Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3500.1
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: 124584
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.30
Warning! 7620 characters in sequence are not A, C, G, or T
Found at i:4578 original size:14 final size:14
Alignment explanation
Indices: 4556--4587 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4546 TCCAATCACC
4556 GGGCAAGTTTGGTT
1 GGGCAAGTTTGGTT
*
4570 GGGCCAGTTTGGTT
1 GGGCAAGTTTGGTT
4584 GGGC
1 GGGC
4588 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCAAGTTTGGTT
Found at i:7975 original size:30 final size:30
Alignment explanation
Indices: 7934--8002 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
7924 CACACAGGTA
* *
7934 GACACACGGGCATGTGACTAGGTCGTGTGT
1 GACACATGGGCATGTGACTAGGCCGTGTGT
*
7964 GACACATGGGCATGTGGCTAGGCCGTGTGT
1 GACACATGGGCATGTGACTAGGCCGTGTGT
7994 GACACATGG
1 GACACATGG
8003 TCTGTCCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (30 bp):
GACACATGGGCATGTGACTAGGCCGTGTGT
Found at i:14902 original size:222 final size:222
Alignment explanation
Indices: 14516--14956 Score: 810
Period size: 222 Copynumber: 2.0 Consensus size: 222
14506 GCCCCGTTTT
14516 TAATGTTCTTTACGTTTTTGGAATCCCGGAAGCTCGATTAAGCTTATGCTAGCAATAATTCAACC
1 TAATGTTCTTTACGTTTTTGGAATCCCGGAAGCTCGATTAAGCTTATGCTAGCAATAATTCAACC
14581 TAGGGTTTATATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGATAGAA
66 TAGGGTTTATATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGATAGAA
* * *
14646 TATGGGGTTTTAAATTATGTTAGGCAACTTGTGCTACTCGGTTTTTAGTGAAAACGAGTAAAAGG
131 TATGGGGTTTTAAATTATGTTAGACAACTTGTGCTACTCGGTTTTGAGTGAAAACGAGTAAAAGA
*
14711 GCTTAATCGGTAAAAATACCTAATCGC
196 GCTTAATCGGCAAAAATACCTAATCGC
*
14738 TAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTAAGCTTATGCTAGCAATAATTCAACC
1 TAATGTTCTTTACGTTTTTGGAATCCCGGAAGCTCGATTAAGCTTATGCTAGCAATAATTCAACC
*
14803 TAGGGTTTATATTTGGAAAAATACCCATAGGTGAAATTTTTGTATTTTGATGTTTTATGATAGAA
66 TAGGGTTTATATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGATAGAA
* *
14868 TATGGGGTTTTAAATTATGTTAGACATCTTGTGCTACTCGGTTTTGAGTGAAAAGGAGTAAAAGA
131 TATGGGGTTTTAAATTATGTTAGACAACTTGTGCTACTCGGTTTTGAGTGAAAACGAGTAAAAGA
14933 GCTTAATCGGCAAAAATACCTAAT
196 GCTTAATCGGCAAAAATACCTAAT
14957 AGTCACAAGT
Statistics
Matches: 211, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 211 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (222 bp):
TAATGTTCTTTACGTTTTTGGAATCCCGGAAGCTCGATTAAGCTTATGCTAGCAATAATTCAACC
TAGGGTTTATATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGATAGAA
TATGGGGTTTTAAATTATGTTAGACAACTTGTGCTACTCGGTTTTGAGTGAAAACGAGTAAAAGA
GCTTAATCGGCAAAAATACCTAATCGC
Found at i:15597 original size:46 final size:46
Alignment explanation
Indices: 15547--15714 Score: 138
Period size: 46 Copynumber: 3.7 Consensus size: 46
15537 TGGTTGAGCA
*
15547 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
15593 TCCGAACTC-----GTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
15635 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
15681 -CTCGAGCTTGTTGAGTTGAGTCAGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
15715 GGGGCGGGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 26
0.70 0.10 0.19
Matches are distributed among these distances:
38 6 0.06
40 3 0.03
41 15 0.16
42 9 0.09
45 1 0.01
46 38 0.40
47 15 0.16
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:15976 original size:19 final size:20
Alignment explanation
Indices: 15939--15976 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15929 ATAAGGTGGT
15939 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
15959 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
15977 TGGTAGTACC
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:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:18114 original size:52 final size:52
Alignment explanation
Indices: 18036--18139 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
18026 CGGAAAGTCA
* *
18036 AGAAATATGAATCCTCGTTCCCAAGTTTCAGCTGGGCAATCATATAGAAATT
1 AGAAATATGAATCCTAGTTCCCAAGTTTCAACTGGGCAATCATATAGAAATT
*
18088 AGAAATATGAATCCTAGTTCCCAAGTTTCAACTGGGCAATCATATGGAAATT
1 AGAAATATGAATCCTAGTTCCCAAGTTTCAACTGGGCAATCATATAGAAATT
18140 TCAAGAAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
AGAAATATGAATCCTAGTTCCCAAGTTTCAACTGGGCAATCATATAGAAATT
Found at i:30059 original size:46 final size:46
Alignment explanation
Indices: 29948--30074 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 46
29938 TAACCCGCCC
*
29948 CTAAGTGAACTCGGACTCAACTCAACGAGTTGGGATGCCTAGTTACAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * *
29996 CTCA-CGAACTCGG-CTCAACTCAACGAGTTCGGA-C-ATTTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
30038 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30075 TGCTCAACCC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 6 0.09
43 2 0.03
44 2 0.03
45 8 0.12
46 39 0.57
47 8 0.12
48 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:40909 original size:14 final size:14
Alignment explanation
Indices: 40890--40920 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40880 ATAGGAGTAA
40890 ATAAAGGAAAAATG
1 ATAAAGGAAAAATG
40904 ATAAAGGAAAAATG
1 ATAAAGGAAAAATG
40918 ATA
1 ATA
40921 TCACCCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (14 bp):
ATAAAGGAAAAATG
Found at i:41810 original size:46 final size:47
Alignment explanation
Indices: 41757--42026 Score: 207
Period size: 46 Copynumber: 5.7 Consensus size: 47
41747 GGATTATTAT
*
41757 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATG-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGAA
* *
41803 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGA-CAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGAGATGAA
* * * * *
41851 GTGCTAGTGCAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAA
* * * * *
41898 -AGCCAATGTAAGACATGTCTAGGACATGCATCGGCTACGAGATG-T
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAA
* * *
41943 G-TC-AGTGTAAGATCATGTCTGGGACATGGCATC-GACACAGATATGATA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-GAGATGA-A
* * **
41991 GAACTTGTGTAAGACTATGTCTAAGACATGGCATCG
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCG
42027 ACACCTTACC
Statistics
Matches: 178, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
44 8 0.04
45 17 0.10
46 71 0.40
47 32 0.18
48 22 0.12
49 3 0.02
50 25 0.14
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAA
Found at i:49767 original size:43 final size:43
Alignment explanation
Indices: 49720--49832 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 43
49710 CCTCGATTGA
* *
49720 GATTTACGTATAAGACCATGTCTGGGACATAGGTATCG-TATTT
1 GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATA-TT
* * *
49763 GATTT-CGTATAAGACCTTGTCCGGGATAGAGGCATCGATATT
1 GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATATT
* * *
49805 GAATTACATGTAAGACCATGTCTGGGAC
1 GATTTACGTATAAGACCATGTCTGGGAC
49833 GTCGGCGTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 33 0.58
43 24 0.42
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATATT
Found at i:52004 original size:22 final size:22
Alignment explanation
Indices: 51976--52097 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
51966 TTCCACATCC
51976 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
51998 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
52022 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
52045 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52069 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52092 ATCACA
1 ATCACA
52098 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52011 original size:47 final size:47
Alignment explanation
Indices: 51948--52986 Score: 1397
Period size: 47 Copynumber: 22.3 Consensus size: 47
51938 CCCTTCGGGA
* * *
51948 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
51995 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
52042 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52089 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52136 CTTATCACACATACACATG------TTC-T----GT-GCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52171 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52218 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52265 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52312 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52359 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52406 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52453 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52500 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52547 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52594 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52641 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52688 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52735 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52782 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
52829 CTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52876 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52923 CTTATCACGCATATATATACT-TTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
52972 CCTATCACATATATA
1 CTTATCACATATATA
52987 TACTTGTACA
Statistics
Matches: 958, Mismatches: 18, Indels: 32
0.95 0.02 0.03
Matches are distributed among these distances:
35 29 0.03
36 1 0.00
40 1 0.00
41 6 0.01
42 1 0.00
46 2 0.00
47 877 0.92
49 40 0.04
50 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:52112 original size:94 final size:94
Alignment explanation
Indices: 51975--52980 Score: 1723
Period size: 94 Copynumber: 10.8 Consensus size: 94
51965 CTTCCACATC
* * *
51975 CATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTC
1 CATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCAAATTCATCACATTGGCCATTC
* * ** *
52039 GGCCTTATCTCATATATGCATGTTCACATT
65 GGCCTTATCACACATACACATGTTCAAATT
*
52069 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52134 GCCTTATCACACATACACATG------TT
66 GCCTTATCACACATACACATGTTCAAATT
* *
52157 C-T----GT-GCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52216 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52245 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52310 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52339 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52404 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52433 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52498 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52527 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52592 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52621 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52686 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52715 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
52780 GCCTTATCACACATACACATGTTCAAATT
66 GCCTTATCACACATACACATGTTCAAATT
52809 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
*
52874 GCCTTATCACACATACACATGTTCACATT
66 GCCTTATCACACATACACATGTTCAAATT
* * * * * *
52903 CATCACATTGGCCATTCGGCCTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACT
1 CATCACATTGGCCATTCGGCCTTATCACACATACACAT--GTTCAAATTCATCACATTGGCCATT
*
52968 CGGCCCTATCACA
64 CGGCCTTATCACA
52981 TATATATACT
Statistics
Matches: 880, Mismatches: 17, Indels: 28
0.95 0.02 0.03
Matches are distributed among these distances:
82 76 0.09
83 1 0.00
87 1 0.00
88 6 0.01
89 1 0.00
93 2 0.00
94 759 0.86
96 34 0.04
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (94 bp):
CATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCG
GCCTTATCACACATACACATGTTCAAATT
Found at i:52165 original size:35 final size:35
Alignment explanation
Indices: 52126--52192 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
52116 CATCACATTG
52126 GCCATTCGGCCTTATCACACATACACATGTTCTGT
1 GCCATTCGGCCTTATCACACATACACATGTTCTGT
52161 GCCATTCGGCCTTATCACACATACACATGTTC
1 GCCATTCGGCCTTATCACACATACACATGTTC
52193 ACATTCATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (35 bp):
GCCATTCGGCCTTATCACACATACACATGTTCTGT
Found at i:52326 original size:141 final size:141
Alignment explanation
Indices: 52161--52980 Score: 1541
Period size: 141 Copynumber: 5.8 Consensus size: 141
52151 CATGTTCTGT
*
52161 GCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
52226 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
66 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
52291 TCATCACATTG
131 TCATCACATTG
52302 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
52367 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
66 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
52432 TCATCACATTG
131 TCATCACATTG
52443 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
52508 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
66 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
52573 TCATCACATTG
131 TCATCACATTG
52584 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
52649 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
66 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
52714 TCATCACATTG
131 TCATCACATTG
52725 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
52790 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
66 ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
52855 TCATCACATTG
131 TCATCACATTG
*
52866 GCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
* * * * * * *
52931 GCATATATATACTTTCACATTCATCACATTGGCCACTCGGCCCTATCACA
66 ACATACACAT--GTTCAAATTCATCACATTGGCCATTCGGCCTTATCACA
52981 TATATATACT
Statistics
Matches: 668, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
141 634 0.95
143 34 0.05
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (141 bp):
GCCATTCGGCCTTATCACACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCAC
ACATACACATGTTCAAATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCAAAT
TCATCACATTG
Found at i:57504 original size:27 final size:26
Alignment explanation
Indices: 57466--57557 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 26
57456 TAGGGCAAAT
*
57466 CAGTTATTTTACCTTACAGAGGTATTA
1 CAGTCATTTTACCTTA-AGAGGTATTA
* *
57493 CAGTCATTTTACCTTATAGGGGTATTT
1 CAGTCATTTTACCTTA-AGAGGTATTA
* *
57520 C-GATCATTTTACCCTATGAGGGTATTA
1 CAG-TCATTTTACCTTAAGA-GGTATTA
57547 CAGTCATTTTA
1 CAGTCATTTTA
57558 TCTCATAAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.04
27 51 0.94
28 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (26 bp):
CAGTCATTTTACCTTAAGAGGTATTA
Found at i:57568 original size:27 final size:26
Alignment explanation
Indices: 57486--57568 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
57476 ACCTTACAGA
* *
57486 GGTATTACAGTCATTTTACCTTATAGG
1 GGTATTACAGTCATTTTA-CTCATAAG
* * *
57513 GGTATTTC-GATCATTTTACCCTATGAG
1 GGTATTACAG-TCATTTTACTC-ATAAG
57540 GGTATTACAGTCATTTTATCTCATAAG
1 GGTATTACAGTCATTTTA-CTCATAAG
57567 GG
1 GG
57569 CAAAATTGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
26 2 0.05
27 39 0.89
28 3 0.07
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (26 bp):
GGTATTACAGTCATTTTACTCATAAG
Found at i:57579 original size:27 final size:27
Alignment explanation
Indices: 57548--57622 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
57538 AGGGTATTAC
*
57548 AGTCATTTTATCTCATAAGGGCAAAAT
1 AGTCATTTTATCTCATAAGGGAAAAAT
* * *
57575 TGTCATTTTATCACATAAAGGAAAAAT
1 AGTCATTTTATCTCATAAGGGAAAAAT
* *
57602 AGTTATTTTGTCTCATAAGGG
1 AGTCATTTTATCTCATAAGGG
57623 TTCAGGTACG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (27 bp):
AGTCATTTTATCTCATAAGGGAAAAAT
Found at i:59669 original size:44 final size:44
Alignment explanation
Indices: 59584--59696 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
59574 GGGAGTTACA
* * * *
59584 CGATATGTG-TTTTCGTGTAAGACCACGTCTGGGACATTGGCAT
1 CGATTTGTGATTTACGTGTAAGACCACGTCTAGGACAGTGGCAT
* *
59627 CGATTTGTGATTTACGTGTAAGACCATGTCTAGGATAGTGGCAT
1 CGATTTGTGATTTACGTGTAAGACCACGTCTAGGACAGTGGCAT
* *
59671 CAATATT-TGA-TTACATGTAAGACCAC
1 CGAT-TTGTGATTTACGTGTAAGACCAC
59697 ATCTGGGATG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 22 0.37
44 35 0.59
45 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (44 bp):
CGATTTGTGATTTACGTGTAAGACCACGTCTAGGACAGTGGCAT
Found at i:59712 original size:43 final size:44
Alignment explanation
Indices: 59599--59713 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
59589 TGTGTTTTCG
** * *
59599 TGTAAGACCACGTCTGGGACATTGGCATCGATTTGTGATTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCAATTTGTGATTTACA
* *
59643 TGTAAGACCATGTCTAGGATAG-TGGCATCAATATT-TGA-TTACA
1 TGTAAGACCACGTCTGGGAT-GTTGGCATCAAT-TTGTGATTTACA
*
59686 TGTAAGACCACATCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
59714 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.46
44 29 0.49
45 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCAATTTGTGATTTACA
Found at i:59916 original size:21 final size:22
Alignment explanation
Indices: 59877--59920 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59867 AAAGAATGTT
59877 ATGTGATATATATGGAAATGAA
1 ATGTGATATATATGGAAATGAA
* *
59899 ATGTGA-ATATGTGTAAATGAA
1 ATGTGATATATATGGAAATGAA
59920 A
1 A
59921 CATGAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
ATGTGATATATATGGAAATGAA
Found at i:66559 original size:43 final size:43
Alignment explanation
Indices: 66496--66611 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
66486 TATGTATTTT
** * *
66496 CATGTAAGACCACAACTGGGACTTTGGCATCGGT-TTTGATTTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGA-TTA
* * *
66539 CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTA
*
66582 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACATTGGCAT
66612 TGTACAAGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 56 0.92
44 5 0.08
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTA
Found at i:68856 original size:39 final size:40
Alignment explanation
Indices: 68811--68980 Score: 200
Period size: 40 Copynumber: 4.3 Consensus size: 40
68801 GCTCCTCGTT
* * *
68811 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
68851 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
68890 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
68930 CAAAGGCCTTCGGGGCTTACCCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
*
68970 CAAATGTCTTC
1 CAAATGCCTTC
68981 AGATCTTAGT
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 76 0.66
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:73306 original size:46 final size:46
Alignment explanation
Indices: 73253--73340 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
73243 TTACTTTCAC
*
73253 CGAGCTCGGTCCAAAACAATGGTGTATGGCATTTACGCCCGTCCAA
1 CGAGCTCGGTCCAAAACAATGGTGTATGGCATTTACGACCGTCCAA
73299 CGAGCTCGGTCCAAAACAATGGTGTATGGCATTTACGACCGT
1 CGAGCTCGGTCCAAAACAATGGTGTATGGCATTTACGACCGT
73341 ACAAAGCCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (46 bp):
CGAGCTCGGTCCAAAACAATGGTGTATGGCATTTACGACCGTCCAA
Found at i:78990 original size:40 final size:40
Alignment explanation
Indices: 78890--79061 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
78880 GCTCCTCGTT
* * *
78890 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
78930 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
78969 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
79009 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
79049 CAAATGCCTTCGG
1 CAAATGCCTTCGG
79062 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:83382 original size:49 final size:49
Alignment explanation
Indices: 83329--83595 Score: 203
Period size: 49 Copynumber: 5.6 Consensus size: 49
83319 ACATCAAAGT
*
83329 CGATGCCATGTCCCAGATAGGTCTTACACTAACTTTCATATATCAAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCAAGGC
* * ** * * * *
83378 CGATGCCGTGTCCCAAACAGGTCTTACACTGGCTCTCATCTATCAATGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCAAGGC
* * * *
83427 CGATGCCATGTCCCAGACAGGTCTTACACTGAC--ACACA-A-CAA-GT
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCAAGGC
* * * * * *
83471 TGACGCCATGTCCCAGATAGGTCTTACACTAGCTTGT-ATATCTCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTT-TCATATATCAAGGC
* * * * * * *
83520 CAATG-CATGTCCCAGACATGTCTTACACTAGCTCTC--GTCTCAATGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCAAGGC
* *
83566 TGATG-CATGTCCCAGACATGTCTTACACTA
1 CGATGCCATGTCCCAGACAGGTCTTACACTA
83596 GCACACATAT
Statistics
Matches: 175, Mismatches: 36, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
44 30 0.17
45 3 0.02
46 38 0.22
47 3 0.02
48 28 0.16
49 73 0.42
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCAAGGC
Found at i:83543 original size:48 final size:46
Alignment explanation
Indices: 83477--83597 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
83467 AAGTTGACGC
* * * * *
83477 CATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-CATCTCAAGGCCAATG
* * **
83525 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCAATG
83571 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
83598 ACACATATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 37 0.58
47 2 0.03
48 25 0.39
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCAATG
Found at i:88605 original size:43 final size:42
Alignment explanation
Indices: 88516--88672 Score: 120
Period size: 43 Copynumber: 3.7 Consensus size: 42
88506 TGTGATGACA
* * * **
88516 TGTAAGACCATATCTAGGACATTGGCATTGTATTAAGATTATG
1 TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATT-TG
*
88559 TGTAAGACCATATCTGGGATATTGGCATCGTTTTGTGATTTCG
1 TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATTT-G
* * * * * * * *
88602 TGTAAGACCCTGTCAGAGACAGTGGCATCGAATATGT-ATTTATA
1 TGTAAGACCATATCTGGGACATTGGCATCG-TTTTGTGA-TT-TG
*
88646 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATATCTGGGACATTGGCAT
88673 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 1 0.01
43 66 0.73
44 22 0.24
45 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATTTG
Found at i:93804 original size:37 final size:34
Alignment explanation
Indices: 93766--93828 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
93756 CCTGTTTCAG
*
93766 TACAGT-CCAGTATTAGT-TGGGCCTTAGCCTAT
1 TACAGTACCAGTATCAGTGTGGGCCTTAGCCTAT
93798 TACAGTACCAGTATCAGTGTGGGCCTTAGCC
1 TACAGTACCAGTATCAGTGTGGGCCTTAGCC
93829 CAATTCAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 6 0.21
33 10 0.36
34 12 0.43
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (34 bp):
TACAGTACCAGTATCAGTGTGGGCCTTAGCCTAT
Found at i:93838 original size:34 final size:33
Alignment explanation
Indices: 93766--93849 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
93756 CCTGTTTCAG
* *
93766 TACAGT-CCAGTATTAGTTGGGCCTTAGCCTAT
1 TACAGTACCAGTATCAGTTGGGCCTTAGCCAAT
93798 TACAGTACCAGTATCAGTGTGGGCCTTAGCCCAAT
1 TACAGTACCAGTATCAGT-TGGGCCTTAG-CCAAT
**
93833 T-CAGTAATAGTATCAGT
1 TACAGTACCAGTATCAGT
93850 ATCAATACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.13
33 10 0.22
34 24 0.53
35 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (33 bp):
TACAGTACCAGTATCAGTTGGGCCTTAGCCAAT
Found at i:106278 original size:46 final size:46
Alignment explanation
Indices: 106228--106400 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
106218 TGGTTGAGCA
106228 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
106274 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * * *
106319 CATCCGAGCTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
106367 CCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
106401 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.57
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:106384 original size:93 final size:93
Alignment explanation
Indices: 106225--106395 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
106215 GGATGGTTGA
* * * * *
106225 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTAGTTGAGT
106290 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
106318 GCATCCGAGCTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAGCTAGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTAGTTGAGT
106383 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
106396 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTAGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:108024 original size:54 final size:54
Alignment explanation
Indices: 107939--108224 Score: 360
Period size: 54 Copynumber: 5.3 Consensus size: 54
107929 ACCCCAAATA
* * *
107939 GGTAAAATGATCGTAATACCCCTGTAAGGTAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
** * *
107993 GGTAAAATGACCGTAATGCCATTGTAGGGTAAAATGACCGTAATACCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
** * ** * *
108047 GGTAAAAAT-ACCGTAATGCCGTTGTAGGGTAAAACGACTATAATATCCTGGTAG
1 GGT-AAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
* * *
108101 GG-AAAATGACCGTAATGCCCCTATAGGGTAAAATAACCGTAATGCCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
* * *
108154 GGTAAAATGACCGTAATACCCGTGTAGGGTAAAATGACCGTAATGCCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
*
108208 GATAAAATGACCGTAAT
1 GGTAAAATGACCGTAAT
108225 ATTTTGTATG
Statistics
Matches: 199, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
52 5 0.03
53 37 0.19
54 152 0.76
55 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (54 bp):
GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAG
Found at i:108225 original size:134 final size:133
Alignment explanation
Indices: 107937--108226 Score: 395
Period size: 134 Copynumber: 2.2 Consensus size: 133
107927 AAACCCCAAA
* * * * * *
107937 TAGGTAAAATGATCGTAATACCCCTGTAAGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATG
1 TAGGTAAAATGACCGTAATA-TCCTGTAAGGGAAAATGACCGTAATACCCCTATAGGGTAAAATA
108002 ACCGTAATGCCATTGTAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAAATACCGTAATGCC
65 ACCGTAATGCCATTGTAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAAATACCGTAATGCC
*
108067 GTTG
130 CTTG
* ** *
108071 TAGGGTAAAACGACTATAATATCCTGGT-AGGGAAAATGACCGTAATGCCCCTATAGGGTAAAAT
1 TA-GGTAAAATGACCGTAATATCCT-GTAAGGGAAAATGACCGTAATACCCCTATAGGGTAAAAT
* * *
108135 AACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCGTGTAGGGT-AAAATGACCGTAATG
64 AACCGTAATGCCATTGTAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAAAT-ACCGTAATG
108199 CCCTTG
128 CCCTTG
108205 TAGGATAAAATGACCGTAATAT
1 TAGG-TAAAATGACCGTAATAT
108227 TTTGTATGAT
Statistics
Matches: 135, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
133 7 0.05
134 112 0.83
135 16 0.12
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (133 bp):
TAGGTAAAATGACCGTAATATCCTGTAAGGGAAAATGACCGTAATACCCCTATAGGGTAAAATAA
CCGTAATGCCATTGTAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAAATACCGTAATGCCC
TTG
Found at i:108238 original size:26 final size:26
Alignment explanation
Indices: 107937--108241 Score: 222
Period size: 27 Copynumber: 11.4 Consensus size: 26
107927 AAACCCCAAA
* *
107937 TAGG-TAAAATGATCGTAATACCCCTG
1 TAGGATAAAATGACCGTAATA-CCTTG
107963 TAAGG-TAAAATGACCGTAATACCCTTG
1 T-AGGATAAAATGACCGTAATA-CCTTG
* *
107990 TAGGGTAAAATGACCGTAATGCCATTG
1 TAGGATAAAATGACCGTAATACC-TTG
* * *
108017 TAGGGTAAAATGACCGTAATACCCCTA
1 TAGGATAAAATGACCGTAATA-CCTTG
* *
108044 TAGGGTAAAAAT-ACCGTAATGCCGTTG
1 TAGGAT-AAAATGACCGTAATACC-TTG
* * ** *
108071 TAGGGTAAAACGACTATAATATCCTGG
1 TAGGATAAAATGACCGTAATA-CCTTG
* * * *
108098 TAGG-GAAAATGACCGTAATGCCCCTA
1 TAGGATAAAATGACCGTAAT-ACCTTG
* * *
108124 TAGGGTAAAATAACCGTAATGCCCTTG
1 TAGGATAAAATGACCGTAAT-ACCTTG
* *
108151 TAGGGTAAAATGACCGTAATACCCGTG
1 TAGGATAAAATGACCGTAATA-CCTTG
* *
108178 TAGGGTAAAATGACCGTAATGCCCTTG
1 TAGGATAAAATGACCGTAAT-ACCTTG
**
108205 TAGGATAAAATGACCGTAATATTTTG
1 TAGGATAAAATGACCGTAATACCTTG
*
108231 TATGATAAAAT
1 TAGGATAAAAT
108242 CACGATTATG
Statistics
Matches: 231, Mismatches: 36, Indels: 24
0.79 0.12 0.08
Matches are distributed among these distances:
26 42 0.18
27 180 0.78
28 9 0.04
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (26 bp):
TAGGATAAAATGACCGTAATACCTTG
Found at i:108420 original size:27 final size:27
Alignment explanation
Indices: 108381--108453 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
108371 TGGTGGAAGT
*
108381 ACTG-TACTGGTGGCTATGTCACATTC
1 ACTGTTACTGGTGGCTATGCCACATTC
* *
108407 ACTGTTACTGGTGGCTTTGCCACATTT
1 ACTGTTACTGGTGGCTATGCCACATTC
* **
108434 ACTGTTTCTGGCAGCTATGC
1 ACTGTTACTGGTGGCTATGC
108454 TGCATTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 4 0.10
27 35 0.90
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
ACTGTTACTGGTGGCTATGCCACATTC
Found at i:108701 original size:22 final size:22
Alignment explanation
Indices: 108676--108722 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
108666 ATAGGGCTTA
*
108676 GGCCCAGACTGTTACTGATCTG
1 GGCCCAAACTGTTACTGATCTG
*
108698 GGCCTAAACTGTTACTGATCTG
1 GGCCCAAACTGTTACTGATCTG
108720 GGC
1 GGC
108723 TTAGGCCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (22 bp):
GGCCCAAACTGTTACTGATCTG
Found at i:111834 original size:82 final size:82
Alignment explanation
Indices: 111735--111898 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
111725 AATGTAATAT
* *
111735 ATGACTATTAAGTGATAAGATGACTGTGATGTGTTAAAATATGACCAAATATATATGAGATTGGA
1 ATGACTATTAAGTGATAAGATGACTGAGATGCGTTAAAATATGACCAAATATATATGAGATTGGA
*
111800 AATATATCCTGACATGA
66 AATATATCCGGACATGA
111817 ATGACTATTAAGTGATAAGATGACTGAGATGCGTTAAAATATGACCAAATATATATGAGATTGGA
1 ATGACTATTAAGTGATAAGATGACTGAGATGCGTTAAAATATGACCAAATATATATGAGATTGGA
111882 AATATATCCGGACATGA
66 AATATATCCGGACATGA
111899 GGTCCGCAGG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (82 bp):
ATGACTATTAAGTGATAAGATGACTGAGATGCGTTAAAATATGACCAAATATATATGAGATTGGA
AATATATCCGGACATGA
Found at i:111925 original size:39 final size:39
Alignment explanation
Indices: 111878--111966 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
111868 TATATGAGAT
*
111878 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTACATGC
* *
111917 TGGAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTACATGC
*
111956 TGGAAAAATAT
1 TGGAAATATAT
111967 TCGGGTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (39 bp):
TGGAAATATATCCGGACATGAGGTCCGCAGGCTACATGC
Found at i:115267 original size:43 final size:43
Alignment explanation
Indices: 115205--115289 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
115195 GATTATGGTT
* *
115205 TGTAAATAAGAACTGTGCTAACCAATTGTAGGACATCGGAAGA
1 TGTAAATAAGAACTATGCTAACCAATTGTAGGACATCAGAAGA
*
115248 TGTAAATAAGAACTATGCTAATCAATTGTAGGACATCAGAAG
1 TGTAAATAAGAACTATGCTAACCAATTGTAGGACATCAGAAG
115290 TGATCTCAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (43 bp):
TGTAAATAAGAACTATGCTAACCAATTGTAGGACATCAGAAGA
Found at i:116911 original size:7 final size:7
Alignment explanation
Indices: 116899--116929 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
116889 AAATCTTTTC
116899 AAAAATA
1 AAAAATA
116906 AAAAATA
1 AAAAATA
116913 AAAAATA
1 AAAAATA
116920 AAAAATA
1 AAAAATA
116927 AAA
1 AAA
116930 TTTATGGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Done.