Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4033.1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 85864
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.30
Warning! 8435 characters in sequence are not A, C, G, or T
Found at i:172 original size:6 final size:6
Alignment explanation
Indices: 161--193 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
151 TGAGAGAAGA
161 GATAGG GATAGG GATAGG GATAGG GATAGG GAT
1 GATAGG GATAGG GATAGG GATAGG GATAGG GAT
194 CGAGAACGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.18
Consensus pattern (6 bp):
GATAGG
Found at i:6280 original size:183 final size:180
Alignment explanation
Indices: 5905--6460 Score: 792
Period size: 184 Copynumber: 3.0 Consensus size: 180
5895 GTATTTTCCG
* * * *
5905 ACTTGATTAGTTGGTTAAGGTTTTTGAGACTGAAACAGATCAGTGTTTCCCTTGTTGATGTGGCT
1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCCTTGTTGATGTGGCT
* * * *
5970 CCTTCACAAACAGTGAATGTTGACCA-ACTGGACTGGTCGAGTTTTTCTGAGACAAAACGTAAAA
66 CCTCCACAAACAGTGAA-CTTGA-CAGACCGGACTGGT-GAGTTTTTCTGGGACAAAA-GTAAAA
* *
6034 GGTTTGTATGACCAATCAGAATAATATTTGAGGGAAAATACGAAGTCCATATGCA
127 GGTTTGTAT-AGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
6089 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCCTTGTTGATGTGGCT
1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCCTTGTTGATGTGGCT
**
6154 CCTCCACAAACAGTGAACTTGACAGACCGGACTGGCTGAGTTTTTCTGGGACAGAAAGTGGAAGG
66 CCTCCACAAACAGTGAACTTGACAGACCGGACTGG-TGAGTTTTTCTGGGACA-AAAGTAAAAGG
* *
6219 TTTGTGTAAGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCC
129 TTTGTAT-AGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
* * *
6272 ACTTGATTAGTCAGTTAAGGGTTTTGAGATAGAAACAGATCTGTGTTTGCGC-TGTTGATGTGGC
1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTT-CCCTTGTTGATGTGGC
* *
6336 TCCTCCACAAACAGTGAACGTTGACCGACCGGACTGGTTGAGTCTTTCTGGGACAATAAGTAAAA
65 TCCTCCACAAACAGTGAAC-TTGACAGACCGGACTGG-TGAGTTTTTCTGGGACAA-AAGTAAAA
* *
6401 GGTTTGTATAGTCTATTAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
127 GGTTTGTATAG-CAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
6456 ACTTG
1 ACTTG
6461 TGGTATACTC
Statistics
Matches: 338, Mismatches: 27, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
182 2 0.01
183 162 0.48
184 174 0.51
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (180 bp):
ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCCTTGTTGATGTGGCT
CCTCCACAAACAGTGAACTTGACAGACCGGACTGGTGAGTTTTTCTGGGACAAAAGTAAAAGGTT
TGTATAGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
Found at i:8930 original size:36 final size:36
Alignment explanation
Indices: 8880--8955 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
8870 GAAGATTACG
* **
8880 GGATCGCACCTGGCCAGTTGTCTGGGTTCTTTTGGT
1 GGATCGCACCTGGCCAATTGTCTGGGTTCTCCTGGT
* *
8916 GGATCGCACTTGGCCAATTGTTTGGGTTCTCCTGGT
1 GGATCGCACCTGGCCAATTGTCTGGGTTCTCCTGGT
8952 GGAT
1 GGAT
8956 TGGGATGGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.11, C:0.21, G:0.33, T:0.36
Consensus pattern (36 bp):
GGATCGCACCTGGCCAATTGTCTGGGTTCTCCTGGT
Found at i:9901 original size:35 final size:35
Alignment explanation
Indices: 9825--9904 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
9815 TTCGTTTCTA
*
9825 TTTATTTTTATTGTTATTTCAATTTCAATTATCTCT
1 TTTATTTTTATTGTTA-TTCAATTTAAATTATCTCT
* *
9861 ATTATTTTTACTT-TTA-TCATATTTAAATTTTCTCT
1 TTTATTTTTA-TTGTTATTCA-ATTTAAATTATCTCT
9896 TTTATTTTT
1 TTTATTTTT
9905 GCAAAGATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 21 0.55
36 12 0.32
37 2 0.05
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (35 bp):
TTTATTTTTATTGTTATTCAATTTAAATTATCTCT
Found at i:11033 original size:13 final size:14
Alignment explanation
Indices: 11008--11036 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10998 GACTTATTTT
11008 AAATATATTTAAAA
1 AAATATATTTAAAA
11022 AAATAT-TTTAAAA
1 AAATATATTTAAAA
11035 AA
1 AA
11037 TTCGATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATATTTAAAA
Found at i:21017 original size:21 final size:21
Alignment explanation
Indices: 20991--21037 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
20981 ATGGAGGCGA
*
20991 TCTCCATGTAGATCA-TCAAGG
1 TCTCCAGGTAGAT-ATTCAAGG
21012 TCTCCAGGTAGATATTCAAGG
1 TCTCCAGGTAGATATTCAAGG
21033 TCTCC
1 TCTCC
21038 TTCTGGGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
TCTCCAGGTAGATATTCAAGG
Found at i:39709 original size:40 final size:40
Alignment explanation
Indices: 39658--39739 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
39648 TACTGTATGA
39658 ATAATTAATTTAAAAGTTATTAAAGATATTTATATATGTC
1 ATAATTAATTTAAAAGTTATTAAAGATATTTATATATGTC
39698 ATAATTAATTTAAAAGTTATTAAAGATATTTATATATGTC
1 ATAATTAATTTAAAAGTTATTAAAGATATTTATATATGTC
39738 AT
1 AT
39740 TTTTTATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (40 bp):
ATAATTAATTTAAAAGTTATTAAAGATATTTATATATGTC
Found at i:39728 original size:20 final size:20
Alignment explanation
Indices: 39665--39729 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
39655 TGAATAATTA
39665 ATTTAAAAGTTATTAAAGAT
1 ATTTAAAAGTTATTAAAGAT
* * **
39685 ATTTATATATGTCA-TAATTA-
1 ATTTA-A-AAGTTATTAAAGAT
39705 ATTTAAAAGTTATTAAAGAT
1 ATTTAAAAGTTATTAAAGAT
39725 ATTTA
1 ATTTA
39730 TATATGTCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 15 0.45
21 5 0.15
22 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (20 bp):
ATTTAAAAGTTATTAAAGAT
Found at i:51936 original size:21 final size:21
Alignment explanation
Indices: 51910--51950 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51900 AGACGAGCAA
* *
51910 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
51931 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
51951 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:59397 original size:11 final size:11
Alignment explanation
Indices: 59369--59400 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
59359 ACTAGTGGAG
*
59369 TTAGGTAATGT
1 TTAGGTGATGT
59380 TTAGGTGATGT
1 TTAGGTGATGT
59391 TTAGGTGATG
1 TTAGGTGATG
59401 AATTTATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (11 bp):
TTAGGTGATGT
Found at i:66997 original size:6 final size:6
Alignment explanation
Indices: 66986--67023 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
66976 AACAGTCATG
*
66986 AAAAGA AAAAG- AAAATA AAAA-A AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
67024 AAGGACAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:67005 original size:11 final size:11
Alignment explanation
Indices: 66985--67022 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
66975 CAACAGTCAT
66985 GAAAAGAAAAA
1 GAAAAGAAAAA
*
66996 GAAAATAAAAA
1 GAAAAGAAAAA
*
67007 AAAAAGAAAAA
1 GAAAAGAAAAA
67018 GAAAA
1 GAAAA
67023 AAAGGACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:67010 original size:16 final size:15
Alignment explanation
Indices: 66986--67049 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
66976 AACAGTCATG
*
66986 AAAAGAAAAAGAAAA
1 AAAAAAAAAAGAAAA
67001 TAAAAAAAAAAGAAAA
1 -AAAAAAAAAAGAAAA
* *
67017 AGAAAAAAAGGACAAGA
1 AAAAAAAAAAGA-AA-A
67034 AAAAAACAAAA-AAAA
1 AAAAAA-AAAAGAAAA
67049 A
1 A
67050 TCAAATACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 12 0.30
16 18 0.45
17 7 0.17
18 3 0.08
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:69322 original size:73 final size:73
Alignment explanation
Indices: 69227--69628 Score: 569
Period size: 73 Copynumber: 5.5 Consensus size: 73
69217 TGATGCTTTT
*
69227 ATTTCTG--TTTCAAAAATTCAACTCATGTTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGCTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
69290 GTAATTTCA
65 GTAATTTCA
*
69299 ATTTCTGCTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
69364 TAATTTCA
66 TAATTTCA
*
69372 ATTTCTGCTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
69437 TAATTTCA
66 TAATTTCA
* * *
69445 ATTTTTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAATACACATTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
69509 TATTTTCA
66 TAATTTCA
* * ** * **
69517 ATTTTTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGA
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACACGTTGA
*
69582 GGTATTTTCA
64 GGTAATTTCA
* * *
69592 AATTCTAC-TTTCAAAAAAATCAACTCATATTGCGAGA
1 ATTTCTGCTTTTC--AAAATTCAACTCATATTGCGAGA
69629 GGTGGGTTGA
Statistics
Matches: 306, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
72 75 0.25
73 178 0.58
74 8 0.03
75 22 0.07
76 23 0.08
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (73 bp):
ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTCA
Found at i:69510 original size:145 final size:145
Alignment explanation
Indices: 69227--70519 Score: 694
Period size: 145 Copynumber: 8.9 Consensus size: 145
69217 TGATGCTTTT
*
69227 ATTTCTG--TTTCAAAAATTCAACTCATGTTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGCTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
*
69290 GTAATTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGAC
65 GTAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
*
69355 ACGTTGAGGTAATTTCA
129 ACATTGAGGTAATTTCA
*
69372 ATTTCTGCTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* *
69437 TAATTTCAATTTTTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAATACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
*
69502 ATTGAGGTATTTTCA
131 ATTGAGGTAATTTCA
* * ** * **
69517 ATTTTTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGA
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACACGTTGA
* * ** * * **
69582 GGTATTTTCAAATTCTACTTTCAAAAAAATCAACTCATATTGCGAG--A-G-G-TG-G-GTTGA-
64 GGTAATTTCAATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
69639 AC-CATT----TAATTTCTA
127 ACACATTGAGGTAATTTC-A
* ** * * ** * ** * * ** *
69654 CGTTT-T-CTAAATC--AACTCATATTGC-TAGAG-GTGAGTTGAGCCTCAG-GACACG-CTGA-
1 -ATTTCTGCT-TTTCAAAATTCA-ACT-CATATTGCGAGAAATGAG-TTGAGCCTCAAGAC--AC
* * ** * *** *
69710 GGTAATTTCAATTTC--TGT-TGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
59 GTTGAGGT-AATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
* **
69772 CAGGACACGCTGAGGTAATTTCA
123 CAAGACACATTGAGGTAATTTCA
* * ** * * *
69795 ATTTCTG-TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-TGTTCACATGCTG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGTTG
* * * ** *
69858 AGGTATTTTCAATTTCTGTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
63 AGGTAATTTCAATTTCTGTTTT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-
* * *
69923 ATTACACACTGTGG-----T--
125 A-GACACATTGAGGTAATTTCA
* ** * **
69938 A-------TTTT--AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGA
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACACGTTGA
* * **
69994 GGTATTTTCAATTAAGCCTTTTGATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTG
64 GGTAATTTC-----A--------ATTTCTG-TTTTC--AAAATTCAACTCATATTGCGAGAAATG
* * ** * *
70059 AGTTGAGCCTCAGGTCACACCGAGGTATTTTCC
113 AGTTGAGCCTCAAGACACATTGAGGTAATTTCA
** ** * ** * * ** * *
70092 ATTTCTG-TTTTCATTATT--A-TGTTTTTGAAAGAATCAACTCATATTGCGAGAAAT-GAGTTC
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAG-A--AA-TGA-GTT--GAG-CCTCAAG-AC
* ** ** *
70152 AGCCTCAAGACACATTGAGGT-AATTTCAATTCCTGTTTCAAAAATTCAACTCATATTGCGAGAA
57 A-CGTTGAGGTA-ATT----TCAATTTC---T-GT-TTTC-AAAATTCAACTCATATTGCGAGAA
* *
70216 ATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCA
110 ATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCA
70252 ATTTCT-CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* *
70316 TAATCTCAATTTCTCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
* *
70381 GTTGAGGTAATCTCA
131 ATTGAGGTAATTTCA
70396 ATTTCT-CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
70460 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
66 TAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
70520 NNNNNNNNNN
Statistics
Matches: 880, Mismatches: 160, Indels: 216
0.70 0.13 0.17
Matches are distributed among these distances:
129 22 0.03
131 3 0.00
132 3 0.00
133 4 0.00
134 8 0.01
135 66 0.08
136 17 0.02
137 11 0.01
138 5 0.01
140 10 0.01
141 14 0.02
142 23 0.03
143 8 0.01
144 142 0.16
145 168 0.19
146 71 0.08
147 39 0.04
148 44 0.05
149 64 0.07
150 15 0.02
152 1 0.00
153 2 0.00
154 6 0.01
155 3 0.00
156 5 0.01
157 5 0.01
158 2 0.00
159 9 0.01
160 75 0.09
161 4 0.00
162 4 0.00
163 9 0.01
164 3 0.00
165 3 0.00
166 8 0.01
167 3 0.00
171 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (145 bp):
ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
ATTGAGGTAATTTCA
Found at i:69785 original size:75 final size:74
Alignment explanation
Indices: 69662--69922 Score: 391
Period size: 75 Copynumber: 3.5 Consensus size: 74
69652 TACGTTTTCT
*
69662 AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
69727 TTGTTAAAAA
66 TT-TTAAAAA
**
69737 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
*
69802 TTTT--CAA
66 TTTTAAAAA
* * * * *
69809 AAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCTGTTCACATGCTGAGGTATTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTGAGGTAATTTCAATTTC
69874 TGTTTTAAAAA
64 TGTTTTAAAAA
*
69885 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
69923 ATTACACACT
Statistics
Matches: 167, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
72 36 0.22
74 30 0.18
75 64 0.38
76 37 0.22
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (74 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
TTTTAAAAA
Found at i:69811 original size:203 final size:201
Alignment explanation
Indices: 69451--69839 Score: 523
Period size: 203 Copynumber: 1.9 Consensus size: 201
69441 TTCAATTTTT
* * *
69451 GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAATACACATTGAGGTATTTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTC
* * **
69516 AATTTTTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCG
66 AATTTCTGCTTTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA-ACACGCCG
* *
69581 AGGTATTTTCAAATTCTACTTTCAAAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCATTT
130 AGGTAATTTCAAATTCTACTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCATTT
69646 AATTTCTAC
193 AATTTCTAC
* * ** * *
69655 GTTTTCTAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTC
69719 AATTTCTG-TTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-ACACGC
66 AATTTCTGCTT-TT--AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGAACACGC
* * ** *
69782 TGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGA
128 CGAGGTAATTTCAAATTCTACTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
69840 GCCTCTGTTC
Statistics
Matches: 162, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
201 31 0.19
202 2 0.01
203 81 0.50
204 9 0.06
205 39 0.24
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (201 bp):
GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTC
AATTTCTGCTTTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGAACACGCCGA
GGTAATTTCAAATTCTACTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCATTTAAT
TTCTAC
Found at i:69998 original size:59 final size:60
Alignment explanation
Indices: 69888--70006 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 60
69878 TTAAAAAAAA
* * * *
69888 TCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTATTTT-AATT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACACCGAGGTATTTTCAATT
*
69947 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-CACACGCCGAGGTATTTTCAATT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GATCACACACCGAGGTATTTTCAATT
70007 AAGCCTTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 47 0.89
60 6 0.11
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (60 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACACCGAGGTATTTTCAATT
Found at i:70142 original size:88 final size:88
Alignment explanation
Indices: 69947--70182 Score: 264
Period size: 88 Copynumber: 2.7 Consensus size: 88
69937 TATTTTAATT
69947 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGCC
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAC-CCGAGGTATTTTCAATT-AGCC
* *
70012 TTTTGATTTCTGTTTTTCAAAAAAA
64 TTTTCATTTATGTTTTTCAAAAAAA
* * * *
70037 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACA-CCGAGGTATTTTCCATT-TCTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCCGAGGTATTTTCAATTAGC-CT
* *
70100 TTTCATTATTATGTTTTT-GAAAGAA
65 TTTCA-T-TTATGTTTTTCAAAAAAA
** * * ** *
70125 TCAACTCATATTGCGAGAAATGAGTTCAGCCTCAAGACACA-TTGAGGTAATTTCAATT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCCGAGGTATTTTCAATT
70183 CCTGTTTCAA
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 5 0.04
88 71 0.56
89 9 0.07
90 40 0.32
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (88 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCCGAGGTATTTTCAATTAGCCTT
TTCATTTATGTTTTTCAAAAAAA
Found at i:70242 original size:72 final size:72
Alignment explanation
Indices: 70125--70519 Score: 704
Period size: 72 Copynumber: 5.5 Consensus size: 72
70115 TTTGAAAGAA
* * *
70125 TCAACTCATATTGCGAGAAATGAGTTCAGCCTCAAGACACATTGAGGTAATTTCAA-TTC-CTGT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCT-T
70188 TTCAAAAAT
65 TTC-AAAAT
70197 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
70262 TCAAAAT
66 TCAAAAT
70269 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
70334 TCAAAAT
66 TCAAAAT
70341 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
70406 TCAAAAT
66 TCAAAAT
* *
70413 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCT-CTT
70478 TTCAAAAT
65 TTCAAAAT
70486 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
70520 NNNNNNNNNN
Statistics
Matches: 315, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
72 261 0.83
73 52 0.17
74 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATCTCAATTTCTCTTT
TCAAAAT
Found at i:74920 original size:17 final size:17
Alignment explanation
Indices: 74889--74926 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
74879 TAGAATTGAG
74889 TTAAGAAAATTATTTAA
1 TTAAGAAAATTATTTAA
*
74906 TTAA-AAAATTAATTTAG
1 TTAAGAAAATT-ATTTAA
74923 TTAA
1 TTAA
74927 TTTGATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAAGAAAATTATTTAA
Found at i:81145 original size:30 final size:30
Alignment explanation
Indices: 81109--81169 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
81099 TTTATGTTAC
*
81109 TTCGATTGATCTTATTCATATGAAGTTCTT
1 TTCGATTGATCTTATTCATATAAAGTTCTT
81139 TTCGATTGATCTTATTCATATAAAGTTCTT
1 TTCGATTGATCTTATTCATATAAAGTTCTT
81169 T
1 T
81170 CTTTTCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (30 bp):
TTCGATTGATCTTATTCATATAAAGTTCTT
Done.