Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003609.1 Hibiscus syriacus cultivar Beakdansim tig00007636_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124482
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6167 original size:23 final size:23
Alignment explanation
Indices: 6141--6188 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6131 ATAAAGTACA
*
6141 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
6164 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
6187 AT
1 AT
6189 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:6969 original size:23 final size:23
Alignment explanation
Indices: 6943--7005 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6933 ATATAACCAC
6943 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6966 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6989 TACCTATTACATCATAT
1 TACCTATTACATTATAT
7006 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:7461 original size:39 final size:39
Alignment explanation
Indices: 7407--7492 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
7397 CAAGTTGTAT
*
7407 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
*
7446 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
7485 ATTTTGAT
1 ATTTTGAT
7493 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
Found at i:7767 original size:18 final size:18
Alignment explanation
Indices: 7744--7780 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7734 AGCCGAATAT
7744 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
7762 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
7780 A
1 A
7781 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:8202 original size:25 final size:25
Alignment explanation
Indices: 8168--8218 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
8158 TTTTTCCAAA
*
8168 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
8193 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
8218 T
1 T
8219 GATTGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:8509 original size:21 final size:22
Alignment explanation
Indices: 8484--8535 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
8474 ACACTTTACA
*
8484 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
8507 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
8530 ATATAA
1 ATATAA
8536 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:8520 original size:23 final size:23
Alignment explanation
Indices: 8494--8556 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
8484 ATATAACCAC
8494 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
8517 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
8540 TACCTATTACATCATAT
1 TACCTATTACATTATAT
8557 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:8959 original size:25 final size:25
Alignment explanation
Indices: 8902--8967 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
8892 CACTCAAAAG
* *
8902 ATGTATATACATAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
8927 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
8952 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
8968 TTAATGATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:11744 original size:183 final size:183
Alignment explanation
Indices: 11436--12144 Score: 1283
Period size: 183 Copynumber: 3.9 Consensus size: 183
11426 TTAAAATTAC
* * *
11436 CGACACTTTTTTAAATGGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
11501 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
11566 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
11619 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
11684 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
11749 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
11802 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
11867 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
11932 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* * *
11985 CGACACTTTTTTAAATCGCATTGACACATTTTTCTTCCAATATGAACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
12050 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * **
12115 ATATTGCAAATTTATCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
12145 ATGTTGAAAG
Statistics
Matches: 511, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 511 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:13574 original size:3 final size:3
Alignment explanation
Indices: 13566--13607 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
13556 ACTTGTTTGG
* * *
13566 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
13608 GCCAGCTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:13581 original size:9 final size:9
Alignment explanation
Indices: 13567--13607 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
13557 CTTGTTTGGA
13567 TCATCATCT
1 TCATCATCT
*
13576 TCATCATCA
1 TCATCATCT
*
13585 TCATCATCG
1 TCATCATCT
13594 TCATCATCT
1 TCATCATCT
13603 TCATC
1 TCATC
13608 GCCAGCTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.24, C:0.34, G:0.02, T:0.39
Consensus pattern (9 bp):
TCATCATCT
Found at i:13583 original size:12 final size:12
Alignment explanation
Indices: 13570--13654 Score: 82
Period size: 12 Copynumber: 6.9 Consensus size: 12
13560 GTTTGGATCA
*
13570 TCATCTTCATCA
1 TCATCTTCATCG
*
13582 TCATCATCATCG
1 TCATCTTCATCG
13594 TCATCATCTTCATCG
1 ---TCATCTTCATCG
* *
13609 CCAGCTTCATCG
1 TCATCTTCATCG
*
13621 TCATCATCA-CG
1 TCATCTTCATCG
13632 TCATCTTCATCG
1 TCATCTTCATCG
*
13644 TCAGCTTCATC
1 TCATCTTCATC
13655 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
11 10 0.17
12 38 0.64
15 11 0.19
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:13657 original size:6 final size:6
Alignment explanation
Indices: 13570--13657 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
13560 GTTTGGATCA
* * * * * *
13570 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * * *
13621 TCATCA TCA-CG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
13658 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
5 4 0.06
6 52 0.84
8 1 0.02
9 5 0.08
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (6 bp):
TCATCT
Found at i:15472 original size:198 final size:198
Alignment explanation
Indices: 14975--16485 Score: 2577
Period size: 198 Copynumber: 7.7 Consensus size: 198
14965 ATATCGATAA
14975 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
15040 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
15105 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACA
131 GGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACA
15170 CATT
195 CATT
* *
15174 ATTTAGACATATTCTCTCATAAAATCGATATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
*
15239 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATTGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
15304 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
131 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
15369 ATT
196 ATT
* *
15372 ATTTATATATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
*
15437 CATTATTCTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
* *
15502 GGTGTAACCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
131 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
15567 ATT
196 ATT
*
15570 ATTTATACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
*
15635 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATTGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
* *
15700 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGATATAAACTATATTAGTGTCGACA
131 GGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACA
15765 CATT
195 CATT
15769 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
15834 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
15899 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
131 GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
15964 A-T
196 ATT
*
15966 -TTTATACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
* *
16030 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC----T-T-TATGGGT-GCACCCTGTT-
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG-ACACT-TTA
* * *
16087 T---T----CC---ATT-CATTC--T-GGAAAAAAAATATCGACACAAACTATATTAGTGTCGAC
129 TGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGAC
16138 ACATT
194 ACATT
*
16143 ATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
16208 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
66 CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
*
16273 GGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACA
131 GGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACA
16338 CATT
195 CATT
16342 ATTTAGACATATTCTCTCAT-AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
1 ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
* * *
16406 CATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTTTATATATGGATCGACACTTTA
66 CATTATACTTTTGG-GTTCGATGATTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTA
16471 TGGGTGCACCCTGTT
129 TGGGTGCACCCTGTT
16486 GGCCATATTG
Statistics
Matches: 1242, Mismatches: 40, Indels: 59
0.93 0.03 0.04
Matches are distributed among these distances:
176 39 0.03
177 2 0.00
178 100 0.08
179 5 0.00
180 2 0.00
182 1 0.00
183 5 0.00
184 11 0.01
185 1 0.00
187 2 0.00
189 1 0.00
190 11 0.01
191 5 0.00
192 1 0.00
194 2 0.00
195 5 0.00
196 101 0.08
197 2 0.00
198 478 0.38
199 429 0.35
200 39 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (198 bp):
ATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTA
CATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
ATT
Found at i:16203 original size:178 final size:177
Alignment explanation
Indices: 15883--16248 Score: 691
Period size: 178 Copynumber: 2.1 Consensus size: 177
15873 TTTTATATAT
15883 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACT
*
15948 ATATTAGTGTCGACACA-T-TTTATACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
16011 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
16058 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAAC
*
16123 TATATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
65 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
16188 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
130 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
16236 GGATCGACACTTT
1 GGATCGACACTTT
16249 TTATATATGG
Statistics
Matches: 186, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
175 44 0.24
176 38 0.20
177 1 0.01
178 103 0.55
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (177 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACACAAACT
ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
Found at i:16428 original size:199 final size:200
Alignment explanation
Indices: 16058--16482 Score: 782
Period size: 199 Copynumber: 2.1 Consensus size: 200
16048 GATGATTTTG
*
16058 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
16123 TATATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
16188 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
16252 TATAT
196 TATAT
16257 GGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
*
16322 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
* * *
16386 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTTT
131 GATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTT
16451 ATATAT
195 ATATAT
16457 GGATCGACACTTTATGGGTGCACCCT
1 GGATCGACACTTTATGGGTGCACCCT
16483 GTTGGCCATA
Statistics
Matches: 219, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
198 58 0.26
199 124 0.57
200 37 0.17
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (200 bp):
GGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACAAATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
TATAT
Found at i:16635 original size:19 final size:19
Alignment explanation
Indices: 16589--16637 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16579 TCATATTCAC
*
16589 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
16608 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
16627 ATACAAAATTA
1 ATACAAAATTA
16638 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:18467 original size:33 final size:33
Alignment explanation
Indices: 18430--18495 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
18420 CATCTTAATA
*
18430 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
18463 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
18496 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:18568 original size:21 final size:21
Alignment explanation
Indices: 18528--18592 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
18518 CCCCTTATGC
* *
18528 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
18549 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
18570 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
18591 CT
1 CT
18593 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:21009 original size:20 final size:20
Alignment explanation
Indices: 20983--21028 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
20973 CACTTTTAAA
20983 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
21002 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
21023 TTTACC
1 TTTACC
21029 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:26324 original size:2 final size:2
Alignment explanation
Indices: 26317--26361 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
26307 CATCAAACAT
26317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26358 TA TA
1 TA TA
26362 ACAATATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26555 original size:16 final size:16
Alignment explanation
Indices: 26535--26600 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
26525 TTTGATTGAC
*
26535 AATTAAAATATATTTA
1 AATTAAAATAAATTTA
* *
26551 TATTAGAATAAATTTA
1 AATTAAAATAAATTTA
* * **
26567 GA-TATAATGTGATTTA
1 AATTAAAAT-AAATTTA
26583 AATTAAAATAAATTTA
1 AATTAAAATAAATTTA
26599 AA
1 AA
26601 GAAAATGTAC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
15 5 0.14
16 27 0.73
17 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTAAAATAAATTTA
Found at i:26622 original size:32 final size:32
Alignment explanation
Indices: 26546--26623 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
26536 ATTAAAATAT
* * * * *
26546 ATTTATATTAGAATAAATTTAGATATAATGTG
1 ATTTATATTAAAATAAATTTAAAGAAAATGTC
*
26578 ATTTAAATTAAAATAAATTTAAAGAAAATGTAC
1 ATTTATATTAAAATAAATTTAAAGAAAATGT-C
26611 ATTTATA-TAAAAT
1 ATTTATATTAAAAT
26624 TAGGAGTCGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 32 0.84
33 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (32 bp):
ATTTATATTAAAATAAATTTAAAGAAAATGTC
Found at i:27117 original size:31 final size:31
Alignment explanation
Indices: 27042--27118 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
27032 AATGATAAAT
* ** * *
27042 TTCAATAAGTTTAAGAATTATTTTGTAATAG
1 TTCAATAAGTTTAATAATTATTTTACAACAA
** *
27073 TTTGATAAATTTAATAATTATTTTACAACAA
1 TTCAATAAGTTTAATAATTATTTTACAACAA
27104 TTCAATAAGTTTAAT
1 TTCAATAAGTTTAAT
27119 GATAATTTGT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
TTCAATAAGTTTAATAATTATTTTACAACAA
Found at i:39151 original size:87 final size:87
Alignment explanation
Indices: 39005--39167 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 87
38995 TATGTTATAT
39005 TATTTAACCGAAAATATTATAAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGAAAATATTATAAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
39070 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * * *
39092 TATTTAACCTG-AAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
1 TATTTAACC-GAAAATATTATAAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
39156 TAGCGCTTATAT
65 TAGCGCTTATAT
39168 TGACCTATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 70 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCGAAAATATTATAAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:39610 original size:182 final size:182
Alignment explanation
Indices: 39303--40324 Score: 1750
Period size: 182 Copynumber: 5.6 Consensus size: 182
39293 TGCGTTCACC
** * *
39303 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
39368 TTTATAAAGTATCGGCACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
39432 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
** * *
39485 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTATTTGTTATACTGTTATGGATCGATTCATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
39550 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
39615 TACTTATAATAAATTATCGACACTTTCAAAATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
39667 TTTTTTCATTTCGAGACCGGTTTTGTCATATTATTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
39732 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
39797 TACTTATAATAAATTATCGATACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
39849 TTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
39914 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
39976 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
40029 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
40094 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* * *
40158 TACGTATAATAAATTA-CTGACACTTTCAACATAACCGGTAGCGTTTTACATG
131 TACTTATAATAAATTATC-GACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
40210 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
40275 TTTATAAAGTATCGACACTTTATTGACGATATAACTTCTTATCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
40325 AAAGGTAAAA
Statistics
Matches: 797, Mismatches: 36, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
178 2 0.00
179 19 0.02
180 155 0.19
181 150 0.19
182 469 0.59
183 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:43344 original size:184 final size:184
Alignment explanation
Indices: 43027--43375 Score: 621
Period size: 184 Copynumber: 1.9 Consensus size: 184
43017 GCGTTACTTA
43027 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAATCGG
1 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAATCGG
* *
43092 TATATTTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTGTGGGTTCCGATGTTTTT
66 TATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
43157 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
131 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
*
43211 AAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCTCTCATAAAA-CA
1 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAATC-
* *
43274 GGTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGTTGTTT
64 GGTATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTT
43339 TTTCAATCGACACTTTTTGAAAAGGTATCGACACTTT
129 TTTCAATCGACACTTTTTGAAAAGGTATCGACACTTT
43376 ATGTTGATAT
Statistics
Matches: 158, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
183 2 0.01
184 156 0.99
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (184 bp):
AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAATCGG
TATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
Found at i:44682 original size:12 final size:12
Alignment explanation
Indices: 44661--44700 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
44651 GTTTGGATCA
*
44661 TCATCATCATCG
1 TCATCTTCATCG
44673 TCATCTTCATCG
1 TCATCTTCATCG
* *
44685 TCAGCTTCATCT
1 TCATCTTCATCG
44697 TCAT
1 TCAT
44701 TGACCGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:46744 original size:28 final size:28
Alignment explanation
Indices: 46713--46768 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
46703 CCCATTTATC
*
46713 ATTTTAAAACACACTTAAAACACACACT
1 ATTTTAAAACACACTTAAAACAAACACT
46741 ATTTTAAAACACACTTAAAACAAACACT
1 ATTTTAAAACACACTTAAAACAAACACT
46769 TCTCCCCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (28 bp):
ATTTTAAAACACACTTAAAACAAACACT
Found at i:55596 original size:17 final size:18
Alignment explanation
Indices: 55574--55631 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 18
55564 TTTTGGTGCA
*
55574 GAGGGAATCGA-TCCCCC
1 GAGGGAACCGATTCCCCC
55591 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATTCCCCC
55609 TTTGAAGGGGAACCGATTCCCCC
1 ---G-A-GGGAACCGATTCCCCC
55632 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 10 0.29
18 6 0.18
21 1 0.03
22 1 0.03
23 16 0.47
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (18 bp):
GAGGGAACCGATTCCCCC
Found at i:55657 original size:19 final size:20
Alignment explanation
Indices: 55614--55651 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55604 CCCCCTTTGA
*
55614 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
55634 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
55652 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:65689 original size:200 final size:200
Alignment explanation
Indices: 65346--65933 Score: 1095
Period size: 200 Copynumber: 2.9 Consensus size: 200
65336 GATATTTAAA
65346 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
65411 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
65476 TAGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
65541 GGACC
196 GGACC
65546 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
*
65611 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
* * **
65676 TGGGATCGACACCTTTTATATATGGATCGACACTTTATTGTTACACGTTGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
65741 GGACC
196 GGACC
*
65746 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
*
65811 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATAGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
65876 TGGGATTGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
65934 ATTGTAAATT
Statistics
Matches: 374, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 374 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (200 bp):
AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
GGACC
Found at i:66192 original size:19 final size:19
Alignment explanation
Indices: 66168--66216 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
66158 TTACATTCAC
66168 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
66187 ATACAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
*
66206 ATGCAAAATTA
1 ATACAAAATTA
66217 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:67819 original size:33 final size:33
Alignment explanation
Indices: 67767--67854 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
67757 ATGACATCGA
*
67767 CTTCCTTCCT-CCTCATTTCTTCAATCTCTTCTT
1 CTTCC-TCCTCCCTCTTTTCTTCAATCTCTTCTT
*
67800 CTTCCTCCTCCCTCTTTTCTTCCATCTCTTCTT
1 CTTCCTCCTCCCTCTTTTCTTCAATCTCTTCTT
67833 CTTCCTCCTCCCTCTTTTCTTC
1 CTTCCTCCTCCCTCTTTTCTTC
67855 TTCATATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 4 0.08
33 48 0.92
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (33 bp):
CTTCCTCCTCCCTCTTTTCTTCAATCTCTTCTT
Found at i:68078 original size:33 final size:33
Alignment explanation
Indices: 68041--68106 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
68031 CATCTTAAGA
*
68041 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
68074 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
68107 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:70851 original size:182 final size:179
Alignment explanation
Indices: 70419--70852 Score: 573
Period size: 182 Copynumber: 2.4 Consensus size: 179
70409 GATATCATTT
* *
70419 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATC
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTT--TGGATC
*
70484 GACACTTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAG
63 GACACTTTATAGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAG
** * * * * * **
70549 TTTCGATACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATTATTTTGA
128 TACCGACACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAA
* *
70601 TACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATATA-TTTTTTTGAAAGTAT
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTTTG---G-AT
* *
70665 CGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATTAA
62 CGACACTTTATAGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-TAA
* *
70730 AGTACCGACACTTTAAATATATTCGGTACCGCTTTACCGGTTTTATCATTTCAA
126 AGTACCGACACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAA
* * * *
70784 TACTGGTTTTGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTAATTTGGATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTT--TTTGGATCG
70849 ACAC
64 ACAC
70853 GAACCGACAA
Statistics
Matches: 220, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
178 1 0.00
180 6 0.03
181 11 0.05
182 104 0.47
183 90 0.41
184 4 0.02
186 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (179 bp):
TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTTTGGATCGAC
ACTTTATAGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGTAC
CGACACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAA
Found at i:71007 original size:11 final size:11
Alignment explanation
Indices: 70991--71015 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
70981 ATTCAGTAAC
70991 ACCGTATATTA
1 ACCGTATATTA
71002 ACCGTATATTA
1 ACCGTATATTA
71013 ACC
1 ACC
71016 CGCCGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:72275 original size:20 final size:20
Alignment explanation
Indices: 72250--72359 Score: 114
Period size: 20 Copynumber: 5.4 Consensus size: 20
72240 TGCATTTGGA
* *
72250 GTTGCGATTTTCCAGTTCGT
1 GTTGCGATTTTCCATTTCGC
72270 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* * *
72290 GTTGCTATTTTTCATTTTGC
1 GTTGCGATTTTCCATTTCGC
* * *
72310 GTTGCGATAATCTACAGTT-GTC
1 GTTGCGAT--TTTCCATTTCG-C
72332 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
72352 GTTGCGAT
1 GTTGCGAT
72360 AGTCTACAGT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
20 57 0.77
21 2 0.03
22 15 0.20
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:72337 original size:22 final size:21
Alignment explanation
Indices: 72309--72436 Score: 104
Period size: 22 Copynumber: 6.0 Consensus size: 21
72299 TTTCATTTTG
72309 CGTTGCGATAATCTACAGTTGT
1 CGTTGCGAT-ATCTACAGTTGT
* * *
72331 CGTTGCGAT-TTTCCATTTCG-
1 CGTTGCGATATCTACAGTT-GT
72351 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
* * *
72373 CGTTGCGAT-TTTTCAAATT-T
1 CGTTGCGATATCTAC-AGTTGT
72393 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
*
72414 TGTTGCGATAATCTACAGTTGT
1 CGTTGCGAT-ATCTACAGTTGT
72436 C
1 C
72437 AAAATTCTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
19 8 0.10
20 22 0.27
21 9 0.11
22 43 0.52
23 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (21 bp):
CGTTGCGATATCTACAGTTGT
Found at i:72342 original size:42 final size:42
Alignment explanation
Indices: 72289--72422 Score: 191
Period size: 42 Copynumber: 3.2 Consensus size: 42
72279 TTCCATTTCG
* *
72289 CGTTGCTATTTTTCATTTTGCGTTGCGATAATCTACAGTTGT
1 CGTTGCGATTTTTCATTTTGCGTTGCGATAGTCTACAGTTGT
* *
72331 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTTCATTTTGCGTTGCGATAGTCTACAGTTGT
*
72373 CGTTGCGATTTTTCAAATTT--GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTTC-ATTTTGCGTTGCGATAGTCTACAGTTGT
*
72414 TGTTGCGAT
1 CGTTGCGAT
72423 AATCTACAGT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 29 0.35
42 51 0.61
43 3 0.04
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.44
Consensus pattern (42 bp):
CGTTGCGATTTTTCATTTTGCGTTGCGATAGTCTACAGTTGT
Found at i:72409 original size:41 final size:41
Alignment explanation
Indices: 72289--72422 Score: 173
Period size: 41 Copynumber: 3.2 Consensus size: 41
72279 TTCCATTTCG
* * *
72289 CGTTGCTATTTTTCATTTTGCGTTGCGATAATCTACAGTTGT
1 CGTTGCGATTTTTCAATTT-CGTTGCGATAGTCTACAGTTGT
*
72331 CGTTGCGA-TTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTTCAATTT--CGTTGCGATAGTCTACAGTTGT
72373 CGTTGCGATTTTTCAAATTT-GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTTC-AATTTCGTTGCGATAGTCTACAGTTGT
*
72414 TGTTGCGAT
1 CGTTGCGAT
72423 AATCTACAGT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
41 37 0.45
42 37 0.45
43 5 0.06
44 4 0.05
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.44
Consensus pattern (41 bp):
CGTTGCGATTTTTCAATTTCGTTGCGATAGTCTACAGTTGT
Found at i:72529 original size:6 final size:6
Alignment explanation
Indices: 72518--72561 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
72508 GACACGTATT
72518 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
72562 CGAGACGGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:72743 original size:20 final size:20
Alignment explanation
Indices: 72718--72760 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
72708 CCAATACTAT
72718 GTGGGATTGAGCCTTAAATA
1 GTGGGATTGAGCCTTAAATA
72738 GTGGGATTGAGCCTTAAATA
1 GTGGGATTGAGCCTTAAATA
72758 GTG
1 GTG
72761 ATATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (20 bp):
GTGGGATTGAGCCTTAAATA
Found at i:73232 original size:22 final size:22
Alignment explanation
Indices: 73204--73256 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
73194 AATTTGGAAA
73204 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
73226 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
73248 ATCGCAACG
1 ATCGCAACG
73257 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:73273 original size:20 final size:20
Alignment explanation
Indices: 73248--73320 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
73238 ACTGTAGACT
73248 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
73268 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
73289 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
73309 CTCGCAACGCGA
1 ATCGCAACGCGA
73321 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:73294 original size:21 final size:21
Alignment explanation
Indices: 73268--73341 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
73258 GAAATGGAAA
73268 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** **
73289 ATCGCAACGCGAAATGGAA--
1 ATCGCAACGCGATTTTCAACT
73308 ACTCGCAACGCGATTTTCAACT
1 A-TCGCAACGCGATTTTCAACT
73330 ATCGCAACGCGA
1 ATCGCAACGCGA
73342 ATTTGCGATA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 26 0.62
22 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:73294 original size:41 final size:41
Alignment explanation
Indices: 73245--73342 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
73235 ACAACTGTAG
73245 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
73286 ACTATCGCAACGCGAAATGGAAACTCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
73327 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
73343 TTTGCGATAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:75569 original size:21 final size:23
Alignment explanation
Indices: 75530--75572 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
75520 ATAATCTATG
*
75530 TTATATAATAATTTTAAAAAATC
1 TTATATAATAATTTAAAAAAATC
75553 TTAT-TAAT-ATTTAAAAAAAT
1 TTATATAATAATTTAAAAAAAT
75573 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 4 0.21
23 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATATAATAATTTAAAAAAATC
Found at i:75578 original size:20 final size:22
Alignment explanation
Indices: 75535--75579 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
75525 CTATGTTATA
* *
75535 TAATAATTTTAAAAAATCTTAT
1 TAATAATTTAAAAAAATCTAAT
75557 TAAT-ATTTAAAAAAAT-TAAT
1 TAATAATTTAAAAAAATCTAAT
75577 TAA
1 TAA
75580 AATATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATTTAAAAAAATCTAAT
Found at i:103375 original size:31 final size:30
Alignment explanation
Indices: 103323--103413 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 30
103313 AGTTAATTTT
* *
103323 TAATTTGACC-ATTGAAGTTTAGATAAAATCC
1 TAATTTGACCTA-TAAACTTTAGATAAAAT-C
*
103354 TAATTTGACCTATAAATTTTAGATATAATATC
1 TAATTTGACCTATAAACTTTAGATA-AA-ATC
*
103386 T-ATTTAACTCT-TAAACTTTAGATAAAAT
1 TAATTTGAC-CTATAAACTTTAGATAAAAT
103414 ATCAATTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
29 2 0.04
30 2 0.04
31 39 0.75
32 7 0.13
33 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (30 bp):
TAATTTGACCTATAAACTTTAGATAAAATC
Found at i:103415 original size:31 final size:31
Alignment explanation
Indices: 103340--103423 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
103330 ACCATTGAAG
* * *
103340 TTTAGATAAAAT-CCTAATTTGACCTATAAAT
1 TTTAGATAAAATATCT-ATTTAACCTATAAAC
*
103371 TTTAGATATAATATCTATTTAACTCT-TAAAC
1 TTTAGATAAAATATCTATTTAAC-CTATAAAC
*
103402 TTTAGATAAAATATCAATTTAA
1 TTTAGATAAAATATCTATTTAA
103424 TCCCTAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 41 0.91
32 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (31 bp):
TTTAGATAAAATATCTATTTAACCTATAAAC
Found at i:104282 original size:31 final size:31
Alignment explanation
Indices: 104247--104307 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
104237 AGTTTAGATA
*
104247 TTTTATCTAAAGTTTAG-GAGTTACATTAAAT
1 TTTTATCTAAAGTTTAGAGA-TTAAATTAAAT
* *
104278 TTTTATCTCAATTTTAGAGATTAAATTAAA
1 TTTTATCTAAAGTTTAGAGATTAAATTAAA
104308 AAATTAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (31 bp):
TTTTATCTAAAGTTTAGAGATTAAATTAAAT
Found at i:107510 original size:32 final size:32
Alignment explanation
Indices: 107464--107542 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 32
107454 GCCTTGTTCG
**
107464 TTCATTTACATTCGTGAACGTTCGATAATCCA
1 TTCATTTATGTTCGTGAACGTTCGATAATCCA
*** * *
107496 TTCATTTATGTTCGTTTTCGTTCGGTAATTCA
1 TTCATTTATGTTCGTGAACGTTCGATAATCCA
*
107528 CTCATTTATGTTCGT
1 TTCATTTATGTTCGT
107543 TTGTTTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (32 bp):
TTCATTTATGTTCGTGAACGTTCGATAATCCA
Found at i:107543 original size:32 final size:32
Alignment explanation
Indices: 107482--107544 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
107472 CATTCGTGAA
*
107482 CGTTCGATAATCCATTCATTTATGTTCGTTTT
1 CGTTCGATAATCCACTCATTTATGTTCGTTTT
* *
107514 CGTTCGGTAATTCACTCATTTATGTTCGTTT
1 CGTTCGATAATCCACTCATTTATGTTCGTTT
107545 GTTTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.49
Consensus pattern (32 bp):
CGTTCGATAATCCACTCATTTATGTTCGTTTT
Found at i:113398 original size:29 final size:30
Alignment explanation
Indices: 113366--113439 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
113356 TGATTAAGAT
113366 TAAAAAAATATTTTAAG-TACACATTTTAA
1 TAAAAAAATATTTTAAGATACACATTTTAA
** *
113395 TAAAAAAA-ATCTTT-AGATACTTATTTTGA
1 TAAAAAAATAT-TTTAAGATACACATTTTAA
113424 TAAAAAAATATTTTAA
1 TAAAAAAATATTTTAA
113440 ACATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.11
29 31 0.82
30 3 0.08
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.39
Consensus pattern (30 bp):
TAAAAAAATATTTTAAGATACACATTTTAA
Found at i:115763 original size:30 final size:30
Alignment explanation
Indices: 115683--115765 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
115673 ATAAGGAATG
*
115683 ATATGAACATGTGATATGTGAACATAAGAGA
1 ATATG-ACATGAGATATGTGAACATAAGAGA
* * * * *
115714 TTAAGTGATATGAGCTATGTGACCATATGAGA
1 AT-A-TGACATGAGATATGTGAACATAAGAGA
115746 ATATGACATGAGATATGTGA
1 ATATGACATGAGATATGTGA
115766 TATGTGAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 15 0.37
31 2 0.05
32 22 0.54
33 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
ATATGACATGAGATATGTGAACATAAGAGA
Found at i:116029 original size:18 final size:18
Alignment explanation
Indices: 116006--116040 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
115996 GTTCTTAAGG
*
116006 AGTGGTCCTTCGGGACAT
1 AGTGGTCCATCGGGACAT
116024 AGTGGTCCATCGGGACA
1 AGTGGTCCATCGGGACA
116041 AATTTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCATCGGGACAT
Found at i:116826 original size:32 final size:32
Alignment explanation
Indices: 116794--116916 Score: 88
Period size: 32 Copynumber: 3.8 Consensus size: 32
116784 ATATATATAT
* *
116794 ATATCATATCATCATCTTAAGTGACGTAATAT
1 ATATTATATCATCATCTTAAGTGACGTAATAC
* * * * * * *
116826 ATGTTATCTTATCAT-TATAAGTTATGTAGTGC
1 ATATTATATCATCATCT-TAAGTGACGTAATAC
* * * *
116858 ATATTACATCATTATCTTAAGTGAAGTATTAC
1 ATATTATATCATCATCTTAAGTGACGTAATAC
*
116890 ATATAATATCATCA-CGTTAAGTGACGT
1 ATATTATATCATCATC-TTAAGTGACGT
116917 GACATGTATC
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
31 2 0.03
32 63 0.95
33 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (32 bp):
ATATTATATCATCATCTTAAGTGACGTAATAC
Found at i:117600 original size:2 final size:2
Alignment explanation
Indices: 117593--117624 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
117583 TAAATGTAAT
117593 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117625 TTGAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:118387 original size:19 final size:19
Alignment explanation
Indices: 118352--118388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
118342 ATGACCAACA
* *
118352 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCAATCTCT
118371 AAATCGCAACGCAATCTC
1 AAATCGCAACGCAATCTC
118389 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCT
Found at i:118451 original size:21 final size:21
Alignment explanation
Indices: 118421--118486 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
118411 GATTCGCAAC
*
118421 GCGA-TTTTGATCATCGCATT
1 GCGATTTTTGATAATCGCATT
*
118441 GCGATTTTTGA-AATCCGCGTT
1 GCGATTTTTGATAAT-CGCATT
* *
118462 GCGATTTTAGATAATCGCAAT
1 GCGATTTTTGATAATCGCATT
118483 GCGA
1 GCGA
118487 ATATGTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 29 0.76
22 3 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
GCGATTTTTGATAATCGCATT
Found at i:118541 original size:20 final size:20
Alignment explanation
Indices: 118516--118588 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
118506 ATAACACGTG
118516 ATCACAACGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
118536 ATCACAACGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
* *
118556 ATCGCAACGAGATTCTGACT
1 ATCACAACGCGATTCTGACT
*
118576 ATCGCAACGCGAT
1 ATCACAACGCGAT
118589 AATACGTGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCACAACGCGATTCTGACT
Found at i:118642 original size:81 final size:81
Alignment explanation
Indices: 118495--118644 Score: 178
Period size: 81 Copynumber: 1.9 Consensus size: 81
118485 GAATATGTAA
* ** * *
118495 ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACTATCACAACGCGATTCTGACTATCG
1 ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACTAACACAACGAAATTCTCAATATCG
118560 CAACGAGATTCTGACT
66 CAACGAGATTCTGACT
* * * * *
118576 ATCGCAACGCGATAATACGTGATCGCAACGCGATTTTGACTAACGCATCACTAAATT-TCAAT-T
1 ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACTAACACA--ACGAAATTCTCAATAT
118639 CGCAAC
64 CGCAAC
118645 AGGTTTTAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
81 49 0.86
82 3 0.05
83 5 0.09
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (81 bp):
ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACTAACACAACGAAATTCTCAATATCG
CAACGAGATTCTGACT
Found at i:121671 original size:18 final size:18
Alignment explanation
Indices: 121648--121682 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
121638 AGCAAAAGGC
121648 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
121666 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
121683 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:121908 original size:20 final size:20
Alignment explanation
Indices: 121858--122113 Score: 187
Period size: 20 Copynumber: 13.8 Consensus size: 20
121848 TTACACATTC
121858 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
121878 A--TGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
121896 ATTTGAATATCGCAACG-GG
1 ATTTGACTATCGCAACGCGA
*
121915 A--T-A--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
**
121930 AAATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
121950 ATTTGACTATCGCAACGAG-
1 ATTTGACTATCGCAACGCGA
* *
121969 A--T-A--ATCGCAATGCAA
1 ATTTGACTATCGCAACGCGA
**
121984 AAATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
122004 AAATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
122024 ATTTGACTATCGC-AC-TG-
1 ATTTGACTATCGCAACGCGA
122041 A---GA-TAATCGCAACGCGA
1 ATTTGACT-ATCGCAACGCGA
*
122058 A-ATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
122077 ATTTGATTATCGTAACGGGA
1 ATTTGACTATCGCAACGCGA
122097 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
122114 AGAAAATCGC
Statistics
Matches: 190, Mismatches: 24, Indels: 44
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.01
14 23 0.12
15 5 0.03
16 3 0.02
17 6 0.03
18 20 0.11
19 20 0.11
20 112 0.59
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:121946 original size:54 final size:54
Alignment explanation
Indices: 121877--122020 Score: 234
Period size: 54 Copynumber: 2.7 Consensus size: 54
121867 TCGCAACGCG
* * * *
121877 AATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATAATCGCAATGCGAA
1 AATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCAAA
121931 AATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCAAA
1 AATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCAAA
**
121985 AATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 AATGACTATCGCAACGCGAATTTGACTATCGCAACG
122021 CGAATTTGAC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (54 bp):
AATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCAAA
Found at i:121976 original size:34 final size:34
Alignment explanation
Indices: 121938--122147 Score: 163
Period size: 34 Copynumber: 5.9 Consensus size: 34
121928 GAAAATGACT
121938 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
* * ** *
121972 ATCGCAATGCAAAAATGACTATCGCAACGCGAAAATGA
1 ATCGCAACGCGAATTTGACTATCGCAA--CG-AGAT-A
122010 CTATCGCAACGCGAATTTGACTATCGC-ACTGAGATA
1 --ATCGCAACGCGAATTTGACTATCGCAAC-GAGATA
* *
122046 ATCGCAACGCGAA-ATGACTATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAA--CG-A---GATA
* * *
122085 ATCGTAACGGGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
* * * *
122119 ATCGCAAAGTGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
122148 CGAATATGAT
Statistics
Matches: 139, Mismatches: 22, Indels: 30
0.73 0.12 0.16
Matches are distributed among these distances:
33 10 0.07
34 63 0.45
35 1 0.01
36 5 0.04
37 8 0.06
38 4 0.03
39 15 0.11
40 33 0.24
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGATA
Found at i:121996 original size:74 final size:73
Alignment explanation
Indices: 121918--122125 Score: 310
Period size: 73 Copynumber: 2.8 Consensus size: 73
121908 CAACGGGATA
* *
121918 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCA
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAACGC-
121983 AAAATGACT
65 AAAATGACT
121992 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC-ACTGAGATAATCGCAACGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAAC-GAGATAATCGCAACGC
*
122056 GAAATGACT
65 AAAATGACT
** * * * *
122065 ATCGCAACGCGAATTTGATTATCGTAACGGGAATTTGACTATCGCAACGAGAAAATCGCAA
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAA
122126 AGTGTATTAG
Statistics
Matches: 123, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
73 62 0.50
74 61 0.50
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (73 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAACGCA
AAATGACT
Found at i:122280 original size:36 final size:34
Alignment explanation
Indices: 122239--122314 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 34
122229 ATAAACTTTA
*
122239 ATCAATTAAATAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAATAA--ACAAATAAGAATTATTTACAC
122275 ATCAA-T---TAAACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAACAAATAAGAATTATTTACAC
122305 ATCAATTAAA
1 ATCAATTAAA
122315 CAAATCAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
30 25 0.71
31 1 0.03
32 3 0.09
35 1 0.03
36 5 0.14
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (34 bp):
ATCAATTAAATAAACAAATAAGAATTATTTACAC
Found at i:122288 original size:30 final size:30
Alignment explanation
Indices: 122254--122319 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
122244 TTAAATAAGC
*
122254 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
122284 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
122314 ACAAAT
1 ACAAAT
122320 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:123598 original size:21 final size:21
Alignment explanation
Indices: 123572--123613 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
123562 GGTACTGGCC
123572 GGTAACTTATACGAAAGCCAA
1 GGTAACTTATACGAAAGCCAA
123593 GGTAACTTATACGAAAGCCAA
1 GGTAACTTATACGAAAGCCAA
123614 CGTCATCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
GGTAACTTATACGAAAGCCAA
Found at i:123734 original size:21 final size:21
Alignment explanation
Indices: 123704--123803 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 21
123694 TTGGGAGAGA
*
123704 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGGC
* * *
123725 CTCTTGAACGGTG--GGGGGA
1 CTCTTGAACGATGACAGGGGC
** * *
123744 CTCTTGAGGGATGATAGAGGC
1 CTCTTGAACGATGACAGGGGC
* *
123765 CTCTTGAACGAT-AGGAGAGGC
1 CTCTTGAACGATGA-CAGGGGC
123786 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
123804 TGAGTTGGGC
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
19 14 0.23
20 1 0.02
21 44 0.73
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGGC
Found at i:124299 original size:20 final size:20
Alignment explanation
Indices: 124274--124314 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
124264 AATAGTTTCT
124274 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
124294 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
124314 G
1 G
124315 GAAATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:124327 original size:20 final size:19
Alignment explanation
Indices: 124284--124409 Score: 90
Period size: 20 Copynumber: 6.4 Consensus size: 19
124274 GAAACTTAAA
* **
124284 ATCGCAACACGAAACTTAAA
1 ATCGCAACACGAAA-TGATT
124304 ATCGCAACACGGAAATGATT
1 ATCGCAACAC-GAAATGATT
*
124324 ATCGCAACGCGAAATGATT
1 ATCGCAACACGAAATGATT
** * *
124343 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAA-ATGATT
* * *
124363 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA-ATGATT
* *
124383 ATCGCAACGCGAAATGACT
1 ATCGCAACACGAAATGATT
*
124402 ATCACAAC
1 ATCGCAAC
124410 GAGAAAATCG
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
19 33 0.35
20 57 0.61
21 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (19 bp):
ATCGCAACACGAAATGATT
Found at i:124366 original size:39 final size:38
Alignment explanation
Indices: 124304--124415 Score: 125
Period size: 39 Copynumber: 2.9 Consensus size: 38
124294 GAAACTTAAA
* * *
124304 ATCGCAACACGGAAATGATTATCGCAACGCGAAATGATT
1 ATCGCAACGC-GAAATGACTATCGCAACGCGAAATGACT
* * *
124343 ATCGCAATGCGAATTTGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACTATCGCAACGCGAA-ATGACT
* *
124383 ATCGCAACGCGAAATGACTATCACAACGAGAAA
1 ATCGCAACGCGAAATGACTATCGCAACGCGAAA
124416 ATCGCAACGC
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
38 3 0.05
39 41 0.68
40 16 0.27
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (38 bp):
ATCGCAACGCGAAATGACTATCGCAACGCGAAATGACT
Done.