Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold630
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: 21145
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:5323 original size:14 final size:13
Alignment explanation
Indices: 5304--5335 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5294 CCTTCTCTTC
5304 AAAAAAAAAGCAA
1 AAAAAAAAAGCAA
*
5317 AAAAAAAAAGTAA
1 AAAAAAAAAGCAA
5330 AAAAAA
1 AAAAAA
5336 CAAAACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGCAA
Found at i:6597 original size:27 final size:27
Alignment explanation
Indices: 6512--6597 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
6502 GTTGGTGGCA
6512 TTTTCCAGTCCTCAAAGAGCAGGATGC
1 TTTTCCAGTCCTCAAAGAGCAGGATGC
* * * * * **
6539 CTTTCGAAGCCCACACA-AGTTGG-TGGC
1 TTTTC-CAGTCCTCAAAGAGCAGGAT-GC
6566 ATTTTCCAGTCCTCAAAGAGCAGGATGC
1 -TTTTCCAGTCCTCAAAGAGCAGGATGC
6594 TTTT
1 TTTT
6598 TCTTTTCAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 17 0.43
29 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (27 bp):
TTTTCCAGTCCTCAAAGAGCAGGATGC
Found at i:6749 original size:171 final size:171
Alignment explanation
Indices: 6369--7042 Score: 947
Period size: 171 Copynumber: 4.0 Consensus size: 171
6359 TTCCTTTTAA
* *
6369 AAAGCCTACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTGAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG
* *
6433 CCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCA
66 CCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACC-TTTC----AAAGCCCA
**
6497 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCT-TT
125 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT
* *
6543 CGAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAA
1 -AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAA
* *
6607 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGACCAGGACACCTTTCAAAGCCCACACA
64 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
6672 AGTTGGTGGCATTTTCCAGTCCTCAAACAGTAGGACACCTCTT
129 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT
6715 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG
* * * * * *
6780 CCCACACGAGTTGGTGGCACTTTTTAGTCCCCATAGAGCAGGACATCTTCCAAAGCCCACACAAG
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
*
6845 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTT
131 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT
* *
6886 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG
* ** *
6945 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAG
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
* *
7010 TTGGTGGCACTTTT-TAGTCCTTAAAGAGCAGGA
131 TTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
7043 TACACTTTAT
Statistics
Matches: 454, Mismatches: 39, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
165 88 0.19
166 5 0.01
171 251 0.55
172 5 0.01
175 27 0.06
176 75 0.17
177 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (171 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG
CCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT
Found at i:6751 original size:226 final size:224
Alignment explanation
Indices: 6331--7043 Score: 870
Period size: 226 Copynumber: 3.1 Consensus size: 224
6321 TCCTTCCGCA
* * * *
6331 TTTTAGTCCTTAAAGAGCAGGATGCCTGTTCCTTTTAAAAAGCCTACACAAGTTGGTGGCACC-T
1 TTTTAGTCCTCAAAGAGCAGGATG-CT-TTTCTTTT-CAAAGCCCACACAAGTTGGTGGCACCTT
* *
6395 TCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTGAAAGCCCACACAAGTTGGTGGCATTTTCCAG
63 TCAGTCCTCAAAGAGCAGGA--C----ACCTTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAG
* *
6460 TCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCT
121 TCCTCAAAGAGCAGGACGCC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCT
* *
6524 CAAAGAGCAGGATGCCTTTCGAAGCCCACACAAGTTGGTGGCA-T
180 CAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
*
6568 TTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 TTT-TAGTCCTCAAAGAGCAGGATGC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
6633 CAGTCCCCAAGGACCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
64 CAGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* * *
6698 ACAGTAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAT
128 AGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAT
6763 GCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACT
193 GC-----C-TTTCAAAGCCCACACGAGTTGGTGGCACT
* * * * **
6801 TTTTAGTCCCCATAGAGCAGGA--C--ATC-TTCCAAAGCCCACACAAGTTGGTGGCATTTTTCA
1 TTTTAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
*
6861 GTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
66 GTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
*
6925 GAGCAGGACGCCT-TTCAAATCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAT
129 GAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAT
6989 GCCTTTCAAAGCCCACACGAGTTGGTGGCACT
193 GCCTTTCAAAGCCCACACGAGTTGGTGGCACT
*
7021 TTTTAGTCCTTAAAGAGCAGGAT
1 TTTTAGTCCTCAAAGAGCAGGAT
7044 ACACTTTATT
Statistics
Matches: 425, Mismatches: 36, Indels: 46
0.84 0.07 0.09
Matches are distributed among these distances:
220 48 0.11
221 1 0.00
225 2 0.00
226 190 0.45
227 10 0.02
228 2 0.00
230 1 0.00
231 52 0.12
232 41 0.10
233 4 0.01
235 1 0.00
236 24 0.06
237 29 0.07
238 20 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (224 bp):
TTTTAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
GTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
GCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCC
TTTCAAAGCCCACACGAGTTGGTGGCACT
Found at i:6939 original size:26 final size:26
Alignment explanation
Indices: 6909--6996 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
6899 GTTGGTGGCA
6909 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* * * ** *
6935 CCTTTCAAATCCCACACAAGTTGGTGG-CA
1 CCTTTC-AGT-CCTCA-AAG-AGCAGGACG
*
6964 CCTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
6990 CCTTTCA
1 CCTTTCA
6997 AAGCCCACAC
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 16 0.36
27 6 0.14
28 6 0.14
29 10 0.23
30 3 0.07
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:7043 original size:55 final size:55
Alignment explanation
Indices: 6369--7042 Score: 732
Period size: 55 Copynumber: 11.9 Consensus size: 55
6359 TTCCTTTTAA
* * * *
6369 AAAGCCTACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTG
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTC
*
6429 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACGCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCC-TTTC
*
6485 TTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTC
1 ----AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTC
* *
6544 GAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGC-----C-TTTC
* * * * *
6605 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGACCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* * *
6660 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAACAGTAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTC
* *
6715 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTC
* * * * ** *
6776 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCCCATAGAGCAGGACATCTTCC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* *
6831 AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCT-TTC
*
6886 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* * *
6941 AAATCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* * *
6996 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTTAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
7043 TACACTTTAT
Statistics
Matches: 537, Mismatches: 52, Indels: 55
0.83 0.08 0.09
Matches are distributed among these distances:
54 5 0.01
55 329 0.61
56 13 0.02
59 4 0.01
60 77 0.14
61 106 0.20
62 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (55 bp):
AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
Found at i:7888 original size:19 final size:21
Alignment explanation
Indices: 7840--7894 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
7830 AATTCCAATA
*
7840 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
7861 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
7881 -TTTGTATCGATACA
1 ATTTGTATCGATACA
7895 ATGTATTGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:7964 original size:13 final size:13
Alignment explanation
Indices: 7946--7971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7936 CATTTTTCTA
7946 TGTATCGATACAT
1 TGTATCGATACAT
7959 TGTATCGATACAT
1 TGTATCGATACAT
7972 CTATTCTTTG
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:7989 original size:34 final size:33
Alignment explanation
Indices: 7926--7992 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
7916 ACCAAGGAAA
*
7926 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATTATTCTATGTATCGATACAT
*
7959 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTATGTATCGATACAT
7993 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTATGTATCGATACAT
Found at i:8035 original size:20 final size:20
Alignment explanation
Indices: 8010--8058 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
8000 GTTTACCCAG
8010 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
8030 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
8050 ATGTATCGA
1 ATGTATCGA
8059 CATTCAGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:13113 original size:55 final size:54
Alignment explanation
Indices: 12907--13526 Score: 659
Period size: 55 Copynumber: 10.9 Consensus size: 54
12897 TTCCTTTTAA
* ** * *
12907 AAAGCCTACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTG
1 AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTC
* *
12967 AAAGCCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAAGACGCCTTTTC
1 AAAG-CCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCC-TTTC
*
13024 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTC
1 ----AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCTTTC
* *
13083 GAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGC-----C-TTTC
* *
13144 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTC
* *
13199 AAAGCCCACACAAGTTGGTGGCAACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 AAAGCCCACACAAGTTGGTGGC-A-TTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTC
* * * * **
13261 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCCCATAGAGCAGGACATCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
*
13316 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTC
*
13371 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* **
13426 AAATCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* *
13480 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGA
13527 TACACTTTAT
Statistics
Matches: 492, Mismatches: 41, Indels: 59
0.83 0.07 0.10
Matches are distributed among these distances:
54 57 0.12
55 206 0.42
56 29 0.06
57 8 0.02
59 4 0.01
60 49 0.10
61 98 0.20
62 41 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (54 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
Found at i:13136 original size:27 final size:27
Alignment explanation
Indices: 13051--13136 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
13041 GTTGGTGGCA
13051 TTTTCCAGTCCTCAAAGAGCAGGATGC
1 TTTTCCAGTCCTCAAAGAGCAGGATGC
* * * * * **
13078 CTTTCGAAGCCCACACA-AGTTGG-TGGC
1 TTTTC-CAGTCCTCAAAGAGCAGGAT-GC
13105 ATTTTCCAGTCCTCAAAGAGCAGGATGC
1 -TTTTCCAGTCCTCAAAGAGCAGGATGC
13133 TTTT
1 TTTT
13137 TCTTTTCAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 17 0.43
29 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (27 bp):
TTTTCCAGTCCTCAAAGAGCAGGATGC
Found at i:13326 original size:172 final size:165
Alignment explanation
Indices: 12907--13526 Score: 755
Period size: 172 Copynumber: 3.6 Consensus size: 165
12897 TTCCTTTTAA
* * * *
12907 AAAGCCTACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTGAAAG
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C---ATC-TTTCAAAG
* * *
12971 CCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAAGACGCCTTTTCTTTTAAAGCCCA
60 -CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCA
*
13036 CACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTC
119 CACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCCTTTC
* *
13083 GAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAA
1 AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGA--C---ATC-TTTCAAA
*
13147 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAA
59 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAA
13212 GTTGGTGGCAACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
124 GTTGGTGGC-ACCTTTCAGTCCTCAAAGAGCAGGATGC-----C-TTTC
* * * *
13261 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCCCATAGAGCAGGACATCTTTCAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACATCTTTCAAAGCCCACA
13326 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTG
66 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTG
*
13391 GCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
131 GCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTC
* * **
13426 AAATCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACATCTTTCAAAGCCCACA
* *
13490 CGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGA
66 CAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
13527 TACACTTTAT
Statistics
Matches: 405, Mismatches: 27, Indels: 36
0.87 0.06 0.08
Matches are distributed among these distances:
164 64 0.16
165 30 0.07
166 1 0.00
171 51 0.13
172 103 0.25
173 7 0.02
176 67 0.17
177 37 0.09
178 41 0.10
179 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (165 bp):
AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACATCTTTCAAAGCCCACA
CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTG
GCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTC
Found at i:13424 original size:26 final size:26
Alignment explanation
Indices: 13394--13480 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
13384 GTTGGTGGCA
13394 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* ** **
13420 CCTTTCAAATCC-CACACA-AGTTGGTGG
1 CCTTTC-AGTCCTCA-A-AGAGCAGGACG
*
13447 CACCTTCAGTCCTCAAAGAGCAGGACG
1 C-CTTTCAGTCCTCAAAGAGCAGGACG
13474 CCTTTCA
1 CCTTTCA
13481 AAGCCCACAC
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 14 0.33
27 22 0.51
28 7 0.16
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:14372 original size:18 final size:21
Alignment explanation
Indices: 14321--14374 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
14311 AATTCCAATA
14321 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTCAGT
** *
14342 AAATGTATTGATACA-T-AGT
1 ATTTGTATCGATACATTCAGT
14361 -TTTGTATCGATACA
1 ATTTGTATCGATACA
14375 ATGTATAGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 1 0.04
21 12 0.44
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (21 bp):
ATTTGTATCGATACATTCAGT
Found at i:14440 original size:13 final size:13
Alignment explanation
Indices: 14422--14447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14412 CATTTTTCTG
14422 TGTATCGATACAT
1 TGTATCGATACAT
14435 TGTATCGATACAT
1 TGTATCGATACAT
14448 CTATTCTTTG
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:14465 original size:34 final size:33
Alignment explanation
Indices: 14402--14468 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
14392 ACCAAGGAAA
*
14402 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
14435 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
14469 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:14525 original size:19 final size:20
Alignment explanation
Indices: 14487--14534 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
14477 TTTTACCAAG
14487 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
14507 ATGTATCGATACA-TTTACA
1 ATGTATCGATACATTTTACA
14526 ATGTATCGA
1 ATGTATCGA
14535 CATTCAGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:16967 original size:29 final size:27
Alignment explanation
Indices: 16891--16942 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
16881 ACATTTTTCA
16891 CATCGGGGATACTCCAACCCCGTTAAT
1 CATCGGGGATACTCCAACCCCGTTAAT
16918 CATCGGGGATACTCCAACCCCGTTA
1 CATCGGGGATACTCCAACCCCGTTA
16943 TTTTCTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (27 bp):
CATCGGGGATACTCCAACCCCGTTAAT
Found at i:17002 original size:79 final size:78
Alignment explanation
Indices: 16919--17089 Score: 247
Period size: 79 Copynumber: 2.2 Consensus size: 78
16909 CCCGTTAATC
* * **
16919 ATCGGGGATACTCCAACCCCGTTATTTTCTG-AGAGGATACTCCAACCCCTGCTT-TGTTCTTAA
1 ATCGGGGATACTCCAACCCCGTTA-TTTCCGAAG-GGATACTCCAACCCCGGCTTAT-TTCCAAA
16982 ATATTGATTTCTCATA
63 ATATTGATTTCTCATA
16998 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTT-ATTTCCAAAAT
*
17063 ATTGATTTCTTATA
65 ATTGATTTCTCATA
17077 ATCGGGGATACTC
1 ATCGGGGATACTC
17090 TACCCTGATT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
78 24 0.29
79 59 0.70
80 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTATTTCCAAAATA
TTGATTTCTCATA
Found at i:17164 original size:51 final size:50
Alignment explanation
Indices: 17076--17249 Score: 177
Period size: 52 Copynumber: 3.4 Consensus size: 50
17066 GATTTCTTAT
* * **
17076 AATCGGGGATACTCTACCCTGATTTTAATTTCTAAAACATTAATTTTCCAC
1 AATCGGGGATACTCAACCCTGATTTTATTTTC-AAAACACCAATTTTCCAC
* * **
17127 AATCGGGGATACTGAAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACT-CAACCCTGATTTTATTTTCAAAACACCAATTTTCC-AC
** * *
17179 AATCGGGGATACTCCAATTCTGATTTTATTTCTAAAAACACCAATTTTTCAC
1 AATCGGGGATACT-CAACCCTGATTTTATTT-TCAAAACACCAATTTTCCAC
*
17231 AATCGAGGATACTCCAACC
1 AATCGGGGATACT-CAACC
17250 TCATTATTTC
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 27 0.27
52 57 0.57
53 16 0.16
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (50 bp):
AATCGGGGATACTCAACCCTGATTTTATTTTCAAAACACCAATTTTCCAC
Found at i:17268 original size:28 final size:30
Alignment explanation
Indices: 17232--17315 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 30
17222 ATTTTTCACA
* *
17232 ATCGAGGATACTCCAACCTCATTAT-TTC-
1 ATCGGGGATACTCCAACCCCATTATCTTCG
*
17260 ATCGGGGATACTCCAACCCCGTTATCTTCG
1 ATCGGGGATACTCCAACCCCATTATCTTCG
17290 A--GGGGATACTCCAACCCCATTTATCT
1 ATCGGGGATACTCCAACCCCA-TTATCT
17316 CCAAAATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 39 0.80
29 9 0.18
30 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCATTATCTTCG
Done.