Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3576
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: 56326
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2258 original size:41 final size:39
Alignment explanation
Indices: 2212--2288 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
2202 GAAGCAATCG
*
2212 TGTGCGAGATACAAGTTCACGGGTTAAGCCCCGAAGGCCTT
1 TGTGCGAGATACAA-ATC-CGGGTTAAGCCCCGAAGGCCTT
** *
2253 TGTGCGAGATTTAAATCCGGGTTAAGTCCCGAAGGC
1 TGTGCGAGATACAAATCCGGGTTAAGCCCCGAAGGC
2289 ATCTCGTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 18 0.56
40 2 0.06
41 12 0.38
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (39 bp):
TGTGCGAGATACAAATCCGGGTTAAGCCCCGAAGGCCTT
Found at i:2284 original size:39 final size:39
Alignment explanation
Indices: 2231--2357 Score: 111
Period size: 39 Copynumber: 3.3 Consensus size: 39
2221 TACAAGTTCA
*
2231 CGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATTTAAATC
1 CGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATTTAAATC
* * *
2270 CGGGTTAAGTCCCGAAGGCATCTCGTGC--GATTATTAATC
1 CGGGTTAAGTCCCGAAGGCCT-TTGTGCGAGATT-TAAATC
* * * *
2309 C-GGTTAAGTCCTGAAGG-CATTGTGTGAG-TTTAAAAC
1 CGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATTTAAATC
* *
2345 CGGGCTATGTCCC
1 CGGGTTAAGTCCC
2358 AAGAGGCATT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
36 9 0.13
37 10 0.14
38 20 0.29
39 25 0.36
40 5 0.07
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
CGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATTTAAATC
Found at i:10044 original size:80 final size:78
Alignment explanation
Indices: 9960--10131 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
9950 GGACTAAGAT
*
9960 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
10023 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
10040 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
10105 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
10119 CCGAAGGCATTTG
1 CCGAAGGCATTTG
10132 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:10122 original size:39 final size:39
Alignment explanation
Indices: 9907--10129 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
9897 TTGAATGCTG
* * * * * *
9907 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
9947 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
9987 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
10027 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
10067 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
10106 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10130 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:10149 original size:79 final size:80
Alignment explanation
Indices: 9987--10164 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
9977 AGATACAAGT
* * * *
9987 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
10052 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
10067 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
10131 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
10146 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
10165 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:17560 original size:79 final size:78
Alignment explanation
Indices: 17424--17647 Score: 206
Period size: 79 Copynumber: 2.8 Consensus size: 78
17414 TTGAATGCTG
* * * * * * *
17424 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
17487 TTGTGCGAG-A-TACAA
63 TTGTGCGAGCATTA-AA
* * * *
17502 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
17566 TCGTGCGAGTCATTAAA
63 TTGTGCGAG-CATTAAA
* * *
17583 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
17648 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.01
79 87 0.71
80 28 0.23
81 4 0.03
82 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGCATTAAA
Found at i:17572 original size:40 final size:40
Alignment explanation
Indices: 17424--17647 Score: 210
Period size: 40 Copynumber: 5.7 Consensus size: 40
17414 TTGAATGCTG
* * * *
17424 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ATTAAA
** * *
17464 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATATTAA-A
*
17504 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
*
17543 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAT-ATTAAA
* * *
17583 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
* * *
17622 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
17648 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
39 65 0.42
40 80 0.51
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
Found at i:17665 original size:79 final size:80
Alignment explanation
Indices: 17504--17680 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
17494 AGATACAAGT
* * * *
17504 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
17568 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
17583 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
17647 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
17662 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
17681 TATGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 16 0.20
79 58 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:22500 original size:20 final size:20
Alignment explanation
Indices: 22475--22523 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
22465 TTTAACTTAG
22475 GTCAGCTCACTCGAGCTCAA
1 GTCAGCTCACTCGAGCTCAA
*
22495 GTCAGCTCATTCGAGCTCAA
1 GTCAGCTCACTCGAGCTCAA
*
22515 TTCAGCTCA
1 GTCAGCTCA
22524 ATCTTAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
GTCAGCTCACTCGAGCTCAA
Found at i:22521 original size:10 final size:10
Alignment explanation
Indices: 22488--22525 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
22478 AGCTCACTCG
*
22488 AGCTCAAGTC
1 AGCTCAATTC
22498 AGCTC-ATTC
1 AGCTCAATTC
22507 GAGCTCAATTC
1 -AGCTCAATTC
22518 AGCTCAAT
1 AGCTCAAT
22526 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:23244 original size:22 final size:21
Alignment explanation
Indices: 23215--23262 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
23205 AAGCATGAAC
*
23215 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
23236 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
23257 TGAACA
1 TGAACA
23263 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:23882 original size:10 final size:10
Alignment explanation
Indices: 23877--23906 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
23867 GAAAAAAAGA
23877 TCAAAAAAAT
1 TCAAAAAAAT
23887 TCAAAAAAAT
1 TCAAAAAAAT
23897 TCAAAGAAAA
1 TCAAA-AAAA
23907 AAGTTCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (10 bp):
TCAAAAAAAT
Found at i:25120 original size:28 final size:28
Alignment explanation
Indices: 25064--25128 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
25054 AGGGCGAGCG
*
25064 AGAAAATGAAAATGAAAAAGAAATTGAA
1 AGAAAATGAAAAAGAAAAAGAAATTGAA
* *
25092 AGAAAAT-AAAAAGAAAATGACATTGGAA
1 AGAAAATGAAAAAGAAAAAGAAATT-GAA
25120 AGAAAATGA
1 AGAAAATGA
25129 GTGAAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 14 0.44
28 17 0.53
29 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.18, T:0.14
Consensus pattern (28 bp):
AGAAAATGAAAAAGAAAAAGAAATTGAA
Found at i:36547 original size:28 final size:27
Alignment explanation
Indices: 36481--36547 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
36471 CTTTGATAGT
*
36481 AACAGTACAGTGTGGGCATTAGCCCAA
1 AACAGTACAGTGTGGACATTAGCCCAA
* *
36508 AACAGAAACAGTGTGGAC-TTAAGCCCGA
1 AACAG-TACAGTGTGGACATT-AGCCCAA
*
36536 TACAGTATCAGT
1 AACAGTA-CAGT
36548 ATGGTGCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
AACAGTACAGTGTGGACATTAGCCCAA
Found at i:36781 original size:32 final size:32
Alignment explanation
Indices: 36721--36915 Score: 234
Period size: 32 Copynumber: 6.1 Consensus size: 32
36711 GAATGGCTAC
* * *
36721 AAGCCATAAGTAA-AGTAATATGTTTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
36752 AAGCCATCAGTAGTAGTGATATGA-CTGGCACA
1 AAGCCATCAGTAACAGTAATATGATC-GGCACA
* * *
36784 CAGCCATCAATAACTGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
36816 AAGCCATCAGTAACGGTAGTATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
36848 AAGCCATCAGTAACAGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
36880 AAGCCATCAGTAAC-GATAATATGATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
36912 AAGC
1 AAGC
36916 AGCAAAGCTG
Statistics
Matches: 139, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
31 12 0.09
32 126 0.91
33 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:37079 original size:24 final size:24
Alignment explanation
Indices: 37052--37110 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
37042 CCATGCTCAG
*
37052 AATCGGTCATAGAAATCACAAACA
1 AATCGGTCATAAAAATCACAAACA
* *
37076 AATCAGTCATAAAAATCACAGACA
1 AATCGGTCATAAAAATCACAAACA
37100 AAT-GAGTCATA
1 AATCG-GTCATA
37111 CATAACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (24 bp):
AATCGGTCATAAAAATCACAAACA
Found at i:37278 original size:26 final size:26
Alignment explanation
Indices: 37236--37352 Score: 85
Period size: 26 Copynumber: 4.4 Consensus size: 26
37226 GGGTATATTG
* *
37236 GTCAATTTACCTAACAGAGGTATTACA
1 GTCATTTTACCT-ACAGGGGTATTACA
* *
37263 GTCATTTTACCTACAGGGGCATCACA
1 GTCATTTTACCTACAGGGGTATTACA
* * *
37289 GTTATTTTACCCCACAGGGGTATTTC-
1 GTCATTTTA-CCTACAGGGGTATTACA
* * * *
37315 GATAATTTTACCCTTCA-GGGTATTTCG
1 G-TCATTTTA-CCTACAGGGGTATTACA
37342 GTCATTTTACC
1 GTCATTTTACC
37353 CTACTTTAGG
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.03
26 36 0.49
27 36 0.49
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (26 bp):
GTCATTTTACCTACAGGGGTATTACA
Found at i:37353 original size:26 final size:27
Alignment explanation
Indices: 37292--37356 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
37282 CATCACAGTT
*
37292 ATTTTACCCCACAGGGGTATTTCGATA
1 ATTTTACCCTACAGGGGTATTTCGATA
* * *
37319 ATTTTACCCTTCA-GGGTATTTCGGTC
1 ATTTTACCCTACAGGGGTATTTCGATA
37345 ATTTTACCCTAC
1 ATTTTACCCTAC
37357 TTTAGGGTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 22 0.67
27 11 0.33
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTTCGATA
Found at i:38030 original size:8 final size:8
Alignment explanation
Indices: 38017--38045 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38007 TTTTAAATGA
38017 TATTTTAT
1 TATTTTAT
38025 TATTTTAT
1 TATTTTAT
38033 TATTTTAT
1 TATTTTAT
38041 TATTT
1 TATTT
38046 AATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:44906 original size:37 final size:37
Alignment explanation
Indices: 44856--44934 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
44846 TTATTACGAA
* * * * *
44856 GTCTTACCCGGACATAATCTCCACGCGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
*
44893 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCAG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
44930 GTCTT
1 GTCTT
44935 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
Found at i:45275 original size:47 final size:47
Alignment explanation
Indices: 45053--45254 Score: 323
Period size: 47 Copynumber: 4.3 Consensus size: 47
45043 CCCTTCGGGA
* * * * * *
45053 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45100 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45147 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45194 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45241 CTTATCTCATATAT
1 CTTATCACATATAT
45255 GCATGTTCAT
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 144 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:47924 original size:26 final size:26
Alignment explanation
Indices: 47862--48034 Score: 190
Period size: 27 Copynumber: 6.6 Consensus size: 26
47852 ATATTGAGTC
* *
47862 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAA-T
*
47889 CGCACACTTAGTGCTACGTAATCAAT
1 CGCACACTTAGTGCTACATAATCAAT
47915 CGCACACTTAGTGCTACATAATCAAT
1 CGCACACTTAGTGCTACATAATCAAT
* **
47941 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAA-T
* *
47968 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCA-AT
* *
47995 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATC-AAT
48022 --CACACTTAGTGCT
1 CGCACACTTAGTGCT
48035 GTACAATTTA
Statistics
Matches: 128, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.09
26 49 0.38
27 65 0.51
28 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (26 bp):
CGCACACTTAGTGCTACATAATCAAT
Found at i:55911 original size:54 final size:53
Alignment explanation
Indices: 55800--55973 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 53
55790 ATATTGAGTC
* * * * *
55800 CGCACACTCAGTGCTATATTAATCAA-CTCGCACACTTAGTGCTACGTAATCAAT
1 CGCACACTTAGTGCT-CA-TAATCAATCTCGCACACTTAGTGCAACATAGTCAAT
* *
55854 CGCACACTTAGTGCTCATAATCAATCTCGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTCATAATCAATCTCGCACACTTAGTGCAACATAGTCAA-T
* *
55908 CGCACACTTAGT-CATCATATTC-ATTTCG-ACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGC-TCATAATCAATCTCGCACACTTAGTGCAACATAGTC-AAT
55960 C-CACACTTAGTGCT
1 CGCACACTTAGTGCT
55974 GTACAATTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
51 11 0.10
52 28 0.27
53 32 0.30
54 34 0.32
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (53 bp):
CGCACACTTAGTGCTCATAATCAATCTCGCACACTTAGTGCAACATAGTCAAT
Found at i:55952 original size:26 final size:27
Alignment explanation
Indices: 55800--55972 Score: 140
Period size: 26 Copynumber: 6.5 Consensus size: 27
55790 ATATTGAGTC
* * * *
55800 CGCACACTCAGTGCTATATTAATCAACT
1 CGCACACTTAGTGCAACA-TAATCAAAT
* *
55828 CGCACACTTAGTGCTACGTAATC-AAT
1 CGCACACTTAGTGCAACATAATCAAAT
* *
55854 CGCACACTTAGTGC-TCATAATCAATCT
1 CGCACACTTAGTGCAACATAATCAA-AT
* ** *
55881 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCAACATAATCAAAT
* * **
55908 CGCACACTTAGT-CATCATATTCATTT
1 CGCACACTTAGTGCAACATAATCAAAT
*
55934 CG-ACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCAACATAATCAAAT
55960 C-CACACTTAGTGC
1 CGCACACTTAGTGC
55973 TGTACAATTT
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
25 15 0.12
26 50 0.42
27 33 0.28
28 22 0.18
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAATCAAAT
Done.