC
1 CCTAAAC
4291 CCTAAAC
1 CCTAAAC
4298 CCTAAA-
1 CCTAAAC
4304 CCTAAAC
1 CCTAAAC
4311 CCTAAAC
1 CCTAAAC
4318 CCTAAAC
1 CCTAAAC
4325 CCTAAAC
1 CCTAAAC
4332 CCTAAAC
1 CCTAAAC
4339 CCTAAAC
1 CCTAAAC
4346 CCTAAAC
1 CCTAAAC
4353 CCTAAAC
1 CCTAAAC
4360 CCTAAAC
1 CCTAAAC
4367 CCTAAAC
1 CCTAAAC
4374 CCTAAAC
1 CCTAAAC
4381 CCT-AAC
1 CCTAAAC
4387 CCTAAAC
1 CCTAAAC
4394 CCTAAAC
1 CCTAAAC
4401 CCTAAAC
1 CCTAAAC
4408 CCTAAAC
1 CCTAAAC
4415 CCTAAAC
1 CCTAAAC
4422 CCTAAAC
1 CCTAAAC
4429 CCTAAAC
1 CCTAAAC
4436 CCTAAAC
1 CCTAAAC
4443 CCTAAAC
1 CCTAAAC
4450 CCTAAAC
1 CCTAAAC
4457 CCTAAA-
1 CCTAAAC
4463 CCTAAAC
1 CCTAAAC
4470 CCTAAAC
1 CCTAAAC
4477 CCT-AAC
1 CCTAAAC
4483 CCTAAAC
1 CCTAAAC
4490 CCTAAAC
1 CCTAAAC
*
4497 CCGAAAC
1 CCTAAAC
4504 CCTAAAC
1 CCTAAAC
4511 CCTAAAC
1 CCTAAAC
4518 CCTAAACC
1 CCTAAA-C
4526 CCTAAACCC
1 CCTAAA--C
4535 CCTAAA-
1 CCTAAAC
4541 CCTAAAC
1 CCTAAAC
4548 CCTAAAC
1 CCTAAAC
4555 CCTAAAC
1 CCTAAAC
4562 CCTAAAC
1 CCTAAAC
4569 CCTAAAC
1 CCTAAAC
4576 CCTAAAC
1 CCTAAAC
4583 CCTAAACC
1 CCTAAA-C
4591 CCTAAAC
1 CCTAAAC
4598 CC
1 CC
4600 CCCGAGCCCC
Statistics
Matches: 4407, Mismatches: 17, Indels: 336
0.93 0.00 0.07
Matches are distributed among these distances:
4 2 0.00
5 98 0.02
6 661 0.15
7 3518 0.80
8 81 0.02
9 30 0.01
10 17 0.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:4635 original size:7 final size:7
Alignment explanation
Indices: 4625--4763 Score: 255
Period size: 7 Copynumber: 20.0 Consensus size: 7
4615 CCCCCCCCGA
4625 GAGCCCC
1 GAGCCCC
4632 GAGCCCC
1 GAGCCCC
4639 GAG-CCC
1 GAGCCCC
4645 GAGCCCC
1 GAGCCCC
4652 GAGCCCC
1 GAGCCCC
4659 GAGCCCC
1 GAGCCCC
4666 GAGCCCC
1 GAGCCCC
4673 GAGCCCC
1 GAGCCCC
4680 GAG-CCC
1 GAGCCCC
4686 GAGCCCC
1 GAGCCCC
4693 GAGCCCC
1 GAGCCCC
4700 GAGCCCC
1 GAGCCCC
4707 GAGCCCC
1 GAGCCCC
4714 GAGCCCCC
1 GAG-CCCC
4722 GAGCCCC
1 GAGCCCC
4729 GAGCCCC
1 GAGCCCC
4736 GAGCCCC
1 GAGCCCC
4743 GAGCCCC
1 GAGCCCC
4750 GAGCCCC
1 GAGCCCC
4757 GAGCCCC
1 GAGCCCC
4764 AAACTAAAGT
Statistics
Matches: 129, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.09
7 110 0.85
8 7 0.05
ACGTcount: A:0.14, C:0.57, G:0.29, T:0.00
Consensus pattern (7 bp):
GAGCCCC
Found at i:7799 original size:29 final size:28
Alignment explanation
Indices: 7754--7851 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
7744 TCCACATTCG
*
7754 AAAATTCTCA-AATTGTCATTTGTTTCACA
1 AAAATTCCCAGAA-TGTCATTT-TTTCACA
**
7783 AAAATTCCCAGAATGTCACATTTTCAACA
1 AAAATTCCCAGAATGTCATTTTTTC-ACA
*
7812 AAAATTCCCAGAATATCACCTTTTTTCACA
1 AAAATTCCCAGAATGTCA--TTTTTTCACA
*
7842 AATATTCCCA
1 AAAATTCCCA
7852 TAATATCACT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.07
29 35 0.60
30 14 0.24
31 5 0.09
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATTCCCAGAATGTCATTTTTTCACA
Found at i:7849 original size:30 final size:29
Alignment explanation
Indices: 7776--7860 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
7766 TTGTCATTTG
*
7776 TTTCACAAAAATTCCCAGAATGTCA-CAT
1 TTTCACAAAAATTCCCAGAATATCACCAT
*
7804 TTTCAACAAAAATTCCCAGAATATCACCTTT
1 TTTC-ACAAAAATTCCCAGAATATCACC-AT
* *
7835 TTTCACAAATATTCCCATAATATCAC
1 TTTCACAAAAATTCCCAGAATATCAC
7861 TGGGTCGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.08
29 20 0.40
30 21 0.42
31 5 0.10
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTCACAAAAATTCCCAGAATATCACCAT
Found at i:11070 original size:36 final size:35
Alignment explanation
Indices: 11030--11112 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
11020 TTAATATATT
* *
11030 TTATTATTTGTTAGAAAATTAATAAGTTGGTAGTAA
1 TTATTAGTTGGTAG-AAATTAATAAGTTGGTAGTAA
* *
11066 TTATTAAGTTGGTAGTAATTATTAAGTTGGTAGTAA
1 TTATT-AGTTGGTAGAAATTAATAAGTTGGTAGTAA
11102 TTATTAAGTTG
1 TTATT-AGTTG
11113 TAGTTTATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 35 0.83
37 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (35 bp):
TTATTAGTTGGTAGAAATTAATAAGTTGGTAGTAA
Found at i:11073 original size:18 final size:18
Alignment explanation
Indices: 11046--11116 Score: 126
Period size: 18 Copynumber: 4.0 Consensus size: 18
11036 TTTGTTAGAA
*
11046 AATTAATAAGTTGGTAGT
1 AATTATTAAGTTGGTAGT
11064 AATTATTAAGTTGGTAGT
1 AATTATTAAGTTGGTAGT
11082 AATTATTAAGTTGGTAGT
1 AATTATTAAGTTGGTAGT
11100 AATTATTAAGTT-GTAGT
1 AATTATTAAGTTGGTAGT
11117 TTATCATCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 5 0.10
18 47 0.90
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (18 bp):
AATTATTAAGTTGGTAGT
Found at i:14282 original size:19 final size:19
Alignment explanation
Indices: 14258--14297 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
14248 TTTTGAAATA
14258 ATTTAATAAAATATA-TAAT
1 ATTTAA-AAAATATATTAAT
*
14277 ATTTAAAAAATTTATTAAT
1 ATTTAAAAAATATATTAAT
14296 AT
1 AT
14298 AATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAAAAATATATTAAT
Found at i:14656 original size:2 final size:2
Alignment explanation
Indices: 14649--14679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14639 CCACTATAAT
14649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14680 CTTCTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16507 original size:32 final size:32
Alignment explanation
Indices: 16468--16533 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
16458 TGTACTCTCA
*
16468 AAATGCTAAAATACAGTTCTTCTAGTTAGTTC
1 AAATGCTAAAATACAGTTCTTCTAGTCAGTTC
* *
16500 AAATGCTAAAGTACATTTCTTCTAGTCAGTTC
1 AAATGCTAAAATACAGTTCTTCTAGTCAGTTC
16532 AA
1 AA
16534 TTACCGAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
AAATGCTAAAATACAGTTCTTCTAGTCAGTTC
Found at i:23134 original size:30 final size:30
Alignment explanation
Indices: 23098--23158 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
23088 ATGATACCCC
23098 TAATGTTTCTTATATTCCTAGGTTTAAGTA
1 TAATGTTTCTTATATTCCTAGGTTTAAGTA
23128 TAATGTTTCTTATATTCCTAGGTTTAAGTA
1 TAATGTTTCTTATATTCCTAGGTTTAAGTA
23158 T
1 T
23159 GTCGTCTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (30 bp):
TAATGTTTCTTATATTCCTAGGTTTAAGTA
Found at i:27060 original size:8 final size:8
Alignment explanation
Indices: 27047--27087 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
27037 CTCATTTTCA
27047 GAGAATTT
1 GAGAATTT
27055 GAGAATTT
1 GAGAATTT
*
27063 -AGAGTTT
1 GAGAATTT
*
27070 GGGAATTT
1 GAGAATTT
27078 GAGAATTT
1 GAGAATTT
27086 GA
1 GA
27088 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:27383 original size:128 final size:128
Alignment explanation
Indices: 27155--27657 Score: 970
Period size: 128 Copynumber: 3.9 Consensus size: 128
27145 CTATAATCGG
27155 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
27220 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
27283 TTCACTATTCACATGAAGGCGCGTTCCCGTGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
27348 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
27411 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
27476 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
27539 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
27604 TATCATTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
27658 TTGAATAACT
Statistics
Matches: 369, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 369 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:32425 original size:21 final size:22
Alignment explanation
Indices: 32343--32426 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 22
32333 CAGAACCCCA
*
32343 GGGGGGTATCGATTCCC-C-TGT
1 GGGGGGAATCGATTCCCTCAT-T
* *
32364 GGGGGGAATCGGTTCCCCTTCA-A
1 GGGGGGAATCGATT-CCC-TCATT
* *
32387 AGGGGGAATCGGTTCCCTCATT
1 GGGGGGAATCGATTCCCTCATT
32409 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
32427 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 26 0.51
22 11 0.22
23 13 0.25
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTCATT
Found at i:36272 original size:22 final size:21
Alignment explanation
Indices: 36230--36269 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36220 GAGTTTGTTT
*
36230 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
36251 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
36270 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:38651 original size:70 final size:70
Alignment explanation
Indices: 38571--38728 Score: 244
Period size: 70 Copynumber: 2.3 Consensus size: 70
38561 TTTTGGAGAA
* *
38571 TCGCGTTGCGAATTTGAAAACCGCGCTGTGTGTTTACCTATATCGATAATTAGCGTTGCGAAAAC
1 TCGCGTTGCGAATTTGAAAACCGAGCTGCGTGTTTACCTATATCGATAATTAGCGTTGCGAAAAC
38636 GAAAT
66 GAAAT
* * * *
38641 TTGCGTTGCGAATTTGAAAACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC
1 TCGCGTTGCGAATTTGAAAACCGAGCTGCGTGTTTACCTATATCGATAATTAGCGTTGCGAAAAC
38706 GAAAT
66 GAAAT
* *
38711 TCGCTTTGCGATTTTGAA
1 TCGCGTTGCGAATTTGAA
38729 GAATCACATT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (70 bp):
TCGCGTTGCGAATTTGAAAACCGAGCTGCGTGTTTACCTATATCGATAATTAGCGTTGCGAAAAC
GAAAT
Found at i:38760 original size:20 final size:20
Alignment explanation
Indices: 38706--38761 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
38696 TTGCGAAAAC
* * *
38706 GAAATTCGCTTTGCGATTTT
1 GAAAATCGCATTGCGAATTT
*
38726 GAAGAATCACATTGCGAATTT
1 GAA-AATCGCATTGCGAATTT
*
38747 GAAAATCGCGTTGCG
1 GAAAATCGCATTGCG
38762 TGTTTACCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
GAAAATCGCATTGCGAATTT
Found at i:38802 original size:91 final size:91
Alignment explanation
Indices: 38646--38819 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
38636 GAAATTTGCG
*
38646 TTGCGAATTTGAAAACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAT
1 TTGCGAATTTGAAAACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAAT
* *
38711 TCGCTTTGCGATTTTGAAGAATCACA
66 TCGCGTTGCGAATTTGAAGAATCACA
* * * *
38737 TTGCGAATTTGAAAA-TCGCGTTGCGTGTTTACCTATATCGGTAATTAGTGTTGTGAAATCAAAA
1 TTGCGAATTTGAAAACT-GAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAA
38801 TTCGCGTTGCGAATTTGAA
65 TTCGCGTTGCGAATTTGAA
38820 AACTGCATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
90 1 0.01
91 74 0.99
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (91 bp):
TTGCGAATTTGAAAACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAAT
TCGCGTTGCGAATTTGAAGAATCACA
Found at i:38845 original size:91 final size:91
Alignment explanation
Indices: 38649--38849 Score: 255
Period size: 91 Copynumber: 2.2 Consensus size: 91
38639 ATTTGCGTTG
* *
38649 CGAATTTGAAAA-CTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTC
1 CGAATTTGAAAATC-GCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTC
* * *
38713 GCTTTGCGATTTTGAAGAATCACATTG
65 GCGTTGCGAATTTGAAGAATCACATTA
* * *
38740 CGAATTTGAAAATCGCGTTGCGTGTTTACCTATATCGGTAATTAGTGTTGTGAAATCAAAATTCG
1 CGAATTTGAAAATCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
*
38805 CGTTGCGAATTTGAA-AA-CTGCATTA
66 CGTTGCGAATTTGAAGAATC-ACATTA
* *
38830 CGATTTTGGAGAATCGCGTT
1 CGAATTT-GAAAATCGCGTT
38850 CCGAATTTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
89 1 0.01
90 12 0.12
91 82 0.85
92 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (91 bp):
CGAATTTGAAAATCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
CGTTGCGAATTTGAAGAATCACATTA
Found at i:38929 original size:21 final size:21
Alignment explanation
Indices: 38896--38963 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
38886 TGATAATTAA
38896 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGATTTTGGAGAATCG
* * *
38917 CGTTACGAATTT-GAAAATCG
1 CGTTGCGATTTTGGAGAATCG
38937 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGATTTTGGAGAATCG
*
38958 TGTTGC
1 CGTTGC
38964 AAATTTGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.44
21 22 0.56
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (21 bp):
CGTTGCGATTTTGGAGAATCG
Found at i:38937 original size:20 final size:20
Alignment explanation
Indices: 38896--38974 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 20
38886 TGATAATTAA
* *
38896 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGAATTT-GAAAATCG
*
38917 CGTTACGAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
* *
38937 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGAATTT-GAAAATCG
* *
38958 TGTTGCAAATTTGAAAA
1 CGTTGCGAATTTGAAAA
38975 CTGTGTTGCG
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 21 0.45
21 26 0.55
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCG
Found at i:38955 original size:112 final size:111
Alignment explanation
Indices: 38706--38984 Score: 287
Period size: 111 Copynumber: 2.5 Consensus size: 111
38696 TTGCGAAAAC
* * * * * *
38706 GAAATTCGCTTTGCGATTTTGAAGAATCACATTGCGAATTTGAAAA-TCGCGTTGCGTGTTTACC
1 GAAAATCGCATTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACT-GAGTTGCGTGTTTACC
* ** * *
38770 TATATCGGTAATTAGTGTTGTGAAATCAAAATTCGCGTTGCGAATTT
65 TATATCGATAATTAACGTTGCGAAATCAAAATTCGCGTTACGAATTT
* *
38817 GAAAA-CTGCATTACGATTTTGGAGAATCGCGTTCCGAATTT-AAAAGCTGAGTTGCGTGTTTAC
1 GAAAATC-GCATTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAA-CTGAGTTGCGTGTTTAC
* ** * *
38880 CTATATTGATAATTAACGTTGCGATTTTGGAGAA-TCGCGTTACGAATTT
64 CTATATCGATAATTAACGTTGCGA-AAT-CAAAATTCGCGTTACGAATTT
* * * *
38929 GAAAATCGCGTTGCGATTTTGGAGAATCGTGTTGCAAATTTGAAAACTGTGTTGCG
1 GAAAATCGCATTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTGAGTTGCG
38985 AAACTGGTGT
Statistics
Matches: 137, Mismatches: 24, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
110 5 0.04
111 65 0.47
112 59 0.43
113 8 0.06
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (111 bp):
GAAAATCGCATTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTGAGTTGCGTGTTTACCT
ATATCGATAATTAACGTTGCGAAATCAAAATTCGCGTTACGAATTT
Found at i:38970 original size:21 final size:21
Alignment explanation
Indices: 38896--39029 Score: 91
Period size: 20 Copynumber: 6.6 Consensus size: 21
38886 TGATAATTAA
*
38896 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGAATTTGGAGAATCG
* *
38917 CGTTACGAATTT-GAAAATCG
1 CGTTGCGAATTTGGAGAATCG
*
38937 CGTTGCGATTTTGGAGAATCG
1 CGTTGCGAATTTGGAGAATCG
* * *
38958 TGTTGCAAATTT-GA-AAACTG
1 CGTTGCGAATTTGGAGAATC-G
* ** * *
38978 TGTTGCGAAACTGGTG-TTCG
1 CGTTGCGAATTTGGAGAATCG
*
38998 CGTTGCG-ATTTTGAG-ATCG
1 CGTTGCGAATTTGGAGAATCG
*
39017 CATTGCGAATTTG
1 CGTTGCGAATTTG
39030 TTGGTTATTT
Statistics
Matches: 84, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
19 16 0.19
20 40 0.48
21 28 0.33
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (21 bp):
CGTTGCGAATTTGGAGAATCG
Found at i:38985 original size:41 final size:41
Alignment explanation
Indices: 38896--38974 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
38886 TGATAATTAA
*
38896 CGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAATCG
1 CGTTGCGATTTTGGAGAATCGCGTTACAAATTTGAAAATCG
* *
38937 CGTTGCGATTTTGGAGAATCGTGTTGCAAATTTGAAAA
1 CGTTGCGATTTTGGAGAATCGCGTTACAAATTTGAAAA
38975 CTGTGTTGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (41 bp):
CGTTGCGATTTTGGAGAATCGCGTTACAAATTTGAAAATCG
Found at i:52461 original size:18 final size:18
Alignment explanation
Indices: 52420--52464 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
52410 AAATGGTTGT
** *
52420 GAAAAGAGAAAGGTAATG
1 GAAAAGAGAAAGAAAAAG
*
52438 GGAAAGAGAAAGAAAAAG
1 GAAAAGAGAAAGAAAAAG
52456 GAAAAGAGA
1 GAAAAGAGA
52465 GAGCAGTGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAAAAGAGAAAGAAAAAG
Found at i:52592 original size:38 final size:38
Alignment explanation
Indices: 52545--52624 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
52535 AAATTATTTA
* *
52545 TCTTTAATTTAACCTTGGAGCGACTTGGTCATTGTATC
1 TCTTTAATTTAACCATGGAGCGACTTAGTCATTGTATC
** * *
52583 TCTTTAATTTAGTCATGGAGCGGCTTAGTCATTGTATT
1 TCTTTAATTTAACCATGGAGCGACTTAGTCATTGTATC
52621 TCTT
1 TCTT
52625 ACAATGTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (38 bp):
TCTTTAATTTAACCATGGAGCGACTTAGTCATTGTATC
Found at i:52741 original size:54 final size:54
Alignment explanation
Indices: 52677--52782 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
52667 TATTCTTTGC
*
52677 AGATGAGCTCATTCTTTATGTCAAAGCCGACTTAGAGAATGAAGCTCTTATCAA
1 AGATGAGCTCATTCTTTATGTCAAAGCCGACTTACAGAATGAAGCTCTTATCAA
* *
52731 AGATGAGCTCATTCTTTATGTCAAAGTCGACTTACAGAATGTAGCTCTTATC
1 AGATGAGCTCATTCTTTATGTCAAAGCCGACTTACAGAATGAAGCTCTTATC
52783 GAACAAATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (54 bp):
AGATGAGCTCATTCTTTATGTCAAAGCCGACTTACAGAATGAAGCTCTTATCAA
Found at i:56000 original size:241 final size:240
Alignment explanation
Indices: 55576--56052 Score: 803
Period size: 241 Copynumber: 2.0 Consensus size: 240
55566 ACATTTTTAT
* *
55576 GACTGGAGAGAAAATTCCATTGTAGTCAATACATTCTTTTTGTGTAAACCTTTGACAACCAATCT
1 GACTGGAGAGAAAATTCCATTGTAGTCAATACATTCTTTTTCTGAAAACCTTTGACAACCAATCT
*
55641 TGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCCTGTAAATCCACTTGTTATGAAGCG
66 TGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCCTGTAAATCCACTTGTTATGAAACG
* * *
55706 CTTTCTTGCCTGGTGATAATTCAGCTAATTCCCATGTCTGATTTGACATAAGCGAGTCCATCTCA
131 CTTTCTTGCATGGTGATAATTCAGCTAATTCCCATGTCTGAGTTAACATAAGCGAGTCCATCTCA
55771 TCTTTCATGGAAGAC-TCTCACTTGACTGAATCCTCCACTTGTTAC
196 TCTTTCATGGAAGACTTC-CACTTGACTGAATCCTCCACTTGTTAC
** * * *
55816 GACTGGAGAGAAAATTTTATTGTAGTCGATACATTTTTTTTACTGAAAATCTTTGACAACCAATC
1 GACTGGAGAGAAAATTCCATTGTAGTCAATACATTCTTTTT-CTGAAAACCTTTGACAACCAATC
55881 TTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCCTGTAAATCCACTTGTTATGAAAC
65 TTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCCTGTAAATCCACTTGTTATGAAAC
* * *
55946 GCTTTCTTGCATGGTGGTAATTTAGCTAATTCCCATGTCTGAGTTAATATAAGCGAGTCCATCTC
130 GCTTTCTTGCATGGTGATAATTCAGCTAATTCCCATGTCTGAGTTAACATAAGCGAGTCCATCTC
56011 ATCTTTCATGGAAGACTTCCACTTGACTGAATCCTCCACTTG
195 ATCTTTCATGGAAGACTTCCACTTGACTGAATCCTCCACTTG
56053 CATCGCTTCA
Statistics
Matches: 221, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
240 37 0.17
241 182 0.82
242 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (240 bp):
GACTGGAGAGAAAATTCCATTGTAGTCAATACATTCTTTTTCTGAAAACCTTTGACAACCAATCT
TGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCCTGTAAATCCACTTGTTATGAAACG
CTTTCTTGCATGGTGATAATTCAGCTAATTCCCATGTCTGAGTTAACATAAGCGAGTCCATCTCA
TCTTTCATGGAAGACTTCCACTTGACTGAATCCTCCACTTGTTAC
Found at i:62450 original size:2 final size:2
Alignment explanation
Indices: 62438--62478 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
62428 CACGTATGCC
62438 AT AT A- 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
62479 CATGTTAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62872 original size:31 final size:31
Alignment explanation
Indices: 62821--62929 Score: 132
Period size: 31 Copynumber: 3.5 Consensus size: 31
62811 CAGAGGTCAT
* *
62821 AAAGAACCTCGG-CAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
62851 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
* * * *
62882 GAAGAACCTAGGTAAACTGTCTATATGTCTCG
1 AAAGAACCTAGGTAAACTGTCCATAGGTC-CC
*
62914 AAAG-ACATAGGTAAAC
1 AAAGAACCTAGGTAAAC
62930 CCTCGACTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 11 0.16
31 54 0.78
32 4 0.06
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:64087 original size:64 final size:63
Alignment explanation
Indices: 64000--64140 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
63990 TCTTTAACAT
* *
64000 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
64063 GATGCATCGATGCACT-CCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
64127 GTGCATCGATGCAC
1 GTGCATCGATGCAC
64141 ATTCAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:67131 original size:30 final size:30
Alignment explanation
Indices: 67079--67190 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
67069 AGACCCCGAT
* ***
67079 AACTATCCAGAGGTCATAAAGAACCTCAA-A
1 AACTATCCATAGGTCCCGAAGAACCT-AAGA
*
67109 AATTATCCATAGGTCCCGAAGAACCTAAGTA
1 AACTATCCATAGGTCCCGAAGAACCTAAG-A
* *
67140 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACCTAAG-A
* * *
67171 AACTGTCCATATGTCTCGAA
1 AACTATCCATAGGTCCCGAA
67191 AGACATAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 2 0.03
30 21 0.30
31 47 0.67
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (30 bp):
AACTATCCATAGGTCCCGAAGAACCTAAGA
Found at i:67152 original size:31 final size:31
Alignment explanation
Indices: 67114--67190 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
67104 TCAAAAATTA
67114 TCCATAGGTCCCGAAGAACCTAAGTAAACTG
1 TCCATAGGTCCCGAAGAACCTAAGTAAACTG
*
67145 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCCCGAAGAACCTAAGTAAACTG
* *
67176 TCCATATGTCTCGAA
1 TCCATAGGTCCCGAA
67191 AGACATAGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (31 bp):
TCCATAGGTCCCGAAGAACCTAAGTAAACTG
Found at i:67200 original size:31 final size:31
Alignment explanation
Indices: 67114--67204 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 31
67104 TCAAAAATTA
* *
67114 TCCATAGGTCCCGAAGAACCTAAGTAAACTG
1 TCCATAGGTCCCGAAGAACATAGGTAAACTG
*
67145 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCCCGAAGAACATAGGTAAACTG
* *
67176 TCCATATGTCTCGAA-AGACATAGGTAAAC
1 TCCATAGGTCCCGAAGA-ACATAGGTAAAC
67205 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCCCGAAGAACATAGGTAAACTG
Found at i:68352 original size:64 final size:63
Alignment explanation
Indices: 68265--68405 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
68255 TCTTTAACAT
* *
68265 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * * *
68328 GATGCATCGATGCACT-CCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAATA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
68392 GTGCATCGATGCAC
1 GTGCATCGATGCAC
68406 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:75253 original size:21 final size:21
Alignment explanation
Indices: 75229--75275 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
75219 ATCATTTAAG
75229 TTTCCTTTATAATCAAGTAAC
1 TTTCCTTTATAATCAAGTAAC
75250 TTTCCTTTATAATCAAGTAAC
1 TTTCCTTTATAATCAAGTAAC
75271 TTTCC
1 TTTCC
75276 ATATGAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (21 bp):
TTTCCTTTATAATCAAGTAAC
Found at i:78034 original size:74 final size:76
Alignment explanation
Indices: 77908--78047 Score: 182
Period size: 74 Copynumber: 1.9 Consensus size: 76
77898 GCCCACCCTA
* * * *
77908 AAATCCTAATTTTTTTTGATTAGTTACTTATTTTACTGATGGTGTCTACCCTGAAA-TTT-TTTG
1 AAATCCTAATTTTCTTCGATTAGCTACTTATTTTACTGACGGTGTCTACCCTGAAACTTTATTTG
77971 TGCTCACTCTG
66 TGCTCACTCTG
77982 AAAT-CTAAGTTTTCTTCGATTAGCTACTTATTTTAC-GTACGGTGTCCT-CCCTGAAACTTTAT
1 AAATCCTAA-TTTTCTTCGATTAGCTACTTATTTTACTG-ACGGTGT-CTACCCTGAAACTTTAT
78044 TTGT
63 TTGT
78048 ACCAATACCA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
73 5 0.09
74 42 0.74
75 5 0.09
76 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (76 bp):
AAATCCTAATTTTCTTCGATTAGCTACTTATTTTACTGACGGTGTCTACCCTGAAACTTTATTTG
TGCTCACTCTG
Found at i:86450 original size:26 final size:25
Alignment explanation
Indices: 86410--86459 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
86400 AGCAGCCGGT
*
86410 GGCTGCTTGAATTTCAAAGGTAGGG
1 GGCTGCTTAAATTTCAAAGGTAGGG
*
86435 GGCTGCCTTAAATTTCAAAGTTAGG
1 GGCTG-CTTAAATTTCAAAGGTAGG
86460 CATCCCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (25 bp):
GGCTGCTTAAATTTCAAAGGTAGGG
Found at i:96272 original size:81 final size:81
Alignment explanation
Indices: 96205--96385 Score: 195
Period size: 81 Copynumber: 2.2 Consensus size: 81
96195 CAGTTTTTGA
* * * *
96205 AATCGCAACTCGAA-TTTCCAAATTCGCAATGCTATTTCCAAATTCGTAACTCAGTTTTTGAAAT
1 AATCGCAACGC-AATTTTCCAAATTCGCAACGCGATTTCCAAATTCGCAACTCAGTTTTTGAAAT
96269 CGCAACGCGAATTTCTT
65 CGCAACGCGAATTTCTT
** * ** *
96286 TTTCGCAACGCAATTTTCCAAATTCGCAACGCGATTTCCAAATTCGCAACT-TGATTTCCGAATT
1 AATCGCAACGCAATTTTCCAAATTCGCAACGCGATTTCCAAATTCGCAACTCAG-TTTTTGAAAT
*
96350 CACAACGCGAATTTCTT
65 CGCAACGCGAATTTCTT
** * *
96367 TTTCGCAACACAAGTTTCC
1 AATCGCAACGCAATTTTCC
96386 TTTTCGCAAC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 3 0.04
81 82 0.96
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (81 bp):
AATCGCAACGCAATTTTCCAAATTCGCAACGCGATTTCCAAATTCGCAACTCAGTTTTTGAAATC
GCAACGCGAATTTCTT
Found at i:96283 original size:41 final size:41
Alignment explanation
Indices: 96142--96364 Score: 152
Period size: 40 Copynumber: 5.5 Consensus size: 41
96132 AAATAACCAA
* ** * * *
96142 CAAATTCGTAACGCGAACTCCAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTTC
* * **
96182 CAAATTCGCAACTCAGTTTTTGAAA-TCGCAACTCGAA-TTTC
1 CAAATTCGCAACGC-GATTTCCAAATTCGCAACTC-AATTTTC
* * * * *
96223 CAAATTCGCAATGCTATTTCCAAATTCGTAACTCAGTTTTT
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTTC
* *** *
96264 GAAA-TCGCAACGCGAATTT-CTTTTTCGCAACGCAATTTTC
1 CAAATTCGCAACGCG-ATTTCCAAATTCGCAACTCAATTTTC
**
96304 CAAATTCGCAACGCGATTTCCAAATTCGCAACTTGA-TTTC
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTTC
* *
96344 CGAATTCACAACGCGAATTTC
1 CAAATTCGCAACGCG-ATTTC
96365 TTTTTCGCAA
Statistics
Matches: 137, Mismatches: 37, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
40 73 0.53
41 63 0.46
42 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (41 bp):
CAAATTCGCAACGCGATTTCCAAATTCGCAACTCAATTTTC
Found at i:96304 original size:61 final size:60
Alignment explanation
Indices: 96151--96315 Score: 208
Period size: 61 Copynumber: 2.7 Consensus size: 60
96141 ACAAATTCGT
* *
96151 AACGCGAA-CTCCAATTTCGCAACACAGTTTCCAAATTCGCAACTCAGTTTTTGAAATCGC
1 AACGCGAATTTCCAATTTCGCAACGCA-TTTCCAAATTCGCAACTCAGTTTTTGAAATCGC
* * * *
96211 AACTCGAATTTCCAAATTCGCAATGCTATTTCCAAATTCGTAACTCAGTTTTTGAAATCGC
1 AACGCGAATTTCCAATTTCGCAACGC-ATTTCCAAATTCGCAACTCAGTTTTTGAAATCGC
**
96272 AACGCGAATTT-CTTTTTCGCAACGCAATTTTCCAAATTCGCAAC
1 AACGCGAATTTCCAATTTCGCAACGC-A-TTTCCAAATTCGCAAC
96316 GCGATTTCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 18 0.20
61 70 0.79
62 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (60 bp):
AACGCGAATTTCCAATTTCGCAACGCATTTCCAAATTCGCAACTCAGTTTTTGAAATCGC
Found at i:96341 original size:20 final size:20
Alignment explanation
Indices: 96142--96364 Score: 130
Period size: 20 Copynumber: 11.0 Consensus size: 20
96132 AAATAACCAA
* **
96142 CAAATTCGTAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* *
96162 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-TTTC
* * *
96182 CAAATTCGCAACTCAGTTTTT
1 CAAATTCGCAACGC-GATTTC
* *
96203 GAAA-TCGCAACTCGAATTTC
1 CAAATTCGCAACGCG-ATTTC
* *
96223 CAAATTCGCAATGCTATTTC
1 CAAATTCGCAACGCGATTTC
* * * *
96243 CAAATTCGTAACTCAGTTTTT
1 CAAATTCGCAACGC-GATTTC
*
96264 GAAA-TCGCAACGCGAATTT-
1 CAAATTCGCAACGCG-ATTTC
*** *
96283 CTTTTTCGCAACGCAATTTTC
1 CAAATTCGCAACGCGA-TTTC
96304 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACGCGATTTC
**
96324 CAAATTCGCAACTTGATTTC
1 CAAATTCGCAACGCGATTTC
* *
96344 CGAATTCACAACGCGAATTTC
1 CAAATTCGCAACGCG-ATTTC
96365 TTTTTCGCAA
Statistics
Matches: 151, Mismatches: 41, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.03
20 111 0.74
21 36 0.24
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:96372 original size:40 final size:41
Alignment explanation
Indices: 96271--96385 Score: 117
Period size: 40 Copynumber: 2.8 Consensus size: 41
96261 TTTGAAATCG
*
96271 CAACGCGAATTTCTTTTTCGCAACGCAATTTTCCAAATTCG
1 CAACGCGAATTTCTTTTTCGCAACGCAATTTTCCAAATTCA
*** *** *
96312 CAACGCG-ATTTCCAAATTCGCAACTTGA-TTTCCGAATTCA
1 CAACGCGAATTT-CTTTTTCGCAACGCAATTTTCCAAATTCA
* *
96352 CAACGCGAATTTCTTTTTCGCAACACAAGTTTCC
1 CAACGCGAATTTCTTTTTCGCAACGCAATTTTCC
96386 TTTTCGCAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
40 31 0.54
41 26 0.46
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (41 bp):
CAACGCGAATTTCTTTTTCGCAACGCAATTTTCCAAATTCA
Found at i:98959 original size:20 final size:20
Alignment explanation
Indices: 98934--98975 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
98924 ATTATTGCGG
**
98934 AAGTCAAATTTGCAACGCGA
1 AAGTCAAATTCACAACGCGA
98954 AAGTCAAATTCACAACGCGA
1 AAGTCAAATTCACAACGCGA
98974 AA
1 AA
98976 ATCGTAACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (20 bp):
AAGTCAAATTCACAACGCGA
Found at i:99030 original size:20 final size:20
Alignment explanation
Indices: 98984--99038 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
98974 AAATCGTAAC
*
98984 GCGAATTTAACTTTCGCATT
1 GCGAATTTGACTTTCGCATT
** *
99004 GTAAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
*
99024 GCGAATTTGATTTTC
1 GCGAATTTGACTTTC
99039 TTAAAGGTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:100527 original size:21 final size:21
Alignment explanation
Indices: 100501--100633 Score: 108
Period size: 21 Copynumber: 6.3 Consensus size: 21
100491 AGTATGCCAT
*
100501 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
100522 GTGGATCCTGAACGATGGGA-
1 GTGGATCCTGAACGATGGGAG
*
100542 G-GGACCTCTTGAACGATGGGAG
1 GTGGA--TCCTGAACGATGGGAG
** ** * **
100564 AAGCCTCTTGAACGATGACAG
1 GTGGATCCTGAACGATGGGAG
* *
100585 GTGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
100606 GTGGATCCTGAGCAATGGTAG
1 GTGGATCCTGAACGATGGGAG
100627 GTGGATC
1 GTGGATC
100634 AGGCTTCTTC
Statistics
Matches: 90, Mismatches: 18, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
19 3 0.03
20 1 0.01
21 85 0.94
23 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.38, T:0.20
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:100786 original size:12 final size:12
Alignment explanation
Indices: 100767--100808 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
100757 GTGCCACTAA
100767 AAATAAATTAAT
1 AAATAAATTAAT
* *
100779 ACATAAATTAGT
1 AAATAAATTAAT
*
100791 AAATAAATAAAT
1 AAATAAATTAAT
100803 AAATAA
1 AAATAA
100809 TACCAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:100964 original size:42 final size:41
Alignment explanation
Indices: 100918--101024 Score: 101
Period size: 42 Copynumber: 2.5 Consensus size: 41
100908 GAAACAATCT
100918 CACGTAGAACAACTACCTCATCACGTAAAACAGA-TACCTCAC
1 CACGTA-AACAACTACCTCATCACGTAAAACA-ACTACCTCAC
* ** *
100960 CACGTAAAGC-ACCATTGTCATCACGTAAAACAACTACTTCAC
1 CACGTAAA-CAACTA-CCTCATCACGTAAAACAACTACCTCAC
* *
101002 CACGTAAAGACCCTACCTCATCA
1 CACGTAAACA-ACTACCTCATCA
101025 TGCCATGCAC
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
41 6 0.12
42 43 0.84
43 2 0.04
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (41 bp):
CACGTAAACAACTACCTCATCACGTAAAACAACTACCTCAC
Found at i:101005 original size:21 final size:21
Alignment explanation
Indices: 100918--101009 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
100908 GAAACAATCT
* *
100918 CACGTAGAACAACTACCTCAT
1 CACGTAAAACAACTACCTCAC
100939 CACGTAAAACAGA-TACCTCAC
1 CACGTAAAACA-ACTACCTCAC
* * ** *
100960 CACGTAAAGC-ACCATTGTCAT
1 CACGTAAAACAACTA-CCTCAC
*
100981 CACGTAAAACAACTACTTCAC
1 CACGTAAAACAACTACCTCAC
101002 CACGTAAA
1 CACGTAAA
101010 GACCCTACCT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 49 0.89
22 4 0.07
ACGTcount: A:0.40, C:0.32, G:0.10, T:0.18
Consensus pattern (21 bp):
CACGTAAAACAACTACCTCAC
Found at i:101097 original size:21 final size:21
Alignment explanation
Indices: 101048--101097 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
101038 TATCGTCATG
* * *
101048 TAAAGTACCGACCTCATCACG
1 TAAAGCACTGACCTCATCACA
*
101069 TAAAGCACTGACCTCATTACA
1 TAAAGCACTGACCTCATCACA
*
101090 TAATGCAC
1 TAAAGCAC
101098 CTAACTCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (21 bp):
TAAAGCACTGACCTCATCACA
Found at i:101268 original size:42 final size:42
Alignment explanation
Indices: 101207--101317 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
101197 GTGATGGAAT
* * **
101207 AGGTGATGGCTCTCAGTGTCGAGGTGTAAAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTGGAAAAGAGGCTCGATC
* *
101249 AGGTGATGGCTCTTGGTGTCGAGGTGGAGAAGAGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTGGAAAAGAGGCTCGATC
* *
101291 AGGTGATGGATCTCGGTGTCGAAGTGG
1 AGGTGATGGCTCTCGGTGTCGAGGTGG
101318 GGGTGCTCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGGTGGAAAAGAGGCTCGATC
Found at i:102832 original size:20 final size:20
Alignment explanation
Indices: 102809--102847 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
102799 TTTGAAACTT
102809 AAATTCACAACACGAAAATG
1 AAATTCACAACACGAAAATG
**
102829 AAATTTGCAACACGAAAAT
1 AAATTCACAACACGAAAAT
102848 CGCAACGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATTCACAACACGAAAATG
Found at i:102865 original size:20 final size:21
Alignment explanation
Indices: 102842--102890 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
102832 TTTGCAACAC
102842 GAAAATCGCAACGCGAAAA-T
1 GAAAATCGCAACGCGAAAACT
* *
102862 GAAATTCGCAACGTGAAAACT
1 GAAAATCGCAACGCGAAAACT
102883 -AAAATCGC
1 GAAAATCGC
102891 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (21 bp):
GAAAATCGCAACGCGAAAACT
Found at i:102913 original size:14 final size:14
Alignment explanation
Indices: 102891--102939 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
102881 CTAAAATCGC
102891 GTTGCGATTTTCGT
1 GTTGCGATTTTCGT
* *
102905 GTTGTGATTTTCTT
1 GTTGCGATTTTCGT
102919 GTTGCGATTTTCGT
1 GTTGCGATTTTCGT
102933 GTTGCGA
1 GTTGCGA
102940 ATTTAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.08, C:0.12, G:0.29, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTCGT
Found at i:103315 original size:22 final size:22
Alignment explanation
Indices: 103290--103332 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
103280 AGGGGGGTCG
* *
103290 CCGGATATGGGGACGGATGTCA
1 CCGGAGATGAGGACGGATGTCA
103312 CCGGAGATGAGGACGGATGTC
1 CCGGAGATGAGGACGGATGTC
103333 GCCATAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.16
Consensus pattern (22 bp):
CCGGAGATGAGGACGGATGTCA
Found at i:103392 original size:27 final size:27
Alignment explanation
Indices: 103362--103429 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
103352 GAGACGAGAC
*
103362 TGAGTTGTGATTTAGGGTTTTAGATTA
1 TGAGTTGCGATTTAGGGTTTTAGATTA
* *
103389 TGAGTTACGATTTAGGGTTTTAGGTTA
1 TGAGTTGCGATTTAGGGTTTTAGATTA
*
103416 TAAGTTGCGATTTA
1 TGAGTTGCGATTTA
103430 CGGGATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.03, G:0.28, T:0.46
Consensus pattern (27 bp):
TGAGTTGCGATTTAGGGTTTTAGATTA
Found at i:103561 original size:20 final size:21
Alignment explanation
Indices: 103538--103582 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
103528 TGACTTCTGT
103538 GTTGCAAATCT-GAAAATCGC
1 GTTGCAAATCTGGAAAATCGC
* *
103558 GTTGCGAATTTGGAAAATCGC
1 GTTGCAAATCTGGAAAATCGC
103579 GTTG
1 GTTG
103583 TGTAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
GTTGCAAATCTGGAAAATCGC
Found at i:104186 original size:29 final size:29
Alignment explanation
Indices: 104149--104205 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
104139 TTGACAAGTA
*
104149 TTAATAGTTTAAGGATGAAATT-AAAATGT
1 TTAAAAGTTTAAGGATG-AATTCAAAATGT
*
104178 TTAAAAGTTTAGGGATGAATTCAAAATG
1 TTAAAAGTTTAAGGATGAATTCAAAATG
104206 AGAATCATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (29 bp):
TTAAAAGTTTAAGGATGAATTCAAAATGT
Found at i:110656 original size:43 final size:43
Alignment explanation
Indices: 110608--110693 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
110598 TCCTGTCCTT
* *
110608 GCCAGCAAGAAACTCCAACAGTATATGATGCCTGTGGTAGTAG
1 GCCAGCAAGAAACTCCAACAGTATACGACGCCTGTGGTAGTAG
110651 GCCAGCAAGAAACTCCAACAGTATACGACGCCTGTGGTAGTAG
1 GCCAGCAAGAAACTCCAACAGTATACGACGCCTGTGGTAGTAG
110694 TCGACGATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (43 bp):
GCCAGCAAGAAACTCCAACAGTATACGACGCCTGTGGTAGTAG
Found at i:116450 original size:31 final size:31
Alignment explanation
Indices: 116412--116476 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
116402 TTTTGGCTCC
*
116412 TAAACTTTAGGTAAAATACTAATTTAACTTA
1 TAAACTTTAGATAAAATACTAATTTAACTTA
* * *
116443 TAAACTTTAGATCAATTATTAATTTAACTTA
1 TAAACTTTAGATAAAATACTAATTTAACTTA
116474 TAA
1 TAA
116477 TCGAGTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (31 bp):
TAAACTTTAGATAAAATACTAATTTAACTTA
Found at i:118969 original size:45 final size:46
Alignment explanation
Indices: 118905--118996 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
118895 CATCAAAGTC
118905 GATCGAGTACCTGA-TTTTTTATACTTTTAATCATATTATGACCGA
1 GATCGAGTACCTGATTTTTTTATACTTTTAATCATATTATGACCGA
118950 GATCGAGTACCTGATTTTTTTATACTTTTAATCATATTATGACCGA
1 GATCGAGTACCTGATTTTTTTATACTTTTAATCATATTATGACCGA
118996 G
1 G
118997 CTCTCTCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 14 0.30
46 32 0.70
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (46 bp):
GATCGAGTACCTGATTTTTTTATACTTTTAATCATATTATGACCGA
Found at i:123881 original size:37 final size:36
Alignment explanation
Indices: 123807--123881 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
123797 CAAATCGTAA
**
123807 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTTAAAAAATTAAAAACAT
* *
123843 AATATTTATATAATTTTTTTTACAAAATTAAAAACAT
1 AATATTTATAT-ATTTTCTTTAAAAAATTAAAAACAT
123880 AA
1 AA
123882 AAAATGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAAAACAT
Found at i:129026 original size:14 final size:14
Alignment explanation
Indices: 129009--129055 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
128999 AAATAAAAAA
129009 ACATAAATGAACGC
1 ACATAAATGAACGC
129023 ACATAAATGAACGC
1 ACATAAATGAACGC
*
129037 ACATAAATGAACGA
1 ACATAAATGAACGC
129051 ACATA
1 ACATA
129056 TTACCAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (14 bp):
ACATAAATGAACGC
Found at i:130089 original size:20 final size:20
Alignment explanation
Indices: 130066--130129 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
130056 TAGTATTTAG
130066 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
130086 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
130106 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
130125 TTAAA
1 ATAAA
130130 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:130099 original size:19 final size:20
Alignment explanation
Indices: 130075--130124 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
130065 GATAAATTTA
*
130075 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
130094 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
130115 TT-ATAATTTT
1 TTAATAATTTT
130125 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:130127 original size:31 final size:30
Alignment explanation
Indices: 130042--130128 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
130032 TTTGATAATA
* *
130042 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
130073 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
130104 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
130129 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:130886 original size:31 final size:30
Alignment explanation
Indices: 130851--130935 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
130841 TCAATAAAGT
130851 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
130882 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
130913 TCT-AAATACTATAAAATAATTAT
1 T-TAAAAAATTATAAAAT-ATTAT
130936 AATATTATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:130913 original size:20 final size:20
Alignment explanation
Indices: 130846--130913 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
130836 TTTCGTCAAT
*
130846 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
130864 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
130885 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
130904 ATAA-ATTTAT
1 A-AAGATTTAT
130914 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:135817 original size:2 final size:2
Alignment explanation
Indices: 135810--135851 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
135800 CATTTACTCA
*
135810 AT AT AT AT AT AT A- AT -T GT 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
135850 AT
1 AT
135852 GAGAAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152380 original size:43 final size:43
Alignment explanation
Indices: 152288--152529 Score: 218
Period size: 43 Copynumber: 5.6 Consensus size: 43
152278 CGTTTGTATA
* * * ** *
152288 AAAAACGCCGCTATATATATATGACATTTTGCGGTGTTTTTTTCC
1 AAAAACGCCGCTATAGATCTA-GACCTTTTGCGACG-TTTGTTCC
**
152333 AAAAACGCCATTATAGATCTAGACCTTTTGCGACGTTTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGACGTTTGTTCC
* * *
152376 AAAAACGTCGCTATAGATCTTGACCTTTTGCAACGTTTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGACGTTTGTTCC
* * * * * *
152419 ATAAACGTC-CTATAGATCTCA-ACTTTTTACGGCGTTTGTTCT
1 AAAAACGCCGCTATAGATCT-AGACCTTTTGCGACGTTTGTTCC
* * ** * *
152461 AAAAACGCCGCTATAGATATCGACCTTTTGCGGTGTTTATTTC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGACGTTTGTTCC
* *
152504 AAAAATGCCGCTATAGATCTTGACCT
1 AAAAACGCCGCTATAGATCTAGACCT
152530 CTGGCAGCGT
Statistics
Matches: 161, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
42 33 0.20
43 100 0.62
44 11 0.07
45 17 0.11
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTAGACCTTTTGCGACGTTTGTTCC
Found at i:156540 original size:17 final size:19
Alignment explanation
Indices: 156510--156548 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
156500 CGAGTTTTAA
156510 TATTAAAAAATAAAAT-AT
1 TATTAAAAAATAAAATAAT
*
156528 TATT-AAAACTAAAATAAT
1 TATTAAAAAATAAAATAAT
156546 TAT
1 TAT
156549 AATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTAAAAAATAAAATAAT
Found at i:174485 original size:226 final size:226
Alignment explanation
Indices: 174091--174542 Score: 904
Period size: 226 Copynumber: 2.0 Consensus size: 226
174081 TCAAGTAGGT
174091 TATTGATTTGAGAAAATTGGTAGCTCGAAAGAATCATTTACCAGTAGAGAATTTGAAGCTTATCT
1 TATTGATTTGAGAAAATTGGTAGCTCGAAAGAATCATTTACCAGTAGAGAATTTGAAGCTTATCT
174156 TGCAAGGGAAGGTATTGCATGATCTTGAAGATGAAGATGATGTTTACACTCGACTCAATGATGGT
66 TGCAAGGGAAGGTATTGCATGATCTTGAAGATGAAGATGATGTTTACACTCGACTCAATGATGGT
174221 GGTATAGATCTTGCCTTTAGTTGAAAAAATAATTATGCAGTAGTTTGCTTTCGCTGCTTACATTT
131 GGTATAGATCTTGCCTTTAGTTGAAAAAATAATTATGCAGTAGTTTGCTTTCGCTGCTTACATTT
174286 ATCATTAGTAGTGTGGATGAAATAACGAAGG
196 ATCATTAGTAGTGTGGATGAAATAACGAAGG
174317 TATTGATTTGAGAAAATTGGTAGCTCGAAAGAATCATTTACCAGTAGAGAATTTGAAGCTTATCT
1 TATTGATTTGAGAAAATTGGTAGCTCGAAAGAATCATTTACCAGTAGAGAATTTGAAGCTTATCT
174382 TGCAAGGGAAGGTATTGCATGATCTTGAAGATGAAGATGATGTTTACACTCGACTCAATGATGGT
66 TGCAAGGGAAGGTATTGCATGATCTTGAAGATGAAGATGATGTTTACACTCGACTCAATGATGGT
174447 GGTATAGATCTTGCCTTTAGTTGAAAAAATAATTATGCAGTAGTTTGCTTTCGCTGCTTACATTT
131 GGTATAGATCTTGCCTTTAGTTGAAAAAATAATTATGCAGTAGTTTGCTTTCGCTGCTTACATTT
174512 ATCATTAGTAGTGTGGATGAAATAACGAAGG
196 ATCATTAGTAGTGTGGATGAAATAACGAAGG
174543 AATTAGACTC
Statistics
Matches: 226, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 226 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (226 bp):
TATTGATTTGAGAAAATTGGTAGCTCGAAAGAATCATTTACCAGTAGAGAATTTGAAGCTTATCT
TGCAAGGGAAGGTATTGCATGATCTTGAAGATGAAGATGATGTTTACACTCGACTCAATGATGGT
GGTATAGATCTTGCCTTTAGTTGAAAAAATAATTATGCAGTAGTTTGCTTTCGCTGCTTACATTT
ATCATTAGTAGTGTGGATGAAATAACGAAGG
Found at i:177292 original size:89 final size:89
Alignment explanation
Indices: 177141--177393 Score: 472
Period size: 89 Copynumber: 2.8 Consensus size: 89
177131 TGCTAAGTTA
*
177141 GCTTCTTAGATTAATCGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAAA
1 GCTTCATAGATTAATCGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAAA
177206 TAAAACGTAAGTCGAAACGTTTCG
66 TAAAACGTAAGTCGAAACGTTTCG
177230 GCTTCATAGATTAA-CTGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAA
1 GCTTCATAGATTAATC-GTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAA
*
177294 ATAAAACGTAATTCGAAACGTTTCG
65 ATAAAACGTAAGTCGAAACGTTTCG
177319 GCTTCATAGATTAATCGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAAA
1 GCTTCATAGATTAATCGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAAA
177384 TAAAACGTAA
66 TAAAACGTAA
177394 ATAAAAAACG
Statistics
Matches: 160, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
88 1 0.01
89 158 0.99
90 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (89 bp):
GCTTCATAGATTAATCGTTAATTAACTAACGATTTTCATCTACTAAGAGATCTTTTTGCCCAAAA
TAAAACGTAAGTCGAAACGTTTCG
Found at i:180756 original size:2 final size:2
Alignment explanation
Indices: 180749--180779 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
180739 GACATAATTA
180749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
180780 ATTATCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184824 original size:31 final size:30
Alignment explanation
Indices: 184752--184839 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
184742 CGGATTTGGT
*
184752 CGTTTTAGTATCTAAACTATCATTTTTGTC
1 CGTTTTAGTACCTAAACTATCATTTTTGTC
** *
184782 CGTTTCGGTACCTAAATTATCATTTTTGATC
1 CGTTTTAGTACCTAAACTATCATTTTTG-TC
* *
184813 CGTTTTAGTACCTAAACTTTTATTTTT
1 CGTTTTAGTACCTAAACTATCATTTTT
184840 TTCAAAATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 24 0.50
31 24 0.50
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (30 bp):
CGTTTTAGTACCTAAACTATCATTTTTGTC
Found at i:198764 original size:23 final size:24
Alignment explanation
Indices: 198721--198769 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
198711 TATAATTAAT
*
198721 TAAATTAGAAAATATACATAT-TA
1 TAAATTAGAAAAAATACATATATA
*
198744 TAAATTA-ATAAAAATATATATATA
1 TAAATTAGA-AAAAATACATATATA
198768 TA
1 TA
198770 TTTATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 17 0.77
24 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAATTAGAAAAAATACATATATA
Found at i:200750 original size:37 final size:35
Alignment explanation
Indices: 200705--200775 Score: 115
Period size: 37 Copynumber: 2.0 Consensus size: 35
200695 AACATCTACC
*
200705 AAACTTTACCAAACTTTGAAAAATATTTTTTCAAAT
1 AAACTTTACCAAACTTTGAAAAACA-TTTTTCAAAT
200741 AAACATTTACCAAACTTTGAAAAACATTTTTCAAA
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAA
200776 GTTGGTTGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.35
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAT
Found at i:202106 original size:29 final size:29
Alignment explanation
Indices: 202064--202123 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
202054 TTTCTTCCTC
202064 CAAATCACCATGAAGGAAAGTTGTTTTCA
1 CAAATCACCATGAAGGAAAGTTGTTTTCA
202093 CAAATCACCATGAAGGAAAGTTGTTTTCA
1 CAAATCACCATGAAGGAAAGTTGTTTTCA
202122 CA
1 CA
202124 TCTAACTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (29 bp):
CAAATCACCATGAAGGAAAGTTGTTTTCA
Found at i:204110 original size:15 final size:16
Alignment explanation
Indices: 204082--204113 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
204072 AAAATCTTTC
204082 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
204098 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
204113 T
1 T
204114 CGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:205374 original size:38 final size:35
Alignment explanation
Indices: 205319--205391 Score: 119
Period size: 38 Copynumber: 2.0 Consensus size: 35
205309 AACATCTACC
205319 AAACTTTACCAAACTTTGAAAAAATATTTTTTCAAAG
1 AAACTTTACCAAACTTTG-AAAAATA-TTTTTCAAAG
205356 AAACATTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAATATTTTTCAAAG
205392 TTGGTTGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
36 10 0.29
37 11 0.31
38 14 0.40
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAATATTTTTCAAAG
Found at i:222199 original size:22 final size:22
Alignment explanation
Indices: 222174--222218 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
222164 CACTCACACC
222174 CCTAACACCTATGGTGCTCAAA
1 CCTAACACCTATGGTGCTCAAA
*
222196 CCTAACATCTATGGTGCTCAAA
1 CCTAACACCTATGGTGCTCAAA
222218 C
1 C
222219 TCGAATCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (22 bp):
CCTAACACCTATGGTGCTCAAA
Found at i:223165 original size:14 final size:14
Alignment explanation
Indices: 223143--223172 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
223133 ATGTGTGGGG
*
223143 TTATGATTTAAGGT
1 TTATAATTTAAGGT
223157 TTATAATTTAAGGT
1 TTATAATTTAAGGT
223171 TT
1 TT
223173 GAAGTTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTATAATTTAAGGT
Found at i:226162 original size:60 final size:60
Alignment explanation
Indices: 226054--226175 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
226044 GAACATATAA
** * * *
226054 ATAGTTAGGTGATCATTTTGTAACTTTTAATAGTGGAACGACTTAATAAAATAATACTCT
1 ATAGTTAGAAGATCATTTTGTAACTTTAAATAGTGGAACGACTAAATAAAATAATACCCT
*
226114 ATAGTTAGAAGATCATTTTGTAACTTTAAATAGAT-GAA-GAACTAAATAAAGTAATACCCT
1 ATAGTTAGAAGATCATTTTGTAACTTTAAATAG-TGGAACG-ACTAAATAAAATAATACCCT
226174 AT
1 AT
226176 CAATGACCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
59 1 0.02
60 52 0.96
61 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (60 bp):
ATAGTTAGAAGATCATTTTGTAACTTTAAATAGTGGAACGACTAAATAAAATAATACCCT
Found at i:227140 original size:29 final size:29
Alignment explanation
Indices: 227098--227153 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
227088 CAGTGGCAAC
227098 ATAGGTCGCCATGCACGCCCAGCGTCCTT
1 ATAGGTCGCCATGCACGCCCAGCGTCCTT
*
227127 ATAGGTCGCCATGCACGCCCGGCGTCC
1 ATAGGTCGCCATGCACGCCCAGCGTCC
227154 ATCATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCAGCGTCCTT
Found at i:227211 original size:31 final size:31
Alignment explanation
Indices: 227176--227240 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
227166 CCTGGTTCTT
227176 TGCCCGCTGTTGCTCGCTGATGCTACTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTACTTTGG
*
227207 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTACTTTGG
227238 TGC
1 TGC
227241 TATGCATGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.05, C:0.29, G:0.31, T:0.35
Consensus pattern (31 bp):
TGCCCGCTGTTGCTCGCTGATGCTACTTTGG
Found at i:227505 original size:35 final size:35
Alignment explanation
Indices: 227466--227533 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
227456 TCCTGCATCG
227466 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
227501 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
227534 GTTGCATCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:227995 original size:21 final size:21
Alignment explanation
Indices: 227970--228013 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
227960 AATCTAGTTA
*
227970 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
227991 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
228012 AT
1 AT
228014 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:228436 original size:14 final size:14
Alignment explanation
Indices: 228417--228443 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
228407 AGTAATTTAT
228417 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
228431 TATTTTTTGTTGT
1 TATTTTTTGTTGT
228444 TGTGTATGTG
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:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:228443 original size:17 final size:17
Alignment explanation
Indices: 228414--228446 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
228404 GTGAGTAATT
228414 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
228431 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
228447 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:228581 original size:22 final size:22
Alignment explanation
Indices: 228539--228581 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
228529 TATTGTGTTT
*
228539 AAAAATATTTAGTGTTGTTTAA
1 AAAAATATTTAGTGTTATTTAA
* *
228561 AAAAATATTTTGTTTTATTTA
1 AAAAATATTTAGTGTTATTTA
228582 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AAAAATATTTAGTGTTATTTAA
Found at i:228840 original size:26 final size:25
Alignment explanation
Indices: 228811--228875 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
228801 AAATCATATT
*
228811 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
228837 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
228863 ATTATT-AATAATA
1 ATTATTAAATAATA
228876 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:231826 original size:26 final size:26
Alignment explanation
Indices: 231770--232120 Score: 256
Period size: 26 Copynumber: 14.2 Consensus size: 26
231760 GATGATTTAG
*
231770 TAATGATTTGATAATAATCA-TATAG
1 TAATGATTTGATAATAATCATTATAA
231795 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
231821 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
231847 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
231870 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
231893 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
231919 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
231945 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
231971 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
231994 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
232017 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
232043 TAATGATTTTATAATAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
232068 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
232092 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
232117 TAAT
1 TAAT
232121 TATTACTAAT
Statistics
Matches: 260, Mismatches: 44, Indels: 44
0.75 0.13 0.13
Matches are distributed among these distances:
21 8 0.03
22 6 0.02
23 26 0.10
24 29 0.11
25 57 0.22
26 132 0.51
27 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:231992 original size:124 final size:124
Alignment explanation
Indices: 231712--232104 Score: 686
Period size: 124 Copynumber: 3.2 Consensus size: 124
231702 ATGTATTTAT
231712 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
231777 TTGATAATAATCA-TATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
231835 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
231900 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
231959 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
232024 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
232082 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
232105 CTAATGATTT
Statistics
Matches: 261, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.07
123 95 0.36
124 148 0.57
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:232111 original size:14 final size:14
Alignment explanation
Indices: 231770--232120 Score: 128
Period size: 14 Copynumber: 26.1 Consensus size: 14
231760 GATGATTTAG
*
231770 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
231784 TAATCA--T-ATAG
1 TAATGATTTAATAA
*
231795 TAATGATTTGATAA
1 TAATGATTTAATAA
*
231809 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
231821 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
231835 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
231847 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
231858 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
231874 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
231893 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
231907 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
231919 TAATGATTTGATAA
1 TAATGATTTAATAA
*
231933 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
231945 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
231959 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
231971 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
231982 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
231998 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
232017 TAATGATTTGATAA
1 TAATGATTTAATAA
*
232031 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
232043 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
232057 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
232069 T-ATTATTTAGTAA
1 TAATGATTTAATAA
232082 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
232092 TAATGATTTAATAC
1 TAATGATTTAATAA
232106 TAATGATTTAATAA
1 TAATGATTTAATAA
232120 T
1 T
232121 TATTACTAAT
Statistics
Matches: 260, Mismatches: 42, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
10 4 0.02
11 38 0.15
12 61 0.23
13 26 0.10
14 81 0.31
15 4 0.02
16 22 0.08
18 2 0.01
19 18 0.07
20 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:232143 original size:38 final size:38
Alignment explanation
Indices: 232073--232146 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
232063 TTTAGTTATT
* **
232073 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
232111 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
232147 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:232353 original size:17 final size:17
Alignment explanation
Indices: 232328--232360 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
232318 ACTAAATATT
*
232328 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
232345 TAATGATTTGATACTA
1 TAATGATTTGATACTA
232361 AACATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:232353 original size:25 final size:23
Alignment explanation
Indices: 232274--232353 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
232264 GATTTATTGT
232274 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
232295 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
232322 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
232344 GTAATGATTT
1 -TAAT-ATTT
232354 GATACTAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:234534 original size:15 final size:14
Alignment explanation
Indices: 234511--234541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
234501 TACAACACTA
234511 AACTTTAATATAAT
1 AACTTTAATATAAT
234525 AACTTATAATATAAT
1 AACTT-TAATATAAT
234540 AA
1 AA
234542 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:234549 original size:16 final size:16
Alignment explanation
Indices: 234516--234562 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
234506 CACTAAACTT
*
234516 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
234531 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
234547 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
234563 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:234801 original size:45 final size:45
Alignment explanation
Indices: 234724--234860 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
234714 TCAACAAACA
*
234724 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
234772 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
* * * *
234816 AACTAT-A-TAACTATCAAACATATACTAATTAATTAAATAATTTTT
1 AA-TATAACTAACTAT-TAACA-AAACAAACTAATTAAATAATTTTT
234861 AATTTATGTA
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
43 7 0.09
44 16 0.21
45 26 0.34
46 14 0.18
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:235053 original size:21 final size:21
Alignment explanation
Indices: 235023--235075 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
235013 CCCTTTCTTC
*
235023 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
235044 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
235065 TTCTTTCTTTC
1 TTCTTTCTTTC
235076 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:235066 original size:17 final size:16
Alignment explanation
Indices: 235046--235077 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
235036 TTCTCCCTTT
235046 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
235063 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
235078 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:235110 original size:23 final size:23
Alignment explanation
Indices: 235080--235125 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
235070 TCTTTCTCGG
*
235080 CTGCAATCTCTTCTAACTTTCTT
1 CTGCAATCTATTCTAACTTTCTT
**
235103 CTGCAATCTATTCTCCCTTTCTT
1 CTGCAATCTATTCTAACTTTCTT
235126 TCTTTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTATTCTAACTTTCTT
Found at i:235166 original size:25 final size:25
Alignment explanation
Indices: 235138--235189 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
235128 TTTCTTTTAT
235138 AACCGACTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
235163 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
235188 AA
1 AA
235190 TAATTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.27
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:235373 original size:102 final size:102
Alignment explanation
Indices: 235238--235441 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
235228 TGGTTCAATT
*
235238 ATTGTACCAATTATTTCACATGCATTGGCTCAAATGGTTCACATGGTTTCATTGGGAGCTGTAGG
1 ATTGAACCAATTATTTCACATGCATTGGCTCAAATGGTTCACATGGTTTCATTGGGAGCTGTAGG
*
235303 CATGCAGCATGTAGCGGGGAGCACGTGAAGGAATCTA
66 CATGCAGCATGCAGCGGGGAGCACGTGAAGGAATCTA
235340 ATTGAACCAATTATTTCACATGCATTGGCTCAAATGGTTCACATGGTTTCATTGGGAGCTGTAGG
1 ATTGAACCAATTATTTCACATGCATTGGCTCAAATGGTTCACATGGTTTCATTGGGAGCTGTAGG
*
235405 CATGCAGCATGCAGTGGGGAGCACGTGAAGGAATCTA
66 CATGCAGCATGCAGCGGGGAGCACGTGAAGGAATCTA
235442 TGTGGCTGTG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (102 bp):
ATTGAACCAATTATTTCACATGCATTGGCTCAAATGGTTCACATGGTTTCATTGGGAGCTGTAGG
CATGCAGCATGCAGCGGGGAGCACGTGAAGGAATCTA
Found at i:235589 original size:9 final size:9
Alignment explanation
Indices: 235575--235603 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
235565 CTCTCCCCAT
235575 TGGCTCGTA
1 TGGCTCGTA
235584 TGGCTCGTA
1 TGGCTCGTA
235593 TGGCTCGTA
1 TGGCTCGTA
235602 TG
1 TG
235604 TCACCCCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.34, T:0.34
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:235632 original size:11 final size:12
Alignment explanation
Indices: 235598--235640 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
235588 TCGTATGGCT
235598 CGTATGTCACCC
1 CGTATGTCACCC
235610 CGTATGTCACCC
1 CGTATGTCACCC
235622 CGTAT-TCACCC
1 CGTATGTCACCC
235633 CGTATGTC
1 CGTATGTC
235641 GCCTGGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:236245 original size:24 final size:24
Alignment explanation
Indices: 236218--236264 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
236208 CCCAATGATT
236218 GGGTACTCTTTCATTCTTGTTTTA
1 GGGTACTCTTTCATTCTTGTTTTA
*
236242 GGGTACTCTTTCATTTTTGTTTT
1 GGGTACTCTTTCATTCTTGTTTT
236265 TACTGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (24 bp):
GGGTACTCTTTCATTCTTGTTTTA
Found at i:243981 original size:114 final size:114
Alignment explanation
Indices: 243781--244351 Score: 1142
Period size: 114 Copynumber: 5.0 Consensus size: 114
243771 TTAGCGTCAG
243781 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
1 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
243846 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
66 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
243895 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
1 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
243960 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
66 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
244009 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
1 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
244074 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
66 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
244123 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
1 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
244188 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
66 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
244237 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
1 AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
244302 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
66 GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
244351 A
1 A
244352 TGTTGTTGTG
Statistics
Matches: 457, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 457 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (114 bp):
AGGGAGTGAAAGGGCTTTACAAAGGGTTCGGCCCCGCCATGGCACGAAGCATCCCTGCAAATGCA
GCATGCTTCTTGGCATATGAAGTGACAAGGTCTAGTTTAGGCTAATCAA
Found at i:247617 original size:22 final size:22
Alignment explanation
Indices: 247589--247631 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
247579 ACACCAGCAG
247589 TATACATTATACTTTCCGACCA
1 TATACATTATACTTTCCGACCA
247611 TATACATTATACTTTCCGACC
1 TATACATTATACTTTCCGACC
247632 GAACTTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (22 bp):
TATACATTATACTTTCCGACCA
Found at i:254069 original size:17 final size:21
Alignment explanation
Indices: 254035--254076 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
254025 TTAAAAAGAT
254035 AAAAATAAAGACGTGAT-ATA
1 AAAAATAAAGACGTGATAATA
254055 AAAAATAAA-A-G-GATAATA
1 AAAAATAAAGACGTGATAATA
254073 AAAA
1 AAAA
254077 GCAAGTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 1 0.05
20 9 0.43
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAAATAAAGACGTGATAATA
Found at i:258632 original size:6 final size:6
Alignment explanation
Indices: 258622--258654 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
258612 ATTTTAATGT
*
258622 ATATAT ATATAA ATATAA ATATAA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATA
258655 AAGATTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:259531 original size:13 final size:13
Alignment explanation
Indices: 259513--259537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259503 TTTTTTTTTT
259513 TGGGGGCGGGGGG
1 TGGGGGCGGGGGG
259526 TGGGGGCGGGGG
1 TGGGGGCGGGGG
259538 AGGGTATAGA
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:0.00, C:0.08, G:0.84, T:0.08
Consensus pattern (13 bp):
TGGGGGCGGGGGG
Found at i:269158 original size:123 final size:123
Alignment explanation
Indices: 268837--269320 Score: 337
Period size: 123 Copynumber: 4.0 Consensus size: 123
268827 TATCCAGAAG
* **
268837 ATCCACCCGCACTAGCTCCACCACCACCATTTCCA--CCATGTCCACCGGCTCCTCCATACCCAC
1 ATCCACCTGCACTAGCTCCACCACCACCACCTCCACCCCATGTCCACCGGCTCCTCCATACCCAC
* * * *
268900 CAGCACTGCCAGCTCCAGCTCCTTCACCACCTCCGCTCCCATATCCAGAAGCTCCACCTCCAT
66 C--CA---CCAGCTCCACCTCCTTCACCACCTCCACTGCCATATCCAGAAGCTCCACCACCAT
* * * * ** * * *** * **
268963 ATCCACCTGCACT-GCCTCCACCACCACCTCCAACAACACCAACTTCTCCATATCCACC-GGCTC
1 ATCCACCTGCACTAG-CTCCACCACCACCACC-TCCACCCCATGTCCACCGGCTCCTCCATAC-C
*
269026 CAGCC-CCAGCTCCACCTCCTTCACCACCTCCAGC-GCCATATCCAGAAGCTCCACCACCAT
63 CACCCACCAGCTCCACCTCCTTCACCACCTCCA-CTGCCATATCCAGAAGCTCCACCACCAT
* * *
269086 ATCCACCTGTACTAGCTCCTCCACCACCACCTCCACCTCCATGTCCACCGGCTCCTGCATACCCA
1 ATCCACCTGCACTAGCTCCACCACCACCACCTCCACC-CCATGTCCACCGGCTCCTCCATACCCA
* * *
269151 -CCACCAGCTCCA---CC-T--CCA-CT--A---CCATATCCCGAAGCTCCTCCGCCAT
65 CCCACCAGCTCCACCTCCTTCACCACCTCCACTGCCATATCCAGAAGCTCCACCACCAT
* * * *
269197 ATCCACCTGCAGC-ACCTCCACCACCACCTTTGCCACCACCACCCCCATATCCACCTGCTCCTCC
1 ATCCACCTGCA-CTAGCTCCACCACCA------CCACCTCCA-CCCCATGTCCACCGGCTCCTCC
* *
269261 ATATCC-TCCACCAGCTCCACCTCCTTCACCACCTCCACTTG-CATATCCAGAAGCTCCACC
58 ATACCCACCCACCAGCTCCACCTCCTTCACCACCTCCAC-TGCCATATCCAGAAGCTCCACC
269321 TGCACTAACT
Statistics
Matches: 275, Mismatches: 51, Indels: 61
0.71 0.13 0.16
Matches are distributed among these distances:
111 43 0.16
112 1 0.00
114 1 0.00
116 2 0.01
117 45 0.16
118 2 0.01
119 1 0.00
120 4 0.01
121 1 0.00
122 5 0.02
123 101 0.37
124 5 0.02
125 1 0.00
126 26 0.09
127 3 0.01
128 1 0.00
129 33 0.12
ACGTcount: A:0.22, C:0.51, G:0.08, T:0.18
Consensus pattern (123 bp):
ATCCACCTGCACTAGCTCCACCACCACCACCTCCACCCCATGTCCACCGGCTCCTCCATACCCAC
CCACCAGCTCCACCTCCTTCACCACCTCCACTGCCATATCCAGAAGCTCCACCACCAT
Found at i:269285 original size:18 final size:18
Alignment explanation
Indices: 269264--269298 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
269254 CTCCTCCATA
*
269264 TCCTCCACCAGCTCCACC
1 TCCTCCACCACCTCCACC
*
269282 TCCTTCACCACCTCCAC
1 TCCTCCACCACCTCCAC
269299 TTGCATATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.60, G:0.03, T:0.20
Consensus pattern (18 bp):
TCCTCCACCACCTCCACC
Found at i:277284 original size:30 final size:30
Alignment explanation
Indices: 277245--277346 Score: 159
Period size: 30 Copynumber: 3.4 Consensus size: 30
277235 TAAAAGTCAC
* * *
277245 AAATCGATCACCAATATTATCATTTGTTACA
1 AAAT-GATCACTAACATTATCGTTTGTTACA
277276 AAATGATCACTAACATTATCGTTTGTTACA
1 AAATGATCACTAACATTATCGTTTGTTACA
*
277306 AAATGGTCACTAACATTATCGTTTGTTACA
1 AAATGATCACTAACATTATCGTTTGTTACA
277336 AAATGATCACT
1 AAATGATCACT
277347 CGAAACGTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 62 0.94
31 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATGATCACTAACATTATCGTTTGTTACA
Found at i:281828 original size:21 final size:21
Alignment explanation
Indices: 281804--281843 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
281794 CGTTATTTCA
*
281804 TTCCATTTCTGGGTTTCTGCT
1 TTCCATTTCTGGGCTTCTGCT
*
281825 TTCCGTTTCTGGGCTTCTG
1 TTCCATTTCTGGGCTTCTG
281844 TTCAATTTTC
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:0.03, C:0.25, G:0.23, T:0.50
Consensus pattern (21 bp):
TTCCATTTCTGGGCTTCTGCT
Found at i:283263 original size:28 final size:28
Alignment explanation
Indices: 283231--283296 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
283221 AAACTCTAAG
** * *
283231 TTAGAGTTTAAGGTTTAAGCTTTATGGT
1 TTAGAGTTTAAGGGGTAAGATTTAGGGT
* * *
283259 TTAGAGGTTATGGGGTATGATTTAGGGT
1 TTAGAGTTTAAGGGGTAAGATTTAGGGT
283287 TTAGAGTTTA
1 TTAGAGTTTA
283297 TAATTTAGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (28 bp):
TTAGAGTTTAAGGGGTAAGATTTAGGGT
Found at i:283901 original size:96 final size:96
Alignment explanation
Indices: 283784--283987 Score: 318
Period size: 96 Copynumber: 2.1 Consensus size: 96
283774 TTTATTATAA
* *
283784 AATAATTCAAAAGGTGTAATAACATATAAAAAGGGGTAAATGACGTGTTTAATGCTTAAACTATC
1 AATAATTCAAAAGGTGTAATAACATATAAAAAGGGGTAAATGACGTGTTTAATACCTAAACTATC
* ** *
283849 CGTTTGGGTTTGTTTTAATACATAAAGTTTT
66 AGTTTGGGTTCATTTTAATACATAAACTTTT
283880 AATAATTCAAAAGGTGTAATAACATATAAAAAGGGGTAAATGACGTGTTTAATACCTAAACTATC
1 AATAATTCAAAAGGTGTAATAACATATAAAAAGGGGTAAATGACGTGTTTAATACCTAAACTATC
* *
283945 AGTTTTGGTTCATTTTAATGCATAAACTTTT
66 AGTTTGGGTTCATTTTAATACATAAACTTTT
**
283976 AATTTTTCAAAA
1 AATAATTCAAAA
283988 ACATACTTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (96 bp):
AATAATTCAAAAGGTGTAATAACATATAAAAAGGGGTAAATGACGTGTTTAATACCTAAACTATC
AGTTTGGGTTCATTTTAATACATAAACTTTT
Found at i:284220 original size:14 final size:14
Alignment explanation
Indices: 284201--284257 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
284191 TTAAATATTA
284201 TAATAAATTAAAAT
1 TAATAAATTAAAAT
*
284215 TAATAATTTAAATACT
1 TAATAAATTAAA-A-T
284231 ATAATAAATTAAAAT
1 -TAATAAATTAAAAT
*
284246 TAATAATTTAAA
1 TAATAAATTAAA
284258 TACAGAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 22 0.59
15 2 0.05
16 2 0.05
17 11 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAAATTAAAAT
Found at i:284220 original size:17 final size:17
Alignment explanation
Indices: 284191--284252 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
284181 CATTAAAAAT
284191 TTAAATATTATAATAAA
1 TTAAATATTATAATAAA
*
284208 TTAAA-A-T-TAATAAT
1 TTAAATATTATAATAAA
*
284222 TTAAATACTATAATAAA
1 TTAAATATTATAATAAA
284239 TTAAA-ATTAATAAT
1 TTAAATATT-ATAAT
284253 TTAAATACAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.29
15 2 0.05
16 4 0.11
17 21 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATATTATAATAAA
Done.