Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2676
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: 55639
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:150 original size:19 final size:18
Alignment explanation
Indices: 115--153 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
105 TTGTTGCTGG
*
115 TTTTTCTTTTTCTTTTCT
1 TTTTTCTTTTTCCTTTCT
*
133 TTTTTTTTTTTCACTTTCT
1 TTTTTCTTTTTC-CTTTCT
152 TT
1 TT
154 CTATGTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTCCTTTCT
Found at i:1673 original size:29 final size:29
Alignment explanation
Indices: 1631--1696 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
1621 AAATGATTTT
1631 TTTTATATAATTAAAATTTAAAATTTTAAG
1 TTTTATATAATTAAAA-TTAAAATTTTAAG
* *
1661 TTTTA-ATTATTAAAATTAAAATTTTAATA
1 TTTTATATAATTAAAATTAAAATTTTAA-G
1690 TTTTATA
1 TTTTATA
1697 AGAATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 12 0.38
29 14 0.44
30 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTATATAATTAAAATTAAAATTTTAAG
Found at i:2519 original size:12 final size:11
Alignment explanation
Indices: 2486--2512 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2476 TATTTTTAAA
2486 TTTTAAAATAT
1 TTTTAAAATAT
2497 TTTTAAAATAT
1 TTTTAAAATAT
2508 TTTTA
1 TTTTA
2513 TATATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3516 original size:2 final size:2
Alignment explanation
Indices: 3509--3546 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3499 ATAGTAGTGC
3509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3547 GTTTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4400 original size:36 final size:36
Alignment explanation
Indices: 4336--4432 Score: 124
Period size: 36 Copynumber: 2.6 Consensus size: 36
4326 TAAAAATATT
*
4336 ATTTTAATAATTTTTAATTATTATTTAATGTAAACATA
1 ATTTTAATAA-TTTT-ATTATTATTTAATATAAACATA
* *
4374 ATTTTTATATATTTT-TTATTATTTAATATAAATATA
1 ATTTTAATA-ATTTTATTATTATTTAATATAAACATA
4410 ATTTTAATAATTTTAATTATTAT
1 ATTTTAATAATTTT-ATTATTAT
4433 ATATATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 5 0.10
36 27 0.52
37 7 0.13
38 12 0.23
39 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (36 bp):
ATTTTAATAATTTTATTATTATTTAATATAAACATA
Found at i:4466 original size:15 final size:15
Alignment explanation
Indices: 4416--4466 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
4406 TATAATTTTA
4416 ATAAT-TTTAATTATT
1 ATAATATTT-ATTATT
*
4431 ATATATATTTTTTAATT
1 ATA-ATATTTATT-ATT
4448 -TAATATTTATTATT
1 ATAATATTTATTATT
4462 ATAAT
1 ATAAT
4467 TTATTTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 15 0.50
16 6 0.20
17 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAATATTTATTATT
Found at i:4695 original size:34 final size:32
Alignment explanation
Indices: 4648--4749 Score: 115
Period size: 34 Copynumber: 3.3 Consensus size: 32
4638 AATTCTTTTT
*
4648 ATTTTAATA-ATTTATTTTTAAAATAAACATA
1 ATTTTAATATATTTATTTTTAATATAAACATA
* *
4679 ATTTTAATA-A-TTA--TTTAATATAGATATA
1 ATTTTAATATATTTATTTTTAATATAAACATA
*
4707 ATTTTAATATTTTTTATTATTTAATATAAACATA
1 ATTTTAATA-TATTTATT-TTTAATATAAACATA
4741 ATTTTAATA
1 ATTTTAATA
4750 AATGTAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
28 21 0.36
30 3 0.05
31 13 0.22
34 22 0.37
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (32 bp):
ATTTTAATATATTTATTTTTAATATAAACATA
Found at i:4986 original size:16 final size:16
Alignment explanation
Indices: 4965--4995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4955 GATTTTATTA
*
4965 CTTTTTTAATTGAATG
1 CTTTTTCAATTGAATG
4981 CTTTTTCAATTGAAT
1 CTTTTTCAATTGAAT
4996 TTATAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (16 bp):
CTTTTTCAATTGAATG
Found at i:5457 original size:17 final size:18
Alignment explanation
Indices: 5425--5458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5415 CTTTGTTAAA
*
5425 ATTTTTGTGTACATAATT
1 ATTTTTGTATACATAATT
5443 ATTTTTGTATA-ATAAT
1 ATTTTTGTATACATAAT
5459 CTCTAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTTTGTATACATAATT
Found at i:6193 original size:39 final size:40
Alignment explanation
Indices: 6140--6262 Score: 103
Period size: 38 Copynumber: 3.1 Consensus size: 40
6130 TGATAATATG
* *
6140 ATATTAAAAGTTAATTAATAAATAATA-AAAAATA-AAAT
1 ATATAAAAATTTAATTAATAAATAATATAAAAATATAAAT
* * *
6178 ATAATAAAAATTTAA-T-ATATATGATATAAATATATAAAT
1 AT-ATAAAAATTTAATTAATAAATAATATAAAAATATAAAT
* * * *
6217 ATATCAAAATTTATATTATTATAATAAT-TAAATATATATAT
1 ATATAAAAATTTA-ATTAATA-AATAATATAAAAATATAAAT
6258 ATATA
1 ATATA
6263 TATAAATACA
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
37 8 0.12
38 19 0.28
39 17 0.25
40 1 0.01
41 18 0.27
42 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (40 bp):
ATATAAAAATTTAATTAATAAATAATATAAAAATATAAAT
Found at i:8366 original size:3 final size:3
Alignment explanation
Indices: 8358--8392 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8348 CTTCATCCCT
8358 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
8393 GCCTCCCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.34, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:10920 original size:10 final size:10
Alignment explanation
Indices: 10905--10935 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10895 CCAATGCTCC
10905 AATATATATA
1 AATATATATA
10915 AATATATATA
1 AATATATATA
*
10925 TATATATATA
1 AATATATATA
10935 A
1 A
10936 TAATCTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATATATA
Found at i:13705 original size:3 final size:3
Alignment explanation
Indices: 13699--13730 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13689 TATTATTATT
*
13699 GTC GTC GTC GTC GTC GTC GTC ATC GTC GTC GT
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GT
13731 GGTAGAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.31, G:0.31, T:0.34
Consensus pattern (3 bp):
GTC
Found at i:13871 original size:5 final size:5
Alignment explanation
Indices: 13856--13900 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
13846 ATAATACTAT
13856 TAAAA -AAAA TAAAA TAAAA TTAAAA T--AA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA TA
13901 TATTTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 24 0.67
6 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:13885 original size:19 final size:18
Alignment explanation
Indices: 13858--13900 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
13848 AATACTATTA
*
13858 AAAAAAATAAAATAAAATT
1 AAAATAATAAAATAAAA-T
13877 AAAATAATAAAATAAAAT
1 AAAATAATAAAATAAAAT
13895 AAAATA
1 AAAATA
13901 TATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAATAAAATAAAAT
Found at i:13917 original size:20 final size:20
Alignment explanation
Indices: 13894--13931 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13884 TAAAATAAAA
13894 TAAAATATATTTTA-ATATTT
1 TAAAATAT-TTTTATATATTT
*
13914 TAAATTATTTTTATATAT
1 TAAAATATTTTTATATAT
13932 ATAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAATATTTTTATATATTT
Found at i:13924 original size:18 final size:19
Alignment explanation
Indices: 13896--13945 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13886 AAATAAAATA
*
13896 AAATATATTTTAATAT-TTT
1 AAAT-TATTTTAATATATAT
*
13915 AAATTATTTTTATATATAT
1 AAATTATTTTAATATATAT
*
13934 AAATTTTTTTAA
1 AAATTATTTTAA
13946 AAAATTATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AAATTATTTTAATATATAT
Found at i:17862 original size:2 final size:2
Alignment explanation
Indices: 17857--17887 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17847 GTGTGTGTGT
17857 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
17888 TATAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19070 original size:6 final size:6
Alignment explanation
Indices: 19059--19090 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19049 TAATACATAA
*
19059 ATAAAT ATAAAT ATAACT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
19091 TTAGGGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:21892 original size:78 final size:79
Alignment explanation
Indices: 21755--21922 Score: 239
Period size: 78 Copynumber: 2.1 Consensus size: 79
21745 ACCACGGGGC
* * * *
21755 TGGAGTATCCCAGATTATAGAAAATCGGTGTTTTGGAAATAAAATCGGGGTTAGTGTATCCCCTC
1 TGGAGTATCCCAGATTATAGAAAATCGGTATTTTGAAAATAAAATCGAGGTTAGAGTATCCCCTC
*
21820 GGAAA-AACAGGGT
66 GAAAATAACAGGGT
* * *
21833 TGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAAATAAAATCGAGGTTGGAGTATCCCTTC
1 TGGAGTATCCCAGATTATAGAAAATCGGTATTTTGAAAATAAAATCGAGGTTAGAGTATCCCCTC
**
21898 GAAAATAATGGGGT
66 GAAAATAACAGGGT
21912 TGGAGTATCCC
1 TGGAGTATCCC
21923 CAATTTTGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 62 0.78
79 17 0.22
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (79 bp):
TGGAGTATCCCAGATTATAGAAAATCGGTATTTTGAAAATAAAATCGAGGTTAGAGTATCCCCTC
GAAAATAACAGGGT
Found at i:21952 original size:79 final size:78
Alignment explanation
Indices: 21748--21974 Score: 233
Period size: 78 Copynumber: 2.9 Consensus size: 78
21738 GGAGATGACC
* * * * *
21748 ACGGGGCTGGAGTAT-CCCAGATTATAGAAAATCGGTGTTTTGGAAATAAAATCGGGGTTAGTGT
1 ACGGGGTTGGAGTATCCCCA-ATTATAGAAAATCGGTGATTTAGAAATAAAATCGGGGTTGGAGT
*
21812 ATCCCCTCGGAAAA
65 ATCCCCTCGAAAAA
* ** * *
21826 ACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGT-ATTTTGAAAATAAAATCGAGGTTGGAGT
1 ACGGGGTTGGAGTATCCCCAATTATAGAAAATCGGTGATTTAG-AAATAAAATCGGGGTTGGAGT
*
21890 ATCCCTTCGAAAATA
65 ATCCCCTCGAAAA-A
* * * * * ***
21905 ATGGGGTTGGAGTATCCCCAATTTTGGAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTA
1 ACGGGGTTGGAGTATCCCCAATTATAGAAAATCGGTGATTTAGAAATAAAATCGGGGTTGGAGTA
21970 TCCCC
66 TCCCC
21975 GATTGTGAGA
Statistics
Matches: 120, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
77 4 0.03
78 58 0.48
79 54 0.45
80 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (78 bp):
ACGGGGTTGGAGTATCCCCAATTATAGAAAATCGGTGATTTAGAAATAAAATCGGGGTTGGAGTA
TCCCCTCGAAAAA
Found at i:21998 original size:51 final size:51
Alignment explanation
Indices: 21907--22058 Score: 148
Period size: 51 Copynumber: 3.0 Consensus size: 51
21897 CGAAAATAAT
* * * * **
21907 GGGGTTGGAGTATCCCCAATTTTG-GAAAATCG-ATGCTTTAGAAATAAGGCC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTAT--TTTAGAAATAAAACC
*
21958 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAATC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAACC
* * * * *
22009 GGAGTTGGAGTA-CTCTCGATTGTGAAAAATTGGTATTTTAGAAATGAAAC
1 GGGGTTGGAGTATC-CCCGATTGTGAGAAATTAGTATTTTAGAAATAAAAC
22059 AAAACTACTT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 76 0.89
52 6 0.07
53 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAACC
Found at i:24357 original size:20 final size:19
Alignment explanation
Indices: 24332--24406 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
24322 AAAATGCCTG
*
24332 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
* *
24352 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGA-A
24372 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
24392 AATGTATCGATACAA
1 AATGTATCGATACAA
24407 CAAGCTAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:25070 original size:41 final size:41
Alignment explanation
Indices: 24971--25072 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
24961 ATCCCACTTT
* * * *
24971 TTGAGGACAAAGG-AAAAGAGAATGAAATAGGTCTTTCTCC
1 TTGAGGACAAAGGAAAAAGAAAAGGAAATAGGTCATGCTCC
* * *
25011 TTGAGGACAAAAGAAAAAAGAAAAGGAAAT-TGTCATGCTTC
1 TTGAGGAC-AAAGGAAAAAGAAAAGGAAATAGGTCATGCTCC
25052 TTGAGGACAAAGTGAAAAAGA
1 TTGAGGACAAAG-GAAAAAGA
25073 GTAAGTCCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 12 0.24
41 26 0.51
42 13 0.25
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.20
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAAGAAAAGGAAATAGGTCATGCTCC
Found at i:25143 original size:39 final size:40
Alignment explanation
Indices: 25100--25177 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
25090 AGGACAAAGG
* * *
25100 AAAAAA-AGGAAAATGAATTGCATCCTGCTCTTTGAGGAT
1 AAAAAAGAGGAAAATAAAGTGCATCATGCTCTTTGAGGAT
*
25139 AAAAAAGAGGAAAATAAAGTGCGTCATGCTCTTTGAGGA
1 AAAAAAGAGGAAAATAAAGTGCATCATGCTCTTTGAGGA
25178 CAAATGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (40 bp):
AAAAAAGAGGAAAATAAAGTGCATCATGCTCTTTGAGGAT
Found at i:25254 original size:38 final size:42
Alignment explanation
Indices: 25155--25261 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 42
25145 GAGGAAAATA
25155 AAGTGCGTCATGCTCTTTGAGGACAAATGGGAAAAGAAGGGAATG
1 AAGTGCGTCATGCTCTTTGAGGACAAA--GGAAAAGAAGGGAA-G
* * *
25200 AAGTGTGTCCTGCTCTTTGAGGACAAA-GAAGA-AAGGGAA-
1 AAGTGCGTCATGCTCTTTGAGGACAAAGGAAAAGAAGGGAAG
*
25239 AA-TGCGTCTTGCTCTTTGAGGAC
1 AAGTGCGTCATGCTCTTTGAGGAC
25262 TAAAAAGTGC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
38 19 0.33
39 2 0.04
41 7 0.12
42 4 0.07
45 25 0.44
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (42 bp):
AAGTGCGTCATGCTCTTTGAGGACAAAGGAAAAGAAGGGAAG
Found at i:25318 original size:61 final size:61
Alignment explanation
Indices: 25243--25417 Score: 280
Period size: 61 Copynumber: 2.9 Consensus size: 61
25233 AGGGAAAATG
*
25243 CGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGA
* * *
25304 CGTCCTGCTCTTTGAGGACTAGAAAA-TACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGA
* *
25365 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
1 CGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
25418 GGCATCCTGC
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
60 3 0.03
61 98 0.93
62 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (61 bp):
CGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGA
Found at i:25443 original size:55 final size:56
Alignment explanation
Indices: 25237--25445 Score: 233
Period size: 61 Copynumber: 3.6 Consensus size: 56
25227 GAAGAAAGGG
* * *
25237 AAAATGCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTA
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
25293 AAAAGAAAAGACGTCCTGCTCTTTGAGGACTAGAAA-ATACCACCAACTTGTGTGGGCTTTAAAA
1 AAAAG----G-CGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT---A
*
25357 GGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-
1 --AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
25414 AAAAGGCATCCTGCTCCTTGAGGACTAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGG
25446 CCTGCTCTTT
Statistics
Matches: 132, Mismatches: 9, Indels: 25
0.80 0.05 0.15
Matches are distributed among these distances:
55 30 0.23
56 4 0.03
60 4 0.03
61 84 0.64
62 4 0.03
64 1 0.01
66 5 0.04
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (56 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTA
Found at i:25457 original size:23 final size:23
Alignment explanation
Indices: 25423--25468 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
25413 TAAAAGGCAT
25423 CCTGCTCCTTGAGGACTAAAAGG
1 CCTGCTCCTTGAGGACTAAAAGG
*
25446 CCTGCTCTTTGAGGACTAAAAGG
1 CCTGCTCCTTGAGGACTAAAAGG
25469 TGCCACCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (23 bp):
CCTGCTCCTTGAGGACTAAAAGG
Found at i:25724 original size:121 final size:122
Alignment explanation
Indices: 25446--25805 Score: 562
Period size: 121 Copynumber: 2.9 Consensus size: 122
25436 GACTAAAAGG
* **
25446 CCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGTTGTCC
1 CCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGCGTCC
* * * *
25510 TACTCTTTGAAGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGTGT
64 TGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGTGT
* *
25571 CCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTG
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCTG
25636 CTC-TTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
66 CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
*
25692 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTG
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCTG
*
25757 CTCTTTGAGGACTAGAAAAGTGCTACCAACTTGTGTGGGCTTTAAAAGG
66 CTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGG
25806 CGCCCTGCTC
Statistics
Matches: 219, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
121 74 0.34
122 20 0.09
123 64 0.29
124 12 0.05
125 47 0.21
126 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (122 bp):
CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCTG
CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
Found at i:25734 original size:61 final size:61
Alignment explanation
Indices: 25446--25805 Score: 544
Period size: 61 Copynumber: 5.9 Consensus size: 61
25436 GACTAAAAGG
* * *
25446 CCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGTTGT
1 CCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGT
* * * *
25508 CCTACTCTTTGAAGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGTGT
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGTGT
* * **
25571 CCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCAT
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
25632 CCTGCTC-TTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
*
25692 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
1 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
*
25753 CCTGCTCTTTGAGGACTAGAAAAGTGCTACCAACTTGTGTGGGCTTTAAAAGG
1 CCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGG
25806 CGCCCTGCTC
Statistics
Matches: 277, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
60 56 0.20
61 89 0.32
62 77 0.28
63 55 0.20
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGT
Found at i:26047 original size:117 final size:118
Alignment explanation
Indices: 25894--26176 Score: 363
Period size: 117 Copynumber: 2.4 Consensus size: 118
25884 TGTGAGCTTT
25894 AAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AG-AAGGCG
1 AAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAAAGGCG
*
25957 TCCTACTCTTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTTGAAAAGA
66 TCATACTCTTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTT-AAAAGA
* *
26011 AAAAGGTGTCCTGCTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1 AAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT---AAG--AA
* * ** * *
26076 AGGTGTCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
61 AGGCGTCATACTCTTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTTAAAAGA
** * ** *
26134 TGAAGGTATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACT
1 AAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
26177 TTTGTGCGTC
Statistics
Matches: 143, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
117 53 0.37
121 2 0.01
123 41 0.29
124 47 0.33
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (118 bp):
AAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAAAGGCG
TCATACTCTTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTTAAAAGA
Found at i:26053 original size:62 final size:61
Alignment explanation
Indices: 25846--26182 Score: 376
Period size: 62 Copynumber: 5.7 Consensus size: 61
25836 AGGAGAGAGC
** * *
25846 GTCCTGCTCTTTGAGGACTGGGAA-GTGCCACTAACTTGTGTGAGCTTT------AAAAGGT
1 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGT
* *
25901 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT---AG---AAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGT
* ** *
25956 GTCCTACTCTTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGT
*
26018 GTCCTGCTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGT
* ***
26080 GTCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGT
* ** * *
26141 ATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTTTTGTG
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTG
26183 CGTCCTACTC
Statistics
Matches: 243, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
54 2 0.01
55 87 0.36
59 2 0.01
61 46 0.19
62 106 0.44
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGT
Found at i:26054 original size:266 final size:270
Alignment explanation
Indices: 25569--26069 Score: 712
Period size: 266 Copynumber: 1.8 Consensus size: 270
25559 GAAAAAAGGT
*
25569 GTCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
1 GTCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGAGCTTTAAAAAG---AGG-ATCC
* * *
25634 TGCTCTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTC
62 TGCTCTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTT--AAGG-AAAGGCGTCCTACTC
* * * *
25699 TTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTG
124 TTTGAGGACTAAAAAATGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCGTCCTGCTATTTG
*
25764 AGGACTAGAAAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGCGCCCTGCTCTTTGAGGACCAAA
189 AGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGCCCTGCTCTTTGAGGACCAAA
25829 GGGCGAAAGGAGAGAGC
254 GGGCGAAAGGAGAGAGC
* * *
25846 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACTAACTTGTGTGAGCTTT-AAAAG-GTG-TCCTGC
1 GTCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGAGCTTTAAAAAGAG-GATCCTGC
*
25908 TCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTT-A-G-AAGGCGTCCTACTCTTTG
65 TC-TTGAGGACTAGAAA-ATGCCACCAACTCGTGTGGGCTTTAAGGAAAGGCGTCCTACTCTTTG
*
25969 AGGACTAAAAAATGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGGTGTCCTGCTATTTGAGG
128 AGGACTAAAAAATGCCACCAACTTATGTGGGCTTT-AAAAGAAAAAGGCGTCCTGCTATTTGAGG
*
26034 ACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
192 ACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
26070 AGAAAAAGGT
Statistics
Matches: 205, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
266 79 0.39
267 30 0.15
268 1 0.00
269 1 0.00
271 11 0.05
272 33 0.16
273 1 0.00
276 5 0.02
277 44 0.21
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (270 bp):
GTCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGAGCTTTAAAAAGAGGATCCTGCT
CTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTAAGGAAAGGCGTCCTACTCTTTGAGG
ACTAAAAAATGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCGTCCTGCTATTTGAGGACTA
GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGCCCTGCTCTTTGAGGACCAAAGGGCGAA
AGGAGAGAGC
Found at i:26211 original size:43 final size:43
Alignment explanation
Indices: 26142--26225 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
26132 GGTGAAGGTA
* * *
26142 TCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTTTTGTGCG
1 TCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGCG
*
26185 TCCTACTCTTTGAGGACTGGAAGGTGCCATCAACTTGTGTG
1 TCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTG
26226 GGCTTCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.31
Consensus pattern (43 bp):
TCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGCG
Found at i:26273 original size:104 final size:104
Alignment explanation
Indices: 26086--26280 Score: 255
Period size: 104 Copynumber: 1.9 Consensus size: 104
26076 AGGTGTCATG
* ** * *
26086 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGAAGGTATCCTGCTCT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAGGAAAAAGCATCCTGCTCT
* *
26151 TTGAGGACTGGAGGGTGCCACCAACTTTTGTGCGTCCTA
66 TTGAGGACTGAAAGGTGCCACCAACTTTTGTGCGTCCTA
** * * * *
26190 CTCTTTGAGGACTGGAAGGTGCCATCAACTTGTGTGGGCTTCAGAAGGAAAAAGCGTCCTGTTCT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAGGAAAAAGCATCCTGCTCT
* *
26255 TTGAGGATTGAAATGTGCCACCAACT
66 TTGAGGACTGAAAGGTGCCACCAACT
26281 CGTATGGGCT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
104 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (104 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAGGAAAAAGCATCCTGCTCT
TTGAGGACTGAAAGGTGCCACCAACTTTTGTGCGTCCTA
Found at i:26280 original size:61 final size:61
Alignment explanation
Indices: 26182--26329 Score: 174
Period size: 61 Copynumber: 2.4 Consensus size: 61
26172 CAACTTTTGT
* * * * * *
26182 GCGTCCTACTCTTTGAGGACTGGAAGGTGCCATCAACTTGTGTGGGCTTCAGAAGGAAAAA-
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTCA-AAAGAAAAAG
* * * *
26243 GCGTCCTGTTCTTTGAGGATTGAAATGTGCCACCAACTCGTATGGGCTTGAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTCAAAAGAAAAAG
*
26304 GCATCCTGCTCTTTGAGGACT-AAAGG
1 GCGTCCTGCTCTTTGAGGACTGAAAGG
26330 ACTAAAAGGG
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 12 0.17
61 60 0.83
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTCAAAAGAAAAAG
Found at i:26318 original size:165 final size:166
Alignment explanation
Indices: 26018--26324 Score: 418
Period size: 165 Copynumber: 1.9 Consensus size: 166
26008 AGAAAAAGGT
* * *
26018 GTCCTGCTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTC
1 GTCCTACTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAAGAAAAAGGCGTC
* * * *** *
26083 ATGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGAAGGTATCCTGC
66 ATGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTATGGGCTTGAAAAGAAAAAGGCATCCTGC
26148 TCTTTGAGGACTGGAGGGTGCCACCAACTTTTGTGC
131 TCTTTGAGGACTGGAGGGTGCCACCAACTTTTGTGC
* ** * * *
26184 GTCCTACTCTTTGAGGACTGGAAGGTGCCATCAACTTGTGTGGGCTTCAGAAGGAAAAA-GCGTC
1 GTCCTACTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAAGAAAAAGGCGTC
* * * * *
26248 CTGTTCTTTGAGGATTGAAATGTGCCACCAACTCGTATGGGCTTGAAAAGAAAAAGGCATCCTGC
66 ATGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTATGGGCTTGAAAAGAAAAAGGCATCCTGC
26313 TCTTTGAGGACT
131 TCTTTGAGGACT
26325 AAAGGACTAA
Statistics
Matches: 120, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
165 69 0.57
166 51 0.43
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (166 bp):
GTCCTACTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTCAAAAAGAAAAAGGCGTC
ATGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTATGGGCTTGAAAAGAAAAAGGCATCCTGC
TCTTTGAGGACTGGAGGGTGCCACCAACTTTTGTGC
Found at i:33594 original size:20 final size:19
Alignment explanation
Indices: 33569--33634 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
33559 ATTTGCTTGC
33569 ATGTATCGATACATTGAATA
1 ATGTATCGATACA-TGAATA
33589 ATGTATCG----AT--ATA
1 ATGTATCGATACATGAATA
33602 ATGTATCGATACAGTGAATA
1 ATGTATCGATACA-TGAATA
33622 ATGTATCGATACA
1 ATGTATCGATACA
33635 CATTTCCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 24 0.62
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACATGAATA
Found at i:33604 original size:13 final size:13
Alignment explanation
Indices: 33586--33612 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33576 GATACATTGA
33586 ATAATGTATCGAT
1 ATAATGTATCGAT
33599 ATAATGTATCGAT
1 ATAATGTATCGAT
33612 A
1 A
33613 CAGTGAATAA
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:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATAATGTATCGAT
Found at i:33606 original size:33 final size:33
Alignment explanation
Indices: 33569--33632 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
33559 ATTTGCTTGC
*
33569 ATGTATCGATACATTGAATAATGTATCGATATA
1 ATGTATCGATACAGTGAATAATGTATCGATATA
33602 ATGTATCGATACAGTGAATAATGTATCGATA
1 ATGTATCGATACAGTGAATAATGTATCGATA
33633 CACATTTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACAGTGAATAATGTATCGATATA
Found at i:34260 original size:20 final size:20
Alignment explanation
Indices: 34235--34309 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
34225 TTTTCACAAT
34235 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
* *
34255 TTGTATCAATACATTGCTCA
1 TTGTATCGATACATTGTTCA
**
34275 TTGTATCGATGTATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
34295 ATGTATCGATACATT
1 TTGTATCGATACATT
34310 CAGGCATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:36684 original size:51 final size:50
Alignment explanation
Indices: 36604--36772 Score: 169
Period size: 51 Copynumber: 3.3 Consensus size: 50
36594 TTTTTTCATC
* ** ***
36604 TCGGGGATACTCCAA-TCCCGGTTCCATTTCTGAAACATCAATTTTTTTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCT-AAACATCAATTTTTCGCAA
* * **
36655 TCGGGGATACTTCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCTAAA-CATCAATTTTTCGCAA
* * *
36706 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTT-CTAAACATCAATTTTTCGCAA
*
36757 TTGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
36773 CCCGTTATTT
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
50 3 0.03
51 89 0.92
52 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (50 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCTAAACATCAATTTTTCGCAA
Found at i:36876 original size:28 final size:28
Alignment explanation
Indices: 36845--36912 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
36835 ATCGGGGGGC
*
36845 ACTCCAACCCCGTTATGTCAT-CGGGGAT
1 ACTCCAACCCCGTTATGTC-TGAGGGGAT
* * *
36873 ACTCCAATCCTGTTATTTCTGAGGGGAT
1 ACTCCAACCCCGTTATGTCTGAGGGGAT
36901 ACTCCAACCCCG
1 ACTCCAACCCCG
36913 ATTTTATTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.26
Consensus pattern (28 bp):
ACTCCAACCCCGTTATGTCTGAGGGGAT
Found at i:37013 original size:51 final size:51
Alignment explanation
Indices: 36896--37013 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
36886 TATTTCTGAG
** * * *
36896 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCTATTTCTCAAAATCG
1 GGGATACTCCAACCCTAATTTTATTTCTAAAACACCAATTTCTCAAAATCA
*
36947 GGGATACTCCAACCCTAATTTTATTT-TCAAAACACCAATTT-TCTATAATCA
1 GGGATACTCCAACCCTAATTTTATTTCT-AAAACACCAATTTCTC-AAAATCA
36998 GGGATACTCCAACCCT
1 GGGATACTCCAACCCT
37014 GTTATTTCCG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 3 0.05
51 56 0.95
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCTAATTTTATTTCTAAAACACCAATTTCTCAAAATCA
Found at i:37029 original size:79 final size:78
Alignment explanation
Indices: 36946--37168 Score: 286
Period size: 81 Copynumber: 2.8 Consensus size: 78
36936 TCTCAAAATC
** *
36946 GGGGATACTCCAACCCTAATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTT-TATAATCAGGGATACTCCAAC
37011 CCTGTTATTTCCGA
65 CCTGTTATTTCCGA
* * *
37025 GGGGATACTCCAACCCCCCGATTTTATTTTCAAAATACTGATTTTTTATAATTAGGGATACTCCA
1 GGGGATACTCCAA--CCCCGATTTTATTTTCAAAACACCGA-TTTTTATAATCAGGGATACTCCA
*
37090 ACCCTGTTATTTCTGA
63 ACCCTGTTATTTCCGA
* * * *
37106 GGAGATACTCTAACCCCGATTTTATTTCCAAAACATCGATTTTTCATAATC-GAGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTT-ATAATCAG-GGATACTCCA
37169 CCCCCGTTGT
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 6 0.05
79 50 0.40
81 65 0.52
82 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTTATAATCAGGGATACTCCAACC
CTGTTATTTCCGA
Found at i:50962 original size:61 final size:59
Alignment explanation
Indices: 50633--50962 Score: 381
Period size: 61 Copynumber: 5.6 Consensus size: 59
50623 CCTTTCGCTC
*
50633 TTTAGTCCTCAAAGAGCAGGACGCC----TTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCA-CTT
*
50689 TTTAGTTCTCAAAGAGCAGGACGCC---TTTT-AAAGCCCACACAAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTT
* *
50744 TTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
1 TT-TAGTCCTCAAAGAGCAGGACGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCACTT
* *
50806 TTTAGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTT-T-TTT-CAAAGCCCACACAAGTTGGTGGCACTT
** * ** *
50867 TCCAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAGCCCACATGAGTTGGTGGTACTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTT--TTTTCAAAGCCCACACAAGTTGGTGGCACTT
*
50928 TTTAGTCCTCAAAGAGCAAGACGCACTTTATTTTC
1 TTTAGTCCTCAAAGAGCAGGACGC-CTTT-TTTTC
50963 CTCTTTCCTT
Statistics
Matches: 241, Mismatches: 20, Indels: 21
0.85 0.07 0.07
Matches are distributed among these distances:
55 4 0.02
56 68 0.28
57 3 0.01
59 1 0.00
60 8 0.03
61 117 0.49
62 38 0.16
63 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (59 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTT
Found at i:51093 original size:42 final size:42
Alignment explanation
Indices: 50927--51079 Score: 189
Period size: 42 Copynumber: 3.5 Consensus size: 42
50917 TGGTGGTACT
*
50927 TTTTAGTCCTCAAAGAGCAAGACGCACTTTATTTTCCTCTTTC
1 TTTT-GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTC
* * * * ** *
50970 CTTTGTCCTCAAAGAGCAAGACACACTTAATTCTCTTTTTTTCTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATT-T-TCCTCTT-TC
51015 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTC
*
51057 TTTTGTCCTCAAGGAGCAGGACG
1 TTTTGTCCTCAAAGAGCAGGACG
51080 TATTTCGTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 50 0.54
43 8 0.09
44 5 0.05
45 30 0.32
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTC
Found at i:51706 original size:20 final size:20
Alignment explanation
Indices: 51681--51735 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
51671 TTTACCCATA
*
51681 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
51701 TGTATCGATATATTGCTCAT
1 TGTATCGATACATTGCTCAT
51721 TGTATCGATACATTG
1 TGTATCGATACATTG
51736 TATCGATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:51734 original size:13 final size:13
Alignment explanation
Indices: 51718--51748 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
51708 ATATATTGCT
51718 CATTGTATCGATA
1 CATTGTATCGATA
51731 CATTGTATCGATA
1 CATTGTATCGATA
51744 CATTG
1 CATTG
51749 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:51740 original size:33 final size:33
Alignment explanation
Indices: 51698--51767 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
51688 ATACATTTTG
* *
51698 CATTGTATCGATATATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
*
51731 CATTGTATCGATACATTGCTCATTGTATTAATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
51764 CATT
1 CATT
51768 TTACAATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCAATA
Found at i:53390 original size:51 final size:50
Alignment explanation
Indices: 53313--53478 Score: 172
Period size: 51 Copynumber: 3.3 Consensus size: 50
53303 TTTTCATCTC
* ** **
53313 GGGATACTCCAA-TCCCGGTTCCATTTCTGAAACATCAATTTTTCTTAATTG
1 GGGATACTCCAACT-CCGATTTTATTTCT-AAACATCAATTTTTCACAATTG
* ** * *
53364 GGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGCAATCG
1 GGGATACTCCAACTCCGATTTTATTTCTAAA-CATCAATTTTTCACAATTG
* * *
53415 GGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTTTCACAATTG
1 GGGATACTCCAACTCCGATTTTATTT-CTAAACATCAATTTTTCACAATTG
53466 GGGATACTCCAAC
1 GGGATACTCCAAC
53479 ATCGTTATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.03
51 87 0.92
52 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (50 bp):
GGGATACTCCAACTCCGATTTTATTTCTAAACATCAATTTTTCACAATTG
Found at i:53667 original size:51 final size:51
Alignment explanation
Indices: 53604--53719 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
53594 ATTTCCGAAA
* * *
53604 GGATACTTCAACCCCGATTTTA-TTTCTAAAATACCAA-TTTCTCACAATCG-G
1 GGATACTCCAACCCCAATTTTATTTTC-AAAACACCAATTTTCT-ACAAT-GAG
*
53655 GGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATGAG
1 GGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTACAATGAG
53706 GGATACTCCAACCC
1 GGATACTCCAACCC
53720 TGTTATTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.02
51 48 0.83
52 9 0.16
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTACAATGAG
Found at i:53740 original size:79 final size:79
Alignment explanation
Indices: 53657--53873 Score: 303
Period size: 79 Copynumber: 2.7 Consensus size: 79
53647 ACAATCGGGG
*
53657 ATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATGAGGGATACTCCAACCCTG
1 ATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATGAGGGATACTCCAACCCTG
53722 TTATTT-TCGAGAGA
66 TTATTTCT-GAGAGA
* * * * *
53736 ATACTCCAACCTCGATTTTTTTTTCAAAATACTAATTTTCTATAATCAGGGATACTCCAACCCTG
1 ATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATGAGGGATACTCCAACCCTG
* *
53801 TTATTTCTGAGGGG
66 TTATTTCTGAGAGA
* * *
53815 ATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTCCATAATCG-GGGATACTCCA
1 ATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAAT-GAGGGATACTCCA
53874 CCCCCGTTGT
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
79 119 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (79 bp):
ATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATGAGGGATACTCCAACCCTG
TTATTTCTGAGAGA
Found at i:54577 original size:35 final size:35
Alignment explanation
Indices: 54536--54719 Score: 286
Period size: 35 Copynumber: 5.4 Consensus size: 35
54526 TAAAAAAAAA
54536 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
* **
54571 CATGGAATGATGGGCAT-GAA-ATAAAAA-AAAAA
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
54603 CATGGGATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
54638 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
54673 CATAGAATGATGGGCATGGAATA-AAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
54707 CATGGAATGATGG
1 CATGGAATGATGG
54720 ATAAAAATGA
Statistics
Matches: 135, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
32 18 0.13
33 10 0.07
34 33 0.24
35 74 0.55
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.18
Consensus pattern (35 bp):
CATGGAATGATGGGCATGGAATATAAAAATGAAGG
Found at i:54629 original size:67 final size:67
Alignment explanation
Indices: 54522--54719 Score: 319
Period size: 67 Copynumber: 2.9 Consensus size: 67
54512 TGAAAATCAA
54522 GAAAT-AAAAAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGC
1 GAAATAAAAAAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGC
54586 AT
66 AT
*
54588 GAAATAAAAAAAAAACATGGGATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGC
1 GAAATAAAAAAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGC
54653 AT
66 AT
* * *
54655 GGAATAAAAAAATGAAGGCATAGAATGATGGGCATGGAATA-AAAAATGAAGGCATGGAATGATG
1 GAAATAAAAAAA--AA-ACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATG
54719 G
63 G
54720 ATAAAAATGA
Statistics
Matches: 123, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
66 5 0.04
67 71 0.58
69 26 0.21
70 21 0.17
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.18
Consensus pattern (67 bp):
GAAATAAAAAAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGC
AT
Done.