Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 1 of 27
Found at i:963 original size:18 final size:18
Alignment explanation
Indices: 930--973 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
920 TAATATAATT
*
930 TAATTAGAATTTAATTTTA
1 TAATTA-AAATTAATTTTA
949 TAATTAAAATTAATTTTA
1 TAATTAAAATTAATTTTA
*
967 AAATTAA
1 TAATTAA
974 TTATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATTAAAATTAATTTTA
Found at i:2165 original size:24 final size:24
Alignment explanation
Indices: 2133--2180 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2123 AGTAATTGTC
2133 AAACTTCAAAATTAAAATAAAGCT
1 AAACTTCAAAATTAAAATAAAGCT
2157 AAACTTCAAAATTAAAATAAAGCT
1 AAACTTCAAAATTAAAATAAAGCT
2181 TTCATGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (24 bp):
AAACTTCAAAATTAAAATAAAGCT
Found at i:3080 original size:26 final size:24
Alignment explanation
Indices: 3042--3089 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
3032 TTTGCTGGCG
3042 TTTTTGATTCTTCCTGAGGAATACA
1 TTTTTGATTCTT-CTGAGGAATACA
* *
3067 TTTTTGTTTCCTTCTTAGGAATA
1 TTTTTGATT-CTTCTGAGGAATA
3090 GAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (24 bp):
TTTTTGATTCTTCTGAGGAATACA
Found at i:7039 original size:20 final size:19
Alignment explanation
Indices: 6997--7049 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
6987 GTTACAAGGA
*
6997 ATGTATCGATACAATTCATC
1 ATGTATCGATAC-ATTCACC
*
7017 ATGTATCGATACATTGTACC
1 ATGTATCGATACATT-CACC
*
7037 ATGTATCAATACA
1 ATGTATCGATACA
7050 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTCACC
Found at i:7123 original size:19 final size:19
Alignment explanation
Indices: 7079--7134 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
7069 CTGCCAATTT
**
7079 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
7099 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
7118 CATGTATCGATACAATG
1 CATGTATCGATACAATG
7135 CATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:9614 original size:13 final size:13
Alignment explanation
Indices: 9596--9639 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
9586 GTTAAATAGT
9596 ATACAATGTATCG
1 ATACAATGTATCG
9609 ATACAATGTATCG
1 ATACAATGTATCG
9622 ATACAATGTATCG
1 ATACAATGTATCG
9635 ATACA
1 ATACA
9640 TCTGGGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
ATACAATGTATCG
Found at i:9673 original size:16 final size:16
Alignment explanation
Indices: 9652--9683 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9642 TGGGTTTTCC
9652 AGATGTATCGATACAT
1 AGATGTATCGATACAT
9668 AGATGTATCGATACAT
1 AGATGTATCGATACAT
9684 TTTGGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
AGATGTATCGATACAT
Found at i:10790 original size:13 final size:13
Alignment explanation
Indices: 10774--10798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10764 ATACATTGTT
10774 CATTGTATCGATA
1 CATTGTATCGATA
10787 CATTGTATCGAT
1 CATTGTATCGAT
10799 TTATTCTGGG
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:10844 original size:20 final size:20
Alignment explanation
Indices: 10819--10912 Score: 95
Period size: 20 Copynumber: 4.7 Consensus size: 20
10809 TTTACCCAGA
10819 TGTATCGATACATTTTGTAT
1 TGTATCGATACATTTTGTAT
*
10839 TGTATCGATACATTGCT-TAT
1 TGTATCGATACATT-TTGTAT
10859 TGTATCGATACA--TTGCTCAT
1 TGTATCGATACATTTTG-T-AT
* ** *
10879 TGTATCGATATATTTTACAA
1 TGTATCGATACATTTTGTAT
10899 TGTATCGATACATT
1 TGTATCGATACATT
10913 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.02
19 1 0.02
20 56 0.92
21 1 0.02
22 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTTGTAT
Found at i:13366 original size:51 final size:51
Alignment explanation
Indices: 13262--13374 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
13252 CTTTATCGAT
* * * * *
13262 GATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGCAATCGGG
1 GATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCAGG
* ** *
13313 GATACTCCAACTCTGATTTTATTT-TCAAAACACCAATTTTTCACAATTAGG
1 GATACTCCAACTCCGATTTTATTTCT-AAAACACCAATTTACCACAATCAGG
13364 GATACTCCAAC
1 GATACTCCAAC
13375 CTTGTTATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCAGG
Found at i:13394 original size:28 final size:28
Alignment explanation
Indices: 13362--13431 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
13352 TTCACAATTA
* **
13362 GGGATACTCCAACCTTGTTATTTTATCG
1 GGGATACTCCAACCTCGTTATTTTAGAG
*
13390 GGGATACTCCAACCTCGTTATTTTCGAG
1 GGGATACTCCAACCTCGTTATTTTAGAG
*
13418 GGGATAATCCAACC
1 GGGATACTCCAACC
13432 CCGGTTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (28 bp):
GGGATACTCCAACCTCGTTATTTTAGAG
Found at i:13507 original size:28 final size:28
Alignment explanation
Indices: 13470--13540 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
13460 TTTCATAATC
13470 GGGG-TACTCCAACCCCGTTATTTCATCA
1 GGGGATACTCCAACCCCGTTATTTCA-CA
* * *
13498 -GGGATACTCCAATCTCGTTATTTCAGA
1 GGGGATACTCCAACCCCGTTATTTCACA
*
13525 GGGGATACTCAAACCC
1 GGGGATACTCCAACCC
13541 TAATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 4 0.11
28 31 0.89
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCACA
Found at i:13568 original size:108 final size:107
Alignment explanation
Indices: 13310--13589 Score: 314
Period size: 108 Copynumber: 2.6 Consensus size: 107
13300 TACCGCAATC
* * * * *
13310 GGGGATACTCCAACTCTGATTTTATTT-TCAAAACACCAATTTTTCACAATTAGGGATACTCCAA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAAATACCAATTTTTCACAA-TCGGGGTACTCCAA
** * *
13374 CCTTGTTATTTTATCGGGGATACTCCAACCTCGTTATTTTCGA
65 CCCCGTTATTTCATCAGGGATACTCCAACCTCGTTATTTTCGA
* * * * **** *
13417 GGGGATAATCCAACCCCGGTTTTATATCTAAAAATATTGTTTTTTTCATAATCGGGGTACTCCAA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAAATA-CCAATTTTTCACAATCGGGGTACTCCAA
*
13482 CCCCGTTATTTCATCAGGGATACTCCAATCTCGTTA-TTTCAGA
65 CCCCGTTATTTCATCAGGGATACTCCAACCTCGTTATTTTC-GA
* *
13525 GGGGATACTCAAACCCTAATTTTATTTCT-AAAATACCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAAATACCAATTTTTCACAATCGGGG-TACTCCAA
13589 C
65 C
13590 TCCGATTTTA
Statistics
Matches: 139, Mismatches: 30, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
106 15 0.11
107 41 0.29
108 74 0.53
109 9 0.06
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (107 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAAATACCAATTTTTCACAATCGGGGTACTCCAAC
CCCGTTATTTCATCAGGGATACTCCAACCTCGTTATTTTCGA
Found at i:13585 original size:51 final size:51
Alignment explanation
Indices: 13525--13636 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
13515 TTATTTCAGA
* * *
13525 GGGGATACTCAAAC-CCTAATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCAAACTCC-AATTTTATTTCCAAAACACCAATTTCTCACAATC
* * *
13576 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTCTCACAATC
1 GGGGATACTCAAACTCCAATTTTATTTCCAAAACACCAATTTCTCACAATC
*
13627 AGGGATACTC
1 GGGGATACTC
13637 TAATCCCGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCAAACTCCAATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:13805 original size:81 final size:80
Alignment explanation
Indices: 13576--13798 Score: 245
Period size: 79 Copynumber: 2.8 Consensus size: 80
13566 TTTCACAATC
* * * *
13576 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAA-TTTCTCACAATCAGGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTC-CATAATCAGGGATACTCTAA
* *
13640 TCCC-GTTATTTTCGC
65 ACCCTGTTATTTTCGA
* * * * * *
13655 GGGGGTACTCCAACCCTGATTTTATTTTCAAAATACTAATTTTCTATAATCAGGGATACT-TCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCATAATCAGGGATACTCTAAA
*
13719 CCCTGTTATTTTTGA
66 CCCTGTTATTTTCGA
* * * *
13734 GGGGATACTCCAACCCCGATTTTTTATTTTTAGAACACCGATTTTCCATAATCGGGGATACTCTA
1 GGGGATACTCCAACCCCGA--TTTTATTTTCAAAACACCAATTTTCCATAATCAGGGATACTCTA
13799 GCCCTGTGGT
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
78 5 0.04
79 74 0.63
80 4 0.03
81 34 0.29
82 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCATAATCAGGGATACTCTAAA
CCCTGTTATTTTCGA
Found at i:18899 original size:13 final size:13
Alignment explanation
Indices: 18881--18906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18871 CAATTTTTTG
18881 TGTATCGATACAT
1 TGTATCGATACAT
18894 TGTATCGATACAT
1 TGTATCGATACAT
18907 ACTTGCTGTA
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:18971 original size:21 final size:21
Alignment explanation
Indices: 18945--19020 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
18935 CTGCCAAGAA
*
18945 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
18966 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
18986 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
19007 ATGTATCGATACAT
1 ATGTATCGATACAT
19021 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:18991 original size:20 final size:20
Alignment explanation
Indices: 18966--19038 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
18956 CATCTTTTTT
18966 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
18986 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
19007 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
19027 ATGTATCGATAC
1 ATGTATCGATAC
19039 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:19002 original size:41 final size:41
Alignment explanation
Indices: 18945--19038 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
18935 CTGCCAAGAA
*
18945 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
18986 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
19027 ATGTATCGATAC
1 ATGTATCGATAC
19039 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:21514 original size:20 final size:20
Alignment explanation
Indices: 21489--21565 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
21479 ATAATCACCC
21489 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
21509 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
21534 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
21554 TGTATCGATACA
1 TGTATCGATACA
21566 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:25427 original size:21 final size:21
Alignment explanation
Indices: 25398--25442 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25388 AAGTTTTCAT
*
25398 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
25418 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
25440 TTT
1 TTT
25443 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:27674 original size:13 final size:13
Alignment explanation
Indices: 27656--27681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27646 CAATTTTTTG
27656 TGTATCGATACAT
1 TGTATCGATACAT
27669 TGTATCGATACAT
1 TGTATCGATACAT
27682 ACTTGCTGTA
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:27746 original size:21 final size:21
Alignment explanation
Indices: 27720--27795 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
27710 CTGCCAAGAA
*
27720 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
27741 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
27761 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
27782 ATGTATCGATACAT
1 ATGTATCGATACAT
27796 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:27766 original size:20 final size:20
Alignment explanation
Indices: 27741--27813 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
27731 CATCTTTTTT
27741 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
27761 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
27782 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
27802 ATGTATCGATAC
1 ATGTATCGATAC
27814 TTTTAAGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:27777 original size:41 final size:41
Alignment explanation
Indices: 27720--27813 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
27710 CTGCCAAGAA
*
27720 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
27761 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
27802 ATGTATCGATAC
1 ATGTATCGATAC
27814 TTTTAAGGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:33341 original size:52 final size:52
Alignment explanation
Indices: 33263--33390 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
33253 CAAAATATGA
* *
33263 AAATTTGCCTGTATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
33315 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
33367 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
33391 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:33403 original size:51 final size:50
Alignment explanation
Indices: 33263--33410 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
33253 CAAAATATGA
* *
33263 AAATTTGCCTGTATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
33315 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
33367 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
33411 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:33417 original size:13 final size:13
Alignment explanation
Indices: 33399--33423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33389 CAAAGATCAG
33399 TGTATCGATACAA
1 TGTATCGATACAA
33412 TGTATCGATACA
1 TGTATCGATACA
33424 TTTGAGTAAT
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:33504 original size:13 final size:13
Alignment explanation
Indices: 33486--33510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33476 CAAAAAAATA
33486 TGTATCGATACAT
1 TGTATCGATACAT
33499 TGTATCGATACA
1 TGTATCGATACA
33511 ACATTTTATG
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:35645 original size:20 final size:20
Alignment explanation
Indices: 35620--35673 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
35610 CATTTTAGAC
**
35620 ATGTATCGATACATTCACTT
1 ATGTATCGATACATAAACTT
*
35640 ATGTATCAATACATAAACTT
1 ATGTATCGATACATAAACTT
*
35660 ATTGGATCGATACA
1 A-TGTATCGATACA
35674 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATAAACTT
Found at i:39864 original size:16 final size:16
Alignment explanation
Indices: 39843--39874 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39833 GAAAACTCAA
*
39843 TAATAACATGAAATGT
1 TAATAACATAAAATGT
39859 TAATAACATAAAATGT
1 TAATAACATAAAATGT
39875 CAATCATGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (16 bp):
TAATAACATAAAATGT
Found at i:41739 original size:28 final size:28
Alignment explanation
Indices: 41707--41765 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
41697 TTATGCAAAG
41707 TAAAAGTCATGTGACAAATTAATCCATT
1 TAAAAGTCATGTGACAAATTAATCCATT
41735 TAAAAGTCATGTGACAAATTAATCCATT
1 TAAAAGTCATGTGACAAATTAATCCATT
41763 TAA
1 TAA
41766 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (28 bp):
TAAAAGTCATGTGACAAATTAATCCATT
Found at i:56608 original size:19 final size:20
Alignment explanation
Indices: 56557--56609 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
56547 CTGCCAGTTT
*
56557 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
** * *
56577 TGTTTATCTATACAA-TGAA
1 CATGTATCGATACAATTGAA
56596 CATGTATCGATACA
1 CATGTATCGATACA
56610 TTGTATCGAT
Statistics
Matches: 24, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:56616 original size:13 final size:13
Alignment explanation
Indices: 56598--56623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56588 ACAATGAACA
56598 TGTATCGATACAT
1 TGTATCGATACAT
56611 TGTATCGATACAT
1 TGTATCGATACAT
56624 CTGGATGTGT
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:57248 original size:14 final size:14
Alignment explanation
Indices: 57231--57261 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
57221 TATTAAAAGG
57231 TTTTTAAAGAAAAT
1 TTTTTAAAGAAAAT
57245 TTTTTAAAGAAAAT
1 TTTTTAAAGAAAAT
57259 TTT
1 TTT
57262 CGTTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTTTAAAGAAAAT
Found at i:64862 original size:18 final size:18
Alignment explanation
Indices: 64839--64876 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
64829 GATAAGAACC
64839 TTTCAATCTCTTAAAAAA
1 TTTCAATCTCTTAAAAAA
64857 TTTCAATCTCTTAAAAAA
1 TTTCAATCTCTTAAAAAA
64875 TT
1 TT
64877 ATACCCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTCAATCTCTTAAAAAA
Found at i:65419 original size:20 final size:19
Alignment explanation
Indices: 65394--65458 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
65384 TTCATATATT
*
65394 GATACAATTGAGTGTGTATC
1 GATACAA-TGAGTATGTATC
**
65414 GATACAATGAACATGTATC
1 GATACAATGAGTATGTATC
*
65433 GATACAAAGCA-TAATGTATC
1 GATACAATG-AGT-ATGTATC
65453 GATACA
1 GATACA
65459 TTTGGATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (19 bp):
GATACAATGAGTATGTATC
Found at i:65432 original size:19 final size:20
Alignment explanation
Indices: 65408--65458 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
65398 CAATTGAGTG
*
65408 TGTATCGATACAATG-A-ACA
1 TGTATCGATACAAAGCATA-A
65427 TGTATCGATACAAAGCATAA
1 TGTATCGATACAAAGCATAA
65447 TGTATCGATACA
1 TGTATCGATACA
65459 TTTGGATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
20 14 0.48
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCATAA
Found at i:67660 original size:13 final size:13
Alignment explanation
Indices: 67642--67668 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
67632 ACATTATGCT
67642 TTGTATCGATACA
1 TTGTATCGATACA
67655 TTGTATCGATACA
1 TTGTATCGATACA
67668 T
1 T
67669 GTTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:67698 original size:20 final size:21
Alignment explanation
Indices: 67652--67755 Score: 99
Period size: 20 Copynumber: 5.0 Consensus size: 21
67642 TTGTATCGAT
67652 ACATTGTATCGATACATGT--
1 ACATTGTATCGATACATGTAC
**
67671 TTATTGTATCGATACATGTAC
1 ACATTGTATCGATACATGTAC
*
67692 A-ATTGTATCGATACATCTATC
1 ACATTGTATCGATACATGTA-C
* *
67713 ACTGTTTGTATCGATACATG-GC
1 AC--ATTGTATCGATACATGTAC
67735 ACATTGTATCGATACAATGTA
1 ACATTGTATCGATAC-ATGTA
67756 TTGATGCATG
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
19 17 0.25
20 29 0.43
21 5 0.07
22 3 0.04
24 14 0.21
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (21 bp):
ACATTGTATCGATACATGTAC
Found at i:69975 original size:16 final size:15
Alignment explanation
Indices: 69951--69980 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
69941 GCATAAAAAG
69951 GAAAAAAAATAATTA
1 GAAAAAAAATAATTA
69966 GAAAAGAAAATAATT
1 GAAAA-AAAATAATT
69981 GAATTGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
GAAAAAAAATAATTA
Found at i:73928 original size:13 final size:13
Alignment explanation
Indices: 73910--73936 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
73900 ATAATGTTTT
73910 TTGTATCGATACA
1 TTGTATCGATACA
73923 TTGTATCGATACA
1 TTGTATCGATACA
73936 T
1 T
73937 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:76405 original size:20 final size:19
Alignment explanation
Indices: 76362--76415 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
76352 AAATTATGCT
**
76362 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
76381 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
**
76401 TTGTAAGGATACATG
1 TTGTATCGATACATG
76416 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:77888 original size:19 final size:21
Alignment explanation
Indices: 77864--77911 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
77854 TTTATTGATA
77864 ATTTTG-A-TGAAAATGAAGT
1 ATTTTGAAGTGAAAATGAAGT
*
77883 ATTTTGAAGTGAAAATGAAGA
1 ATTTTGAAGTGAAAATGAAGT
*
77904 AATTTGAA
1 ATTTTGAA
77912 AAAGATTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTGAAAATGAAGT
Found at i:84287 original size:19 final size:19
Alignment explanation
Indices: 84243--84298 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
84233 CTGTCAGTTT
**
84243 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
84263 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
84282 CATGTATCGATACAATG
1 CATGTATCGATACAATG
84299 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:84301 original size:13 final size:13
Alignment explanation
Indices: 84283--84309 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
84273 TACAATGAAC
84283 ATGTATCGATACA
1 ATGTATCGATACA
84296 ATGTATCGATACA
1 ATGTATCGATACA
84309 A
1 A
84310 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:89448 original size:2 final size:2
Alignment explanation
Indices: 89441--89468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
89431 TCAAAAACAA
89441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89469 CTACAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90960 original size:6 final size:6
Alignment explanation
Indices: 90951--90977 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
90941 ATATATAAAG
90951 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
90978 AATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:91468 original size:145 final size:147
Alignment explanation
Indices: 91193--91469 Score: 357
Period size: 145 Copynumber: 1.9 Consensus size: 147
91183 TTCTTTGTTG
* * *
91193 CTAAACTTTTTGAAGTAATTTTATTAATTTATTTTAAATAAGAAACATAATACGTTCATCTCAAC
1 CTAAACTTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
* * * ** ** *
91258 TTTAATATATTGGATAAAAATAAGTTTAAAATATTTAACATGTGTTTGTATTAGAACTAATTTTA
66 GTTAAAATATTGGATAAAAATAAATTTAAAATATTTAACATGTACTTAAATTAGAACTAAATTTA
91323 ATCAATTTCTTTTATCA
131 ATCAATTTCTTTTATCA
*
91340 CTAAA-TTTTT-AAGTAATTTTATTAA-TTATTTCAAATAA-AAAGCATAATACATTTATCTCAA
1 CTAAACTTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAA-CATAATACATTCATCTCAA
* * *
91401 AGTTAAAATATTTGATTAAAAATAAATTTAAAATATTTAGCATGTACTTAAATTATAA-TATAAT
65 AGTTAAAATATTGGA-TAAAAATAAATTTAAAATATTTAACATGTACTTAAATTAGAACTA-AAT
91465 TTAAT
128 TTAAT
91470 TAGAATTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
143 3 0.03
144 42 0.38
145 57 0.51
146 5 0.04
147 5 0.04
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (147 bp):
CTAAACTTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
GTTAAAATATTGGATAAAAATAAATTTAAAATATTTAACATGTACTTAAATTAGAACTAAATTTA
ATCAATTTCTTTTATCA
Found at i:91712 original size:29 final size:29
Alignment explanation
Indices: 91672--91743 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
91662 GGTAAGTATA
91672 TATTTTTC--AAAATATAAAAG-ATAAATG
1 TATTTTTCTGAAAAT-TAAAAGCATAAATG
* *
91699 TATTTTTCTGAAAATTTAAAGCATAAGTG
1 TATTTTTCTGAAAATTAAAAGCATAAATG
* *
91728 TACTTTTCTGTAAATT
1 TATTTTTCTGAAAATT
91744 TAATTTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.21
28 5 0.13
29 25 0.66
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (29 bp):
TATTTTTCTGAAAATTAAAAGCATAAATG
Found at i:91744 original size:29 final size:28
Alignment explanation
Indices: 91688--91746 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
91678 TCAAAATATA
*
91688 AAAGATAAATGTATTTTTCTGAAAATTT
1 AAAGATAAATGTACTTTTCTGAAAATTT
* *
91716 AAAGCATAAGTGTACTTTTCTGTAAATTT
1 AAAG-ATAAATGTACTTTTCTGAAAATTT
91745 AA
1 AA
91747 TTTTGTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (28 bp):
AAAGATAAATGTACTTTTCTGAAAATTT
Found at i:91914 original size:3 final size:3
Alignment explanation
Indices: 91906--91969 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
91896 ATATCTTTAT
91906 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
91955 ATA TATA AT- ATA ATA
1 ATA -ATA ATA ATA ATA
91970 TAAATATATA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:91972 original size:18 final size:18
Alignment explanation
Indices: 91906--91981 Score: 86
Period size: 18 Copynumber: 4.1 Consensus size: 18
91896 ATATCTTTAT
91906 ATAATAATA-ATAATAATA
1 ATAATAATATA-AATAATA
91924 ATAATAATA-ATAATAATA
1 ATAATAATATA-AATAATA
91942 ATAATAATAATAAATATATA
1 ATAATAAT-ATAAATA-ATA
91962 AT-ATAATATAAATATATA
1 ATAATAATATAAATA-ATA
91980 AT
1 AT
91982 TAACTTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
18 39 0.71
19 10 0.18
20 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATATAAATAATA
Found at i:93650 original size:25 final size:25
Alignment explanation
Indices: 93605--93652 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
93595 TTTGCTGCCC
93605 TTTTTGATTCTTCCTGAGGAATATA
1 TTTTTGATTCTTCCTGAGGAATATA
* *
93630 TTTTTGTTTCCTTCTTG-GGAATA
1 TTTTTGATT-CTTCCTGAGGAATA
93653 GAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (25 bp):
TTTTTGATTCTTCCTGAGGAATATA
Found at i:99081 original size:40 final size:40
Alignment explanation
Indices: 99026--99118 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
99016 ATCTTATTCA
99026 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
1 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
*
99066 AAATGATTTTCAATATCAAATATGTTTTAGAGTTATGTAT
1 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
*
99106 AAATGTTTTTCAA
1 AAATGATTTTCAA
99119 GCATTAAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (40 bp):
AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
Found at i:99111 original size:21 final size:21
Alignment explanation
Indices: 99047--99114 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
99037 AATATCAAAG
99047 ATGTTTTAGAGTTATGTATAA
1 ATGTTTTAGAGTTATGTATAA
*
99068 ATGATTTTCA-A--TAT-CA-AA
1 ATG-TTTT-AGAGTTATGTATAA
99086 TATGTTTTAGAGTTATGTATAA
1 -ATGTTTTAGAGTTATGTATAA
99108 ATGTTTT
1 ATGTTTT
99115 TCAAGCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 4 0.11
20 6 0.16
21 11 0.30
22 7 0.19
23 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (21 bp):
ATGTTTTAGAGTTATGTATAA
Found at i:99332 original size:18 final size:18
Alignment explanation
Indices: 99275--99332 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 18
99265 CTTTGTATAG
* **
99275 TGTATCGATACATGATCT
1 TGTATCGATATATGAAAT
*
99293 TGTTATCGATATATAGCGAAT
1 TG-TATCGATATAT-G-AAAT
99314 TGTATCGATATATGAAAT
1 TGTATCGATATATGAAAT
99332 T
1 T
99333 AACAGTAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 12 0.38
21 3 0.09
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTATCGATATATGAAAT
Found at i:99381 original size:20 final size:20
Alignment explanation
Indices: 99356--99409 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
99346 CTACTATTGC
99356 TTGTATCGATACATGCGACA
1 TTGTATCGATACATGCGACA
99376 TTGTATCGATACATGCGACA
1 TTGTATCGATACATGCGACA
99396 TTGTATCGATACAT
1 TTGTATCGATACAT
99410 TGTATCGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGCGACA
Found at i:99411 original size:13 final size:13
Alignment explanation
Indices: 99393--99422 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
99383 GATACATGCG
99393 ACATTGTATCGAT
1 ACATTGTATCGAT
99406 ACATTGTATCGAT
1 ACATTGTATCGAT
99419 ACAT
1 ACAT
99423 AGTAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:100693 original size:142 final size:141
Alignment explanation
Indices: 100178--100686 Score: 650
Period size: 141 Copynumber: 3.6 Consensus size: 141
100168 TAAGCTTTTA
* * * * **
100178 CTAATATTCTTATGGTTTTCTGTAGGGATATAGAAAATTTCAAAACTTTTCATATCTTTTTGGTT
1 CTAATATTCTTATAGTTTT-TTTAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
* * * * *
100243 C-CTTATTAAGCTACGAAATGATTTTTTTTGAAAATTAAAAATTAAATATATATTATTATCTTAA
65 CTC-CATTAAGGTACGAAATGAATTTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAA
*
100307 TTTTTTAAAATTT
129 TTTTTCAAAATTT
* *
100320 CTAATATTCCTATAGTTTTTTGTAGGGGTATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
1 CTAATATTCTTATAGTTTTTT-TAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
* * * *
100385 CTCCATTAAGTTACAAAATAAATTTTTTT-AAAATTAGAAATTAAATAAAAATTATTATCTTAAT
65 CTCCATTAAGGTACGAAATGAATTTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAAT
100449 TTTTCAAGAA-TT
130 TTTTCAA-AATTT
* * * *
100461 CTAATATTCATATAGTTTTTCATAGGGATATACAAATCTTT-AAAACTTTTCGTATCTTTTCAAT
1 CTAATATTCTTATAGTTTTT-TTAGGGATATAGAAAT-TTTCAAAACTTTTCGTATCTTTTCAGT
* * *
100525 TCTCTATTAAGGTATGAAATGAATTTTTTTGAAAATTAAAAATTAAATAAAAATTATTATATTAA
64 TCTCCATTAAGGTACGAAATGAATTTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAA
*
100590 TTTTTCAATATTT
129 TTTTTCAAAATTT
* * * *
100603 CTAATATTCTTATAGTTTTCTTTAGGGGTATAGAAATGTTC-AAACTTTTTGTATCTTTTTAGTT
1 CTAATATTCTTATAGTTTT-TTTAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
100667 CTCCATTAAGGTACGAAATG
65 CTCCATTAAGGTACGAAATG
100687 GGATTTTCGA
Statistics
Matches: 318, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
141 161 0.51
142 155 0.49
143 2 0.01
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (141 bp):
CTAATATTCTTATAGTTTTTTTAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTTC
TCCATTAAGGTACGAAATGAATTTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAATT
TTTCAAAATTT
Found at i:102409 original size:72 final size:72
Alignment explanation
Indices: 102240--102698 Score: 534
Period size: 73 Copynumber: 6.3 Consensus size: 72
102230 ACGCTGTGAC
* * *
102240 AAACTTCTACAAATAAAAATAAATTATGCCATAAAAAATTTAAACTTGTATAATCATACCCAAAA
1 AAACTTCTACAAATAAAAATAAATTATACC-T-TAAAATTTAAACTCGTATAATCATACCCAAAA
102305 AA-ACATATTT
64 AATA-A-ATTT
* *
102315 AAACTTTTACAAATAAAAATAAATTATACCTTAAAATTTAAACTCCTATAATCATACCCAAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACCTTAAAATTTAAACTCGTATAATCATACCCAAAAAA
102380 TAAATTT
66 TAAATTT
* * * * *
102387 AAACTTCTACAAATAAAGATAAATAATACTCTAAAAATTTAAACTCATATAATCA-AACCAAAAA
1 AAACTTCTACAAATAAAAATAAATTATAC-CTTAAAATTTAAACTCGTATAATCATACCCAAAAA
102451 ATAAATTT
65 ATAAATTT
* * * * * ** *
102459 AAATTTCTAAAAATAAAAATAAATTACACCTTCAAAATTTAAACTCATATAGTCATACCGTACAA
1 AAACTTCTACAAATAAAAATAAATTATACCTT-AAAATTTAAACTCGTATAATCATACCCAAAAA
*
102524 ATATATTT
65 ATAAATTT
* **
102532 AAACTTCTACAAAGT-AAAATAAATTATACCTTTAAAATTTAAACTCGAATAATCA-A-ATAAAA
1 AAACTTCTACAAA-TAAAAATAAATTATACC-TTAAAATTTAAACTCGTATAATCATACCCAAAA
102594 AATAAATTT
64 AATAAATTT
* * * * * *
102603 AAACTTC-AAAAATAAAAATAAATTATACCTTCAAAATTTAAATTTGTGTAATCATACCCTACAA
1 AAACTTCTACAAATAAAAATAAATTATACCTT-AAAATTTAAACTCGTATAATCATACCCAAAAA
*
102667 ATAAGTTT
65 ATAAATTT
102675 AAACTTCTACAAATAAAAATAAAT
1 AAACTTCTACAAATAAAAATAAAT
102699 AATATCGTTA
Statistics
Matches: 328, Mismatches: 45, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
69 3 0.01
70 37 0.11
71 20 0.06
72 109 0.33
73 126 0.38
74 5 0.02
75 28 0.09
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (72 bp):
AAACTTCTACAAATAAAAATAAATTATACCTTAAAATTTAAACTCGTATAATCATACCCAAAAAA
TAAATTT
Found at i:102532 original size:145 final size:144
Alignment explanation
Indices: 102240--102702 Score: 573
Period size: 145 Copynumber: 3.2 Consensus size: 144
102230 ACGCTGTGAC
* * ** *
102240 AAACTTCTACAAATAAAAATAAATTATGCCATAAAAAATTTAAACTTGTATAATCATACCCAAAA
1 AAACTTCTACAAATAAAAATAAATAATACCAT-AAAAATTTAAACTCATATAATCA-AACCAAAA
* *
102305 AA-ACATATTTAAACTTT-TACAAATAAAAATAAATTATACCTT-AAAATTTAAACTCCTATAAT
64 AATA-A-ATTTAAA-TTTCTAAAAATAAAAATAAATTATACCTTCAAAATTTAAACTCATATAAT
* *
102367 CATACCCAAAAAATAAATTT
126 CATACCCTACAAAT-AATTT
*
102387 AAACTTCTACAAATAAAGATAAATAATACTC-TAAAAATTTAAACTCATATAATCAAACCAAAAA
1 AAACTTCTACAAATAAAAATAAATAATAC-CATAAAAATTTAAACTCATATAATCAAACCAAAAA
* *
102451 ATAAATTTAAATTTCTAAAAATAAAAATAAATTACACCTTCAAAATTTAAACTCATATAGTCATA
65 ATAAATTTAAATTTCTAAAAATAAAAATAAATTATACCTTCAAAATTTAAACTCATATAATCATA
*
102516 CCGTACAAATATATTT
130 CCCTACAAATA-ATTT
* * * *
102532 AAACTTCTACAAAGT-AAAATAAATTATACCTTTAAAATTTAAACTCGA-ATAATCAAA-TAAAA
1 AAACTTCTACAAA-TAAAAATAAATAATACCATAAAAATTTAAACTC-ATATAATCAAACCAAAA
* * ** *
102594 AATAAATTTAAACTTC-AAAAATAAAAATAAATTATACCTTCAAAATTTAAATTTGTGTAATCAT
64 AATAAATTTAAATTTCTAAAAATAAAAATAAATTATACCTTCAAAATTTAAACTCATATAATCAT
102658 ACCCTACAAATAAGTTT
129 ACCCTACAAATAA-TTT
102675 AAACTTCTACAAATAAAAATAAATAATA
1 AAACTTCTACAAATAAAAATAAATAATA
102703 TCGTTAATCA
Statistics
Matches: 280, Mismatches: 26, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
142 2 0.01
143 84 0.30
144 51 0.18
145 91 0.32
146 24 0.09
147 27 0.10
148 1 0.00
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (144 bp):
AAACTTCTACAAATAAAAATAAATAATACCATAAAAATTTAAACTCATATAATCAAACCAAAAAA
TAAATTTAAATTTCTAAAAATAAAAATAAATTATACCTTCAAAATTTAAACTCATATAATCATAC
CCTACAAATAATTT
Found at i:103208 original size:67 final size:67
Alignment explanation
Indices: 103064--103210 Score: 181
Period size: 69 Copynumber: 2.2 Consensus size: 67
103054 GATTTTTTTT
* **
103064 AAAATTTTTT-AATTTAAATTTTTTTATTATATTAAAAATTAATAATTAATATTTTGATTTTTCA
1 AAAATTTTTTAAATTTAAATTTTTTTATTATATTAAAAATAAATAATTAATACGTTGA-TTTTCA
103128 ATA
65 ATA
* * * *
103131 AAAATATTTTAAATTTTATTTTATTTTATTTTATTAAAAATAAATAATTAATACGTTG-TTTTCA
1 AAAATTTTTTAAATTTAAATTT-TTTTATTATATTAAAAATAAATAATTAATACGTTGATTTTCA
*
103195 ATT
65 ATA
*
103198 TAAATTTTTTAAA
1 AAAATTTTTTAAA
103211 ATCTAATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
67 28 0.41
68 9 0.13
69 31 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (67 bp):
AAAATTTTTTAAATTTAAATTTTTTTATTATATTAAAAATAAATAATTAATACGTTGATTTTCAA
TA
Found at i:105239 original size:11 final size:11
Alignment explanation
Indices: 105225--105249 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
105215 TTGTAATAAT
105225 AAAATAAAATA
1 AAAATAAAATA
105236 AAAATAAAATA
1 AAAATAAAATA
105247 AAA
1 AAA
105250 TAATTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:105241 original size:6 final size:5
Alignment explanation
Indices: 105222--105252 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
105212 ATTTTGTAAT
105222 AATAA AATAA AATAAA AATAA AATAA AATAA
1 AATAA AATAA AAT-AA AATAA AATAA AATAA
105253 TTATAGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:105243 original size:16 final size:16
Alignment explanation
Indices: 105222--105252 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
105212 ATTTTGTAAT
105222 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
105238 AATAAAATAAAATAA
1 AATAAAATAAAATAA
105253 TTATAGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:112021 original size:27 final size:28
Alignment explanation
Indices: 111988--112058 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
111978 GCCACCCATT
111988 TATTTGTCAAAAATGGTGG-TTATTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
* *
112015 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
*
112043 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
112059 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTGGTTTATTTTG
Found at i:114676 original size:21 final size:22
Alignment explanation
Indices: 114647--114692 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
114637 TGTTCAGACA
** *
114647 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
114669 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
114690 AGT
1 AGT
114693 TTCAACAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:116631 original size:28 final size:27
Alignment explanation
Indices: 116576--116646 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
116566 GCCACCCATT
116576 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
116603 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
*
116631 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
116647 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:121115 original size:2 final size:2
Alignment explanation
Indices: 121108--121140 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
121098 GCATCAAATT
121108 TA 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 TA T
121141 CTAACTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:124476 original size:277 final size:276
Alignment explanation
Indices: 123978--124530 Score: 908
Period size: 277 Copynumber: 2.0 Consensus size: 276
123968 TCTTTAAAGA
* *
123978 AATAATATCACGCACTCATTACTGGCCAGCTTCTCATTTTGGTCACTTTGCTCCAATGCCTCTTC
1 AATAATATCACGCACTCATTACTGGCCAGCTTCTCATTTTGGTCACTTTGCTCCAATACCACTTC
* *
124043 CTCAATCATGCCATGGTCAGATTCCAGAAGTCCTTCCTCATGTGCCAGCTCTTCTATTTTCTTCT
66 CTCAATCATGCCATGATCAGATTCCAGAAGTCCTTCCTCATGTGCCAGCTCTTCGATTTTCTTCT
* * *
124108 TCGACATTAAAGCATTATCAACGCCAAGCGCATCCTCTTGTTTTTCTCCATTCCTAATGCCTGAT
131 TCGACATTAAAGCATTATCAACACCAAGCACATCCTCTTGTTTTTCTCCATTCCTAATGCCTGAG
* * *
124173 TTACTGTAAGCCAATAAGAGTTAACAAAAAGTCAAACACAATTAAGTGTAAGCCAGAAATGATGA
196 TTACTGCAAGCCAATAAGAATTAACAAAAAGTCAAACACAATCAAGTGTAA-CCAGAAATGATGA
124238 TTAATAAAGCAAACAAC
260 TTAATAAAGCAAACAAC
* *
124255 AATAATATCACGCACTCATTACTGGCCAGCTTCTGATTTTGGTCATTTTGCTCCAATACCACTTC
1 AATAATATCACGCACTCATTACTGGCCAGCTTCTCATTTTGGTCACTTTGCTCCAATACCACTTC
* * *
124320 TTCAATCATGCCATGATCAGATTCCAGAAGTCCTTCCTCATGTGCCAGCTCTTCGCTTTTGTTCT
66 CTCAATCATGCCATGATCAGATTCCAGAAGTCCTTCCTCATGTGCCAGCTCTTCGATTTTCTTCT
* *
124385 TTGACATTAAAGCATTATCAACACCAAGCACATGCTCTTGTTTTTCTCCATTCCTAATGCCTGAG
131 TCGACATTAAAGCATTATCAACACCAAGCACATCCTCTTGTTTTTCTCCATTCCTAATGCCTGAG
* * *
124450 TTACTGCAAGCCAATAAGAATTAACAAAAAGTCAAACACAATCAAGTTTAACCAGAATTGATGCT
196 TTACTGCAAGCCAATAAGAATTAACAAAAAGTCAAACACAATCAAGTGTAACCAGAAATGATGAT
*
124515 TAATGAAGCAAACAAC
261 TAATAAAGCAAACAAC
124531 CATATGTTAT
Statistics
Matches: 255, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
276 27 0.11
277 228 0.89
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (276 bp):
AATAATATCACGCACTCATTACTGGCCAGCTTCTCATTTTGGTCACTTTGCTCCAATACCACTTC
CTCAATCATGCCATGATCAGATTCCAGAAGTCCTTCCTCATGTGCCAGCTCTTCGATTTTCTTCT
TCGACATTAAAGCATTATCAACACCAAGCACATCCTCTTGTTTTTCTCCATTCCTAATGCCTGAG
TTACTGCAAGCCAATAAGAATTAACAAAAAGTCAAACACAATCAAGTGTAACCAGAAATGATGAT
TAATAAAGCAAACAAC
Found at i:126226 original size:2 final size:2
Alignment explanation
Indices: 126219--126248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
126209 CCCCGGGAAG
126219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126249 TTAATCAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128601 original size:2 final size:2
Alignment explanation
Indices: 128594--128630 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
128584 TTAGATCCCT
128594 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
128631 TTAAGACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:128619 original size:17 final size:17
Alignment explanation
Indices: 128597--128630 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
128587 GATCCCTGAG
128597 AGAGAGAGAGAGAGAGA
1 AGAGAGAGAGAGAGAGA
128614 AGAGAGAGAGAGAGAGA
1 AGAGAGAGAGAGAGAGA
128631 TTAAGACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
AGAGAGAGAGAGAGAGA
Found at i:135692 original size:16 final size:17
Alignment explanation
Indices: 135662--135697 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
135652 TTGAATTGTT
135662 TTTGGGTTTAGGGATTA
1 TTTGGGTTTAGGGATTA
*
135679 TTTGGTTTTA-GGATTA
1 TTTGGGTTTAGGGATTA
135695 TTT
1 TTT
135698 TACAATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (17 bp):
TTTGGGTTTAGGGATTA
Found at i:143535 original size:21 final size:22
Alignment explanation
Indices: 143495--143536 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
143485 TCAACTCTGT
*
143495 TCAATATCTTTTGAAATAAAAA
1 TCAATATCTTCTGAAATAAAAA
*
143517 TCAATAT-TTCTGTAATAAAA
1 TCAATATCTTCTGAAATAAAA
143537 TCCAATAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (22 bp):
TCAATATCTTCTGAAATAAAAA
Found at i:144332 original size:21 final size:21
Alignment explanation
Indices: 144294--144334 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
144284 TAAGGAAGTT
*
144294 GAAAAGAAAAAGACAAAAAGG
1 GAAAAGAAAAAGAAAAAAAGG
*
144315 GAAAAGGAAAAAAAAAAAAA
1 GAAAA-GAAAAAGAAAAAAA
144335 AAAAGAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
GAAAAGAAAAAGAAAAAAAGG
Found at i:145002 original size:28 final size:28
Alignment explanation
Indices: 144960--145020 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
144950 CCCATCTATC
* *
144960 TATATACACACACAT-ATAATTGATAATA
1 TATATACACAAACATGA-AACTGATAATA
*
144988 TATATACATAAACATGAAACTGATAATA
1 TATATACACAAACATGAAACTGATAATA
145016 TATAT
1 TATAT
145021 GTACCTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (28 bp):
TATATACACAAACATGAAACTGATAATA
Found at i:146348 original size:21 final size:21
Alignment explanation
Indices: 146315--146372 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
146305 TATATATTTT
*
146315 ATAATTAAAATTAAATAAA-A
1 ATAATTATAATTAAATAAATA
146335 A-AATTATTTAATTAAATAAATA
1 ATAATTA--TAATTAAATAAATA
146357 ATAATTATAATTAAAT
1 ATAATTATAATTAAAT
146373 TAATTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 5 0.15
20 1 0.03
21 20 0.61
22 2 0.06
23 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTATAATTAAATAAATA
Found at i:146373 original size:26 final size:26
Alignment explanation
Indices: 146313--146386 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
146303 TCTATATATT
146313 TTATAATTAAAATTAAATAAA-AA-AA
1 TTATAATT-AAATTAAATAAATAATAA
146338 TTAT--TT-AATTAAATAAATAATAA
1 TTATAATTAAATTAAATAAATAATAA
*
146361 TTATAATTAAATTAATTAAATAATAA
1 TTATAATTAAATTAAATAAATAATAA
146387 AATATTTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 11 0.26
22 2 0.05
23 8 0.19
25 6 0.14
26 16 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTATAATTAAATTAAATAAATAATAA
Found at i:146377 original size:30 final size:31
Alignment explanation
Indices: 146342--146414 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
146332 AAAAAATTAT
*
146342 TTAATTAAATAA-ATAATAATTATAATTAAA
1 TTAATTAAATAATAAAATAATTATAATTAAA
* *
146372 TTAATTAAATAATAAAATATTTATATTTAAA
1 TTAATTAAATAATAAAATAATTATAATTAAA
146403 TATAATATAAAT
1 T-TAAT-TAAAT
146415 CAGAACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.32
31 16 0.43
32 4 0.11
33 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAATTAAATAATAAAATAATTATAATTAAA
Found at i:146401 original size:26 final size:24
Alignment explanation
Indices: 146323--146394 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 24
146313 TTATAATTAA
*
146323 AATTAAATAAAAAAATTATTTAATT
1 AATTAAATAATAAAA-TATTTAATT
* * *
146348 AAATAAATAATAATTATAATTAAATT
1 AATTAAATAATAA-AAT-ATTTAATT
146374 AATTAAATAATAAAATATTTA
1 AATTAAATAATAAAATATTTA
146395 TATTTAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 4 0.11
25 14 0.37
26 20 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTAAATAATAAAATATTTAATT
Found at i:146867 original size:15 final size:14
Alignment explanation
Indices: 146830--146883 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
146820 TTTTTTAGAT
146830 AATTTTAAAATTAA
1 AATTTTAAAATTAA
* *
146844 AAATGTAAAATGTAA
1 AATTTTAAAAT-TAA
146859 AATTTTAAAATTATTA
1 AATTTTAAAATTA--A
146875 AATTTTAAA
1 AATTTTAAA
146884 TAATACTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.33
15 12 0.36
16 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
AATTTTAAAATTAA
Found at i:147050 original size:12 final size:14
Alignment explanation
Indices: 147033--147066 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
147023 AAAAGTTTTT
147033 AAATTAAAAG-A-A
1 AAATTAAAAGCATA
147045 AAATTAAAAGCATA
1 AAATTAAAAGCATA
147059 AAATTAAA
1 AAATTAAA
147067 CTCTTAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 1 0.05
14 9 0.45
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (14 bp):
AAATTAAAAGCATA
Found at i:147255 original size:13 final size:13
Alignment explanation
Indices: 147239--147265 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
147229 ATTTTTTATT
147239 TATTTTTTAAAAA
1 TATTTTTTAAAAA
147252 TATTTTTTAAAAA
1 TATTTTTTAAAAA
147265 T
1 T
147266 TTTAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTTTTAAAAA
Found at i:156533 original size:17 final size:16
Alignment explanation
Indices: 156502--156544 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
156492 CATATGTTTT
**
156502 TTTTTTCTTTTTCTTCC
1 TTTTTTCTTCATCTT-C
156519 TTTTTTCTTCATCTTC
1 TTTTTTCTTCATCTTC
156535 TTTCTTTCTT
1 TTT-TTTCTT
156545 ACGTATAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTTCATCTTC
Found at i:158728 original size:32 final size:33
Alignment explanation
Indices: 158690--158753 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
158680 CAATTCAATG
* *
158690 TGTATCGATACTATG-AACATGTATTGGTACAA
1 TGTATCGATACTAGGCAACATGTATTGATACAA
*
158722 TGTATCGATACTAGGCAATATGTATTGATACA
1 TGTATCGATACTAGGCAACATGTATTGATACA
158754 TCTGGTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACTAGGCAACATGTATTGATACAA
Found at i:165378 original size:20 final size:20
Alignment explanation
Indices: 165355--165427 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
165345 ACAATTCAAA
165355 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
165375 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
165396 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
165416 GTATCGATACAT
1 GTATCGATACAT
165428 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:165399 original size:21 final size:21
Alignment explanation
Indices: 165373--165448 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
165363 ACATGTTGCA
165373 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
165394 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
165414 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
165435 TTGTATCGATACAT
1 ATGTATCGATACAT
165449 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:165406 original size:41 final size:41
Alignment explanation
Indices: 165355--165448 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
165345 ACAATTCAAA
*
165355 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
165396 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
165437 GTATCGATACAT
1 GTATCGATACAT
165449 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:165505 original size:13 final size:13
Alignment explanation
Indices: 165487--165512 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165477 TACAGCAAGT
165487 ATGTATCGATACA
1 ATGTATCGATACA
165500 ATGTATCGATACA
1 ATGTATCGATACA
165513 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:169594 original size:15 final size:15
Alignment explanation
Indices: 169574--169604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
169564 TAAAAATGTC
*
169574 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
169589 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
169604 C
1 C
169605 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:171697 original size:20 final size:21
Alignment explanation
Indices: 171618--171696 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
171608 AATGTCCAAA
*
171618 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
171638 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
171663 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
171683 TTGTATCGATACAT
1 ATGTATCGATACAT
171697 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:171701 original size:13 final size:13
Alignment explanation
Indices: 171683--171721 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
171673 ACATTTTTCT
171683 TTGTATCGATACA
1 TTGTATCGATACA
171696 TTGTATCGATACA
1 TTGTATCGATACA
*
171709 CTGTATCGATACA
1 TTGTATCGATACA
171722 GGGTGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:174187 original size:20 final size:20
Alignment explanation
Indices: 174164--174236 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
174154 ACAATTCAAA
174164 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
174184 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
174205 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
174225 GTATCGATACAT
1 GTATCGATACAT
174237 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:174208 original size:21 final size:21
Alignment explanation
Indices: 174182--174257 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
174172 ACATGTTGCA
174182 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
174203 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
174223 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
174244 TTGTATCGATACAT
1 ATGTATCGATACAT
174258 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:174215 original size:41 final size:41
Alignment explanation
Indices: 174164--174257 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
174154 ACAATTCAAA
*
174164 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
174205 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
174246 GTATCGATACAT
1 GTATCGATACAT
174258 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:174314 original size:13 final size:13
Alignment explanation
Indices: 174296--174321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
174286 TACAGCAAGT
174296 ATGTATCGATACA
1 ATGTATCGATACA
174309 ATGTATCGATACA
1 ATGTATCGATACA
174322 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:181535 original size:130 final size:128
Alignment explanation
Indices: 181279--181514 Score: 285
Period size: 130 Copynumber: 1.8 Consensus size: 128
181269 AAAAAAAAAG
* * * * ** *
181279 AAAGAAAAAATGAGTGGCCTCGGTTTAAAACTCAGGCCACCTTTATGGAAAGCGTCATTGTGACC
1 AAAGAAAAAATGAATGGCCTAGGTTTAAAACCCAGGCCACCTTAATGGAAAAAGCCATTGTGACC
* ** *
181344 CTTGCACCAAAGTTTAACTTTCGTCATAAAACATAAAAAAATGTAAAAAAGAAACAAAAATGGGA
66 CTTACACCAAAGCCTAACTTTCGTCATAAAACACAAAAAAA--TAAAAAAGAAACAAAAATGGGA
* *
181409 AAAGAAAAAATGAATGGCCTAGGTTTCAAACCCAGGCCACCTTAATGGTAAAAAGCCCTTGTGAC
1 AAAGAAAAAATGAATGGCCTAGGTTTAAAACCCAGGCCACCTTAATGG-AAAAAGCCATTGTGAC
* *
181474 CCTTACATCAAAGCCTAACTTT-GATCATAAAATGACAAAAA
65 CCTTACACCAAAGCCTAACTTTCG-TCATAAAA-CACAAAAA
181515 CAAAACAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
130 44 0.50
131 38 0.43
132 6 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (128 bp):
AAAGAAAAAATGAATGGCCTAGGTTTAAAACCCAGGCCACCTTAATGGAAAAAGCCATTGTGACC
CTTACACCAAAGCCTAACTTTCGTCATAAAACACAAAAAAATAAAAAAGAAACAAAAATGGGA
Found at i:182154 original size:19 final size:19
Alignment explanation
Indices: 182127--182167 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
182117 TTAGGTTTTG
* *
182127 AACCTAAGCCACTCGTGTA
1 AACCCAAGCCACTCATGTA
182146 AACCCAAGCCACTCATGTA
1 AACCCAAGCCACTCATGTA
182165 AAC
1 AAC
182168 TAAAAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.34, G:0.12, T:0.17
Consensus pattern (19 bp):
AACCCAAGCCACTCATGTA
Found at i:187885 original size:21 final size:21
Alignment explanation
Indices: 187833--187895 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
187823 AAAAAAAAAT
*
187833 TTATCCAAATGTATCGATACA
1 TTATACAAATGTATCGATACA
***
187854 TT-TGTGGAATGTATCGATACA
1 TTAT-ACAAATGTATCGATACA
*
187875 TTATACAAATGTATCAATACA
1 TTATACAAATGTATCGATACA
187896 AGGTCCCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (21 bp):
TTATACAAATGTATCGATACA
Found at i:187956 original size:19 final size:19
Alignment explanation
Indices: 187932--187995 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
187922 TTTCAGCGAT
187932 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
187951 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
187965 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
187983 TTGTATCGATACA
1 TTGTATCGATACA
187996 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
19 24 0.63
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:187969 original size:32 final size:32
Alignment explanation
Indices: 187933--188003 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
187923 TTCAGCGATT
187933 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
187965 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
187997 TGTATCG
1 TGTATCG
188004 CTAGGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:187970 original size:13 final size:13
Alignment explanation
Indices: 187952--187976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187942 ACATAAGTAT
187952 TGTATCGATACAA
1 TGTATCGATACAA
187965 TGTATCGATACA
1 TGTATCGATACA
187977 TAAGTTTTGT
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:188065 original size:13 final size:13
Alignment explanation
Indices: 188047--188072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
188037 CATTTTTCTG
188047 TGTATCGATACAT
1 TGTATCGATACAT
188060 TGTATCGATACAT
1 TGTATCGATACAT
188073 GATTCTTTGT
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:188069 original size:33 final size:33
Alignment explanation
Indices: 188027--188092 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
188017 GCCAAGGAAA
**
188027 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGATTCTGTGTATCGATACAT
*
188060 TGTATCGATACATGATTCTTTGTATCGATACAT
1 TGTATCGATACATGATTCTGTGTATCGATACAT
188093 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATGATTCTGTGTATCGATACAT
Found at i:190497 original size:51 final size:51
Alignment explanation
Indices: 190440--190560 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
190430 CAATTCTCCG
* *
190440 CAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACA-CTAATTTTCTA
1 CAATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCGAATTTTC-A
* * * *
190491 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGCACCGACTTTTCA
1 CAATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCGAATTTTCA
190542 CAATCGGGGATATTCCAAC
1 CAATCGGGGATATTCCAAC
190561 CCCGTTATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 54 0.89
52 7 0.11
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
CAATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCGAATTTTCA
Found at i:190656 original size:27 final size:27
Alignment explanation
Indices: 190618--190670 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
190608 CATCAATTTT
*
190618 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
190645 TCATCGGGGATACTCCAACCTCGTTA
1 TCATCGGGGATACTCCAACCCCGTTA
190671 CCTCCGAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:190723 original size:103 final size:105
Alignment explanation
Indices: 190544--190746 Score: 250
Period size: 103 Copynumber: 1.9 Consensus size: 105
190534 ACTTTTCACA
* * * * * ** *
190544 ATCGGGGATATTCCAACCCCGTTATTTCTAGGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTACTCCGAGGGGGACACTCAAACCCCGACTTTATTTCCAAAAC
190609 ATCAATTTTTCAT-T-GGGGATACTCCAACCCCGTTAATC
66 ATCAATTTTTCATATCGGGGATACTCCAACCCCGTTAATC
* *
190647 ATCGGGGATACTCCAACCTCGTTACCTCCGA-GGGGATACTCAAACCCCGACTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTA-CTCCGAGGGGGACACTCAAACCCCGACTTTATTTCCAAAA
* **
190711 TATTGATTTTTCATAATCGGGGATACTCCAACCCCG
65 CATCAATTTTTCAT-ATCGGGGATACTCCAACCCCG
190747 GTTTTATTGC
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
103 61 0.73
104 3 0.04
105 1 0.01
106 18 0.22
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (105 bp):
ATCGGGGATACTCCAACCCCGTTACTCCGAGGGGGACACTCAAACCCCGACTTTATTTCCAAAAC
ATCAATTTTTCATATCGGGGATACTCCAACCCCGTTAATC
Found at i:190744 original size:51 final size:51
Alignment explanation
Indices: 190678--190899 Score: 255
Period size: 52 Copynumber: 4.3 Consensus size: 51
190668 TTACCTCCGA
* * * *** *
190678 GGGGATACTCAAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * *
190729 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTTCACAATC
* ***
190781 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT-TCACAATC
* *
190833 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATC
*
190885 GAGGATACTCCAACC
1 GGGGATACTCCAACC
190900 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
51 35 0.24
52 95 0.66
53 13 0.09
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:190918 original size:28 final size:28
Alignment explanation
Indices: 190882--190958 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
190872 ATTTTTCACA
* * *
190882 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
190910 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
190938 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
190959 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:191024 original size:107 final size:107
Alignment explanation
Indices: 190833--191032 Score: 251
Period size: 107 Copynumber: 1.9 Consensus size: 107
190823 TCTTTTAATC
* * *
190833 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
190898 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
190941 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
191005 CCCCGTTATTTTCGA-GGGGATACTCCAA
66 CCCCGTTA-TTTC-ACGGGGATACTCCAA
191033 TCCTGATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
107 52 0.67
108 25 0.32
109 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:193849 original size:20 final size:20
Alignment explanation
Indices: 193824--193897 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
193814 AAAGACAGAT
*
193824 TGTATCGATACATTGAAGAA
1 TGTATCGATACATTGAAAAA
* *
193844 TGTATCGATACATTCATACAA
1 TGTATCGATACATTGA-AAAA
193865 -GTATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
*
193884 TGTATCAATACATT
1 TGTATCGATACATT
193898 TGGGTAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.06
20 41 0.87
21 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATTGAAAAA
Found at i:196083 original size:21 final size:19
Alignment explanation
Indices: 196037--196092 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
196027 AAAAACCAAT
*
196037 AATGTATCGATACAATGAA
1 AATGTATCGATACATTGAA
196056 AATGTATCGATACATTGCAA
1 AATGTATCGATACATTG-AA
* *
196076 GCATGTATCAATACATT
1 -AATGTATCGATACATT
196093 CACTTATGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 2 0.06
21 14 0.44
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:196176 original size:20 final size:21
Alignment explanation
Indices: 196151--196201 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
196141 CAGGGTCCAA
* *
196151 TATCGATATATTTAGTT-ATG
1 TATCGATACATTTACTTGATG
*
196171 TATCGATACATTTACTTGTTG
1 TATCGATACATTTACTTGATG
196192 TATCGATACA
1 TATCGATACA
196202 AATTATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (21 bp):
TATCGATACATTTACTTGATG
Found at i:197563 original size:20 final size:22
Alignment explanation
Indices: 197515--197564 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
197505 AAAATATTTA
* *
197515 TGATTTTGTTGTTGAAAGATTT
1 TGATATTGTTGTTGAAAGAGTT
*
197537 TGTTATTGTTGTT-AAA-AGTT
1 TGATATTGTTGTTGAAAGAGTT
197557 TGATATTG
1 TGATATTG
197565 ATTTATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 11 0.46
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (22 bp):
TGATATTGTTGTTGAAAGAGTT
Found at i:201230 original size:154 final size:155
Alignment explanation
Indices: 201021--201317 Score: 388
Period size: 154 Copynumber: 1.9 Consensus size: 155
201011 CTCCTAAAAA
* * * * *
201021 ACTTGAAAAGGATTATAAAAAGGATGAACCTATCCTAAATTCTCACTTTCGGCATAAAAGTGGAC
1 ACTTAAAAAGGATTATAAAAAGGATGAACCAATCCTAAATTCCCACCTTCGGCATAAAAGCGGAC
* * * * *
201086 TCGGTGGCAACCTAAGGCTCAGTTATAAAAAAATACTAGAATGC-CCTA-AGGTCTA-CTTTCGA
66 CCGATGGCAACCTAAGACTCAGTTATAAAAAAATACTAAAATGCTCCTATA-GTATATC-TTCGA
201148 CATGAAAGTATCTCGGCAAACTTAAAG
129 CATGAAAGTATCTCGGCAAACTTAAAG
* * *
201175 ACTTAAAAAGGATTGTAAAAGGGATGAACCAAT-CTTAATTACCCACCTT-GAGCATAAAAGCGG
1 ACTTAAAAAGGATTATAAAAAGGATGAACCAATCCTAAATT-CCCACCTTCG-GCATAAAAGCGG
* *
201238 ACCCGATGGCAACCTAAGACTCAGTTCTAAAAAATTACTAAAATGCTCCTATAGTATATCTTCGA
64 ACCCGATGGCAACCTAAGACTCAGTTATAAAAAAATACTAAAATGCTCCTATAGTATATCTTCGA
201303 CATGAAAGTATCTCG
129 CATGAAAGTATCTCG
201318 CTAATCTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
153 7 0.06
154 86 0.70
155 28 0.23
156 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (155 bp):
ACTTAAAAAGGATTATAAAAAGGATGAACCAATCCTAAATTCCCACCTTCGGCATAAAAGCGGAC
CCGATGGCAACCTAAGACTCAGTTATAAAAAAATACTAAAATGCTCCTATAGTATATCTTCGACA
TGAAAGTATCTCGGCAAACTTAAAG
Found at i:201350 original size:18 final size:18
Alignment explanation
Indices: 201327--201361 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
201317 GCTAATCTTA
201327 AAGGAAACAAAAGTGATC
1 AAGGAAACAAAAGTGATC
**
201345 AAGGAAATGAAAGTGAT
1 AAGGAAACAAAAGTGAT
201362 AAACAATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.26, T:0.14
Consensus pattern (18 bp):
AAGGAAACAAAAGTGATC
Found at i:202208 original size:166 final size:165
Alignment explanation
Indices: 201772--202167 Score: 598
Period size: 166 Copynumber: 2.4 Consensus size: 165
201762 ACGAATTACC
* ** *
201772 CCCTAAACTTT-TTGAATTTACAAATTAGTCCTTGCATAATTAAAACA-AAAACTTAAGCATCAA
1 CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATATAATTAAAATACAAAA-TTAA-CATCAA
* * * *
201835 AGAAATCAAAATTAGCACACAAATCAGATCCAAAAATTATAAAGCAAATTCGGTCAATGATCATT
64 AGAAATCAAAATTAGCACACAAATCAAATCCAAAAATTACAAAGCAGATTCGGCCAATGATCATT
* *
201900 GGCCTTGGAATAAATTTTTCAATATTTACATTTAAAT
129 GGCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
* * * *
201937 CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATATACTTAAAATACAAAATTAAACATTAAA
1 CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATATAATTAAAATACAAAATT-AACATCAAA
*
202002 GAAATCAAAATTAGCACACAAATCAAATCCAAAAATTACAAAGCAGATTCGGCCAATGATCTTTG
65 GAAATCAAAATTAGCACACAAATCAAATCCAAAAATTACAAAGCAGATTCGGCCAATGATCATTG
202067 GCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
130 GCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
*
202103 CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATACAATTAAAATACAAAATTGAACATCAAA
1 CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATATAATTAAAATACAAAATT-AACATCAAA
202168 CATATCATAA
Statistics
Matches: 207, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
165 10 0.05
166 191 0.92
167 6 0.03
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.31
Consensus pattern (165 bp):
CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATATAATTAAAATACAAAATTAACATCAAAG
AAATCAAAATTAGCACACAAATCAAATCCAAAAATTACAAAGCAGATTCGGCCAATGATCATTGG
CCTTGGAACAAATTTTTCAATATTTACACTTAAAT
Found at i:202235 original size:166 final size:166
Alignment explanation
Indices: 201772--202261 Score: 497
Period size: 166 Copynumber: 3.0 Consensus size: 166
201762 ACGAATTACC
* * * ** * * *
201772 CCCTAAACTT-TTTGAATTTACAAATTAGTCCTTGCATAATTAAAACA-AAAACTTAAGCATCAA
1 CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATACAATTAAAATACAAAA-TTAAACATCAA
* * * * * * * *** *
201835 AGAAATCAAAATTAGCACACAAATCAGATCCAAAAATTATAAAGCAA-ATTCGGTCAATGATCAT
65 ACAAATCAAAATCAACAAAAAAATCAAATCCAAAAATTACAAAG-AAGATTCAACCAATGATCTT
* *
201899 TGGCCTTGGAATAAATTTTTCAATATTTACATTTAAAT
129 TGGCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
* * *
201937 CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATATACTTAAAATACAAAATTAAACATTAAA
1 CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATACAATTAAAATACAAAATTAAACATCAAA
* * * * * * **
202002 GAAATCAAAATTAGCACACAAATCAAATCCAAAAATTACAAAGCAGATTCGGCCAATGATCTTTG
66 CAAATCAAAATCAACAAAAAAATCAAATCCAAAAATTACAAAGAAGATTCAACCAATGATCTTTG
202067 GCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
131 GCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
* * *
202103 CCCTAAACTTTCTTGAATTTGCAAATTAGTCCTTATACAATTAAAATACAAAATTGAACATCAAA
1 CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATACAATTAAAATACAAAATTAAACATCAAA
* * * * * * *
202168 CATATCATAATCAATAAAAAAATCAAATCTAAAGATTACAAGGAAGATTCAACCAAATGCT-TTT
66 CAAATCAAAATCAACAAAAAAATCAAATCCAAAAATTACAAAGAAGATTCAACC-AATGATCTTT
* *
202232 GGCC-TCGAGACAAAATTTTT-TATATTTACA
130 GGCCTTGGA-AC-AAATTTTTCAATATTTACA
202262 AATTTACCCT
Statistics
Matches: 280, Mismatches: 39, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
165 14 0.05
166 249 0.89
167 17 0.06
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.31
Consensus pattern (166 bp):
CCCTAAACTTCCTTGAATTTGCAAATTAGTACTTATACAATTAAAATACAAAATTAAACATCAAA
CAAATCAAAATCAACAAAAAAATCAAATCCAAAAATTACAAAGAAGATTCAACCAATGATCTTTG
GCCTTGGAACAAATTTTTCAATATTTACACTTAAAT
Done.