Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023927.1 Corchorus olitorius cultivar O-4 contig23960, 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: 86643
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:343 original size:29 final size:31
Alignment explanation
Indices: 311--384 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
301 TTGAAAGCTG
*
311 AGGGATTTATTTGGCCC-AAA-AAAAAGATC
1 AGGGATTTATTTGGCCCAAAATAAAAAGATA
*
340 AGGGATTTATTTGTCCCAAAATAAAAAGATA
1 AGGGATTTATTTGGCCCAAAATAAAAAGATA
371 AGGGATTTATTTGG
1 AGGGATTTATTTGG
385 TATTTAAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.40
30 3 0.08
31 21 0.52
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (31 bp):
AGGGATTTATTTGGCCCAAAATAAAAAGATA
Found at i:7790 original size:25 final size:25
Alignment explanation
Indices: 7762--7811 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
7752 TAAGCCTATA
*
7762 GGAATTTATTTAATGAATTCGTTTT
1 GGAATTTATTTAATAAATTCGTTTT
7787 GGAATTTATTTAATAAATTCGTTTT
1 GGAATTTATTTAATAAATTCGTTTT
7812 TACCATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (25 bp):
GGAATTTATTTAATAAATTCGTTTT
Found at i:10744 original size:22 final size:22
Alignment explanation
Indices: 10719--10761 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10709 ATATTCTTTT
10719 AAATTTATTATT-TCTTTTTATC
1 AAATTTATTATTAT-TTTTTATC
*
10741 AAATTTTTTATTATTTTTTAT
1 AAATTTATTATTATTTTTTAT
10762 AGTTAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (22 bp):
AAATTTATTATTATTTTTTATC
Found at i:12580 original size:23 final size:24
Alignment explanation
Indices: 12537--12592 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
12527 CTTAACCCAA
12537 ATAACCCAAAATCTTAAAGAACCC-
1 ATAACCCAAAA-CTTAAAGAACCCT
12561 ATAACCCAGAAA-TTAAAGAACCCTT
1 ATAACCCA-AAACTTAAAGAACCC-T
12586 ATAACCC
1 ATAACCC
12593 TTAGCTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 10 0.34
ACGTcount: A:0.48, C:0.29, G:0.05, T:0.18
Consensus pattern (24 bp):
ATAACCCAAAACTTAAAGAACCCT
Found at i:12641 original size:17 final size:16
Alignment explanation
Indices: 12619--12660 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
12609 TAACCCAGAT
12619 AACCCTGAATCTTAAAG
1 AACCCTGAAT-TTAAAG
*
12636 AACCCTGGAATTTAATG
1 AACCCT-GAATTTAAAG
12653 AACCCTGA
1 AACCCTGA
12661 TAACCCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (16 bp):
AACCCTGAATTTAAAG
Found at i:13850 original size:49 final size:49
Alignment explanation
Indices: 13737--13921 Score: 309
Period size: 49 Copynumber: 3.8 Consensus size: 49
13727 TTTTTTTTAA
13737 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCTCTTTTTTTTGGT
1 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAA-C-CTCTTTTTTTTGGT
*
13788 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCGTTTTTTTGGT
1 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCTTTTTTTTGGT
* **
13837 AGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACCT-TTTTTTTTTTT
1 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCTTTTTTTTGGT
13885 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCT
1 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCT
13922 TTATTTTCCT
Statistics
Matches: 128, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
48 44 0.34
49 49 0.38
50 1 0.01
51 34 0.27
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (49 bp):
AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCTTTTTTTTGGT
Found at i:13898 original size:48 final size:48
Alignment explanation
Indices: 13725--13928 Score: 309
Period size: 48 Copynumber: 4.2 Consensus size: 48
13715 ACTCTTTCTT
**
13725 TTTTTTTTTTAAAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
1 TTTTTTTTTTGTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
13773 TCTCTTTTTTTTGGTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
1 T-T-TTTTTTTT-GTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
* * *
13824 TCGTTTTTTTGGTAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACC
1 T-TTTTTTTTTGTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
*
13873 TTTTTTTTTTTTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
1 TTTTTTTTTTGTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
*
13921 TTTATTTT
1 TTTTTTTT
13929 CCTCTTAAGT
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
48 51 0.36
49 39 0.27
50 15 0.10
51 38 0.27
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.46
Consensus pattern (48 bp):
TTTTTTTTTTGTAGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACC
Found at i:13907 original size:97 final size:100
Alignment explanation
Indices: 13737--13921 Score: 331
Period size: 97 Copynumber: 1.9 Consensus size: 100
13727 TTTTTTTTAA
*
13737 AGTTTGAGCCGCCCTTTCGGGTTTTCAACTCAAACCTCTCTTTTTTTTGGTAGTTTGAGCCGCCC
1 AGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACCTCTCTTTTTTTTGGTAGTTTGAGCCGCCC
13802 TTTCGGGTTTTCAACTCAAACCTCGTTTTTTTGGT
66 TTTCGGGTTTTCAACTCAAACCTCGTTTTTTTGGT
*
13837 AGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACCT-T-TTTTTTTT-TTAGTTTGAGCCGCCC
1 AGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACCTCTCTTTTTTTTGGTAGTTTGAGCCGCCC
13899 TTTCGGGTTTTCAACTCAAACCT
66 TTTCGGGTTTTCAACTCAAACCT
13922 TTATTTTCCT
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
97 38 0.46
98 8 0.10
99 1 0.01
100 36 0.43
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (100 bp):
AGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAAACCTCTCTTTTTTTTGGTAGTTTGAGCCGCCC
TTTCGGGTTTTCAACTCAAACCTCGTTTTTTTGGT
Found at i:17626 original size:31 final size:30
Alignment explanation
Indices: 17534--17618 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
17524 TTTTTAGAAA
* *
17534 TTAAAACAACCCAACAAACAGTTCCATAAAT
1 TTAAAATAACCCAAGAAA-AGTTCCATAAAT
17565 TTAAAAT-ACCCAAGAAAAAGTTCCATAAAT
1 TTAAAATAACCCAAG-AAAAGTTCCATAAAT
17595 TTAAAATAACCCAAGAAAATGTTC
1 TTAAAATAACCCAAGAAAA-GTTC
17619 AACAAATTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
30 29 0.59
31 20 0.41
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (30 bp):
TTAAAATAACCCAAGAAAAGTTCCATAAAT
Found at i:20029 original size:30 final size:30
Alignment explanation
Indices: 19995--20087 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
19985 CTGGCTTTGG
*
19995 TAAAGGTTTTGGTTTTAATAAGGATTCTGA
1 TAAAGGTTTTGGTTTGAATAAGGATTCTGA
* * *
20025 TAAAGGTTTTCGCTTGGATAAGGATTCTGA
1 TAAAGGTTTTGGTTTGAATAAGGATTCTGA
* * * *
20055 TAAAGGTTTTGGTTAGGATAAGGGTTTTGA
1 TAAAGGTTTTGGTTTGAATAAGGATTCTGA
20085 TAA
1 TAA
20088 GCTAGATACG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (30 bp):
TAAAGGTTTTGGTTTGAATAAGGATTCTGA
Found at i:23131 original size:21 final size:21
Alignment explanation
Indices: 23101--23141 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23091 TATTCTTTTA
23101 AATTTATTATT-TCTTTTTATC
1 AATTTATTATTAT-TTTTTATC
*
23122 AATTTTTTATTATTTTTTAT
1 AATTTATTATTATTTTTTAT
23142 AGTTAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTATTATTATTTTTTATC
Found at i:23152 original size:24 final size:24
Alignment explanation
Indices: 23103--23152 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
23093 TTCTTTTAAA
* *
23103 TTTATTATTTCTTTTTATCAATTT
1 TTTATTATTTCTTTATATCAAGTT
*
23127 TTTATTATTT-TTTATAGTTAAGTT
1 TTTATTATTTCTTTATA-TCAAGTT
23151 TT
1 TT
23153 CTCATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTATTTCTTTATATCAAGTT
Found at i:23771 original size:3 final size:3
Alignment explanation
Indices: 23763--23802 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
23753 TTAACAAAAT
23763 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
23803 AACAAAACGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25539 original size:18 final size:18
Alignment explanation
Indices: 25516--25553 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25506 CGCGTGGGGA
25516 ATGTTTACAAATATGTTG
1 ATGTTTACAAATATGTTG
*
25534 ATGTTTCCAAATATGTTG
1 ATGTTTACAAATATGTTG
25552 AT
1 AT
25554 TCAATGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (18 bp):
ATGTTTACAAATATGTTG
Found at i:29034 original size:8 final size:8
Alignment explanation
Indices: 29023--29051 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29013 CATCTTTTAG
29023 TTTTTTGA
1 TTTTTTGA
29031 TTTTTTGA
1 TTTTTTGA
29039 TTTTTTGA
1 TTTTTTGA
29047 TTTTT
1 TTTTT
29052 ACCATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (8 bp):
TTTTTTGA
Found at i:31806 original size:21 final size:22
Alignment explanation
Indices: 31782--31823 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31772 AATTGAATGT
* *
31782 AAGTGATATGTGAT-ATGTGTG
1 AAGTGAAACGTGATGATGTGTG
31803 AAGTGAAACGTGATGATGTGT
1 AAGTGAAACGTGATGATGTGT
31824 TGCCTGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (22 bp):
AAGTGAAACGTGATGATGTGTG
Found at i:32615 original size:23 final size:23
Alignment explanation
Indices: 32581--32624 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
32571 GAACCGTAGT
*
32581 CCAACTAGATTAATATGAGCTTC
1 CCAACTAAATTAATATGAGCTTC
32604 CCAACTAAATTAATATGAGCT
1 CCAACTAAATTAATATGAGCT
32625 AAATCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (23 bp):
CCAACTAAATTAATATGAGCTTC
Found at i:33150 original size:50 final size:50
Alignment explanation
Indices: 33087--33464 Score: 607
Period size: 50 Copynumber: 7.5 Consensus size: 50
33077 CGATCAACTT
* * * * * *
33087 CTTTGAA-TCGTCTTCTAATCCAATATAAAAAGGATCGTCTTTCGCTTATC
1 CTTTGAACT-GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
33137 CTTTGAACTGTCTTCCAATTTAATCTTGAAAGGACCTTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
33187 CTTTGAACTGTCTTCCAATTCAATCTTGAAAGGACCGTCTTCCACTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
33237 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
33287 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
33337 CTTTGAACTGTCTTCCAATTCGATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
33388 CTTTGGAA-TGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTT-GAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
33438 CTTTGAACTGTCTTCCAATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
33465 GAGAAAATCA
Statistics
Matches: 308, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
49 3 0.01
50 256 0.83
51 46 0.15
52 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:33215 original size:23 final size:23
Alignment explanation
Indices: 33189--33263 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 23
33179 CGCTTATCCT
33189 TTGAACTGTCTTCCAATTCAATC
1 TTGAACTGTCTTCCAATTCAATC
* *
33212 TTGAAAGGACCGTCTTCCACTT--ATCC
1 TTG--A--ACTGTCTTCCAATTCAAT-C
33238 TTTGAACTGTCTTCCAATTCAATC
1 -TTGAACTGTCTTCCAATTCAATC
33262 TT
1 TT
33264 AAAAGGACCG
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
23 17 0.43
24 1 0.03
25 6 0.15
26 1 0.03
27 15 0.38
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.39
Consensus pattern (23 bp):
TTGAACTGTCTTCCAATTCAATC
Found at i:33226 original size:27 final size:27
Alignment explanation
Indices: 33196--33329 Score: 85
Period size: 27 Copynumber: 5.3 Consensus size: 27
33186 CCTTTGAACT
33196 GTCTTCCAATTCAATCTTGAAAGGACC
1 GTCTTCCAATTCAATCTTGAAAGGACC
* *
33223 GTCTTCCACTT--ATCCTTTG--A--ACT
1 GTCTTCCAATTCAAT-C-TTGAAAGGACC
*
33246 GTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCAATTCAATCTTGAAAGGACC
** *
33273 GTCTTCCGCTT--ATCCTTTG--A--ACT
1 GTCTTCCAATTCAAT-C-TTGAAAGGACC
*
33296 GTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCAATTCAATCTTGAAAGGACC
33323 GTCTTCC
1 GTCTTCC
33330 GCTTATCCTT
Statistics
Matches: 78, Mismatches: 13, Indels: 32
0.63 0.11 0.26
Matches are distributed among these distances:
23 27 0.35
24 2 0.03
25 12 0.15
26 2 0.03
27 35 0.45
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (27 bp):
GTCTTCCAATTCAATCTTGAAAGGACC
Found at i:33299 original size:23 final size:23
Alignment explanation
Indices: 33273--33352 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
33263 TAAAAGGACC
33273 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * * *
33296 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
33323 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
33346 GTCTTCC
1 GTCTTCC
33353 AATTCGATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:33854 original size:64 final size:64
Alignment explanation
Indices: 33697--34369 Score: 841
Period size: 64 Copynumber: 10.5 Consensus size: 64
33687 GCATCTCTTA
* * * * *
33697 ACAAGATCATCTTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTACTTTTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACTTTTTG
* * * * *
33762 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTTAGAAACCTTCTTCTTGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* ** * * * * *
33826 ACACGATCAACTTCTGATTC-ACTCCTGAAACCTCTTGAGAAACCATCTTCTAGTGTACTTCTTG
1 ACAAGATCGTCTTCCGA-TCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * * *
33890 ACAAGATCGTCCTCCGATTC-ACTCCTGAAAACTCTTGAGAAACCGTCTTTTGGTGTACTTCTTT
1 ACAAGATCGTCTTCCGA-TCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTT-TTT
33954 G
64 G
* * * * *
33955 ACAAGATCGTCCTCCGATTAACTTCTAAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * *
34019 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTCCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* *
34083 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * * * *
34147 ACAAGATCGTTTTCCGATCAACTTCTGAAAACTGTTGCGAAACCTTCTCCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
*
34211 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGA-AAACCCATCTTCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAA-CCATCTTCTGGTGTACTTTTTG
* * * *
34275 ACAAGATCGTCTTCCGATCAACTTCTGAAAGCTCTTGAGAAAACCATTTTCTGGTGTACTCTTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAG-AAACCATCTTCTGGTGTACTTTTTG
** * *
34340 ATGAGATTGTCTTCCAATCAACATT-TGAAA
1 ACAAGATCGTCTTCCGATCAAC-TTCTGAAA
34370 GTTCTTTCTA
Statistics
Matches: 539, Mismatches: 62, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
63 3 0.01
64 400 0.74
65 131 0.24
66 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (64 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
Found at i:34129 original size:257 final size:256
Alignment explanation
Indices: 33697--34369 Score: 859
Period size: 257 Copynumber: 2.6 Consensus size: 256
33687 GCATCTCTTA
* * * *
33697 ACAAGATCATCTTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTACTTTTTA
1 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACTTTTTG
* * * * * *
33762 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTTAGAAACCTTCTTCTTGTGTACTTTTTGA
65 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTTCTGGTGTACTTTTTGA
* ** * * * *
33827 CACGATCAACTTCTGATTC-ACTCCTGAAACCTCTTGAGAAACCATCTTCTAGTGTACTTCTTGA
130 CAAGATCGTCTTCCGA-TCAACTTCTGAAAACTCTTGAGAAACCATCTCCTAGTGTACTTCTTGA
**
33891 CAAGATCGTCCTCCGATTC-ACTCCTGAAAACTCTTGAGAAACCGTCTTTTGGTGTACTTCTTTG
194 CAAGATCGTCCTCCGA-TCAACTCCTGAAAACTCTTGAGAAACCGTCTCCTGGTGTACTT-TTTG
* * * * * *
33955 ACAAGATCGTCCTCCGATTAACTTCTAAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTGA
1 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTGA
*
34020 CAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTCCTGGTGTACTTTTTGAC
66 CAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTTCTGGTGTACTTTTTGAC
* * *
34085 AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTGACA
131 AAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTCCTAGTGTACTTCTTGACA
** * * * *
34150 AGATCGTTTTCCGATCAACTTCTGAAAACTGTTGCGAAACCTTCTCCTGGTGTACTTTTTG
196 AGATCGTCCTCCGATCAACTCCTGAAAACTCTTGAGAAACCGTCTCCTGGTGTACTTTTTG
34211 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGA-AAACCCATCTTCTGGTGTACTTTTTG
1 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAA-CCATCTTCTGGTGTACTTTTTG
* * * * *
34275 ACAAGATCGTCTTCCGATCAACTTCTGAAAGCTCTTGAGAAAACCATTTTCTGGTGTACTCTTTA
65 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAA-CATCTTCTGGTGTACTTTTTG
** * *
34340 ATGAGATTGTCTTCCAATCAACATT-TGAAA
129 ACAAGATCGTCTTCCGATCAAC-TTCTGAAA
34370 GTTCTTTCTA
Statistics
Matches: 360, Mismatches: 50, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
255 3 0.01
256 103 0.29
257 222 0.62
258 32 0.09
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (256 bp):
ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTGA
CAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTTCTGGTGTACTTTTTGAC
AAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTCCTAGTGTACTTCTTGACA
AGATCGTCCTCCGATCAACTCCTGAAAACTCTTGAGAAACCGTCTCCTGGTGTACTTTTTG
Found at i:34226 original size:192 final size:192
Alignment explanation
Indices: 33697--34369 Score: 886
Period size: 193 Copynumber: 3.5 Consensus size: 192
33687 GCATCTCTTA
* * * * *
33697 ACAAGATCATCTTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTACTTTTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACTTTTTG
* * * * *
33762 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTTAGAAACCTTCTTCTTGTGTACTTTTTGA
65 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCTTCTCCTGGTGTACTTTTTGA
* * * * * * *
33827 CACGATCAACTTCTGATTC-ACTCCTGAAACCTCTTGAGAAACCATCTTCTAGTGTACTTCTTG
130 CAAGATCATCTTCCGA-TCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * * *
33890 ACAAGATCGTCCTCCGATTC-ACTCCTGAAAACTCTTGAGAAACCGTCTTTTGGTGTACTTCTTT
1 ACAAGATCGTCTTCCGA-TCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTT-TTT
* * * *
33954 GACAAGATCGTCCTCCGATTAACTTCTAAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTG
64 GACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCTTCTCCTGGTGTACTTTTTG
* * * *
34019 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAAACATCTCCTGGTGTACTTTTTG
129 ACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
* *
34083 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTCCTGGTGTACTTTTTGA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTGA
* *
34148 CAAGATCGTTTTCCGATCAACTTCTGAAAACTGTTGCGAAACCTTCTCCTGGTGTACTTTTTGAC
66 CAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCTTCTCCTGGTGTACTTTTTGAC
34213 AAGATCATCTTCCGATCAACTTCTGAAAACTCTTGA-AAACCCATCTTCTGGTGTACTTTTTG
131 AAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAA-CCATCTTCTGGTGTACTTTTTG
* * * *
34275 ACAAGATCGTCTTCCGATCAACTTCTGAAAGCTCTTGAGAAAACCATTTTCTGGTGTACTCTTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAG-AAACCATCTTCTGGTGTACTTTTTG
** * *
34340 ATGAGATTGTCTTCCAATCAACATT-TGAAA
65 ACAAGATCGTCTTCCGATCAAC-TTCTGAAA
34370 GTTCTTTCTA
Statistics
Matches: 417, Mismatches: 56, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
191 3 0.01
192 180 0.43
193 230 0.55
194 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (192 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTGA
CAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCTTCTCCTGGTGTACTTTTTGAC
AAGATCATCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTG
Found at i:41669 original size:23 final size:23
Alignment explanation
Indices: 41643--41686 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41633 GAACCGTAGT
*
41643 CCAACTAGATTAATATGAGCTTC
1 CCAACTAAATTAATATGAGCTTC
41666 CCAACTAAATTAATATGAGCT
1 CCAACTAAATTAATATGAGCT
41687 AAATCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (23 bp):
CCAACTAAATTAATATGAGCTTC
Found at i:41994 original size:20 final size:20
Alignment explanation
Indices: 41969--42030 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
41959 AAGACTGAAA
41969 AATTGAAGAAACCAAACTGG
1 AATTGAAGAAACCAAACTGG
* * **
41989 AATTGATTGAAA-AAAAAGGG
1 AATTGA-AGAAACCAAACTGG
42009 AATTGAAGAAACCAAACTGG
1 AATTGAAGAAACCAAACTGG
42029 AA
1 AA
42031 AGTGGAACTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.53, C:0.10, G:0.21, T:0.16
Consensus pattern (20 bp):
AATTGAAGAAACCAAACTGG
Found at i:43638 original size:368 final size:368
Alignment explanation
Indices: 42961--43698 Score: 1404
Period size: 368 Copynumber: 2.0 Consensus size: 368
42951 ACAAGACCGG
42961 ATATAGCCTTTACAGTGAGCAAATTATCAAGATTTACTAGTAATCCTAGTATGGCTCATTGGATA
1 ATATAGCCTTTACAGTGAGCAAATTATCAAGATTTACTAGTAATCCTAGTATGGCTCATTGGATA
43026 GCGGTTGAAAGAGGACTTGGGTACCATAAACAAACCACTAAGTTCAAGTTATGTTATACTAACTT
66 GCGGTTGAAAGAGGACTTGGGTACCATAAACAAACCACTAAGTTCAAGTTATGTTATACTAACTT
* * * *
43091 TCCCGCTGTTTTGGAAGGCTATTCCGATGCTAGTTGGATCTCCAATATTGGAGATAGTATTTCAA
131 TCCCGCTGTTTTGGAAGGCTATTCCGATGCTAGTTGGATCTCCAATATTAGAAATAATATGTCAA
* *
43156 CTTCGGGTTGGATATTTTCTATAGCGGGTGGTGCTATTAGTTGGGCATCTCAGAAGCAAACATGT
196 CTTCGGGTTGGATATTTTCTATAGCAGGTGGTGCTATTAGTTGGGCATCTAAGAAGCAAACATGT
43221 CTTGCACATTCAACCATGGAAGCCGAGTTTATAGCCTTGGCAGCAGCGGGTAAAGAGGCCGAATG
261 CTTGCACATTCAACCATGGAAGCCGAGTTTATAGCCTTGGCAGCAGCGGGTAAAGAGGCCGAATG
43286 GCTTAGAAACATGTTGCTTGAAATTGATTTATGGCCTCAGCCC
326 GCTTAGAAACATGTTGCTTGAAATTGATTTATGGCCTCAGCCC
43329 ATATAGCCTTTACAGTGAGCAAATTATCAAGATTTACTAGTAATCCTAGTATGGCTCATTGGATA
1 ATATAGCCTTTACAGTGAGCAAATTATCAAGATTTACTAGTAATCCTAGTATGGCTCATTGGATA
*
43394 GTGGTTGAAAGAGGACTTGGGTACCATAAACAAACCACTAAGTTCAAGTTATGTTATACTAACTT
66 GCGGTTGAAAGAGGACTTGGGTACCATAAACAAACCACTAAGTTCAAGTTATGTTATACTAACTT
*
43459 TCCCGCTGTTTTGGAAGGCTATTCCGATGCTAGTTGGATCTCTAATATTAGAAATAATATGTCAA
131 TCCCGCTGTTTTGGAAGGCTATTCCGATGCTAGTTGGATCTCCAATATTAGAAATAATATGTCAA
43524 CTTCGGGTTGGATATTTTCTATAGCAGGTGGTGCTATTAGTTGGGCATCTAAGAAGCAAACATGT
196 CTTCGGGTTGGATATTTTCTATAGCAGGTGGTGCTATTAGTTGGGCATCTAAGAAGCAAACATGT
43589 CTTGCACATTCAACCATGGAAGCCGAGTTTATAGCCTTGGCAGCAGCGGGTAAAGAGGCCGAATG
261 CTTGCACATTCAACCATGGAAGCCGAGTTTATAGCCTTGGCAGCAGCGGGTAAAGAGGCCGAATG
43654 GCTTAGAAACATGTTGCTTGAAATTGATTTATGGCCTCAGCCC
326 GCTTAGAAACATGTTGCTTGAAATTGATTTATGGCCTCAGCCC
43697 AT
1 AT
43699 GCCACCCGTT
Statistics
Matches: 362, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
368 362 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (368 bp):
ATATAGCCTTTACAGTGAGCAAATTATCAAGATTTACTAGTAATCCTAGTATGGCTCATTGGATA
GCGGTTGAAAGAGGACTTGGGTACCATAAACAAACCACTAAGTTCAAGTTATGTTATACTAACTT
TCCCGCTGTTTTGGAAGGCTATTCCGATGCTAGTTGGATCTCCAATATTAGAAATAATATGTCAA
CTTCGGGTTGGATATTTTCTATAGCAGGTGGTGCTATTAGTTGGGCATCTAAGAAGCAAACATGT
CTTGCACATTCAACCATGGAAGCCGAGTTTATAGCCTTGGCAGCAGCGGGTAAAGAGGCCGAATG
GCTTAGAAACATGTTGCTTGAAATTGATTTATGGCCTCAGCCC
Found at i:45590 original size:19 final size:17
Alignment explanation
Indices: 45546--45594 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
45536 AAAAAAAGAT
45546 TTTTTTATTTTAACTATTA
1 TTTTTTA-TTT-ACTATTA
*
45565 TTATTTATTTACTATTTA
1 TTTTTTATTTACTA-TTA
45583 TCTTTTTATTTA
1 T-TTTTTATTTA
45595 TTAATTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 15 0.58
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTATTTACTATTA
Found at i:45595 original size:27 final size:27
Alignment explanation
Indices: 45565--45621 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
45555 TTAACTATTA
* **
45565 TTATTTATTTA-CTATTTATCTTTTTAT
1 TTATTAATTTAGCTA-TTATCTACTTAT
45592 TTATTAATTTAGCTATTATCTACTTAT
1 TTATTAATTTAGCTATTATCTACTTAT
45619 TTA
1 TTA
45622 CTATTATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATTAATTTAGCTATTATCTACTTAT
Found at i:45629 original size:45 final size:44
Alignment explanation
Indices: 45545--45638 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 44
45535 CAAAAAAAGA
* *
45545 TTTTT-TTATTTTAACTATTATTATTTATTTACTATTTATCTTT
1 TTTTTATTAATTTAACTATTATTACTTATTTACTATTTATCTTT
*
45588 TTATTTATTAATTTAGCTATTATCTACTTATTTACTA-TTATCTTT
1 TT-TTTATTAATTTAACTATTAT-TACTTATTTACTATTTATCTTT
45633 TTTTTA
1 TTTTTA
45639 CCTACCTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 2 0.04
44 7 0.16
45 24 0.53
46 12 0.27
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (44 bp):
TTTTTATTAATTTAACTATTATTACTTATTTACTATTTATCTTT
Found at i:48268 original size:11 final size:11
Alignment explanation
Indices: 48252--48288 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
48242 AAAGCAAGTG
48252 GAAAAAAAAAA
1 GAAAAAAAAAA
48263 G-AAAAAAAAA
1 GAAAAAAAAAA
*
48273 GAAGAAAAAAA
1 GAAAAAAAAAA
48284 GAAAA
1 GAAAA
48289 TAGACTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:48269 original size:10 final size:10
Alignment explanation
Indices: 48254--48288 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
48244 AGCAAGTGGA
48254 AAAAAAAAAG
1 AAAAAAAAAG
48264 AAAAAAAAAG
1 AAAAAAAAAG
48274 AAGAAAAAAAG
1 AA-AAAAAAAG
48285 AAAA
1 AAAA
48289 TAGACTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:48269 original size:13 final size:13
Alignment explanation
Indices: 48253--48288 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
48243 AAGCAAGTGG
48253 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
*
48266 AAAAAAAGAAGAA
1 AAAAAAAAAAGAA
48279 AAAAAGAAAA
1 AAAAA-AAAA
48289 TAGACTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:48753 original size:26 final size:25
Alignment explanation
Indices: 48724--48786 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 25
48714 AGGGAAAGAA
48724 AAAAAGAAAAAAGAAGAAAAGAA-TTG
1 AAAAAGAAAAAA-AAG-AAAGAAGTTG
48750 AAAAAGAAAAGAAAAGAAAGAAGTTG
1 AAAAAGAAAA-AAAAGAAAGAAGTTG
*
48776 AAAAAGCAAAA
1 AAAAAGAAAAA
48787 GATGGAGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.21
26 25 0.74
27 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (25 bp):
AAAAAGAAAAAAAAGAAAGAAGTTG
Found at i:48761 original size:21 final size:20
Alignment explanation
Indices: 48729--48767 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
48719 AAGAAAAAAA
*
48729 GAAAAAAGAAGAAAAGAATT
1 GAAAAAAAAAGAAAAGAATT
48749 GAAAAAGAAAAGAAAAGAA
1 GAAAAA-AAAAGAAAAGAA
48768 AGAAGTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
GAAAAAAAAAGAAAAGAATT
Found at i:49015 original size:41 final size:42
Alignment explanation
Indices: 48970--49051 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
48960 ATGGAAAATA
* *
48970 TTTTCTTCAAAGTGTGATCTTTTCAAAAGAAA-AAGTTTTTT
1 TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAATAAGTTTTTT
*
49011 TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAATATGTTTTT
1 TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAATAAGTTTTT
49052 CAAAAAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (42 bp):
TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAATAAGTTTTTT
Found at i:50229 original size:25 final size:25
Alignment explanation
Indices: 50180--50229 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
50170 TAAGCCAATA
**
50180 GGAATTTATTTAATAAATTTGTTTT
1 GGAATTTATTTAATAAATTCATTTT
50205 GGAATTTATTTAATAAATTCATTTT
1 GGAATTTATTTAATAAATTCATTTT
50230 TACCATGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (25 bp):
GGAATTTATTTAATAAATTCATTTT
Found at i:56165 original size:11 final size:11
Alignment explanation
Indices: 56149--56181 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
56139 CTTTCTCCTC
56149 CAAATCTTCAA
1 CAAATCTTCAA
56160 CAAATCTTCAA
1 CAAATCTTCAA
*
56171 CAATTCTTCAA
1 CAAATCTTCAA
56182 AATACAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (11 bp):
CAAATCTTCAA
Found at i:63150 original size:19 final size:18
Alignment explanation
Indices: 63117--63152 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
63107 TTGAGATAAT
63117 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
63135 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
63153 TAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:74663 original size:26 final size:23
Alignment explanation
Indices: 74633--74679 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
74623 CTTGAAAATT
74633 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
74659 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
74680 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Done.