Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1159
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: 94638
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4954 original size:21 final size:21
Alignment explanation
Indices: 4921--4993 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
4911 TAGCCCATTA
* * *
4921 TATCAATATATGTTAGGATTG
1 TATCGATACATGTTAAGATTG
*
4942 TATCGATACATGTCAAGATTG
1 TATCGATACATGTTAAGATTG
* *
4963 TATCGATATATGATAAGATTG
1 TATCGATACATGTTAAGATTG
4984 TATCGATACA
1 TATCGATACA
4994 AATAAAGGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
TATCGATACATGTTAAGATTG
Found at i:6817 original size:19 final size:19
Alignment explanation
Indices: 6793--6886 Score: 104
Period size: 19 Copynumber: 5.6 Consensus size: 19
6783 AACTGTAACG
6793 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
6812 GTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
6825 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
6844 GTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
6857 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
6876 GTATCGATACA
1 GTATCGATACA
6887 ATGTATCGCT
Statistics
Matches: 63, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.35
15 4 0.06
17 4 0.06
19 33 0.52
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (19 bp):
GTATCGATACATAAGTGTT
Found at i:6829 original size:13 final size:13
Alignment explanation
Indices: 6811--6867 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
6801 ACATAAGTGT
6811 TGTATCGATACAA
1 TGTATCGATACAA
6824 TGTATCGATACATAA
1 TGTATCGATAC--AA
6839 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
6856 TGTATCGATACA
1 TGTATCGATACA
6868 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6834 original size:32 final size:32
Alignment explanation
Indices: 6793--6894 Score: 204
Period size: 32 Copynumber: 3.2 Consensus size: 32
6783 AACTGTAACG
6793 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
6825 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
6857 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
6889 GTATCG
1 GTATCG
6895 CTACGAAGCT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GTATCGATACATAAGTGTTGTATCGATACAAT
Found at i:12740 original size:18 final size:18
Alignment explanation
Indices: 12719--12773 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
12709 GTCAAAAGTA
12719 AACACACAAAAAAAAAAC
1 AACACACAAAAAAAAAAC
* *
12737 AACAGCA-ACACAAAAAAC
1 AACA-CACAAAAAAAAAAC
12755 AA-A-ACAAAAATAAAAAC
1 AACACACAAAAA-AAAAAC
12772 AA
1 AA
12774 AAAAATACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 9 0.30
18 15 0.50
19 2 0.07
ACGTcount: A:0.76, C:0.20, G:0.02, T:0.02
Consensus pattern (18 bp):
AACACACAAAAAAAAAAC
Found at i:12785 original size:12 final size:11
Alignment explanation
Indices: 12724--12791 Score: 64
Period size: 12 Copynumber: 5.9 Consensus size: 11
12714 AAGTAAACAC
12724 ACAAAAAAAAA
1 ACAAAAAAAAA
* ** *
12735 ACAACAGCAAC
1 ACAAAAAAAAA
12746 ACAAAAAACAAA
1 ACAAAAAA-AAA
12758 ACAAAAATAAAA
1 ACAAAAA-AAAA
*
12770 ACAAAAAAATAC
1 ACAAAAAAA-AA
12782 ACAAAAAAAA
1 ACAAAAAAAA
12792 GGAAAAGAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 15 0.33
12 29 0.64
13 1 0.02
ACGTcount: A:0.79, C:0.16, G:0.01, T:0.03
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:14067 original size:64 final size:67
Alignment explanation
Indices: 13999--14325 Score: 299
Period size: 64 Copynumber: 5.0 Consensus size: 67
13989 CTCTCCTTCA
* *
13999 AAGTCCACAACTCAGTGGCATCCCTTTTTC-CTAT-AAGTCCACAACTCAGTGGTATCTC-TTTT
1 AAGTCCACAACTCAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTT
14061 CT
66 CT
* * * *
14063 AAGTCCACGACTCCA-TGGCA--CCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CTCTTTT
1 AAGTCCACAACT-CAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTT
14124 TCCTTTT
65 T-C---T
* * * * *
14131 AAGCCCACAACTTC-GTGGCA-CTCTTTTTCTTTTTAAAGTCCACGACTCCGTGGCATCTCTTTC
1 AAGTCCACAAC-TCAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCATCTCTTT-
*
14194 CTTCA
64 -TTCT
*
14199 AAGTCCACAACTCAGTGGCATCCCTTTTTC-CTGT-AAGTCCACAACTCAGTGGCATCTCTTTTT
1 AAGTCCACAACTCAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTT
14262 -T
66 CT
* * * * *
14263 AAGTCCACGACTCAGTGGCAT--ATTTTTCTTTTTAAAGCCCACAACTCCGT-G-ATACTCTTTT
1 AAGTCCACAACTCAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCAT-CTCTTTT
14324 TC
65 TC
14326 CCTTTTAAGT
Statistics
Matches: 218, Mismatches: 25, Indels: 40
0.77 0.09 0.14
Matches are distributed among these distances:
62 16 0.07
63 16 0.07
64 71 0.33
65 5 0.02
67 27 0.12
68 34 0.16
69 40 0.18
70 6 0.03
71 1 0.00
72 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.35
Consensus pattern (67 bp):
AAGTCCACAACTCAGTGGCATCCCTTTTTCTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTT
CT
Found at i:14131 original size:35 final size:34
Alignment explanation
Indices: 13999--14378 Score: 280
Period size: 34 Copynumber: 11.6 Consensus size: 34
13989 CTCTCCTTCA
* * *
13999 AAGTCCACAACTCAGTGGCATCCCTTTTTCC-TAT
1 AAGTCCACAACTCCGTGGCA-CTCTTTTTCCTTTT
* *
14033 AAGTCCACAACTCAGTGGTA-TCTCTTTT-C---T
1 AAGTCCACAACTCCGTGGCACTCT-TTTTCCTTTT
* * *
14063 AAGTCCACGACTCCATGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
14096 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
14131 AAGCCCACAACTTCGTGGCACTCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * **
14165 AAAGTCCACGACTCCGTGGCA-TCTCTTTCCTTCA
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
14199 AAGTCCACAACTCAGTGGCATCCCTTTTTCC-TGT
1 AAGTCCACAACTCCGTGGCA-CTCTTTTTCCTTTT
* *
14233 AAGTCCACAACTCAGTGGCA-TC-TCTT--TTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * *
14263 AAGTCCACGACTCAGTGGCA-TATTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* **
14296 AAAGCCCACAACTCCGTGATACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTT-CCTTTT
* *
14332 AAGTCCATAACTCCATGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
14359 AAGTCCACAACTCCGTGGCA
1 AAGTCCACAACTCCGTGGCA
14379 TCAAGTCAGT
Statistics
Matches: 282, Mismatches: 46, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
27 24 0.09
29 4 0.01
30 41 0.15
31 6 0.02
32 4 0.01
33 28 0.10
34 114 0.40
35 56 0.20
36 5 0.02
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:14355 original size:27 final size:27
Alignment explanation
Indices: 14325--14378 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
14315 TACTCTTTTT
*
14325 CCCTTTTAAGTCCATAACTCCATGGCA
1 CCCTTTTAAGTCCACAACTCCATGGCA
*
14352 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCATGGCA
14379 TCAAGTCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCATGGCA
Found at i:14622 original size:21 final size:21
Alignment explanation
Indices: 14598--14666 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
14588 ATGTCGCTGG
14598 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
14619 CCTTTAAGTCCAATATCGTTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
14641 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
14662 CCTTG
1 CCTTG
14667 TTTTTAAGAC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 12 0.35
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:14642 original size:43 final size:43
Alignment explanation
Indices: 14585--15088 Score: 477
Period size: 43 Copynumber: 10.9 Consensus size: 43
14575 GTCTTTAACA
*
14585 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGT
* * *
14628 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-----TTTAAGT
*
14676 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGT
* * *
14719 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-C----CTTTAAGT
* *
14767 CCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGT
* *
14810 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-C----CTTTAAGT
* *
14858 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGT
* *
14901 CCAATGTCGCTGGCCTTGAATCAGTATATTAGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGT
* * *
14950 CCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCATATT---G-----G-CACCTTTAAGT
* *
15002 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGT
* *
15051 CCAGTATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTT
15089 CGTCATCTTT
Statistics
Matches: 383, Mismatches: 42, Indels: 72
0.77 0.08 0.14
Matches are distributed among these distances:
43 151 0.39
44 3 0.01
45 1 0.00
47 1 0.00
48 115 0.30
49 74 0.19
52 35 0.09
57 1 0.00
58 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGT
Found at i:14714 original size:91 final size:91
Alignment explanation
Indices: 14525--15088 Score: 804
Period size: 91 Copynumber: 6.0 Consensus size: 91
14515 GCACCTTTAT
*
14525 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTTGTCTTTAACACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TTGTCTTTAAGACCAAT
14590 GTCGCTGGCCTTGAATCAGCACATTGGCAC
62 GTCGCTGGCCTTGAATCAGCACATTGGCAC
* *
14620 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
14685 CTGGCCTTGAATCAGCACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
*
14711 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
*
14776 CTGGCCTTGAATCAACACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
14802 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
*
14867 CTGGCCTTGAATCAGCACATTGGCAT
66 CTGGCCTTGAATCAGCACATTGGCAC
* * * * * * *
14893 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTATATTAGCACCTTCATCTTTAAGTCCAATATT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTC
* *
14958 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
65 GCTGGCCTTGAATCAGCACATT---G-----G-CAC
* * * * *
14994 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTC
*
15059 GCTGGCCTTGAATCAGCATATTGGCAC
65 GCTGGCCTTGAATCAGCACATTGGCAC
15086 CTT
1 CTT
15089 CGTCATCTTT
Statistics
Matches: 434, Mismatches: 25, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
91 263 0.61
92 40 0.09
93 1 0.00
95 44 0.10
98 1 0.00
100 1 0.00
101 84 0.19
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (91 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:14836 original size:182 final size:182
Alignment explanation
Indices: 14429--15088 Score: 906
Period size: 182 Copynumber: 3.5 Consensus size: 182
14419 GGCATCTTCT
* * *
14429 TTTAAGCCCAATATCGCTGGCCTTGAATAAGCATATTGGCACCTCATCTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
14494 TGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
66 TGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
*
14559 TATTGGCACCTTTGTTGTCTTTAACACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
125 TATTGGCACC----TTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* * *
14621 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
*
14686 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
14751 CACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACC
131 CACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
*
14803 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
* * * *
14868 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTATATTAG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
* * * * * *
14933 CACCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
131 CACCTT-GTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CACC
* * * *
14995 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCG
*
15060 CTGGCCTTGAATCAGCATATTGGCACCTT
65 CTGGCCTTGAATCAGCACATTGGCACCTT
15089 CGTCATCTTT
Statistics
Matches: 427, Mismatches: 30, Indels: 21
0.89 0.06 0.04
Matches are distributed among these distances:
182 175 0.41
183 34 0.08
186 44 0.10
191 2 0.00
192 129 0.30
193 43 0.10
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (182 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
CACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:15201 original size:105 final size:100
Alignment explanation
Indices: 14914--15245 Score: 261
Period size: 101 Copynumber: 3.2 Consensus size: 100
14904 ATGTCGCTGG
* * * * * * * * *
14914 CCTTGAATCAGTATATTAGCACCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATAT
1 CCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACCAATATCGCTGACCGTGAATCAGCACAT
* * ** ** * ** *
14979 TGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGG
66 TGACACC-TTCACATCTTTAAACCCAATATCATTGA
* * * * *
15015 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATAT
1 CCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACCAATATCGCTGACCGTGAATCAGCACAT
* * *
15080 TGGCACCTTCGTCATCTTTAAAACCCAATGTCATTGA
66 TGACACCTTC-ACATCTTT-AAACCCAATATCATTGA
* * * *
15117 CCTTGAATCAGCACATTGGCATTCTTTTCATCTTCAAGACTAATGTCGCTGATCGTGAATCAGCA
1 CCTTGAATCAGCACATTGGCA--C-CTTCATCTTCAAGACCAATATCGCTGACCGTGAATCAGCA
* * *
15182 CATTGACATTCCTT-ACATCTTTAAGCCCAATATCGTTGG
63 CATTGACA--CCTTCACATCTTTAAACCCAATATCATTGA
* *
15221 CCGTGAATCAGCATATTGGCACCTT
1 CCTTGAATCAGCACATTGGCACCTT
15246 TATCACTCTT
Statistics
Matches: 193, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
100 2 0.01
101 75 0.39
102 34 0.18
104 33 0.17
105 45 0.23
107 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (100 bp):
CCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACCAATATCGCTGACCGTGAATCAGCACAT
TGACACCTTCACATCTTTAAACCCAATATCATTGA
Found at i:15888 original size:19 final size:19
Alignment explanation
Indices: 15864--15924 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
15854 AAACAGTAAC
15864 TGTATCGATATATAAGTGT
1 TGTATCGATATATAAGTGT
*
15883 TGTATCG--ATACAA----
1 TGTATCGATATATAAGTGT
15896 TGTATCGATATATAAGTGT
1 TGTATCGATATATAAGTGT
15915 TGTATCGATA
1 TGTATCGATA
15925 CAATGTATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 7 0.21
15 5 0.15
17 5 0.15
19 17 0.50
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (19 bp):
TGTATCGATATATAAGTGT
Found at i:15905 original size:32 final size:32
Alignment explanation
Indices: 15864--15933 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
15854 AAACAGTAAC
15864 TGTATCGATATATAAGTGTTGTATCGATACAA
1 TGTATCGATATATAAGTGTTGTATCGATACAA
15896 TGTATCGATATATAAGTGTTGTATCGATACAA
1 TGTATCGATATATAAGTGTTGTATCGATACAA
15928 TGTATC
1 TGTATC
15934 TCTACGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATATATAAGTGTTGTATCGATACAA
Found at i:23448 original size:20 final size:20
Alignment explanation
Indices: 23419--23472 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
23409 TACCCAGATG
23419 TGTATCGATACATGTA-TGAA
1 TGTATCGATACAT-TATTGAA
* *
23439 TGTATTGATACATTATTTAA
1 TGTATCGATACATTATTGAA
23459 TGTATCGATACATT
1 TGTATCGATACATT
23473 CTGTCTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATTGAA
Found at i:26911 original size:22 final size:22
Alignment explanation
Indices: 26879--26921 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
26869 TCCAACATAT
26879 GTAACAAATCACATACAATTAC
1 GTAACAAATCACATACAATTAC
*
26901 GTAACACATCACATACAATTA
1 GTAACAAATCACATACAATTA
26922 AGGTATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (22 bp):
GTAACAAATCACATACAATTAC
Found at i:27574 original size:13 final size:12
Alignment explanation
Indices: 27556--27585 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
27546 AAAATAAAAT
27556 ATTATATTTAATA
1 ATTATATTTAA-A
27569 ATTATATTTAAA
1 ATTATATTTAAA
27581 ATTAT
1 ATTAT
27586 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATATTTAAA
Found at i:29344 original size:19 final size:19
Alignment explanation
Indices: 29320--29358 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29310 TATTTAAGTT
*
29320 TAAAAAT-TTATAGTTTAAA
1 TAAAAATATTA-AATTTAAA
29339 TAAAAATATTAAATTTAAA
1 TAAAAATATTAAATTTAAA
29358 T
1 T
29359 GAGAGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATATTAAATTTAAA
Found at i:29856 original size:2 final size:2
Alignment explanation
Indices: 29849--29888 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29839 TTAAGCAAAG
29849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29889 ATAATGTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32777 original size:27 final size:27
Alignment explanation
Indices: 32737--32789 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
32727 AGTTAATTTT
* * *
32737 TTTTATTCATAAAATTTAAATTTAAAA
1 TTTTATTCAAAAAATTAAAAATTAAAA
*
32764 TTTTATTTAAAAAATTAAAAATTAAA
1 TTTTATTCAAAAAATTAAAAATTAAA
32790 TTATTTGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTTATTCAAAAAATTAAAAATTAAAA
Found at i:34082 original size:8 final size:8
Alignment explanation
Indices: 34069--34130 Score: 54
Period size: 8 Copynumber: 7.2 Consensus size: 8
34059 TATTTCTGTC
34069 AAGAAAAA
1 AAGAAAAA
34077 AAGAAAAA
1 AAGAAAAA
*
34085 AAGAAAGA
1 AAGAAAAA
34093 AAGAAAGGAGA
1 AAGAAA--A-A
34104 AA-AAAAGGA
1 AAGAAAA--A
*
34113 AACAAAAA
1 AAGAAAAA
34121 AAGAAAAA
1 AAGAAAAA
34129 AA
1 AA
34131 TTATATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 32 0.70
9 4 0.09
10 7 0.15
11 3 0.07
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:34108 original size:23 final size:21
Alignment explanation
Indices: 34072--34130 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
34062 TTCTGTCAAG
*
34072 AAAAAAAGAAAAAAA-GAAAG
1 AAAAAAAGAAAAAAAGGAAAC
34092 AAAGAAAGGAGAAAAAAAGGAAAC
1 AAA-AAA--AGAAAAAAAGGAAAC
34116 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
34131 TTATATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
23 12 0.35
24 7 0.21
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAGGAAAC
Found at i:34434 original size:20 final size:22
Alignment explanation
Indices: 34390--34446 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
34380 TATTCGTGTA
34390 TTCATATTATGTTTATATTATTT
1 TTCATATTATGTTTATA-TATTT
*
34413 TTCATATTGTGTTT-TA-ATTT
1 TTCATATTATGTTTATATATTT
*
34433 TTTATATATATGTT
1 TTCATAT-TATGTT
34447 GAGTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.33
21 5 0.17
22 2 0.07
23 13 0.43
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.65
Consensus pattern (22 bp):
TTCATATTATGTTTATATATTT
Found at i:34926 original size:14 final size:14
Alignment explanation
Indices: 34907--34958 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
34897 TCAATCCGTG
34907 ATATTTTTATATAA
1 ATATTTTTATATAA
* *
34921 ATATTTATATATTA
1 ATATTTTTATATAA
34935 ATAATTCATTTTATATAA
1 AT-A-T--TTTTATATAA
34953 ATATTT
1 ATATTT
34959 ACATGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 16 0.53
15 1 0.03
16 2 0.07
17 1 0.03
18 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTTTATATAA
Found at i:35101 original size:13 final size:14
Alignment explanation
Indices: 35061--35138 Score: 65
Period size: 13 Copynumber: 5.6 Consensus size: 14
35051 TTTATCTTAT
35061 ATTTTATATAATTAA
1 ATTTTAT-TAATTAA
*
35076 ATTTTA--ACTTTAA
1 ATTTTATTA-ATTAA
*
35089 ATTTT-TTTATTAA
1 ATTTTATTAATTAA
*
35102 ATATTT-TTAAATAA
1 AT-TTTATTAATTAA
35116 ATTTTATTAATTATA
1 ATTTTATTAATTA-A
35131 ATTTTATT
1 ATTTTATT
35139 TAATAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 1 0.02
13 18 0.35
14 17 0.33
15 15 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTATTAATTAA
Found at i:35134 original size:27 final size:27
Alignment explanation
Indices: 35061--35135 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 27
35051 TTTATCTTAT
*
35061 ATTTTATATAATTAAA-TTTTAACTTTAA
1 ATTTTAT-TAATTAAATTTTTAAC-ATAA
*
35089 ATTTT-TTTATTAAATATTTTTAA-ATAA
1 ATTTTATTAATT-AA-ATTTTTAACATAA
35116 ATTTTATTAATTATAATTTT
1 ATTTTATTAATTA-AATTTT
35136 ATTTAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
26 4 0.10
27 17 0.44
28 12 0.31
29 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTTATTAATTAAATTTTTAACATAA
Found at i:35587 original size:29 final size:30
Alignment explanation
Indices: 35546--35611 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
35536 AAATATTAAA
*
35546 TTTTTGATAAAAATTAAAT-TGATTTTATAT
1 TTTTTTATAAAAATTAAATATGA-TTTATAT
**
35576 TTTTTTAT-AAAATTTTATATGATTTATAT
1 TTTTTTATAAAAATTAAATATGATTTATAT
*
35605 TTATTTA
1 TTTTTTA
35612 ATCTGGTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTTTATAAAAATTAAATATGATTTATAT
Found at i:43219 original size:32 final size:32
Alignment explanation
Indices: 43182--43296 Score: 117
Period size: 32 Copynumber: 3.7 Consensus size: 32
43172 ATTGACACGT
**
43182 TTTAATAACCATTAAATTTATAAGTAATTATG
1 TTTAATATTCATTAAATTTATAAGTAATTATG
* ** * *
43214 TTTAATATTTATTAAATTTACGAGTAATTTTA
1 TTTAATATTCATTAAATTTATAAGTAATTATG
* * *
43246 TTTGATATTCATTATATTTATAAATAATTATG
1 TTTAATATTCATTAAATTTATAAGTAATTATG
*
43278 TCT-A-ATTCATTAAATTTAT
1 TTTAATATTCATTAAATTTAT
43297 GATCAATATC
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 14 0.21
31 1 0.02
32 51 0.77
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTAATATTCATTAAATTTATAAGTAATTATG
Found at i:43975 original size:13 final size:12
Alignment explanation
Indices: 43957--43988 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
43947 GGCCAATTAT
43957 AAAAAAAAAATAG
1 AAAAAAAAAA-AG
43970 AAAAAAAAAAAG
1 AAAAAAAAAAAG
43982 AAAAAAA
1 AAAAAAA
43989 GAGAGCCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:44631 original size:18 final size:18
Alignment explanation
Indices: 44604--44638 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44594 CTCATATTCG
*
44604 AAAATTTATTAAACTTCA
1 AAAATCTATTAAACTTCA
44622 AAAATCTATTAAACTTC
1 AAAATCTATTAAACTTC
44639 GACTAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATCTATTAAACTTCA
Found at i:44828 original size:2 final size:2
Alignment explanation
Indices: 44821--44845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44811 ATTAATTTTC
44821 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 T
44846 TCAAGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46199 original size:19 final size:18
Alignment explanation
Indices: 46152--46207 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
46142 TATATTTAAA
46152 TAAAATAGTAAAAAAAAT
1 TAAAATAGTAAAAAAAAT
* *
46170 T-AATTATTAAAAATCAAAT
1 TAAAATAGTAAAAA--AAAT
46189 TAAAATA-T-AAAAAAAT
1 TAAAATAGTAAAAAAAAT
46205 TAA
1 TAA
46208 TATTTGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 7 0.22
17 10 0.31
18 5 0.16
19 6 0.19
20 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAATAGTAAAAAAAAT
Found at i:46760 original size:11 final size:10
Alignment explanation
Indices: 46735--46762 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46725 TATTCTATTT
46735 ATTTTTAAGG
1 ATTTTTAAGG
46745 ATTTTTAAGG
1 ATTTTTAAGG
46755 ATTTTTAA
1 ATTTTTAA
46763 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (10 bp):
ATTTTTAAGG
Found at i:47473 original size:68 final size:68
Alignment explanation
Indices: 47341--47542 Score: 336
Period size: 67 Copynumber: 3.0 Consensus size: 68
47331 TTTAACTAAC
* * * *
47341 GGTGTTAATTTAAAAAGTAATATGCTCGATAAAATACAAGTTTAAGTACTAAATTAATAATTTTT
1 GGTGTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTT
47406 TCT
66 TCT
47409 GGTGTTAGTCTAAAAAGTAATATGCTTGAT-AAATAAAAGTTTAAGTACTAAATTAATAATTTTT
1 GGTGTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTT
47473 TCT
66 TCT
* *
47476 AGTGTTAGTCT-AAAAGTAATATGTTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTT
1 GGTGTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTT
47540 TCT
66 TCT
47543 TTAGATATCA
Statistics
Matches: 127, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
66 17 0.13
67 83 0.65
68 27 0.21
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (68 bp):
GGTGTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTT
TCT
Found at i:51755 original size:21 final size:21
Alignment explanation
Indices: 51722--51775 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
51712 CTATAATTTA
* * *
51722 TATCAATATAAACAGTAAATG
1 TATCGATACAAACAATAAATG
51743 TATCGATACAAACAATAAATG
1 TATCGATACAAACAATAAATG
51764 TATCGATACAAA
1 TATCGATACAAA
51776 GCTACCCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (21 bp):
TATCGATACAAACAATAAATG
Found at i:55641 original size:18 final size:18
Alignment explanation
Indices: 55618--55652 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55608 TTATTAAGAA
* *
55618 TATTTTTTTGAAAAATTC
1 TATTTTCTTAAAAAATTC
55636 TATTTTCTTAAAAAATT
1 TATTTTCTTAAAAAATT
55653 ACACCATTTA
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:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTTCTTAAAAAATTC
Found at i:56471 original size:14 final size:16
Alignment explanation
Indices: 56436--56472 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
56426 TTTCTCATTT
56436 TTCTTTTTCTTTCATCC
1 TTCTTTTTCTTT-ATCC
56453 TTCTTTTTCTTT-T-C
1 TTCTTTTTCTTTATCC
56467 TTCTTT
1 TTCTTT
56473 AGCAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 1 0.05
17 12 0.60
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTTTCTTTATCC
Found at i:57733 original size:44 final size:44
Alignment explanation
Indices: 57670--57757 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
57660 GCTCAAAATA
57670 AGGGATTGCATGACATTGTTTGCCTTTCCGAATTTATTTCGGAT
1 AGGGATTGCATGACATTGTTTGCCTTTCCGAATTTATTTCGGAT
*
57714 AGGGATTGCATGACATTGTTTGCCTTTTCGAATTTATTTCGGAT
1 AGGGATTGCATGACATTGTTTGCCTTTCCGAATTTATTTCGGAT
57758 TCATCTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (44 bp):
AGGGATTGCATGACATTGTTTGCCTTTCCGAATTTATTTCGGAT
Found at i:59918 original size:53 final size:52
Alignment explanation
Indices: 59817--59936 Score: 123
Period size: 53 Copynumber: 2.3 Consensus size: 52
59807 TGAAATTGCC
** * * * *
59817 TAAATGTATCAATACAATAAGGTATTGTATCCATAAATTTGTCTTTTTTGAAT
1 TAAATGTATTGATACAATAAGGTATTGTATCCATAAATTGGCCCTTTTTG-AG
* * ** * *
59870 TGAATGTATTGATACAATAAGGTATTTTATTGATACATTGGCCCTTTTTGGG
1 TAAATGTATTGATACAATAAGGTATTGTATCCATAAATTGGCCCTTTTTGAG
59922 TAAATGTATTGATAC
1 TAAATGTATTGATAC
59937 TTAAGTGGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
52 14 0.26
53 40 0.74
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (52 bp):
TAAATGTATTGATACAATAAGGTATTGTATCCATAAATTGGCCCTTTTTGAG
Found at i:66871 original size:59 final size:59
Alignment explanation
Indices: 66742--66871 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 59
66732 CCTCATGGTT
** * * ** **
66742 ATCTGAGTTTGAGTGACTTGGCATCACTTGATATTTAAATTTGGGTCGTCTTGGTGGCG
1 ATCTGAGTTTGAACGACTTGGCATCACTTAATATTTAAATTTGAGTCACCTCAGTGGCG
* * *
66801 ATCTAAATTTGAACGACTTGGCATCACTTAATGTTTAAATTTGAGTCACCTCAGTGGCG
1 ATCTGAGTTTGAACGACTTGGCATCACTTAATATTTAAATTTGAGTCACCTCAGTGGCG
66860 ATCTGAGTTTGA
1 ATCTGAGTTTGA
66872 GTGACTCAGT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (59 bp):
ATCTGAGTTTGAACGACTTGGCATCACTTAATATTTAAATTTGAGTCACCTCAGTGGCG
Found at i:66887 original size:59 final size:59
Alignment explanation
Indices: 66824--67097 Score: 316
Period size: 59 Copynumber: 4.7 Consensus size: 59
66814 CGACTTGGCA
* * * * * * *
66824 TCACTTAATGTTTAAATTTGAGTCACCTCAGTGGCGATCTGAGTTTGAGTGACTCAGTG
1 TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTAGTG
* * * * * *
66883 TCACTTAACATTTGAATTTGGGTTGCCTCGGTGGCGATCTGAATTTAAGTGACTTAGTA
1 TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTAGTG
* * * * *
66942 TCATTTGACGTTTGAATTCGAGTTGCCTTAGTGGCGATCTGAATTTGAGTGACTTAGTG
1 TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTAGTG
* * * * *
67001 TCACTCGACATTTGATTTTGGGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTGGTG
1 TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTAGTG
* *
67060 TCACTTGACGTTTGAATTTG-GTCGTCTCGGTGGCGATC
1 TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATC
67098 AGGGCATATA
Statistics
Matches: 180, Mismatches: 35, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
58 16 0.09
59 164 0.91
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (59 bp):
TCACTTGACGTTTGAATTTGAGTCGCCTCAGTGGCGATCTGAATTTAAGTGACTTAGTG
Found at i:66975 original size:118 final size:118
Alignment explanation
Indices: 66742--67077 Score: 413
Period size: 118 Copynumber: 2.8 Consensus size: 118
66732 CCTCATGGTT
* ** * * * * *
66742 ATCTGAGTTTGAGTGACTTGGCATCACTTGATATTTAAATTTGGGTCGTCTTGGTGGCGATCTAA
1 ATCTGAGTTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCGCCTCGGTGGCGATCTGA
* * * * * *
66807 ATTTGAA-CGACTTGGCATCACTTAATGTTTAAATTTGAGTCACCTCAGTGGCG
66 ATTT-AAGTGACTTGGTATCACTTGACGTTTGAATTCGAGTCACCTCAGTGGCG
* * *
66860 ATCTGAGTTTGAGTGACTCAGTGTCACTTAACATTTGAATTTGGGTTGCCTCGGTGGCGATCTGA
1 ATCTGAGTTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCGCCTCGGTGGCGATCTGA
* * ** *
66925 ATTTAAGTGACTTAGTATCATTTGACGTTTGAATTCGAGTTGCCTTAGTGGCG
66 ATTTAAGTGACTTGGTATCACTTGACGTTTGAATTCGAGTCACCTCAGTGGCG
* * * *
66978 ATCTGAATTTGAGTGACTTAGTGTCACTCGACATTTGATTTTGGGTCGCCTCAGTGGCGATCTGA
1 ATCTGAGTTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCGCCTCGGTGGCGATCTGA
*
67043 ATTTAAGTGACTTGGTGTCACTTGACGTTTGAATT
66 ATTTAAGTGACTTGGTATCACTTGACGTTTGAATT
67078 TGGTCGTCTC
Statistics
Matches: 185, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
117 2 0.01
118 183 0.99
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (118 bp):
ATCTGAGTTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCGCCTCGGTGGCGATCTGA
ATTTAAGTGACTTGGTATCACTTGACGTTTGAATTCGAGTCACCTCAGTGGCG
Found at i:69488 original size:13 final size:13
Alignment explanation
Indices: 69470--69495 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69460 ACATTTTATG
69470 ATGTATCGATACA
1 ATGTATCGATACA
69483 ATGTATCGATACA
1 ATGTATCGATACA
69496 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:69490 original size:33 final size:32
Alignment explanation
Indices: 69448--69515 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
69438 CGTTACAAGC
**
69448 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
69481 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
69513 CAA
1 CAA
69516 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:71933 original size:20 final size:21
Alignment explanation
Indices: 71904--71944 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
71894 TGTTTTTGAA
71904 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
71923 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
71945 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:72088 original size:13 final size:13
Alignment explanation
Indices: 72072--72104 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
72062 CCCCTATATT
*
72072 GATACAGTGTATC
1 GATACAATGTATC
72085 GATACAATGTATC
1 GATACAATGTATC
72098 GATACAA
1 GATACAA
72105 AGAATGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (13 bp):
GATACAATGTATC
Found at i:78302 original size:13 final size:13
Alignment explanation
Indices: 78284--78309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78274 ACATTTTATG
78284 ATGTATCGATACA
1 ATGTATCGATACA
78297 ATGTATCGATACA
1 ATGTATCGATACA
78310 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:78304 original size:33 final size:32
Alignment explanation
Indices: 78262--78329 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
78252 CGTTACAAGC
**
78262 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
78295 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
78327 CAA
1 CAA
78330 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:81857 original size:13 final size:13
Alignment explanation
Indices: 81839--81869 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
81829 CCATCAACTA
81839 ATCTTATTCTTGG
1 ATCTTATTCTTGG
81852 ATCTTATTCTTGG
1 ATCTTATTCTTGG
81865 ATCTT
1 ATCTT
81870 GTTCGTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55
Consensus pattern (13 bp):
ATCTTATTCTTGG
Found at i:87711 original size:14 final size:14
Alignment explanation
Indices: 87689--87726 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
87679 ATTAGAAGTT
*
87689 ATAAGAAAAAAATA
1 ATAATAAAAAAATA
87703 ATAATAAAAAAATA
1 ATAATAAAAAAATA
*
87717 AAAATAAAAA
1 ATAATAAAAA
87727 CTTTGGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (14 bp):
ATAATAAAAAAATA
Found at i:88373 original size:13 final size:13
Alignment explanation
Indices: 88333--88377 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
88323 GTATGAAAGT
* *
88333 AAAATTAAAAAAAT
1 AAAA-TAAAATAAC
88347 AAAATAATAATAAC
1 AAAATAA-AATAAC
88361 AAAATAAAATAAC
1 AAAATAAAATAAC
88374 AAAA
1 AAAA
88378 AATTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 13 0.46
14 15 0.54
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAATAAC
Done.