Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3064
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: 37345
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Found at i:3851 original size:59 final size:58
Alignment explanation
Indices: 3759--3875 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 58
3749 TTGTAGGGAA
3759 AAGGTATATGTATAAGAGTATGTTCAAACTGAATATTATTATAAGAATAAAAATACTAT
1 AAGGTATATGTATAAGAGTATGTTCAAACTGAATATTA-TATAAGAATAAAAATACTAT
3818 AAGGTATATGTATAAGAGTATGTTCAAACTGAATATTATATAAGAATAAAAATACTAT
1 AAGGTATATGTATAAGAGTATGTTCAAACTGAATATTATATAAGAATAAAAATACTAT
3876 TTTTGCTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 20 0.34
59 38 0.66
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (58 bp):
AAGGTATATGTATAAGAGTATGTTCAAACTGAATATTATATAAGAATAAAAATACTAT
Found at i:6365 original size:18 final size:19
Alignment explanation
Indices: 6342--6379 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6332 TGGTACCACC
6342 AAACAT-ATATCA-CATCTT
1 AAACATCAT-TCATCATCTT
6360 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
6379 A
1 A
6380 CACCTTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (19 bp):
AAACATCATTCATCATCTT
Found at i:8120 original size:37 final size:37
Alignment explanation
Indices: 8070--8148 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
8060 TTATTACGAA
* *
8070 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
8107 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
8144 GTCTT
1 GTCTT
8149 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:8380 original size:47 final size:47
Alignment explanation
Indices: 8316--8821 Score: 813
Period size: 47 Copynumber: 11.0 Consensus size: 47
8306 ACTCGCCCCG
8316 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
8363 TCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
8410 -CAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
8454 TCACAATATATACACTTTCACATTCATCACATCGACTATTAGGCCTTA
1 TCAC-ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
8502 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
8549 TCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
* *
8596 TC-CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
8642 TCACATATATACACTTTCACATTCATCACATCGGCTA-TAGG-CTTGA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT-A
*
8688 -CAC--ATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
8731 TCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
* *
8777 T--CATATATACACTTTCACATTCAACACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
8822 CTATCATTTC
Statistics
Matches: 436, Mismatches: 11, Indels: 26
0.92 0.02 0.05
Matches are distributed among these distances:
43 31 0.07
44 78 0.18
45 32 0.07
46 84 0.19
47 168 0.39
48 43 0.10
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
Found at i:8521 original size:139 final size:139
Alignment explanation
Indices: 8316--8820 Score: 846
Period size: 139 Copynumber: 3.7 Consensus size: 139
8306 ACTCGCCCCG
* *
8316 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
8381 ACATTCATCACATCGGCTATTAGGCCTT-ACACATATACACTTTCACATTCATCACATCGGCCAT
66 ACATTCATCACATCGGCTATTAGGCCTTCACACATATACACTTTCACATTCATCACATCGGCCAT
8445 TAGGCCTTA
131 TAGGCCTTA
* *
8454 TCACAATATATACACTTTCACATTCATCACATCGACTATTAGGCCTTATCACATATATACACTTT
1 TCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
8519 CACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGC
65 CACATTCATCACATCGGCTATTAGGCC-T-TCACACATATACACTTTCACATTCATCACATCGGC
*
8584 TATTAGGCCTTA
128 CATTAGGCCTTA
*
8596 TC-CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
8660 ACATTCATCACATCGGCTA-TAGG-CTTGACACATATACACTTTCACATTCATCACATCGGCCAT
66 ACATTCATCACATCGGCTATTAGGCCTTCACACATATACACTTTCACATTCATCACATCGGCCAT
8723 TAGG-CTTA
131 TAGGCCTTA
8731 TCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTAT--CATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
* *
8793 ACATTCAACACATCGGCCATTAGGCCTT
66 ACATTCATCACATCGGCTATTAGGCCTT
8821 ACTATCATTT
Statistics
Matches: 349, Mismatches: 11, Indels: 17
0.93 0.03 0.05
Matches are distributed among these distances:
133 32 0.09
134 4 0.01
135 24 0.07
136 68 0.19
137 1 0.00
138 5 0.01
139 89 0.26
140 78 0.22
141 2 0.01
142 46 0.13
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (139 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCTATTAGGCCTTCACACATATACACTTTCACATTCATCACATCGGCCAT
TAGGCCTTA
Found at i:11371 original size:40 final size:40
Alignment explanation
Indices: 11314--11496 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
11304 CCAGCATGAT
* *
11314 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
11354 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
11394 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
11435 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
11475 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
11497 CATCATTCAA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.03
40 96 0.81
41 20 0.17
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:11840 original size:29 final size:29
Alignment explanation
Indices: 11801--11879 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
11791 CTTAATAATC
*
11801 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
11831 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
11860 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
11880 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:11922 original size:43 final size:43
Alignment explanation
Indices: 11861--11949 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
11851 TGCATTTCAA
*
11861 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTAGT
11904 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTAGT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTAGT
11947 GCC
1 GCC
11950 AATCTCACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTAGT
Found at i:11950 original size:28 final size:28
Alignment explanation
Indices: 11910--11977 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
11900 TATTGCCCGC
11910 ACACTTAGTGCCAATCTCACAACCGTGA
1 ACACTTAGTGCCAATCTCACAACCGTGA
11938 ACACTTAGTGCCAATCTCACAACCGTGA
1 ACACTTAGTGCCAATCTCACAACCGTGA
*
11966 ACACTTATTGCC
1 ACACTTAGTGCC
11978 CGCACACTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24
Consensus pattern (28 bp):
ACACTTAGTGCCAATCTCACAACCGTGA
Found at i:11953 original size:71 final size:71
Alignment explanation
Indices: 11867--12020 Score: 299
Period size: 71 Copynumber: 2.2 Consensus size: 71
11857 TCAAGCCCGC
11867 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATCTCACAA
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATCTCACAA
11932 CCGTGA
66 CCGTGA
11938 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATCTCACAA
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATCTCACAA
12003 CCGTGA
66 CCGTGA
*
12009 ACACTTATTGCC
1 ACACTTAGTGCC
12021 CGCACACTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (71 bp):
ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATCTCACAA
CCGTGA
Found at i:11985 original size:43 final size:43
Alignment explanation
Indices: 11938--12034 Score: 194
Period size: 43 Copynumber: 2.3 Consensus size: 43
11928 ACAACCGTGA
11938 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
11981 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
12024 ACACTTAGTGC
1 ACACTTAGTGC
12035 TGAAAACCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (43 bp):
ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
Found at i:13928 original size:37 final size:37
Alignment explanation
Indices: 13878--13956 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
13868 TTATTACGAA
* *
13878 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
13915 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
13952 GTCTT
1 GTCTT
13957 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:14192 original size:47 final size:47
Alignment explanation
Indices: 14075--14638 Score: 965
Period size: 47 Copynumber: 12.1 Consensus size: 47
14065 CCCTTCGGGA
* * * * * * *
14075 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
14122 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14168 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14215 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14262 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14309 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
14356 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14403 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
14450 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14497 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14542 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14589 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14635 CTTA
1 CTTA
14639 CTATCATTTC
Statistics
Matches: 497, Mismatches: 17, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
45 44 0.09
46 58 0.12
47 395 0.79
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:25728 original size:40 final size:40
Alignment explanation
Indices: 25673--25865 Score: 243
Period size: 39 Copynumber: 4.9 Consensus size: 40
25663 GGATATAGCT
* * *
25673 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
25713 ACTCGCACAATTGCCTTCGGGACTTAG-CCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
*
25752 ACTCGCACAAATGCCTTCGGGACTTAGCCCGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
25791 ACTCGCACAAATGCCTTCGGGACTT-GCCCGG-AACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* * *
25830 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
25866 CATCCAAATA
Statistics
Matches: 134, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 5 0.04
39 92 0.69
40 36 0.27
41 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:25767 original size:39 final size:39
Alignment explanation
Indices: 25647--25858 Score: 232
Period size: 39 Copynumber: 5.4 Consensus size: 39
25637 AAATCACGTA
* * * * *
25647 CCTTCGGAATTTAACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCGGATTTAG-TAACTCGCACAAATG
* * *
25686 CCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACAATTG
1 CCTTCGGGACTTAG-CCGGATT-TAGTAACTCGCACAAATG
25726 CCTTCGGGACTTAGCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATTTAGTAACTCGCACAAATG
*
25765 CCTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATTTAGTAACTCGCACAAATG
** * * * *
25804 CCTTCGGGACTT-GCCCGGAACTAGTCACTAGCGCAGATG
1 CCTTCGGGACTTAG-CCGGATTTAGTAACTCGCACAAATG
25843 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
25859 CGGTTATCAT
Statistics
Matches: 148, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 114 0.77
40 33 0.22
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATTTAGTAACTCGCACAAATG
Found at i:25780 original size:79 final size:78
Alignment explanation
Indices: 25647--25864 Score: 262
Period size: 78 Copynumber: 2.8 Consensus size: 78
25637 AAATCACGTA
* * * * *
25647 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGT
1 CCTTCGGGACTTAGCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAGAGT
*
25712 AACTCGCACAATTG
65 AACTCGCACAAATG
* * *
25726 CCTTCGGGACTTAGCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGATT-TAGT
1 CCTTCGGGACTTAGCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAGAGT
25790 AACTCGCACAAATG
65 AACTCGCACAAATG
* * *
25804 CCTTCGGGACTT-GCCCGGA-ACTAGTCACTAGCGCAGATGCCTTCGGGACTTAGCCCGGTTA
1 CCTTCGGGACTTAG-CCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA
25865 TCATCCAAAT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
77 1 0.01
78 68 0.57
79 51 0.43
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAGAGTA
ACTCGCACAAATG
Found at i:33837 original size:78 final size:79
Alignment explanation
Indices: 33717--33908 Score: 255
Period size: 78 Copynumber: 2.4 Consensus size: 79
33707 CGATATAGCT
* * *
33717 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTCGCACAATTGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAGAGTAACTCGCACAAATGCCTTCGGGACTT
**
33782 AGCCCGGATTTAGTA
66 -GCCCGGAACTAGTA
*
33797 ACTCGCACAAATGCC-TC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTAGAGTAACTCGCACAAATGCCTTCGGGACT
*
33859 TGCCCGGAACTAGTC
65 TGCCCGGAACTAGTA
* * *
33874 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGGTTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA
33909 TCATCCAAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
77 23 0.23
78 44 0.45
79 17 0.17
80 14 0.14
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (79 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAGAGTAACTCGCACAAATGCCTTCGGGACTT
GCCCGGAACTAGTA
Found at i:33888 original size:39 final size:40
Alignment explanation
Indices: 33717--33905 Score: 251
Period size: 40 Copynumber: 4.8 Consensus size: 40
33707 CGATATAGCT
* * *
33717 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
33757 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
33797 ACTCGCACAAATGCC-TC-GGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
33835 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
33874 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
33906 TTATCATCCA
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
38 36 0.27
39 37 0.28
40 59 0.44
41 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:35872 original size:19 final size:20
Alignment explanation
Indices: 35848--35885 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35838 GGTACCATCA
35848 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
35867 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
35886 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:36223 original size:93 final size:93
Alignment explanation
Indices: 36113--36283 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
36103 GCCCCTAAGT
* *
36113 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATAAATGAACTCGGACTAAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTAAACTCAA
*
36178 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * * * *
36206 GAACTCGGACTCAACTCAAGGAGTTCGGACATTTGCATCCATAATTGAACTGGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTAAACTCAA
36271 CGAGTTCGGATGC
66 CGAGTTCGGATGC
36284 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTAAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:36268 original size:46 final size:45
Alignment explanation
Indices: 36112--36280 Score: 162
Period size: 46 Copynumber: 3.7 Consensus size: 45
36102 CGCCCCTAAG
* * * *
36112 TGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCAT-AA
* * * * *
36158 TGAACTCGGACTAAACTCAATGAGTTCGGATGCCTAGTTACAT-C-TCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAA
* *
36205 CGAACTCGGACTCAACTCAAGGAGTTCGGACATTTGCATCCATAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAA
*
36250 TTGAACTGGGACTCAACTCAACGAGTTCGGA
1 -TGAACTCGGACTCAACTCAACGAGTTCGGA
36281 TGCTCAACCA
Statistics
Matches: 98, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 53 0.54
47 28 0.29
48 1 0.01
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAA
Done.