Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 2 of 29
Found at i:169988 original size:29 final size:29
Alignment explanation
Indices: 169941--170039 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
169931 ATGTTATAAG
169941 ATTT-TTT-AATATAATTTAAAAATTAAAA
1 ATTTATTTAAATATAA-TTAAAAATTAAAA
* * ** **
169969 ATTTATTTGAGTATAATTAAATCTCGAAA
1 ATTTATTTAAATATAATTAAAAATTAAAA
169998 ATTTATTTAAATATAA-TAAAAATATAAAA
1 ATTTATTTAAATATAATTAAAAAT-TAAAA
170027 ATTTATTTAAATA
1 ATTTATTTAAATA
170040 AAATAATAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 9 0.16
29 42 0.74
30 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
ATTTATTTAAATATAATTAAAAATTAAAA
Found at i:170835 original size:15 final size:14
Alignment explanation
Indices: 170810--170853 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
170800 AATATATTAA
170810 AAAAATATTAAATT
1 AAAAATATTAAATT
*
170824 AAAAATATTTAATT
1 AAAAATATTAAATT
*
170838 ATAAACTAATTAAATT
1 A-AAAAT-ATTAAATT
170854 TAAGTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 14 0.56
15 4 0.16
16 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATATTAAATT
Found at i:171898 original size:16 final size:16
Alignment explanation
Indices: 171877--171910 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
171867 TATATTTTAT
*
171877 AATTTAAATAATAATA
1 AATTTAAATAAGAATA
*
171893 AATTTAATTAAGAATA
1 AATTTAAATAAGAATA
171909 AA
1 AA
171911 ATTTCTGGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTTAAATAAGAATA
Found at i:176201 original size:27 final size:27
Alignment explanation
Indices: 176128--176204 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
176118 AAAGCCACCA
* * * *
176128 TTTGTATTTGTAAAAAATGATGATTTT
1 TTTGTGTTTGTAAAAAATGGTGGTTCT
176155 TTTGTGTTTGTAAAAAATGGTGGTTCCT
1 TTTGTGTTTGTAAAAAATGGTGGTT-CT
176183 TTT-TGTTTGTAAAAAATGGTGG
1 TTTGTGTTTGTAAAAAATGGTGG
176205 CTTATTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 41 0.91
28 4 0.09
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.48
Consensus pattern (27 bp):
TTTGTGTTTGTAAAAAATGGTGGTTCT
Found at i:176215 original size:24 final size:24
Alignment explanation
Indices: 176161--176230 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
176151 TTTTTTTGTG
* *
176161 TTTGTAAAAAATGGTGGTTCCTTTTTG
1 TTTGTAAAAAATGGTGG---CTTATTA
176188 TTTGTAAAAAATGGTGGCTTATTA
1 TTTGTAAAAAATGGTGGCTTATTA
* *
176212 TTTGTCAAAATTGGTGGCT
1 TTTGTAAAAAATGGTGGCT
176231 AATTTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 22 0.56
27 17 0.44
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (24 bp):
TTTGTAAAAAATGGTGGCTTATTA
Found at i:179222 original size:19 final size:19
Alignment explanation
Indices: 179186--179223 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
179176 CTTAACAAGA
*
179186 AAGATGTTCGCTACAAGGC
1 AAGATGTTAGCTACAAGGC
179205 AAGATTGTTAGCTA-AAGGC
1 AAGA-TGTTAGCTACAAGGC
179224 TACGCTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
AAGATGTTAGCTACAAGGC
Found at i:180704 original size:27 final size:27
Alignment explanation
Indices: 180671--180772 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 27
180661 AAAAGCCAGC
*
180671 CTTTGTGTTTGTCAAAAATGGTGATTT
1 CTTTGTGTTTGTCAAAAATGGTGACTT
* *
180698 CTTTGTGTTTGTAAAAATATGGTGGCTT
1 CTTTGTGTTTGTCAAAA-ATGGTGACTT
* * * *
180726 CTTTTTATTTGTCGAAAATGGTGGC-T
1 CTTTGTGTTTGTCAAAAATGGTGACTT
* *
180752 -TGT-TGTTTGTCAAAATTGGTG
1 CTTTGTGTTTGTCAAAAATGGTG
180773 GCTAATTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
24 15 0.24
25 2 0.03
26 1 0.02
27 24 0.38
28 21 0.33
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGACTT
Found at i:181796 original size:17 final size:18
Alignment explanation
Indices: 181760--181801 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
181750 TCTAAATTAT
181760 TATT-AAAAATATTAAAA
1 TATTAAAAAATATTAAAA
**
181777 TA-TAAAAAATATTACTA
1 TATTAAAAAATATTAAAA
181794 TATTAAAA
1 TATTAAAA
181802 TTTATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAAAAATATTAAAA
Found at i:182210 original size:26 final size:25
Alignment explanation
Indices: 182167--182234 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
182157 ATTATATTAT
182167 AAATAAAATAAATTAATAAAATAGAA
1 AAAT-AAATAAATTAATAAAATAGAA
* * * **
182193 AAATGAATAATTTAAATATAATTTAA
1 AAATAAATAAATT-AATAAAATAGAA
*
182219 AAATAAATAAAATAAT
1 AAATAAATAAATTAAT
182235 TTAAAGTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
25 10 0.30
26 23 0.70
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (25 bp):
AAATAAATAAATTAATAAAATAGAA
Found at i:182215 original size:11 final size:10
Alignment explanation
Indices: 182198--182244 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
182188 TAGAAAAATG
182198 AATAATTTAA
1 AATAATTTAA
182208 ATATAATTTAAA
1 A-ATAATTT-AA
*
182220 AATAA-ATAA
1 AATAATTTAA
182229 AATAATTTAA
1 AATAATTTAA
*
182239 AGTAAT
1 AATAAT
182245 AAATTACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 11 0.35
12 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AATAATTTAA
Found at i:182245 original size:22 final size:21
Alignment explanation
Indices: 182205--182248 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 21
182195 ATGAATAATT
182205 TAAATATAATTTAAAAATAAA
1 TAAATATAATTTAAAAATAAA
182226 TAAA-ATAATTTAAAGTAATAAA
1 TAAATATAATTTAAA--AATAAA
182248 T
1 T
182249 TACTTAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATATAATTTAAAAATAAA
Found at i:183857 original size:15 final size:15
Alignment explanation
Indices: 183837--183867 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
183827 ATGTTAACAA
*
183837 CCTATTGACGCAAGT
1 CCTATTGACACAAGT
183852 CCTATTGACACAAGT
1 CCTATTGACACAAGT
183867 C
1 C
183868 TTTATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (15 bp):
CCTATTGACACAAGT
Found at i:186044 original size:88 final size:87
Alignment explanation
Indices: 185790--186054 Score: 261
Period size: 88 Copynumber: 3.0 Consensus size: 87
185780 TTTGTCATGT
* * * *
185790 CATTAGTTAAATATTTTCTAT--TGTCAAAAAGAATCTGATACCTCATGTATCTATCACATCTTT
1 CATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATCTGATACC-CATGCATCTATCACATTTTT
185853 C-GAGTTGTAAGAAATTTATTAGG
65 CAGAGTT-TAAGAAATTTATTAGG
* * * * * **
185876 CACTAGTCAAATATTTTTTATCGTGTCAGAAGAAATATTTTACCCCATGCATCTATCACATCTTT
1 CATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATCTGATA-CCCATGCATCTATCACAT-TTT
* *
185941 T-AGAATTAAAGAAATTTATTAGG
64 TCAGAGTTTAAGAAATTTATTAGG
* * * * *
185964 TATTAGTCAAATATCTTCTATCGTGTCAAAAGGAATCCGATATCCCATACATCTATCATATTTTT
1 CATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATCTGATA-CCCATGCATCTATCACATTTTT
* *
186029 CAG-GTTCTAACAAATTTATTATG
65 CAGAGTT-TAAGAAATTTATTAGG
186052 CAT
1 CAT
186055 CTTTTCTTAA
Statistics
Matches: 141, Mismatches: 31, Indels: 12
0.77 0.17 0.07
Matches are distributed among these distances:
86 18 0.13
87 6 0.04
88 108 0.77
89 9 0.06
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (87 bp):
CATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATCTGATACCCATGCATCTATCACATTTTTC
AGAGTTTAAGAAATTTATTAGG
Found at i:188330 original size:15 final size:15
Alignment explanation
Indices: 188310--188338 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
188300 CTATCTTAAC
188310 AATAATGATGATGAT
1 AATAATGATGATGAT
188325 AATAATGATGATGA
1 AATAATGATGATGA
188339 AGCCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (15 bp):
AATAATGATGATGAT
Found at i:189955 original size:13 final size:13
Alignment explanation
Indices: 189939--190004 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
189929 ATATTAAAGA
*
189939 TAAATATAATTTT
1 TAAAAATAATTTT
189952 T-AAAAT--TTTT
1 TAAAAATAATTTT
189962 TAAAAATAAAATTTT
1 TAAAAAT--AATTTT
* *
189977 TAAAAATAACTGT
1 TAAAAATAATTTT
*
189990 TAAAAATACTTTT
1 TAAAAATAATTTT
190003 TA
1 TA
190005 TCCCCAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 4 0.10
13 17 0.40
15 11 0.26
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (13 bp):
TAAAAATAATTTT
Found at i:189978 original size:15 final size:16
Alignment explanation
Indices: 189952--189985 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
189942 ATATAATTTT
189952 TAAAATTTTTTAAAAA
1 TAAAATTTTTTAAAAA
189968 TAAAA-TTTTTAAAAA
1 TAAAATTTTTTAAAAA
189983 TAA
1 TAA
189986 CTGTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATTTTTTAAAAA
Found at i:190433 original size:30 final size:30
Alignment explanation
Indices: 190397--190458 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
190387 GCAATTACCT
190397 AATTGTCTTTAACTTCATTTACACAAAGTG
1 AATTGTCTTTAACTTCATTTACACAAAGTG
*
190427 AATTGTCTTTAACTTCATTTACACAAGGTG
1 AATTGTCTTTAACTTCATTTACACAAAGTG
190457 AA
1 AA
190459 CCAACTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (30 bp):
AATTGTCTTTAACTTCATTTACACAAAGTG
Found at i:190564 original size:22 final size:21
Alignment explanation
Indices: 190508--190569 Score: 52
Period size: 25 Copynumber: 2.8 Consensus size: 21
190498 TGGAAGATGC
190508 AAATAATTAAAAATTATTTTA
1 AAATAATTAAAAATTATTTTA
* * *
190529 TAGTAAATCATAAATTATTATTTTA
1 AAAT-AAT--TAAA-AATTATTTTA
*
190554 AAATAATTAAAGATTA
1 AAATAATTAAAAATTA
190570 AAAATGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
21 6 0.19
22 7 0.23
24 7 0.23
25 11 0.35
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (21 bp):
AAATAATTAAAAATTATTTTA
Found at i:190588 original size:52 final size:51
Alignment explanation
Indices: 190512--190626 Score: 151
Period size: 51 Copynumber: 2.2 Consensus size: 51
190502 AGATGCAAAT
*
190512 AATTAAAAATTATTTTATAGTAAATCAT-AAATTATTATTTTAAAATAATTAAA
1 AATTAAAAA-TATTTTATAGTAAAT-ATCAAATTATTA-TTTAAAATAATAAAA
* * *
190565 GATTAAAAATGTTTTATATTAAATATCAAATTATTATTTAAAATAATAAAA
1 AATTAAAAATATTTTATAGTAAATATCAAATTATTATTTAAAATAATAAAA
*
190616 AATAAAAAATA
1 AATTAAAAATA
190627 AAAAATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 24 0.44
52 22 0.41
53 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (51 bp):
AATTAAAAATATTTTATAGTAAATATCAAATTATTATTTAAAATAATAAAA
Found at i:190629 original size:6 final size:7
Alignment explanation
Indices: 190603--190633 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
190593 AATTATTATT
190603 TAAAATAA
1 TAAAA-AA
190611 TAAAAAA
1 TAAAAAA
190618 TAAAAAA
1 TAAAAAA
190625 TAAAAAA
1 TAAAAAA
190632 TA
1 TA
190634 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAAAAA
Found at i:190771 original size:52 final size:51
Alignment explanation
Indices: 190714--190860 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 51
190704 AATAGATATA
* *
190714 TAAAAATAATAAAAAATAAATAATATTTTATATTAAATCCTGAATTAGTATT
1 TAAAAATAATAAAAAATAAA-AATATTTTATATTAAATCATGAATTACTATT
* * *
190766 TAAAAATAATAAAATATTAAAAATATTTTATAATAAATCTTGAATTACTATT
1 TAAAAATAATAAAA-AATAAAAATATTTTATATTAAATCATGAATTACTATT
* * *
190818 TAAAAAT-TTACAAAATAAAAACA--TTATATTAAATCATGAATTA
1 TAAAAATAATAAAAAATAAAAATATTTTATATTAAATCATGAATTA
190861 TTGTCAATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
48 18 0.21
50 8 0.10
51 4 0.05
52 49 0.58
53 5 0.06
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (51 bp):
TAAAAATAATAAAAAATAAAAATATTTTATATTAAATCATGAATTACTATT
Found at i:191147 original size:25 final size:25
Alignment explanation
Indices: 191101--191148 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
191091 AAAAATTACA
*
191101 ATTTAAAAATAATAAATTTTTTATT
1 ATTTAAAAATAATAAATATTTTATT
191126 ATTTAAAAATAAT-AATAATTTTA
1 ATTTAAAAATAATAAAT-ATTTTA
191149 AAAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTAAAAATAATAAATATTTTATT
Found at i:191156 original size:28 final size:25
Alignment explanation
Indices: 191101--191157 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
191091 AAAAATTACA
** *
191101 ATTTAAAAATAATAAATTTTTTATT
1 ATTTAAAAATAATAAATTTTAAAAT
191126 ATTTAAAAATAATAATAATTTTAAAAAT
1 ATTTAAAAATAAT-A-AATTTT-AAAAT
191154 ATTT
1 ATTT
191158 TATATATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 13 0.50
26 1 0.04
27 6 0.23
28 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTAAAAATAATAAATTTTAAAAT
Found at i:191404 original size:20 final size:20
Alignment explanation
Indices: 191379--191417 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
191369 ACTAAAAATA
*
191379 TCATTTTTGTTATATGCCTT
1 TCATTTTTATTATATGCCTT
191399 TCATTTTTATTATATGCCT
1 TCATTTTTATTATATGCCT
191418 GAAGAGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.59
Consensus pattern (20 bp):
TCATTTTTATTATATGCCTT
Found at i:192041 original size:27 final size:27
Alignment explanation
Indices: 192011--192087 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
192001 AAAGTTACCT
*
192011 TTTGTGTTTGTAAAAAAT-GATGATTAC
1 TTTGTGTTTGTCAAAAATAG-TGATTAC
* * *
192038 TTTGTATTTGTCAAAAATAGTGGTTCC
1 TTTGTGTTTGTCAAAAATAGTGATTAC
* *
192065 TTTTTGTTTGTCAAAAATTGTGA
1 TTTGTGTTTGTCAAAAATAGTGA
192088 CTTGTTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATAGTGATTAC
Found at i:196613 original size:27 final size:26
Alignment explanation
Indices: 196582--196675 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 26
196572 AAAAGCCACC
196582 CTTTGTGTTTGTCAAAAATGGTGGTT
1 CTTTGTGTTTGTCAAAAATGGTGGTT
* *
196608 ACTTTGTATTTGTCAAAAATGGTAGTT
1 -CTTTGTGTTTGTCAAAAATGGTGGTT
* *
196635 CTTTTTTGTTTGTAAAAAATGGTGG--
1 C-TTTGTGTTTGTCAAAAATGGTGGTT
196660 C-TTGTTGTTTGTCAAA
1 CTTTG-TGTTTGTCAAA
196676 TTTGGTGGCT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
23 2 0.04
24 10 0.18
25 1 0.02
26 1 0.02
27 43 0.75
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.47
Consensus pattern (26 bp):
CTTTGTGTTTGTCAAAAATGGTGGTT
Found at i:196681 original size:24 final size:24
Alignment explanation
Indices: 196640--196685 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
196630 TAGTTCTTTT
196640 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* **
196664 TTGTTTGTCAAATTTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
196686 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:197592 original size:2 final size:2
Alignment explanation
Indices: 197587--197633 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
197577 AAAAAGAAAA
197587 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
197629 AG AG A
1 AG AG A
197634 ATAGGTCGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:198258 original size:21 final size:23
Alignment explanation
Indices: 198229--198272 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
198219 ATTGGATAAT
*
198229 AAAAGATGAAAA-AT-GTAAAAA
1 AAAAAATGAAAATATAGTAAAAA
198250 AAAAAATGAAAATATAGTAAAAA
1 AAAAAATGAAAATATAGTAAAAA
198273 CCTCCAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 2 0.10
23 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAAAATGAAAATATAGTAAAAA
Found at i:199564 original size:28 final size:32
Alignment explanation
Indices: 199498--199575 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 32
199488 AATTGTTTTA
199498 TTTTTTAAATTTAAAATTAATTCTGATTTAATT
1 TTTTTTAAATTTAAAATT-ATTCTGATTTAATT
199531 TATTTTTAAATTTAAAA-T-TT-TGATTTAA-T
1 T-TTTTTAAATTTAAAATTATTCTGATTTAATT
199560 TTTTTTAAATTCTAAA
1 TTTTTTAAATT-TAAA
199576 TTACGTTCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
28 10 0.23
29 6 0.14
30 8 0.19
31 2 0.05
33 2 0.05
34 15 0.35
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (32 bp):
TTTTTTAAATTTAAAATTATTCTGATTTAATT
Found at i:199577 original size:28 final size:30
Alignment explanation
Indices: 199516--199575 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
199506 ATTTAAAATT
199516 AATTCTGATTTAATTTATTTTTAAATTTAA
1 AATTCTGATTTAATTTATTTTTAAATTTAA
*
199546 AATTTTGATTTAA-TT-TTTTTAAATTCTAA
1 AATTCTGATTTAATTTATTTTTAAATT-TAA
199575 A
1 A
199576 TTACGTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.36
29 6 0.21
30 12 0.43
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (30 bp):
AATTCTGATTTAATTTATTTTTAAATTTAA
Found at i:199968 original size:20 final size:20
Alignment explanation
Indices: 199919--199961 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
199909 ACATATTACA
* *
199919 AATAAATA-ATTTTTTAAAT
1 AATAAATATAATTTTTAATT
199938 AATAAATATAATTTTTAATT
1 AATAAATATAATTTTTAATT
199958 AATA
1 AATA
199962 TCTATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAATATAATTTTTAATT
Found at i:207163 original size:21 final size:20
Alignment explanation
Indices: 207125--207162 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207115 AATAATATTT
207125 AAAAAAATAAACATTTTTCA
1 AAAAAAATAAACATTTTTCA
*
207145 AAAAAAATAAAGATTTTT
1 AAAAAAATAAACATTTTT
207163 TATTATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAAAATAAACATTTTTCA
Found at i:207320 original size:14 final size:15
Alignment explanation
Indices: 207290--207322 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
207280 TTAAAATTGT
*
207290 AATATTAATATTTTA
1 AATAATAATATTTTA
207305 AATAATAATA-TTTA
1 AATAATAATATTTTA
207319 AATA
1 AATA
207323 TATTTAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATATTTTA
Found at i:207825 original size:2 final size:2
Alignment explanation
Indices: 207818--207851 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
207808 TTATTTTAAA
207818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
207852 TTTGACTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208895 original size:14 final size:14
Alignment explanation
Indices: 208878--208905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
208868 AAATATAAAA
208878 ATATAAAAATATTT
1 ATATAAAAATATTT
208892 ATATAAAAATATTT
1 ATATAAAAATATTT
208906 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAAAAATATTT
Found at i:210621 original size:16 final size:16
Alignment explanation
Indices: 210591--210624 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
210581 GTTGCTTATA
**
210591 TTATTTTTTTTATTTT
1 TTATTTTTTAGATTTT
210607 TTATTTTTTAGATTTT
1 TTATTTTTTAGATTTT
210623 TT
1 TT
210625 TGGTTATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTATTTTTTAGATTTT
Found at i:211135 original size:22 final size:22
Alignment explanation
Indices: 211107--211149 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
211097 CAAGTGCATA
211107 GAATAACTATCTTTATAAGAAT
1 GAATAACTATCTTTATAAGAAT
211129 GAATAACTATCTTTATAAGAA
1 GAATAACTATCTTTATAAGAA
211150 AGTAAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (22 bp):
GAATAACTATCTTTATAAGAAT
Found at i:217202 original size:51 final size:51
Alignment explanation
Indices: 217109--217211 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
217099 ATAATATAGG
* * *
217109 CTTTAACTATCCATAGAAAATTATTAATCAATAAAATATGCTTCAATCATT
1 CTTTAACCATCCATAGAAAATAATTAATCAATAAAACATGCTTCAATCATT
* * * *
217160 CTTTAACCATCCATAGAAAATAATTAATCACTCATACGTGCTTCAATCATT
1 CTTTAACCATCCATAGAAAATAATTAATCAATAAAACATGCTTCAATCATT
217211 C
1 C
217212 AGTCAAACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (51 bp):
CTTTAACCATCCATAGAAAATAATTAATCAATAAAACATGCTTCAATCATT
Found at i:218706 original size:13 final size:15
Alignment explanation
Indices: 218683--218716 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
218673 TAAAGACATA
218683 ATTTTAGAGAATGAT
1 ATTTTAGAGAATGAT
218698 -TTTTA-AGAATGAT
1 ATTTTAGAGAATGAT
218711 ATTTTA
1 ATTTTA
218717 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (15 bp):
ATTTTAGAGAATGAT
Found at i:218728 original size:29 final size:30
Alignment explanation
Indices: 218696--218755 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
218686 TTAGAGAATG
*
218696 ATTTTT-AAGAATGATATTTTAT-TTTTAAA
1 ATTTTTAAAG-ATAATATTTTATATTTTAAA
*
218725 ATTTTTAAAGATAATTTTTTATATTTTAAA
1 ATTTTTAAAGATAATATTTTATATTTTAAA
218755 A
1 A
218756 ATAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
ATTTTTAAAGATAATATTTTATATTTTAAA
Found at i:218750 original size:22 final size:22
Alignment explanation
Indices: 218716--218776 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
218706 ATGATATTTT
* *
218716 ATTTTTAAAATTTTTAAAGATA
1 ATTTTTAATATTTTTAAAAATA
*
218738 ATTTTTTATA-TTTTAAAAATA
1 ATTTTTAATATTTTTAAAAATA
*
218759 ATTATTAATTATTTTTAA
1 ATTTTTAA-TATTTTTAA
218777 TTTTTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 16 0.50
22 10 0.31
23 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTTTAATATTTTTAAAAATA
Found at i:223043 original size:7 final size:7
Alignment explanation
Indices: 223031--223056 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
223021 TAGAATCCCT
223031 CTTCATA
1 CTTCATA
223038 CTTCATA
1 CTTCATA
223045 CTTCATA
1 CTTCATA
223052 CTTCA
1 CTTCA
223057 ACCTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
CTTCATA
Found at i:225175 original size:22 final size:21
Alignment explanation
Indices: 225150--225204 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
225140 AAGCAAAAAA
225150 AGAGAAAAACTGAGAAAGACTC
1 AGAGAAAAACTGAG-AAGACTC
** *
225172 AGAGATGACCTGAGAAGACTC
1 AGAGAAAAACTGAGAAGACTC
225193 AGAGAGAAAACT
1 AGAGA-AAAACT
225205 CGCAGGCAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
AGAGAAAAACTGAGAAGACTC
Found at i:225365 original size:22 final size:23
Alignment explanation
Indices: 225339--225398 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
225329 AAAATTTGGA
225339 TATTTTAATATTTAATTTA-AT-T
1 TATTTTAAT-TTTAATTTAGATAT
*
225361 TATTTATAAGTTTAA-TTAGATAT
1 TATTT-TAATTTTAATTTAGATAT
*
225384 TTTTTTAATTTTAAT
1 TATTTTAATTTTAAT
225399 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (23 bp):
TATTTTAATTTTAATTTAGATAT
Found at i:225443 original size:17 final size:15
Alignment explanation
Indices: 225410--225459 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
225400 TATTTTTATT
*
225410 ATAAATTAATATTAAA
1 ATAATTTAAT-TTAAA
225426 ATAATTCTCAATTTAAA
1 ATAATT-T-AATTTAAA
*
225443 AAAATTTAATTTAAA
1 ATAATTTAATTTAAA
225458 AT
1 AT
225460 TAATCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.31
16 6 0.21
17 11 0.38
18 3 0.10
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTTAATTTAAA
Found at i:225607 original size:36 final size:35
Alignment explanation
Indices: 225531--225621 Score: 83
Period size: 36 Copynumber: 2.5 Consensus size: 35
225521 AATATTTTTT
* * *
225531 TAAAATTAAATAAAATTTTTAAAAATAAAATTCAAT
1 TAAATTTAAATAAAA-TTTAAAAAATAAAATTCAAA
* * *
225567 TAAATTTAAATTAAATTTAAAATAATAAATTTTAAA
1 TAAATTTAAATAAAATTTAAAA-AATAAAATTCAAA
* *
225603 TAAATATAAACTCAAATTT
1 TAAATTTAAA-TAAAATTT
225622 TTTACTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
35 6 0.13
36 32 0.71
37 7 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
TAAATTTAAATAAAATTTAAAAAATAAAATTCAAA
Found at i:225979 original size:24 final size:25
Alignment explanation
Indices: 225925--225982 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
225915 AGTAATATAT
* **
225925 ATAAATATAATTAATATATTTTTTAA
1 ATAAATAAAATTAATATA-TTTACAA
*
225951 TTAAATAAAATTAATATA-TTACAA
1 ATAAATAAAATTAATATATTTACAA
225975 ATAAATAA
1 ATAAATAA
225983 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 11 0.41
26 16 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAATAAAATTAATATATTTACAA
Found at i:226219 original size:2 final size:2
Alignment explanation
Indices: 226206--226252 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
226196 GGACAAAAAC
*
226206 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
226248 AT AT A
1 AT AT A
226253 CACGGAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:227425 original size:2 final size:2
Alignment explanation
Indices: 227391--227416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
227381 ATACCTTTAA
227391 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
227417 GTGTATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230365 original size:33 final size:33
Alignment explanation
Indices: 230323--230392 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
230313 TTCAACGATT
230323 TGTATCGATACATAAAATGTCGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
*** * *
230356 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
230389 TGTA
1 TGTA
230393 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTCGTATCGATACAA
Found at i:230450 original size:13 final size:13
Alignment explanation
Indices: 230432--230456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230422 ATTACTCACA
230432 TGTATCGATACAT
1 TGTATCGATACAT
230445 TGTATCGATACA
1 TGTATCGATACA
230457 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:230521 original size:52 final size:52
Alignment explanation
Indices: 230465--230585 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
230455 CACTGATCTT
*
230465 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
230517 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
230569 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
230586 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:233844 original size:21 final size:21
Alignment explanation
Indices: 233819--233861 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
233809 CATGTCAGGA
233819 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
233840 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
233861 G
1 G
233862 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:237797 original size:10 final size:11
Alignment explanation
Indices: 237763--237797 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
237753 TTCCAAACAC
*
237763 AAAAAAAGGAA
1 AAAAAAAAGAA
237774 AAAAAAAAGAA
1 AAAAAAAAGAA
*
237785 AAAAAACAGAA
1 AAAAAAAAGAA
237796 AA
1 AA
237798 TCTCGATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:237845 original size:1 final size:1
Alignment explanation
Indices: 237839--237870 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
237829 TAATCTTCAC
*
237839 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
237871 CCCCTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:238843 original size:30 final size:31
Alignment explanation
Indices: 238807--238888 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
238797 ATACCTTTTT
238807 AAAGTCCACGACTCAGTGGCATTTTGTC-TC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
238837 AAAGTCCACGACTCAGTGGCATTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* * *
238868 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
238889 CCTTGTTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTTC
Found at i:238972 original size:34 final size:34
Alignment explanation
Indices: 238804--239656 Score: 756
Period size: 34 Copynumber: 25.8 Consensus size: 34
238794 CAAATACCTT
* * * *
238804 TTTAAAGTCCACGACTCAGTGGCA-TTTTGTCTC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
238837 ---AAAGTCCACGACTCAGTGGCA--TTTTT-TC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
238865 TTTAAAGCCCACAACTCCGTGGCACCTTGTTC-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
238898 TTTTAAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
238926 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
* *
238961 TTT-AAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
238988 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
*
239023 TTT-AAGTCCACAACTCCGTGGCAC------C-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239049 GTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 -TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
239083 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239116 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
*
239151 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239186 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
239221 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
239257 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
*
239292 TTTTCAAAGCCCACGACTCCGTGGCA-------CTC
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239321 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239354 TTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTT-AAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
239390 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
239426 TTTAAAGCCCACAACTCTGTGGCACCTTCTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
239459 TTTCAAAGCCCACGACTCTGTGGCAC-----TCTT
1 TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
239489 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
239523 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
239558 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
239593 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
239628 TTTTAAGTCCACAACTCCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCA-CTTT
239657 CTCCCTTCTC
Statistics
Matches: 692, Mismatches: 62, Indels: 130
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.00
27 46 0.07
28 48 0.07
29 31 0.04
30 24 0.03
31 18 0.03
33 108 0.16
34 214 0.31
35 54 0.08
36 38 0.05
37 110 0.16
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
Found at i:239061 original size:27 final size:27
Alignment explanation
Indices: 239023--239074 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
239013 TTTTTTCATC
*
239023 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
239050 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
239075 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:239170 original size:70 final size:68
Alignment explanation
Indices: 238837--239656 Score: 923
Period size: 70 Copynumber: 12.4 Consensus size: 68
238827 ATTTTGTCTC
* * * * *
238837 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCACAACTCCGTGGCAC-CTTGTTCCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
238899 TTT
66 TTT
* * *
238902 -AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCCGTGGCACT-TTTTTCAT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
238960 CTTT
66 -TTT
* * * *
238964 -AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCTGTGGCACT-TTTTTCAT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
239022 CTTT
66 -TTT
* * *
239026 -AAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
239083 TTT
66 TTT
*
239086 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
239151 TTTT
65 TTTT
*
239155 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
239220 CTTTT
64 CTTTT
239225 CAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
239290 TCTTTT
64 -CTTTT
* *
239296 CAAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-C
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
239353 TTTT
65 TTTT
*
239357 CAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTT
1 -AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACTCTTT
239421 TT-CTGTTT
61 TTCCT-TTT
* * * *
239429 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCACTC----T--
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
239488 TTTT
65 TTTT
239492 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
239557 CTTTT
64 CTTTT
*
239562 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
239627 CTTTT
64 CTTTT
* *
239632 -AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
239657 CTCCCTTCTC
Statistics
Matches: 685, Mismatches: 32, Indels: 73
0.87 0.04 0.09
Matches are distributed among these distances:
60 4 0.01
61 102 0.15
62 90 0.13
63 59 0.09
64 47 0.07
65 1 0.00
66 6 0.01
67 22 0.03
68 54 0.08
69 7 0.01
70 153 0.22
71 137 0.20
72 3 0.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (68 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TTT
Found at i:239505 original size:97 final size:100
Alignment explanation
Indices: 239053--239677 Score: 647
Period size: 105 Copynumber: 6.1 Consensus size: 100
239043 GCACCCGTTT
239053 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-T
1 AAGCCCACAACTCCGTGGCA-C---TTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGT
* *
239117 TTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
62 TTAAAGCCCACAACTCCGTGGCACTCTTCTT-CCTTTTCA
* *
239157 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCA-C-TTCT-TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CT
*
239222 -TTTCAAAGCCCACAACTCCGTGGCAC-CTT-TTTCTGTTT-A
60 GTTT-AAAGCCCACAACTCCGTGGCACTCTTCTTCCT-TTTCA
*
239261 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 AAGCCCACAACTCCGTGGCA--C---TTCT-TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
239321 --TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CTTTTCA
59 TGTTTAAAGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
* *
239359 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 AAGCCCACAACTCCGTGGCA--C---TT--CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
239424 TGTTTAAAGCCCACAACTCTGTGGCAC-CTTCTT-CTTTTCA
59 TGTTTAAAGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
* *
239464 AAGCCCACGACTCTGTGGCAC-TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
1 AAGCCCACAACTCCGTGGCACTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
*
239528 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
66 AGCCCACAACTCCGTGGCACTCTTCTT-CCTTTTCA
* **
239564 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCAC--TTCT-TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGT
* * * *
239629 TTTAAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCTCTA
62 TTAAAGCCCACAACTCCGTGGCACTC-TTCTTCCTTTTC-A
239669 AAGCCCACA
1 AAGCCCACA
239678 CAAGTCGGTG
Statistics
Matches: 464, Mismatches: 26, Indels: 61
0.84 0.05 0.11
Matches are distributed among these distances:
97 63 0.14
98 80 0.17
99 10 0.02
100 29 0.06
102 5 0.01
103 30 0.06
104 85 0.18
105 104 0.22
106 9 0.02
107 30 0.06
108 19 0.04
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (100 bp):
AAGCCCACAACTCCGTGGCACTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
AGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
Found at i:239744 original size:33 final size:33
Alignment explanation
Indices: 239659--239798 Score: 210
Period size: 33 Copynumber: 4.2 Consensus size: 33
239649 GCATCTTTCT
239659 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
* *
239693 CCATTCTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
* *
239726 TCCCTTC-CCAAAGCCCACACAAGTTGGTGGCAA
1 -CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
239759 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
239792 CCCTTCT
1 CCCTTCT
239799 AAGCCCAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 5 0.05
33 57 0.59
34 34 0.35
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (33 bp):
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:239779 original size:66 final size:68
Alignment explanation
Indices: 239658--239798 Score: 234
Period size: 66 Copynumber: 2.1 Consensus size: 68
239648 GGCATCTTTC
* *
239658 TCCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTTGGTGG
1 TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
239723 CAA
66 CAA
*
239726 TCCCTTC-CCAAAGCCCACACAAGTTGGTGGC-AACCATTCTCTAAAGCCCACACAAGTCGGTGG
1 TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
239789 CAA
66 CAA
239792 -CCCTTCT
1 TCCCTTCT
239799 AAGCCCAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
65 6 0.09
66 34 0.49
67 22 0.32
68 7 0.10
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.21
Consensus pattern (68 bp):
TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
CAA
Found at i:240131 original size:49 final size:49
Alignment explanation
Indices: 239798--240123 Score: 423
Period size: 49 Copynumber: 6.8 Consensus size: 49
239788 GCAACCCTTC
* *
239798 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
239847 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
239895 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
239938 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
239987 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
240036 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
240085 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
240124 TCTTTATCAC
Statistics
Matches: 244, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
43 40 0.16
45 1 0.00
48 43 0.18
49 160 0.66
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:240219 original size:49 final size:49
Alignment explanation
Indices: 240140--240427 Score: 385
Period size: 49 Copynumber: 6.0 Consensus size: 49
240130 TCACTTTTCT
*
240140 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
240189 CACCTTCACCATTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
240238 CACCTTCATCTTTAAGCCCAATGTAGCTGGCCTTG-ATCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
240286 CACC-TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * *
240333 -A----CACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
240377 CACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CACC--TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
240428 ACATCCTTTT
Statistics
Matches: 207, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
43 37 0.18
44 1 0.00
45 1 0.00
46 1 0.00
47 30 0.14
48 27 0.13
49 73 0.35
52 37 0.18
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (49 bp):
CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
Found at i:240228 original size:116 final size:116
Alignment explanation
Indices: 240024--240239 Score: 297
Period size: 116 Copynumber: 1.9 Consensus size: 116
240014 AGCACATTGG
* * * *
240024 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
1 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
***
240089 CCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
66 CCCAATATAACTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
* * * * *
240140 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
* * *
240205 TCCAATATAACTGGCCTTGAATCAGCATATTGGCA
66 CCCAATATAACTGGCCGTGAATCAACATATTGGCA
240240 CCTTCATCTT
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
116 85 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (116 bp):
CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
CCCAATATAACTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
Found at i:240355 original size:43 final size:43
Alignment explanation
Indices: 240247--240436 Score: 175
Period size: 43 Copynumber: 4.1 Consensus size: 43
240237 GCACCTTCAT
* *
240247 CTTTAAGCCCAATGTAGCTGGCCTTG-ATCAGCACATTGGCACCTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A---CAC
240294 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
* * * *
240337 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A-------CAC
*
240389 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-C
240433 CTTT
1 CTTT
240437 TTCATCATCT
Statistics
Matches: 121, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
43 39 0.32
44 5 0.04
45 1 0.01
46 1 0.01
47 26 0.21
48 11 0.09
50 1 0.01
51 1 0.01
52 36 0.30
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
Found at i:240410 original size:95 final size:91
Alignment explanation
Indices: 240247--240436 Score: 283
Period size: 95 Copynumber: 2.0 Consensus size: 91
240237 GCACCTTCAT
* *
240247 CTTTAAGCCCAATGTAGCTGGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
1 CTTTAAGCCCAATATAGCTAGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
240312 TGGCCTTGAATCAGCACATTGACA-C
66 TGGCCTTGAATCAGCACATTGACATC
* * *
240337 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGCCCAATATAGCTAGCCTTG-ATCAGCACATTGGCACC---T-CATCTTTAAGTCCAAT
240402 GTAGCTGGCCTTGAATCAGCACATTGACATC
61 GTAGCTGGCCTTGAATCAGCACATTGACATC
240433 CTTT
1 CTTT
240437 TTCATCATCT
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
90 23 0.26
91 16 0.18
94 1 0.01
95 44 0.49
96 5 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (91 bp):
CTTTAAGCCCAATATAGCTAGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGACATC
Found at i:240415 original size:52 final size:53
Alignment explanation
Indices: 240337--240496 Score: 178
Period size: 52 Copynumber: 3.0 Consensus size: 53
240327 ACATTGACAC
*
240337 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
* * * *
240389 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCA-CAT
* * * * * *
240445 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCAC
240497 TTTTCTCATC
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 37 0.42
53 2 0.02
54 9 0.10
55 4 0.05
56 36 0.41
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
Found at i:240467 original size:56 final size:56
Alignment explanation
Indices: 240337--240673 Score: 259
Period size: 67 Copynumber: 5.7 Consensus size: 56
240327 ACATTGACAC
* * *
240337 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCA-CC-TTTTC--CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* *
240389 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* * * * * *
240445 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TCATC
240510 AT
55 AT
*
240512 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* * * * * * *
240568 CTTTAAGCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TCATC
240633 AT
55 AT
* *
240635 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
240674 GCTTATCATC
Statistics
Matches: 225, Mismatches: 34, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
52 37 0.16
53 2 0.01
54 5 0.02
56 70 0.31
57 2 0.01
58 3 0.01
59 5 0.02
60 1 0.00
61 3 0.01
62 6 0.03
63 2 0.01
64 7 0.03
65 3 0.01
66 2 0.01
67 77 0.34
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (56 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
Found at i:240605 original size:123 final size:123
Alignment explanation
Indices: 240386--240673 Score: 531
Period size: 123 Copynumber: 2.3 Consensus size: 123
240376 GCACCTTTTC
*
240386 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
*
240451 GCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
66 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
240509 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
240574 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
66 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
* * *
240632 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTG
240674 GCTTATCATC
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 160 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (123 bp):
CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
Found at i:241521 original size:33 final size:33
Alignment explanation
Indices: 241479--241548 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
241469 TTCAACGATT
241479 TGTATCGATACATAAAATGTCGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
*** * *
241512 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
241545 TGTA
1 TGTA
241549 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTCGTATCGATACAA
Found at i:241606 original size:13 final size:13
Alignment explanation
Indices: 241588--241612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241578 ATTACTCACA
241588 TGTATCGATACAT
1 TGTATCGATACAT
241601 TGTATCGATACA
1 TGTATCGATACA
241613 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:241677 original size:52 final size:52
Alignment explanation
Indices: 241621--241741 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
241611 CACTGATCTT
*
241621 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
241673 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
241725 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
241742 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:245000 original size:21 final size:21
Alignment explanation
Indices: 244975--245017 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
244965 CATGTCAGGA
244975 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
244996 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
245017 G
1 G
245018 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:248953 original size:10 final size:11
Alignment explanation
Indices: 248919--248953 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
248909 TTCCAAACAC
*
248919 AAAAAAAGGAA
1 AAAAAAAAGAA
248930 AAAAAAAAGAA
1 AAAAAAAAGAA
*
248941 AAAAAACAGAA
1 AAAAAAAAGAA
248952 AA
1 AA
248954 TCTCGATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:249001 original size:1 final size:1
Alignment explanation
Indices: 248995--249028 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
248985 TAATCTTCAC
*
248995 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
249029 CCCCTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:250001 original size:30 final size:31
Alignment explanation
Indices: 249965--250046 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
249955 ATACCTTTTT
249965 AAAGTCCACGACTCAGTGGCATTTTGTC-TC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
249995 AAAGTCCACGACTCAGTGGCATTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* * *
250026 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
250047 CCTTGTTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTTC
Found at i:250130 original size:34 final size:34
Alignment explanation
Indices: 249962--250814 Score: 756
Period size: 34 Copynumber: 25.8 Consensus size: 34
249952 CAAATACCTT
* * * *
249962 TTTAAAGTCCACGACTCAGTGGCA-TTTTGTCTC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
249995 ---AAAGTCCACGACTCAGTGGCA--TTTTT-TC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250023 TTTAAAGCCCACAACTCCGTGGCACCTTGTTC-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
250056 TTTTAAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
250084 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
* *
250119 TTT-AAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250146 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
*
250181 TTT-AAGTCCACAACTCCGTGGCAC------C-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250207 GTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 -TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
250241 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250274 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
*
250309 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250344 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
250379 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
250415 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
*
250450 TTTTCAAAGCCCACGACTCCGTGGCA-------CTC
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250479 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250512 TTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTT-AAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
250548 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
250584 TTTAAAGCCCACAACTCTGTGGCACCTTCTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
250617 TTTCAAAGCCCACGACTCTGTGGCAC-----TCTT
1 TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
250647 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
250681 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
250716 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
250751 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
250786 TTTTAAGTCCACAACTCCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCA-CTTT
250815 CTCCCTTCTC
Statistics
Matches: 692, Mismatches: 62, Indels: 130
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.00
27 46 0.07
28 48 0.07
29 31 0.04
30 24 0.03
31 18 0.03
33 108 0.16
34 214 0.31
35 54 0.08
36 38 0.05
37 110 0.16
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
Found at i:250219 original size:27 final size:27
Alignment explanation
Indices: 250181--250232 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
250171 TTTTTTCATC
*
250181 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
250208 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
250233 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:250328 original size:70 final size:68
Alignment explanation
Indices: 249995--250814 Score: 923
Period size: 70 Copynumber: 12.4 Consensus size: 68
249985 ATTTTGTCTC
* * * * *
249995 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCACAACTCCGTGGCAC-CTTGTTCCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
250057 TTT
66 TTT
* * *
250060 -AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCCGTGGCACT-TTTTTCAT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
250118 CTTT
66 -TTT
* * * *
250122 -AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCTGTGGCACT-TTTTTCAT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
250180 CTTT
66 -TTT
* * *
250184 -AAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
250241 TTT
66 TTT
*
250244 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
250309 TTTT
65 TTTT
*
250313 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
250378 CTTTT
64 CTTTT
250383 CAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
250448 TCTTTT
64 -CTTTT
* *
250454 CAAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-C
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
250511 TTTT
65 TTTT
*
250515 CAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTT
1 -AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACTCTTT
250579 TT-CTGTTT
61 TTCCT-TTT
* * * *
250587 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCACTC----T--
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
250646 TTTT
65 TTTT
250650 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
250715 CTTTT
64 CTTTT
*
250720 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
250785 CTTTT
64 CTTTT
* *
250790 -AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
250815 CTCCCTTCTC
Statistics
Matches: 685, Mismatches: 32, Indels: 73
0.87 0.04 0.09
Matches are distributed among these distances:
60 4 0.01
61 102 0.15
62 90 0.13
63 59 0.09
64 47 0.07
65 1 0.00
66 6 0.01
67 22 0.03
68 54 0.08
69 7 0.01
70 153 0.22
71 137 0.20
72 3 0.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (68 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TTT
Found at i:250663 original size:97 final size:100
Alignment explanation
Indices: 250211--250835 Score: 647
Period size: 105 Copynumber: 6.1 Consensus size: 100
250201 GCACCCGTTT
250211 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-T
1 AAGCCCACAACTCCGTGGCA-C---TTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGT
* *
250275 TTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
62 TTAAAGCCCACAACTCCGTGGCACTCTTCTT-CCTTTTCA
* *
250315 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCA-C-TTCT-TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CT
*
250380 -TTTCAAAGCCCACAACTCCGTGGCAC-CTT-TTTCTGTTT-A
60 GTTT-AAAGCCCACAACTCCGTGGCACTCTTCTTCCT-TTTCA
*
250419 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 AAGCCCACAACTCCGTGGCA--C---TTCT-TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
250479 --TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CTTTTCA
59 TGTTTAAAGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
* *
250517 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 AAGCCCACAACTCCGTGGCA--C---TT--CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
250582 TGTTTAAAGCCCACAACTCTGTGGCAC-CTTCTT-CTTTTCA
59 TGTTTAAAGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
* *
250622 AAGCCCACGACTCTGTGGCAC-TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
1 AAGCCCACAACTCCGTGGCACTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
*
250686 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
66 AGCCCACAACTCCGTGGCACTCTTCTT-CCTTTTCA
* **
250722 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCAC--TTCT-TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGT
* * * *
250787 TTTAAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCTCTA
62 TTAAAGCCCACAACTCCGTGGCACTC-TTCTTCCTTTTC-A
250827 AAGCCCACA
1 AAGCCCACA
250836 CAAGTCGGTG
Statistics
Matches: 464, Mismatches: 26, Indels: 61
0.84 0.05 0.11
Matches are distributed among these distances:
97 63 0.14
98 80 0.17
99 10 0.02
100 29 0.06
102 5 0.01
103 30 0.06
104 85 0.18
105 104 0.22
106 9 0.02
107 30 0.06
108 19 0.04
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (100 bp):
AAGCCCACAACTCCGTGGCACTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAA
AGCCCACAACTCCGTGGCACTCTTCTTCCTTTTCA
Found at i:250902 original size:33 final size:33
Alignment explanation
Indices: 250817--250956 Score: 210
Period size: 33 Copynumber: 4.2 Consensus size: 33
250807 GCATCTTTCT
250817 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
* *
250851 CCATTCTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
* *
250884 TCCCTTC-CCAAAGCCCACACAAGTTGGTGGCAA
1 -CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
250917 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
250950 CCCTTCT
1 CCCTTCT
250957 AAGCCCAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 5 0.05
33 57 0.59
34 34 0.35
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (33 bp):
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:250937 original size:66 final size:68
Alignment explanation
Indices: 250816--250956 Score: 234
Period size: 66 Copynumber: 2.1 Consensus size: 68
250806 GGCATCTTTC
* *
250816 TCCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTTGGTGG
1 TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
250881 CAA
66 CAA
*
250884 TCCCTTC-CCAAAGCCCACACAAGTTGGTGGC-AACCATTCTCTAAAGCCCACACAAGTCGGTGG
1 TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
250947 CAA
66 CAA
250950 -CCCTTCT
1 TCCCTTCT
250957 AAGCCCAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
65 6 0.09
66 34 0.49
67 22 0.32
68 7 0.10
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.21
Consensus pattern (68 bp):
TCCCTTCTCCAAAGCCCACACAAGTCGGTGGCAAACCATTCTCTAAAGCCCACACAAGTCGGTGG
CAA
Found at i:251289 original size:49 final size:49
Alignment explanation
Indices: 250956--251281 Score: 423
Period size: 49 Copynumber: 6.8 Consensus size: 49
250946 GCAACCCTTC
* *
250956 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
251005 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
251053 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
251096 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
251145 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
251194 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
251243 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
251282 TCTTTATCAC
Statistics
Matches: 244, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
43 40 0.16
45 1 0.00
48 43 0.18
49 160 0.66
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:251377 original size:49 final size:49
Alignment explanation
Indices: 251298--251585 Score: 385
Period size: 49 Copynumber: 6.0 Consensus size: 49
251288 TCACTTTTCT
*
251298 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
251347 CACCTTCACCATTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
251396 CACCTTCATCTTTAAGCCCAATGTAGCTGGCCTTG-ATCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
251444 CACC-TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * *
251491 -A----CACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
251535 CACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CACC--TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
251586 ACATCCTTTT
Statistics
Matches: 207, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
43 37 0.18
44 1 0.00
45 1 0.00
46 1 0.00
47 30 0.14
48 27 0.13
49 73 0.35
52 37 0.18
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (49 bp):
CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
Found at i:251386 original size:116 final size:116
Alignment explanation
Indices: 251182--251397 Score: 297
Period size: 116 Copynumber: 1.9 Consensus size: 116
251172 AGCACATTGG
* * * *
251182 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
1 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
***
251247 CCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
66 CCCAATATAACTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
* * * * *
251298 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
* * *
251363 TCCAATATAACTGGCCTTGAATCAGCATATTGGCA
66 CCCAATATAACTGGCCGTGAATCAACATATTGGCA
251398 CCTTCATCTT
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
116 85 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (116 bp):
CACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
CCCAATATAACTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
Found at i:251513 original size:43 final size:43
Alignment explanation
Indices: 251405--251594 Score: 175
Period size: 43 Copynumber: 4.1 Consensus size: 43
251395 GCACCTTCAT
* *
251405 CTTTAAGCCCAATGTAGCTGGCCTTG-ATCAGCACATTGGCACCTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A---CAC
251452 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
* * * *
251495 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A-------CAC
*
251547 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-C
251591 CTTT
1 CTTT
251595 TTCATCATCT
Statistics
Matches: 121, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
43 39 0.32
44 5 0.04
45 1 0.01
46 1 0.01
47 26 0.21
48 11 0.09
50 1 0.01
51 1 0.01
52 36 0.30
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
Found at i:251568 original size:95 final size:91
Alignment explanation
Indices: 251405--251594 Score: 283
Period size: 95 Copynumber: 2.0 Consensus size: 91
251395 GCACCTTCAT
* *
251405 CTTTAAGCCCAATGTAGCTGGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
1 CTTTAAGCCCAATATAGCTAGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
251470 TGGCCTTGAATCAGCACATTGACA-C
66 TGGCCTTGAATCAGCACATTGACATC
* * *
251495 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGCCCAATATAGCTAGCCTTG-ATCAGCACATTGGCACC---T-CATCTTTAAGTCCAAT
251560 GTAGCTGGCCTTGAATCAGCACATTGACATC
61 GTAGCTGGCCTTGAATCAGCACATTGACATC
251591 CTTT
1 CTTT
251595 TTCATCATCT
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
90 23 0.26
91 16 0.18
94 1 0.01
95 44 0.49
96 5 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (91 bp):
CTTTAAGCCCAATATAGCTAGCCTTGATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGACATC
Found at i:251573 original size:52 final size:53
Alignment explanation
Indices: 251495--251654 Score: 178
Period size: 52 Copynumber: 3.0 Consensus size: 53
251485 ACATTGACAC
*
251495 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
* * * *
251547 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCA-CAT
* * * * * *
251603 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCAC
251655 TTTTCTCATC
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 37 0.42
53 2 0.02
54 9 0.10
55 4 0.05
56 36 0.41
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
Found at i:251625 original size:56 final size:56
Alignment explanation
Indices: 251495--251831 Score: 259
Period size: 67 Copynumber: 5.7 Consensus size: 56
251485 ACATTGACAC
* * *
251495 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCA-CC-TTTTC--CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* *
251547 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* * * * * *
251603 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TCATC
251668 AT
55 AT
*
251670 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
* * * * * * *
251726 CTTTAAGCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TCATC
251791 AT
55 AT
* *
251793 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
251832 GCTTATCATC
Statistics
Matches: 225, Mismatches: 34, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
52 37 0.16
53 2 0.01
54 5 0.02
56 70 0.31
57 2 0.01
58 3 0.01
59 5 0.02
60 1 0.00
61 3 0.01
62 6 0.03
63 2 0.01
64 7 0.03
65 3 0.01
66 2 0.01
67 77 0.34
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (56 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
Found at i:251763 original size:123 final size:123
Alignment explanation
Indices: 251544--251831 Score: 531
Period size: 123 Copynumber: 2.3 Consensus size: 123
251534 GCACCTTTTC
*
251544 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
*
251609 GCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
66 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
251667 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
251732 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
66 GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
* * *
251790 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTG
251832 GCTTATCATC
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 160 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (123 bp):
CATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAA
GCCCAATATCGTTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
Found at i:252682 original size:33 final size:33
Alignment explanation
Indices: 252640--252709 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
252630 TTCAACGATT
252640 TGTATCGATACATAAAATGTCGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
*** * *
252673 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTCGTATCGATACAA
252706 TGTA
1 TGTA
252710 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTCGTATCGATACAA
Found at i:252767 original size:13 final size:13
Alignment explanation
Indices: 252749--252773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252739 ATTACTCACA
252749 TGTATCGATACAT
1 TGTATCGATACAT
252762 TGTATCGATACA
1 TGTATCGATACA
252774 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:252838 original size:52 final size:52
Alignment explanation
Indices: 252782--252902 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
252772 CACTGATCTT
*
252782 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
252834 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
252886 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
252903 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:256164 original size:21 final size:21
Alignment explanation
Indices: 256139--256181 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
256129 CATGTCAGGA
256139 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
256160 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
256181 G
1 G
256182 TCATTTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:260119 original size:10 final size:11
Alignment explanation
Indices: 260086--260119 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
260076 TTCCAAACAC
*
260086 AAAAAAGGAAA
1 AAAAAAAGAAA
260097 AAAAAAAGAAA
1 AAAAAAAGAAA
*
260108 AAAAACAGAAA
1 AAAAAAAGAAA
260119 A
1 A
260120 TCTCGATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:260167 original size:1 final size:1
Alignment explanation
Indices: 260161--260192 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
260151 TAATCTTCAC
*
260161 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
260193 CCCCTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:261236 original size:34 final size:33
Alignment explanation
Indices: 261168--261982 Score: 529
Period size: 34 Copynumber: 24.8 Consensus size: 33
261158 GTCTCAAAGT
* * *
261168 CCACGACTCAGTGGCA--TTTTT-CTTTAAAG-
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
* *
261197 CC-CAACTCCGTGGCACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
* *
261229 CCACCAACTCCGTGGCAAAC-----CCTTTAAAGC
1 CCA-CAACTCCGTGGC-ACCTTTTTCCTTTTAAGC
* * *
261259 CCACAATTCCGTGGCA-CTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCT-TTTAAGC
* *
261292 CCACAACTCCGTGGCACC-----CGTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
* * * * * *
261320 CCACAATTCTGTGGCACTTTTTTCATCTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
*
261353 CCAC-ACTCCGTGGCA-C-----CCGTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
*
261379 CCACAACTCTCCGTGGCACCTTTTT-CTTTAAAGC
1 CCACAA--CTCCGTGGCACCTTTTTCCTTTTAAGC
*
261413 CCACAAACTCCGTGGCAAACC-TTTT-CTTTAAAGC
1 CCAC-AACTCCGTGGC--ACCTTTTTCCTTTTAAGC
*
261447 CCACAACTCTGT-GCACTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGC
*
261483 CCACAACTCCGTGGCACCTTTTT--TTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
*
261514 CCACAACTCTGTGGCACCTTTTTTCCTTTTCAAAGC
1 CCACAACTCCGTGGCACC-TTTTTCCTTTT--AAGC
*
261550 CCACAACTCCGTGGCACC-TTTTCTGTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTC-CTTTT-AAGC
*
261584 CCACAACTCCGT-GCACTCTTTTTCTCTTTCAAAGC
1 CCACAACTCCGTGGCAC-CTTTTTC-CTTT-TAAGC
*
261619 CC-CGAACTCCGTGGCA-C----T-CTTTAAAGC
1 CCAC-AACTCCGTGGCACCTTTTTCCTTTTAAGC
*
261646 CCACAACTCCGTGGC-CCTTCTTTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACCTT-TTTCCTTTT--AAGC
*
261681 CCACAACTCTGTGGCACTCTTTTTCCCTTTTTCAAAGC
1 CCACAACTCCGTGGCAC-CTTTTT-CC-TTTT--AAGC
*
261719 CCACAACTCCCGTGGCACCTTTTTCTGTTTTAAAGC
1 CCACAACT-CCGTGGCACCTTTTTC-CTTTT-AAGC
* *
261755 CCACAACTCTGTGGCACCTTCTT-CTTTTCAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTT--AAGC
* * * *
261789 CCACGACTCTGTGGCA-C-TCTT--TTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
261818 CCACAACTCCGTGGCACCTTTTT-CTGTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCT-TTT-AAGC
261852 CCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGC
*
261889 CCAC-ACTCCCGTGGCA-CTTTTTTCTTTTAAAGC
1 CCACAACT-CCGTGGCACCTTTTTCCTTTT-AAGC
*
261922 CCAC-ACTCCGTGGCACTCTTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCAC-C-TTTTT-CCTTTTAAGC
*
261957 CCACAACTCCGTGGCATCTTTCTTCC
1 CCACAACTCCGTGGCACCTTT-TTCC
261983 CTTCTCTCAA
Statistics
Matches: 645, Mismatches: 59, Indels: 159
0.75 0.07 0.18
Matches are distributed among these distances:
26 10 0.02
27 21 0.03
28 37 0.06
29 43 0.07
30 20 0.03
31 35 0.05
32 38 0.06
33 76 0.12
34 125 0.19
35 92 0.14
36 84 0.13
37 32 0.05
38 24 0.04
39 8 0.01
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
CCACAACTCCGTGGCACCTTTTTCCTTTTAAGC
Found at i:261344 original size:62 final size:61
Alignment explanation
Indices: 261189--261972 Score: 462
Period size: 62 Copynumber: 12.0 Consensus size: 61
261179 TGGCATTTTT
* * * *
261189 CTTTAAAG-CC-CAACTCCGTGGCACCTTGTTC-CTTTTAAGTCCACCAACTCCGTGGCAAACC
1 CTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCA-CAACTCCGTGGC--ACC
* *
261250 CTTTAAAGCCCACAATTCCGTGGCAC-TTTTTCATCTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACC
* * *
261310 CGTTTAAAGCCCACAATTCTGTGGCACTTTTTTCATC-TT-AAGTCCAC-ACTCCGTGGCACC
1 C-TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACC
*
261370 CGTTT-AAGCCCACAACTCTCCGTGGCAC-CTTTT-TCTTTAAAGCCCACAAACTCCGTGGCAAA
1 C-TTTAAAGCCCACAA--CTCCGTGGCACTTTTTTCTCTTTAAAGCCCAC-AACTCCGTGGC--A
261432 CC
60 CC
* *
261434 TTTTCTTTAAAGCCCACAACTCTGT-GCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGC
1 ----CTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGC
261498 ACC
59 ACC
* *
261501 TTTTTTTTAAAGCCCACAACTCTGTGGCACCTTTTTTC-CTTTTCAAAGCCCACAACTCCGTGGC
1 ----CTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTC-TTT-AAAGCCCACAACTCCGTGGC
261565 ACC
59 ACC
261568 TTTTCTGTTTTAAAGCCCACAACTCCGT-GCACTCTTTTTCTCTTTCAAAGCCC-CGAACTCCGT
1 ----C---TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTCTTT-AAAGCCCAC-AACTCCGT
*
261631 GGCACT
56 GGCACC
* *
261637 CTTTAAAGCCCACAACTCCGTGGCCCTTCTTTTCT-TTTCAAAGCCCACAACTCTGTGGCACTCT
1 CTTTAAAGCCCACAACTCCGTGGCACTT-TTTTCTCTTT-AAAGCCCACAACTCCGTGGCA----
261701 TTTTCC
60 ----CC
* * *
261707 CTTTTTCAAAGCCCACAACTCCCGTGGCACCTTTTTCTGTTTTAAAGCCCACAACTCTGTGGCAC
1 C--TTT-AAAGCCCACAACT-CCGTGGCACTTTTTTCT-CTTTAAAGCCCACAACTCCGTGGCA-
261772 CTTC
60 C--C
* * *
261776 TTCTTTTCAAAGCCCACGACTCTGTGGCAC-----TCTTTTTAAAGCCCACAACTCCGTGGCACC
1 --C-TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACC
*
261836 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCAC-ACTCCCG
1 -----C--TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT-AAAGCCCACAACT-CCG
261900 TGGCACTTTTTTC
55 TGGCAC------C
* * * *
261913 TTTTAAAGCCCAC-ACTCCGTGGCACTCTTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 CTTTAAAGCCCACAACTCCGTGGCA--CTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCA
261973 TCTTTCTTCC
Statistics
Matches: 617, Mismatches: 31, Indels: 143
0.78 0.04 0.18
Matches are distributed among these distances:
58 2 0.00
59 12 0.02
60 34 0.06
61 51 0.08
62 82 0.13
63 78 0.13
64 13 0.02
65 5 0.01
66 5 0.01
67 68 0.11
68 39 0.06
69 77 0.12
70 74 0.12
71 21 0.03
72 3 0.00
73 19 0.03
74 30 0.05
75 3 0.00
77 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (61 bp):
CTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACC
Found at i:261484 original size:36 final size:34
Alignment explanation
Indices: 261375--261982 Score: 576
Period size: 34 Copynumber: 17.9 Consensus size: 34
261365 GCACCCGTTT
261375 AAGCCCACAACTCTCCGTGGCACCTTTTT-C-TTTA
1 AAGCCCACAA--CTCCGTGGCACCTTTTTCCTTTTA
261409 AAGCCCACAAACTCCGTGGCAAACC-TTTT-C-TTTA
1 AAGCCCAC-AACTCCGTGGC--ACCTTTTTCCTTTTA
*
261443 AAGCCCACAACTCTGT-GCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT-A
261479 AAGCCCACAACTCCGTGGCACC-TTTT--TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
*
261510 AAGCCCACAACTCTGTGGCACCTTTTTTCCTTTTCA
1 AAGCCCACAACTCCGTGGCACC-TTTTTCCTTTT-A
*
261546 AAGCCCACAACTCCGTGGCACC-TTTTCTGTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTTTA
*
261580 AAGCCCACAACTCCGT-GCACTCTTTTTCTCTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTTC-CTTTTA
261615 AAGCCC-CGAACTCCGTGGCA-C----T-C-TTTA
1 AAGCCCAC-AACTCCGTGGCACCTTTTTCCTTTTA
*
261642 AAGCCCACAACTCCGTGGC-CCTTCTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTT-TTTCCTTTT-A
*
261677 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CC-TTTT-A
*
261715 AAGCCCACAACTCCCGTGGCACCTTTTTCTGTTTTA
1 AAGCCCACAACT-CCGTGGCACCTTTTTC-CTTTTA
* *
261751 AAGCCCACAACTCTGTGGCACCTTCTT-CTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-A
* * *
261785 AAGCCCACGACTCTGTGGCA-C----TCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
261814 AAGCCCACAACTCCGTGGCACCTTTTT-CTGTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTA
261848 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT-A
*
261885 AAGCCCAC-ACTCCCGTGGCA-CTTTTTTCTTTTA
1 AAGCCCACAACT-CCGTGGCACCTTTTTCCTTTTA
261918 AAGCCCAC-ACTCCGTGGCACTCTTTTTTCCCTTTT-
1 AAGCCCACAACTCCGTGGCAC-C-TTTTT-CCTTTTA
* *
261953 AAGTCCACAACTCCGTGGCATCTTTCTTCC
1 AAGCCCACAACTCCGTGGCACCTTT-TTCC
261983 CTTCTCTCAA
Statistics
Matches: 495, Mismatches: 24, Indels: 110
0.79 0.04 0.17
Matches are distributed among these distances:
27 21 0.04
28 2 0.00
29 20 0.04
30 8 0.02
31 23 0.05
32 19 0.04
33 43 0.09
34 111 0.22
35 103 0.21
36 81 0.16
37 32 0.06
38 24 0.05
39 8 0.02
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
Found at i:261644 original size:27 final size:28
Alignment explanation
Indices: 261607--261702 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 28
261597 CACTCTTTTT
261607 CTCTTTCAAAGCCC-CGAACTCCGTGGCA
1 CTCTTTCAAAGCCCAC-AACTCCGTGGCA
*
261635 CTCTTT-AAAGCCCACAACTCCGTGGCCCTT
1 CTCTTTCAAAGCCCACAACTCCGTGG--C-A
*
261665 CTTTTCTTTTCAAAGCCCACAACTCTGTGGCA
1 C---TC-TTTCAAAGCCCACAACTCCGTGGCA
261697 CTCTTT
1 CTCTTT
261703 TTCCCTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
27 17 0.30
28 10 0.18
29 3 0.05
30 1 0.02
32 1 0.02
33 3 0.05
34 3 0.05
35 18 0.32
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.30
Consensus pattern (28 bp):
CTCTTTCAAAGCCCACAACTCCGTGGCA
Found at i:261824 original size:63 final size:62
Alignment explanation
Indices: 261375--261944 Score: 378
Period size: 63 Copynumber: 8.5 Consensus size: 62
261365 GCACCCGTTT
*
261375 AAGCCCACAACTCTCCGTGGCACCTTTTTCTTTAAAGCCCACAAACTCCGTGGCAAACC-TTTTC
1 AAGCCCACAA--CTCCGTGGCA-C-TCTT-TTTAAAGCCCAC-AACTCCGTGGC--ACCTTTTTC
261439 -TTTA
58 TTTTA
*
261443 AAGCCCACAACTCTGT-GCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC-TTTT-
1 AAGCCCACAACTCCGTGGCACTC----T---TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
261505 TTTTA
58 TTTTA
* * *
261510 AAGCCCACAACTCTGTGGCACCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTCTG
1 AAGCCCACAACTCCGTGGCA-C-----T-CTTTTTAAAGCCCACAACTCCGTGGCACCTTTT-TC
261575 TTTTA
58 TTTTA
261580 AAGCCCACAACTCCGT-GCACTCTTTTTCTCTTTCAAAGCCC-CGAACTCCGTGGCA-C----TC
1 AAGCCCACAACTCCGTGGCACTC----T-T-TTT-AAAGCCCAC-AACTCCGTGGCACCTTTTTC
261638 -TTTA
58 TTTTA
* *
261642 AAGCCCACAACTCCGTGGCCCTTCTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAGCCCACAACTCCGTGGCAC-TC---T-TTTT-AAAGCCCACAACTCCGTGGCAC-CTTTTT--
261707 CTTTTTCA
57 C-TTTT-A
* *
261715 AAGCCCACAACTCCCGTGGCACCTTTTTCTGTTTTAAAGCCCACAACTCTGTGGCACCTTCTTCT
1 AAGCCCACAACT-CCGTGGCA-C----TCT-TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT
261780 TTTCA
59 TTT-A
* *
261785 AAGCCCACGACTCTGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTA
*
261848 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCAC-ACTCCCGTGGCACTTTTTT
1 AAGCCCACAACTCCGTGGCACTC----T---TTTT-AAAGCCCACAACT-CCGTGGCACCTTTTT
261912 CTTTTA
57 CTTTTA
261918 AAGCCCAC-ACTCCGTGGCACTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT
261945 TCCCTTTTAA
Statistics
Matches: 427, Mismatches: 18, Indels: 120
0.76 0.03 0.21
Matches are distributed among these distances:
62 47 0.11
63 67 0.16
64 10 0.02
65 4 0.01
66 6 0.01
67 53 0.12
68 26 0.06
69 59 0.14
70 67 0.16
71 27 0.06
72 3 0.01
73 18 0.04
74 30 0.07
75 7 0.02
78 3 0.01
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (62 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTA
Found at i:261945 original size:70 final size:70
Alignment explanation
Indices: 261809--261977 Score: 256
Period size: 70 Copynumber: 2.4 Consensus size: 70
261799 GTGGCACTCT
*
261809 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTT
261874 TTCCC
66 TTCCC
261879 TTTTCAAAGCCCAC-ACTCCCGTGGCACTTTTTTCT-TTTAAAGCCCAC-ACTCCGTGGCACTCT
1 TTTT-AAAGCCCACAACT-CCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC-
261941 TTTTTCCC
63 TTTTTCCC
*
261949 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTT
261978 CTTCCCTTCT
Statistics
Matches: 92, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
68 15 0.16
69 21 0.23
70 31 0.34
71 25 0.27
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.35
Consensus pattern (70 bp):
TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTT
TTCCC
Found at i:262029 original size:33 final size:34
Alignment explanation
Indices: 261984--262120 Score: 183
Period size: 33 Copynumber: 4.1 Consensus size: 34
261974 CTTTCTTCCC
261984 TTCTCTCAAAG-CCACACAAGTCGGTGGCAAACCA
1 TTCTCT-AAAGCCCACACAAGTCGGTGGCAAACCA
* * *
262018 TTCTCTAAAG-CCACACAAGTTGGTGGCAATCCC
1 TTCTCTAAAGCCCACACAAGTCGGTGGCAAACCA
* *
262051 TTC-CCAAAGCCCACACAAGTTGGTGGC-AACCA
1 TTCTCTAAAGCCCACACAAGTCGGTGGCAAACCA
*
262083 TTCTCTAAAGCCCACACAAGTCGGTGGCAAACCC
1 TTCTCTAAAGCCCACACAAGTCGGTGGCAAACCA
262117 TTCT
1 TTCT
262121 AAGCCCAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 11 0.12
33 66 0.73
34 14 0.15
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (34 bp):
TTCTCTAAAGCCCACACAAGTCGGTGGCAAACCA
Found at i:262070 original size:66 final size:67
Alignment explanation
Indices: 261980--262120 Score: 216
Period size: 66 Copynumber: 2.1 Consensus size: 67
261970 GCATCTTTCT
*
261980 TCCCTTCTCTCAAAGCCACACAAGTCGGTGGCAAACCATTCTCTAAAG-CCACACAAGTTGGTGG
1 TCCCTTCTCTCAAAGCCACACAAGTCGGTGGC-AACCATTCTCTAAAGCCCACACAAGTCGGTGG
262044 CAA
65 CAA
*
262047 TCCCTTC-C-CAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGG
1 TCCCTTCTCTCAAAG-CCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGG
262110 CAA
65 CAA
*
262113 ACCCTTCT
1 TCCCTTCT
262121 AAGCCCAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
65 20 0.29
66 41 0.60
67 7 0.10
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (67 bp):
TCCCTTCTCTCAAAGCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGC
AA
Found at i:262178 original size:49 final size:49
Alignment explanation
Indices: 262120--262436 Score: 318
Period size: 49 Copynumber: 6.6 Consensus size: 49
262110 CAAACCCTTC
* * *
262120 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
262169 TAAGTCCAATATAGCTGGCCTTGAATCAGGCACATTGACACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCA-GCACATTGGCACCTTCATCTT
*
262218 TAAGTCCAATGTAGCTGGCCTTGAATCATCAGCACATTGGCA----C--C-T
1 TAAGTCCAATATAGCTGGCCTTG-A--ATCAGCACATTGGCACCTTCATCTT
*
262263 T-AGTCCAATATAGCTGGCC-TGAAATCAG--CATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTG-AATCAGCACATTGGCACCTTCATCTT
* * * *
262309 TAAGTAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 T-A--AGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
262361 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
262410 TAAG-CCAATATCGTTGGCCGTGAATCA
1 TAAGTCCAATATAGCTGGCCTTGAATCA
262437 TAATATTGGC
Statistics
Matches: 226, Mismatches: 24, Indels: 37
0.79 0.08 0.13
Matches are distributed among these distances:
39 8 0.04
41 5 0.02
43 4 0.02
44 17 0.08
45 3 0.01
46 3 0.01
48 21 0.09
49 98 0.43
50 34 0.15
51 13 0.06
52 20 0.09
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:262301 original size:39 final size:42
Alignment explanation
Indices: 262220--262302 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 42
262210 CTCACCTTTA
*
262220 AGTCCAATGTAGCTGGCCTTGAATCATCAGCACATTGGCACCTT
1 AGTCCAATATAGCTGGCCTTGAA-CATCAG-ACATTGGCACCTT
262264 AGTCCAATATAGCTGGCC-TGAA-ATCAG-CATTGGCACCTT
1 AGTCCAATATAGCTGGCCTTGAACATCAGACATTGGCACCTT
262303 TATCTTTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
39 12 0.32
41 5 0.13
43 4 0.11
44 17 0.45
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (42 bp):
AGTCCAATATAGCTGGCCTTGAACATCAGACATTGGCACCTT
Found at i:262382 original size:143 final size:138
Alignment explanation
Indices: 262125--262403 Score: 384
Period size: 143 Copynumber: 2.0 Consensus size: 138
262115 CCTTCTAAGC
262125 CCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
1 CCAATATAGCTGGCCCTGAATCAGCA-ATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
* * *
262190 TGAATCAGGCACATTGACACCTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCATCAGCACAT
65 TGAATCAGGCACATTGACACCTCACCATTAAGCCCAATATAGCTGGCCTTG-A--ATCAGCACAT
262255 TGGCACCTTAGT
127 TGGCACCTTAGT
* *
262267 CCAATATAGCTGG-CCTGAAATCAGC-ATTGGCACCTTTATCTTTAAGTAGTCCAATGTAGCTGG
1 CCAATATAGCTGGCCCTG-AATCAGCAATTGGCACCTTCATCTTT-A--AGTCCAATATAGCTGG
* * *
262330 CCTTGACTCA-GCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATA
62 CCTTGAATCAGGCACATTGACACC-TCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACA
262394 TTGGCACCTT
126 TTGGCACCTT
262404 TATCTTTAAG
Statistics
Matches: 124, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
140 35 0.28
141 5 0.04
142 33 0.27
143 51 0.41
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (138 bp):
CCAATATAGCTGGCCCTGAATCAGCAATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGGCACATTGACACCTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGC
ACCTTAGT
Found at i:262560 original size:47 final size:48
Alignment explanation
Indices: 262464--262746 Score: 279
Period size: 47 Copynumber: 6.0 Consensus size: 48
262454 TCACTTTTCT
*
262464 CACCTTCATCTTTAAGTCCAATGGTAGCTGGCCTTGACTCAGCACATTGG
1 CACCTTCATC-TTAAGTCCAAT-GTAGCTGGCCTTGAATCAGCACATTGG
* * * *
262514 CACCTTCACCATTAA-TCCAATATAACTGGCC-TGAATCAGCATATTGG
1 CACCTTCATC-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
262561 CACCTTCATCTTAAGCCCAATGTAGCTGGCCTTG-ATCAGCACATTGG
1 CACCTTCATCTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
*
262608 CACC-TCATCTTTAAGTCCAATGTA---GGCCTTGAATCAGCACA-TGA
1 CACCTTCATC-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * *
262652 CA-C--C-T-TTAAGTCCAATATAGCTAGCCTTGAAATCAGCATATTGG
1 CACCTTCATCTTAAGTCCAATGTAGCTGGCCTTG-AATCAGCACATTGG
*
262696 CAACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCC-TGAATCAGCACATTG
1 C-ACC--TT-CATC-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
262747 ACATCCTTTT
Statistics
Matches: 193, Mismatches: 21, Indels: 36
0.77 0.08 0.14
Matches are distributed among these distances:
39 13 0.07
41 1 0.01
42 7 0.04
43 10 0.05
44 14 0.07
45 10 0.05
46 10 0.05
47 65 0.34
48 10 0.05
49 6 0.03
50 13 0.07
51 1 0.01
52 13 0.07
53 2 0.01
54 18 0.09
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (48 bp):
CACCTTCATCTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
Found at i:262765 original size:54 final size:56
Alignment explanation
Indices: 262655--262915 Score: 203
Period size: 54 Copynumber: 4.6 Consensus size: 56
262645 CACATGACAC
* * * * *
262655 CTTTAAGTCCAATATAGCTAGCCTTGAAATCAGCATATTGGCAACC-TTTTC--CAT
1 CTTTAAGTCCAATATAGCTGGCCATG-AATCAGCACATTGACATCCTTTTTCATCAT
* *
262709 CTTTAAGTTCAATGTAGCTGGCC-TGAATCAGCACATTGACATCCTTTTTCAT-AT
1 CTTTAAGTCCAATATAGCTGGCCATGAATCAGCACATTGACATCCTTTTTCATCAT
* * * *
262763 CTTTAAGCCCAATATCG-TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCATGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TCATC
262827 AT
55 AT
* *
262829 CTTTAAGTTCAATATAGCTGG-CTTGAATCAAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCATGAATC-AGCACATTGACATCCTTTTTCATCAT
* * * *
262885 CTTTAAGCCCAATATCGTTGCCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCATGAATCA
262916 ACAATTGGCA
Statistics
Matches: 164, Mismatches: 24, Indels: 36
0.73 0.11 0.16
Matches are distributed among these distances:
52 16 0.10
53 12 0.07
54 47 0.29
55 1 0.01
56 25 0.15
57 8 0.05
58 1 0.01
59 3 0.02
60 4 0.02
61 4 0.02
62 3 0.02
63 1 0.01
64 1 0.01
65 5 0.03
66 24 0.15
67 9 0.05
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (56 bp):
CTTTAAGTCCAATATAGCTGGCCATGAATCAGCACATTGACATCCTTTTTCATCAT
Found at i:262929 original size:122 final size:120
Alignment explanation
Indices: 262706--262988 Score: 469
Period size: 122 Copynumber: 2.3 Consensus size: 120
262696 CAACCTTTTC
* *
262706 CATCTTTAAGTTCAATGTAGCTGGCCTGAATCAGCACATTGACATCCTTTTTCATATCTTTAAGC
1 CATCTTTAAGTTCAATATAGCTGGCTTGAATCAGCACATTGACATCCTTTTTCATATCTTTAAGC
*
262771 CCAATATCGTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
66 CCAATATCGTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
262826 CATCTTTAAGTTCAATATAGCTGGCTTGAATCAAGCACATTGACATCCTTTTTCATCATCTTTAA
1 CATCTTTAAGTTCAATATAGCTGGCTTGAATC-AGCACATTGACATCCTTTTTCAT-ATCTTTAA
262891 GCCCAATATCGTTGCCCATGAATCAACA-ATTGGCATCTTTATCACTTTTCTCATCAT
64 GCCCAATATCG-TGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
* * * *
262948 CATCTTTAAGTCCAATATTGCTGCCTTGAATCAGCATATTG
1 CATCTTTAAGTTCAATATAGCTGGCTTGAATCAGCACATTG
262989 GCTATCATCT
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
120 30 0.20
121 31 0.20
122 77 0.50
123 15 0.10
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (120 bp):
CATCTTTAAGTTCAATATAGCTGGCTTGAATCAGCACATTGACATCCTTTTTCATATCTTTAAGC
CCAATATCGTGCCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
Found at i:263834 original size:31 final size:32
Alignment explanation
Indices: 263799--263863 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
263789 TTCAACGATT
263799 TGTATCGATACATAA-AGTTGTATCGATACAA
1 TGTATCGATACATAATAGTTGTATCGATACAA
**
263830 TGTATCGATACATAATTTTTTGTATCGATACAA
1 TGTATCGATACATAA-TAGTTGTATCGATACAA
263863 T
1 T
263864 TAAGCTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAATAGTTGTATCGATACAA
Found at i:263835 original size:13 final size:13
Alignment explanation
Indices: 263817--263841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
263807 TACATAAAGT
263817 TGTATCGATACAA
1 TGTATCGATACAA
263830 TGTATCGATACA
1 TGTATCGATACA
263842 TAATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:263922 original size:13 final size:13
Alignment explanation
Indices: 263904--263928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
263894 ATTACTCACA
263904 TGTATCGATACAT
1 TGTATCGATACAT
263917 TGTATCGATACA
1 TGTATCGATACA
263929 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:264020 original size:51 final size:52
Alignment explanation
Indices: 263937--264057 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
263927 CACTGATCTT
*
263937 TGTATCGATACATGCATGGCAAATTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCA-GGCAAATTTGCCCAGATGTATCGATACACTATTAAA
263989 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
264041 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
264058 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
51 30 0.45
52 37 0.55
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:267334 original size:21 final size:21
Alignment explanation
Indices: 267309--267351 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
267299 CATGTCAGGA
267309 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
267330 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
267351 G
1 G
267352 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:271267 original size:12 final size:11
Alignment explanation
Indices: 271250--271279 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
271240 TTCCAAACAC
*
271250 AAAAAAAGGAA
1 AAAAAAAAGAA
271261 AAAAAAAAGAA
1 AAAAAAAAGAA
271272 AAAAAAAA
1 AAAAAAAA
271280 CAGAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:271284 original size:13 final size:12
Alignment explanation
Indices: 271250--271286 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
271240 TTCCAAACAC
*
271250 AAAAAAAGGAAA
1 AAAAAAAGAAAA
271262 AAAAAAAGAAAA
1 AAAAAAAGAAAA
271274 AAAAAACAGAAAA
1 AAAAAA-AGAAAA
271287 TCTCGATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:271334 original size:1 final size:1
Alignment explanation
Indices: 271328--271358 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
271318 TAATCTTCAC
*
271328 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
271359 CCCCTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Done.