Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2051
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: 82950
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:3308 original size:32 final size:32
Alignment explanation
Indices: 3253--3315 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3243 TAGCCAAACT
* * *
3253 TGTATCGATACACCAAGTATGTATGGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
3285 TGTATCGATACACAAAA-ATTGTATCGATACA
1 TGTATCGATACACAAAATA-TGTATCGATACA
3316 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATACAA
Found at i:5674 original size:55 final size:55
Alignment explanation
Indices: 5512--6615 Score: 1153
Period size: 55 Copynumber: 19.4 Consensus size: 55
5502 CTTTTAGCCT
*
5512 TTCCAGTCCTCAAAGAGCAGGACGCCTTCACCTTTTAAAGCGCACACAAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCATC
*
5572 TTCCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCATC
1 TT-CCAGTCCTCAAAGAGCAGGACG-C--CT--TT-TAAAGCCCACACAAGTTGGTGGCATC
*
5634 CTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* **
5688 TTCCTAATCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT-
1 TTCC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
5743 TTCCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCGCACAAGTTGGTGGCATT
1 TT-CCAGTCCTCAAAGAGCAGGACG-C--C-T-TTT-AAAGCCCACACAAGTTGGTGGCATC
* * * *
5805 TTCCAATCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * *
5860 TT-CGGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGGTGGCATC
* *
5920 TTCCAGTCCTCAAAGAGCAGGACACCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGAC-GC------C-TTTTAAAGCCCACACAAGTTGGTGGCATC
* *
5983 TT-TAGTCCTCAAGGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * * *
6037 CTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
6092 TTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
6147 TTTC-GTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCTACACAAGTTGGTGGCATC
1 TTCCAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * * * *
6207 CTCTAGTCCTCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
6262 TTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
6317 TTCCAATCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * * *
6372 TTCCAATCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACG-C----CTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * * *
6432 TT-CAGTCCTCGAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGAGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
6486 TTCCAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
6541 TTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
**
6595 TTTTTAGTCCTCAAAGAGCAG
1 -TTCCAGTCCTCAAAGAGCAG
6616 AATACACTTT
Statistics
Matches: 905, Mismatches: 97, Indels: 89
0.83 0.09 0.08
Matches are distributed among these distances:
54 98 0.11
55 475 0.52
56 10 0.01
57 1 0.00
58 7 0.01
59 23 0.03
60 88 0.10
61 145 0.16
62 23 0.03
63 31 0.03
64 4 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
Found at i:6274 original size:225 final size:222
Alignment explanation
Indices: 5540--6615 Score: 1238
Period size: 225 Copynumber: 4.7 Consensus size: 222
5530 AGGACGCCTT
* * * *
5540 CACCTTTTAAAGCGCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGC-CTTCTC
1 CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--CAC--CT-
** * *
5604 CTTCTAAAGCCCACACAAGTTGGTGGCATCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGC
61 -TTC-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
* ** *
5669 CCACACAAGTTGGTGGCACTTCCTAATCCTCAAAGAGCAGGA-----TACCTTTTAAAGCCCACA
124 CCACACAAGTTGGTGGCA-TT-TTCGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACA
** *
5729 CAAGTTGGTGGCATTTCCCAGTCCTCAAAGAGCAGGA
187 CAAGTTGGTGGCACCT-CTAGTCCTCAAAGAGCAGGA
* * * **
5766 CGCCTTCTTCTTTCAAAGCCCGCACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
1 ---C-AC--CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
* * ** * * *
5831 TTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CGGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
60 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTTTC
* *
5895 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTTTCTTTTTAA
119 AAAGCCCACACAAGTTGGTGGCATTTT-C-GTCCTCAAAGAGCAGGACGCC---TTTCCTTTTAA
* *
5960 AGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAGGAGCAGGA
179 AGCCCACACAAGTTGGTGGCACCTCTAGTCCTCAAAGAGCAGGA
* * ** *
6004 CGCCTTTTAAAGCCCACACAAGTTGGTGGCATCCTCCAATCCTCAAAGAGCAGGACACCTTTCAA
1 CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAA
*
6069 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACA
66 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
6134 AGTTGGTGGCACCTTTCGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCTACACAAGTTG
131 AGTTGGTGGCA-TTTTCGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTG
6199 GTGGCATCCTCTAGTCCTCAAAGAGCAGGA
194 GTGGCA-CCTCTAGTCCTCAAAGAGCAGGA
* *
6229 CACCATTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTCAA
1 CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAA
*
6294 AGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACAC
66 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACAC
* * * * *
6358 AAGTTGGTGGCATTTTCCAATCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTT
130 AAGTTGGTGGCATTTT-C-GTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTT
*
6423 GGTGGCACCT-TCAGTCCTCGAAGAGCAGGA
193 GGTGGCACCTCT-AGTCCTCAAAGAGCAGGA
* *
6453 CACCTTTCAAAGCCCACACAAGTTGGAGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTCTT-A
1 CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCA
* **
6517 AAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACA
65 AAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACA
* *
6581 CGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAG
129 CAAGTTGGTGGCA--TTTTCGTCCTCAAAGAGCAG
6616 AATACACTTT
Statistics
Matches: 738, Mismatches: 76, Indels: 71
0.83 0.09 0.08
Matches are distributed among these distances:
223 5 0.01
224 187 0.25
225 200 0.27
226 70 0.09
227 31 0.04
228 3 0.00
229 4 0.01
230 3 0.00
231 45 0.06
232 123 0.17
233 18 0.02
234 1 0.00
235 1 0.00
238 17 0.02
239 30 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (222 bp):
CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAA
AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
AGTTGGTGGCATTTTCGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGT
GGCACCTCTAGTCCTCAAAGAGCAGGA
Found at i:7375 original size:21 final size:21
Alignment explanation
Indices: 7351--7427 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
7341 AATTTATCCA
7351 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
7372 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
7393 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
7414 AATGTATCGATACA
1 AATGTATCGATACA
7428 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:7556 original size:13 final size:13
Alignment explanation
Indices: 7538--7563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7528 CATTTTTCTG
7538 TGTATCGATACAT
1 TGTATCGATACAT
7551 TGTATCGATACAT
1 TGTATCGATACAT
7564 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7560 original size:33 final size:33
Alignment explanation
Indices: 7518--7583 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
7508 GCCAAGGAAA
***
7518 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
7551 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
7584 CTGGAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:10064 original size:27 final size:28
Alignment explanation
Indices: 10034--10109 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
10024 AATTTTCACA
10034 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
10061 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
10089 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
10110 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:10155 original size:79 final size:79
Alignment explanation
Indices: 10063--10267 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
10053 CGTTAATCAT
* *
10063 CGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT-
1 CGGGGATACTCCAACCCCGTTATTTTC-GAGGGAATACTCCAACCCCGACTTTATTCCC-AAATC
* * *
10126 ATTGATTTCTCATAAT
64 ATCGATTTCTCACAAC
* * * * ** *
10142 TGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAATCCCGATTTTTTTTTCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGACTTTATTCCCAAATCAT
10207 CGATTTCTCACAAC
66 CGATTTCTCACAAC
* * *
10221 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCG
10268 TTATTATCTC
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.03
79 100 0.93
80 4 0.04
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGACTTTATTCCCAAATCAT
CGATTTCTCACAAC
Found at i:11558 original size:22 final size:24
Alignment explanation
Indices: 11533--11584 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
11523 AATTGTTGAC
11533 GTTCTTGAAGTTGATGTTATG-A-
1 GTTCTTGAAGTTGATGTTATGCAT
* *
11555 GTTCGTGAATTTGATGTTATGCAT
1 GTTCTTGAAGTTGATGTTATGCAT
11579 GTTCTT
1 GTTCTT
11585 TAAATGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 1 0.04
24 5 0.20
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.48
Consensus pattern (24 bp):
GTTCTTGAAGTTGATGTTATGCAT
Found at i:11753 original size:19 final size:19
Alignment explanation
Indices: 11704--11753 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
11694 TTTCCAGATC
*
11704 TATCGATACA-AAGAAATTG
1 TATCGATACATTA-AAATTG
11723 TATCGATACATTAAAATTG
1 TATCGATACATTAAAATTG
*
11742 TATTGATACATT
1 TATCGATACATT
11754 TTGACCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TATCGATACATTAAAATTG
Found at i:13618 original size:30 final size:30
Alignment explanation
Indices: 13577--13634 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
13567 AATAGGGTGA
13577 AATTCACAAAAGGGGAGAAATAGAGATTTT
1 AATTCACAAAAGGGGAGAAATAGAGATTTT
*
13607 AATTCATAAAAGGGGAGAAATAGAGATT
1 AATTCACAAAAGGGGAGAAATAGAGATT
13635 CTTTCATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.22
Consensus pattern (30 bp):
AATTCACAAAAGGGGAGAAATAGAGATTTT
Found at i:13649 original size:28 final size:29
Alignment explanation
Indices: 13578--13653 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
13568 ATAGGGTGAA
* *
13578 ATTCACAAAAGGGGAGAAATAGAGATTTT
1 ATTCATAAAAGGGGAGAAATAGAGATTCT
13607 AATTCATAAAAGGGGAGAAATAGAGATTCT
1 -ATTCATAAAAGGGGAGAAATAGAGATTCT
* *
13637 -TTCATTAAGGGGGAGAA
1 ATTCATAAAAGGGGAGAA
13654 TATTCATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 15 0.36
30 27 0.64
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (29 bp):
ATTCATAAAAGGGGAGAAATAGAGATTCT
Found at i:14912 original size:36 final size:35
Alignment explanation
Indices: 14865--14956 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 35
14855 TGATTGAGAT
14865 GTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAA-AG
1 GTTCTATCTTAGCCTTTGAAAAAGATA--GAGAAGAG
*
14901 GTTCTATCTTAGCCTGTG-AAAAGATAGAGAAGAG
1 GTTCTATCTTAGCCTTTGAAAAAGATAGAGAAGAG
14935 GTTCTATCTTAG-CTTGTGAAAA
1 GTTCTATCTTAGCCTT-TGAAAA
14957 GATTGTGAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.14
34 16 0.31
35 11 0.22
36 17 0.33
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (35 bp):
GTTCTATCTTAGCCTTTGAAAAAGATAGAGAAGAG
Found at i:14942 original size:34 final size:34
Alignment explanation
Indices: 14865--14991 Score: 138
Period size: 34 Copynumber: 3.8 Consensus size: 34
14855 TGATTGAGAT
*
14865 GTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAA-AG
1 GTTCTATCTTAGCCTGTG-AAAAGATA--GAGAAGAG
14901 GTTCTATCTTAGCCTGTGAAAAGATAGAGAAGAG
1 GTTCTATCTTAGCCTGTGAAAAGATAGAGAAGAG
* * *
14935 GTTCTATCTTAGCTTGTGAAAAGAT--TG-TGAG
1 GTTCTATCTTAGCCTGTGAAAAGATAGAGAAGAG
* *
14966 GTTTTATCTTAGCCT-TCAAAAGATAG
1 GTTCTATCTTAGCCTGTGAAAAGATAG
14992 TGTTATAAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.10
31 16 0.20
32 1 0.01
33 5 0.06
34 26 0.32
35 8 0.10
36 17 0.21
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (34 bp):
GTTCTATCTTAGCCTGTGAAAAGATAGAGAAGAG
Found at i:16319 original size:58 final size:58
Alignment explanation
Indices: 16153--16350 Score: 166
Period size: 58 Copynumber: 3.4 Consensus size: 58
16143 TAAAAGTCTG
* * * ***
16153 TAAAACATGACAAATTACTAAAATAA-GCCTAAAATGCATAAAATTGCATAA-AGAGTTT
1 TAAATCATGAAAAATGACTAAAATAATG-CTAAAATGCATAAAATTGCATAATA-AACAT
** * * * * * ** * **
16211 TAAATCATGGCAAATGACTAAAATGATGCAAAAATACATGAGATCACATAATAACCCC
1 TAAATCATGAAAAATGACTAAAATAATGCTAAAATGCATAAAATTGCATAATAAACAT
* *
16269 TAAATTATGAAAAATGACTAAAATAATGCTAAAATGCATCAAATTGCATAATAAACAT
1 TAAATCATGAAAAATGACTAAAATAATGCTAAAATGCATAAAATTGCATAATAAACAT
* *
16327 TAAATCATGAAAACTTACTAAAAT
1 TAAATCATGAAAAATGACTAAAAT
16351 GGCTTTAAAA
Statistics
Matches: 108, Mismatches: 30, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
58 106 0.98
59 2 0.02
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.25
Consensus pattern (58 bp):
TAAATCATGAAAAATGACTAAAATAATGCTAAAATGCATAAAATTGCATAATAAACAT
Found at i:17612 original size:20 final size:19
Alignment explanation
Indices: 17587--17662 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
17577 TTTTACCTAG
17587 ATGTATCGATACACTTTTCA
1 ATGTATCGATACA-TTTTCA
** *
17607 ATGTATCGATACATGGATGA
1 ATGTATCGATACAT-TTTCA
17627 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
*
17647 ATGTATCGATATATTT
1 ATGTATCGATACATTT
17663 AGTTAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 45 0.96
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:18592 original size:19 final size:19
Alignment explanation
Indices: 18568--18635 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
18558 AATTCAACGA
18568 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
18587 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
18602 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
18619 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
18636 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:18606 original size:32 final size:32
Alignment explanation
Indices: 18570--18632 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
18560 TTCAACGATT
*
18570 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
18602 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
18633 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:18607 original size:13 final size:13
Alignment explanation
Indices: 18589--18613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18579 ACATAAGTTT
18589 TGTATCGATACAA
1 TGTATCGATACAA
18602 TGTATCGATACA
1 TGTATCGATACA
18614 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:18693 original size:13 final size:13
Alignment explanation
Indices: 18675--18700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18665 CATTTTTCTG
18675 TGTATCGATACAT
1 TGTATCGATACAT
18688 TGTATCGATACAT
1 TGTATCGATACAT
18701 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18712 original size:33 final size:33
Alignment explanation
Indices: 18655--18721 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
18645 GCCAAGGAAA
*** *
18655 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGAAACAT
*
18688 TGTATCGATACATGGATCTTTGTATCGAAACAT
1 TGTATCGATACATGGATCTGTGTATCGAAACAT
18721 T
1 T
18722 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGAAACAT
Found at i:21287 original size:51 final size:51
Alignment explanation
Indices: 21201--21372 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
21191 CTCGTTAATC
* * * **
21201 ATCGGGGATACTTCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATA
1 ATCGGGGATACTCCAACACCGATTTTATTTCCAAAATATAAATTTTTCATA
* * * * * *
21252 ATCGGGGATACTCCAACTCCGGTTTTAATTT-CAAAACACAAATTTTCCTTTA
1 ATCGGGGATACTCCAACACCGATTTT-ATTTCCAAAATATAAATTTTTC-ATA
** *
21304 ATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATATCCATTTTTCACA
1 ATCGGGGATACTCCAACACCGATTTTATTTCC-AAAATATAAATTTTTCATA
***
21356 ATTAAGGATACTCCAAC
1 ATCGGGGATACTCCAAC
21373 CTCGTCAATT
Statistics
Matches: 95, Mismatches: 22, Indels: 7
0.77 0.18 0.06
Matches are distributed among these distances:
51 38 0.40
52 46 0.48
53 11 0.12
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (51 bp):
ATCGGGGATACTCCAACACCGATTTTATTTCCAAAATATAAATTTTTCATA
Found at i:22596 original size:20 final size:20
Alignment explanation
Indices: 22560--22597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22550 AGCCTTTGAT
*
22560 CATGCATTTTCACTATGTTC
1 CATGCATTTTCAATATGTTC
*
22580 CATGCATTTTTAATATGT
1 CATGCATTTTCAATATGT
22598 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (20 bp):
CATGCATTTTCAATATGTTC
Found at i:28716 original size:21 final size:22
Alignment explanation
Indices: 28685--28746 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
28675 ATGAAAAAGT
*
28685 CAAAAGCAAAAGCACAAAAAATG
1 CAAAAGCAAAAACA-AAAAAATG
28708 -AAAAG-AAAAACAAAAAAATG
1 CAAAAGCAAAAACAAAAAAATG
*
28728 CAAAAGC-AAAATAAAAAAA
1 CAAAAGCAAAAACAAAAAAA
28747 GGGAACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.23
21 22 0.63
22 5 0.14
ACGTcount: A:0.74, C:0.11, G:0.10, T:0.05
Consensus pattern (22 bp):
CAAAAGCAAAAACAAAAAAATG
Found at i:30265 original size:55 final size:55
Alignment explanation
Indices: 30138--30930 Score: 705
Period size: 55 Copynumber: 14.2 Consensus size: 55
30128 CAGTGGCATT
* * * * *
30138 CCTTTTTAAGTCCACAACTCCGTGGTAACTTTTTAAGTCCACAACTCCGTGGCAA
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* *
30193 CCTTTT-AAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
** * *
30247 CCTTTTAAAGTCCACAACTCCGTGGCGCCCTTTAAAGTCTACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* *
30302 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCTACAACTCCATGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* *
30357 CCTTTT-AAGTCCATAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCAC
* * *
30412 CCTTTT-AAGTCCACAACTTCGTGGCACCCTTTTAAAGTTCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCAC
* * **
30467 GCTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTTTGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* * *
30522 CCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACCACTCGGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCAC
* * * *
30578 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAAGTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* * * * * * * * * *
30632 CCTTTCAAAGCCCACAAGTCTGTGACATCATTTCAAAGCCCACAAGTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCCGTGGCAC
* * * * * * * * * *
30688 CATTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAATCCCACAAGTCAGTGGCAAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT-CCACAACTCCGTGGC-AC
* * * * * * *
30745 TCATTTTAAAGCCCACACAAGT-CGATGGCAACTCATTTGAAAGCTCACACAAGTCAGTGGCAAC
1 -CCTTTTAAAG-TC-CACAACTCCG-TGGC-A-TCCTTT-TAAG-TC-CACAACTCCGTGGC-AC
* * * * * * * * *
30809 CCATTTCAAAGCCCATAACTCCGTGTCATCTTTTTAAGCCCACAAGTCAGTGGCAT
1 CC-TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
* * * * * * * * * *
30865 CCTTTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCCGTGGCAC
*
30921 CCTTTCAAAG
1 CCTTTTAAAG
30931 CTCACAAGTC
Statistics
Matches: 635, Mismatches: 83, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
54 97 0.15
55 297 0.47
56 144 0.23
57 16 0.03
58 10 0.02
59 6 0.01
60 16 0.03
61 2 0.00
62 14 0.02
63 8 0.01
64 25 0.04
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.27
Consensus pattern (55 bp):
CCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:30650 original size:28 final size:28
Alignment explanation
Indices: 30176--31388 Score: 804
Period size: 28 Copynumber: 43.2 Consensus size: 28
30166 CTTTTTAAGT
* * * * *
30176 CCACAACTCCGTGGCAACCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
30203 CCACAACTCCGTGGCATTCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
30230 CCACAACTCCGTGGCATCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * ** *
30258 CCACAACTCCGTGGCGCCCTTT-AAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * * *
30285 CTACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
30313 CCACAACTCCGTGGCATCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
30340 CTACAACTCCA-TGGCACCCTTT-TAAGT
1 CCACAAGT-CAGTGGCATCCTTTCAAAGC
* * * * *
30367 CCATAACTCCGTGGCATCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * * *
30395 CCATAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
30422 CCACAACTTC-GTGGCACCCTTTTAAAGT
1 CCACAA-GTCAGTGGCATCCTTTCAAAGC
* * * * *
30450 TCACAACTCCGTGGCA-CGCTTTTAAAGT
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * * *
30478 CCACAACTCTGTGGCATCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* ** * * *
30505 CCACAACTTTGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
30533 CCACAACTCCA-TGGCATCCTTTTAAAGT
1 CCACAAGT-CAGTGGCATCCTTTCAAAGC
* * * * * *
30561 CCACCACTCGGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
30588 CCACAACTCCGTGGCACCCTTT-AAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
30615 CCACAAGTCCGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
30643 CCACAAGTCTGTGACATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
30671 CCACAAGTCTGTGGCA-CCATTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* *
30699 CCACAAGTCAGTGGCATCATTTCAAATC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
30727 CCACAAGTCAGTGGCAACTCATTTTAAAGCC
1 CCACAAGTCAGTGGC-A-TCCTTTCAAAG-C
* *
30758 CACACAAGTC-GATGGCAACTCATTTGAAAGC
1 C-CACAAGTCAG-TGGC-A-TCCTTTCAAAGC
*
30789 TCACACAAGTCAGTGGCAACCCATTTCAAAGC
1 -C-CACAAGTCAGTGGC-ATCC-TTTCAAAGC
* * * * **
30821 CCATAACTCCGTGTCAT-CTTTTTAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
30848 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
30876 CCACAAGTCAGTGGTACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
30904 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
30932 TCACAAGTCAATGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
30960 CCATAAGTCAGTGGCATCTTTTTC-AAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * *
30988 CCACAAGTTAATGGCA-CATTTTTC-AAGC
1 CCACAAGTCAGTGGCATC--CTTTCAAAGC
* * * * *
31016 CCACAGGTTAATGGCA-CTTTTTCCAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
*
31044 CCACAAGTCAATGGCA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
*
31072 CCACAAGTCAGTGGTACAT--TTTTAAAGC
1 CCACAAGTCAGTGG--CATCCTTTCAAAGC
* *
31100 CCACAAGTCAGTGGCATCTTTTCTAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
31128 CCAAAAGTCAGTGGCA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
*
31156 CCACAAGTCAGTGGCATCTTTTTC-AAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * * *
31184 CCACAAGTTAGTGCCATCTTTTCCAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
31212 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
31240 CCACAAGCCAGTAGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
31268 CCACAAGTTAGTGGCA-CTATTTCAAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
*
31296 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
31324 CCACAAGTCGGTGGCACCCTTTCAAAGCC
1 CCACAAGTCAGTGGCATCCTTTCAAAG-C
* *
31353 CACACAAGTCAATGGCAATTCTTTGCAAAGC
1 C-CACAAGTCAGTGGC-ATCCTTT-CAAAGC
31384 CCACA
1 CCACA
31389 CAAGTTAGTG
Statistics
Matches: 1022, Mismatches: 120, Indels: 85
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.00
27 245 0.24
28 652 0.64
29 16 0.02
30 37 0.04
31 13 0.01
32 54 0.05
33 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:32302 original size:20 final size:20
Alignment explanation
Indices: 32277--32332 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
32267 TTTTCACCCA
32277 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
32297 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
* *
32317 AATGTATCAATACATT
1 GATGTATCGATACATT
32333 CTACACAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (20 bp):
GATGTATCGATACATTTTTC
Found at i:33856 original size:21 final size:21
Alignment explanation
Indices: 33815--33858 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33805 CTCTCCTTTA
* *
33815 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
33836 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
33857 TC
1 TC
33859 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:35684 original size:13 final size:13
Alignment explanation
Indices: 35666--35701 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35656 ATCACCCTGT
35666 ATCGATACAATGC
1 ATCGATACAATGC
* *
35679 ATCGATATAATGT
1 ATCGATACAATGC
35692 ATCGATACAA
1 ATCGATACAA
35702 AGAAAAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
ATCGATACAATGC
Found at i:38763 original size:21 final size:21
Alignment explanation
Indices: 38734--38778 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38724 AAGTTTTCAT
*
38734 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
38754 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
38776 TTT
1 TTT
38779 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:41024 original size:13 final size:13
Alignment explanation
Indices: 41006--41031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40996 CAATTTTTTG
41006 TGTATCGATACAT
1 TGTATCGATACAT
41019 TGTATCGATACAT
1 TGTATCGATACAT
41032 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:48277 original size:16 final size:16
Alignment explanation
Indices: 48258--48288 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48248 GCATTCACAT
*
48258 TCACATGCATTTGCAA
1 TCACATCCATTTGCAA
48274 TCACATCCATTTGCA
1 TCACATCCATTTGCA
48289 CCTACACGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (16 bp):
TCACATCCATTTGCAA
Found at i:48564 original size:16 final size:16
Alignment explanation
Indices: 48545--48598 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
48535 CATTCATAAG
*
48545 TATTTGCACTCATGTA
1 TATTCGCACTCATGTA
* *
48561 TATTCCCACTCATGTC
1 TATTCGCACTCATGTA
*
48577 CATTCGCACTCAATGGTA
1 TATTCGCACTC-AT-GTA
48595 TATT
1 TATT
48599 TTCTAACTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 22 0.76
17 2 0.07
18 5 0.17
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (16 bp):
TATTCGCACTCATGTA
Found at i:48659 original size:16 final size:16
Alignment explanation
Indices: 48640--48689 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
48630 TCATACACAA
*
48640 GCATTTGCATTCATGT
1 GCATTCGCATTCATGT
* *
48656 GCATTCCCTTTCATGT
1 GCATTCGCATTCATGT
*
48672 GCAGTCGCATTCATGT
1 GCATTCGCATTCATGT
48688 GC
1 GC
48690 GATCGCGTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (16 bp):
GCATTCGCATTCATGT
Found at i:49429 original size:35 final size:34
Alignment explanation
Indices: 49337--49496 Score: 96
Period size: 35 Copynumber: 4.5 Consensus size: 34
49327 TTAAAATTTA
* * * *
49337 TCTTAAGGATATTTCAACAATGACCATGTTAAAGTCTT
1 TCTTAAGGAT-TTTCATCAATCA-C-T-TTAAAGCCTC
49375 TCTTAAGGACATTTT-ATCAATCACTTTAAAGCCTC
1 TCTTAAGG--ATTTTCATCAATCACTTTAAAGCCTC
49410 TCTTAAGGATTATTCATCAAGT-ACTTTAGAA-CCTC
1 TCTTAAGGATT-TTCATCAA-TCACTTTA-AAGCCTC
** * *
49445 TCTCGAGGATGTTTCA-CCATGCACTTTAGAGCCTC
1 TCTTAAGGAT-TTTCATCAAT-CACTTTAAAGCCTC
49480 T-TTCAAGGATATTTCAT
1 TCTT-AAGGAT-TTTCAT
49497 TAAAGGTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
33 4 0.04
34 6 0.06
35 64 0.65
36 5 0.05
37 1 0.01
38 14 0.14
39 3 0.03
40 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTTAAGGATTTTCATCAATCACTTTAAAGCCTC
Found at i:49921 original size:16 final size:16
Alignment explanation
Indices: 49900--49932 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
49890 AACAATGTTT
49900 AGGTCCTTTTATCCAA
1 AGGTCCTTTTATCCAA
49916 AGGTCCTTTTATCCAA
1 AGGTCCTTTTATCCAA
49932 A
1 A
49933 ACCTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (16 bp):
AGGTCCTTTTATCCAA
Found at i:51555 original size:32 final size:32
Alignment explanation
Indices: 51516--51582 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
51506 CCGTTACAAG
51516 CAATGTATCGATACATTTA-TG-GTGTATCGATA
1 CAATGTATCGATACA--TACTGTGTGTATCGATA
51548 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTGTGTGTATCGATA
51580 CAA
1 CAA
51583 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 2 0.06
31 2 0.06
32 29 0.88
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (32 bp):
CAATGTATCGATACATACTGTGTGTATCGATA
Found at i:51556 original size:13 final size:13
Alignment explanation
Indices: 51538--51562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51528 ACATTTATGG
51538 TGTATCGATACAA
1 TGTATCGATACAA
51551 TGTATCGATACA
1 TGTATCGATACA
51563 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:51661 original size:20 final size:21
Alignment explanation
Indices: 51614--51666 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
51604 GCCAATGACC
**
51614 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
51635 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
51655 TGTATCGATACA
1 TGTATCGATACA
51667 ATATATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:61316 original size:16 final size:17
Alignment explanation
Indices: 61295--61328 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61285 ACATTTAATA
61295 TATTT-CAAATTAATTT
1 TATTTACAAATTAATTT
61311 TATTTCACAAATTAATTT
1 TATTT-ACAAATTAATTT
61329 ATAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTACAAATTAATTT
Found at i:61774 original size:30 final size:30
Alignment explanation
Indices: 61740--61798 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
61730 TTAATAAACT
61740 TATCACATGTAGGTCTATTAATCCATGTAA
1 TATCACATGTAGGTCTATTAATCCATGTAA
* * * * *
61770 TATCATATTTAGGTTTATTAGTCTATGTA
1 TATCACATGTAGGTCTATTAATCCATGTA
61799 TTTGTATTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (30 bp):
TATCACATGTAGGTCTATTAATCCATGTAA
Found at i:63711 original size:2 final size:2
Alignment explanation
Indices: 63704--63730 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63694 AAATAATTAA
63704 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
63731 AATTCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73088 original size:19 final size:18
Alignment explanation
Indices: 73063--73127 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
73053 ATTTCAACGA
73063 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
73081 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
73097 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
73113 TTTTGTATCGATACA
1 -TTTGTATCGATACA
73128 ATGTAAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:73101 original size:32 final size:32
Alignment explanation
Indices: 73065--73132 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
73055 TTCAACGATT
73065 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
73097 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
73129 TGTA
1 TGTA
73133 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:73102 original size:13 final size:13
Alignment explanation
Indices: 73084--73108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73074 ACATAAGTGT
73084 TGTATCGATACAA
1 TGTATCGATACAA
73097 TGTATCGATACA
1 TGTATCGATACA
73109 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:73188 original size:13 final size:13
Alignment explanation
Indices: 73170--73194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73160 ATTACTCAAA
73170 TGTATCGATACAT
1 TGTATCGATACAT
73183 TGTATCGATACA
1 TGTATCGATACA
73195 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:73247 original size:52 final size:52
Alignment explanation
Indices: 73203--73331 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
73193 CACTGATCTT
73203 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
73255 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
73307 TGTATCGATACATGTAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
73332 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.