Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3083
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: 46699
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:1725 original size:104 final size:96
Alignment explanation
Indices: 1370--1800 Score: 386
Period size: 104 Copynumber: 4.4 Consensus size: 96
1360 TATAACATTC
* * * *
1370 TATACACTTTCACATCCATCACGTT-GG-CA-TCGGCCCTGTA-CA-ATATATACATTCTTCA-A
1 TATACACTTTCACATTCATCACATTCGGCCATTAGG-CCT-TATCACATATATACACT-TTCATA
* *
1429 TGTCATCACATCG-CATTAGCCCTTATCAC--ATA
63 T-TCATCACATCGCCTTTAGGCCTTATCACATATA
*
1461 TATACACTGTTCACA-TCATCACATGCGGCCATTAGGCCTTATCACATATATACACTTTTCATAT
1 TATACACT-TTCACATTCATCACATTCGGCCATTAGGCCTTATCACATATATACAC-TTTCATAT
*
1525 TCATCACAT-GCGCATTAGGCCTTGATCACATAATA
64 TCATCACATCGC-CTTTAGGCCTT-ATCACAT-ATA
* * * *
1560 TATACATTTTCACACTTTCATCACATTCTGCCATTAGGTCCCTATCACATATTATACACTTTCAC
1 TATACACTTTCACA--TTCATCACATTCGGCCATTAGG-CCTTATCACATA-TATACACTTTCAT
* *
1625 ATTCAGCACATCAGCCTTTAGGCCCTATTCTACATATCA
62 ATTCATCACATC-GCCTTTAGGCCTTA-TC-ACATAT-A
1664 TATACACTATTC-CATTCATCACATATTCGGCCCATTAGGCCTTTATCACATATATACACTTTCA
1 TATACACT-TTCACATTCATCAC--ATTCGG-CCATTAGGCC-TTATCACATATATACACTTTCA
1728 TATTCAATCACATCGGCCATTTAGGCCTTAATCACA-ATA
61 TATTC-ATCACATC-GCC-TTTAGGCCTT-ATCACATATA
*
1767 TATACACTTTCACATGTCATCACA-TCGGTCATTA
1 TATACACTTTCACAT-TCATCACATTCGGCCATTA
1801 CGCCATTACT
Statistics
Matches: 284, Mismatches: 22, Indels: 59
0.78 0.06 0.16
Matches are distributed among these distances:
91 15 0.05
92 10 0.04
93 8 0.03
94 25 0.09
95 13 0.05
96 5 0.02
98 6 0.02
99 10 0.04
100 5 0.02
101 23 0.08
102 39 0.14
103 32 0.11
104 48 0.17
105 33 0.12
106 11 0.04
107 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (96 bp):
TATACACTTTCACATTCATCACATTCGGCCATTAGGCCTTATCACATATATACACTTTCATATTC
ATCACATCGCCTTTAGGCCTTATCACATATA
Found at i:1752 original size:50 final size:48
Alignment explanation
Indices: 1370--1800 Score: 332
Period size: 52 Copynumber: 8.7 Consensus size: 48
1360 TATAACATTC
* * * * *
1370 TATACACTTTCACATCCATCACGTTGG-CA-TCGGCCCTGTA-CA-ATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGG-CCTTTATCACATA
* *
1415 TATACATTCTTCA-ATGTCATCACATC-G-CATTA-GCCCTTATCACATA
1 TATACACT-TTCACAT-TCATCACATCGGCCATTAGGCCTTTATCACATA
1461 TATACACTGTTCACA-TCATCACATGCGGCCATTAGGCC-TTATCACATA
1 TATACACT-TTCACATTCATCACAT-CGGCCATTAGGCCTTTATCACATA
* *
1509 TATACACTTTTCATATTCATCACAT--GCGCATTAGGCCTTGATCACATAATA
1 TATACAC-TTTCACATTCATCACATCGGC-CATTAGGCCTTTATCAC---ATA
* * *
1560 TATACATTTTCACACTTTCATCACATTCTGCCATTAGGTCC-CTATCACATA
1 TATACACTTTCACA--TTCATCACA-TCGGCCATTAGG-CCTTTATCACATA
* * * * *
1611 TTATACACTTTCACATTCAGCACATCAGCCTTTAGGCCCTATTCTACATATCA
1 -TATACACTTTCACATTCATCACATCGGCCATTAGG-CCT-TTAT-CACAT-A
1664 TATACACTATTC-CATTCATCACATATTCGGCCCATTAGGCCTTTATCACATA
1 TATACACT-TTCACATTCATCAC--A-TCGG-CCATTAGGCCTTTATCACATA
* *
1716 TATACACTTTCATATTCAATCACATCGGCCATTTAGGCCTTAATCACAATA
1 TATACACTTTCACATTC-ATCACATCGGCCA-TTAGGCCTTTATCAC-ATA
*
1767 TATACACTTTCACATGTCATCACATCGGTCATTA
1 TATACACTTTCACAT-TCATCACATCGGCCATTA
1801 CGCCATTACT
Statistics
Matches: 316, Mismatches: 32, Indels: 71
0.75 0.08 0.17
Matches are distributed among these distances:
44 4 0.01
45 24 0.08
46 29 0.09
47 11 0.03
48 33 0.10
49 28 0.09
50 35 0.11
51 47 0.15
52 58 0.18
53 14 0.04
54 16 0.05
55 10 0.03
56 7 0.02
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (48 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTTATCACATA
Found at i:5444 original size:43 final size:42
Alignment explanation
Indices: 5414--5593 Score: 155
Period size: 42 Copynumber: 4.4 Consensus size: 42
5404 ACGGATAATT
* *
5414 ACTAGCACGGAATGCTCTTCGGAAACTTAGCCCGGAATACATC
1 ACTAGCAC-GAATGCTCCTCGGAAACTTAGCACGGAATACATC
*
5457 ACTAGCACGAATGCTCCTCGG--AC-TAGCCCGG-ATACCAAT-
1 ACTAGCACGAATGCTCCTCGGAAACTTAGCACGGAATA-C-ATC
* *
5496 ACTAGCACGAATATGCTCCTCGG--ACTTAGCCCGGAATTATATC
1 ACTAGCACG-A-ATGCTCCTCGGAAACTTAGCACGGAA-TACATC
* * *
5539 ACTAGCACGAATGCTCCTCGG-GACTTAAGCCCGG-AT-TATC
1 ACTAGCACGAATGCTCCTCGGAAACTT-AGCACGGAATACATC
5579 ACTAGCACGAATGCT
1 ACTAGCACGAATGCT
5594 GCCTGGACTT
Statistics
Matches: 125, Mismatches: 2, Indels: 23
0.83 0.01 0.15
Matches are distributed among these distances:
38 3 0.02
39 18 0.14
40 24 0.19
41 25 0.20
42 28 0.22
43 25 0.20
44 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (42 bp):
ACTAGCACGAATGCTCCTCGGAAACTTAGCACGGAATACATC
Found at i:5503 original size:82 final size:85
Alignment explanation
Indices: 5413--5574 Score: 244
Period size: 82 Copynumber: 1.9 Consensus size: 85
5403 AACGGATAAT
* *
5413 TACTAGCACGGA-ATGCTCTTCGGAAACTTAGCCCGGAA-TACATCACTAGCACGAATGCTCCTC
1 TACTAGCACGAATATGCTCCTCGG--ACTTAGCCCGGAATTACATCACTAGCACGAATGCTCCTC
5476 -GGAC-T-AGCCCGGATACCAA
64 GGGACTTAAGCCCGGATACCAA
*
5495 TACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAATTATATCACTAGCACGAATGCTCCTCGG
1 TACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAATTACATCACTAGCACGAATGCTCCTCGG
5560 GACTTAAGCCCGGAT
66 GACTTAAGCCCGGAT
5575 TATCACTAGC
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
81 13 0.18
82 35 0.49
83 14 0.19
84 1 0.01
85 9 0.12
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (85 bp):
TACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAATTACATCACTAGCACGAATGCTCCTCGG
GACTTAAGCCCGGATACCAA
Found at i:5602 original size:81 final size:79
Alignment explanation
Indices: 5414--5606 Score: 225
Period size: 82 Copynumber: 2.4 Consensus size: 79
5404 ACGGATAATT
* *
5414 ACTAGCACGGA-ATGCTCTTCGGAAACTTAGCCCGGAATACATCACTAGCACGAATGCTCCTCGG
1 ACTAGCACGAATATGCTCCTCGG--ACTTAGCCCGGAATACATCACTAGCACGAATGCTCCTCGG
5478 ACTAGCCCGGATACCAA
64 ACTAGCCCGGATACC-A
*
5495 TACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAATTATATCACTAGCACGAATGCTCCTCGG
1 -ACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAA-TACATCACTAGCACGAATGCTCCTC-G
*
5560 GACTTAAGCCCGGATTATC-
63 GAC-T-AGCCCGGA-TACCA
5579 ACTAGCACG-A-ATGCTGCCT-GGACTTAGC
1 ACTAGCACGAATATGCT-CCTCGGACTTAGC
5607 GCCGATATAT
Statistics
Matches: 100, Mismatches: 4, Indels: 15
0.84 0.03 0.13
Matches are distributed among these distances:
81 27 0.27
82 38 0.38
83 23 0.23
84 1 0.01
85 8 0.08
86 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (79 bp):
ACTAGCACGAATATGCTCCTCGGACTTAGCCCGGAATACATCACTAGCACGAATGCTCCTCGGAC
TAGCCCGGATACCA
Found at i:7387 original size:47 final size:46
Alignment explanation
Indices: 7260--7580 Score: 350
Period size: 47 Copynumber: 6.6 Consensus size: 46
7250 GATACCAAAT
7260 CTTTCACATTCCATCACAT-GGCCATTAGGCCCCTTAATCACATATATATACA
1 CTTTCACATT-CATCACATCGGCCATTAGG--CC-T-ATCAC--ATATATACA
*
7312 CTTTTCACATTCATCAACATGCGGCCATTA-GCCTGATCACATACATTACA
1 C-TTTCACATTCATC-ACAT-CGGCCATTAGGCCT-ATCACATATA-TACA
7362 CTTTC-CATTCAATCACATCGGCCATTAGGCTCATTAGCCTATCACATATATATACA
1 CTTTCACATTC-ATCACATCGGCCATTA-G-------GCCTATCAC--ATATATACA
7418 C-TTCACATTCATCACATC-GCCATTAGGCCCTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGG-CCTATCACATATATACA
7463 C-TTCACATTCATCACATCGGCCATTA-GCCTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACA
7507 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCC-TATCACATATATACA
*
7554 CTTTCACATTCATCACATCGGTCATTA
1 CTTTCACATTCATCACATCGGCCATTA
7581 CGCCATACTA
Statistics
Matches: 242, Mismatches: 4, Indels: 51
0.81 0.01 0.17
Matches are distributed among these distances:
44 18 0.07
45 53 0.22
46 11 0.05
47 58 0.24
48 9 0.04
49 11 0.05
50 5 0.02
51 6 0.02
52 7 0.03
53 14 0.06
54 8 0.03
55 24 0.10
56 14 0.06
57 4 0.02
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (46 bp):
CTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACA
Found at i:7443 original size:45 final size:46
Alignment explanation
Indices: 7393--7580 Score: 296
Period size: 45 Copynumber: 4.1 Consensus size: 46
7383 CCATTAGGCT
7393 CATTA-GCCTATCACATATATATACAC-TTCACATTCATCACATC-GC
1 CATTAGGCCTATCAC--ATATATACACTTTCACATTCATCACATCGGC
7438 CATTAGGCCCTATCACATATATACAC-TTCACATTCATCACATCGGC
1 CATTAGG-CCTATCACATATATACACTTTCACATTCATCACATCGGC
7484 CATTA-GCCTATCACATATATACACTTTCACATTCATCACATCGGC
1 CATTAGGCCTATCACATATATACACTTTCACATTCATCACATCGGC
*
7529 CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGT
1 CATTAGGCC-TATCACATATATACACTTTCACATTCATCACATCGGC
7576 CATTA
1 CATTA
7581 CGCCATACTA
Statistics
Matches: 136, Mismatches: 1, Indels: 10
0.93 0.01 0.07
Matches are distributed among these distances:
44 18 0.13
45 58 0.43
46 11 0.08
47 49 0.36
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.31
Consensus pattern (46 bp):
CATTAGGCCTATCACATATATACACTTTCACATTCATCACATCGGC
Found at i:7531 original size:91 final size:91
Alignment explanation
Indices: 7393--7580 Score: 317
Period size: 91 Copynumber: 2.1 Consensus size: 91
7383 CCATTAGGCT
7393 CATTAGCCTATCACATATATATACACTTCACATTCATCACATCGCCATTAGGCCCTATCACATAT
1 CATTAGCCTATCACA-ATATATACACTTCACATTCATCACATCGCCATTAGGCCCTATCACATAT
7458 ATACAC-TTCACATTCATCACATCGGC
65 ATACACTTTCACATTCATCACATCGGC
*
7484 CATTAGCCTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
1 CATTAGCCTATCACAATATATACAC-TTCACATTCATCACATC-GCCATTAGGCCCTATCACATA
*
7548 TATACACTTTCACATTCATCACATCGGT
64 TATACACTTTCACATTCATCACATCGGC
7576 CATTA
1 CATTA
7581 CGCCATACTA
Statistics
Matches: 92, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
89 10 0.11
90 17 0.18
91 41 0.45
92 24 0.26
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.31
Consensus pattern (91 bp):
CATTAGCCTATCACAATATATACACTTCACATTCATCACATCGCCATTAGGCCCTATCACATATA
TACACTTTCACATTCATCACATCGGC
Found at i:11011 original size:40 final size:40
Alignment explanation
Indices: 10985--11249 Score: 408
Period size: 40 Copynumber: 6.7 Consensus size: 40
10975 TGATTACTCT
* * * *
10985 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* * * *
11025 TCGAGG-TTTAGCACGGATATATTACTAGCACGAATGCTCT
1 TCG-GGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* *
11065 TCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
11105 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
11145 TCGGGACTTAGCCC-GATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
11184 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
11224 TCGGGACTTAGCCCGGATATATCACT
1 TCGGGACTTAGCCCGGATATATCACT
11250 CTCAATTCTC
Statistics
Matches: 208, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 39 0.19
40 167 0.80
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
Found at i:11201 original size:119 final size:120
Alignment explanation
Indices: 10985--11249 Score: 408
Period size: 119 Copynumber: 2.2 Consensus size: 120
10975 TGATTACTCT
* * * * * * *
10985 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGAGGTTTAGCACGGATATATTAC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAGGCTTAGCACCGATATATCAC
*
11050 TAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
66 TAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
*
11105 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCG-GGACTTAGC-CCGATATATCA
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAGG-CTTAGCACCGATATATCA
* *
11168 CTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
65 CTAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
11224 TCGGGACTTAGCCCGGATATATCACT
1 TCGGGACTTAGCCCGGATATATCACT
11250 CTCAATTCTC
Statistics
Matches: 132, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
119 89 0.67
120 43 0.33
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (120 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAGGCTTAGCACCGATATATCAC
TAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
Found at i:12512 original size:37 final size:37
Alignment explanation
Indices: 12462--12540 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
12452 TTATTACGAA
* * *
12462 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
12499 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
12536 GTCTT
1 GTCTT
12541 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:12736 original size:47 final size:47
Alignment explanation
Indices: 12658--13032 Score: 642
Period size: 47 Copynumber: 7.9 Consensus size: 47
12648 CCCTTCGGGA
* * * * * *
12658 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12705 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12752 CTTATCACATATATAAACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12799 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12846 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12895 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12942 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12989 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
13033 CGCCATACTA
Statistics
Matches: 313, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 266 0.85
49 47 0.15
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12992 original size:190 final size:188
Alignment explanation
Indices: 12658--13032 Score: 651
Period size: 190 Copynumber: 2.0 Consensus size: 188
12648 CCCTTCGGGA
* * * *
12658 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
12723 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAAACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAAACTTTCACATTCATCACATC
12788 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
12846 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
*
12911 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAAACTTTCACATTCATCACA
*
12976 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGTCATTA
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
13033 CGCCATACTA
Statistics
Matches: 176, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 10 0.06
189 1 0.01
190 165 0.94
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAAACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18551 original size:49 final size:49
Alignment explanation
Indices: 18335--18559 Score: 200
Period size: 49 Copynumber: 4.5 Consensus size: 49
18325 CTGGTACGCA
* * * *
18335 TAGTAGCCTGCAATTAGTACTACACATGCGATCAATTATCCGGTATACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATCATCCGGTACACG
* * * * *
18384 TAGTTGCCTGCACTTAGTACTACACACT-TGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACA-TGCGACC-AATCATCCGGTACACG
* * * ** * ** * *
18434 TAGTAGCTTGCACTTAGTACTACACACGTGATTGAAGTTATTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TCATCCGGTACACG
*
18485 TAGTAGCCTGCACTTAGTACTGCACATGCGACCAATCATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATCATCCGGTACACG
* * *
18534 TAGTAGCATGAAATTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
18560 CGTGACCTCA
Statistics
Matches: 135, Mismatches: 36, Indels: 10
0.75 0.20 0.06
Matches are distributed among these distances:
49 58 0.43
50 43 0.32
51 34 0.25
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATCATCCGGTACACG
Found at i:18551 original size:100 final size:101
Alignment explanation
Indices: 18384--18564 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 101
18374 CCGGTATACG
* * * * * *
18384 TAGTTGCCTGCACTTAGTACTACACACTTGACCTAACCATCTGATACACGTAGTAGCTTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACTCGACCTAACCATCCGATACACGTAGTAGCATGAAATT
18449 AGTACTACACACGTGATTGAAGTTATTGGGTACGCA
66 AGTACTACACACGTGATTGAAGTTATTGGGTACGCA
* * *
18485 TAGTAGCCTGCACTTAGTACTGCACA-TGCGACC-AATCATCCGGTACACGTAGTAGCATGAAAT
1 TAGTAGCCTGCACTTAGTACTACACACT-CGACCTAACCATCCGATACACGTAGTAGCATGAAAT
18548 TAGTACTACACACGTGA
65 TAGTACTACACACGTGA
18565 CCTCACAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
100 42 0.60
101 28 0.40
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACTCGACCTAACCATCCGATACACGTAGTAGCATGAAATT
AGTACTACACACGTGATTGAAGTTATTGGGTACGCA
Found at i:24337 original size:49 final size:49
Alignment explanation
Indices: 24265--24452 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
24255 TAGACAAGGC
* * *
24265 TATCTGGTACGCATAGTAACCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
24314 TATCCGGCACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* ** * *
24365 TATCGGGTATGCATAGTAGCCTACACTTAGTAATACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
24414 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
24453 CGTGACCTAC
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 74 0.65
50 2 0.02
51 38 0.33
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:24413 original size:100 final size:100
Alignment explanation
Indices: 24265--24457 Score: 323
Period size: 100 Copynumber: 1.9 Consensus size: 100
24255 TAGACAAGGC
* * * *
24265 TATCTGGTACGCATAGTAACCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACACGTAG
1 TATCGGGTACGCATAGTAACCTACACTTAGTAATACACATGCGACCAATTATCCGGCACACATAG
24330 TAGCCTGCACTTAGTACTACACACGTGATCGAAAT
66 TAGCCTGCACTTAGTACTACACACGTGATCGAAAT
* * *
24365 TATCGGGTATGCATAGTAGCCTACACTTAGTAATACACATGCGACCAATTATCCGGTACACATAG
1 TATCGGGTACGCATAGTAACCTACACTTAGTAATACACATGCGACCAATTATCCGGCACACATAG
24430 TAGCCTGCACTTAGTACTACACACGTGA
66 TAGCCTGCACTTAGTACTACACACGTGA
24458 CCTACAATAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 86 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAACCTACACTTAGTAATACACATGCGACCAATTATCCGGCACACATAG
TAGCCTGCACTTAGTACTACACACGTGATCGAAAT
Found at i:24735 original size:27 final size:27
Alignment explanation
Indices: 24705--24758 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24695 TCATACAACC
* *
24705 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
24732 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
24759 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:26908 original size:19 final size:19
Alignment explanation
Indices: 26873--26910 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
26863 TTGCAATTTA
*
26873 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
26892 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
26911 TCTGACAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:40752 original size:22 final size:22
Alignment explanation
Indices: 40722--40771 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
40712 CACGTTGAGC
**
40722 TATTACCTTGGGTTGGGTTCAG
1 TATTACCTTGGGTAAGGTTCAG
*
40744 TATTCCCTTGGGTAAGGTTCAG
1 TATTACCTTGGGTAAGGTTCAG
40766 TATTAC
1 TATTAC
40772 TTCGCTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (22 bp):
TATTACCTTGGGTAAGGTTCAG
Done.