Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1850
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: 46659
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:88 original size:19 final size:20
Alignment explanation
Indices: 64--101 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
54 TGCCAAGGAA
64 ATGTATCGATACAT-TATCC
1 ATGTATCGATACATGTATCC
83 ATGTATCGATACATGTATC
1 ATGTATCGATACATGTATC
102 GATACATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATGTATCC
Found at i:99 original size:12 final size:12
Alignment explanation
Indices: 64--109 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
54 TGCCAAGGAA
64 ATGTATCGATAC
1 ATGTATCGATAC
76 AT-TATC----C
1 ATGTATCGATAC
83 ATGTATCGATAC
1 ATGTATCGATAC
95 ATGTATCGATAC
1 ATGTATCGATAC
107 ATG
1 ATG
110 GATCTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
11 4 0.14
12 18 0.62
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:125 original size:32 final size:31
Alignment explanation
Indices: 64--128 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
54 TGCCAAGGAA
*
64 ATGTATCGATACATTATCCATGTATCGATAC
1 ATGTATCGATACATGATCCATGTATCGATAC
**
95 ATGTATCGATACATGGATCTTTGTATCGATAC
1 ATGTATCGATACAT-GATCCATGTATCGATAC
127 AT
1 AT
129 TTAGGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (31 bp):
ATGTATCGATACATGATCCATGTATCGATAC
Found at i:1555 original size:52 final size:52
Alignment explanation
Indices: 1499--1800 Score: 154
Period size: 51 Copynumber: 5.8 Consensus size: 52
1489 CAAAATCGGT
1499 GATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTTTAATCAGG
1 GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTT-CTTTAATCAGG
* * * ** *
1551 GATACTCCAGCTCCGATTTTATTTTCAAAAACACCAATTTT-TCACAATCGGG
1 GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTTCT-TTAATCAGG
* * * ** * * * ** * *
1603 GATACTCTAACCCC--ATTAATCATCGAGGATACTCCAA-CCTCGTTATTTCCGAAGG
1 GATACTCCAACCCCGGTTTTATTTTC-A-AAAACACCAATTTTCTTTA-AT-C--AGG
* * * * *** ** *
1658 GATACTCCAACCCCGGCTTCA-TTTCCAAAATATTGA-TTTCTCAAAATCGGG
1 GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTTCT-TTAATCAGG
*
1709 GATACTCTAACCCCGGTTTTA-TTTC-AAAACACCAATTTTCCTTTAATCAGG
1 GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTT-CTTTAATCAGG
* * * *
1760 GATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
1 GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTT
1801 TTCACAATCG
Statistics
Matches: 176, Mismatches: 58, Indels: 31
0.66 0.22 0.12
Matches are distributed among these distances:
50 12 0.07
51 54 0.31
52 53 0.30
53 30 0.17
54 6 0.03
55 16 0.09
56 2 0.01
57 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (52 bp):
GATACTCCAACCCCGGTTTTATTTTCAAAAACACCAATTTTCTTTAATCAGG
Found at i:1780 original size:209 final size:208
Alignment explanation
Indices: 1307--1934 Score: 940
Period size: 210 Copynumber: 3.0 Consensus size: 208
1297 CCATCTCTGA
* * * * * *
1307 TTTATTTTCAAAACACTAA-TTTCCTATAATCGGGGATACCCCAACTTCGATTTTATTTCCAAAA
1 TTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAA
1371 ACACCAATTTTTCACAATCGGGGATACTAACAACCCCGTTAATCATCGGGATACTCCAACCCCGT
66 ACACCAATTTTTCACAATCGGGGATACT--CAACCCCGTTAATCATCGGGATACTCCAACCCCGT
*
1436 TATTT-CGAAGGGATACTCCAAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGTG
129 TATTTCCGAAGGGATACTCC-AACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAG
1500 ATACTCCAACCCCGGT
193 ATACTCCAACCCCGGT
*
1516 TTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTTCAAAA
1 TTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAA
* *
1581 ACACCAATTTTTCACAATCGGGGATACTCTAACCCCATTAATCATCGAGGATACTCCAACCTCGT
66 ACACCAATTTTTCACAATCGGGGATACTC-AACCCCGTTAATCATCG-GGATACTCCAACCCCGT
*
1646 TATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGGGA
129 TATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAGA
*
1711 TACTCTAACCCCGGT
194 TACTCCAACCCCGGT
1726 TTTA-TTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAA
1 TTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAA
* * * *
1790 ACACCAATTTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCCACCCC
66 ACACCAA-TTTTTCACAATCGGGGATACT-CAACCCCGTTA-ATCATC-GGGATACTCCAACCCC
** * * * *
1855 GTTACCTCCGAGGGGATACTCCAACCCCGGCTTTA-TTCTCAAAATATTGATTTCTCATAATTGG
127 GTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTC-CAAAATATTGATTTCTCAAAATCGG
1919 AGATACTCCAACCCCG
191 AGATACTCCAACCCCG
1935 TTATTTCCGA
Statistics
Matches: 384, Mismatches: 26, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
208 1 0.00
209 100 0.26
210 181 0.47
211 101 0.26
212 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (208 bp):
TTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAA
ACACCAATTTTTCACAATCGGGGATACTCAACCCCGTTAATCATCGGGATACTCCAACCCCGTTA
TTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAAAATCGGAGATA
CTCCAACCCCGGT
Found at i:2002 original size:78 final size:79
Alignment explanation
Indices: 1838--2006 Score: 193
Period size: 78 Copynumber: 2.2 Consensus size: 79
1828 TTATTTCATC
* *
1838 GGGGATACTCCCACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATT
1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATC
* *
1903 GATTTCTCATAATT
66 GATTTCTCACAACT
* ** * * *
1917 GGAGATACTCCAACCCCGTTATTTCCGA-GGGATACTCCAATCCCGATG-TTT-TTTTC-TAATC
1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCG--GCTTTATTCTCAAAAT-
1978 ATCGATTTCTCACAACT
63 ATCGATTTCTCACAACT
1995 GGGGATACTCCA
1 GGGGATACTCCA
2007 GCCTCGTCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 3 0.04
78 45 0.59
79 27 0.36
80 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATC
GATTTCTCACAACT
Found at i:7106 original size:13 final size:13
Alignment explanation
Indices: 7088--7148 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
7078 ATACAAAGAT
7088 CAATGTATCGATA
1 CAATGTATCGATA
7101 CAATGTATCGATA
1 CAATGTATCGATA
7114 C-A--T-T-GA-A
1 CAATGTATCGATA
*
7121 TAATGTATCGATA
1 CAATGTATCGATA
7134 CAATGTATCGATA
1 CAATGTATCGATA
7147 CA
1 CA
7149 TTGAATAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 1 0.03
10 2 0.05
11 1 0.03
12 3 0.08
13 29 0.73
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:7112 original size:33 final size:33
Alignment explanation
Indices: 7070--7168 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
7060 AAATTCCCAG
**
7070 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACATTGAAT-AATGTATCGATACA
7103 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
7136 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
7169 TTTCCTTGGC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 61 0.97
34 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACATTGAATAATGTATCGATACA
Found at i:7127 original size:20 final size:20
Alignment explanation
Indices: 7102--7170 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
7092 GTATCGATAC
7102 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
7122 AATGTATCGATAC-------
1 AATGTATCGATACATTGAAT
7135 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
7155 AATGTATCGATACATT
1 AATGTATCGATACATT
7171 TCCTTGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.31
20 29 0.69
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:7315 original size:21 final size:20
Alignment explanation
Indices: 7289--7327 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
7279 GTTGGGACCT
7289 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
7310 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
7328 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:9708 original size:20 final size:20
Alignment explanation
Indices: 9634--9708 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
9624 ACCCAGAATA
* *
9634 TATCGATACAATGAGAAATG
1 TATCGATACATTTAGAAATG
* *
9654 TATCGATTCATTTGAAAACATG
1 TATCGATACATTT-AGAA-ATG
* *
9676 TATCGATATATTTAGTAATG
1 TATCGATACATTTAGAAATG
9696 TATCGATACATTT
1 TATCGATACATTT
9709 CCTTAGCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 25 0.57
21 5 0.11
22 14 0.32
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
TATCGATACATTTAGAAATG
Found at i:12376 original size:21 final size:21
Alignment explanation
Indices: 12350--12389 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12340 TTTGCTTCCT
12350 CTTGAATCTGTGAGATTGTTA
1 CTTGAATCTGTGAGATTGTTA
12371 CTTGAATCTGTGAGATTGT
1 CTTGAATCTGTGAGATTGT
12390 AAGTGCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (21 bp):
CTTGAATCTGTGAGATTGTTA
Found at i:14942 original size:2 final size:2
Alignment explanation
Indices: 14930--14970 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
14920 ATTGAATTGG
* *
14930 AT AT CT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14971 AAAGAGAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15916 original size:2 final size:2
Alignment explanation
Indices: 15909--15937 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15899 TGAAATTAGC
15909 AT 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 AT A
15938 ATGAGGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16399 original size:2 final size:2
Alignment explanation
Indices: 16351--16379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16341 ATTGAATTGC
16351 AT 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 AT A
16380 AAAGAGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16401 original size:33 final size:33
Alignment explanation
Indices: 16359--16425 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
16349 GCATATATAT
16359 ATATATATATATATATATATAA-AAGAGAAGTCA
1 ATATATATATATATATATA-AATAAGAGAAGTCA
16392 ATATATATATATATATATAAATAAGAGAAGTCA
1 ATATATATATATATATATAAATAAGAGAAGTCA
16425 A
1 A
16426 AGTCAGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (33 bp):
ATATATATATATATATATAAATAAGAGAAGTCA
Found at i:19054 original size:16 final size:16
Alignment explanation
Indices: 19029--19123 Score: 102
Period size: 16 Copynumber: 5.9 Consensus size: 16
19019 ATATAAAATC
*
19029 TTAAACTTAAAATAAT
1 TTAAATTTAAAATAAT
* *
19045 TTAAATTTAAAATTAC
1 TTAAATTTAAAATAAT
*
19061 TTAAATATAAAA-AATT
1 TTAAATTTAAAATAA-T
*
19077 TTAAATTCAAAATAAT
1 TTAAATTTAAAATAAT
* *
19093 TTCAATTTAATATAAT
1 TTAAATTTAAAATAAT
*
19109 TTAAATTCAAAATAA
1 TTAAATTTAAAATAA
19124 CCTACGTCAG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
15 1 0.02
16 60 0.95
17 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:19113 original size:48 final size:48
Alignment explanation
Indices: 19015--19114 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
19005 AATAAAATAA
* *
19015 AAATATATAAAATCTTAAACTTAAAATAATTTAAATTTAAAATTACTT
1 AAATATAAAAAATCTTAAACTTAAAATAATTTAAATTTAAAATAACTT
* * * *
19063 AAATATAAAAAATTTTAAA-TTCAAAATAATTTCAATTTAATATAATTT
1 AAATATAAAAAATCTTAAACTT-AAAATAATTTAAATTTAAAATAACTT
19111 AAAT
1 AAAT
19115 TCAAAATAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.04
48 43 0.96
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (48 bp):
AAATATAAAAAATCTTAAACTTAAAATAATTTAAATTTAAAATAACTT
Found at i:29791 original size:18 final size:18
Alignment explanation
Indices: 29752--29791 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29742 TATTTTTATT
**
29752 AAATAATTAATTATTTTC
1 AAATAATTAATTATTTAA
*
29770 AAATAATTATTTATTTAA
1 AAATAATTAATTATTTAA
29788 AAAT
1 AAAT
29792 TATAGTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATTAATTATTTAA
Found at i:29968 original size:2 final size:2
Alignment explanation
Indices: 29961--30138 Score: 50
Period size: 2 Copynumber: 97.0 Consensus size: 2
29951 CAAAATTTAC
* * * *
29961 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT TT TT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
30002 -T AT GAT -T AT AT TT A- AA AT AT -T AT AT AT TT AT AT -T A- AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
30039 AT TT AT TT AT -T AT -T A- AT TT AT AT -T AT AT AA AT -T TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
30075 AT AT AT TT AT AT AT TT AT AT -T AT TT AT AT -T AT AGT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
30114 TT AT TT AT AT -T AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30139 TAAAAATTTA
Statistics
Matches: 126, Mismatches: 30, Indels: 40
0.64 0.15 0.20
Matches are distributed among these distances:
1 18 0.14
2 105 0.83
3 3 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (2 bp):
AT
Found at i:30049 original size:20 final size:20
Alignment explanation
Indices: 30007--30132 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 20
29997 TGTATTATGA
* *
30007 TTATATTTAAAATATTATATAT
1 TTATA-TTAATAT-TTATTTAT
30029 TTATATTAATATTTATTTA-
1 TTATATTAATATTTATTTAT
*
30048 TTATTAATTTATATTATATAAATT-T
1 TTA-T-ATTAATATT-TAT---TTAT
30073 TAATATATTTATATATTTATATTAT
1 T--TATA-TTA-ATATTTAT-TTAT
*
30098 TTATATT-ATAGTTATTTTAT
1 TTATATTAATATTTA-TTTAT
30118 TTATATT-ATATTTAT
1 TTATATTAATATTTAT
30133 ATATATTAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 29
0.71 0.05 0.24
Matches are distributed among these distances:
19 4 0.05
20 30 0.35
21 15 0.18
22 10 0.12
23 4 0.05
24 3 0.04
25 6 0.07
26 6 0.07
27 7 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
TTATATTAATATTTATTTAT
Found at i:30058 original size:43 final size:45
Alignment explanation
Indices: 29973--30074 Score: 106
Period size: 43 Copynumber: 2.4 Consensus size: 45
29963 ATATATATAT
**
29973 ATATATATATATTTTATATTTTTATGTATTATGATTATATTTAAA
1 ATATATATATATTTTATATTAATATGTATTATGATTATATTTAAA
* * *
30018 ATAT-TATATA-TTTATATTAATATTTATTTATTATTA-ATTT-AT
1 ATATATATATATTTTATATTAATATGTA-TTATGATTATATTTAAA
*
30060 AT-TATATAAATTTTA
1 ATATATATATATTTTA
30075 ATATATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
41 1 0.02
42 8 0.17
43 21 0.44
44 14 0.29
45 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (45 bp):
ATATATATATATTTTATATTAATATGTATTATGATTATATTTAAA
Found at i:30080 original size:68 final size:71
Alignment explanation
Indices: 30008--30138 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 71
29998 GTATTATGAT
30008 TATATTTAAA-ATATTATA-TATTTATATTA-A-TA-TTTATTTATTATTA-ATTTATATTATAT
1 TATATTTAAATAT-TTATATTATTTATATTATAGTATTTTATTTA-TATTATATTTATA-TATAT
30067 AAATTTTAA
63 AAATTTTAA
*
30076 TATATTTATATATTTATATTATTTATATTATAGTTATTTTATTTATATTATATTTATATATAT
1 TATATTTAAATATTTATATTATTTATATTATAG-TATTTTATTTATATTATATTTATATATAT
30139 TAAAAATTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
68 14 0.25
69 13 0.24
70 1 0.02
72 12 0.22
73 15 0.27
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (71 bp):
TATATTTAAATATTTATATTATTTATATTATAGTATTTTATTTATATTATATTTATATATATAAA
TTTTAA
Found at i:30127 original size:42 final size:43
Alignment explanation
Indices: 30026--30136 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 43
30016 AAATATTATA
30026 TATTTATATTAATATTTATTTATTATTAATTTATATTATATAAATTT
1 TATTTATATT-ATA--TATTTA-TATTAATTTATATTATATAAATTT
* *
30073 TA-ATATATTTATATATTTATATT-ATTTATATTATAGT-TATTT
1 TATTTATA-TTATATATTTATATTAATTTATATTATA-TAAATTT
30115 TATTTATATTATAT-TTATATAT
1 TATTTATATTATATATT-TATAT
30137 ATTAAAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
41 2 0.04
42 29 0.51
43 9 0.16
44 6 0.11
46 7 0.12
47 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (43 bp):
TATTTATATTATATATTTATATTAATTTATATTATATAAATTT
Found at i:30960 original size:37 final size:34
Alignment explanation
Indices: 30906--31004 Score: 117
Period size: 37 Copynumber: 2.8 Consensus size: 34
30896 TTATTAAGTG
* *
30906 TGTTAGTTAAACATATTAAGTGTGTTAGGTGGTA
1 TGTTAGGTAAATATATTAAGTGTGTTAGGTGGTA
* *
30940 TGTTAGGTGAGTAATATATTAAGTGTGTTAAGTGGTG
1 TGTTAGGT-A--AATATATTAAGTGTGTTAGGTGGTA
* *
30977 TGTTAGGTAAATATATTAGGTATGTTAG
1 TGTTAGGTAAATATATTAAGTGTGTTAG
31005 ATAAACATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 23 0.42
35 1 0.02
36 1 0.02
37 30 0.55
ACGTcount: A:0.29, C:0.01, G:0.28, T:0.41
Consensus pattern (34 bp):
TGTTAGGTAAATATATTAAGTGTGTTAGGTGGTA
Found at i:31009 original size:22 final size:22
Alignment explanation
Indices: 30977--31026 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
30967 TTAAGTGGTG
* *
30977 TGTTAGGTAAATATATTAGGTA
1 TGTTAGATAAACATATTAGGTA
*
30999 TGTTAGATAAACATATTAGGTG
1 TGTTAGATAAACATATTAGGTA
31021 TGTTAG
1 TGTTAG
31027 GTGAACTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (22 bp):
TGTTAGATAAACATATTAGGTA
Found at i:35606 original size:34 final size:34
Alignment explanation
Indices: 35566--35657 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 34
35556 TTATTAAGTG
35566 TGTTAGGTAAACATATTAGGTGTGTTA-AGTGATA
1 TGTTAGGTAAACATATTAGGTGTGTTAGA-TGATA
* * *
35600 TGTTAGGTGAGTAATATATTAAGTGTGTTAGATGATG
1 TGTTAGGT-A--AACATATTAGGTGTGTTAGATGATA
35637 TGTTAGGTAAACATATTAGGT
1 TGTTAGGTAAACATATTAGGT
35658 ATATTAGGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
34 18 0.37
35 1 0.02
36 1 0.02
37 28 0.57
38 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (34 bp):
TGTTAGGTAAACATATTAGGTGTGTTAGATGATA
Found at i:35657 original size:13 final size:13
Alignment explanation
Indices: 35639--35679 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
35629 AGATGATGTG
35639 TTAGGTAAACATA
1 TTAGGTAAACATA
35652 TTAGGT----ATA
1 TTAGGTAAACATA
35661 TTAGGTAAACATA
1 TTAGGTAAACATA
35674 TTAGGT
1 TTAGGT
35680 GTGTTAGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 9 0.38
13 15 0.62
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (13 bp):
TTAGGTAAACATA
Found at i:35664 original size:22 final size:22
Alignment explanation
Indices: 35639--35688 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
35629 AGATGATGTG
35639 TTAGGTAAACATATTAGGTATA
1 TTAGGTAAACATATTAGGTATA
* *
35661 TTAGGTAAACATATTAGGTGTG
1 TTAGGTAAACATATTAGGTATA
35683 TTAGGT
1 TTAGGT
35689 GAACTTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (22 bp):
TTAGGTAAACATATTAGGTATA
Found at i:36935 original size:36 final size:37
Alignment explanation
Indices: 36889--36962 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
36879 TAATTACAGA
* * *
36889 TTTTATGAATCATATA-TTTTTTAAAAATCTTAAATT
1 TTTTAAGAATCATAGATTTTTTTAAAAATCATAAATT
*
36925 TTTTAAGAATCATAGATTTTTTTAAGAATCATAAATT
1 TTTTAAGAATCATAGATTTTTTTAAAAATCATAAATT
36962 T
1 T
36963 CATGGATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 14 0.42
37 19 0.58
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (37 bp):
TTTTAAGAATCATAGATTTTTTTAAAAATCATAAATT
Found at i:36962 original size:19 final size:18
Alignment explanation
Indices: 36889--36962 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
36879 TAATTACAGA
* *
36889 TTTTATGAATCATATATT
1 TTTTAAGAATCATAAATT
* *
36907 TTTTAAAAATCTTAAATT
1 TTTTAAGAATCATAAATT
*
36925 TTTTAAGAATCATAGATTT
1 TTTTAAGAATCATA-AATT
36944 TTTTAAGAATCATAAATT
1 TTTTAAGAATCATAAATT
36962 T
1 T
36963 CATGGATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 30 0.64
19 17 0.36
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTTAAGAATCATAAATT
Found at i:38660 original size:26 final size:26
Alignment explanation
Indices: 38624--38676 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
38614 AAAAAGAACC
38624 CTGGCTACGTCA-CATCATCTTCCATA
1 CTGGCTACGTCACCA-CATCTTCCATA
38650 CTGGCTACGTCACCACATCTTCCATA
1 CTGGCTACGTCACCACATCTTCCATA
38676 C
1 C
38677 CCGATGCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (26 bp):
CTGGCTACGTCACCACATCTTCCATA
Found at i:39836 original size:18 final size:18
Alignment explanation
Indices: 39809--39893 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
39799 CAAATTTTAG
39809 GAATTATAGATTTTCTAA
1 GAATTATAGATTTTCTAA
*
39827 GAATTTTAGATTTTCTAA
1 GAATTATAGATTTTCTAA
*
39845 GAATTACAGATTTT-TCAA
1 GAATTATAGATTTTCT-AA
*
39863 GAATCATAGA-TTTCT-A
1 GAATTATAGATTTTCTAA
* *
39879 TAATTATAAATTTTC
1 GAATTATAGATTTTC
39894 AACCTTAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
16 8 0.14
17 8 0.14
18 40 0.71
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (18 bp):
GAATTATAGATTTTCTAA
Found at i:42689 original size:10 final size:10
Alignment explanation
Indices: 42674--42699 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42664 TTTCTAACAA
42674 AATTAAAAAT
1 AATTAAAAAT
42684 AATTAAAAAT
1 AATTAAAAAT
42694 AATTAA
1 AATTAA
42700 TCATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAAAAAT
Found at i:43991 original size:2 final size:2
Alignment explanation
Indices: 43984--44012 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43974 TTCTCTTTTA
43984 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44013 GCAATTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44634 original size:20 final size:20
Alignment explanation
Indices: 44594--44635 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44584 AAATAAAAAA
*
44594 TATATTTTTATATTCATATT
1 TATATTTTTATATTCAAATT
44614 TATATTTTTATAATT-AAATT
1 TATATTTTTAT-ATTCAAATT
44634 TA
1 TA
44636 AATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTTTTATATTCAAATT
Found at i:45935 original size:23 final size:24
Alignment explanation
Indices: 45908--45955 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
45898 TTAATATTTA
*
45908 TTAAATTTATAATTAA-ATTAAAT
1 TTAAATATATAATTAATATTAAAT
*
45931 TTAAATATATTATTAATTATTAAAT
1 TTAAATATATAATTAA-TATTAAAT
45956 AATAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAAATATATAATTAATATTAAAT
Done.