Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1750
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: 41927
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:5862 original size:40 final size:40
Alignment explanation
Indices: 5799--6002 Score: 222
Period size: 40 Copynumber: 5.1 Consensus size: 40
5789 CGGAATTTAA
** *
5799 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
5839 CCGG-TCATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGAT-ATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5879 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5918 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5958 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5998 CCGGA
1 CCGGA
6003 CATCATTCGA
Statistics
Matches: 139, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 91 0.65
41 13 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5929 original size:79 final size:79
Alignment explanation
Indices: 5820--6002 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 79
5810 TACTCGTTCA
* *
5820 AATGCCTTCGGGACATAGCCCGGTCATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
* *
5884 TTTAGTAAC-TCGCACC
64 TATAGTAACTTAGCA-C
* **
5900 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
5964 ATGGTCACTTAGCAC
65 ATAGTAACTTAGCAC
*
5979 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
6003 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 4 0.04
79 58 0.65
80 27 0.30
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:10664 original size:50 final size:49
Alignment explanation
Indices: 10559--10686 Score: 177
Period size: 50 Copynumber: 2.6 Consensus size: 49
10549 GGTACGGATT
* * * * *
10559 GTAGACTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACGTA
1 GTAGCCTGAACTTAGTACTACACACGTGACCAACAGTCTAATACACGTA
*
10608 GTAGCCTGAACTTAGTACTACACACGTGACCTCACCA-TCTAATACACGTA
1 GTAGCCTGAACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACGTA
10658 GTAGCCTGAACTTAGTACTACACACGTGA
1 GTAGCCTGAACTTAGTACTACACACGTGA
10687 TCATAGTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
49 25 0.35
50 42 0.59
51 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (49 bp):
GTAGCCTGAACTTAGTACTACACACGTGACCAACAGTCTAATACACGTA
Found at i:14306 original size:43 final size:43
Alignment explanation
Indices: 14152--14307 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
14142 TGTGTTATCG
* * * *
14152 TGTAAG-CCACGTCTGGGATATTGGCATCGACT-TATGATTTACG
1 TGTAAGACCACGTTTGGGACATTGGCATCGA-TATTTGA-TTACA
* * * ** *
14195 TGTAAAACCATGTTTAGGATGTTGGCATC-ATATTTGATTTCA
1 TGTAAGACCACGTTTGGGACATTGGCATCGATATTTGATTACA
* *
14237 TGTAAGACC-CTGTATGAGAC-TGTGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTTTGGGACAT-TGGCATCGATATTTGATTACA
14280 TGTAAGACCACGTTTGGGACATTGGCAT
1 TGTAAGACCACGTTTGGGACATTGGCAT
14308 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
42 24 0.27
43 44 0.49
44 20 0.22
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTAAGACCACGTTTGGGACATTGGCATCGATATTTGATTACA
Found at i:24613 original size:37 final size:37
Alignment explanation
Indices: 24563--24641 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
24553 TTATTACGAA
* * *
24563 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
24600 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
24637 GTCTT
1 GTCTT
24642 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:24838 original size:47 final size:47
Alignment explanation
Indices: 24760--25270 Score: 817
Period size: 47 Copynumber: 10.7 Consensus size: 47
24750 CCCTTCGGGA
* * * * * *
24760 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24807 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24854 CTTATCGCATAAATACACTTTCACATTCATCACATCGTCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24901 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24950 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24997 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25044 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25093 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25140 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25189 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
25236 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
25271 AGAATCCTAA
Statistics
Matches: 438, Mismatches: 19, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 298 0.68
49 139 0.32
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:24948 original size:96 final size:94
Alignment explanation
Indices: 24760--25270 Score: 799
Period size: 96 Copynumber: 5.4 Consensus size: 94
24750 CCCTTCGGGA
** * * * * * * *
24760 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATAAATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
24825 TTTCACATTCATCACATTGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
24854 CTTATCGCATAAATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATAAATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
24919 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
24950 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATAAATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
25015 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
25044 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATA-A-ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
25109 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
25140 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATA-A-ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
25205 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
25236 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATAAATACACT-TTCACATTCATCACAT
25271 AGAATCCTAA
Statistics
Matches: 392, Mismatches: 20, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
93 1 0.00
94 113 0.29
96 278 0.71
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATAAATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:25029 original size:143 final size:143
Alignment explanation
Indices: 24760--25270 Score: 834
Period size: 143 Copynumber: 3.6 Consensus size: 143
24750 CCCTTCGGGA
* * * * * * *
24760 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* * *
24823 ACTTTCACATTCATCACATTGGCCATTAGGCCTTATCGCATAAATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
24888 TCGTCCATTAGGC
131 TCGGCCATTAGGC
24901 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
24966 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
25031 TCGGCCATTAGGC
131 TCGGCCATTAGGC
25044 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
25109 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
25174 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
* *
25189 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
25252 A-TGTTCACATCCATCACAT
66 ACT-TTCACATTCATCACAT
25271 AGAATCCTAA
Statistics
Matches: 351, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
141 10 0.03
142 2 0.01
143 292 0.83
145 47 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:29273 original size:39 final size:39
Alignment explanation
Indices: 29121--29537 Score: 620
Period size: 39 Copynumber: 10.8 Consensus size: 39
29111 CCAGCATGAT
* * * *
29121 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
** * *
29161 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
*
29201 TG--C-TCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
29238 TGCTCTTCGAGACTTAGCCC-GATACATCACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
*
29277 TGCTCTTCGAGACTTAGCCCGGATACATTACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
29317 TGCTCTTC-GACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
29355 TGCTCTTCGAGACTTAGCCCGGAT--ATCACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
29393 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
29432 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
29471 TGCTCTTCGGACTTAGCCCGGAT--ATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
29508 TGCTCTTCGGA-TTAGCCCGGATACATCACT
1 TGCTCTTCGGACTTAGCCCGGATACATCACT
29538 CAATTCTCAT
Statistics
Matches: 351, Mismatches: 14, Indels: 26
0.90 0.04 0.07
Matches are distributed among these distances:
36 13 0.04
37 67 0.19
38 67 0.19
39 116 0.33
40 87 0.25
41 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:29464 original size:194 final size:191
Alignment explanation
Indices: 29121--29537 Score: 628
Period size: 194 Copynumber: 2.2 Consensus size: 191
29111 CCAGCATGAT
* * * * * **
29121 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGA-A
*
29186 TATCACTAGCACGAATGCTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGAGAC
64 TATCACTAGCACGAATGCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGAC
*
29251 TTAGCCCGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACATTACTAGCACGA
129 TTAGCCCGATACATCACTAGCACGAATGCTCTTCG-GACTTAGCCCGGAT--ATCACTAGCACGA
29316 A
191 A
*
29317 TGCTCTTC-GACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGG-ATA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGAATA
29380 TCACTAGCACGAATGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG-GA
66 TCACTAGCACGAATG--C-TCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGA
29443 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATATCACTAGCACGAA
128 CTTAGCCC-GATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATATCACTAGCACGAA
29508 TGCTCTTCGGA-TTAGCCCGGATACATCACT
1 TGCTCTTCGGACTTAGCCCGGATACATCACT
29538 CAATTCTCAT
Statistics
Matches: 206, Mismatches: 10, Indels: 15
0.89 0.04 0.06
Matches are distributed among these distances:
191 40 0.19
192 20 0.10
193 24 0.12
194 110 0.53
195 4 0.02
196 8 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (191 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGAATA
TCACTAGCACGAATGCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTT
AGCCCGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATATCACTAGCACGAA
Found at i:29572 original size:115 final size:114
Alignment explanation
Indices: 29121--29537 Score: 619
Period size: 116 Copynumber: 3.6 Consensus size: 114
29111 CCAGCATGAT
* * * ** *
29121 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGAGACTTAGCCCGGATAT--CACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATA
* *
29186 TATCACTAGCACGAATGCTC--GGAACTTAGTCCGGATACATCACTAGCACGAA
63 CATCACTAGCACGAATGCTCTTCG-ACTTAG-CCGGATACATCACTAGCACGAA
29238 TGCTCTTCGAGACTTAGCCC-GATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATA
1 TGCTCTTCGAGACTTAGCCCGGAT--ATCACTAGCACGAATGCTCTTCG-GACTTAGCCCGGATA
*
29302 CATTACTAGCACGAATGCTCTTCGACTTAGCCCGGATACATCACTAGCACGAA
63 CATCACTAGCACGAATGCTCTTCGACTTAG-CCGGATACATCACTAGCACGAA
29355 TGCTCTTCGAGACTTAGCCCGGATATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACAT
1 TGCTCTTCGAGACTTAGCCCGGATATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACAT
29420 CACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
66 CACTAGCACGAATGCTCTTC-GACTTAG-CCGGATACATCACTAGCACGAA
29471 TGCTCTTCG-GACTTAGCCCGGATATCACTAGCACGAATGCTCTTCGGA-TTAGCCCGGATACAT
1 TGCTCTTCGAGACTTAGCCCGGATATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACAT
29534 CACT
66 CACT
29538 CAATTCTCAT
Statistics
Matches: 282, Mismatches: 11, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
114 19 0.07
115 77 0.27
116 114 0.40
117 66 0.23
118 6 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (114 bp):
TGCTCTTCGAGACTTAGCCCGGATATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACAT
CACTAGCACGAATGCTCTTCGACTTAGCCGGATACATCACTAGCACGAA
Found at i:30814 original size:36 final size:37
Alignment explanation
Indices: 30742--30819 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
30732 TTATTACGAA
* *
30742 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
30779 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
30815 GTCTT
1 GTCTT
30820 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:31016 original size:47 final size:47
Alignment explanation
Indices: 30938--31350 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
30928 CCCTTCGGGA
* * * * * *
30938 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30985 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31032 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31079 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31126 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31173 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31269 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31316 CTTATCACATATATACACTTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
31351 AGAATCCTAA
Statistics
Matches: 353, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 306 0.87
49 47 0.13
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:36842 original size:82 final size:81
Alignment explanation
Indices: 36726--36881 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
36716 AAATTGTACA
* * * *
36726 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
36790 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
36807 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
36872 TGCGAGTTGA
65 TGCGAATTGA
36882 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:36849 original size:55 final size:52
Alignment explanation
Indices: 36725--36878 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
36715 TAAATTGTAC
* *
36725 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
36778 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
36833 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
36879 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:36883 original size:27 final size:27
Alignment explanation
Indices: 36726--36881 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
36716 AAATTGTACA
*
36726 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
36753 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
36780 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
36807 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
36835 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
36862 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
36882 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:36892 original size:27 final size:27
Alignment explanation
Indices: 36718--36902 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
36708 GCGGGATTAA
*
36718 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
36745 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
36772 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
36799 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
36827 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
36854 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
36881 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
36903 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:36893 original size:82 final size:81
Alignment explanation
Indices: 36718--36902 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
36708 GCGGGATTAA
* * * *
36718 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
36783 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
36799 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
36863 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
36881 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
36903 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Done.