Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold975
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: 287369
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1459 original size:1 final size:1
Alignment explanation
Indices: 1453--1508 Score: 67
Period size: 1 Copynumber: 56.0 Consensus size: 1
1443 CGTCCTCCAC
* * * * *
1453 AAAAAAAAAAAAAAAAAACAAAACAAAAAAAACAAAACAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1509 GGGGTCCGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1475 original size:14 final size:14
Alignment explanation
Indices: 1453--1508 Score: 87
Period size: 14 Copynumber: 4.0 Consensus size: 14
1443 CGTCCTCCAC
1453 AAAAA-AAAAAAAA
1 AAAAACAAAAAAAA
*
1466 AAAAACAAAACAAA
1 AAAAACAAAAAAAA
1480 AAAAACAAAACAAAA
1 AAAAACAAAA-AAAA
1495 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
1509 GGGGTCCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
13 5 0.13
14 21 0.54
15 13 0.33
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:1478 original size:24 final size:24
Alignment explanation
Indices: 1451--1508 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
1441 GGCGTCCTCC
1451 ACAAAAAAAA-AAAAAAAAAACAAA
1 ACAAAAAAAACAAAAAAAAAA-AAA
*
1475 ACAAAAAAAACAAAACAAAAAAAA
1 ACAAAAAAAACAAAAAAAAAAAAA
1499 ACAAAAAAAA
1 ACAAAAAAAA
1509 GGGGTCCGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (24 bp):
ACAAAAAAAACAAAAAAAAAAAAA
Found at i:2985 original size:29 final size:29
Alignment explanation
Indices: 2946--3118 Score: 174
Period size: 29 Copynumber: 6.0 Consensus size: 29
2936 TCACCCTTCA
2946 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
2975 AAAGCCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3002 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
3030 AAAGCCTACAAGTCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
** *
3059 AGAAGCCCACAAGTTGGTGGCATCTTTTCC
1 A-AAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
3089 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
3119 TTTTGTAAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
27 24 0.20
28 27 0.22
29 42 0.34
30 30 0.24
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:3009 original size:57 final size:57
Alignment explanation
Indices: 2940--3109 Score: 209
Period size: 57 Copynumber: 3.0 Consensus size: 57
2930 CATTCCTCAC
2940 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* * * *
2997 CCTTCAAAAGCCCACAAGTCAGTGGCAAC--CTTCAAAGCCTACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAA
* ** * * * *
3052 CCTTTTCAGAAGCCCACAAGTTGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCA
3110 CTCTTTTTCT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
55 25 0.26
57 51 0.54
59 19 0.20
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (57 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:3041 original size:27 final size:28
Alignment explanation
Indices: 2940--3072 Score: 171
Period size: 28 Copynumber: 4.7 Consensus size: 28
2930 CATTCCTCAC
*
2940 CCTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
2968 CTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
2997 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
3025 CCTTC-AAAGCCTACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
3052 CCTTTTCAGAAGCCCACAAGT
1 CC--TTCAAAAGCCCACAAGT
3073 TGGTGGCATC
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
27 25 0.27
28 28 0.30
29 25 0.27
30 14 0.15
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:3230 original size:33 final size:32
Alignment explanation
Indices: 3164--3258 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
3154 CTTTTAAGCC
* * * *
3164 CACAAGTTAGTGGCACCCTTTTTCAAAGCCCA
1 CACAAGTTGGTGGCAACCATTCTCAAAGCCCA
3196 CACAAGTTGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTTGGTGGCAACCATTCTC-AAAGCCCA
* *
3229 CACAAGTCGGTGGCAACCCTTCT--AAGCCCA
1 CACAAGTTGGTGGCAACCATTCTCAAAGCCCA
3259 ATATAGCTGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.12
32 20 0.36
33 29 0.52
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (32 bp):
CACAAGTTGGTGGCAACCATTCTCAAAGCCCA
Found at i:3315 original size:49 final size:49
Alignment explanation
Indices: 3251--3818 Score: 723
Period size: 49 Copynumber: 11.7 Consensus size: 49
3241 GCAACCCTTC
* * * *
3251 TAAGCCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCACCTTCTTCGT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCA-CATTGGCACCTTCATCTT
*
3300 TAAGACCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3343 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * * *
3395 TAAGTCCAATGTAGCTTGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3444 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3493 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3542 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3591 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3640 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3688 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3731 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
3783 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3819 ACATCCTTTT
Statistics
Matches: 452, Mismatches: 48, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
43 77 0.17
45 2 0.00
48 45 0.10
49 248 0.55
50 4 0.01
52 76 0.17
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:3533 original size:98 final size:96
Alignment explanation
Indices: 3251--3818 Score: 805
Period size: 98 Copynumber: 5.9 Consensus size: 96
3241 GCAACCCTTC
* * * *
3251 TAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCACCTTCT-TCGTTAAGACCAATGTAGC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTTTAAGTCCAATGTAGC
3315 TGGCCTTGAATCAGCACATTGGCACC-T---T
65 TGGCCTTGAATCAGCACATTGGCACCTTCACT
3343 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGTA
* *
3408 GCTTGCCTTGACTCAGCACATTGGCACCTTCACCAT
63 GCTGGCCTTGAATCAGCACATTGGCACCTTCA-C-T
3444 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
*
3509 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
66 GGCCTTGAATCAGCACATTGGCACCTTCA-C-T
*
3542 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
* *
3607 GGCCTTGACTCAGCACATTGGCACTTTCATCTT
66 GGCCTTGAATCAGCACATTGGCACCTTCA-C-T
* * * * *
3640 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAACGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
3704 GGCCTTGAATCAGCACATTGGCACC-T---T
66 GGCCTTGAATCAGCACATTGGCACCTTCACT
*
3731 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGTA
3796 GCTGGCCTTGAATCAGCACATTG
63 GCTGGCCTTGAATCAGCACATTG
3819 ACATCCTTTT
Statistics
Matches: 437, Mismatches: 25, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
91 40 0.09
92 40 0.09
93 3 0.01
95 79 0.18
96 2 0.00
97 42 0.10
98 186 0.43
100 3 0.01
101 42 0.10
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (96 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTCACT
Found at i:3767 original size:91 final size:94
Alignment explanation
Indices: 3637--3827 Score: 289
Period size: 91 Copynumber: 2.0 Consensus size: 94
3627 GCACTTTCAT
*
3637 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-CACCTTTAAGTCCAACGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCACCTTTAAGTCCAACGT
*
3700 AGCTGGCCTTGAATCAGCACATTGGCA-C
66 AGCTGGCCTTGAATCAGCACATTGACATC
* * * *
3728 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TTCCACCTTTAAGTCCAAC
3793 GTAGCTGGCCTTGAATCAGCACATTGACATC
64 GTAGCTGGCCTTGAATCAGCACATTGACATC
3824 CTTT
1 CTTT
3828 TTCTCATCTT
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
91 42 0.47
94 1 0.01
95 41 0.46
96 5 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (94 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCACCTTTAAGTCCAACGT
AGCTGGCCTTGAATCAGCACATTGACATC
Found at i:3857 original size:55 final size:51
Alignment explanation
Indices: 3728--3865 Score: 145
Period size: 52 Copynumber: 2.6 Consensus size: 51
3718 ACATTGGCAC
* *
3728 CTTTAAGTCCAATATAGC-TGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCC-A-ATAGCGTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
*
3780 CTTTAAGTTCAATGTAGC-TGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAA--TAGCGTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* *
3835 CTTTAAGCCCAATAGCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATAGCG-TGGCCTTGAATCA
3866 ACATATTGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 35 0.48
53 6 0.08
54 5 0.07
55 25 0.34
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (51 bp):
CTTTAAGTCCAATAGCGTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:3939 original size:67 final size:68
Alignment explanation
Indices: 3831--3957 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3821 ATCCTTTTTC
* *
3831 TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
3895 TCT
66 TCT
* ** * *
3898 TCATCTTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
3958 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:4787 original size:13 final size:13
Alignment explanation
Indices: 4769--4793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4759 CATAAAGTGT
4769 TGTATCGATACAA
1 TGTATCGATACAA
4782 TGTATCGATACA
1 TGTATCGATACA
4794 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4875 original size:13 final size:13
Alignment explanation
Indices: 4857--4881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4847 ATCACTTAAA
4857 TGTATCGATACAT
1 TGTATCGATACAT
4870 TGTATCGATACA
1 TGTATCGATACA
4882 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4932 original size:52 final size:52
Alignment explanation
Indices: 4870--5070 Score: 323
Period size: 52 Copynumber: 3.9 Consensus size: 52
4860 ATCGATACAT
** *
4870 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* ** *
4922 TGTATCGATACATTATAAAATGTATCGATATATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
4974 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
5026 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
5071 TCATATTTCG
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
51 1 0.01
52 136 0.99
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:12115 original size:19 final size:19
Alignment explanation
Indices: 12093--12131 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12083 TTTTCTAGTT
*
12093 TTATTCATTTTTTGTTATA
1 TTATTCACTTTTTGTTATA
12112 TTATTCACTTTTTGTTATA
1 TTATTCACTTTTTGTTATA
12131 T
1 T
12132 CAAAACCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTATTCACTTTTTGTTATA
Found at i:14364 original size:20 final size:20
Alignment explanation
Indices: 14339--14391 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
14329 TCTTTTTCAA
14339 GTATCGATACAATGCAACAT
1 GTATCGATACAATGCAACAT
**
14359 GTATCGATACTGTGCAACAT
1 GTATCGATACAATGCAACAT
14379 GTATCGATACAAT
1 GTATCGATACAAT
14392 TAAATGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
GTATCGATACAATGCAACAT
Found at i:16689 original size:20 final size:21
Alignment explanation
Indices: 16660--16700 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16650 TGTTTTTGAA
16660 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
16679 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
16701 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:16840 original size:13 final size:13
Alignment explanation
Indices: 16822--16860 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
16812 ATAATCCCCC
*
16822 TGTATCGATACAG
1 TGTATCGATACAA
16835 TGTATCGATACAA
1 TGTATCGATACAA
16848 TGTATCGATACAA
1 TGTATCGATACAA
16861 AGAATTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23034 original size:13 final size:13
Alignment explanation
Indices: 23016--23041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23006 CATTTTATGG
23016 TGTATCGATACAT
1 TGTATCGATACAT
23029 TGTATCGATACAT
1 TGTATCGATACAT
23042 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23152 original size:33 final size:33
Alignment explanation
Indices: 23115--23179 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
23105 CTTTTTCAAG
23115 TATCGATA-TAATGCAACATGTATCGATACAATA
1 TATCGATACT-ATGCAACATGTATCGATACAATA
23148 TATCGATACTATGCAACATGTATCGATACAAT
1 TATCGATACTATGCAACATGTATCGATACAAT
23180 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (33 bp):
TATCGATACTATGCAACATGTATCGATACAATA
Found at i:24185 original size:3 final size:3
Alignment explanation
Indices: 24179--24212 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
24169 AGCTTTGGGT
*
24179 GGA GGA GGA GGA TGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
24213 CATCTTCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.65, T:0.03
Consensus pattern (3 bp):
GGA
Found at i:25477 original size:22 final size:21
Alignment explanation
Indices: 25442--25491 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
25432 TTTGTTGATG
*
25442 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
25462 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
25483 AATTTGAAG
1 ATTTTGAAG
25492 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:25488 original size:21 final size:22
Alignment explanation
Indices: 25449--25491 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
25439 ATGATTTTGA
* *
25449 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
25471 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
25492 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:31788 original size:20 final size:20
Alignment explanation
Indices: 31763--31816 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
31753 GTTATAAGCA
* *
31763 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTACC
*
31783 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
31803 ATGTATCGATACAA
1 ATGTATCGATACAA
31817 ACAATGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:33158 original size:14 final size:14
Alignment explanation
Indices: 33139--33166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33129 GACAGGTATT
33139 TATTTTTTTGAAAA
1 TATTTTTTTGAAAA
33153 TATTTTTTTGAAAA
1 TATTTTTTTGAAAA
33167 AGGAGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTTTTTGAAAA
Found at i:33410 original size:2 final size:2
Alignment explanation
Indices: 33403--33433 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33393 TAAAGGAATG
33403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33434 TCTAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35731 original size:20 final size:21
Alignment explanation
Indices: 35703--35753 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
35693 CATGGTCCTA
*
35703 TATCGATACATTCACTTA-TG
1 TATCGATACATTCACTAATTG
*
35723 TATCAATACATTCACTAATTG
1 TATCGATACATTCACTAATTG
35744 TATCGATACA
1 TATCGATACA
35754 AATTGCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (21 bp):
TATCGATACATTCACTAATTG
Found at i:36690 original size:132 final size:130
Alignment explanation
Indices: 36287--36728 Score: 473
Period size: 132 Copynumber: 3.4 Consensus size: 130
36277 AGACTTAAAA
* * * *
36287 AAAT-AAAAATTCAAT-TTTTGG-TG-AAAACCGGGGTTGAATTATCCCCTTCGAGATGGTGGGG
1 AAATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGGTTGAAGTAT-CCCTTC-AGA-GGTGAGG
* * * * *
36348 TTGGAGTATCCCCT-GAGGTAAAGAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTATC
63 TTGGAGTAT-CCCTAGAGATGAAGAATTTGGTATTGTGGAAGTAAAAATATGGGGTTAGAGTATC
36412 CC-C
127 CCAC
* * * *
36415 ATAGATGAAAAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATCCCTTTAAAGGTAGAGG
1 A-A-ATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGGTTGAAGTATCCCTTCAGAGGT-GAGG
* *
36480 TTGGAGTATCCCTAGAGATGAAGAATTCGGTATTGTGGAAGTACAAAATATGGGGTTAGAATATC
63 TTGGAGTATCCCTAGAGATGAAGAATTTGGTATTGTGGAAGTA-AAAATATGGGGTTAGAGTATC
* *
36545 CAAG
127 CCAC
* * *
36549 AGATGAAAAATTCGATGTTTTGGAAGTAAAAACGGGGTTGGAGTATCCCTTCAGAGGTGATGGTT
1 AAATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGGTTGAAGTATCCCTTCAGAGGTGA-GGTT
* * *
36614 GGAGTATCCTTAGAGATGAAGAATTTGGTATTGTAGAAGTAAAAATTATAGGGTTAGAGTATCCC
65 GGAGTATCCCTAGAGATGAAGAATTTGGTATTGTGGAAGTAAAAA-TATGGGGTTAGAGTATCCC
36679 AC
129 AC
* ** * * * * *
36681 AAATTAAAAATTTGATGTCTTGAAAGTAAAGACAGGGTTAAAGTATCC
1 AAATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGGTTGAAGTATCC
36729 TCTTGGAGAT
Statistics
Matches: 264, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
128 1 0.00
129 1 0.00
130 2 0.01
131 24 0.09
132 194 0.73
133 25 0.09
134 17 0.06
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (130 bp):
AAATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGGTTGAAGTATCCCTTCAGAGGTGAGGTTG
GAGTATCCCTAGAGATGAAGAATTTGGTATTGTGGAAGTAAAAATATGGGGTTAGAGTATCCCAC
Found at i:40838 original size:154 final size:154
Alignment explanation
Indices: 40510--40855 Score: 349
Period size: 154 Copynumber: 2.2 Consensus size: 154
40500 TCGATCTTAA
** * *
40510 AAAAATTATGAAAACGCTCCTAGAGGATACCTTCGACTTAAAAGTGCCTGATACCCCTAAAGAAC
1 AAAAATTATGAAAATACTCCAAGAGGATACCTTCGACGTAAAAGTGCCTGATACCCCTAAAGAAC
* ** * * * * *
40575 TTAAAAATGATTATAGATGGGATGAACAGATCCTAAATACCCACCTTTGCCATAAAAGTAGGCTC
66 TTAAAAAGGATTATAGAAAGGATAAACAGATCCTAAATACCCACCTTCGACATAAAAGGAGACTC
* *
40640 GGTGACAAATTAGGACTAAATTCT
131 GATGACAAACTAGGACTAAATTCT
** * * * *
40664 AAAAACTTACAAAAATACTCCAA-AGGGATACTTTTGACGTAAAAGTGTCTGATACCCCTAAAGG
1 AAAAA-TTATGAAAATACTCCAAGA-GGATACCTTCGACGTAAAAGTGCCTGATACCCCTAAAGA
* **
40728 ACTTGAAAAGGATTATA-AAAGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCGA-A
64 ACTTAAAAAGGATTATAGAAAGGATAAACAGATCCTAAATACCCACCTTCGACATAAAAG-GAGA
* * * * * *
40791 CTCGATTACAACCTAGGAGTTAGTTTT
128 CTCGATGACAAACTAGGACTAAATTCT
*
40818 GAAAAATTATGAAAATACTCCTAG-GGTATACCTTCGAC
1 -AAAAATTATGAAAATACTCCAAGAGG-ATACCTTCGAC
40856 ATGAAAGCAT
Statistics
Matches: 152, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
153 2 0.01
154 83 0.55
155 67 0.44
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (154 bp):
AAAAATTATGAAAATACTCCAAGAGGATACCTTCGACGTAAAAGTGCCTGATACCCCTAAAGAAC
TTAAAAAGGATTATAGAAAGGATAAACAGATCCTAAATACCCACCTTCGACATAAAAGGAGACTC
GATGACAAACTAGGACTAAATTCT
Found at i:43984 original size:84 final size:84
Alignment explanation
Indices: 43892--44135 Score: 221
Period size: 83 Copynumber: 2.9 Consensus size: 84
43882 AATCGACAAT
*
43892 TCAACAAAGTATAAAGAAATTTACCCA-GGACTAAGCCGATAGGTAAATAAGGGATGAAAGGTTG
1 TCAACAAAG-ATAAAGAAATTTACCTAGGGACTAAGCCGATAGGTAAATAAGGGATGAAAGGTTG
*
43956 ACCAGGGCTGAACCGATAAG
65 ACTAGGGCTGAACCGATAAG
* * ** * * * * *
43976 TTAACAAAGGGT-AAGAGTTTTTA-CTAGGGACTAAGCCGACAAGTAAAT-AGAGAGGAAAAGTT
1 TCAACAAA-GATAAAGA-AATTTACCTAGGGACTAAGCCGATAGGTAAATAAGGGATGAAAGGTT
* *
44038 GACTAGGGCTAAATCGATAAG
64 GACTAGGGCTGAACCGATAAG
* * * ** *
44059 TCACCAAAAGATAAA-AAAGTT-CACTAGGGACTGAGTTGATAGGTAAACAAGGGATGAAAGGTT
1 TCAAC-AAAGATAAAGAAATTTAC-CTAGGGACTAAGCCGATAGGTAAATAAGGGATGAAAGGTT
*
44122 GACTAGGGTTGAAC
64 GACTAGGGCTGAAC
44136 TAATATGTCC
Statistics
Matches: 121, Mismatches: 31, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
82 2 0.02
83 60 0.50
84 58 0.48
85 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (84 bp):
TCAACAAAGATAAAGAAATTTACCTAGGGACTAAGCCGATAGGTAAATAAGGGATGAAAGGTTGA
CTAGGGCTGAACCGATAAG
Found at i:44641 original size:16 final size:16
Alignment explanation
Indices: 44588--44707 Score: 102
Period size: 16 Copynumber: 7.6 Consensus size: 16
44578 AGTTCAGCTG
44588 GTTCAGGTTCGGGCTC
1 GTTCAGGTTCGGGCTC
* ** *
44604 GTTC-GGGTCAAGTTC
1 GTTCAGGTTCGGGCTC
*
44619 GTTCAGGTTCGAGCTC
1 GTTCAGGTTCGGGCTC
* *
44635 ATTCAGGTTTGGGCTC
1 GTTCAGGTTCGGGCTC
*
44651 GTTCAGGTTTGGGCTC
1 GTTCAGGTTCGGGCTC
* *
44667 ATTC-GAGTTCAGGCTC
1 GTTCAG-GTTCGGGCTC
44683 GTTC-GAGTTCGGGCTC
1 GTTCAG-GTTCGGGCTC
*
44699 GTTCGGGTT
1 GTTCAGGTT
44708 TGAACTTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.14
16 72 0.85
17 1 0.01
ACGTcount: A:0.10, C:0.22, G:0.34, T:0.34
Consensus pattern (16 bp):
GTTCAGGTTCGGGCTC
Found at i:45270 original size:99 final size:100
Alignment explanation
Indices: 45166--45353 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 100
45156 TATGAAATAT
* * *
45166 TTACGTGAATAAAGAATTCAGGTA-CAATAAGAAAATTATTTC-ATGTTTTAATCTAAATAAAAA
1 TTACGTGAATAAAGAATTCA-ATATCAATAAGAAAATTA-CTCAATATTTTAATCTAAATAAAAA
*
45229 -ATCATTAATTAATTAAGAACATAATGGTCTATACTA
64 TATCATTAATTAATTAAAAACATAATGGTCTATACTA
* * * * *
45265 TTACGTTAATAAAGAATTCAATATTAATAATAAAATTACTCAATATTTTAATTTTAATAAAAATA
1 TTACGTGAATAAAGAATTCAATATCAATAAGAAAATTACTCAATATTTTAATCTAAATAAAAATA
*
45330 TCATTAATTAATTAAAAATATAAT
66 TCATTAATTAATTAAAAACATAAT
45354 AATCAATACT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
98 4 0.05
99 49 0.64
100 23 0.30
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (100 bp):
TTACGTGAATAAAGAATTCAATATCAATAAGAAAATTACTCAATATTTTAATCTAAATAAAAATA
TCATTAATTAATTAAAAACATAATGGTCTATACTA
Found at i:45356 original size:19 final size:19
Alignment explanation
Indices: 45318--45361 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
45308 TATTTTAATT
*
45318 TTAATAAAAATATCATTAA
1 TTAATAAAAATATCAATAA
45337 TTAATTAAAAATAT-AATAA
1 TTAA-TAAAAATATCAATAA
*
45356 TCAATA
1 TTAATA
45362 CTATAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAATAAAAATATCAATAA
Found at i:49034 original size:16 final size:16
Alignment explanation
Indices: 49010--49055 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
49000 TCAGTCTCGG
*
49010 GTTTGGGTTCTTTCGA
1 GTTTAGGTTCTTTCGA
*
49026 GTTTAGGTTCTTTCGG
1 GTTTAGGTTCTTTCGA
*
49042 GTTCAGGTTCTTTC
1 GTTTAGGTTCTTTC
49056 AGGGTCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (16 bp):
GTTTAGGTTCTTTCGA
Found at i:49365 original size:44 final size:44
Alignment explanation
Indices: 49264--50313 Score: 488
Period size: 44 Copynumber: 24.1 Consensus size: 44
49254 AAAAGGCGGA
* ** * * * *
49264 TTTGACCAGAGTGGTAACCATGTGTCAAATCAGAATGAAAAAAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* ** * * * *
49308 ATTGAGTAAGGTGGTAACCATACGTCAGACCAAAATTAGAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* *
49352 TTTGACCAGGGTGGTAACCATACGTTAAA-CAAGAAAGAGGCAA-A-
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAA-AATGA-G-AAGAG
* * * * * * *
49396 TTTAAACAAGGTGGCAACCATATGTCAAATCAAAATGAAAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* ** * * * * * * *
49440 TCTGATTAGGGTAGTAACCATACATTAGACCGAAATAAGAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * *
49484 TTTGACTAAGGTGGTAACCATACATTAAA-CAGGAA-GA-AGGCAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCA-AAATGAGAAG-AG
* * * * * *
49527 ATTTGACTAGGTTGGTAACCATACATCAAATCAGAATGAAAAGAA
1 -TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * *
49572 TTTGACAAAGGTGGTAACCATACGTCAGACCGAAATGAAAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * *
49616 TTTGACTAGGGTGATAACCATACGTCAAAT-AGGAAA-GAGGTAGA-
1 TTTGACCAGGGTGGTAACCATACGTCAAATCA--AAATGA-GAAGAG
* * ** * *
49660 TTTGACTAGGGTAGTAACCATGTGTCAAATCAAAATGAAAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * *
49704 TCTAACCAAGGTGGTAACCATACATCAAACCAAAATAAGAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
*
49748 TTTGACCATGGTGGTAACCATACGTCAAA-CAAGAA-G-G-AG-G
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAA-AATGAGAAGAG
* * * * * * *
49788 -CTG---A--TTTG-AACCATGCATCAAATCAGAATGCA-AAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATG-AGAAGAG
* * * *
49825 TCTGACCAGGGTGGTAACCATATGTCAGATCAAAATGAAAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* **
49869 TTTGACCAGGGTGGTAACCATACATCAAAT-AAGAAAAAGGCAA-A-
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAA-AATGA-G-AAGAG
* * * * * * * *
49913 TTTGACCAGAGTGGTAACCATGCATCAAATCAGAATAAAAATAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * *
49957 TCTGACCAGGGTGGTAACCAAACGTCAAA-CAAGAA-GA-AGGCAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAA-AATGAGAAG-AG
* * * * * * *
50000 ATTTGACTAGGGTGGTAACCATGCATCAAATCAGAATGAAAAAAA
1 -TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * *
50045 TCTGACCAGGGTAGTAACCATACGTCAGACCAAAATGAAAAGAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * *
50089 TTTGACTAGGGTGGTAACCATACGTCAAAT-AGGAAGGAGGTAGA-
1 TTTGACCAGGGTGGTAACCATACGTCAAATCA-AAATGA-GAAGAG
* * * * * * *
50133 TTTGACTAGGGTGGTAACAATGCATCAAATTAAAATGAAAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * *
50177 TCTGACCAGGGTGTTAACCATACGTTAGATCGAAATGAGAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * * * * *
50221 TTTAACTAAGG-GGTAACCCTGCGTTAAATCAGAATGAAAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
* * * * * *
50264 TCTGACTAGGGTGGTAACCATACGTTAGACCAAAATGAGAAAAG
1 TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
50308 TTTGAC
1 TTTGAC
50314 TAGATACAGT
Statistics
Matches: 750, Mismatches: 206, Indels: 100
0.71 0.20 0.09
Matches are distributed among these distances:
33 14 0.02
34 5 0.01
36 3 0.00
38 3 0.00
39 2 0.00
40 1 0.00
41 3 0.00
42 8 0.01
43 64 0.09
44 612 0.82
45 28 0.04
46 7 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (44 bp):
TTTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAAGAG
Found at i:49470 original size:132 final size:131
Alignment explanation
Indices: 49234--50021 Score: 703
Period size: 132 Copynumber: 6.1 Consensus size: 131
49224 GCCACTTTTA
* * * * * *
49234 GTAACCATACATCAAAC-AGAAAAAGGCGGATTTGACCAGAGTGGTAACCATGTGTCAAATCAGA
1 GTAACCATACGTCAAACAAGAAAGAGGCAGATTTAACAAG-GTGGTAACCATATGTCAAATCAGA
* ** *
49298 ATGAAAAAAAAT-TGAGTAAGGTGGTAACCATACGTCAGACCAAAATTAGAAGAGTTTGACCAGG
65 ATG-AAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAATAAGAAGAGTTTGACCAGG
49362 GTG
129 GTG
* * * *
49365 GTAACCATACGTTAAACAAGAAAGAGGCAAATTTAAACAAGGTGGCAACCATATGTCAAATCAAA
1 GTAACCATACGTCAAACAAGAAAGAGGCAGATTT-AACAAGGTGGTAACCATATGTCAAATCAGA
** * * * * * * *
49430 ATGAAAAGAATCTGATTAGGGTAGTAACCATACATTAGACCGAAATAAGAAGAGTTTGACTAAGG
65 ATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAATAAGAAGAGTTTGACCAGGG
49495 TG
130 TG
* * * * * **
49497 GTAACCATACATTAAAC-AGGAAGAAGGCAGATTTGACTAGGTTGGTAACCATACATCAAATCAG
1 GTAACCATACGTCAAACAAGAAAG-AGGCAGATTTAACAAGG-TGGTAACCATATGTCAAATCAG
* * * *
49561 AATGAAAAGAATTTGACAAAGGTGGTAACCATACGTCAGACCGAAATGAA-AAGAGTTTGACTAG
64 AATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAAT-AAGAAGAGTTTGACCAG
49625 GGTG
128 GGTG
* * * * * * * * *
49629 ATAACCATACGTCAAATAGGAAAGAGGTAGATTTGACTAGGGTAGTAACCATGTGTCAAATCAAA
1 GTAACCATACGTCAAACAAGAAAGAGGCAGATTTAAC-AAGGTGGTAACCATATGTCAAATCAGA
* * * *
49694 ATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAAACCAAAATAAGAAGAGTTTGACCATGG
65 ATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAATAAGAAGAGTTTGACCAGGG
49759 TG
130 TG
* * *
49761 GTAACCATACGTCAAACAAGAAGGAGGCTGATTTGAACCA--T-G----C--A--TCAAATCAGA
1 GTAACCATACGTCAAACAAGAAAGAGGCAGATTT-AACAAGGTGGTAACCATATGTCAAATCAGA
* * * *
49815 ATGCAAAGAATCTGACCAGGGTGGTAACCATATGTCAGATCAAAATGAA-AAGAGTTTGACCAGG
65 ATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAAT-AAGAAGAGTTTGACCAGG
49879 GTG
129 GTG
* * * * * * ***
49882 GTAACCATACATCAAATAAGAAAAAGGCAAATTTGACCAGAGTGGTAACCATGCATCAAATCAGA
1 GTAACCATACGTCAAACAAGAAAGAGGCAGATTTAACAAG-GTGGTAACCATATGTCAAATCAGA
* * * * * * * *
49947 ATAAAAATAATCTGACCAGGGTGGTAACCAAACGTCA-AACAAGAAGAAGGCAGA-TTTGACTAG
65 ATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAA-AATAA-GAAGAGTTTGACCAG
50010 GGTG
128 GGTG
50014 GTAACCAT
1 GTAACCAT
50022 GCATCAAATC
Statistics
Matches: 536, Mismatches: 95, Indels: 51
0.79 0.14 0.07
Matches are distributed among these distances:
120 4 0.01
121 93 0.17
122 2 0.00
123 1 0.00
124 1 0.00
125 1 0.00
128 1 0.00
129 1 0.00
130 1 0.00
131 40 0.07
132 374 0.70
133 17 0.03
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (131 bp):
GTAACCATACGTCAAACAAGAAAGAGGCAGATTTAACAAGGTGGTAACCATATGTCAAATCAGAA
TGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAGACCAAAATAAGAAGAGTTTGACCAGGGT
G
Found at i:49889 original size:121 final size:121
Alignment explanation
Indices: 49675--49903 Score: 325
Period size: 121 Copynumber: 1.9 Consensus size: 121
49665 CTAGGGTAGT
**
49675 AACCATGTGTCAAATCAAAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAAACCAAAAT
1 AACCATGCATCAAATCAAAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAAACCAAAAT
* *
49740 AAGAAGAGTTTGACCATGGTGGTAACCATACGTCAAACAAGAAGGAGGCTGATTTG
66 AAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAAGAAGGAGGCTGATTTG
* * * * ** * *
49796 AACCATGCATCAAATCAGAATGCAAAGAATCTGACCAGGGTGGTAACCATATGTCAGATCAAAAT
1 AACCATGCATCAAATCAAAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAAACCAAAAT
*
49861 GAA-AAGAGTTTGACCAGGGTGGTAACCATACATCAAATAAGAA
66 -AAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAAGAA
49904 AAAGGCAAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 92 0.98
122 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (121 bp):
AACCATGCATCAAATCAAAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAAACCAAAAT
AAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAAGAAGGAGGCTGATTTG
Found at i:50345 original size:35 final size:35
Alignment explanation
Indices: 50302--50496 Score: 168
Period size: 35 Copynumber: 5.7 Consensus size: 35
50292 ACCAAAATGA
* *
50302 GAAA-AGTTTGACTAGATACAGTCCAACAATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACAATGATG
* * * * *
50336 GAATGAGTTTGACTAGATGCAGTTAAACGATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACAATGATG
*
50371 GAAAGAGTTTGACCAGATACAATC--A-AATGAT-
1 GAAAGAGTTTGACCAGATACAGTCAAACAATGATG
* * * * * *
50402 TAAAAAGGATTTGACTAGATATAGTTAAATAATGATG
1 GAAAGA-G-TTTGACCAGATACAGTCAAACAATGATG
*
50439 GAAAGTGTTTGACCAGATACAGTCAAACAATGAT-
1 GAAAGAGTTTGACCAGATACAGTCAAACAATGATG
* *
50473 AAAACGAGTTTGACCAAATACAGT
1 GAAA-GAGTTTGACCAGATACAGT
50497 TAAATGAGAG
Statistics
Matches: 126, Mismatches: 27, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
31 4 0.03
32 6 0.05
33 14 0.11
34 6 0.05
35 86 0.68
36 7 0.06
37 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (35 bp):
GAAAGAGTTTGACCAGATACAGTCAAACAATGATG
Found at i:50487 original size:103 final size:103
Alignment explanation
Indices: 50308--50503 Score: 250
Period size: 103 Copynumber: 1.9 Consensus size: 103
50298 ATGAGAAAAG
* * * * * * *
50308 TTTGACTAGATACAGTCCAACAATGATGGAATGAGTTTGACTAGATGCAGTTAAACGATGATGGA
1 TTTGACTAGATACAGTCAAACAATGATGGAAAGAGTTTGACCAGATACAGTCAAACAATGATGAA
*
50373 AAGAGTTTGACCAGATACAATCAAATGATTAAAAAGGA
66 AAGAGTTTGACCAAATACAATCAAATGATTAAAAAGGA
* * * *
50411 TTTGACTAGATATAGTTAAATAATGATGGAAAGTGTTTGACCAGATACAGTCAAACAATGAT-AA
1 TTTGACTAGATACAGTCAAACAATGATGGAAAGAGTTTGACCAGATACAGTCAAACAATGATGAA
* *
50475 AACGAGTTTGACCAAATACAGTTAAATGA
66 AA-GAGTTTGACCAAATACAATCAAATGA
50504 GAGAAAATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
102 3 0.04
103 75 0.96
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (103 bp):
TTTGACTAGATACAGTCAAACAATGATGGAAAGAGTTTGACCAGATACAGTCAAACAATGATGAA
AAGAGTTTGACCAAATACAATCAAATGATTAAAAAGGA
Found at i:50515 original size:30 final size:30
Alignment explanation
Indices: 50481--50569 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
50471 ATAAAACGAG
*
50481 TTTGACCAAATACAGTTAAATGAGAGAAAA
1 TTTGACCAAATATAGTTAAATGAGAGAAAA
* * ** *
50511 TTTGATCAATTATAGTCCAATGATGA-AATA
1 TTTGACCAAATATAGTTAAATGA-GAGAAAA
* *
50541 TTTGACCGAATATAGTTAAGTGAG-GAAAA
1 TTTGACCAAATATAGTTAAATGAGAGAAAA
50570 ACTTGATGAG
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
29 4 0.09
30 38 0.86
31 2 0.05
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (30 bp):
TTTGACCAAATATAGTTAAATGAGAGAAAA
Found at i:50809 original size:92 final size:89
Alignment explanation
Indices: 50678--50964 Score: 307
Period size: 89 Copynumber: 3.2 Consensus size: 89
50668 TGGTCACGTA
* * *
50678 ATGCATCAAT-CCATCTAGTGTCTAAAAGAAAGGGATATGATTAGGAATGAGTGGTCGGGATATC
1 ATGCATCAATACCATCTAGTGT-TGAATGAAAGGGATATGATTGGGAATGAGTGGTC-GGATATC
50742 CTTGCTAC-AAGAAAATCTAGCTTTGTG
64 CTTGCT-CTAAGAAAATC-AGCTTTGTG
** * * *
50769 ATGCATCAATACCATCTAGTGGTTGAATG-AAGGGAATATGATTGGGAATGTACAGG-CTG-CAC
1 ATGCATCAATACCATCTAGT-GTTGAATGAAAGGG-ATATGATTGGGAATG-AGTGGTCGGATAT
50831 CCTTGCTCTAAGAAAATCAAGC-TTGTG
63 CCTTGCTCTAAGAAAATC-AGCTTTGTG
* * * *
50858 ATGCATCAATACCATCTAGTACTTGAATGAAAGGGATATGATTGGGAATGTGTGGTCAGAATGTC
1 ATGCATCAATACCATCTAGT-GTTGAATGAAAGGGATATGATTGGGAATGAGTGGTC-GGATATC
* *
50923 CTTGCCCTAAGCAAATCAGGCTTTGTG
64 CTTGCTCTAAGAAAATCA-GCTTTGTG
50950 ATGCATCAATACCAT
1 ATGCATCAATACCAT
50965 TTAGGAGTTA
Statistics
Matches: 164, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
88 2 0.01
89 49 0.30
90 26 0.16
91 34 0.21
92 48 0.29
93 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (89 bp):
ATGCATCAATACCATCTAGTGTTGAATGAAAGGGATATGATTGGGAATGAGTGGTCGGATATCCT
TGCTCTAAGAAAATCAGCTTTGTG
Found at i:53787 original size:79 final size:77
Alignment explanation
Indices: 53663--54050 Score: 367
Period size: 79 Copynumber: 5.0 Consensus size: 77
53653 AAAGAGGCAA
** * **
53663 GGTTGGAGTGCCCCTTC-AGAAT-ATGGGGTTGGAGTATCCTTGAGATGAAAATTTTAATATTTT
1 GGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCGAGATGAAAA-TTTAATATTTT
*
53726 TGAAGTAAAAACG
65 TGAAATAAAAACG
* * *
53739 AGGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCTCCGAGATGAAAAATCAATATTTT
1 -GGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCGAGATGAAAATTTAATATTTT
*
53804 TGGAAATAAAAATG
65 T-GAAATAAAAACG
** ** * * **
53818 GGATTGGAGTATTCCC-TC-AGAAATAATGGGGTTAAAGTATCATCGAGATAAAAAATCGATATT
1 GG-TTGGAGTA-TCCCTTCGA-AAATAATGGGGTTGGAGTATCCCCGAGATGAAAATTTAATATT
53881 TTTGGAAATAAAAACGG
63 TTT-GAAATAAAAAC-G
* * * *
53898 GGCTAGAGTATCCCTTCGAAAATAATGAGGTTGGAGTACCCCCCGAGA--AAAATTTAATATTTT
1 GGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTA-TCCCCGAGATGAAAATTTAATATTTT
* *
53961 GGAAATAAAAATG
65 TGAAATAAAAACG
* * * *
53974 GAATTGGAGTAT-CCTCTCGAAATTGATGGGGTTGGAGTATCCCCGAAATGAAAAATTTAATATT
1 G-GTTGGAGTATCCCT-TCGAAAATAATGGGGTTGGAGTATCCCCGAGATG-AAAATTTAATATT
54038 TTTGAAATAAAAA
63 TTTGAAATAAAAA
54051 TTTAGAAATT
Statistics
Matches: 257, Mismatches: 39, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
76 12 0.05
77 52 0.20
78 33 0.13
79 146 0.57
80 14 0.05
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (77 bp):
GGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCGAGATGAAAATTTAATATTTTT
GAAATAAAAACG
Found at i:54028 original size:156 final size:156
Alignment explanation
Indices: 53678--54050 Score: 452
Period size: 158 Copynumber: 2.4 Consensus size: 156
53668 GAGTGCCCCT
* * *
53678 TCAG-AAT-ATGGGGTTGGAGTATCCTTGAGATGAAAATTTTAATATTTTTGAAGTAAAAACGAG
1 TCAGAAATAATGGGGTTGGAGTATCCTCGAGATGAAAA-ATTAATATTTTTGAAATAAAAACGAG
* * * * *
53741 GTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCTCCGAGATGAAAAATCAATATTTTTG
65 GCTAGAGTATCCCTTCGAAAATAATGAGGTTGGAGTACCCCCGAGA-GAAAAATCAATATTTTTG
*
53806 GAAATAAAAATGGGATTGGAGTATTCCC
129 GAAATAAAAATGGAATTGGAGTATTCCC
** * * ** *
53834 TCAGAAATAATGGGGTTAAAGTATCATCGAGATAAAAAATCGATATTTTTGGAAATAAAAACGGG
1 TCAGAAATAATGGGGTTGGAGTATCCTCGAGATGAAAAATTAATATTTTT-GAAATAAAAACGAG
* *
53899 GCTAGAGTATCCCTTCGAAAATAATGAGGTTGGAGTACCCCCCGAGA-AAAATTTAATA-TTTTG
65 GCTAGAGTATCCCTTCGAAAATAATGAGGTTGGAGTA-CCCCCGAGAGAAAAATCAATATTTTTG
53962 GAAATAAAAATGGAATTGGAGTA-TCCTC
129 GAAATAAAAATGGAATTGGAGTATTCC-C
* * *
53990 TC-GAAATTGATGGGGTTGGAGTATCCCCGAAATGAAAAATTTAATATTTTTGAAATAAAAA
1 TCAGAAA-TAATGGGGTTGGAGTATCCTCGAGATGAAAAA-TTAATATTTTTGAAATAAAAA
54051 TTTAGAAATT
Statistics
Matches: 183, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
155 7 0.04
156 69 0.38
157 30 0.16
158 70 0.38
159 7 0.04
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (156 bp):
TCAGAAATAATGGGGTTGGAGTATCCTCGAGATGAAAAATTAATATTTTTGAAATAAAAACGAGG
CTAGAGTATCCCTTCGAAAATAATGAGGTTGGAGTACCCCCGAGAGAAAAATCAATATTTTTGGA
AATAAAAATGGAATTGGAGTATTCCC
Found at i:54061 original size:23 final size:23
Alignment explanation
Indices: 54018--54061 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54008 GAGTATCCCC
*
54018 GAAATGAAAAATTTAATATTTTT
1 GAAATGAAAAATTTAAAATTTTT
54041 GAAAT-AAAAATTTAGAAATTT
1 GAAATGAAAAATTTA-AAATTT
54062 GACAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
GAAATGAAAAATTTAAAATTTTT
Found at i:56919 original size:23 final size:23
Alignment explanation
Indices: 56876--56918 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
56866 TTATTTCATT
*
56876 TATTTCTTTTCTTTTCTTTTTCA
1 TATTTCATTTCTTTTCTTTTTCA
56899 TATTTCATTTC-TTTCTTTTT
1 TATTTCATTTCTTTTCTTTTT
56919 TTTGTGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTTCATTTCTTTTCTTTTTCA
Found at i:59181 original size:22 final size:22
Alignment explanation
Indices: 59118--59194 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 22
59108 ACTGCAAGGA
* *
59118 AATGTATTGATACATTAAT-A-
1 AATGTATCGATACATTTATCAT
*
59138 AATGTATCGATACATGCT-TCAT
1 AATGTATCGATACAT-TTATCAT
*
59160 AATATATCGATACATTTATCAT
1 AATGTATCGATACATTTATCAT
59182 --TGTATCGATACAT
1 AATGTATCGATACAT
59195 CTGGGTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 27 0.57
21 2 0.04
22 18 0.38
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (22 bp):
AATGTATCGATACATTTATCAT
Found at i:61533 original size:95 final size:95
Alignment explanation
Indices: 61366--61601 Score: 328
Period size: 95 Copynumber: 2.5 Consensus size: 95
61356 TTTATTGGCG
* * * * *
61366 ACACTCCAACCCCATTCTTCCGAGAGAATACTCCAACCCCATTTTTAAACTTATTAAGATACTTC
1 ACACTCCAACTCCATTCTTCCGAGGGGATACTCCAACCTCATTTTTAAACTTATCAAGATACTTC
* *
61431 CTATTTTTTCCTAAAATATCATTATCGGGG
66 CTATTTTTGCCTAAAATATCATTATCGGGA
* * * * * * *
61461 ACATTCCAACTTCATTCTTCCAAGGGGATACTCTAATCTCATTTTTAAATTTGTCAAGATACTTC
1 ACACTCCAACTCCATTCTTCCGAGGGGATACTCCAACCTCATTTTTAAACTTATCAAGATACTTC
61526 CTATTTTTGCCTAAAATATCATTATCGGGA
66 CTATTTTTGCCTAAAATATCATTATCGGGA
* *
61556 ACACTCTAACTCCATTCCTCCGAGGGGATACTCCAACCTCATTTTT
1 ACACTCCAACTCCATTCTTCCGAGGGGATACTCCAACCTCATTTTT
61602 CAACAAAAAA
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 120 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (95 bp):
ACACTCCAACTCCATTCTTCCGAGGGGATACTCCAACCTCATTTTTAAACTTATCAAGATACTTC
CTATTTTTGCCTAAAATATCATTATCGGGA
Found at i:73528 original size:153 final size:153
Alignment explanation
Indices: 73244--73521 Score: 389
Period size: 153 Copynumber: 1.8 Consensus size: 153
73234 GAAATGCCCA
* * * * *
73244 ATACCCCTAAAGGACTTAAAAATGATTATAGATAGGATGAAATTATCCTAAATACCCACCTTCGG
1 ATACCCCTAAAGGACATAAAAAGGATTATAGAAAGGATGAAACTATCCTAAATACCCACCTTCCG
* ** *
73309 CATAAAAGCATACCTGGTGACAACCTAAGACTTGGTTCTAAAAAATTATGAAATGCCCCAAGGGA
66 CATAAAAGCATACCTGGTGACAACCTAAGACTTGATTCTAAAAAATTAAAAAATACCCCAAGGGA
73374 TACCTTTAATGTAGAAGTGTCTG
131 TACCTTTAATGTAGAAGTGTCTG
* *
73397 ATACTCCTAAAGGACATGAAAAGGATTATAGAAAGGAT-AAACCTATCCTAAATACCCACCTTCC
1 ATACCCCTAAAGGACATAAAAAGGATTATAGAAAGGATGAAA-CTATCCTAAATACCCACCTTCC
* * *
73461 GCATAAAAGCGA-ACCTGGTGACAACCTAGGAGTTGATTTTAAAAAATTACAAAAATACCCC
65 GCATAAAAGC-ATACCTGGTGACAACCTAAGACTTGATTCTAAAAAATTA-AAAAATACCCC
73522 TAGGATATAC
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
152 3 0.03
153 96 0.89
154 9 0.08
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (153 bp):
ATACCCCTAAAGGACATAAAAAGGATTATAGAAAGGATGAAACTATCCTAAATACCCACCTTCCG
CATAAAAGCATACCTGGTGACAACCTAAGACTTGATTCTAAAAAATTAAAAAATACCCCAAGGGA
TACCTTTAATGTAGAAGTGTCTG
Found at i:75006 original size:14 final size:13
Alignment explanation
Indices: 74970--75026 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
74960 ATTATATAAC
*
74970 AAAAATT-AATAA
1 AAAAATTAAATAT
74982 AAAAGATTAAATTAT
1 AAAA-ATTAAA-TAT
*
74997 AAAAATTAAAGATT
1 AAAAATTAAATA-T
*
75011 AAAAATTAAATTT
1 AAAAATTAAATAT
75024 AAA
1 AAA
75027 TTTTATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.11
13 8 0.22
14 19 0.51
15 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:75020 original size:21 final size:19
Alignment explanation
Indices: 74970--75020 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
74960 ATTATATAAC
74970 AAAAATTAATAAAAAAGATT
1 AAAAATTAA-AAAAAAGATT
*
74990 -AAATTATAAAAATTAAAGATT
1 AAAAAT-TAAAAA--AAAGATT
75011 AAAAATTAAA
1 AAAAATTAAA
75021 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 7 0.28
20 3 0.12
21 11 0.44
22 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAATTAAAAAAAAGATT
Found at i:75132 original size:15 final size:15
Alignment explanation
Indices: 75108--75143 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
75098 GCAAATTCTT
75108 AAAATTTTTTT-AAA
1 AAAATTTTTTTGAAA
75122 AAAACTTTTTTTGAAA
1 AAAA-TTTTTTTGAAA
75138 AAAATT
1 AAAATT
75144 ATTATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
AAAATTTTTTTGAAA
Found at i:77454 original size:23 final size:23
Alignment explanation
Indices: 77411--77455 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
77401 ATCTCTCAAT
*
77411 TTCTTCAAGAGTTATATCCCAAA
1 TTCTTCAAGAGTTATAACCCAAA
*
77434 TTCTT-AAGAGATTGTAACCCAA
1 TTCTTCAAGAG-TTATAACCCAA
77456 GGTTAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
TTCTTCAAGAGTTATAACCCAAA
Found at i:77891 original size:13 final size:13
Alignment explanation
Indices: 77873--77903 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
77863 ACTTTTCACT
*
77873 ATGTATCGATACA
1 ATGTATCAATACA
77886 ATGTATCAATACA
1 ATGTATCAATACA
77899 ATGTA
1 ATGTA
77904 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:78673 original size:22 final size:21
Alignment explanation
Indices: 78646--78693 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
78636 TTATAACTCT
78646 CCCTTAATTAAAAAAT-TTTCTC
1 CCCTTAA-TAAAAAATCTTTC-C
*
78668 CCCTTAATAAAATATCTTTCC
1 CCCTTAATAAAAAATCTTTCC
78689 CCCTT
1 CCCTT
78694 TTTGTTTCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
CCCTTAATAAAAAATCTTTCC
Found at i:88010 original size:22 final size:22
Alignment explanation
Indices: 87949--88075 Score: 78
Period size: 22 Copynumber: 5.8 Consensus size: 22
87939 AATTGCTATT
*
87949 ATCACAATAATAGTATGTACAT
1 ATCACAATAATAGTATGTACAC
* * *
87971 ATGACTATAACT-GAATGTACAC
1 ATCACAATAA-TAGTATGTACAC
* * *
87993 ATCACAATATTAGTATGTATAT
1 ATCACAATAATAGTATGTACAC
* * * ** *
88015 ATTACTATAAAAGTATGTGTAT
1 ATCACAATAATAGTATGTACAC
*
88037 ATCACAATAATA-TAATGTACAA
1 ATCACAATAATAGT-ATGTACAC
* *
88059 ATCATAATAACAGTATG
1 ATCACAATAATAGTATG
88076 GAAACCAACC
Statistics
Matches: 78, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
21 2 0.03
22 74 0.95
23 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACAATAATAGTATGTACAC
Found at i:88041 original size:44 final size:44
Alignment explanation
Indices: 87948--88057 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
87938 TAATTGCTAT
**
87948 TATCACAATAATAGTATGTACATATGACTATAACTGAATGTACA
1 TATCACAATAATAGTATGTACATATGACTATAAAAGAATGTACA
* * * * * **
87992 CATCACAATATTAGTATGTATATATTACTATAAAAGTATGTGTA
1 TATCACAATAATAGTATGTACATATGACTATAAAAGAATGTACA
88036 TATCACAATAATA-TAATGTACA
1 TATCACAATAATAGT-ATGTACA
88058 AATCATAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (44 bp):
TATCACAATAATAGTATGTACATATGACTATAAAAGAATGTACA
Found at i:88230 original size:22 final size:22
Alignment explanation
Indices: 88140--88218 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
88130 TCACTATAAA
* **
88140 AGTATGTACATATCATTGTAAC
1 AGTATGTATATATCACAGTAAC
*
88162 AGTA--CATATATCACAGTAAC
1 AGTATGTATATATCACAGTAAC
88182 AGTATGTATATATCACAGTAAC
1 AGTATGTATATATCACAGTAAC
88204 AGTATGTATATATCA
1 AGTATGTATATATCA
88219 TGATAATAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 16 0.32
22 34 0.68
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (22 bp):
AGTATGTATATATCACAGTAAC
Found at i:90617 original size:59 final size:59
Alignment explanation
Indices: 90554--90819 Score: 271
Period size: 59 Copynumber: 4.6 Consensus size: 59
90544 TAAATAACCA
* ** *
90554 TAGATTATGTAAACTATTTTAAAT-ATCCCTAAAATGCAAATAAAATACTAAAGTGACCC
1 TAGATTATGTAAAATAACTTAAATGAT-CCTAAAATGCATATAAAATACTAAAGTGACCC
** *
90613 TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCATGGAAAATGA-TAAAGTAACCC
1 TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCATATAAAAT-ACTAAAGTGACCC
* *
90672 TAGATTATGTTAAATAACCTAAATGAT-CTAAAAT--ATATGAAAATACTAAAGTGACCC
1 TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCATAT-AAAATACTAAAGTGACCC
* * * * ** *
90729 TAAATTATATAAAATAACTTAAATGACCCTAAAATGCATGA-AAATTACTAAA-TGGTCT
1 TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCAT-ATAAAATACTAAAGTGACCC
* *
90787 TAGA-TATGAAAAATAAC-CAAATGATCCTAAAAT
1 TAGATTATGTAAAATAACTTAAATGATCCTAAAAT
90820 ACTTAGAAAT
Statistics
Matches: 173, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
56 17 0.10
57 48 0.28
58 20 0.12
59 82 0.47
60 5 0.03
61 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (59 bp):
TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCATATAAAATACTAAAGTGACCC
Found at i:90731 original size:29 final size:28
Alignment explanation
Indices: 90595--90782 Score: 111
Period size: 29 Copynumber: 6.5 Consensus size: 28
90585 AAATGCAAAT
*
90595 AAAAT-ACTAAAGTGACCCT-AGATTATG
1 AAAATAACTAAA-TGACCCTAAAATTATG
* *
90622 TAAAATAACTTAAATGATCCTAAAATGCATGG
1 -AAAATAAC-TAAATGACCCTAAAAT-TAT-G
* * *
90654 AAAATGA-TAAAGTAACCCT-AGATTATG
1 AAAATAACTAAA-TGACCCTAAAATTATG
* *
90681 TTAAATAACCTAAATGA-TCTAAAATATATG
1 -AAAATAA-CTAAATGACCCTAAAAT-TATG
*
90711 AAAAT-ACTAAAGTGACCCT-AAATTATAT
1 AAAATAACTAAA-TGACCCTAAAATTAT-G
*
90739 AAAATAACTTAAATGACCCTAAAATGCATG
1 AAAATAAC-TAAATGACCCTAAAAT-TATG
*
90769 AAAATTACTAAATG
1 AAAATAACTAAATG
90783 GTCTTAGATA
Statistics
Matches: 123, Mismatches: 19, Indels: 35
0.69 0.11 0.20
Matches are distributed among these distances:
27 9 0.07
28 27 0.22
29 41 0.33
30 35 0.28
31 10 0.08
32 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAATAACTAAATGACCCTAAAATTATG
Found at i:90800 original size:57 final size:58
Alignment explanation
Indices: 90554--90905 Score: 197
Period size: 59 Copynumber: 6.1 Consensus size: 58
90544 TAAATAACCA
* * ** **
90554 TAGATTATGTAAACTATTTTAAAT-ATCCCTAAAATGCAAAT-AAAA-TACTAAAGTGACCC
1 TAGATTATGAAAAATAACTTAAATGA-CCCTAAAATGC--ATGAAAATTACTAAA-TGGTCC
* * * ***
90613 TAGATTATGTAAAATAACTTAAATGATCCTAAAATGCATGGAAAATGA-TAAAGTAACCC
1 TAGATTATGAAAAATAACTTAAATGACCCTAAAATGCAT-GAAAATTACTAAA-TGGTCC
** * * ** **
90672 TAGATTATGTTAAATAACCTAAATGA-TCTAAAATATATGAAAA-TACTAAAGTGACCC
1 TAGATTATGAAAAATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAA-TGGTCC
* *
90729 TAAATTAT-ATAAAATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAATGGTCT
1 TAGATTATGA-AAAATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAATGGTCC
* * * * ** *
90787 TAGA-TATGAAAAATAAC-CAAATGATCCTAAAATAC-TTAGAAATTAAAAAATAGTCCC
1 TAGATTATGAAAAATAACTTAAATGACCCTAAAATGCATGA-AAATTACTAAATGGT-CC
* * * * * *
90844 TTAGAGTATGAAAAGA-AACTTAAATGACCCT-AAATGAATGGAAATTGCAAAATGGTTC
1 -TAGATTATGAAAA-ATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAATGGTCC
90902 TAGA
1 TAGA
90906 GTTGACCAAC
Statistics
Matches: 235, Mismatches: 42, Indels: 34
0.76 0.14 0.11
Matches are distributed among these distances:
55 2 0.01
56 28 0.12
57 54 0.23
58 35 0.15
59 103 0.44
60 13 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (58 bp):
TAGATTATGAAAAATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAATGGTCC
Found at i:90896 original size:59 final size:57
Alignment explanation
Indices: 90739--90896 Score: 153
Period size: 56 Copynumber: 2.8 Consensus size: 57
90729 TAAATTATAT
* * * *
90739 AAAATAACTTAAATGACCCTAAAATGCATGAAAATTACTAAATGGTCTTAGATATGA
1 AAAATAACTTAAATGACCCTAAAATGAATGGAAATTACAAAATAGTCTTAGATATGA
* * * * *
90796 AAAATAAC-CAAATGATCCTAAAAT-ACTTAGAAATTAAAAAATAGTCCCTTAGAGTATGA
1 AAAATAACTTAAATGACCCTAAAATGA-ATGGAAATTACAAAATAGT--CTTAGA-TATGA
*
90855 AAAGA-AACTTAAATGACCCT-AAATGAATGGAAATTGCAAAAT
1 AAA-ATAACTTAAATGACCCTAAAATGAATGGAAATTACAAAAT
90897 GGTTCTAGAG
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
56 27 0.34
57 8 0.10
58 6 0.08
59 27 0.34
60 11 0.14
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (57 bp):
AAAATAACTTAAATGACCCTAAAATGAATGGAAATTACAAAATAGTCTTAGATATGA
Found at i:91502 original size:11 final size:10
Alignment explanation
Indices: 91484--91538 Score: 76
Period size: 10 Copynumber: 5.4 Consensus size: 10
91474 GAACAATTCA
91484 TTTTTTTTCT
1 TTTTTTTTCT
91494 TTCTTTTTTC-
1 TT-TTTTTTCT
91504 TTTTTTTTCT
1 TTTTTTTTCT
91514 TTTTTTTTCT
1 TTTTTTTTCT
*
91524 TTTCTTTTGCT
1 TTT-TTTTTCT
91535 TTTT
1 TTTT
91539 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
9 7 0.17
10 18 0.44
11 16 0.39
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:91509 original size:19 final size:19
Alignment explanation
Indices: 91485--91547 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
91475 AACAATTCAT
91485 TTTTTTTCTTTCTTTTTTC
1 TTTTTTTCTTTCTTTTTTC
91504 TTTTTTTTCTTT-TTTTTTC
1 -TTTTTTTCTTTCTTTTTTC
* *
91523 TTTTCTT-TTGC-TTTTTC
1 TTTTTTTCTTTCTTTTTTC
91540 TATTTTTT
1 T-TTTTTT
91548 TGGTCAAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.24
18 11 0.29
19 7 0.18
20 11 0.29
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTTTTC
Found at i:91549 original size:17 final size:17
Alignment explanation
Indices: 91487--91549 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 17
91477 CAATTCATTT
91487 TTTTTC-TTTCTTTT--
1 TTTTTCTTTTCTTTTGC
*
91501 TTCTTTTTTTTCTTTT--
1 TT-TTTCTTTTCTTTTGC
91517 TTTTTCTTTTCTTTTGC
1 TTTTTCTTTTCTTTTGC
91534 TTTTTCTATTT-TTTTG
1 TTTTTCT-TTTCTTTTG
91550 GTCAAGACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.05
15 15 0.36
16 10 0.24
17 12 0.29
18 3 0.07
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTGC
Found at i:92346 original size:5 final size:5
Alignment explanation
Indices: 92333--92370 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
92323 TTTCGCAGGA
*
92333 AAACG AAACT AAACG AAACG AAACG AAACG AAACG AAA
1 AAACG AAACG AAACG AAACG AAACG AAACG AAACG AAA
92371 AGGAAAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.63, C:0.18, G:0.16, T:0.03
Consensus pattern (5 bp):
AAACG
Found at i:96461 original size:80 final size:78
Alignment explanation
Indices: 96356--96553 Score: 204
Period size: 78 Copynumber: 2.5 Consensus size: 78
96346 TAATACAATG
* * *
96356 CTAATGGACTCGATTTTAAT-AAAAATGACTAAAATGACCTAAACG-GAA-AAATTTTGACATGA
1 CTAA-GGACTTGATTTTAATGGAAAATAACTAAAATGACCT-AA-GTGAACAAATTTTGACATG-
96418 AAATGTGCTAATATCACC
62 AAAT-TGCTAATATCACC
* * * * *
96436 CTAAGGGCTTGATTTTAATGGAAAATAACTAAAACGACCTTAGTTAACATATTTTGACATGAAAT
1 CTAAGGACTTGATTTTAATGGAAAATAACTAAAATGACCTAAGTGAACAAATTTTGACATGAAAT
** *
96501 TTTTAATATGACC
66 TGCTAATATCACC
* * *
96514 CTAAGGATTTGGTTTTAATGGAAAATAACTCAAATGACCT
1 CTAAGGACTTGATTTTAATGGAAAATAACTAAAATGACCT
96554 TAACAAGCAT
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
78 46 0.46
79 20 0.20
80 33 0.33
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (78 bp):
CTAAGGACTTGATTTTAATGGAAAATAACTAAAATGACCTAAGTGAACAAATTTTGACATGAAAT
TGCTAATATCACC
Found at i:96541 original size:78 final size:80
Alignment explanation
Indices: 96406--96555 Score: 214
Period size: 78 Copynumber: 1.9 Consensus size: 80
96396 AAACGGAAAA
*
96406 ATTTTGACATGAAAATGTGCTAATATCACCCTAAGGGCTTGATTTTAATGGAAAATAACTAAAAC
1 ATTTTGACATGAAAATGTGCTAATATCACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAAC
96471 GACCTTAGTTAACAT
66 GACCTTAGTTAACAT
** * * * * *
96486 ATTTTGACATG-AAAT-TTTTAATATGACCCTAAGGATTTGGTTTTAATGGAAAATAACTCAAAT
1 ATTTTGACATGAAAATGTGCTAATATCACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAAC
96549 GACCTTA
66 GACCTTA
96556 ACAAGCATGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 47 0.76
79 4 0.06
80 11 0.18
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (80 bp):
ATTTTGACATGAAAATGTGCTAATATCACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAAC
GACCTTAGTTAACAT
Found at i:96590 original size:78 final size:78
Alignment explanation
Indices: 96406--96590 Score: 192
Period size: 78 Copynumber: 2.3 Consensus size: 78
96396 AAACGGAAAA
* * *
96406 ATTTTGACATGAAAATGTGCTAATATCACCCTAAGGGCTTGATTTTAATGGAAAATAACTAAAAC
1 ATTTGGACATGAAAA--TGCTAATATGACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAAC
**
96471 GACCTTAGTTAACAT
64 GACCTTAGACAACAT
* * ** * * * *
96486 ATTTTGACATGAAATTTTTAATATGACCCTAAGGATTTGGTTTTAATGGAAAATAACTCAAATGA
1 ATTTGGACATGAAAATGCTAATATGACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAACGA
96551 CCTTA-ACAAGCAT
66 CCTTAGACAA-CAT
* * *
96564 GTTTGGATATGAAAATGCTAACATGAC
1 ATTTGGACATGAAAATGCTAATATGAC
96591 TTAAAATGAG
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
77 2 0.02
78 70 0.81
80 14 0.16
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (78 bp):
ATTTGGACATGAAAATGCTAATATGACCCTAAGGACTTGATTTTAATGGAAAATAACTAAAACGA
CCTTAGACAACAT
Found at i:101403 original size:20 final size:20
Alignment explanation
Indices: 101358--101409 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
101348 GTAGCCAAAC
**
101358 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
101378 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
101397 TTGTATCGATACA
1 TTGTATCGATACA
101410 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:105476 original size:15 final size:15
Alignment explanation
Indices: 105456--105486 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
105446 TAAAAATGTC
*
105456 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
105471 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
105486 C
1 C
105487 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:107564 original size:13 final size:13
Alignment explanation
Indices: 107546--107586 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
107536 TCTGGAAATT
107546 CAATGTATCGATA
1 CAATGTATCGATA
107559 CAATGTATCGATA
1 CAATGTATCGATA
*
107572 CACTGTATCGATA
1 CAATGTATCGATA
107585 CA
1 CA
107587 GAGGGATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:109248 original size:23 final size:21
Alignment explanation
Indices: 109206--109248 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
109196 GTTTAATGTT
**
109206 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
109227 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
109249 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:109478 original size:19 final size:19
Alignment explanation
Indices: 109454--109491 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
109444 TACGAATTTG
109454 TTAAGGGGGAGATTTTTTA
1 TTAAGGGGGAGATTTTTTA
109473 TTAAGGGGGAGATTTTTTA
1 TTAAGGGGGAGATTTTTTA
109492 ATAAAATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TTAAGGGGGAGATTTTTTA
Found at i:109502 original size:20 final size:19
Alignment explanation
Indices: 109459--109504 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
109449 ATTTGTTAAG
* *
109459 GGGGAGATTTTTTATTAAG
1 GGGGAGATTTTTTATAAAA
109478 GGGGAGATTTTTTAATAAAA
1 GGGGAGATTTTTT-ATAAAA
*
109498 TGGGAGA
1 GGGGAGA
109505 ATGTACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (19 bp):
GGGGAGATTTTTTATAAAA
Found at i:110157 original size:13 final size:13
Alignment explanation
Indices: 110139--110164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110129 TACACCAAGT
110139 ATGTATCGATACA
1 ATGTATCGATACA
110152 ATGTATCGATACA
1 ATGTATCGATACA
110165 CAAAAAATTG
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:110162 original size:32 final size:33
Alignment explanation
Indices: 110121--110184 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
110111 TAGCCAAACT
* **
110121 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
110153 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
110185 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:112417 original size:21 final size:21
Alignment explanation
Indices: 112384--112428 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
112374 TTGCAAGATG
*
112384 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
112406 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
112426 AAA
1 AAA
112429 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:114252 original size:15 final size:15
Alignment explanation
Indices: 114232--114262 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
114222 TAAAAATGTC
*
114232 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
114247 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
114262 C
1 C
114263 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:116532 original size:20 final size:20
Alignment explanation
Indices: 116489--116534 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
116479 AAATCTTTTG
116489 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
116510 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
116530 CAAAA
1 CAAAA
116535 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:118030 original size:23 final size:21
Alignment explanation
Indices: 117988--118030 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
117978 GTTTAATGTT
**
117988 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
118009 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
118031 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:118260 original size:19 final size:19
Alignment explanation
Indices: 118236--118273 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
118226 TACGAATTTG
118236 TTAAGGGGGAGATTTTTTA
1 TTAAGGGGGAGATTTTTTA
118255 TTAAGGGGGAGATTTTTTA
1 TTAAGGGGGAGATTTTTTA
118274 ATAAAATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TTAAGGGGGAGATTTTTTA
Found at i:118284 original size:20 final size:19
Alignment explanation
Indices: 118241--118286 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
118231 ATTTGTTAAG
* *
118241 GGGGAGATTTTTTATTAAG
1 GGGGAGATTTTTTATAAAA
118260 GGGGAGATTTTTTAATAAAA
1 GGGGAGATTTTTT-ATAAAA
*
118280 TGGGAGA
1 GGGGAGA
118287 ATGTACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (19 bp):
GGGGAGATTTTTTATAAAA
Found at i:118939 original size:13 final size:13
Alignment explanation
Indices: 118921--118946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118911 TACACCAAGT
118921 ATGTATCGATACA
1 ATGTATCGATACA
118934 ATGTATCGATACA
1 ATGTATCGATACA
118947 CAAAAAATTG
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:118944 original size:32 final size:33
Alignment explanation
Indices: 118903--118966 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
118893 TAGCCAAACT
* **
118903 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
118935 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
118967 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:120120 original size:13 final size:13
Alignment explanation
Indices: 120102--120126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120092 TAGCCAAACT
120102 TGTATCGATACAA
1 TGTATCGATACAA
120115 TGTATCGATACA
1 TGTATCGATACA
120127 CAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:124063 original size:13 final size:13
Alignment explanation
Indices: 124047--124072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
124037 TAGGGTAATT
124047 TTGTATCGATACA
1 TTGTATCGATACA
124060 TTGTATCGATACA
1 TTGTATCGATACA
124073 AAACTTATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:124918 original size:61 final size:61
Alignment explanation
Indices: 124801--124918 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
124791 GGTAACGACA
* * * *
124801 TTGGACTTAAAGATGTGAAGAATGATAAAGGTGCCAACATGCTAATTGACGACTAGCAATG
1 TTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAACATGCTAATTCAAGACTAGCAATG
* * * * * *
124862 TTGGGCTTGAAGATGAGAAGAATGATAAAGATGCTAATATGCTGATTCAAGGCTAGC
1 TTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAACATGCTAATTCAAGACTAGC
124919 GATATTGGTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.25
Consensus pattern (61 bp):
TTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAACATGCTAATTCAAGACTAGCAATG
Found at i:125016 original size:52 final size:51
Alignment explanation
Indices: 124897--125397 Score: 206
Period size: 52 Copynumber: 9.7 Consensus size: 51
124887 TAAAGATGCT
* * * ** ***
124897 AATATGCTGATTCAAGGCTAGCGATATTGG-TTTAAGGAAAAAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATAAGCC
* ** * * *
124947 AATGTATTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAATAAGCT
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAATAAGCC
* * * **
124999 AATATGCTGATTCAAGGCTAGCGATATTGGACTTAAGAAAGGAAAATGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAA-AGATGAAAATAAGCC
* * *
125051 AATGTGCTGATTCAAGGACAGCGATATTGGACTTGAAGATGAGAAGAATGATAAAGATGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G-A-AA--AT--A-A-GCC
* * * * * *
125112 AATATGCTGATTCAAGGCTATCGATATAGGGCTT-AAGAAAGAAAA-AAGTGTC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-ATGAAAATAA--GCC
* * * *
125164 AATTTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATAAAGT-CGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAA-TAAGCC
* * * **
125216 AATATGCTGATTCCAA----A--GACATTGGACTT-AAGAAAGAAATTGGTGCC
1 AATATGCTGATT-CAAGGCCAGCGATATTGGACTTAAAG-ATGAAAAT-AAGCC
* * * * *
125263 AATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAATATGGTAAAGGT-A-CC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G-AAA-ATAAGCC
* * * * *** *
125315 AATATACTGATTCAAGGCCAACAATATTAGACTTAAA-A--AAAAGGTGTC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATAAGCC
* * *
125363 AATATGCTGATTCAAGGCCAGTGACATTGGGCTTA
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTA
125398 GAAGGGTTGC
Statistics
Matches: 336, Mismatches: 80, Indels: 72
0.69 0.16 0.15
Matches are distributed among these distances:
45 1 0.00
46 8 0.02
47 31 0.09
48 29 0.09
49 1 0.00
50 25 0.07
51 11 0.03
52 164 0.49
53 17 0.05
54 4 0.01
55 4 0.01
57 4 0.01
58 1 0.00
59 1 0.00
60 3 0.01
61 32 0.10
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (51 bp):
AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAATAAGCC
Found at i:125197 original size:113 final size:113
Alignment explanation
Indices: 124999--125205 Score: 315
Period size: 113 Copynumber: 1.8 Consensus size: 113
124989 CAAATAAGCT
* * *
124999 AATATGCTGATTCAAGGCTAGCGATATTGGACTTAAGAAAGGAAAATGTGCCAATGTGCTGATTC
1 AATATGCTGATTCAAGGCTAGCGATATAGGACTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTC
* * *
125064 AAGGACAGCGATATTGGACTTGAAGATGAGAAGAATGATAAAGATGCC
66 AAGGACAGCAACATTGGACTTAAAGATGAGAAGAATGATAAAGATGCC
* * * *
125112 AATATGCTGATTCAAGGCTATCGATATAGGGCTTAAGAAAGAAAAAAGTGTCAATTTGCTGATTC
1 AATATGCTGATTCAAGGCTAGCGATATAGGACTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTC
*
125177 AAGGCCAGCAACATTGGACTTAAAGATGA
66 AAGGACAGCAACATTGGACTTAAAGATGA
125206 TAAAGTCGCC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
113 83 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (113 bp):
AATATGCTGATTCAAGGCTAGCGATATAGGACTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTC
AAGGACAGCAACATTGGACTTAAAGATGAGAAGAATGATAAAGATGCC
Found at i:125278 original size:99 final size:99
Alignment explanation
Indices: 125143--125327 Score: 255
Period size: 99 Copynumber: 1.9 Consensus size: 99
125133 CGATATAGGG
* *
125143 CTTAAGAAAGAAAAAAGTGTCAATTTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATA
1 CTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATA
* *
125208 AA-GTCGCCAATATGCTGATTCCAAAGACATTGGA
66 AAGGT-ACCAATATACTGATTCCAAAGACATTGGA
*** * * * *
125242 CTTAAGAAAGAAATTGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAATATGGTA
1 CTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATA
125307 AAGGTACCAATATACTGATTC
66 AAGGTACCAATATACTGATTC
125328 AAGGCCAACA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 72 0.97
100 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (99 bp):
CTTAAGAAAGAAAAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATA
AAGGTACCAATATACTGATTCCAAAGACATTGGA
Found at i:125519 original size:62 final size:64
Alignment explanation
Indices: 125397--125542 Score: 224
Period size: 62 Copynumber: 2.3 Consensus size: 64
125387 CATTGGGCTT
* * * * * *
125397 AGAAGGGTTGCCACTAACTTGTATGGGCTTTGGGAAGGGTGCCACCCGACTTGTGTAGGCTTTG
1 AGAAGGGTTGCCACCAGCTTGTATAGGATTTGAGAAGGGTGCCACCCGACTTATGTAGGCTTTG
125461 AGAAGGGTTGCCACCAGCTTGTATAGGATTT-AGAAGGGTGCCA-CCGACTTATGTAGGCTTTG
1 AGAAGGGTTGCCACCAGCTTGTATAGGATTTGAGAAGGGTGCCACCCGACTTATGTAGGCTTTG
125523 AGAAGGGTTGCCACCAGCTT
1 AGAAGGGTTGCCACCAGCTT
125543 CTGTGGGTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
62 38 0.50
63 11 0.14
64 27 0.36
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (64 bp):
AGAAGGGTTGCCACCAGCTTGTATAGGATTTGAGAAGGGTGCCACCCGACTTATGTAGGCTTTG
Found at i:125555 original size:32 final size:32
Alignment explanation
Indices: 125397--125542 Score: 165
Period size: 32 Copynumber: 4.6 Consensus size: 32
125387 CATTGGGCTT
* * * *
125397 AGAAGGGTTGCCACTAACTTGTATGGGCTTTG
1 AGAAGGGTTGCCACCAGCTTGTGTAGGCTTTG
* *
125429 GGAAGGG-TGCCACCCGACTTGTGTAGGCTTTG
1 AGAAGGGTTGCCACCAG-CTTGTGTAGGCTTTG
* *
125461 AGAAGGGTTGCCACCAGCTTGTATAGGATTT-
1 AGAAGGGTTGCCACCAGCTTGTGTAGGCTTTG
*
125492 AGAAGGG-TGCCACC-GACTTATGTAGGCTTTG
1 AGAAGGGTTGCCACCAG-CTTGTGTAGGCTTTG
125523 AGAAGGGTTGCCACCAGCTT
1 AGAAGGGTTGCCACCAGCTT
125543 CTGTGGGTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.01
30 18 0.19
31 20 0.21
32 47 0.49
33 9 0.09
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (32 bp):
AGAAGGGTTGCCACCAGCTTGTGTAGGCTTTG
Found at i:125590 original size:34 final size:33
Alignment explanation
Indices: 125555--125977 Score: 297
Period size: 34 Copynumber: 12.8 Consensus size: 33
125545 GTGGGTTTTG
* *
125555 AAAAGAAAAAGGTGCCACGGAGTTATGGGCTTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
125588 GAAAAGAAAAAGGTGCTACGGAGTTGCGGAC-TT
1 -AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
125621 AAAAG-----GGTGCCATGGAGTTATGGGCTTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
125649 AAAAAGAAAAAGGTGCTACGGAGTTGCGGAC-TT
1 -AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
*
125682 AAAAG-----GGTGCCACAGAGTTGTGGACTTTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTT
* * **
125711 AGAAG-AAAAGGTGCCACGAAGTTGTGGGTTTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* **
125743 GAAAATAAAAAGGTGCCATAGAGTTGTGGAC-TT
1 -AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
*
125776 AAAAGGAAAAATGGTGTCACGGAGTTGTAGG-CTTT
1 AAAA-GAAAAA-GGTGCCACGGAGTTGT-GGACTTT
* * * *
125811 GAAAAGAAAAATGTGCCACGTAATTGTGGAC-TC
1 -AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
125844 AAAAGGAAAAAAGGGTGCCACAGAGTTATGGAC-TT
1 AAAA-G-AAAAA-GGTGCCACGGAGTTGTGGACTTT
* * *
125879 AAAACGAAAGAAGATGCCACCGAGTTGTGGGCTTT
1 AAAA-GAAA-AAGGTGCCACGGAGTTGTGGACTTT
*
125914 AAAAAGAAAAAGGTGCCATGGAGTTGTGGAC-TT
1 -AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
125947 AAAAGCAAAAAAGGATGCCATGGAGTAGTGG
1 AAAAG--AAAAAGG-TGCCACGGAGTTGTGG
125978 GCTAAAATAG
Statistics
Matches: 305, Mismatches: 54, Indels: 59
0.73 0.13 0.14
Matches are distributed among these distances:
27 32 0.10
28 2 0.01
29 11 0.04
32 26 0.09
33 36 0.12
34 136 0.45
35 54 0.18
36 8 0.03
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (33 bp):
AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
Found at i:125637 original size:27 final size:27
Alignment explanation
Indices: 125594--125708 Score: 86
Period size: 27 Copynumber: 4.0 Consensus size: 27
125584 CTTTGAAAAG
* *
125594 AAAAAGGTGCTACGGAGTTGCGGACTT
1 AAAAGGGTGCCACGGAGTTGCGGACTT
* ** *
125621 AAAAGGGTGCCATGGAGTTATGGGCTTT
1 AAAAGGGTGCCACGGAGTTGCGGAC-TT
*
125649 AAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGCGGACTT
* *
125682 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGCGGACTT
125709 TTAGAAGAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
27 38 0.57
28 2 0.03
29 5 0.07
32 5 0.07
33 2 0.03
34 15 0.22
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGCGGACTT
Found at i:125639 original size:61 final size:61
Alignment explanation
Indices: 125560--125734 Score: 253
Period size: 61 Copynumber: 2.9 Consensus size: 61
125550 TTTTGAAAAG
* *
125560 AAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
1 AAAAGGGTGCCACGGAGTTATGGGCTTTAAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
*
125621 AAAAGGGTGCCATGGAGTTATGGGCTTTAAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
1 AAAAGGGTGCCACGGAGTTATGGGCTTTAAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
* * * * * * *
125682 AAAAGGGTGCCACAGAGTTGTGGACTTTTAGAAG-AAAAGGTGCCACGAAGTTG
1 AAAAGGGTGCCACGGAGTTATGGGCTTTAAAAAGAAAAAGGTGCTACGGAGTTG
125735 TGGGTTTTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
60 17 0.17
61 86 0.83
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.22
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTATGGGCTTTAAAAAGAAAAAGGTGCTACGGAGTTGCGGACTT
Found at i:125879 original size:103 final size:103
Alignment explanation
Indices: 125749--125966 Score: 278
Period size: 103 Copynumber: 2.1 Consensus size: 103
125739 TTTTGAAAAT
* * * * * * *
125749 AAAAA-GGTGCCATAGAGTTGTGGACTTAAAAGGAAA-AATGGTGTCACGGAGTTGTAGGCTTTG
1 AAAAAGGGTGCCACAGAGTTATGGACTTAAAACGAAAGAA-GATGCCACCGAGTTGTAGGCTTTA
* * *
125812 AAAAGAAAAATGTGCCACGTAATTGTGGACTCAAAAGGA
65 AAAAGAAAAAGGTGCCACGGAATTGTGGACTCAAAAGCA
*
125851 AAAAAGGGTGCCACAGAGTTATGGACTTAAAACGAAAGAAGATGCCACCGAGTTGTGGGCTTTAA
1 AAAAAGGGTGCCACAGAGTTATGGACTTAAAACGAAAGAAGATGCCACCGAGTTGTAGGCTTTAA
* * *
125916 AAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGCA
66 AAAGAAAAAGGTGCCACGGAATTGTGGACTCAAAAGCA
*
125954 AAAAAGGATGCCA
1 AAAAAGGGTGCCA
125967 TGGAGTAGTG
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
102 5 0.05
103 92 0.93
104 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.20
Consensus pattern (103 bp):
AAAAAGGGTGCCACAGAGTTATGGACTTAAAACGAAAGAAGATGCCACCGAGTTGTAGGCTTTAA
AAAGAAAAAGGTGCCACGGAATTGTGGACTCAAAAGCA
Found at i:126073 original size:91 final size:91
Alignment explanation
Indices: 125928--126142 Score: 362
Period size: 91 Copynumber: 2.4 Consensus size: 91
125918 AGAAAAAGGT
* *
125928 GCCATGGAGTTGTGGACTTAAAA-G-CAAAAAAGGATGCCATGGAGTAGTGGGCTAAAATAGGTA
1 GCCATAGAGTTGTGGACTTAAAAGGAAAAAAAAGGATGCCATGGAGTAGTGGGCTAAAATAGGTA
125991 CCACGAAGTTGTGGACTTAAAAGGGC
66 CCACGAAGTTGTGGACTTAAAAGGGC
*
126017 GCCATAGATTTGTGGACTTAAAAGGAAAAAAAAGGATGCCATGGAGTAGTGGGCTAAAATAGGTA
1 GCCATAGAGTTGTGGACTTAAAAGGAAAAAAAAGGATGCCATGGAGTAGTGGGCTAAAATAGGTA
*
126082 CCACGGAGTTGTGGACTTAAAAGGGC
66 CCACGAAGTTGTGGACTTAAAAGGGC
* *
126108 GCCACAGAGTTATGGACTTAAAAGGAAAAAAAAGG
1 GCCATAGAGTTGTGGACTTAAAAGGAAAAAAAAGG
126143 TGCTACAAAG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
89 21 0.18
90 1 0.01
91 95 0.81
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.20
Consensus pattern (91 bp):
GCCATAGAGTTGTGGACTTAAAAGGAAAAAAAAGGATGCCATGGAGTAGTGGGCTAAAATAGGTA
CCACGAAGTTGTGGACTTAAAAGGGC
Found at i:126272 original size:27 final size:27
Alignment explanation
Indices: 126215--126495 Score: 145
Period size: 27 Copynumber: 9.7 Consensus size: 27
126205 AGGTGCTATA
* * * *
126215 GAGTTGTGGGCTTTAAAA-GATGGCACA
1 GAGTTGTGGAC-TTAAAAGGGTGCCACG
* *
126242 GAGTTGTGGGCTTAAAAGGGTGCCATG
1 GAGTTGTGGACTTAAAAGGGTGCCACG
* *
126269 GAGTTATAGACTTAAAAGGAAAAAGGTGCCACG
1 GAGTTGTGGACTTAAAA-G-----GGTGCCACG
* *
126302 GAGTTGTGGGCTT-AAAGGATGCCACG
1 GAGTTGTGGACTTAAAAGGGTGCCACG
* * * *
126328 GAGTTGTGGAATTAAAAAGGTGTCATG
1 GAGTTGTGGACTTAAAAGGGTGCCACG
* *
126355 AAGTTGTGGACTTAAAAGGAAAAAGATGACACG
1 GAGTTGTGGACTTAAAAGG-----G-TGCCACG
* ** * *
126388 AAGTTGTGGGTTTAAAAAGAAAAATGTGCCACA
1 GAGTTGTGGACTT-AAAAG-----GGTGCCACG
126421 GAGTTGTGGACTTAAAAGGGTGCCACG
1 GAGTTGTGGACTTAAAAGGGTGCCACG
*
126448 GTGTTGTAGG-CTTTAAAAAGGGTGCCACG
1 GAGTTGT-GGAC-TT-AAAAGGGTGCCACG
126477 GAGTTGTGGACTTAAAAGG
1 GAGTTGTGGACTTAAAAGG
126496 AAAAAGGGTA
Statistics
Matches: 195, Mismatches: 35, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
26 25 0.13
27 75 0.38
28 9 0.05
29 21 0.11
31 1 0.01
32 9 0.05
33 49 0.25
34 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.24
Consensus pattern (27 bp):
GAGTTGTGGACTTAAAAGGGTGCCACG
Found at i:126316 original size:33 final size:33
Alignment explanation
Indices: 126255--126502 Score: 139
Period size: 33 Copynumber: 8.2 Consensus size: 33
126245 TTGTGGGCTT
* * * *
126255 AAAAGGGTGCCATGGAGTTATAGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
126288 AAAAAGGTGCCACGGAGTTGTGGGCTT-AAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
126320 ----A--TGCCACGGAGTTGTGGAATT------
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
126341 AAAAAGGTGTCATGAAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * * ** *
126374 AAAAAGATGACACGAAGTTGTGGGTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
126407 AAAAATGTGCCACAGAGTTGTGGACTTAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
126439 -----GGTGCCACGGTGTTGTAGG-CTT--TA--
1 AAAAAGGTGCCACGGAGTTGT-GGACTTAAAAGG
*
126463 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
126496 AAAAAGG
1 AAAAAGG
126503 GTACCACAGA
Statistics
Matches: 161, Mismatches: 31, Indels: 46
0.68 0.13 0.19
Matches are distributed among these distances:
25 2 0.01
26 18 0.11
27 32 0.20
28 5 0.03
29 18 0.11
31 1 0.01
32 6 0.04
33 79 0.49
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.22
Consensus pattern (33 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:126317 original size:86 final size:85
Alignment explanation
Indices: 126174--126494 Score: 297
Period size: 86 Copynumber: 3.7 Consensus size: 85
126164 AAAATGACAA
* * * **
126174 GGTGCCATAGAGTTATAGACTTAAAAAAAAAAGGTGCTATAGAGTTGTGGGCTTTAAAAGATGGC
1 GGTGCCATGGAGTTATAGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAAAGATGGC
*
126239 ACAGAGTTGTGGGCTTAAAAG
65 ACAGAGTTGTGGACTTAAAAG
* *
126260 GGTGCCATGGAGTTATAGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAGGATGCC
1 GGTGCCATGGAGTTATAGACTTAAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGATGGC
* * *
126325 ACGGAGTTGTGGAATTAAAAA
65 ACAGAGTTGTGGACTTAAAAG
* * * * * * * *
126346 GGTGTCATGAAGTTGTGGACTTAAAAGGAAAAAGATGACACGAAGTTGTGGGTTTAAAAAGAAAA
1 GGTGCCATGGAGTTATAGACTTAAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTT-AAAAG----
126411 ATGTGCCACAGAGTTGTGGACTTAAAAG
60 ATG-G-CACAGAGTTGTGGACTTAAAAG
* * * * * * *
126439 GGTGCCACGGTGTTGTAGGCTT--TA-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCATGGAGTTATAGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAG
126495 GAAAAAGGGT
Statistics
Matches: 190, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
86 99 0.52
87 26 0.14
88 5 0.03
89 21 0.11
91 4 0.02
93 35 0.18
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (85 bp):
GGTGCCATGGAGTTATAGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGATGGCA
CAGAGTTGTGGACTTAAAAG
Found at i:126342 original size:26 final size:25
Alignment explanation
Indices: 126290--126370 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 25
126280 TTAAAAGGAA
**
126290 AAAGGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGAATT
126315 AAAGGATGCCACGGAGTTGTGGAATT
1 AAAGG-TGCCACGGAGTTGTGGAATT
* * * *
126341 AAAAAGGTGTCATGAAGTTGTGGACTT
1 --AAAGGTGCCACGGAGTTGTGGAATT
126368 AAA
1 AAA
126371 AGGAAAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.17
26 18 0.38
27 16 0.34
28 5 0.11
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.25
Consensus pattern (25 bp):
AAAGGTGCCACGGAGTTGTGGAATT
Found at i:127687 original size:26 final size:26
Alignment explanation
Indices: 127665--127715 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
127655 ACTTTTTTGT
127665 ATTTTTT-TGCCTTTTTTTGTTTTTC
1 ATTTTTTGTGCCTTTTTTTGTTTTTC
**
127690 ATTTTTTGTGTTTTTTTTTGTGTTTT
1 ATTTTTTGTGCCTTTTTTTGT-TTTT
127716 TCTTTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.04, C:0.06, G:0.12, T:0.78
Consensus pattern (26 bp):
ATTTTTTGTGCCTTTTTTTGTTTTTC
Found at i:127696 original size:14 final size:13
Alignment explanation
Indices: 127677--127722 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
127667 TTTTTTGCCT
127677 TTTTTTGTTTTTC
1 TTTTTTGTTTTTC
127690 ATTTTTTGTGTTTT-
1 -TTTTTTGT-TTTTC
127704 TTTTTGTGTTTTTC
1 TTTTT-TGTTTTTC
127718 TTTTT
1 TTTTT
127723 GACTTTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.31
14 16 0.55
15 4 0.14
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTTTTC
Found at i:127729 original size:26 final size:26
Alignment explanation
Indices: 127676--127729 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
127666 TTTTTTTGCC
**
127676 TTTTTTTGTTTTTCATTTTTTGTGTTT
1 TTTTTTTGTTTTTCA-TTTTTGACTTT
127703 TTTTTTGTGTTTTTC-TTTTTGACTTT
1 TTTTTT-TGTTTTTCATTTTTGACTTT
127729 T
1 T
127730 CCATCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 6 0.25
28 8 0.33
ACGTcount: A:0.04, C:0.06, G:0.11, T:0.80
Consensus pattern (26 bp):
TTTTTTTGTTTTTCATTTTTGACTTT
Found at i:131205 original size:80 final size:79
Alignment explanation
Indices: 131106--131428 Score: 321
Period size: 78 Copynumber: 4.1 Consensus size: 79
131096 ATACACCAAA
* * * *
131106 TTTCTACAATCGGGAATACTCCAACCCCGTCATTT-TCGAGGGGATACTCTAACGTCAGCTTTAT
1 TTTC-ACAATCGGGGATACTCCAACCCCGTCATTTCT-GAGGGGATACTCCAACGCCGGCTTTAT
131170 TTCTAAAAACATCAATT
64 TTCT-AAAACATCAATT
* * * * *
131187 TTTCACAATCGGGGATACTTCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTGTTT
1 TTTCACAATCGGGGATACTCCAACCCCGTCATTTCTGAGGGGATACTCCAACGCCGGCTTTATTT
131252 C-AAAACATCAATT
66 CTAAAACATCAATT
* * * * * * *
131265 TTTCATAATTGGGGATACTTCAACCCCGTTATTTCTGAGGGAATACTCCAATGCCGGTTTTATTT
1 TTTCACAATCGGGGATACTCCAACCCCGTCATTTCTGAGGGGATACTCCAACGCCGGCTTTATTT
*
131330 -TCAAAACATCGATT
66 CT-AAAACATCAATT
* * * * * ** *
131344 TTCCACCATAGCGGATACTCCAACCCCGTCATTT-TCGAGGGGATACTCCAACCCCGTTTTTATC
1 TTTCACAATCGGGGATACTCCAACCCCGTCATTTCT-GAGGGGATACTCCAACGCCGGCTTTATT
* *
131408 TCCAAAACATTAAATT
65 TCTAAAACA-TCAATT
131424 TTTCA
1 TTTCA
131429 TCGGGGAATG
Statistics
Matches: 202, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
78 70 0.35
79 68 0.34
80 59 0.29
81 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TTTCACAATCGGGGATACTCCAACCCCGTCATTTCTGAGGGGATACTCCAACGCCGGCTTTATTT
CTAAAACATCAATT
Found at i:131368 original size:79 final size:79
Alignment explanation
Indices: 131106--131428 Score: 319
Period size: 79 Copynumber: 4.1 Consensus size: 79
131096 ATACACCAAA
* * * ** *
131106 TTTCTACAATCGGGAATACTCCAACCCCGTCATTTTCGAGGGGATACTCTAACGTCAGCTTTATT
1 TTTC-ACAATAGGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGGCTTTATT
*
131171 TCTAAAAACATCAATT
65 T-TCAAAACATCAATT
* * * * *
131187 TTTCACAATCGGGGATACTTCAACCCTGTTA-TTTCTGAGGGGATACTCCAACCCCGGCTTT-GT
1 TTTCACAATAGGGGATACTCCAACCCCGTCATTTTC-GAGGGGATACTCCAACCCCGGCTTTATT
131250 TTCAAAACATCAATT
65 TTCAAAACATCAATT
* * * * * ** *
131265 TTTCATAATTGGGGATACTTCAACCCCGTTA-TTTCTGAGGGAATACTCCAATGCCGGTTTTATT
1 TTTCACAATAGGGGATACTCCAACCCCGTCATTTTC-GAGGGGATACTCCAACCCCGGCTTTATT
*
131329 TTCAAAACATCGATT
65 TTCAAAACATCAATT
* * * ** *
131344 TTCCACCATAGCGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGTTTTTATCT
1 TTTCACAATAGGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGGCTTTATTT
* *
131409 CCAAAACATTAAATT
66 TCAAAACA-TCAATT
131424 TTTCA
1 TTTCA
131429 TCGGGGAATG
Statistics
Matches: 203, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
78 67 0.33
79 76 0.37
80 56 0.28
81 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TTTCACAATAGGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGGCTTTATTT
TCAAAACATCAATT
Found at i:136675 original size:20 final size:21
Alignment explanation
Indices: 136647--136685 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
136637 TTCCCGTGTA
*
136647 AATGTATCGATACA-ATTTTT
1 AATGCATCGATACATATTTTT
136667 AATGCATCGATACATATTT
1 AATGCATCGATACATATTT
136686 GAAAATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (21 bp):
AATGCATCGATACATATTTTT
Found at i:136763 original size:33 final size:32
Alignment explanation
Indices: 136720--136783 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
136710 TACAAGCCAA
*
136720 TGTATCGATACA-ATTTTTGGTGTATCGATACAT
1 TGTATCGATACATA-CTTT-GTGTATCGATACAT
*
136753 TGTATTGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
136784 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:139338 original size:13 final size:13
Alignment explanation
Indices: 139320--139358 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
139310 ATAATCCCCC
*
139320 TGTATCGATACAG
1 TGTATCGATACAA
139333 TGTATCGATACAA
1 TGTATCGATACAA
139346 TGTATCGATACAA
1 TGTATCGATACAA
139359 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:143220 original size:22 final size:20
Alignment explanation
Indices: 143171--143222 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
143161 ATCATGCAAG
143171 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
143192 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
143214 TTTTTATTT
1 TTTTTATTT
143223 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:159608 original size:8 final size:8
Alignment explanation
Indices: 159594--159635 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
159584 CATGGATTTT
159594 CAAAAAAA
1 CAAAAAAA
159602 -AAAAAAA
1 CAAAAAAA
159609 CAAAAAAA
1 CAAAAAAA
*
159617 CAAAAAGA
1 CAAAAAAA
*
159625 CAAAAAGA
1 CAAAAAAA
159633 CAA
1 CAA
159636 GGAAAATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:159993 original size:23 final size:23
Alignment explanation
Indices: 159968--160010 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
159958 GAAACACAAA
*
159968 AAAAAG-AAAGAAATGAAATATG
1 AAAAAGAAAAGAAAAGAAATATG
159990 AAAAAGAAAAGAAAAGAAATA
1 AAAAAGAAAAGAAAAGAAATA
160011 AATGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAGAAATATG
Found at i:162889 original size:26 final size:27
Alignment explanation
Indices: 162860--162911 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
162850 TAAATTTTTC
162860 ATTTC-GGGGATACTCCAACCCCATCA
1 ATTTCAGGGGATACTCCAACCCCATCA
*
162886 ATTTCGAGGGGATACTCCAATCCCAT
1 ATTTC-AGGGGATACTCCAACCCCAT
162912 TTTTATTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
28 18 0.78
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (27 bp):
ATTTCAGGGGATACTCCAACCCCATCA
Found at i:163037 original size:155 final size:157
Alignment explanation
Indices: 162832--163218 Score: 473
Period size: 158 Copynumber: 2.5 Consensus size: 157
162822 AATTTCTAAA
* *
162832 TTTTTATTTCAAAAATATTAAATTTTTCATTTCGGGGATACTCCAACCCCATCAATTTC-GAGGG
1 TTTTTATTTCAAAAATATTAAATTTTTCATCTCGAGGATACTCCAACCCCAT-AATTTCTGAGGG
* * * * *
162896 GATACTCCAATCCCATTTTTA-TTTCCAAAATATTAAATTTT-TCTCGGGGGTACTCCAACCTCA
65 GATACTCCAACCCCATTTTTATTTTCAAAAATATTAAATTTTATCTCGGAGATACTCCAACCCCA
* * * *
162959 TTATTTTTGAAGGGATACTCTAGCCTCG
130 TTATTTTCGAAGGGATACTCCAACCCCG
* * ** *
162987 TTTTTATTTTCAAAAATA-TCAATTTTTTATCTCGAGGATACTTTAACCCCATTATTTCTGAGGG
1 TTTTTA-TTTCAAAAATATTAAATTTTTCATCTCGAGGATACTCCAACCCCATAATTTCTGAGGG
* * *
163051 GATACTCCAACCCCATTTTTATTTTCAAAAATATTGATTTTTCATCTCGGAGATACTCCAGCCCC
65 GATACTCCAACCCCATTTTTATTTTCAAAAATATTAAATTTT-ATCTCGGAGATACTCCAACCCC
163116 ATTATTTTCGAAGGGATACTCCAACCCCG
129 ATTATTTTCGAAGGGATACTCCAACCCCG
* * * *
163145 TCTTTACTTCAAAAATATTAAAATTTTCATCTCAAGGATACTCCAACCCCAT-A-TTCTGAAGGG
1 TTTTTATTTCAAAAATATTAAATTTTTCATCTCGAGGATACTCCAACCCCATAATTTCTG-AGGG
*
163208 G-CACTCCAACC
65 GATACTCCAACC
163219 TTGCCTCTTT
Statistics
Matches: 197, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
154 5 0.03
155 59 0.30
156 42 0.21
157 16 0.08
158 75 0.38
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (157 bp):
TTTTTATTTCAAAAATATTAAATTTTTCATCTCGAGGATACTCCAACCCCATAATTTCTGAGGGG
ATACTCCAACCCCATTTTTATTTTCAAAAATATTAAATTTTATCTCGGAGATACTCCAACCCCAT
TATTTTCGAAGGGATACTCCAACCCCG
Found at i:163056 original size:79 final size:78
Alignment explanation
Indices: 162831--163218 Score: 380
Period size: 79 Copynumber: 5.0 Consensus size: 78
162821 AAATTTCTAA
* * *
162831 ATTTTTATTTCAAAAATATTAAATTTTTCATTTCGGGGATACTCCAACCCCATCAATTTC-GAGG
1 ATTTTTATTTCAAAAATA-TAAATTTTTCATCTCGAGGATACTCCAACCCCAT-TATTTCTGAGG
*
162895 GGATACTCCAATCCC
64 GGATACTCCAACCCC
* * * * * *
162910 ATTTTTATTTCCAAAATATTAAA-TTTT--TCTCGGGGGTACTCCAACCTCATTATTTTTGAAGG
1 ATTTTTATTTCAAAAATA-TAAATTTTTCATCTCGAGGATACTCCAACCCCATTATTTCTGAGGG
* * *
162972 GATACTCTAGCCTC
65 GATACTCCAACCCC
* * * **
162986 GTTTTTATTTTCAAAAATATCAATTTTTTATCTCGAGGATACTTTAACCCCATTATTTCTGAGGG
1 ATTTTTA-TTTCAAAAATATAAATTTTTCATCTCGAGGATACTCCAACCCCATTATTTCTGAGGG
163051 GATACTCCAACCCC
65 GATACTCCAACCCC
** * *
163065 ATTTTTATTTTCAAAAATATTGATTTTTCATCTCG-GAGATACTCCAGCCCCATTATTT-TCGAA
1 ATTTTTA-TTTCAAAAATATAAATTTTTCATCTCGAG-GATACTCCAACCCCATTATTTCT-GAG
163128 GGGATACTCCAACCCC
63 GGGATACTCCAACCCC
* * * * *
163144 GTCTTTACTTCAAAAATATTAAAATTTTCATCTCAAGGATACTCCAACCCCA-TA-TTCTGAAGG
1 ATTTTTATTTCAAAAATA-TAAATTTTTCATCTCGAGGATACTCCAACCCCATTATTTCTG-AGG
*
163207 GG-CACTCCAACC
64 GGATACTCCAACC
163219 TTGCCTCTTT
Statistics
Matches: 256, Mismatches: 42, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
75 4 0.02
76 43 0.17
77 26 0.10
78 23 0.09
79 159 0.62
80 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (78 bp):
ATTTTTATTTCAAAAATATAAATTTTTCATCTCGAGGATACTCCAACCCCATTATTTCTGAGGGG
ATACTCCAACCCC
Found at i:166227 original size:30 final size:29
Alignment explanation
Indices: 166188--166275 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
166178 TCATCAAGTT
166188 TTTCCTCATTTAACTATATTCGGTCAAATA
1 TTTCCTCATTTAACTATATT-GGTCAAATA
* ** * *
166218 TTTCATCATTGGACTATAATTGATC-AATT
1 TTTCCTCATTTAACTAT-ATTGGTCAAATA
*
166247 TTTCTCTCATTTAACTGTATTTGGTCAAA
1 TTTC-CTCATTTAACTATA-TTGGTCAAA
166276 CTCGTTTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
29 8 0.18
30 31 0.70
31 5 0.11
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTCCTCATTTAACTATATTGGTCAAATA
Found at i:166299 original size:35 final size:34
Alignment explanation
Indices: 166260--166459 Score: 183
Period size: 35 Copynumber: 5.9 Consensus size: 34
166250 CTCTCATTTA
* *
166260 ACTGTATTTGGTCAAACTCGTTTTATCATTGTTTG
1 ACTGTATCTGGTCAAACTC-TTTCATCATTGTTTG
* * *
166295 ACTGTATCTGGTCAAACACTTTCCATCATTATTTA
1 ACTGTATCTGGTCAAACTCTTT-CATCATTGTTTG
* * * * *
166330 ACTATATCTAGTCAAA-TCCTTT-TTAATTATTTG
1 ACTGTATCTGGTCAAACT-CTTTCATCATTGTTTG
* *
166363 ATTGTATCTGGTCAAACTCTTTCCATCATTGTTTA
1 ACTGTATCTGGTCAAACTCTTT-CATCATTGTTTG
* * * *
166398 ACTGCATCTAGTCAAACTCATTCCATCATTGTTGG
1 ACTGTATCTGGTCAAACTC-TTTCATCATTGTTTG
166433 ACTGTATCTGGTCAAACT-TTTC-TCATT
1 ACTGTATCTGGTCAAACTCTTTCATCATT
166460 TTGGTCTGAC
Statistics
Matches: 132, Mismatches: 27, Indels: 15
0.76 0.16 0.09
Matches are distributed among these distances:
32 5 0.04
33 28 0.21
34 4 0.03
35 93 0.70
36 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (34 bp):
ACTGTATCTGGTCAAACTCTTTCATCATTGTTTG
Found at i:166378 original size:68 final size:70
Alignment explanation
Indices: 166255--166449 Score: 232
Period size: 68 Copynumber: 2.8 Consensus size: 70
166245 TTTTTCTCTC
* * * * *
166255 ATTTAACTGTATTTGGTCAAACTCGTTTTATCATTGTTTGACTGTATCTGGTCAAACACTTTCCA
1 ATTTAACTGTATCTAGTCAAACTCCTTTTATAATTATTTGACTGTATCTGGTCAAACACTTTCCA
166320 TCATT
66 TCATT
* * *
166325 ATTTAACTATATCTAGTCAAA-TCCTTTT-TAATTATTTGATTGTATCTGGTCAAACTCTTTCCA
1 ATTTAACTGTATCTAGTCAAACTCCTTTTATAATTATTTGACTGTATCTGGTCAAACACTTTCCA
166388 TCATT
66 TCATT
* * * ** * * *
166393 GTTTAACTGCATCTAGTCAAACTCATTCCATCATTGTTGGACTGTATCTGGTCAAAC
1 ATTTAACTGTATCTAGTCAAACTCCTTTTATAATTATTTGACTGTATCTGGTCAAAC
166450 TTTTCTCATT
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
68 54 0.51
69 10 0.10
70 41 0.39
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (70 bp):
ATTTAACTGTATCTAGTCAAACTCCTTTTATAATTATTTGACTGTATCTGGTCAAACACTTTCCA
TCATT
Found at i:166441 original size:103 final size:103
Alignment explanation
Indices: 166262--166448 Score: 250
Period size: 103 Copynumber: 1.8 Consensus size: 103
166252 CTCATTTAAC
* * * * * *
166262 TGTATTTGGTCAAACTCGTTTTATCATTGTTTGACTGTATCTGGTCAAACACTTTCCATCATTAT
1 TGTATCTGGTCAAACTCGTTTCATCATTGTTTAACTGCATCTAGTCAAACACATTCCATCATTAT
*
166327 TTAACTATATCTAGTCAAATCCTTTTTAATTATTTGAT
66 TGAACTATATCTAGTCAAATCCTTTTTAATTATTTGAT
* *
166365 TGTATCTGGTCAAACTC-TTTCCATCATTGTTTAACTGCATCTAGTCAAACTCATTCCATCATTG
1 TGTATCTGGTCAAACTCGTTT-CATCATTGTTTAACTGCATCTAGTCAAACACATTCCATCATTA
* * *
166429 TTGGACTGTATCTGGTCAAA
65 TTGAACTATATCTAGTCAAA
166449 CTTTTCTCAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
102 3 0.04
103 68 0.96
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (103 bp):
TGTATCTGGTCAAACTCGTTTCATCATTGTTTAACTGCATCTAGTCAAACACATTCCATCATTAT
TGAACTATATCTAGTCAAATCCTTTTTAATTATTTGAT
Done.