Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2486
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: 43778
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1378 original size:20 final size:20
Alignment explanation
Indices: 1353--1457 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
1343 TTTTTACAAT
1353 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1373 TTGTATCGATACATTCTGGGTTTTACCCA
1 TTGTATCGATACA-T-T--G--TT---CA
*
1402 GATGTATCGATACATT-TCTCA
1 -TTGTATCGATACATTGT-TCA
*
1423 TTGTATCGATACGTTGTTCA
1 TTGTATCGATACATTGTTCA
1443 TTGTATCGATACATT
1 TTGTATCGATACATT
1458 CTGGGTTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
20 43 0.62
21 4 0.06
22 1 0.01
23 1 0.01
24 2 0.03
26 2 0.03
28 1 0.01
29 3 0.04
30 12 0.17
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1427 original size:70 final size:70
Alignment explanation
Indices: 1353--1507 Score: 256
Period size: 70 Copynumber: 2.2 Consensus size: 70
1343 TTTTTACAAT
1353 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATT
1418 TCTCA
66 TCTCA
* * *
1423 TTGTATCGATACGTTGTTCATTGTATCGATACATTCTGGGTTTTACCTAGATGTATTGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATT
*
1488 TTTCA
66 TCTCA
* *
1493 ATGTATCAATACATT
1 TTGTATCGATACATT
1508 CAAGTATTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 78 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (70 bp):
TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATT
TCTCA
Found at i:3659 original size:79 final size:79
Alignment explanation
Indices: 3528--3684 Score: 215
Period size: 79 Copynumber: 2.0 Consensus size: 79
3518 TCTTTCAAGT
** *
3528 TTTTATTTTTAAAACACCGATTTTCCACAATCGAGGATAATCAAACCCCGTTATTTTCGAAGGGA
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATAATCAAACCCCGTTATTTTCGAAGGGA
*
3593 TACTCCAACCCCGA
66 TACTCAAACCCCGA
* * * * * * *
3607 TTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATAATCAAACCCCGTTATTTTCGAAGGGA
3672 TACTCAAACCCCG
66 TACTCAAACCCCG
3685 CTATTTCCGA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (79 bp):
TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATAATCAAACCCCGTTATTTTCGAAGGGA
TACTCAAACCCCGA
Found at i:3681 original size:28 final size:28
Alignment explanation
Indices: 3639--3710 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
3629 TTTCACAATC
* * *
3639 GGGGATACTCCAACCTCGTTATTTTCGA
1 GGGGATACTCCAACCCCGCTATTTCCGA
*
3667 GGGGATACTCAAACCCCGCTATTTCCGA
1 GGGGATACTCCAACCCCGCTATTTCCGA
3695 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
3711 TGGTTTTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGCTATTTCCGA
Found at i:3690 original size:107 final size:107
Alignment explanation
Indices: 3562--3898 Score: 460
Period size: 107 Copynumber: 3.1 Consensus size: 107
3552 CCACAATCGA
*
3562 GGATAATCAAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAA
1 GGATACTCAAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAA
* *
3627 TTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGAGG
66 TTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGG
* * * * * *
3669 GGATACTCAAACCCCGCTATTTCCGAGGGGATACTCCAACCCTGGTTTTGTTTCCAAAACATCAA
1 GGATACTCAAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAA
* * *
3734 TTTTTCACAACCGAGGATACTCCAACCCCGTTATTTTTGAAG
66 TTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGG
* * * * * *
3776 GGATACTCCAACCCTGTTA-TTTCCAAGGGGATACTCCAACCCCAATTTTATTTTCAAAATATCA
1 GGATACTCAAACCCCGTTATTTTCGAA-GGGATACTCCAACCCCGATTTTATTTCCAAAACATCA
* * *
3840 ATTTTTCATAATCAAGGATACTCCAACCCCGTTGTTTTCGAGG
65 ATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGG
*
3883 GGATACTCCAACCCCG
1 GGATACTCAAACCCCG
3899 GTTTTATTTC
Statistics
Matches: 198, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
106 4 0.02
107 194 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGATACTCAAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAA
TTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGG
Found at i:3788 original size:28 final size:28
Alignment explanation
Indices: 3748--3818 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
3738 TCACAACCGA
**
3748 GGATACTCCAACCCCGTTATTTTTGAA-G
1 GGATACTCCAACCCCGTTA-TTTCCAAGG
*
3776 GGATACTCCAACCCTGTTATTTCCAAGG
1 GGATACTCCAACCCCGTTATTTCCAAGG
3804 GGATACTCCAACCCC
1 GGATACTCCAACCCC
3819 AATTTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 5 0.13
28 33 0.87
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCCAAGG
Found at i:3859 original size:79 final size:79
Alignment explanation
Indices: 3776--3923 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 79
3766 ATTTTTGAAG
* * * *
3776 GGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTTCAAAATATCAA
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAA
3841 TTTTTCATAATCAA
66 TTTTTCATAATCAA
* * * **
3855 GGATACTCCAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAA
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAA
3920 TTTT
66 TTTT
3924 CCACCATTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 60 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAA
TTTTTCATAATCAA
Found at i:3938 original size:79 final size:79
Alignment explanation
Indices: 3774--3947 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 79
3764 TTATTTTTGA
* * * *
3774 AGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTTCAAAATATC
1 AGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACC
* *
3839 AATTTTTCATAATC
66 AATTTTCCACAATC
* * * * **
3853 AAGGATACTCCAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACC
1 AGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACC
* *
3918 AATTTTCCACCATT
66 AATTTTCCACAATC
* *
3932 GGGGATACTCTAACCC
1 AGGGATACTCCAACCC
3948 TGATTTTATT
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (79 bp):
AGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACC
AATTTTCCACAATC
Found at i:3941 original size:51 final size:51
Alignment explanation
Indices: 3881--4000 Score: 150
Period size: 51 Copynumber: 2.4 Consensus size: 51
3871 TTGTTTTCGA
* * *
3881 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* * * * * *
3932 GGGGATACTCTAACCCTGATTTTATTTCCAGAACATCGATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
3983 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
4001 TTATTTTTGA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:3956 original size:130 final size:128
Alignment explanation
Indices: 3802--4202 Score: 525
Period size: 130 Copynumber: 3.1 Consensus size: 128
3792 TTATTTCCAA
* * * *
3802 GGGGATACTCCAACCCCAATTTTATTTTCAAAATATCAATTTTTCATAATCAAGGATACTCCAAC
1 GGGGATACTCCAACCCTAATTTTATTTCCAAAA-ATCGATTTTTCA-AATCAGGGATACTCCAAC
* * *
3867 CCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATT
64 CCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATC
* * *
3932 GGGGATACTCTAACCCTGATTTTATTTCCAGAACATCGATTTTTCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCTAATTTTATTTCCA-AAAATCGATTTTTCA-AATCAGGGATACTCCAAC
* * *
3997 CCCGTTATTTTTGAGGGGATACTCCAACCCCAATTTTATTTTCAAAACA-CAATTTTCCACCATC
64 CCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATC
** * * ** *
4061 AAGGAAACTCCATCTTTAATTTTATTTCCAGAAAATCGATTTTTCAATATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTAATTTTATTTCCA-AAAATCGATTTTTCAA-ATCAGGGATACTCCAAC
* * *
4126 CCCGTTATTTTCGAAGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCGATTTTCCACAATC
64 CCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATC
*
4191 GGAGATACTCCA
1 GGGGATACTCCA
4203 GCCCCGTTAT
Statistics
Matches: 234, Mismatches: 34, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
128 1 0.00
129 112 0.48
130 119 0.51
131 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (128 bp):
GGGGATACTCCAACCCTAATTTTATTTCCAAAAATCGATTTTTCAAATCAGGGATACTCCAACCC
CGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATC
Found at i:4124 original size:129 final size:130
Alignment explanation
Indices: 3808--4186 Score: 505
Period size: 129 Copynumber: 2.9 Consensus size: 130
3798 CCAAGGGGAT
* * * *
3808 ACTCCAACCCCAATTTTATTTTCA-AAATATCAATTTTTC-ATAATCAAGGATACTCCAACCCCG
1 ACTCCAACCCTAATTTTATTTCCAGAAA-ATCGATTTTTCAAT-ATCAGGGATACTCCAACCCCG
* * ***
3871 TTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATTGGGG
64 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGG
*
3936 AT
129 AA
* * *
3938 ACTCTAACCCTGATTTTATTTCCAGAACATCGATTTTTCACA-ATCAGGGATACTCCAACCCCGT
1 ACTCCAACCCTAATTTTATTTCCAGAAAATCGATTTTTCA-ATATCAGGGATACTCCAACCCCGT
* * *
4002 TATTTTTGAGGGGATACTCCAACCCCAATTTTATTTTCAAAACA-CAATTTTCCACCATCAAGGA
65 TATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGGA
4066 A
130 A
* ** *
4067 ACTCCATCTTTAATTTTATTTCCAGAAAATCGATTTTTCAATATCGGGGATACTCCAACCCCGTT
1 ACTCCAACCCTAATTTTATTTCCAGAAAATCGATTTTTCAATATCAGGGATACTCCAACCCCGTT
* *
4132 ATTTTCGAAGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCGATTTTCCAC
66 ATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCAC
4187 AATCGGAGAT
Statistics
Matches: 216, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
128 1 0.00
129 112 0.52
130 100 0.46
131 2 0.01
132 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.33
Consensus pattern (130 bp):
ACTCCAACCCTAATTTTATTTCCAGAAAATCGATTTTTCAATATCAGGGATACTCCAACCCCGTT
ATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGGAA
Found at i:4198 original size:79 final size:77
Alignment explanation
Indices: 4080--4251 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 77
4070 CCATCTTTAA
* * *
4080 TTTTATTTCCAGAAAATCGATTTTTCAATATCGGGGATACTCCAACCCCGTTATTT-TCGAAGGG
1 TTTTATTTCCA-AAAACCGATTTTCCAATATCGGAGATACTCCAACCCCGTTATTTCT-GAAGGG
4144 ATACTCCAACCCCAG
64 ATACTCCAACCCC-G
*
4159 TTTTATTTCCAAAACACCGATTTTCCACA-ATCGGAGATACTCCAGCCCCGTTATTTCTGAAGGG
1 TTTTATTTCCAAAA-ACCGATTTTCCA-ATATCGGAGATACTCCAACCCCGTTATTTCTGAAGGG
* *
4223 CTACTCTAACCCCG
64 ATACTCCAACCCCG
*
4237 TCTTTATCTCCAAAA
1 T-TTTATTTCCAAAA
4252 TATTAAATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
78 5 0.06
79 75 0.91
80 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (77 bp):
TTTTATTTCCAAAAACCGATTTTCCAATATCGGAGATACTCCAACCCCGTTATTTCTGAAGGGAT
ACTCCAACCCCG
Found at i:6797 original size:34 final size:35
Alignment explanation
Indices: 6759--6825 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
6749 CCGTACAACA
6759 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
6793 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
6826 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:7301 original size:13 final size:13
Alignment explanation
Indices: 7283--7308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7273 CAATTTTTTG
7283 TGTATCGATACAT
1 TGTATCGATACAT
7296 TGTATCGATACAT
1 TGTATCGATACAT
7309 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:7320 original size:32 final size:33
Alignment explanation
Indices: 7263--7326 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
7253 TACAAGCCAA
**
7263 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
7296 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
7327 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:7403 original size:20 final size:21
Alignment explanation
Indices: 7355--7410 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
7345 AAATCCCAAT
**
7355 AACATGTATCGATACATCTTT
1 AACATGTATCGATACATCTGC
**
7376 TTCATGTATCGATACAT-TGC
1 AACATGTATCGATACATCTGC
7396 AACATGTATCGATAC
1 AACATGTATCGATAC
7411 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (21 bp):
AACATGTATCGATACATCTGC
Found at i:9558 original size:84 final size:84
Alignment explanation
Indices: 9406--9567 Score: 195
Period size: 84 Copynumber: 1.9 Consensus size: 84
9396 TTTCCACTTG
* * * *
9406 CAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAACTCA
1 CAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACTCA
9471 TTGATTTACTTTCATTTTC
66 TTGATTTACTTTCATTTTC
* * *
9490 CAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTACAC
1 CAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTAAAC
* *
9552 TTATTGATTTATTTTC
63 TCATTGATTTACTTTC
9568 TTCTTTGAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.14
84 51 0.77
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.52
Consensus pattern (84 bp):
CAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACTCA
TTGATTTACTTTCATTTTC
Found at i:11637 original size:13 final size:13
Alignment explanation
Indices: 11619--11644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11609 CAATTTTTTG
11619 TGTATCGATACAT
1 TGTATCGATACAT
11632 TGTATCGATACAT
1 TGTATCGATACAT
11645 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:11656 original size:32 final size:33
Alignment explanation
Indices: 11599--11662 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
11589 TACAAGCCAA
**
11599 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
11632 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
11663 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:15524 original size:70 final size:70
Alignment explanation
Indices: 15450--15604 Score: 229
Period size: 70 Copynumber: 2.2 Consensus size: 70
15440 TTTTCACAAT
* * **
15450 TTGTATTGATACATTGTTCATTGTATCGATACATTCTAGGTTTTTCCCAGATGTTTTGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTACTGATACATT
*
15515 GTTCG
66 GTTCA
* *
15520 TTGTATCGATACGTTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTACTGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTACTGATACATT
*
15585 TTTCA
66 GTTCA
*
15590 ATGTATCGATACATT
1 TTGTATCGATACATT
15605 CAGGCATTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (70 bp):
TTGTATCGATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTACTGATACATT
GTTCA
Found at i:15536 original size:20 final size:20
Alignment explanation
Indices: 15507--15554 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
15497 CAGATGTTTT
*
15507 GATACATTGTTCGTTGTATC
1 GATACATTGTTCATTGTATC
*
15527 GATACGTTGTTCATTGTATC
1 GATACATTGTTCATTGTATC
15547 GATACATT
1 GATACATT
15555 CTGGGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (20 bp):
GATACATTGTTCATTGTATC
Found at i:17305 original size:79 final size:79
Alignment explanation
Indices: 17194--17341 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 79
17184 TCACTCATGT
* * * * **
17194 TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCAAACCCCGTTATTTTTGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCGTTATTTTCAAGGGGA
17259 TACTTTAACCCCAG
66 TACTTTAACCCCAG
* * * *
17273 TTTTGTTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTCAAGGGGA
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCGTTATTTTCAAGGGGA
17338 TACT
66 TACT
17342 CAAACCCCGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (79 bp):
TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCGTTATTTTCAAGGGGA
TACTTTAACCCCAG
Found at i:17347 original size:28 final size:28
Alignment explanation
Indices: 17305--17376 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
17295 TTCCACAATC
* *
17305 GGGGATACTCCAACCTCGTTATTTTCAA
1 GGGGATACTCAAACCCCGTTATTTTCAA
**
17333 GGGGATACTCAAACCCCGTTATTTTTGA
1 GGGGATACTCAAACCCCGTTATTTTCAA
*
17361 GGGGATACTCGAACCC
1 GGGGATACTCAAACCC
17377 GATTTTGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (28 bp):
GGGGATACTCAAACCCCGTTATTTTCAA
Found at i:17421 original size:106 final size:106
Alignment explanation
Indices: 17226--17565 Score: 475
Period size: 107 Copynumber: 3.2 Consensus size: 106
17216 TTTCATAATC
** *
17226 GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTTTAACCCCAGTTTTGTTTCCAAAACATC
1 GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTCCAACCCGA-TTTTGTTTCCAAAACATC
**
17291 AATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTCAA
65 AATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTTGA
*
17333 GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTCGAACCCGATTTTGTTTCCAAAACATCA
1 GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTCCAACCCGATTTTGTTTCCAAAACATCA
*
17398 ATTTTCCACAACCGGGGATACTCCAACCTCGTTATTTTTGA
66 ATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTTGA
* * * * ** * * * *
17439 GGAGATACTCTAACCCTGTTATCTCCGAGGGGATACCCCAACCTCGGTTTTATTTTCAAAACATC
1 GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTCCAACC-CGATTTTGTTTCCAAAACATC
*
17504 AATTTTCCACAATCGGGGATACTCCAACC-CTATTATTTTTGA
65 AATTTTCCACAATCGGGGATACTCCAACCTC-GTTATTTTTGA
*
17546 GGGGATACTCCAACCCCGTT
1 GGGGATACTCAAACCCCGTT
17566 TTTATTTTCA
Statistics
Matches: 209, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
106 93 0.44
107 116 0.56
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (106 bp):
GGGGATACTCAAACCCCGTTATTTTTGAGGGGATACTCCAACCCGATTTTGTTTCCAAAACATCA
ATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTTGA
Found at i:17573 original size:79 final size:79
Alignment explanation
Indices: 17442--17690 Score: 309
Period size: 79 Copynumber: 3.2 Consensus size: 79
17432 TTTTTGAGGA
* * * * * *
17442 GATACTCTAACCCTGTTATCTCCGAGGGGATACCCCAACCTCGGTTTTATTTTCAAAACATCAAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAACATCAAT
*
17507 TTTCCACAATCGGG
66 TTTCCACAATCAGG
* * * *
17521 GATACTCCAACCCTATTATTTTTGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAATATCGAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAACATCAAT
*
17586 TTTCCACAATCAAG
66 TTTCCACAATCAGG
* * * * * *
17600 AATACTACAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGTTTTTATTTCCAAAACACCAAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAACATCAAT
* **
17665 TTTCCACCATTTGG
66 TTTCCACAATCAGG
17679 GATACTCCAACC
1 GATACTCCAACC
17691 TTGATTTTAT
Statistics
Matches: 142, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 142 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAACATCAAT
TTTCCACAATCAGG
Found at i:17689 original size:51 final size:51
Alignment explanation
Indices: 17625--17743 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
17615 TTGTTTTCGA
* * *
17625 GGGGATACTCCAACCCCGTTTTTATTTCCAAAACACCAATTTTCCACCATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* ** * ** * *
17676 TGGGATACTCCAACCTTGATTTTATTTTCTGAACATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
17727 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
17744 ATTATTTTTG
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:17856 original size:129 final size:130
Alignment explanation
Indices: 17548--17920 Score: 478
Period size: 129 Copynumber: 2.9 Consensus size: 130
17538 ATTTTTGAGG
* * * ** * *
17548 GGATACTCCAACCCCGTTTTTATTTTCAAAATATCGATTTTCCACAATCAAGAATACTACAACCC
1 GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCC
* * * ***
17613 CGTTGTTTTCGAGGGGATACTCCAACCCCGTTTTTATTTCCAAAACACCAATTTTCCACCATTTG
66 CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
* **
17678 GGATACTCCAACCTTGATTTTATTTTCTGAACATCGATTTTCCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCC
* * * *
17743 CATTATTTTTGAGGGAAAACTCCAACCCCGGTTTTATTTTCAAAACA-CAATTTTCCACCATCAA
66 CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
* * * * *
17807 GGATACTCCATCCCTGATTTTATTTCCAAAACATCAATTTTCCACAATCGGGGACACTCCAACCA
1 GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCC
* * * *
17872 CATTATTTTCGAGGGGATACTTCAACCCCAGTTTTATTTCTAGAACACC
66 CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACC
17921 GTTATTTCTC
Statistics
Matches: 206, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
129 110 0.53
130 96 0.47
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (130 bp):
GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCC
CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
Found at i:23780 original size:19 final size:20
Alignment explanation
Indices: 23736--23780 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
23726 TGTTTCAATT
*
23736 CATTGTTCATTGTATTGATA
1 CATTGTTCATTGTATCGATA
*
23756 CGTTGTTCATT-TATCGATA
1 CATTGTTCATTGTATCGATA
23775 CATTGT
1 CATTGT
23781 ATCGATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (20 bp):
CATTGTTCATTGTATCGATA
Found at i:25670 original size:28 final size:28
Alignment explanation
Indices: 25638--25736 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
25628 TTCCAAAAAC
25638 GGGGATACTCCAACCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
25666 GGGGATACTCCAACCCTATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
* * *
25694 GGGGATACTCAAACCACATTATTTCCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
25722 GGGGATACTCCAACC
1 GGGGATACTCCAACC
25737 TCGATTTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:25803 original size:135 final size:134
Alignment explanation
Indices: 25560--25843 Score: 424
Period size: 135 Copynumber: 2.1 Consensus size: 134
25550 TTTCACAATC
* * * * *
25560 GGGGATACTCAAACCCCGTTATTTTCGAAAGGATCTCCAATCTTGATTTTATTTCCAAAACATCA
1 GGGGATACTCAAACCACATTATTTCCGAAAGGATCTCCAACCTCGATTTTATTTCCAAAACATCA
* *
25625 ACTTTCCAAAAACGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTATTATTT
66 ACTTTCCAAAAACGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCAAACCCCATTATTT
25690 TCGA
131 TCGA
**
25694 GGGGATACTCAAACCACATTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACATC
1 GGGGATACTCAAACCACATTATTTCCGAAAGGAT-CTCCAACCTCGATTTTATTTCCAAAACATC
* * * * *
25759 AATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCAAACCCCATTATT
65 AACTTTCCAAAAACGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCAAACCCCATTATT
25824 TTCGA
130 TTCGA
*
25829 GGGGATACTCCAACC
1 GGGGATACTCAAACC
25844 CCAGTTTTAT
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
134 29 0.22
135 105 0.78
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (134 bp):
GGGGATACTCAAACCACATTATTTCCGAAAGGATCTCCAACCTCGATTTTATTTCCAAAACATCA
ACTTTCCAAAAACGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCAAACCCCATTATTT
TCGA
Found at i:25815 original size:28 final size:28
Alignment explanation
Indices: 25773--25846 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
25763 TTCCACAATC
* *
25773 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
25801 GGGGATACTCAAACCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
25829 GGGGATACTCCAACCCCA
1 GGGGATACTCCAACCCCA
25847 GTTTTATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:25884 original size:79 final size:78
Alignment explanation
Indices: 25801--25975 Score: 251
Period size: 79 Copynumber: 2.2 Consensus size: 78
25791 TTATTTTTGA
* *
25801 GGGGATACTCAAACCCCATTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATC
1 GGGGATACTC-AACCCCATTATTTTCGAGAGGATACTCCAACCCCAGCTTTATTTCCAAAACATC
25866 GATTTTTCACAATC
65 GATTTTTCACAATC
** ** * *
25880 GGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCTGGCTTTATTTTCAAAATATC
1 GGGGATACT-CAACCCCATTATTTTCGAGAGGATACTCCAACCCCAGCTTTATTTCCAAAACATC
25945 GATTTTTCACAATC
65 GATTTTTCACAATC
25959 GGGGATACTTCAACCCC
1 GGGGATAC-TCAACCCC
25976 GATTTTATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 83 0.98
80 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (78 bp):
GGGGATACTCAACCCCATTATTTTCGAGAGGATACTCCAACCCCAGCTTTATTTCCAAAACATCG
ATTTTTCACAATC
Found at i:25923 original size:107 final size:107
Alignment explanation
Indices: 25666--25923 Score: 410
Period size: 107 Copynumber: 2.4 Consensus size: 107
25656 TTATTTTCGA
* *
25666 GGGGATACTCCAACCCTATTATTTTCGAGGGGATACTCAAACCACATTATTTCCGAGGGGATACT
1 GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCAAACCCCATTATTTCCGAGGGGATACT
*
25731 CCAACCTCGATTTTATTTCCAAAACATCAATTTTCCACAATC
66 CCAACCCCGATTTTATTTCCAAAACATCAATTTTCCACAATC
* * *
25773 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCAAACCCCATTATTTTCGAGGGGATACT
1 GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCAAACCCCATTATTTCCGAGGGGATACT
* *
25838 CCAACCCC-AGTTTTATTTCCAAAACATCGATTTTTCACAATC
66 CCAACCCCGA-TTTTATTTCCAAAACATCAATTTTCCACAATC
* *
25880 GGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCC
1 GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCAAACCC
25924 TGGCTTTATT
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
106 1 0.01
107 137 0.99
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCAAACCCCATTATTTCCGAGGGGATACT
CCAACCCCGATTTTATTTCCAAAACATCAATTTTCCACAATC
Found at i:25973 original size:51 final size:51
Alignment explanation
Indices: 25910--26078 Score: 205
Period size: 51 Copynumber: 3.3 Consensus size: 51
25900 ATTTTCGAGA
** *
25910 GGATACTCCAACCCTGGCTTTATTTTCAAAATATCGATTTTTCACAATCGG
1 GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTTCACAATCGG
* * * * * * *
25961 GGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACCATTGG
1 GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTTCACAATCGG
* * *
26012 GGATACTCCAACTCTGATTTTA-TTTCTATAACATCGATTTTCCACAATCGG
1 GGATACTCCAACCCTGATTTTATTTTC-AAAACATCGATTTTTCACAATCGG
26063 GGATACTCCAACCCTG
1 GGATACTCCAACCCTG
26079 TTATTTTTGA
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
50 3 0.03
51 93 0.97
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
GGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTTCACAATCGG
Found at i:26072 original size:181 final size:180
Alignment explanation
Indices: 25829--26207 Score: 458
Period size: 181 Copynumber: 2.1 Consensus size: 180
25819 TTATTTTCGA
*
25829 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAAC
* * *
25894 CCTGTTATTTTCG-AGAGGATACTCCAACC-CTGGCTTTATTTTCAAAATATCGATTTTTCACAA
66 CCTGTTATTTTCGAAG-GGATACTCCAACCTC-GGCTTTATTTTCAAAACA-CAATTTTCCACAA
* * *
25957 TCGGGGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACCATT
128 TCGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACCATT
* * * *
26010 GGGGATACTCCAA-CTCTGATTTTATTTCTATAACATCGATTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAA
* * * * *
26074 CCCTGTTATTTTTGAAGGGATACTTCAACTTCGGTTTTATTTTCAAAACACAATTTTCCACCATC
65 CCCTGTTATTTTCGAAGGGATACTCCAACCTCGGCTTTATTTTCAAAACACAATTTTCCACAATC
* * * * ** * * ** *
26139 GAGGATACTCCATCCCTAATTTTATTTTCAGAACTTCGATTTTCCATAATC
130 GAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACCATT
26190 GGGGATACTCCAACCCCA
1 GGGGATACTCCAACCCCA
26208 TTATTTTCGA
Statistics
Matches: 165, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
180 65 0.39
181 97 0.59
182 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (180 bp):
GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAAC
CCTGTTATTTTCGAAGGGATACTCCAACCTCGGCTTTATTTTCAAAACACAATTTTCCACAATCG
AGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACCATT
Found at i:26103 original size:79 final size:78
Alignment explanation
Indices: 26011--26155 Score: 186
Period size: 78 Copynumber: 1.8 Consensus size: 78
26001 TTCACCATTG
* * *
26011 GGGATACTCCAAC-TCTGATTTTA-TTTCTATAACATCGATTTTCCACAATCGGGGATACTCCAA
1 GGGATACTCCAACTTC-GATTTTATTTTC-AAAACA-CAATTTTCCACAATCGAGGATACTCCAA
26074 CCCTGTTATTTTTGAA
63 CCCTGTTATTTTTGAA
* * * *
26090 GGGATACTTCAACTTCGGTTTTATTTTCAAAACACAATTTTCCACCATCGAGGATACTCCATCCC
1 GGGATACTCCAACTTCGATTTTATTTTCAAAACACAATTTTCCACAATCGAGGATACTCCAACCC
26155 T
66 T
26156 AATTTTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
78 28 0.49
79 23 0.40
80 6 0.11
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (78 bp):
GGGATACTCCAACTTCGATTTTATTTTCAAAACACAATTTTCCACAATCGAGGATACTCCAACCC
TGTTATTTTTGAA
Found at i:26191 original size:129 final size:129
Alignment explanation
Indices: 25960--26263 Score: 405
Period size: 129 Copynumber: 2.3 Consensus size: 129
25950 TTCACAATCG
* * * * * *
25960 GGGATACTTCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACCATTGGGGATACTCCAACT
1 GGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACCATCGAGGATACTCCAACC
* * ** *
26025 CTGATTTTATTTCTATAACATCGATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTTTGAA
66 CTAATTTTATTTCTAGAACATCGATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCG-A
** *
26090 GGGATACTTCAACTTCGGTTTTATTTTCAAAACA-CAATTTTCCACCATCGAGGATACTCCATCC
1 GGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACCATCGAGGATACTCCAACC
* *
26154 CTAATTTTATTT-TCAGAACTTCGATTTTCCATAATCGGGGATACTCCAACCCCATTATTTTCGA
66 CTAATTTTATTTCT-AGAACATCGATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCGA
* *
26218 GTGGATACTTAAACCCCAGTTTTATTTTCAAAACACCAATTTTCCA
1 G-GGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCA
26264 AAACCGGGGA
Statistics
Matches: 151, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
128 3 0.02
129 108 0.72
130 40 0.26
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (129 bp):
GGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACCATCGAGGATACTCCAACC
CTAATTTTATTTCTAGAACATCGATTTTCCACAATCGGGGATACTCCAACCCCATTATTTTCGA
Found at i:32095 original size:7 final size:7
Alignment explanation
Indices: 32083--32108 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
32073 TTGAAAATAA
32083 ATTTGGC
1 ATTTGGC
32090 ATTTGGC
1 ATTTGGC
32097 ATTTGGC
1 ATTTGGC
32104 ATTTG
1 ATTTG
32109 ACAAAGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (7 bp):
ATTTGGC
Found at i:32206 original size:16 final size:16
Alignment explanation
Indices: 32185--32221 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
32175 TTTAATTATT
*
32185 TTATTAAGGGGGAGAA
1 TTATTAAAGGGGAGAA
*
32201 TTATTAAAGGGGAGAT
1 TTATTAAAGGGGAGAA
32217 TTATT
1 TTATT
32222 GAAAATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (16 bp):
TTATTAAAGGGGAGAA
Found at i:32966 original size:13 final size:13
Alignment explanation
Indices: 32948--32977 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
32938 GATACATGGG
*
32948 ACATTGTATCTAT
1 ACATTGTATCGAT
32961 ACATTGTATCGAT
1 ACATTGTATCGAT
32974 ACAT
1 ACAT
32978 GGTAAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:32975 original size:33 final size:33
Alignment explanation
Indices: 32932--33000 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
32922 CTAAGTGAAA
* * * *
32932 TGTATGGATACATGGGACATTGTATCTATACAT
1 TGTATCGATACATGGGAAAATGTATCGATACAT
*
32965 TGTATCGATACATGGTAAAATGTATCGATACAT
1 TGTATCGATACATGGGAAAATGTATCGATACAT
32998 TGT
1 TGT
33001 GCCCAACGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATGGGAAAATGTATCGATACAT
Found at i:33930 original size:21 final size:21
Alignment explanation
Indices: 33901--33941 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33891 TATCAGTAAG
*
33901 TTAATATAAAATTTTTAACAC
1 TTAACATAAAATTTTTAACAC
33922 TTAACATAAAATTTTTAACA
1 TTAACATAAAATTTTTAACA
33942 TTGTTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAACATAAAATTTTTAACAC
Found at i:34990 original size:22 final size:21
Alignment explanation
Indices: 34955--34996 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
34945 AAAAATGATA
*
34955 CATAATTTTATTATAATAATT
1 CATAATTATATTATAATAATT
34976 CATACATTATATTATAATAAT
1 CATA-ATTATATTATAATAAT
34997 ATGGTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
CATAATTATATTATAATAATT
Found at i:40395 original size:20 final size:22
Alignment explanation
Indices: 40370--40420 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
40360 TTCGTATTTT
40370 TATTATTTTTATAT-TTAA-AA
1 TATTATTTTTATATATTAATAA
40390 TATTATATTTTATATATTAATAA
1 TATTAT-TTTTATATATTAATAA
40413 T-TTATTTT
1 TATTATTTT
40421 ATTTTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 11 0.39
22 8 0.29
23 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTTTTATATATTAATAA
Found at i:40406 original size:14 final size:14
Alignment explanation
Indices: 40378--40448 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
40368 TTTATTATTT
* *
40378 TTATATTTAAAATA
1 TTATATTTTATATA
40392 TTATATTTTATATA
1 TTATATTTTATATA
*
40406 TTAATAATTTAT-T-
1 TT-ATATTTTATATA
40419 TTAT-TTTATATATA
1 TTATATTT-TATATA
*
40433 TT-TATATGTATATA
1 TTATAT-TTTATATA
40447 TT
1 TT
40449 CGTATTATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
11 2 0.04
12 5 0.11
13 4 0.09
14 26 0.57
15 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (14 bp):
TTATATTTTATATA
Found at i:40418 original size:25 final size:24
Alignment explanation
Indices: 40368--40431 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
40358 GATTCGTATT
40368 TTTATTAT-TTTTATAT-TTAAAA
1 TTTATTATATTTTATATATTAAAA
40390 --TATTATATTTTATATATTAATAA
1 TTTATTATATTTTATATATTAA-AA
*
40413 TTTATTTTATTTTATATAT
1 TTTATTATATTTTATATAT
40432 ATTTATATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 6 0.17
21 8 0.22
22 4 0.11
23 2 0.06
25 16 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATTATATTTTATATATTAAAA
Found at i:40468 original size:3 final size:3
Alignment explanation
Indices: 40460--40531 Score: 53
Period size: 3 Copynumber: 23.3 Consensus size: 3
40450 GTATTATGTG
*
40460 TTA TTA TTA TTA TTG TT- TT- TTA TTA TCTA TTTA TT- TATA TCTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA T-TA TTA
40505 TTTA TTA TTA TTA TTA TTA TTTA TTA T
1 -TTA TTA TTA TTA TTA TTA -TTA TTA T
40532 CTATCTATCT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
2 7 0.12
3 39 0.66
4 12 0.20
5 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40508 original size:16 final size:17
Alignment explanation
Indices: 40478--40535 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
40468 ATTATTGTTT
40478 TTTATTATC--TATTTA
1 TTTATTATCTATATTTA
40493 TTTA-TATCTATATTTA
1 TTTATTATCTATATTTA
40509 -TTATTAT-TAT-TATTA
1 TTTATTATCTATAT-TTA
40524 TTTATTATCTAT
1 TTTATTATCTAT
40536 CTATCTATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 16 0.43
17 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATCTATATTTA
Found at i:40510 original size:46 final size:46
Alignment explanation
Indices: 40460--40549 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
40450 GTATTATGTG
* * * * *
40460 TTATTATTATTATTGTTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
40506 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
40550 CTAACATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (46 bp):
TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
Found at i:41620 original size:23 final size:23
Alignment explanation
Indices: 41593--41637 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41583 AAAATTTACA
**
41593 TATTTATGTTTTTTATTATTTAT
1 TATTTATAATTTTTATTATTTAT
41616 TATTTATAATTTTTATTATTTA
1 TATTTATAATTTTTATTATTTA
41638 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTATAATTTTTATTATTTAT
Found at i:42801 original size:13 final size:12
Alignment explanation
Indices: 42783--42827 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
42773 AAAAACTTCA
42783 TATTTTTTATTT
1 TATTTTTTATTT
42795 GTATTTTTTATTTT
1 -TATTTTTTA-TTT
* *
42809 TAATTTTAATTT
1 TATTTTTTATTT
42821 TATTTTT
1 TATTTTT
42828 AAATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.32
13 16 0.57
14 3 0.11
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:42808 original size:6 final size:6
Alignment explanation
Indices: 42786--42828 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
42776 AACTTCATAT
* * *
42786 TTTTTA TTTGTA TTTTTTA TTTTTA ATTTTA ATTTTA TTTTTA
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
42829 AATTATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:42832 original size:13 final size:12
Alignment explanation
Indices: 42783--42839 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
42773 AAAAACTTCA
*
42783 TATTTTTTATTT
1 TATTTTTAATTT
*
42795 GTATTTTTTATTTT
1 -TA-TTTTTAATTT
*
42809 TAATTTTAATTT
1 TATTTTTAATTT
42821 TATTTTTAAATTAT
1 TATTTTT-AATT-T
42835 TATTT
1 TATTT
42840 AATGTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 14 0.39
13 8 0.22
14 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TATTTTTAATTT
Found at i:43748 original size:15 final size:15
Alignment explanation
Indices: 43716--43753 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
43706 ACTAATTAAT
43716 TTTTATTTATAATAAA
1 TTTT-TTTATAATAAA
43732 TTTTTTTA-AATATAA
1 TTTTTTTATAATA-AA
43747 TTTTTTT
1 TTTTTTT
43754 CATTGCACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTTATAATAAA
Done.