Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007916.1 Kokia drynarioides strain JFW-HI SEQ_122560, whole genome shotgun sequence
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: 68753
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2323 original size:17 final size:17
Alignment explanation
Indices: 2301--2339 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2291 GGATAATTTT
*
2301 AAATATTGTGTTTAAAA
1 AAATATTATGTTTAAAA
*
2318 AAATATTATTTTTAAAA
1 AAATATTATGTTTAAAA
*
2335 GAATA
1 AAATA
2340 GTAATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (17 bp):
AAATATTATGTTTAAAA
Found at i:2395 original size:24 final size:23
Alignment explanation
Indices: 2351--2404 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
2341 TAATATTATG
*
2351 AAATATTTTTAAAACAATTTAATA
1 AAATATATTTAAAACAATTTAA-A
*
2375 AAATATATTTACAAAC-TTTTAAA
1 AAATATATTTA-AAACAATTTAAA
*
2398 ATATATA
1 AAATATA
2405 GATTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 7 0.27
24 15 0.58
25 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATATTTAAAACAATTTAAA
Found at i:13575 original size:61 final size:62
Alignment explanation
Indices: 13315--13575 Score: 355
Period size: 62 Copynumber: 4.2 Consensus size: 62
13305 TGGAAAATGA
* * * * * * * *
13315 AAAGATCCGATGTCTTTATGATATCGTGAGAATTACACGGGAAATGAATCCTTTTACGAATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAAACCTATTACGGATT
* * * *
13377 AAAGGTCCAATGCCTTTGTGATATCGTGAGTATTACATGAGAAA-AAAATCCTTTTACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAAA-CCTATTACGGATT
* *
13439 AAAGGTTCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAAACCTATTACGGATT
*
13501 AAAGGTTCGATGTCTTTGTG-TATCGTGAGTATTACATGAGAAATGAAACCTATTACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAAACCTATTACGGATT
*
13562 AAAGGTCCAATGTC
1 AAAGGTCCGATGTC
13576 GGGAATCTTA
Statistics
Matches: 178, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
61 54 0.30
62 122 0.69
63 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (62 bp):
AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAAACCTATTACGGATT
Found at i:17997 original size:48 final size:45
Alignment explanation
Indices: 17920--18081 Score: 252
Period size: 45 Copynumber: 3.5 Consensus size: 45
17910 TTTCCTAGCT
* *
17920 TCTTGAAGCTCCTCATCAGCATCACCATCTGATAAGTAAATATCA
1 TCTTGAAGCTCCTCATCATCATCACCATCTGATAAGTTAATATCA
17965 TCTTGAAGCTCCTTCTCATCATCATCACCATCTGATAAGTTAATATCA
1 TCTTGAAGCT-C--CTCATCATCATCACCATCTGATAAGTTAATATCA
* *
18013 TCTTGAAGCTCCTCATCATCATCACCATTTGATAAGTTAATACCA
1 TCTTGAAGCTCCTCATCATCATCACCATCTGATAAGTTAATATCA
*
18058 TCTTGAAACTCCTCATCATCATCA
1 TCTTGAAGCTCCTCATCATCATCA
18082 TCACCACCTC
Statistics
Matches: 109, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
45 65 0.60
46 1 0.01
47 1 0.01
48 42 0.39
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.33
Consensus pattern (45 bp):
TCTTGAAGCTCCTCATCATCATCACCATCTGATAAGTTAATATCA
Found at i:18082 original size:48 final size:47
Alignment explanation
Indices: 17920--18087 Score: 245
Period size: 48 Copynumber: 3.6 Consensus size: 47
17910 TTTCCTAGCT
* *
17920 TCTTGAAGCT-C-CTCATCAGCATCACCATCTGATAAGTAAATATCA
1 TCTTGAAGCTCCTCTCATCATCATCACCATCTGATAAGTTAATATCA
17965 TCTTGAAGCTCCTTCTCATCATCATCACCATCTGATAAGTTAATATCA
1 TCTTGAAGCTCC-TCTCATCATCATCACCATCTGATAAGTTAATATCA
* *
18013 TCTTGAAGCT-C-CTCATCATCATCACCATTTGATAAGTTAATACCA
1 TCTTGAAGCTCCTCTCATCATCATCACCATCTGATAAGTTAATATCA
*
18058 TCTTGAAACTCCTCATCATCATCATCACCA
1 TCTTGAAGCTCCTC-TCATCATCATCACCA
18088 CCTCCATCAC
Statistics
Matches: 112, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
45 51 0.46
46 2 0.02
47 2 0.02
48 57 0.51
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
TCTTGAAGCTCCTCTCATCATCATCACCATCTGATAAGTTAATATCA
Found at i:18102 original size:93 final size:93
Alignment explanation
Indices: 17920--18091 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
17910 TTTCCTAGCT
* *
17920 TCTTGAAGCTCCTCATCAGCATCACCATCTGATAAGTAAATATCATCTTGAAGCTCCTTCTCATC
1 TCTTGAAGCTCCTCATCAGCATCACCATCTGATAAGTAAATACCATCTTGAAACTCCTTCTCATC
* * *
17985 ATCATCACCATCTGATAAGTTAATATCA
66 ATCATCACCACCTCATAAGCTAATATCA
* * *
18013 TCTTGAAGCTCCTCATCATCATCACCATTTGATAAGTTAATACCATCTTGAAACTCC-TCATCAT
1 TCTTGAAGCTCCTCATCAGCATCACCATCTGATAAGTAAATACCATCTTGAAACTCCTTC-TCAT
18077 CATCATCACCACCTC
65 CATCATCACCACCTC
18092 CATCACTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (93 bp):
TCTTGAAGCTCCTCATCAGCATCACCATCTGATAAGTAAATACCATCTTGAAACTCCTTCTCATC
ATCATCACCACCTCATAAGCTAATATCA
Found at i:22970 original size:49 final size:46
Alignment explanation
Indices: 22867--22957 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
22857 AAACAATATA
** *
22867 ATAGTTTTGCCTTTTAACTTAATGAGTAAATATTTATCTAAACGAC
1 ATAGTTTTGCCTTTTAACTTAAAAAGTAAATATTTATCAAAACGAC
22913 ATAGTTTTGCCTTTTAACTTTAGAAAATGTAAA-ATTTTATCAAAA
1 ATAGTTTTGCCTTTTAAC-TTA-AAAA-GTAAATA-TTTATCAAAA
22958 TGATGTAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
46 18 0.47
47 3 0.08
48 3 0.08
49 14 0.37
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (46 bp):
ATAGTTTTGCCTTTTAACTTAAAAAGTAAATATTTATCAAAACGAC
Found at i:28188 original size:11 final size:11
Alignment explanation
Indices: 28174--28213 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
28164 ACTTAAAATT
28174 ATTAAATATAA
1 ATTAAATATAA
28185 ATTAAATGA-AA
1 ATTAAAT-ATAA
*
28196 ATTAAATATAT
1 ATTAAATATAA
28207 ATTAAAT
1 ATTAAAT
28214 TTGAAATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 1 0.04
11 24 0.92
12 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
ATTAAATATAA
Found at i:29108 original size:10 final size:11
Alignment explanation
Indices: 29086--29114 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29076 TTATTTCTTT
29086 AAAAT-TTTAA
1 AAAATATTTAA
29096 AAAATATTTAA
1 AAAATATTTAA
29107 AAAATATT
1 AAAATATT
29115 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:35625 original size:20 final size:22
Alignment explanation
Indices: 35600--35641 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35590 AAGTTATTTA
35600 ATAATTTT-AT-ATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
35620 ATAATTTTAATAATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
35642 CATTTGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAT
Found at i:36200 original size:23 final size:23
Alignment explanation
Indices: 36149--36209 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
36139 TTTTATATGT
*
36149 CTTTGTGGCACGCTTTTTCTCTG
1 CTTTGTGGTACGCTTTTTCTCTG
*
36172 CCTTGTGGTACGCTTTTTCTCTG
1 CTTTGTGGTACGCTTTTTCTCTG
* *
36195 TTTTGTGGTATGCTT
1 CTTTGTGGTACGCTT
36210 CTGCCTTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.05, C:0.21, G:0.23, T:0.51
Consensus pattern (23 bp):
CTTTGTGGTACGCTTTTTCTCTG
Found at i:39648 original size:29 final size:30
Alignment explanation
Indices: 39585--39735 Score: 105
Period size: 30 Copynumber: 5.1 Consensus size: 30
39575 GAAATTCAAA
* * * *
39585 TTTTTAGAAAGTTATTGGGTCAAATC-TAAA
1 TTTTTGGAAAGTTA-AGGGTCAAAACATAAT
*
39615 TTTTTGGAAAGTTCAGGGT-AAAACATAAT
1 TTTTTGGAAAGTTAAGGGTCAAAACATAAT
* * * *
39644 TTTTT-GAAAGTTTGAGGGTCGAATC-TAAA
1 TTTTTGGAAAG-TTAAGGGTCAAAACATAAT
*
39673 TTTTTGGATAATTTAAGGGTCAAAACAT-AT
1 TTTTTGGA-AAGTTAAGGGTCAAAACATAAT
* * * *
39703 TTTTTTGATAGTTTAGAGGTTAAAACATAAT
1 TTTTTGGAAAGTTAAG-GGTCAAAACATAAT
39734 TT
1 TT
39736 CTAAATAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
28 9 0.10
29 32 0.34
30 46 0.49
31 7 0.07
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (30 bp):
TTTTTGGAAAGTTAAGGGTCAAAACATAAT
Found at i:39673 original size:58 final size:60
Alignment explanation
Indices: 39583--39721 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 60
39573 TTGAAATTCA
* * *
39583 AATTTTTAGAAAGTTAT-TGGGTCAAATCTAAATTTTTGGA-AAGTTCAGGGT-AAAACAT
1 AATTTTTTGAAAGTT-TGAGGGTCAAATCTAAATTTTTGGATAAGTTAAGGGTCAAAACAT
* *
39641 AATTTTTTGAAAGTTTGAGGGTCGAATCTAAATTTTTGGATAATTTAAGGGTCAAAACAT
1 AATTTTTTGAAAGTTTGAGGGTCAAATCTAAATTTTTGGATAAGTTAAGGGTCAAAACAT
* *
39701 ATTTTTTTGATAGTTTAGAGG
1 AATTTTTTGAAAGTTT-GAGG
39722 TTAAAACATA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.01
58 35 0.50
59 9 0.13
60 21 0.30
61 4 0.06
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.40
Consensus pattern (60 bp):
AATTTTTTGAAAGTTTGAGGGTCAAATCTAAATTTTTGGATAAGTTAAGGGTCAAAACAT
Found at i:40178 original size:13 final size:13
Alignment explanation
Indices: 40162--40188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40152 AAGGGGAGTT
40162 GCCATGCTCCATC
1 GCCATGCTCCATC
40175 GCCATGCTCCATC
1 GCCATGCTCCATC
40188 G
1 G
40189 AAGGCCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.44, G:0.19, T:0.22
Consensus pattern (13 bp):
GCCATGCTCCATC
Found at i:41551 original size:46 final size:46
Alignment explanation
Indices: 41499--41601 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 46
41489 CCCCATGATC
* * * *
41499 AGGGTAAGATATTGGATGAT-GTCTTCAATCTTCCCTTCTTAACTTA
1 AGGGTAAAAGATTGGATGATGGT-TTCAATCTCCCCCTCTTAACTTA
*
41545 AGGGTAAAAGATTGGATGATGGTTTCAATCTCCCCCTCTTGACTTA
1 AGGGTAAAAGATTGGATGATGGTTTCAATCTCCCCCTCTTAACTTA
* *
41591 GGGGTGAAAGA
1 AGGGTAAAAGA
41602 CTAAATGATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 47 0.96
47 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (46 bp):
AGGGTAAAAGATTGGATGATGGTTTCAATCTCCCCCTCTTAACTTA
Found at i:41610 original size:46 final size:47
Alignment explanation
Indices: 41514--41611 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 47
41504 AAGATATTGG
* * * **
41514 ATGAT-GTCTTCAATCTTCCCTTCTTAACTTAAGGGTAAAAGATTGG
1 ATGATGGTCTTCAATCTCCCCCTCTTAACTTAAGGGTAAAAGACTAA
* * *
41560 ATGATGGT-TTCAATCTCCCCCTCTTGACTTAGGGGTGAAAGACTAA
1 ATGATGGTCTTCAATCTCCCCCTCTTAACTTAAGGGTAAAAGACTAA
41606 ATGATG
1 ATGATG
41612 ATGTAACTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 41 0.95
47 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (47 bp):
ATGATGGTCTTCAATCTCCCCCTCTTAACTTAAGGGTAAAAGACTAA
Found at i:41809 original size:48 final size:48
Alignment explanation
Indices: 41734--41825 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
41724 TAAACTTCAC
** * *
41734 TTCATTGTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACCAT
1 TTCATTGTTTTGACCTACTTCTCTGTATCTAATCAGGAAGATGACCAT
*
41782 TTCATTGTTTTGACCTACTTCTCTGTATCTAATTAGGAAGATGA
1 TTCATTGTTTTGACCTACTTCTCTGTATCTAATCAGGAAGATGA
41826 GGTTTGAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (48 bp):
TTCATTGTTTTGACCTACTTCTCTGTATCTAATCAGGAAGATGACCAT
Found at i:41860 original size:123 final size:123
Alignment explanation
Indices: 41675--41900 Score: 371
Period size: 123 Copynumber: 1.8 Consensus size: 123
41665 TATTTGGCCC
* *
41675 ACTTCTCTGTATCTCATCAGGAAGATGGGGTTGGAAGTTTCACTCGCATTAAACTTCACTTCATT
1 ACTTCTCTGTATCTAATCAGGAAGATGAGGTTGGAAGTTTCACTCGCATTAAACTTCACTTCATT
41740 GTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACCATTTCATTGTTTTGACCT
66 GTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACCATTTCATTGTTTTGACCT
* * * **
41798 ACTTCTCTGTATCTAATTAGGAAGATGAGGTTTGAAGTTTCACTCGCATTAAGCTTTGCTTCATT
1 ACTTCTCTGTATCTAATCAGGAAGATGAGGTTGGAAGTTTCACTCGCATTAAACTTCACTTCATT
* *
41863 GTTTTGGTTTGCTTCTTTGTATCTTATCAGGAAGATGA
66 GTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGA
41901 GGCTTGAAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (123 bp):
ACTTCTCTGTATCTAATCAGGAAGATGAGGTTGGAAGTTTCACTCGCATTAAACTTCACTTCATT
GTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACCATTTCATTGTTTTGACCT
Found at i:41908 original size:75 final size:75
Alignment explanation
Indices: 41782--41975 Score: 282
Period size: 75 Copynumber: 2.6 Consensus size: 75
41772 AGATGACCAT
*** * *
41782 TTCATTGTTTTGACCTACTTCTCTGTATCTAATTAGGAAGATGAGGTTTGAAGTTTCACTCGCAT
1 TTCATTGTTTTGGTTTACTTCTCTGTATCTAATCAGGAAGATGAGGCTTGAAGTTTCACTCGCAT
41847 TAAGCTTT-GC
66 TAAG-TTTCGC
* * *
41857 TTCATTGTTTTGGTTTGCTTCTTTGTATCTTATCAGGAAGATGAGGCTTGAAGTTTCACTCGCAT
1 TTCATTGTTTTGGTTTACTTCTCTGTATCTAATCAGGAAGATGAGGCTTGAAGTTTCACTCGCAT
*
41922 TGAGTTTCGC
66 TAAGTTTCGC
*
41932 TTCATTGTTTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGA
1 TTCATTGTTTTGGTTTACTTCTCTGTATCTAATCAGGAAGATGA
41976 CCACTTTATT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 3 0.03
75 103 0.97
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (75 bp):
TTCATTGTTTTGGTTTACTTCTCTGTATCTAATCAGGAAGATGAGGCTTGAAGTTTCACTCGCAT
TAAGTTTCGC
Found at i:41991 original size:123 final size:123
Alignment explanation
Indices: 41874--43146 Score: 1316
Period size: 123 Copynumber: 10.4 Consensus size: 123
41864 TTTTGGTTTG
* * * * *
41874 CTTCTTTGTATCTTATCAGGAAGATGAGGCTTGAAGTTTCACTCGCATTGAGTTTCGCTTCATTG
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTG
* * *
41939 TTTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCA
66 TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* * * * * * *
41997 -TATCTCTGTATCTTATCAGGAAGTTGGGGTTTGAAGTTTCACTCGCATTGAGGTTTGCTTTATT
1 CT-TCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATT
* * * * * * *
42061 ATTTTGGTCTACTTTTCTGTATCTCATAAGGAAGATGACCACTTAATTTTTTTGATCGA
65 GTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* * * * *
42120 CTT-TCTATATCTAATCAGGAA-ATTAGGGTTTGAAGTTTTACACACATTGAGCTTCGCTTCATT
1 CTTCTCTGTATCTCATCAGGAAGATGA-GGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATT
** * * *
42183 GTTTTTGACCTACTTCTTTGTATCTCATCAAGAAGATTACCACTTCATTGTTTTGACCCA
65 G-TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* * * * * *
42243 CTTCTCTATATCTCATCAAGTACAT-AGGGTTTGAAGCTTCACTCACATTGAGC-TCTGCTTCTT
1 CTTCTCTGTATCTCATCAGGAAGATGA-GGTTTGAAGTTTCACTCACATTGAGCTTC-GCTTCAT
* * * *
42306 TGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCA
64 TGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* ** * *
42366 TTTCTCTGTATCTCATCAGGAAGAT-AGGATTTGAAGTTTTTCTCATATTGAGCTTCGCTTCCTT
1 CTTCTCTGTATCTCATCAGGAAGATGAGG-TTTGAAGTTTCACTCACATTGAGCTTCGCTTCATT
* ** * * * *
42430 TTTTTATTCTATTTCTCTGTATCTTATCAAGAAGATGACCACTTCATTGTTTTGAGCCA
65 GTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
** * *
42489 CTTCTCTGTATCTCATCAGGAAGAT-AGGGTTTGAAGTTTCACTCGTATTGAGC-TCTGTTTCGT
1 CTTCTCTGTATCTCATCAGGAAGATGA-GGTTTGAAGTTTCACTCACATTGAGCTTC-GCTTCAT
* * ** * * *
42552 TGATTTAGTGAACTTCTCTGTATCTCA-CTAGGAAGATTACCGCTTCATTGTCTTGACCCA
64 TGTTTTGGTCTACTTCTCTGTATCTCATC-AGGAAGATGACCACTTCATTGTTTTGACCCA
* * * *
42612 CTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCATATTGAGTTTCGCTTCATTG
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTG
* * * *
42677 TTTTGGTTTACTTCTTTGTATCTCATCAGAAAGATGACCACTTCATTATTTTGACCCA
66 TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* * * * * *
42735 CTTTTTTGTATCTCATTAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTTGTTTCATTG
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTG
* * * *
42800 TTCTGGTCTACTTCTCTGTACCTCAAT-AGGAAG-TGACC-GTTCCATTATTTTGACCCA
66 TTTTGGTCTACTTCTCTGTATCTC-ATCAGGAAGATGACCACTT-CATTGTTTTGACCCA
* * * *
42857 CTTTTTTGTATCTCATCAGGAAAATGAGGTTTGAAGTTTCACTCATATTGAGCTTCGCTTTC-TT
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGC-TTCATT
* * * *
42921 GTTTTGGTATACTTCTCTGTATATTATTAGGAAGATGACCACTTCATTGTTTTGACCCA
65 GTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
* * * * * * * *
42980 CTTCTCTGAATCTTATCAAGAAGATGAGGTTTGAAG-TTCGCTCATATTGAGCTCCGTTTCGTTG
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTG
* * ** * * ** * *
43044 ATTTAGTGAACTTCTCTGTATCTCA-CTAGGAAGATTATCGTTTTATTATTTTGACCCA
66 TTTTGGTCTACTTCTCTGTATCTCATC-AGGAAGATGACCACTTCATTGTTTTGACCCA
* * *
43102 CTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACTCA
1 CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCA
43147 TATCAAGAAG
Statistics
Matches: 966, Mismatches: 160, Indels: 48
0.82 0.14 0.04
Matches are distributed among these distances:
121 8 0.01
122 251 0.26
123 645 0.67
124 60 0.06
125 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (123 bp):
CTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTG
TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGACCCA
Found at i:42030 original size:198 final size:199
Alignment explanation
Indices: 41675--42098 Score: 579
Period size: 198 Copynumber: 2.1 Consensus size: 199
41665 TATTTGGCCC
* *
41675 ACTTCTCTGTATCTCATCAGGAAGATG-GGGTTGGAAGTTTCACTCGCATTAAACTTCACTTCAT
1 ACTTCTTTGTATCTCATCAGGAAGATGAGGCTTGGAAGTTTCACTCGCATTAAACTTCACTTCAT
* * * *
41739 TGTTTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACCATTTCATTGTTTTGACCTACTTCT
66 TGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCATTTCATTATTTTGACCCACTTCT
* *
41804 CTGTATCTAATTAGGAAGATGAGGTTTGAAGTTTCACTCGCATTAAGCTTTGCTTCATTGTTTTG
131 CTGTATCTAATCAGGAAGATGAGGTTTGAAGTTTCACTCGCATTAAGCTTTGCTTCATTATTTTG
*
41869 GTTT
196 GTCT
* * * ** *
41873 GCTTCTTTGTATCTTATCAGGAAGATGAGGCTT-GAAGTTTCACTCGCATTGAGTTTCGCTTCAT
1 ACTTCTTTGTATCTCATCAGGAAGATGAGGCTTGGAAGTTTCACTCGCATTAAACTTCACTTCAT
*
41937 TGTTTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCACTTT-ATTATTTTGACCCA-TAT
66 TGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCA-TTTCATTATTTTGACCCACT-T
* * * * * *
42000 CTCTGTATCTTATCAGGAAGTTGGGGTTTGAAGTTTCACTCGCATTGAGGTTTGCTTTATTATTT
129 CTCTGTATCTAATCAGGAAGATGAGGTTTGAAGTTTCACTCGCATTAAGCTTTGCTTCATTATTT
42065 TGGTCT
194 TGGTCT
*
42071 ACTT-TTCTGTATCTCATAAGGAAGATGA
1 ACTTCTT-TGTATCTCATCAGGAAGATGA
42099 CCACTTAATT
Statistics
Matches: 197, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
197 3 0.02
198 187 0.95
199 7 0.04
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (199 bp):
ACTTCTTTGTATCTCATCAGGAAGATGAGGCTTGGAAGTTTCACTCGCATTAAACTTCACTTCAT
TGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCATTTCATTATTTTGACCCACTTCT
CTGTATCTAATCAGGAAGATGAGGTTTGAAGTTTCACTCGCATTAAGCTTTGCTTCATTATTTTG
GTCT
Found at i:43230 original size:202 final size:202
Alignment explanation
Indices: 42951--43351 Score: 511
Period size: 202 Copynumber: 2.0 Consensus size: 202
42941 ATATTATTAG
* *
42951 GAAGATGACCACTTCATTGTTTTGACCCACTTCTCTGAATCTTATCAAGAAGATGAGGTTTGAAG
1 GAAGATGACCACTTCACTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGAGGTTTGAAG
* * * *
43016 TTCGCTCATATTGAGCTCCG-TTTCGTTGATTTAGTGAACTTCTCTGTATCTCACTAGGAAGATT
66 TTCACTCATATTGAGCTCCGCTTT-ATTGATTTAGTGAACTTCTCTATATCTCACTAAGAAGATT
* **
43080 ATCGTTTTATTATTTTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACT
130 ATCGCTCCATTATTTTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACT
43145 CATATCAA
195 CATATCAA
* * * * *
43153 GAAGATGATCAGTTCACTGTTTTGA-CCACTTTTTTGTATCTCATCAAGAAGAT-AGGGTTTGAA
1 GAAGATGACCACTTCACTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGA-GGTTTGAA
** * * ** * * *
43216 GTTTCACTCATATTGAGCTTTGCTTTATTGTTTTGGTTTACTTTTTTATATCTCATTAAGAAGAT
65 G-TTCACTCATATTGAGCTCCGCTTTATTGATTTAGTGAACTTCTCTATATCTCACTAAGAAGAT
* * * *
43281 TATCGCTCCATTGTTTTGACCCACTTCTCTGTATCTCATCATGAAGATGGGGTTTGAAGTTTCAC
129 TATCGCTCCATTATTTTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCAC
43346 TCATAT
194 TCATAT
43352 TAAGCTCCGC
Statistics
Matches: 169, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
200 1 0.01
201 33 0.20
202 132 0.78
203 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (202 bp):
GAAGATGACCACTTCACTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGAGGTTTGAAG
TTCACTCATATTGAGCTCCGCTTTATTGATTTAGTGAACTTCTCTATATCTCACTAAGAAGATTA
TCGCTCCATTATTTTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACTC
ATATCAA
Found at i:43321 original size:123 final size:123
Alignment explanation
Indices: 43148--44038 Score: 964
Period size: 123 Copynumber: 7.2 Consensus size: 123
43138 CTTCACTCAT
* * * *
43148 ATCAAGAAGATGATCAGTTCACTGTTTTGA-CCACTTTTTTGTATCTCATCAAGAAGATAGGGTT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTT
* * * * * * *
43212 TGAAGTTTCACTCATATTGAGCTTTGCTTTATTGTTTTGGTTTACTTTTTTATATCTC
66 TGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* * * * * *
43270 ATTAAGAAGATTATCGCTCCATTGTTTTGACCCACTTCTCTGTATCTCATCATGAAGATGGGGTT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTT
* * *
43335 TGAAGTTTCACTCATATTAAGCTCCGCTTCATTATTTTGGTCTACTTGTCTGTATCTC
66 TGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* * * *
43393 ATCAAGGAGATGACCACTTCATTGTTTTGACCCATTTCTCTGTATCTCATCAAGAAGATGGGGTT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTT
** * * * *
43458 TGAAGTTTCGTTCGTATTTAGCTTCGCTTCATTGTTTTAGTTTACTTCTCTGTATCTC
66 TGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* * * *
43516 ATCAAGAAGATGATTACTTCATTGTTTTAATCCACTTCTCTGTATCTCAT-ATGAAAGATAGGGT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAG-AAGATAGGGT
* * * * * * *
43580 TTGAAGTTTCAATCACATTAAGCTCCGCTTCGTTGATTTGGTCCACTTCTCTATATCTC
65 TTGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* ** * * * **
43639 ATCAGGAAGATGATCGTTTCATTGTTTTGACTCACTTTTCTGTATCTCATC-AGAAATATAAAGT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAG-AAGATAGGGT
* * * * * * * * * *
43703 TTGATGTTTCATTCATATTGAGCTTCTCTCCCTTGTTTTGTTTTTCTTCTTTGTATCTC
65 TTGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* * * * * *
43762 ATCAAGAAGATGATCATTTCATTGTTTTGACCCACTACTTTGTATCTCATTAGGAAGAT-GAGGC
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAG-GGT
** * * *
43826 TTGAAGTTTCACTCGCATTGAGCTTCGCTTCATTGTTTTGGTCTACTTCTTTGTATCTT
65 TTGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
* * * * * * * *
43885 ATCAGGAAGATGACCACTTTATTGTTTTGACCCACATCTCTGTATCTCATTAGGAAGTTGGGGTT
1 ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTT
***
43950 TGAAGTTTCACTTGCATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
66 TGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
*
44008 AT-AAGGAAGATGACCACTTCATTTGTTTTGA
1 ATCAA-GAAGATGATCACTTCA-TTGTTTTGA
44039 TCTAACCGAT
Statistics
Matches: 640, Mismatches: 121, Indels: 14
0.83 0.16 0.02
Matches are distributed among these distances:
122 27 0.04
123 602 0.94
124 11 0.02
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (123 bp):
ATCAAGAAGATGATCACTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTT
TGAAGTTTCACTCATATTAAGCTTCGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
Found at i:43351 original size:447 final size:448
Alignment explanation
Indices: 42707--43516 Score: 1135
Period size: 447 Copynumber: 1.8 Consensus size: 448
42697 TCTCATCAGA
* * * *
42707 AAGATGACCACTTCATTATTTTGACCCACTTTTTTGTATCTCATTAGGAAGATGGGGTTTGAAGT
1 AAGATGACCACTTCACTATTTTGACCCACTTTTTTGTATCTCATCAAGAAGATAGGGTTTGAAGT
* *
42772 TTCACTCACATTGAGCTTTGTTTCATTGTTCTGGTCTACTTCTCTGTACCTCAATAGGAAGTGAC
66 TTCACTCACATTGAGCTTTGTTTCATTGTTCTGGTCTACTTCTCTATACCTCAATAAGAAGTGAC
* * *
42837 CGTTCCATTATTTTGACCCACTTTTTTGTATCTCATCAGGAAAATGAGGTTTGAAGTTTCACTCA
131 CGCTCCATTATTTTGACCCACTTCTCTGTATCTCATCAGGAAAATGAGGTTTGAAGTTTCACTCA
* * * * *
42902 TATTGAGCTTCGCTTTC-TTGTTTTGGTATACTTCTCTGTATATTAT-TAGGAAGATGACCACTT
196 TATTAAGCTCCGC-TTCATTATTTTGGTATACTTCTCTGTATATCATCAAGG-AGATGACCACTT
*
42965 CATTGTTTTGACCCACTTCTCTGAATCTTATCAAGAAGATGAGGTTTGAAG-TTCGCTCATATTG
259 CATTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGAGGTTTGAAGTTTCGCTCATATTG
* *
43029 AGCTCCGTTTCGTTGATTTAGTGAACTTCTCTGTATCTCACTAGGAAGATTATCGTTTTATTATT
324 AGCTCCGCTTCATTGATTTAGTGAACTTCTCTGTATCTCACTAGGAAGATTATCGTTTTATTATT
43094 TTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACTCATATCAAG
389 TTGACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACTCATATCAAG
* * *
43154 AAGATGATCAGTTCACTGTTTTGA-CCACTTTTTTGTATCTCATCAAGAAGATAGGGTTTGAAGT
1 AAGATGACCACTTCACTATTTTGACCCACTTTTTTGTATCTCATCAAGAAGATAGGGTTTGAAGT
* * * * * * * *
43218 TTCACTCATATTGAGCTTTGCTTT-ATTGTTTTGGTTTACTTTTTTATATCTCATTAAGAAGATT
66 TTCACTCACATTGAGCTTTG-TTTCATTGTTCTGGTCTACTTCTCTATACCTCAATAAGAAG-TG
* * * * *
43282 ATCGCTCCATTGTTTTGACCCACTTCTCTGTATCTCATCATGAAGATGGGGTTTGAAGTTTCACT
129 ACCGCTCCATTATTTTGACCCACTTCTCTGTATCTCATCAGGAAAATGAGGTTTGAAGTTTCACT
* * *
43347 CATATTAAGCTCCGCTTCATTATTTTGGTCTACTTGTCTGTATCTCATCAAGGAGATGACCACTT
194 CATATTAAGCTCCGCTTCATTATTTTGGTATACTTCTCTGTATATCATCAAGGAGATGACCACTT
* * * * * *
43412 CATTGTTTTGACCCATTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCGTTCGTATTT
259 CATTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGAGGTTTGAAGTTTCGCTCATATTG
* * **
43477 AGCTTCGCTTCATTGTTTTAGTTTACTTCTCTGTATCTCA
324 AGCTCCGCTTCATTGATTTAGTGAACTTCTCTGTATCTCA
43517 TCAAGAAGAT
Statistics
Matches: 312, Mismatches: 46, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
446 88 0.28
447 177 0.57
448 47 0.15
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (448 bp):
AAGATGACCACTTCACTATTTTGACCCACTTTTTTGTATCTCATCAAGAAGATAGGGTTTGAAGT
TTCACTCACATTGAGCTTTGTTTCATTGTTCTGGTCTACTTCTCTATACCTCAATAAGAAGTGAC
CGCTCCATTATTTTGACCCACTTCTCTGTATCTCATCAGGAAAATGAGGTTTGAAGTTTCACTCA
TATTAAGCTCCGCTTCATTATTTTGGTATACTTCTCTGTATATCATCAAGGAGATGACCACTTCA
TTGTTTTGACCCACTTCTCTGAATCTCATCAAGAAGATGAGGTTTGAAGTTTCGCTCATATTGAG
CTCCGCTTCATTGATTTAGTGAACTTCTCTGTATCTCACTAGGAAGATTATCGTTTTATTATTTT
GACCCACTTCTCTGAATCTCATCAGGAAGATGGGGTTTGAAGCTTCACTCATATCAAG
Found at i:43421 original size:48 final size:48
Alignment explanation
Indices: 43361--43452 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
43351 TTAAGCTCCG
** * * *
43361 CTTCATTATTTTGGTCTACTTGTCTGTATCTCATCAAGGAGATGACCA
1 CTTCATTATTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGACCA
* *
43409 CTTCATTGTTTTGACCCATTTCTCTGTATCTCATCAAGAAGATG
1 CTTCATTATTTTGACCCACTTCTCTGTATCTCATCAAGAAGATG
43453 GGGTTTGAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (48 bp):
CTTCATTATTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGACCA
Found at i:44317 original size:49 final size:49
Alignment explanation
Indices: 44264--44550 Score: 197
Period size: 49 Copynumber: 5.9 Consensus size: 49
44254 CTTCATCTTC
44264 AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
1 AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* ** * ** * * *
44313 AAGGTATAAGGTTCACCGTTGCGTCCTTGACCTTTCCCTTCACATTTTT
1 AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * * ** ** *
44362 AGGGT-TCAAGATTCT-TCGTTACGGCTTCAATC-TGACCTTCTTATTTCT
1 AAGGTAT-AAGATT-TGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * ** * * *
44410 AAGGTATAAGGTTCGCCGTTGCATCCTTAACCTTTCCTTTCACATCTC-
1 AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * * *
44458 AAGGGTACAAGATTTGTCGTTGCGACCTCAATCTTTCCCTTAACAT-TATT
1 AA-GGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCT-CT
* * * *
44508 AAGGTACAAGATTTGTCATTGCGGCCTTAATCTTTCCCTTCAC
1 AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCAC
44551 GTCTTTAGAG
Statistics
Matches: 175, Mismatches: 55, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
48 34 0.19
49 139 0.79
50 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (49 bp):
AAGGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
Found at i:44478 original size:97 final size:98
Alignment explanation
Indices: 44257--44492 Score: 262
Period size: 97 Copynumber: 2.4 Consensus size: 98
44247 AAGTCTGCTT
* * * **
44257 CATCTTCAA-GGTATAAGATTTGCCGTTGCGGCCTCAATCTTTCCCTTCACATCTCTAAGGTATA
1 CATC-TCAAGGGTACAAGATTTGTCGTTACGGCCTCAATCTTGACCTTCACATCTCTAAGGTATA
* *
44321 AGGTTCACCGTTGCGTCCTTGACCTTTCCCTTCA
65 AGGTTCACCGTTGCATCCTTAACCTTTCCCTTCA
* ** * * ** *
44355 CATTTTTAGGGTTCAAGATTCT-TCGTTACGGCTTCAATC-TGACCTTCTTATTTCTAAGGTATA
1 CATCTCAAGGGTACAAGATT-TGTCGTTACGGCCTCAATCTTGACCTTCACATCTCTAAGGTATA
* *
44418 AGGTTCGCCGTTGCATCCTTAACCTTTCCTTTCA
65 AGGTTCACCGTTGCATCCTTAACCTTTCCCTTCA
* *
44452 CATCTCAAGGGTACAAGATTTGTCGTTGCGACCTCAATCTT
1 CATCTCAAGGGTACAAGATTTGTCGTTACGGCCTCAATCTT
44493 TCCCTTAACA
Statistics
Matches: 110, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
96 1 0.01
97 81 0.74
98 27 0.25
99 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (98 bp):
CATCTCAAGGGTACAAGATTTGTCGTTACGGCCTCAATCTTGACCTTCACATCTCTAAGGTATAA
GGTTCACCGTTGCATCCTTAACCTTTCCCTTCA
Found at i:45769 original size:7 final size:7
Alignment explanation
Indices: 45759--45798 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
45749 TTCTTTTTCA
45759 TTCTTTT
1 TTCTTTT
45766 TTCTTTT
1 TTCTTTT
45773 TTCCTTTCT
1 TT-CTTT-T
45782 TTCTTTT
1 TTCTTTT
45789 TTCTCTTT
1 TTCT-TTT
45797 TT
1 TT
45799 TTTGACCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.47
8 13 0.43
9 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:45771 original size:23 final size:22
Alignment explanation
Indices: 45745--45801 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
45735 TCATCTCGAC
45745 CTTTTTCTTTTTCATTCTTTTTT
1 CTTTTT-TTTTTCATTCTTTTTT
* *
45768 CTTTTTTCCTTTCTTTCTTTTTT
1 CTTTTTT-TTTTCATTCTTTTTT
*
45791 CTCTTTTTTTT
1 CTTTTTTTTTT
45802 GACCTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
CTTTTTTTTTTCATTCTTTTTT
Found at i:45784 original size:16 final size:16
Alignment explanation
Indices: 45746--45799 Score: 67
Period size: 16 Copynumber: 3.3 Consensus size: 16
45736 CATCTCGACC
45746 TTTTTC-TTTTTCATTCT
1 TTTTTCTTTTTTC--TCT
45763 TTTTTCTTTTTTC-CT
1 TTTTTCTTTTTTCTCT
45778 TTCTTTCTTTTTTCTCT
1 TT-TTTCTTTTTTCTCT
45795 TTTTT
1 TTTTT
45800 TTGACCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.12
16 14 0.41
17 10 0.29
18 6 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCT
Found at i:45789 original size:17 final size:15
Alignment explanation
Indices: 45746--45799 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 15
45736 CATCTCGACC
45746 TTTTTCTTTTTCATTCT
1 TTTTTCTTTTT--TTCT
*
45763 TTTTTCTTTTTTCCT
1 TTTTTCTTTTTTTCT
45778 TTCTTTCTTTTTTCTCT
1 TT-TTTCTTTTTT-TCT
45795 TTTTT
1 TTTTT
45800 TTGACCTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 5 0.15
16 13 0.39
17 15 0.45
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:50013 original size:12 final size:14
Alignment explanation
Indices: 49976--50018 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
49966 CACGAATAAA
* *
49976 AAATACATAAAAAC
1 AAATATATAAAAAT
49990 AAATATATAAAAAT
1 AAATATATAAAAAT
50004 AAA-A-ATAAAAAT
1 AAATATATAAAAAT
50016 AAA
1 AAA
50019 CAAAATACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
14 15 0.56
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATATATAAAAAT
Found at i:50233 original size:30 final size:29
Alignment explanation
Indices: 50176--50359 Score: 104
Period size: 30 Copynumber: 6.2 Consensus size: 29
50166 GTTAAAAATG
*
50176 AAATTTTGGAAAGTTTGAGGG-CTAAATTCA
1 AAATTTTGGAAAGTTTGGGGGTC-AAA-TCA
*
50206 AAATTTTGGAAAGTTTGGGGGTCAAATTTGA
1 AAATTTTGGAAAGTTTGGGGGTCAAA--TCA
** * * * *
50237 ATTTTTTGG-AAGTTCGAGGGTTAAAACA
1 AAATTTTGGAAAGTTTGGGGGTCAAATCA
* ** * *
50265 TAATTTGTAAAAAGTTTAGGGGTCAAAACA
1 AAATTT-TGGAAAGTTTGGGGGTCAAATCA
* * *
50295 TAATTTTTGGAAAGTTTGGGGGTTAAATCT
1 -AAATTTTGGAAAGTTTGGGGGTCAAATCA
* * *
50325 AAATTTTTGAATAGTTT-GAGGTCAAAACA
1 AAATTTTGGAA-AGTTTGGGGGTCAAATCA
*
50354 CAATTT
1 AAATTT
50360 CTAAATAAAA
Statistics
Matches: 115, Mismatches: 33, Indels: 13
0.71 0.20 0.08
Matches are distributed among these distances:
28 4 0.03
29 23 0.20
30 73 0.63
31 15 0.13
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (29 bp):
AAATTTTGGAAAGTTTGGGGGTCAAATCA
Found at i:50330 original size:60 final size:57
Alignment explanation
Indices: 50179--50359 Score: 159
Period size: 60 Copynumber: 3.0 Consensus size: 57
50169 AAAAATGAAA
* * **
50179 TTTTGGAAAGTTTGAGGGCTAAATTCAAAATTTTGGAAAGTTTGGGGGTC-AAATTTGAATT
1 TTTTGGAAAGTTTGAGGGTTAAA-TC-AAATTTTGAAAAGTTT-GGGGTCAAAACAT-AA-T
* * *
50240 TTTTGG-AAGTTCGAGGGTTAAAACATAATTTGTAAAAAGTTTAGGGGTCAAAACATAAT
1 TTTTGGAAAGTTTGAGGGTTAAATCA-AATTT-TGAAAAGTTT-GGGGTCAAAACATAAT
* * * *
50299 TTTTGGAAAGTTTGGGGGTTAAATCTAAATTTTTGAATAGTTTGAGGTCAAAACACAAT
1 TTTTGGAAAGTTTGAGGGTTAAATC-AAA-TTTTGAAAAGTTTGGGGTCAAAACATAAT
50358 TT
1 TT
50360 CTAAATAAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
58 1 0.01
59 29 0.29
60 55 0.56
61 14 0.14
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.36
Consensus pattern (57 bp):
TTTTGGAAAGTTTGAGGGTTAAATCAAATTTTGAAAAGTTTGGGGTCAAAACATAAT
Found at i:57306 original size:21 final size:20
Alignment explanation
Indices: 57261--57307 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
57251 GAGTTAATTG
*
57261 TTTGTAATTTAGAAAATTTA
1 TTTGCAATTTAGAAAATTTA
* *
57281 GTTGCAATTTAGGAAATTTCA
1 TTTGCAATTTAGAAAATTT-A
57302 TTTGCA
1 TTTGCA
57308 TTTTGGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTGCAATTTAGAAAATTTA
Found at i:60266 original size:13 final size:13
Alignment explanation
Indices: 60256--60285 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
60246 TAATTATTGT
60256 AATTTATTATTTA
1 AATTTATTATTTA
60269 AATTTATTATTTA
1 AATTTATTATTTA
60282 AATT
1 AATT
60286 GTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTTATTATTTA
Found at i:61894 original size:30 final size:31
Alignment explanation
Indices: 61858--61915 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
61848 ATTCGAATTC
61858 GTTAAATAATT-AAATG-TATATGTTTGACTT
1 GTTAAATAATTGAAATGAT-TATGTTTGACTT
*
61888 GTTAAATGATTGAAATGATTATGTTTGA
1 GTTAAATAATTGAAATGATTATGTTTGA
61916 AAGGTACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 14 0.56
32 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (31 bp):
GTTAAATAATTGAAATGATTATGTTTGACTT
Found at i:64388 original size:24 final size:24
Alignment explanation
Indices: 64334--64388 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
64324 ATAACTTGAG
64334 ATTTTATGTTAATAAATAATAAAT
1 ATTTTATGTTAATAAATAATAAAT
* * *
64358 ATATTATTTTAATAAATACTAAAT
1 ATTTTATGTTAATAAATAATAAAT
*
64382 CTTTTAT
1 ATTTTAT
64389 AAAAAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTATGTTAATAAATAATAAAT
Found at i:67962 original size:11 final size:11
Alignment explanation
Indices: 67948--67973 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
67938 TTATTATTTA
67948 TTATGTTTAAT
1 TTATGTTTAAT
67959 TTATGTTTAAT
1 TTATGTTTAAT
67970 TTAT
1 TTAT
67974 ACCTATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TTATGTTTAAT
Done.