Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2563
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: 56441
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:2019 original size:15 final size:15
Alignment explanation
Indices: 1999--2029 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1989 ATTATATGCA
*
1999 TCTTTTTTTTCTTTT
1 TCTTTTTCTTCTTTT
2014 TCTTTTTCTTCTTTT
1 TCTTTTTCTTCTTTT
2029 T
1 T
2030 TTATACCTAC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTTTTCTTCTTTT
Found at i:10644 original size:10 final size:9
Alignment explanation
Indices: 10627--10677 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 9
10617 TTAACTTAGT
10627 TCAGCTCAA
1 TCAGCTCAA
10636 TCGAGCTCAA
1 TC-AGCTCAA
*
10646 GTCAGCTCAT
1 -TCAGCTCAA
10656 TCGAGCTCAA
1 TC-AGCTCAA
10666 TTCAGCTCAA
1 -TCAGCTCAA
10676 TC
1 TC
10678 TTAACCGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 6 0.17
10 26 0.72
11 4 0.11
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (9 bp):
TCAGCTCAA
Found at i:10652 original size:20 final size:20
Alignment explanation
Indices: 10627--10677 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
10617 TTAACTTAGT
10627 TCAGCTCAATCGAGCTCAAG
1 TCAGCTCAATCGAGCTCAAG
* *
10647 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCAATCGAGCTCAAG
10667 TCAGCTCAATC
1 TCAGCTCAATC
10678 TTAACCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (20 bp):
TCAGCTCAATCGAGCTCAAG
Found at i:12486 original size:21 final size:21
Alignment explanation
Indices: 12443--12487 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12433 AAGTGTTTGT
** **
12443 ATTGAAAAAAAAAGTTACGAA
1 ATTGAAAAAAAAAGAAAAAAA
12464 ATTGAAAAAAAAAGAAAAAAA
1 ATTGAAAAAAAAAGAAAAAAA
12485 ATT
1 ATT
12488 TCAAAGTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (21 bp):
ATTGAAAAAAAAAGAAAAAAA
Found at i:13531 original size:5 final size:6
Alignment explanation
Indices: 13496--13556 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
13486 TTCCAAGCGA
* *
13496 GAAAAT GAAAAT GAAAAA GAAATT G-AAA- GAAAA- GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
*
13541 GAAAAT GAAAAA GAAA
1 GAAAAT GAAAAT GAAA
13557 GAGGGTTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
4 1 0.02
5 10 0.21
6 37 0.77
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11
Consensus pattern (6 bp):
GAAAAT
Found at i:13536 original size:27 final size:28
Alignment explanation
Indices: 13495--13550 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
13485 ATTCCAAGCG
*
13495 AGAAAATGAAAATGAAAAAGAAATTGAA
1 AGAAAATGAAAATGAAAAAGAAAATGAA
*
13523 AGAAAA-GAAAATGAAAATGAAAATGAA
1 AGAAAATGAAAATGAAAAAGAAAATGAA
13550 A
1 A
13551 AAGAAAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (28 bp):
AGAAAATGAAAATGAAAAAGAAAATGAA
Found at i:13538 original size:21 final size:22
Alignment explanation
Indices: 13502--13544 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13492 GCGAGAAAAT
*
13502 GAAAATGAAAAAGAAATTGAAA
1 GAAAATGAAAAAGAAAATGAAA
*
13524 GAAAA-GAAAATGAAAATGAAA
1 GAAAATGAAAAAGAAAATGAAA
13545 ATGAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.12
Consensus pattern (22 bp):
GAAAATGAAAAAGAAAATGAAA
Found at i:13557 original size:33 final size:33
Alignment explanation
Indices: 13495--13558 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
13485 ATTCCAAGCG
**
13495 AGAAAATGAAAATGAAAAAGAAATTGAAAGAAA
1 AGAAAATGAAAATGAAAAAGAAAAAGAAAGAAA
*
13528 AGAAAATGAAAATGAAAATGAAAAAGAAAGA
1 AGAAAATGAAAATGAAAAAGAAAAAGAAAGA
13559 GGGTTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (33 bp):
AGAAAATGAAAATGAAAAAGAAAAAGAAAGAAA
Found at i:15797 original size:27 final size:27
Alignment explanation
Indices: 15767--15944 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15757 ATATTAAGTC
* * *
15767 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
15794 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
15822 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
15849 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
15876 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
15903 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
15930 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15945 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:15851 original size:55 final size:54
Alignment explanation
Indices: 15767--15944 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
15757 ATATTAAGTC
* * *
15767 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
15822 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
15876 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
15930 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15945 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:15933 original size:81 final size:82
Alignment explanation
Indices: 15788--15943 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
15778 TGCTATATAA
* *
15788 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
15853 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
15870 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
15933 ACACTTAGTGC
65 ACACTTAGTGC
15944 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:23970 original size:27 final size:27
Alignment explanation
Indices: 23940--24115 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
23930 ATATTAAGTC
* * * *
23940 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
23967 CGCACACTTAGTGC-ACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
23993 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
24020 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
24047 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
24074 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24101 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24116 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 24 0.19
27 104 0.81
28 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:24104 original size:81 final size:80
Alignment explanation
Indices: 23961--24114 Score: 245
Period size: 81 Copynumber: 1.9 Consensus size: 80
23951 TGCTATATAA
* *
23961 TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCACA
1 TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACA
24026 CTTAGTGCCGCATGG
66 CTTAGTGCCGCATGG
* * **
24041 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
24106 ACTTAGTGC
65 ACTTAGTGC
24115 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 20 0.30
81 47 0.70
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACA
CTTAGTGCCGCATGG
Found at i:31119 original size:46 final size:46
Alignment explanation
Indices: 31067--31159 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
31057 CAAAGAAAAG
31067 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
31113 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
31159 A
1 A
31160 TGCCACACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:32928 original size:10 final size:10
Alignment explanation
Indices: 32915--32944 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
32905 TCATTGTGCC
32915 GAATTGAGCT
1 GAATTGAGCT
32925 GAATTGAGCT
1 GAATTGAGCT
*
32935 GGATTGAGCT
1 GAATTGAGCT
32945 TTATTTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.30
Consensus pattern (10 bp):
GAATTGAGCT
Found at i:34846 original size:18 final size:18
Alignment explanation
Indices: 34823--34868 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
34813 TTGGACACGT
34823 TCTTTTCTTTCTTCAA-TC
1 TCTTTTCTTT-TTCAACTC
*
34841 TCTTTTTCTTTTTCAACTT
1 TC-TTTTCTTTTTCAACTC
34860 TCTTTTCTT
1 TCTTTTCTT
34869 GCTCGCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTCTTTTTCAACTC
Found at i:34914 original size:10 final size:10
Alignment explanation
Indices: 34896--34946 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
34886 ATCTCGATCC
* *
34896 CTTTTTTTTT
1 CTTTCTTTTA
34906 CTTTCTTTTA
1 CTTTCTTTTA
34916 CTTTCTTTTA
1 CTTTCTTTTA
34926 C--T-TTTTA
1 CTTTCTTTTA
*
34933 CTTTCTTTTT
1 CTTTCTTTTA
34943 CTTT
1 CTTT
34947 TGTTTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
7 6 0.17
8 1 0.03
9 1 0.03
10 27 0.77
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTCTTTTA
Found at i:34924 original size:23 final size:23
Alignment explanation
Indices: 34897--34954 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 23
34887 TCTCGATCCC
34897 TTTTTTTTTCTTTCTTTTACTTT
1 TTTTTTTTTCTTTCTTTTACTTT
*
34920 CTTTTACTTTTTACTTTCTTTTTCTTT
1 -TTTT--TTTTT-CTTTCTTTTACTTT
*
34947 TGTTTTTT
1 TTTTTTTT
34955 CATTACAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 8 0.28
26 8 0.28
27 13 0.45
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTCTTTCTTTTACTTT
Found at i:34933 original size:17 final size:17
Alignment explanation
Indices: 34911--34947 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
34901 TTTTTCTTTC
34911 TTTTACTTTCTTTTACT
1 TTTTACTTTCTTTTACT
*
34928 TTTTACTTTCTTTTTCT
1 TTTTACTTTCTTTTACT
34945 TTT
1 TTT
34948 GTTTTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTACTTTCTTTTACT
Found at i:36135 original size:9 final size:10
Alignment explanation
Indices: 36117--36159 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
36107 ATCACGTTCA
36117 CAATTTTTTT
1 CAATTTTTTT
*
36127 GAATTTTTTT
1 CAATTTTTTT
*
36137 TAATTTTTTT
1 CAATTTTTTT
36147 CAATTTTTTT
1 CAATTTTTTT
36157 CAA
1 CAA
36160 ATACTTACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (10 bp):
CAATTTTTTT
Found at i:36367 original size:24 final size:25
Alignment explanation
Indices: 36321--36367 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
36311 AGGAATTTGG
*
36321 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
36346 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
36368 TTGGCTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:37891 original size:20 final size:20
Alignment explanation
Indices: 37840--37880 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
37830 AAACATGTAA
*
37840 TAAATTAAGACAAATTTAAT
1 TAAACTAAGACAAATTTAAT
* *
37860 TAAACTAGGACACATTTAAT
1 TAAACTAAGACAAATTTAAT
37880 T
1 T
37881 CGGCTAAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (20 bp):
TAAACTAAGACAAATTTAAT
Found at i:38255 original size:24 final size:25
Alignment explanation
Indices: 38209--38255 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
38199 AGGAATTTGG
*
38209 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
38234 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
38256 TTGGCTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:40393 original size:27 final size:27
Alignment explanation
Indices: 40376--40553 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
40366 ATATTAAGTC
40376 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
40403 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
40430 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
40458 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
40485 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
40512 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
40539 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40554 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40515 original size:82 final size:81
Alignment explanation
Indices: 40397--40552 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40387 TGCTATATAA
* *
40397 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40462 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40479 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40543 CACTTAGTGC
65 CACTTAGTGC
40553 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40536 original size:54 final size:54
Alignment explanation
Indices: 40376--40552 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
40366 ATATTAAGTC
* * * *
40376 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
40430 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
40485 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
40539 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40553 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:48228 original size:27 final size:27
Alignment explanation
Indices: 48211--48388 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
48201 ATATTAAGTC
48211 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
48238 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
48265 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
48293 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
48320 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
48347 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
48374 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
48389 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:48350 original size:82 final size:81
Alignment explanation
Indices: 48232--48387 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
48222 TGCTATATAA
* *
48232 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
48297 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
48314 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
48378 CACTTAGTGC
65 CACTTAGTGC
48388 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:48371 original size:54 final size:54
Alignment explanation
Indices: 48211--48387 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
48201 ATATTAAGTC
* * * *
48211 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
48265 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
48320 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
48374 CGCACACTTAGTGC
1 CGCACACTTAGTGC
48388 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:52162 original size:20 final size:20
Alignment explanation
Indices: 52111--52151 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52101 AAACATGTAA
*
52111 TAAATTAAGACAAATTTAAT
1 TAAACTAAGACAAATTTAAT
* *
52131 TAAACTAGGACACATTTAAT
1 TAAACTAAGACAAATTTAAT
52151 T
1 T
52152 CGGCTAAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (20 bp):
TAAACTAAGACAAATTTAAT
Found at i:53558 original size:19 final size:19
Alignment explanation
Indices: 53534--53572 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
53524 AATAAATTAC
53534 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
53553 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
53572 T
1 T
53573 GCTGGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Done.