Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004557.1 Hibiscus syriacus cultivar Beakdansim tig00010127_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: 145868
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5151 original size:21 final size:19
Alignment explanation
Indices: 5104--5158 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
5094 TGACCAGACC
5104 CTTGACTTTGACCCATTGA
1 CTTGACTTTGACCCATTGA
5123 CTAATGACTTTGACCCATTGAA
1 CT--TGACTTTGACCCATTG-A
5145 CGTTGACTTTGACC
1 C-TTGACTTTGACC
5159 AAAAAGTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.06
21 27 0.84
22 2 0.06
23 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (19 bp):
CTTGACTTTGACCCATTGA
Found at i:6497 original size:2 final size:2
Alignment explanation
Indices: 6490--6545 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
6480 TTTGACTTGT
6490 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6531 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
6546 CCTGATTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8460 original size:3 final size:3
Alignment explanation
Indices: 8452--8490 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
8442 TATTTTTAAT
8452 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8491 GTTTTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8798 original size:17 final size:18
Alignment explanation
Indices: 8764--8798 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8754 CAACTCCTCA
*
8764 GCTTCCCAGCCGTGAGCC
1 GCTTCCAAGCCGTGAGCC
8782 GCTTCCAAGCC-TGAGCC
1 GCTTCCAAGCCGTGAGCC
8799 ACCGCCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.43, G:0.26, T:0.17
Consensus pattern (18 bp):
GCTTCCAAGCCGTGAGCC
Found at i:10284 original size:5 final size:5
Alignment explanation
Indices: 10259--10296 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
10249 TTGTGTTGAG
*
10259 TTTTA -TTTA TTTATG TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTT
10297 ACTTCATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:10496 original size:2 final size:2
Alignment explanation
Indices: 10489--10533 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
10479 ATGTAAATAG
10489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10531 AT A
1 AT A
10534 ATACAATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13529 original size:20 final size:20
Alignment explanation
Indices: 13504--13564 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
13494 ACATTCCCTC
13504 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
13524 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
* *
13544 TCTTTGCGGCCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
13564 T
1 T
13565 GCATTTATCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:14194 original size:14 final size:14
Alignment explanation
Indices: 14160--14245 Score: 66
Period size: 14 Copynumber: 5.7 Consensus size: 14
14150 AATAAAAGCG
14160 AAGAACAAAGAAAATCA
1 AAGAA-AAA-AAAA-CA
* *
14177 AAGAGAAAGAAACA
1 AAGAAAAAAAAACA
*
14191 AAGAGAAAAACAAGCAGA
1 AAGA-AAAAA-AA--ACA
*
14209 AAGAAAAAGAAA-A
1 AAGAAAAAAAAACA
14222 AAGAAAAAAAAACA
1 AAGAAAAAAAAACA
14236 AAGAAAAAAA
1 AAGAAAAAAA
14246 GTGGACAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
13 12 0.21
14 18 0.32
15 6 0.11
16 7 0.12
17 8 0.14
18 6 0.11
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (14 bp):
AAGAAAAAAAAACA
Found at i:14201 original size:12 final size:12
Alignment explanation
Indices: 14168--14244 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 12
14158 CGAAGAACAA
*
14168 AGAAAATCAAAG
1 AGAAAAACAAAG
14180 AGAAAGAAACAAAG
1 AG-AA-AAACAAAG
14194 AGAAAAAC-AAG
1 AGAAAAACAAAG
14205 CAGAAAGAA-AAAG
1 -AGAAA-AACAAAG
*
14218 A-AAAAAGAAA-
1 AGAAAAACAAAG
14228 A-AAAAACAAAG
1 AGAAAAACAAAG
14239 A-AAAAA
1 AGAAAAA
14245 AGTGGACAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
10 11 0.20
11 15 0.27
12 12 0.21
13 9 0.16
14 9 0.16
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (12 bp):
AGAAAAACAAAG
Found at i:14226 original size:13 final size:14
Alignment explanation
Indices: 14208--14245 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
14198 AAACAAGCAG
*
14208 AAAGAAAAAGAAA-
1 AAAGAAAAAAAAAC
14221 AAAGAAAAAAAAAC
1 AAAGAAAAAAAAAC
14235 AAAGAAAAAAA
1 AAAGAAAAAAA
14246 GTGGACAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:15142 original size:24 final size:23
Alignment explanation
Indices: 15089--15145 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
15079 TGAAAGGGGT
15089 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
15112 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
15136 GATATTTTCA
1 AATATTTTCA
15146 TACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:15866 original size:35 final size:36
Alignment explanation
Indices: 15776--16092 Score: 144
Period size: 36 Copynumber: 8.9 Consensus size: 36
15766 GTTTCTCTCG
* * *
15776 AAACAAAATGTTGTCTCGCTAGAGACAGCTTCTTTTGAA
1 AAAC-AAATTTTGTCTCGCTTGAGACAG-TT-TTCTGAA
15815 AAACAAATCTTT-TCTCGCTTGAGACAGTTTTCT-AA
1 AAACAAAT-TTTGTCTCGCTTGAGACAGTTTTCTGAA
* * *
15850 AATCAAATTTTGTCTCGTTTGAGAC-GATTTCTTGAA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTTC-TGAA
* * *
15886 AAAAAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTT-C--TGAA
* * ** *
15925 ATACAAATTTCGAAT---TT------GTTTTCAT-ATT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTTC-TGA-A
* * ** *
15953 AAACAAA-GTTGATCTCACTTGAGATTGTTTTCTCAA
1 AAACAAATTTTG-TCTCGCTTGAGACAGTTTTCTGAA
** *
15989 AAACAAACGTTGTCTCGCTTGAGACAATTTCTCT-AA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTT-TCTGAA
* * * *
16025 AAACAATTTTTGTGTCGTTTGAGACAATTTCTCT-AA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTT-TCTGAA
* * *
16061 AAACAAATGTTGTCTCACTTGAGACAATTTTC
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTTC
16093 CAAATTATGA
Statistics
Matches: 218, Mismatches: 39, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
27 3 0.01
28 8 0.04
29 1 0.00
30 4 0.02
31 2 0.01
34 8 0.04
35 24 0.11
36 108 0.50
37 19 0.09
38 19 0.09
39 22 0.10
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTTCTGAA
Found at i:15874 original size:73 final size:71
Alignment explanation
Indices: 15781--15917 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
15771 TCTCGAAACA
* * * *
15781 AAATGTTGTCTCGCTAGAGACAGCTTCTTTTGAAAAACAAATCTT-TTCTCGCTTGAGACAGTTT
1 AAATGTTGTCTCGCTAGAGAC-GATT-TCTTGAAAAAAAAAT-TTCGTCTCGCTTGAGACAGTTT
15845 TCTAAAATC
63 TCTAAAATC
* * * *
15854 AAATTTTGTCTCGTTTGAGACGATTTCTTGAAAAAAAAATTTCGTCTCGCTTGAGACATTTTTC
1 AAATGTTGTCTCGCTAGAGACGATTTCTTGAAAAAAAAATTTCGTCTCGCTTGAGACAGTTTTC
15918 CTTTGAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 2 0.04
71 32 0.58
72 3 0.05
73 18 0.33
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (71 bp):
AAATGTTGTCTCGCTAGAGACGATTTCTTGAAAAAAAAATTTCGTCTCGCTTGAGACAGTTTTCT
AAAATC
Found at i:16027 original size:36 final size:36
Alignment explanation
Indices: 15981--16090 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 36
15971 TTGAGATTGT
*
15981 TTTCTC-AAAAACAAACGTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
* * * *
16016 TTTCTCTAAAAACAATTTTTGTGTCGTTTGAGACAA
1 TTTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
*
16052 TTTCTCTAAAAACAAATGTTGTCTCACTTGAGACAA
1 TTTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
16088 TTT
1 TTT
16091 TCCAAATTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
35 6 0.09
36 58 0.91
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
Found at i:16143 original size:32 final size:30
Alignment explanation
Indices: 16107--16168 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
16097 TTATGAATTT
16107 GTTTCACTGGAAACAAACATCATCTTTGAGTC
1 GTTTCACTGGAAAC-AA-ATCATCTTTGAGTC
** * *
16139 GTTTCTTTTGAAACAAATGATCTTTGAGTC
1 GTTTCACTGGAAACAAATCATCTTTGAGTC
16169 TATTTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 13 0.50
31 2 0.08
32 11 0.42
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (30 bp):
GTTTCACTGGAAACAAATCATCTTTGAGTC
Found at i:16164 original size:30 final size:31
Alignment explanation
Indices: 16128--16186 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
16118 AACAAACATC
*
16128 ATCTTTGAGTC-GTTTCTTTTGAAACAAATG
1 ATCTTTGAGTCTATTTCTTTTGAAACAAATG
16158 ATCTTTGAGTCTATTTCTTTTGAAACAAA
1 ATCTTTGAGTCTATTTCTTTTGAAACAAA
16187 ACTTTGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCTTTTGAAACAAATG
Found at i:16422 original size:66 final size:64
Alignment explanation
Indices: 16250--16435 Score: 230
Period size: 64 Copynumber: 2.9 Consensus size: 64
16240 TTAAAAAAAA
* * * * *
16250 TGAAAAAATATTTGAGCATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTT
1 TGAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTT
* * * *
16314 TGAAAGAATCATTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTTTTTTGAGACAGTTCCTTT
1 TGAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTT
* **
16378 TGAAGAAAAATCTTTAAGTATGTTT-TTATGAAAACAAAGGTTTGTCTCTTTTGAGACA
1 TG-A-AAAAATCTTTGAGTATGTTTCTT-TGAAAACAAAATTTTGTCTCTTTTGAGACA
16436 ATTTCTCTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
64 57 0.55
65 3 0.03
66 43 0.42
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (64 bp):
TGAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTT
Found at i:16676 original size:66 final size:66
Alignment explanation
Indices: 16606--16890 Score: 170
Period size: 66 Copynumber: 4.5 Consensus size: 66
16596 ATTTCTGTTA
* *
16606 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAAACAACCTTTGAGATTGTTTCCTTT
1 AAACAAATTTTGTCTCTCTTAAGACAGTTTCTTATGAAAAAACAACCTTTGAGATTGTTTCCTTT
16671 G
66 G
* * * * * * * *
16672 AAACAAATTTCGTCTCACTT---A-AG------ATG--TAATCCATCTTTGAGTTTGTTTCTTTT
1 AAACAAATTTTGTCTCTCTTAAGACAGTTTCTTATGAAAAAACAACCTTTGAGATTGTTTCCTTT
16725 G
66 G
* * * * * * * *
16726 AAACAAAATTT-TATATCTTAATGACAATTTCTTTTGAGAAAAAAAATCTTTGAGTTTGTTTCCT
1 AAACAAATTTTGTCTCTCTTAA-GACAGTTTCTTATGA-AAAAACAACCTTTGAGATTGTTTCCT
16790 TTG
64 TTG
* * * * * *
16793 AAACAAAATTTTGTCTCTC--GAGACAATTTCTTTTGAAAATACCCACCTTTGAGATCGTTT-CT
1 AAAC-AAATTTTGTCTCTCTTAAGACAGTTTCTTATGAAAA-AACAACCTTTGAGATTGTTTCCT
*
16855 ATTA
64 -TTG
* *
16859 AAACAAATTTTGTCTCCCTTAAGGCAGTTTCT
1 AAACAAATTTTGTCTCTCTTAAGACAGTTTCT
16891 CTAAAAATAC
Statistics
Matches: 164, Mismatches: 35, Indels: 39
0.69 0.15 0.16
Matches are distributed among these distances:
53 5 0.03
54 31 0.19
56 3 0.02
57 1 0.01
58 1 0.01
62 2 0.01
63 1 0.01
64 2 0.01
65 18 0.11
66 53 0.32
67 37 0.23
68 6 0.04
69 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (66 bp):
AAACAAATTTTGTCTCTCTTAAGACAGTTTCTTATGAAAAAACAACCTTTGAGATTGTTTCCTTT
G
Found at i:16920 original size:31 final size:31
Alignment explanation
Indices: 16885--16945 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
16875 CCTTAAGGCA
16885 GTTTCTCTAAAAATACAAA-ATCTTTGAGTTT
1 GTTTCTCTAAAAATA-AAACATCTTTGAGTTT
**
16916 GTTTCTCTTGAAATAAAACTATCTTTGAGT
1 GTTTCTCTAAAAATAAAAC-ATCTTTGAGT
16946 CGTTTCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.12
31 13 0.50
32 10 0.38
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (31 bp):
GTTTCTCTAAAAATAAAACATCTTTGAGTTT
Found at i:17323 original size:38 final size:37
Alignment explanation
Indices: 17231--17337 Score: 110
Period size: 36 Copynumber: 2.9 Consensus size: 37
17221 TTCTTTGAGA
* * **
17231 AAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTAC
1 AAAATCTTTGAGTATGTTTCCTT-GAAACAAAATAAAC
* *
17269 --CATCTTTGAGTTTGTTTCCCTTGAAACAAAATAAAC
1 AAAATCTTTGAGTATGTTT-CCTTGAAACAAAATAAAC
*
17305 AAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1 AAAATCTTTGAGTATG-TTTCCTTGAAACAAAA
17338 ACATCTTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
36 27 0.47
37 3 0.05
38 24 0.42
39 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (37 bp):
AAAATCTTTGAGTATGTTTCCTTGAAACAAAATAAAC
Found at i:17526 original size:31 final size:28
Alignment explanation
Indices: 17488--17568 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
17478 GAGACAATTG
*
17488 CTTTTGAAACACATCACCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ACCTTTGAGTATGTTT
*
17519 -TTCTTGAAACAAATCTTTGAGTATGTTT
1 CTT-TTGAAACAAACCTTTGAGTATGTTT
*
17547 CTTTTGAAACAAATCTTTGAGT
1 CTTTTGAAACAAACCTTTGAGT
17569 CGGTTTCCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 33 0.72
29 2 0.04
30 3 0.07
31 8 0.17
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (28 bp):
CTTTTGAAACAAACCTTTGAGTATGTTT
Found at i:17575 original size:28 final size:28
Alignment explanation
Indices: 17505--17568 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
17495 AACACATCAC
*
17505 CTTTGAGTTTGTTT-TTCTTGAAACAAAT
1 CTTTGAGTATGTTTCTT-TTGAAACAAAT
17533 CTTTGAGTATGTTTCTTTTGAAACAAAT
1 CTTTGAGTATGTTTCTTTTGAAACAAAT
17561 CTTTGAGT
1 CTTTGAGT
17569 CGGTTTCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 32 0.94
29 2 0.06
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (28 bp):
CTTTGAGTATGTTTCTTTTGAAACAAAT
Found at i:17581 original size:28 final size:28
Alignment explanation
Indices: 17521--17584 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
17511 GTTTGTTTTT
* *
17521 CTTGAAACAAATCTTTGAGTATGTTTCT
1 CTTGAAACAAATCTTTGAGTAGGTTTCC
* *
17549 TTTGAAACAAATCTTTGAGTCGGTTTCC
1 CTTGAAACAAATCTTTGAGTAGGTTTCC
17577 CTTGAAAC
1 CTTGAAAC
17585 CATAATCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (28 bp):
CTTGAAACAAATCTTTGAGTAGGTTTCC
Found at i:17698 original size:43 final size:42
Alignment explanation
Indices: 17644--17842 Score: 129
Period size: 43 Copynumber: 4.5 Consensus size: 42
17634 ATCAACCGAA
17644 CAGACCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAAC
1 CAGA-CTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAAC
* ** * **
17687 CAGACGTCCTCATCATGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGC
1 CAGAC-TCCTCATCACGTAGGAGTCGTG---TC-ACC--CCT--AGATAAC
* * *
17738 CAGAACTCTTCATCACGTATGAGTCGTGTCATCCCC-CG---AC
1 CAG-ACTCCTCATCACGTAGGAGTCGTGTCA-CCCCTAGATAAC
17778 CAGATCTCCTCATCACGTAGGA-TCCGTGTCACCCCTAGATAAC
1 CAGA-CTCCTCATCACGTAGGAGT-CGTGTCACCCCTAGATAAC
* *
17821 CAGCCGTCCTCATCGCGTAGGA
1 CAGAC-TCCTCATCACGTAGGA
17843 ACCGAGTTAT
Statistics
Matches: 119, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
39 6 0.05
40 27 0.23
42 2 0.02
43 44 0.37
46 4 0.03
47 2 0.02
48 4 0.03
49 3 0.03
51 25 0.21
52 2 0.02
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.23
Consensus pattern (42 bp):
CAGACTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAAC
Found at i:17792 original size:40 final size:39
Alignment explanation
Indices: 17737--17812 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
17727 CTAAAGATGG
* *
17737 CCAGAACTCTTCATCACGTATGAGT-CGTGTCATCCCCCGA
1 CCAGAACTCCTCATCACGTAGGA-TCCGTGTCA-CCCCCGA
*
17777 CCAGATCTCCTCATCACGTAGGATCCGTGTCACCCC
1 CCAGAACTCCTCATCACGTAGGATCCGTGTCACCCC
17813 TAGATAACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 5 0.16
40 27 0.84
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (39 bp):
CCAGAACTCCTCATCACGTAGGATCCGTGTCACCCCCGA
Found at i:17833 original size:134 final size:134
Alignment explanation
Indices: 17593--17869 Score: 439
Period size: 134 Copynumber: 2.1 Consensus size: 134
17583 ACCATAATCA
*
17593 CTAAAGATGGCCATAACTCTTCATCAAGTATGAGTCGTGTCATCAACCGAACAGACCTCCTCATC
1 CTAAAGATGGCCAGAACTCTTCATCAAGTATGAGTCGTGTCATCAACCGAACAGACCTCCTCATC
* * *
17658 ACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCATGTAGGAACCGTGTTATCGCC
66 ACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACC
17723 CTTC
131 CTTC
* ** * *
17727 CTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATC
1 CTAAAGATGGCCAGAACTCTTCATCAAGTATGAGTCGTGTCATCAACCGAACAGACCTCCTCATC
* *
17792 ACGTAGGA-TCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAC
66 ACGTAGGAGT-CGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
17856 CCTTC
130 CCTTC
17861 CTAAAGATG
1 CTAAAGATG
17870 ATGTTGAAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 1 0.01
134 130 0.99
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (134 bp):
CTAAAGATGGCCAGAACTCTTCATCAAGTATGAGTCGTGTCATCAACCGAACAGACCTCCTCATC
ACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACC
CTTC
Found at i:23995 original size:23 final size:21
Alignment explanation
Indices: 23943--24004 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
23933 TTTTGGTGCA
*
23943 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
23963 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
23984 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
24005 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:24030 original size:20 final size:20
Alignment explanation
Indices: 23945--24030 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
23935 TTGGTGCAGA
* *
23945 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
23964 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
23988 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
24009 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
24029 GG
1 GG
24031 TTCTAGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:27549 original size:43 final size:40
Alignment explanation
Indices: 27434--27554 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
27424 CCCAACAGAT
* *
27434 GACCAGAACTCGTCATCACGTATGAGCCGTGTCATCCCCC
1 GACCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCAC
** * *
27474 GACCAGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAAAC
1 GACCAGAACTCCTCATCACGTATGAGCCGTGTCATCCC----AC
* * * *
27517 GACCAGAACTCTTCATCATGTATGAGCAGTGTCGTCCC
1 GACCAGAACTCCTCATCACGTATGAGCCGTGTCATCCC
27555 CAACAAACCT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
39 3 0.05
40 29 0.47
43 27 0.44
44 3 0.05
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (40 bp):
GACCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCAC
Found at i:27723 original size:3 final size:3
Alignment explanation
Indices: 27715--27767 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
27705 TATTTTTAAT
27715 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27763 TTA TT
1 TTA TT
27768 TTGAAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29531 original size:15 final size:15
Alignment explanation
Indices: 29511--29577 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
29501 CTTGTGTTGA
29511 GTTTTA-TTTATTTAT
1 GTTTTATTTTATTT-T
29526 GTTTTATTTTATTTT
1 GTTTTATTTTATTTT
*
29541 ATTTTATTTTATTTT
1 GTTTTATTTTATTTT
* * *
29556 -ATTTACTTCATCTTT
1 GTTTTATTTTAT-TTT
29571 GTTTTAT
1 GTTTTAT
29578 GAACTAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.19
15 24 0.56
16 11 0.26
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (15 bp):
GTTTTATTTTATTTT
Found at i:29537 original size:5 final size:5
Alignment explanation
Indices: 29512--29559 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
29502 TTGTGTTGAG
*
29512 TTTTA -TTTA TTTATG TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
29560 ACTTCATCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 4 0.10
5 31 0.79
6 4 0.10
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:29780 original size:2 final size:2
Alignment explanation
Indices: 29773--29805 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29763 GTGTAAGTAA
*
29773 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29806 ATACAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33242 original size:15 final size:17
Alignment explanation
Indices: 33211--33242 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
33201 TTTGCTAAGG
33211 ATTTCTATTATGATTTT
1 ATTTCTATTATGATTTT
33228 ATTTCT-TTA-GATTTT
1 ATTTCTATTATGATTTT
33243 CTCAAGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (17 bp):
ATTTCTATTATGATTTT
Found at i:35010 original size:24 final size:24
Alignment explanation
Indices: 34978--35037 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
34968 TCTATAATCT
* * *
34978 GAGTCAACTTAGACAGAGTTGGCG
1 GAGTCAACTCAGACAGAGTTGACC
**
35002 GAGTCAACTCAGATTGAGTTGACC
1 GAGTCAACTCAGACAGAGTTGACC
35026 GAGTCAACTCAG
1 GAGTCAACTCAG
35038 TCTAGTGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (24 bp):
GAGTCAACTCAGACAGAGTTGACC
Found at i:36763 original size:22 final size:22
Alignment explanation
Indices: 36735--36787 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
36725 AATATTTGTT
36735 CCGAAGGACCACTAGATACGTC
1 CCGAAGGACCACTAGATACGTC
*
36757 CCGAAGGACCACTGGATACGTC
1 CCGAAGGACCACTAGATACGTC
36779 CCGAAGGAC
1 CCGAAGGAC
36788 TAATATACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.26, T:0.11
Consensus pattern (22 bp):
CCGAAGGACCACTAGATACGTC
Found at i:41508 original size:22 final size:22
Alignment explanation
Indices: 41480--41578 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
41470 TTAGTATTTA
* *
41480 TCCCGAATGACCACTAGATACG
1 TCCCGAAGGACCACTGGATACG
41502 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
41524 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
41546 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
*
41568 TCCCTAAGGAC
1 TCCCGAAGGAC
41579 TAATATACCC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.15
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACG
Found at i:43435 original size:36 final size:36
Alignment explanation
Indices: 43389--43461 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
43379 TGTGCCTATT
43389 TTTTTTTGTTATAACAGTTTTATGGACCGCTTCCTA
1 TTTTTTTGTTATAACAGTTTTATGGACCGCTTCCTA
43425 TTTTTTTGTTATAACAGTTTTATGGACCGCTTCCTA
1 TTTTTTTGTTATAACAGTTTTATGGACCGCTTCCTA
43461 T
1 T
43462 CATATCTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (36 bp):
TTTTTTTGTTATAACAGTTTTATGGACCGCTTCCTA
Found at i:47059 original size:23 final size:23
Alignment explanation
Indices: 47029--47082 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
47019 ACTTCTCCCT
47029 TCTGCACCTCCTCCTCGGCCTCG
1 TCTGCACCTCCTCCTCGGCCTCG
47052 TCTGCACCTCCTCCTCGGCCTCG
1 TCTGCACCTCCTCCTCGGCCTCG
47075 TCTGCACC
1 TCTGCACC
47083 AGACACTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.06, C:0.52, G:0.17, T:0.26
Consensus pattern (23 bp):
TCTGCACCTCCTCCTCGGCCTCG
Found at i:54690 original size:2 final size:2
Alignment explanation
Indices: 54678--54722 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
54668 CTGTGTTCTG
54678 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54719 TA TA
1 TA TA
54723 AGCTCAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57841 original size:25 final size:24
Alignment explanation
Indices: 57813--57885 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
57803 GTTTAGGGTC
57813 TTTGAAAAGATAGA-ATAGGATTTTA
1 TTTGAAAA-AT-GATATAGGATTTTA
* *
57838 TTTGGAAAATGATTTAGGATTTTA
1 TTTGAAAAATGATATAGGATTTTA
* * *
57862 TTTGGAAAATGATTTAGGGTTTTA
1 TTTGAAAAATGATATAGGATTTTA
57886 AATATTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.05
24 35 0.80
25 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (24 bp):
TTTGAAAAATGATATAGGATTTTA
Found at i:57856 original size:24 final size:24
Alignment explanation
Indices: 57828--57885 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
57818 AAAGATAGAA
57828 TAGGATTTTATTTGGAAAATGATT
1 TAGGATTTTATTTGGAAAATGATT
57852 TAGGATTTTATTTGGAAAATGATT
1 TAGGATTTTATTTGGAAAATGATT
*
57876 TAGGGTTTTA
1 TAGGATTTTA
57886 AATATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (24 bp):
TAGGATTTTATTTGGAAAATGATT
Found at i:68404 original size:21 final size:22
Alignment explanation
Indices: 68374--68416 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
68364 CCCTAAAAAA
68374 TTTTGCCCCCAATGTTC-AATTT
1 TTTTGCCCCCAAT-TTCTAATTT
68396 TTTTG-CCCCAATTTCTAATTT
1 TTTTGCCCCCAATTTCTAATTT
68417 CAAGCTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 12 0.60
22 5 0.25
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTTGCCCCCAATTTCTAATTT
Found at i:83798 original size:2 final size:2
Alignment explanation
Indices: 83791--83822 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83781 TTTAATATTC
83791 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
83823 GCGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84679 original size:13 final size:14
Alignment explanation
Indices: 84646--84681 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
84636 AAATAAAGTC
84646 ATAATTATTTAAAA
1 ATAATTATTTAAAA
*
84660 ATGATTATTTAAAA
1 ATAATTATTTAAAA
84674 A-AATTATT
1 ATAATTATT
84682 ATGACAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
ATAATTATTTAAAA
Found at i:90090 original size:23 final size:23
Alignment explanation
Indices: 90064--90109 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
90054 TTTTAATAGT
90064 TTTTTTAAACAATATTTAAAATA
1 TTTTTTAAACAATATTTAAAATA
90087 TTTTTTAAACAATATTTAAAATA
1 TTTTTTAAACAATATTTAAAATA
90110 GTTAAACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTTTAAACAATATTTAAAATA
Found at i:93041 original size:2 final size:2
Alignment explanation
Indices: 92953--93022 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
92943 TATGCATAAC
92953 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93023 ATTTTTCAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 64 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93950 original size:167 final size:166
Alignment explanation
Indices: 93610--93929 Score: 561
Period size: 167 Copynumber: 1.9 Consensus size: 166
93600 ATCTTTTCTC
93610 AACTTAAGCTATGTCAGAATCTAGGATGGGAAATAGTTTATTATTGTTAAATCACAGCCAATGTG
1 AACTTAAGCTATGTCAGAATCTAGGATGGGAAATAGTTTATTATTGTTAAATCACAGCCAATGTG
93675 GGTATTCTCTAGACTTGAAGACCTTAGTTTAAATTTGACCAGAAAGTAGTTCCTCGGTTTCTACC
66 GGTATTCTCTAGACTTGAAGACCTTAGTTTAAATTTGACCAGAAAGTAGTTCCTCGGTTTCTACC
** **
93740 ATTGGTCAATGTGCTTTTGAGAAAAATATCTTTTCTC
131 ATTGGTCAATGTGCTTTTGAGAAAAATA-CAATTCGA
93777 AACTTAAGCTATGTCAGAATCTAGGATGGGAAATAGTTTATTATTGTTAAATCACAGCCAATGTG
1 AACTTAAGCTATGTCAGAATCTAGGATGGGAAATAGTTTATTATTGTTAAATCACAGCCAATGTG
93842 GGTATTCTTCTAGACTTGAAGACCTTAGTTTAAATTTTGACCAGAAAGTAGTTCCTCGG-TTCTA
66 GGTATTC-TCTAGACTTGAAGACCTTAGTTTAAA-TTTGACCAGAAAGTAGTTCCTCGGTTTCTA
93906 CCAATTGGTCAATGTGCTTTTGAG
129 CC-ATTGGTCAATGTGCTTTTGAG
93930 TTGAGTGAAA
Statistics
Matches: 150, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
167 72 0.48
168 33 0.22
169 45 0.30
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (166 bp):
AACTTAAGCTATGTCAGAATCTAGGATGGGAAATAGTTTATTATTGTTAAATCACAGCCAATGTG
GGTATTCTCTAGACTTGAAGACCTTAGTTTAAATTTGACCAGAAAGTAGTTCCTCGGTTTCTACC
ATTGGTCAATGTGCTTTTGAGAAAAATACAATTCGA
Found at i:94167 original size:74 final size:74
Alignment explanation
Indices: 94062--94276 Score: 256
Period size: 74 Copynumber: 2.9 Consensus size: 74
94052 CAAACAAGAT
* ** * * * *
94062 GACTCCTCTTCATAGTTTAAGCCAATATTGATTCTTTAGATGACTCCCCTTTGAGGGTCTAAGTC
1 GACTTCTCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTTGAGGGTCTAAGTC
94127 AAGTGAGAC
66 AAGTGAGAC
* * * **
94136 -A-TCTCTCATTCACGGTTTAAGCTGGTCTTGATTATTTGGATGACTCCCCTTCGCTGGTCTAAG
1 GACT-TCTC-TTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTTGAGGGTCTAAG
94199 TCAAGTGAGAC
64 TCAAGTGAGAC
* *
94210 GACTTCTCTTCGCGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCC-TTCATGGGTCTAAGT
1 GACTTCTCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTTGA-GGGTCTAAGT
94274 CAA
65 CAA
94277 ATTAAATGAC
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
72 1 0.01
73 5 0.04
74 105 0.90
75 5 0.04
76 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (74 bp):
GACTTCTCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTTGAGGGTCTAAGTC
AAGTGAGAC
Found at i:94301 original size:74 final size:74
Alignment explanation
Indices: 94060--94304 Score: 237
Period size: 74 Copynumber: 3.3 Consensus size: 74
94050 TCCAAACAAG
* ** * * * * *
94060 ATGACTCCTCTTCATAGTTTAAGCCAATATTGATTCTTTAGATGACTCCCCTTTGA-GGGTCTAA
1 ATGACTCCCCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCC-TTCATGGGTCTAA
94124 GTCAAGTGAGA
65 GTCAAGTGA-A
* * * * *
94135 CAT--CTCTCATTCACGGTTTAAGCTGGTCTTGATTATTTGGATGACTCCCCTTCGCT-GGTCTA
1 -ATGACTCCCCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTC-ATGGGTCTA
*
94197 AGTCAAGTGAG
64 AGTCAAGTGAA
* * * *
94208 ACGACTTCTCTTCGCGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTCATGGGTCTAAG
1 ATGACTCCCCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTCATGGGTCTAAG
* *
94273 TCAAATTAA
66 TCAAGTGAA
*
94282 ATGACTCCCCTTCATGGTTTAAG
1 ATGACTCCCCTTCACGGTTTAAG
94305 ACAATCTTAA
Statistics
Matches: 133, Mismatches: 31, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
72 1 0.01
73 3 0.02
74 127 0.95
76 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (74 bp):
ATGACTCCCCTTCACGGTTTAAGCTAGTCTTGATTCTTTGGATGACTCCCCTTCATGGGTCTAAG
TCAAGTGAA
Found at i:103698 original size:74 final size:76
Alignment explanation
Indices: 103589--103753 Score: 176
Period size: 74 Copynumber: 2.2 Consensus size: 76
103579 CCACTACACA
* * * * * *
103589 GGTCTAAATCAAGTAAGAGGACTCCTCTTTGCAGTTTAAGTC-GGT-CTTGATTCTTTGGGTGAC
1 GGTCTAAGTCAAGTAACACGACTCCTCTTTACAGTTTAAGTCAGGTACATGATTATTTGGGTGAC
103652 -TCCCATTCGCG
66 TTCCC-TTCGCG
* *
103663 GGTCTAAGTCAAGTGACACGACTACC-CTTTACAGTTTAAGTCATGTAACATGATTATTTGGGTG
1 GGTCTAAGTCAAGTAACACGACT-CCTCTTTACAGTTTAAGTCAGGT-ACATGATTATTTGGGTG
* *
103727 ACTTCCCTTTGTG
64 ACTTCCCTTCGCG
*
103740 GGTTTAAGTCAAGT
1 GGTCTAAGTCAAGT
103754 TCCTCATATA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
74 34 0.45
75 4 0.05
77 33 0.44
78 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
GGTCTAAGTCAAGTAACACGACTCCTCTTTACAGTTTAAGTCAGGTACATGATTATTTGGGTGAC
TTCCCTTCGCG
Found at i:103896 original size:6 final size:6
Alignment explanation
Indices: 103889--105192 Score: 1864
Period size: 6 Copynumber: 217.3 Consensus size: 6
103879 CAAAATTTTA
* * * * * * * *
103889 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* ** * * * * *
103937 TATGTA TATGCA TAT-TG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * ** *
103984 TATATG TATATG TATATG CATAT-TG TATATG CATATGTA TATGCA TATGTA
1 TATGTG TATGTG TATGTG --TATGTG TATGTG --TATGTG TATGTG TATGTG
* * * * * * * *
104035 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
104083 TATGTA TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104131 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104179 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104227 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104275 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104323 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104371 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104419 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104467 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104515 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104563 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104611 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104659 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104707 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104755 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104803 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
104851 TATATGTG TATGTG TATGTG TATGTG TATGTG TA--TG TATGTG TATGTG
1 --TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
104899 TATGTG TA--TG TATGTA TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * *
104945 TATGTG TATGTG TATGTG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
104993 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
105041 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
105089 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
105137 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
105185 TATATG TA
1 TATGTG TA
105193 ACTTCCGAAA
Statistics
Matches: 1275, Mismatches: 11, Indels: 24
0.97 0.01 0.02
Matches are distributed among these distances:
4 8 0.01
5 6 0.00
6 1246 0.98
7 2 0.00
8 13 0.01
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:105431 original size:18 final size:18
Alignment explanation
Indices: 105408--105447 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
105398 CTTTTTACCT
*
105408 ACGCGTGAAAATCATTAC
1 ACGCGTGAAAATCATCAC
105426 ACGCGTGAAAATCATCAC
1 ACGCGTGAAAATCATCAC
105444 ACGC
1 ACGC
105448 TAAGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (18 bp):
ACGCGTGAAAATCATCAC
Found at i:112150 original size:32 final size:36
Alignment explanation
Indices: 112087--112163 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 36
112077 CTGGGCTGGG
112087 TATATATATTTAAATTAAATATATAAATATT-AT-T
1 TATATATATTTAAATTAAATATATAAATATTAATAT
* *
112121 TATATAT-TTTAATTTAAAT-TA-AATTTATTAATAT
1 TATATATATTTAAATTAAATATATAA-ATATTAATAT
112155 TATATATAT
1 TATATATAT
112164 ATAATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 2 0.05
32 6 0.16
33 13 0.35
34 15 0.41
35 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TATATATATTTAAATTAAATATATAAATATTAATAT
Found at i:112172 original size:38 final size:37
Alignment explanation
Indices: 112087--112172 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 37
112077 CTGGGCTGGG
*
112087 TATATAT-ATTTAAATTAAATATATAAATATTATTTA
1 TATATATAATTTAAATTAAATATATAAATATTATATA
* * *
112123 TATATTTTAATTTAAATTAAATTTATTAATATTATATA
1 TATA-TATAATTTAAATTAAATATATAAATATTATATA
112161 TATATAATAATT
1 TATAT-ATAATT
112173 ATTTTTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 4 0.10
37 3 0.07
38 35 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATAATTTAAATTAAATATATAAATATTATATA
Found at i:119489 original size:14 final size:13
Alignment explanation
Indices: 119454--119503 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
119444 AATGATGATA
*
119454 ATAATGATATAAAT
1 ATAAT-ATATATAT
*
119468 AAAATATATATACT
1 ATAATATATATA-T
119482 ATAATATATATAT
1 ATAATATATATAT
119495 AT-ATATATA
1 ATAATATATA
119504 ATTTTTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 7 0.22
13 9 0.28
14 16 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:119522 original size:2 final size:2
Alignment explanation
Indices: 119471--119503 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
119461 TATAAATAAA
119471 AT AT AT AT ACT AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
119504 ATTTTTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:119578 original size:2 final size:2
Alignment explanation
Indices: 119551--119636 Score: 124
Period size: 2 Copynumber: 44.0 Consensus size: 2
119541 ATTTTCAAAA
* *
119551 AT AT A- AT AT AT A- AA AT AG AT AT -T 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
119590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
119633 AT AT
1 AT AT
119637 TAAAACTCAA
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.04
2 72 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Done.