Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 128 of 144
Found at i:31457594 original size:17 final size:17
Alignment explanation
Indices: 31457553--31457615 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
31457543 TTTTAAATGT
31457553 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
* *
31457570 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
31457586 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
31457603 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
31457616 TCTAAGTTGG
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:31458361 original size:3 final size:3
Alignment explanation
Indices: 31458355--31458381 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31458345 ATAATAATAA
31458355 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
31458382 CCACGACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31462475 original size:6 final size:7
Alignment explanation
Indices: 31462464--31462500 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
31462454 ATTATATATA
31462464 AAATTT-
1 AAATTTG
31462470 AAATTTG
1 AAATTTG
31462477 AAATTTG
1 AAATTTG
*
31462484 AAATTTA
1 AAATTTG
31462491 AAATTT-
1 AAATTTG
31462497 AAAT
1 AAAT
31462501 ATATGTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (7 bp):
AAATTTG
Found at i:31462665 original size:20 final size:20
Alignment explanation
Indices: 31462642--31462679 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31462632 AATTCAATAA
*
31462642 TTTCTTTAAAATTTCAAAGT
1 TTTCTTTAAAAATTCAAAGT
31462662 TTTCTTTAAAAATTCAAA
1 TTTCTTTAAAAATTCAAA
31462680 TTTCAATAAA
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:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTCTTTAAAAATTCAAAGT
Found at i:31463175 original size:2 final size:2
Alignment explanation
Indices: 31463168--31463202 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31463158 ACAAAATAGC
31463168 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 T
31463203 TACTGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31465316 original size:31 final size:31
Alignment explanation
Indices: 31465279--31465343 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
31465269 CCATATTAGT
* *
31465279 TTTTAATTTTTAA-AATATCTAT-ATTGTTTTA
1 TTTTAATATTTAATAAT-TCAATAATT-TTTTA
31465310 TTTTAATATTTAATAATTCAATAATTTTTTA
1 TTTTAATATTTAATAATTCAATAATTTTTTA
31465341 TTT
1 TTT
31465344 ATTGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTAATATTTAATAATTCAATAATTTTTTA
Found at i:31474010 original size:3 final size:3
Alignment explanation
Indices: 31474002--31474034 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
31473992 TGGATGGCCA
31474002 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31474035 CTTCAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31479807 original size:14 final size:14
Alignment explanation
Indices: 31479788--31479817 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31479778 GAATAGATTT
31479788 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
31479802 TTAATTAATTAAAA
1 TTAATTAAATAAAA
31479816 TT
1 TT
31479818 TTTAAATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:31487277 original size:6 final size:6
Alignment explanation
Indices: 31487266--31487292 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31487256 TATAATTTGA
31487266 TTAATT TTAATT TTAATT TTAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTA
31487293 GGGTTTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:31495235 original size:14 final size:13
Alignment explanation
Indices: 31495216--31495249 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31495206 CCCCCCCCCC
31495216 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
*
31495229 CACAAAAACAAAAA
1 CA-AAAAAAAAAAA
31495243 CAAAAAA
1 CAAAAAA
31495250 CAGTCCTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:31509742 original size:18 final size:19
Alignment explanation
Indices: 31509716--31509751 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31509706 TTAGGCCTTT
31509716 ATTTAATCATTTT-GAAAG
1 ATTTAATCATTTTCGAAAG
*
31509734 ATTTGATCATTTTCGAAA
1 ATTTAATCATTTTCGAAA
31509752 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (19 bp):
ATTTAATCATTTTCGAAAG
Found at i:31511123 original size:21 final size:20
Alignment explanation
Indices: 31511099--31511144 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
31511089 TTGATATACG
*
31511099 AAAATACGAGAATTTGAAAAA
1 AAAATACGAAAATTT-AAAAA
**
31511120 AAAATTGGAAAATTTAAAAA
1 AAAATACGAAAATTTAAAAA
31511140 AAAAT
1 AAAAT
31511145 TCTCGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (20 bp):
AAAATACGAAAATTTAAAAA
Found at i:31514723 original size:15 final size:15
Alignment explanation
Indices: 31514705--31514740 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
31514695 ACCAGACCCT
31514705 GAGAAGAAACCCGAG
1 GAGAAGAAACCCGAG
*
31514720 GAGAAGAAGCCCGAG
1 GAGAAGAAACCCGAG
31514735 GAGAAG
1 GAGAAG
31514741 GGAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.39, T:0.00
Consensus pattern (15 bp):
GAGAAGAAACCCGAG
Found at i:31515500 original size:21 final size:21
Alignment explanation
Indices: 31515476--31515527 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
31515466 TCCGCCTAAA
* *
31515476 AAAGACGACGGCGGTGAGAAG
1 AAAGACGACGGCGGAGAAAAG
31515497 -AA-A-GACGGCGGAGAAAAG
1 AAAGACGACGGCGGAGAAAAG
*
31515515 AAAGACGCCGGCG
1 AAAGACGACGGCG
31515528 CTGATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 3 0.12
21 6 0.24
ACGTcount: A:0.40, C:0.17, G:0.40, T:0.02
Consensus pattern (21 bp):
AAAGACGACGGCGGAGAAAAG
Found at i:31515505 original size:18 final size:18
Alignment explanation
Indices: 31515482--31515521 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31515472 TAAAAAAGAC
* *
31515482 GACGGCGGTGAGAAGAAA
1 GACGGCGGAGAAAAGAAA
31515500 GACGGCGGAGAAAAGAAA
1 GACGGCGGAGAAAAGAAA
31515518 GACG
1 GACG
31515522 CCGGCGCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.42, T:0.03
Consensus pattern (18 bp):
GACGGCGGAGAAAAGAAA
Found at i:31515807 original size:33 final size:33
Alignment explanation
Indices: 31515765--31515839 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
31515755 TGAACATGAG
31515765 TCAAGGGTATATGTCTCATCCTGGGTATGCGAA
1 TCAAGGGTATATGTCTCATCCTGGGTATGCGAA
* *
31515798 TCAAGGGTATATGTCTCATCCTGGTTATGTGAA
1 TCAAGGGTATATGTCTCATCCTGGGTATGCGAA
31515831 TCAAGGGTA
1 TCAAGGGTA
31515840 CATGGTGGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (33 bp):
TCAAGGGTATATGTCTCATCCTGGGTATGCGAA
Found at i:31516160 original size:5 final size:5
Alignment explanation
Indices: 31516150--31516178 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31516140 TGTTGGGACG
31516150 GTTTT GTTTT GTTTT GTTTT GTTTT GTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTT
31516179 CTATAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
GTTTT
Found at i:31524864 original size:103 final size:103
Alignment explanation
Indices: 31524685--31524892 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
31524675 CTACAAGATG
31524685 TAGATCACTTATAAAAAGTTTTTAAATTCTCAATGTGTGTTTGTAGTCTGGACCCACGTGCACCC
1 TAGATCACTTATAAAAAGTTTTTAAATTCTCAATGTGTGTTTGTAGTCTGGACCCACGTGCACCC
31524750 CAATTCAAATTCTGTTTAGTCTAACCCTTAGGGCCAAA
66 CAATTCAAATTCTGTTTAGTCTAACCCTTAGGGCCAAA
31524788 TAGATCACTTATAAAAAGTTTTTAAATTCTCAATGTGTGTTTGTAGTCTGGACCCACGTGCACCC
1 TAGATCACTTATAAAAAGTTTTTAAATTCTCAATGTGTGTTTGTAGTCTGGACCCACGTGCACCC
31524853 CAATTCAAATTCTGTTTAGTCTAACCCTTAGGGCCAAA
66 CAATTCAAATTCTGTTTAGTCTAACCCTTAGGGCCAAA
31524891 TA
1 TA
31524893 TTCAAGGGTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (103 bp):
TAGATCACTTATAAAAAGTTTTTAAATTCTCAATGTGTGTTTGTAGTCTGGACCCACGTGCACCC
CAATTCAAATTCTGTTTAGTCTAACCCTTAGGGCCAAA
Found at i:31579334 original size:82 final size:82
Alignment explanation
Indices: 31579231--31579396 Score: 251
Period size: 82 Copynumber: 2.0 Consensus size: 82
31579221 GAGACCAAAT
* * * **
31579231 TATGTTAGAGATTAAAGTATAAGGATTAAATATCAAATTTAAGCATATTAGATTGATCAAAACTA
1 TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAGAAAGATCAAAACTA
* * *
31579296 AAAGTTAATCATTTTTA
66 AAAATCAATCACTTTTA
*
31579313 TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAGAAAGATCAAAATTA
1 TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAGAAAGATCAAAACTA
31579378 AAAATCAATCACTTTTA
66 AAAATCAATCACTTTTA
31579395 TA
1 TA
31579397 AAATGTAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (82 bp):
TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAGAAAGATCAAAACTA
AAAATCAATCACTTTTA
Found at i:31594526 original size:26 final size:26
Alignment explanation
Indices: 31594494--31594543 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
31594484 AATTTTTTAT
31594494 AATTTTTA-AAA-AATATATAAATTTGG
1 AATTTTTATAAATAAT-T-TAAATTTGG
31594520 AATTTTTATAAATAATTTAAATTT
1 AATTTTTATAAATAATTTAAATTT
31594544 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.68
27 4 0.18
28 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
AATTTTTATAAATAATTTAAATTTGG
Found at i:31596073 original size:20 final size:18
Alignment explanation
Indices: 31596034--31596069 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31596024 CCACCCAAAA
31596034 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
31596052 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
31596070 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:31596295 original size:94 final size:92
Alignment explanation
Indices: 31596142--31596344 Score: 241
Period size: 93 Copynumber: 2.2 Consensus size: 92
31596132 AAAAATATAC
31596142 ATTTAAATTTTTAAATAATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGC
1 ATTTAAATTTTTAAA-AATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGC
*** *
31596207 GTTATTTGATATGGCACCATC-CAAAAA
65 ACCATTTGATATGACACCATCACAAAAA
* * * * * **
31596234 ATTTTAACTTTTTAAAAATAAATAATAAATTATTAAAAA-AATTAAAATTTGTAGGGGAAGTGGT
1 A-TTTAAATTTTTAAAAATAAATAATAAATAAATAAAAAGAA-AAAAAATT-TA-GAAAAGTGGT
31596298 GGCACCATTTGATATGACACCATCACAAAAA
62 GGCACCATTTGATATGACACCATCACAAAAA
31596329 A-TTAAATTTTTAAAAA
1 ATTTAAATTTTTAAAAA
31596345 ATTAAAAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
91 2 0.02
92 28 0.30
93 29 0.31
94 28 0.30
95 7 0.07
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (92 bp):
ATTTAAATTTTTAAAAATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGCA
CCATTTGATATGACACCATCACAAAAA
Found at i:31596345 original size:94 final size:92
Alignment explanation
Indices: 31596142--31596361 Score: 236
Period size: 94 Copynumber: 2.4 Consensus size: 92
31596132 AAAAATATAC
*
31596142 ATTTAAATTTTTAAATAATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGC
1 ATTTAAATTTTTAAAAAATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGC
*** *
31596207 GTTATTTGATATGGCACCATCCAAAAA
66 ACCATTTGATATGACACCATCCAAAAA
* * * * * **
31596234 ATTTTAACTTTTT-AAAAATAAATAATAAATTATTAAAAA-AATTAAAATTTGTAGGGGAAGTGG
1 A-TTTAAATTTTTAAAAAATAAATAATAAATAAATAAAAAGAA-AAAAAATT-TA-GAAAAGTGG
31596297 TGGCACCATTTGATATGACACCATCACAAAAA
62 TGGCACCATTTGATATGACACCATC-CAAAAA
*
31596329 A-TTAAATTTTTAAAAAATTAA-AA-AAAT-AATAAA
1 ATTTAAATTTTTAAAAAATAAATAATAAATAAATAAA
31596362 TCATGGAAAG
Statistics
Matches: 107, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
91 7 0.07
92 34 0.32
93 23 0.21
94 36 0.34
95 7 0.07
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (92 bp):
ATTTAAATTTTTAAAAAATAAATAATAAATAAATAAAAAGAAAAAAAATTTAGAAAAGTGGTGGC
ACCATTTGATATGACACCATCCAAAAA
Found at i:31596828 original size:18 final size:19
Alignment explanation
Indices: 31596805--31596843 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31596795 TACCTTTATT
*
31596805 AATTTAAAATTTTAAA-AA
1 AATTTAAAAGTTTAAATAA
*
31596823 AATTTAAGAGTTTAAATAA
1 AATTTAAAAGTTTAAATAA
31596842 AA
1 AA
31596844 AAAAATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AATTTAAAAGTTTAAATAA
Found at i:31597187 original size:21 final size:22
Alignment explanation
Indices: 31597157--31597198 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31597147 TATTGGTTTG
*
31597157 AAAAAGAAAATTAA-TTATTTC
1 AAAAAGAAAAATAATTTATTTC
*
31597178 AAAAATAAAAATAATTTATTT
1 AAAAAGAAAAATAATTTATTT
31597199 GTGCTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAAGAAAAATAATTTATTTC
Found at i:31598928 original size:30 final size:30
Alignment explanation
Indices: 31598893--31598955 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
31598883 ATAGTCTATA
*
31598893 TTTTTATAATTTTTGAAGAATTAAAT-TAAT
1 TTTTTATAATTTTTG-AGAATAAAATGTAAT
* *
31598923 TTTTTATTATTTTTGAGGATAAAATGTAAT
1 TTTTTATAATTTTTGAGAATAAAATGTAAT
31598953 TTT
1 TTT
31598956 ATCATTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (30 bp):
TTTTTATAATTTTTGAGAATAAAATGTAAT
Found at i:31599647 original size:6 final size:6
Alignment explanation
Indices: 31599636--31599670 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31599626 AGGCAGGCTT
31599636 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC TGCCA
1 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC TGCCA
31599671 GAGATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (6 bp):
TGCCAC
Found at i:31606823 original size:2 final size:2
Alignment explanation
Indices: 31606816--31606859 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
31606806 AGGTTAAACC
31606816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31606858 TA
1 TA
31606860 GGACACAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31612484 original size:16 final size:17
Alignment explanation
Indices: 31612458--31612491 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31612448 CACAAAATTT
*
31612458 TAAATTATAAAATTAAA
1 TAAATTATAAAATAAAA
31612475 TAAA-TATAAAATAAAA
1 TAAATTATAAAATAAAA
31612491 T
1 T
31612492 TTTATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTATAAAATAAAA
Found at i:31617760 original size:5 final size:5
Alignment explanation
Indices: 31617750--31617780 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31617740 ATACGTGTGT
31617750 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
31617781 ACACTTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:31621087 original size:16 final size:16
Alignment explanation
Indices: 31621052--31621081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31621042 TATTCTTTTA
31621052 TATAACAACTATTTCC
1 TATAACAACTATTTCC
31621068 TATAACAA-TATTTC
1 TATAACAACTATTTC
31621082 ATTATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAACAACTATTTCC
Found at i:31621952 original size:19 final size:18
Alignment explanation
Indices: 31621902--31621952 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
31621892 TTGAATTTTA
*
31621902 TTTAATATTTTTATAAAT
1 TTTAATATTTTTACAAAT
31621920 TTTAATATTTTTTACAAAT
1 TTTAATA-TTTTTACAAAT
31621939 TTATAATATTTTTA
1 TT-TAATATTTTTA
31621953 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.23
19 18 0.60
20 5 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATATTTTTACAAAT
Found at i:31622557 original size:3 final size:3
Alignment explanation
Indices: 31622549--31622579 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31622539 CTTCAACTTA
31622549 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
31622580 TATTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31628092 original size:42 final size:42
Alignment explanation
Indices: 31628045--31628129 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
31628035 TCCAAAAAAA
31628045 TCCCACAACCGCCTTACCATTTGATTAATGGATAAATTAATT
1 TCCCACAACCGCCTTACCATTTGATTAATGGATAAATTAATT
31628087 TCCCACAACCGCCTTACCATTTGATTAATGGATAAATTAATT
1 TCCCACAACCGCCTTACCATTTGATTAATGGATAAATTAATT
31628129 T
1 T
31628130 AATTATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (42 bp):
TCCCACAACCGCCTTACCATTTGATTAATGGATAAATTAATT
Found at i:31633393 original size:4 final size:4
Alignment explanation
Indices: 31633384--31633409 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31633374 ATTCCATTGA
31633384 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
31633410 TATCTCTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:31639723 original size:7 final size:7
Alignment explanation
Indices: 31639711--31639735 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31639701 TTATAAAAAG
31639711 AATGGGA
1 AATGGGA
31639718 AATGGGA
1 AATGGGA
31639725 AATGGGA
1 AATGGGA
31639732 AATG
1 AATG
31639736 AGAGAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (7 bp):
AATGGGA
Found at i:31640688 original size:29 final size:28
Alignment explanation
Indices: 31640651--31640705 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
31640641 CCAAATCATC
*
31640651 ATTTATTATTTATATTATT-TTTTAAATGT
1 ATTTATTATATA-ATT-TTGTTTTAAATGT
*
31640680 ATTTGTTATATAATTTTGTTTTAAAT
1 ATTTATTATATAATTTTGTTTTAAAT
31640706 CCTCATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 11 0.48
29 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
ATTTATTATATAATTTTGTTTTAAATGT
Found at i:31641827 original size:21 final size:21
Alignment explanation
Indices: 31641803--31641847 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
31641793 AAAAACTAGG
31641803 AAAA-AAAAACAAAAATATAAA
1 AAAATAAAAAC-AAAATATAAA
*
31641824 AAAATAAAAACTAAATATAAA
1 AAAATAAAAACAAAATATAAA
31641845 AAA
1 AAA
31641848 TTAAGGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAATAAAAACAAAATATAAA
Found at i:31648788 original size:15 final size:15
Alignment explanation
Indices: 31648768--31648801 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31648758 ACCAAGGAAC
* *
31648768 GGAAAGAGAGGAGGA
1 GGAAAGAAAGGAAGA
31648783 GGAAAGAAAGGAAGA
1 GGAAAGAAAGGAAGA
31648798 GGAA
1 GGAA
31648802 TGTGAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGGAAGA
Found at i:31650145 original size:60 final size:60
Alignment explanation
Indices: 31650071--31650242 Score: 215
Period size: 58 Copynumber: 2.9 Consensus size: 60
31650061 TTAATATAAC
* * * *
31650071 ATTTGGTACCTGAACTTGGCCTTTTTTCCTAATTTGATACCTAAACTTTTTTTTGACCAA
1 ATTTGGTACTTGAACTTGACCTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAACCAA
* * *
31650131 ATTTGGTACTTGAACTTGACAC-TTTTTCCTAATTCGGTACTTAAAC--TTTTTTAACCCA
1 ATTTGGTACTTGAACTTGAC-CTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAACCAA
* * * *
31650189 ATTTGGTACTTGAAGTTGACATTTTTTCCTATTTTGGTACCTAAGCTTTTTTTT
1 ATTTGGTACTTGAACTTGACCTTTTTTCCTAATTTGGTACCTAAACTTTTTTTT
31650243 TAGATTCAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 49 0.52
60 45 0.47
61 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGACCTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAACCAA
Found at i:31650226 original size:31 final size:30
Alignment explanation
Indices: 31650130--31650228 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
31650120 TTTTTGACCA
*
31650130 AATTTGGTACTTGAACTTGACACTTTTTCCT
1 AATTTGGTACTTGAA-TTGACATTTTTTCCT
* *
31650161 AATTCGGTACTT-AA---AC-TTTTTTAACCC
1 AATTTGGTACTTGAATTGACATTTTTT--CCT
31650188 AATTTGGTACTTGAAGTTGACATTTTTTCCT
1 AATTTGGTACTTGAA-TTGACATTTTTTCCT
*
31650219 ATTTTGGTAC
1 AATTTGGTAC
31650229 CTAAGCTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
25 5 0.09
26 2 0.04
27 13 0.24
28 2 0.04
30 2 0.04
31 22 0.41
32 2 0.04
33 6 0.11
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.45
Consensus pattern (30 bp):
AATTTGGTACTTGAATTGACATTTTTTCCT
Found at i:31652591 original size:11 final size:11
Alignment explanation
Indices: 31652575--31652599 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31652565 ATAAAAAGGC
31652575 AACTTATAAGA
1 AACTTATAAGA
31652586 AACTTATAAGA
1 AACTTATAAGA
31652597 AAC
1 AAC
31652600 AAGGAAAAAT
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
AACTTATAAGA
Found at i:31660065 original size:21 final size:22
Alignment explanation
Indices: 31660034--31660074 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
31660024 CGACCCGACC
31660034 TAAATAAATTA-ATTATTTTTAA
1 TAAATAAATTATA-TATTTTTAA
31660056 TAAA-AAATTATATATTTTT
1 TAAATAAATTATATATTTTT
31660075 TAGTGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATAAATTATATATTTTTAA
Found at i:31660109 original size:22 final size:22
Alignment explanation
Indices: 31660084--31660154 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
31660074 TTAGTGTTAT
31660084 TTTTTTACTATTTTGGTTGCTG
1 TTTTTTACTATTTTGGTTGCTG
**
31660106 TTTTTTGGTATTTTGGTAT--TG
1 TTTTTTACTATTTTGGT-TGCTG
*
31660127 TTTTTTACTATTTT-GATGCTG
1 TTTTTTACTATTTTGGTTGCTG
31660148 CTTTTTT
1 -TTTTTT
31660155 TTTACTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 16 0.40
22 21 0.52
23 1 0.03
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.66
Consensus pattern (22 bp):
TTTTTTACTATTTTGGTTGCTG
Found at i:31660152 original size:21 final size:21
Alignment explanation
Indices: 31660084--31660201 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 21
31660074 TTAGTGTTAT
*
31660084 TTTTTTACTATTTTGGTTGCTG
1 TTTTTTACTATTTT-GATGCTG
** * **
31660106 TTTTTTGGTATTTTGGTATTG
1 TTTTTTACTATTTTGATGCTG
31660127 TTTTTTACTATTTTGATGCTG
1 TTTTTTACTATTTTGATGCTG
* *
31660148 CTTTTTTTTTACTGTTTTGATGTTG
1 ----TTTTTTACTATTTTGATGCTG
* *
31660173 TTTTTGTTATTATTTTTATTGCTG
1 -TTTT-TTACTATTTTGA-TGCTG
31660197 TTTTT
1 TTTTT
31660202 GTTGTTATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
21 20 0.27
22 18 0.24
23 13 0.18
24 4 0.05
25 19 0.26
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (21 bp):
TTTTTTACTATTTTGATGCTG
Found at i:31660158 original size:25 final size:24
Alignment explanation
Indices: 31660127--31660201 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 24
31660117 TTTGGTATTG
31660127 TTTTTTACTATTTTGATGCTGCTTT
1 TTTTTTACTATTTTGATGCTG-TTT
* *
31660152 TTTTTTACTGTTTTGATGTTG-TT
1 TTTTTTACTATTTTGATGCTGTTT
* * *
31660175 TTTGTTATTATTTTTATTGCTGTTT
1 TTTTTTACTATTTTGA-TGCTGTTT
31660200 TT
1 TT
31660202 GTTGTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 14 0.34
24 4 0.10
25 23 0.56
ACGTcount: A:0.11, C:0.07, G:0.13, T:0.69
Consensus pattern (24 bp):
TTTTTTACTATTTTGATGCTGTTT
Found at i:31660212 original size:11 final size:12
Alignment explanation
Indices: 31660162--31660252 Score: 69
Period size: 12 Copynumber: 7.7 Consensus size: 12
31660152 TTTTTTACTG
* *
31660162 TTTTGATGTTGT
1 TTTTGTTGTTAT
*
31660174 TTTTGTTATTAT
1 TTTTGTTGTTAT
* * *
31660186 TTTTATTGCTGT
1 TTTTGTTGTTAT
31660198 TTTTGTTGTTA-
1 TTTTGTTGTTAT
*
31660209 TTTTGCTGTTAT
1 TTTTGTTGTTAT
** *
31660221 TTTTGCCGTT-G
1 TTTTGTTGTTAT
31660232 TTTTGATTGTTAT
1 TTTTG-TTGTTAT
31660245 TTTTGTTG
1 TTTTGTTG
31660253 ATTGGATGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
11 15 0.25
12 40 0.67
13 5 0.08
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:31660987 original size:6 final size:6
Alignment explanation
Indices: 31660958--31661003 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
31660948 TTATTTAGAT
*
31660958 TATAAC TATAAA TTATAAA TTATAAA TATAAA TATAAA TATAAA TA
1 TATAAA TATAAA -TATAAA -TATAAA TATAAA TATAAA TATAAA TA
31661004 GATTATAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 25 0.66
7 13 0.34
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:31662543 original size:19 final size:19
Alignment explanation
Indices: 31662519--31662562 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
31662509 TATTATAAAT
*
31662519 AAATTATTAAAAA-GTTGTA
1 AAATTATTAAAAACATT-TA
31662538 AAATTA-TAAAAACATTTA
1 AAATTATTAAAAACATTTA
31662556 AAATTAT
1 AAATTAT
31662563 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTATTAAAAACATTTA
Found at i:31664902 original size:30 final size:29
Alignment explanation
Indices: 31664858--31665136 Score: 174
Period size: 30 Copynumber: 9.4 Consensus size: 29
31664848 ACCCGGGGGC
31664858 AAAATGGTAA-TTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
* **
31664887 AAAAATAGAATTTTTGAG-G-CTTCGAGGG-T
1 -AAAATGGAATTTTTG-GTGAAATCG-GGGTT
31664916 -AAATGGTAATTTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTTGGTGAAATCGGGGTT
*
31664946 AAAAATGGAA-TTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGAATTTTTGGTGAAA--TCGGGGTT
31664975 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
* * *
31665005 AAAAATAGAA-TTTT--AGAAAGTTTGAGGGTT
1 -AAAATGGAATTTTTGGTGAAA--TCG-GGGTT
*
31665035 -AAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
*
31665064 AAAAATGGAA-TTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGAATTTTTGGTGAAA--TCGGGGTT
*
31665093 AAAATGGTAATTTTTGGTGAAATCGAGGTTT
1 AAAATGG-AATTTTTGGTGAAATCG-GGGTT
*
31665124 AAAATAGAATTTT
1 AAAATGGAATTTT
31665137 GGAAAGTTTG
Statistics
Matches: 196, Mismatches: 20, Indels: 66
0.70 0.07 0.23
Matches are distributed among these distances:
27 17 0.09
28 24 0.12
29 53 0.27
30 58 0.30
31 26 0.13
32 18 0.09
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGTGAAATCGGGGTT
Found at i:31664949 original size:59 final size:59
Alignment explanation
Indices: 31664858--31665168 Score: 457
Period size: 59 Copynumber: 5.3 Consensus size: 59
31664848 ACCCGGGGGC
* *
31664858 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTG-AGGCTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAG-TTCGAGGGT
* *
31664916 -AAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
* *
31664975 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
* * * *
31665034 TAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
* * * *
31665093 AAAATGGTAATTTTTGGTGAAATCGAGGTTTAAAATAGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
31665152 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
31665169 ACTGTTTGGG
Statistics
Matches: 231, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
57 9 0.04
59 211 0.91
60 11 0.05
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
Found at i:31665138 original size:29 final size:29
Alignment explanation
Indices: 31664858--31665138 Score: 134
Period size: 29 Copynumber: 9.5 Consensus size: 29
31664848 ACCCGGGGGC
* *
31664858 AAAATGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTGGTGAAATCGAGGTTT
* * * *** *
31664888 AAAATAGAATTTTTGAGGCTTCGAGG-GT
1 AAAATGGAATTTTGGTGAAATCGAGGTTT
* *
31664916 -AAATGGTAATTTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA--TTTTGGTGAAATCGAGGTTT
**
31664947 AAAATGGAATTTT-G-GAAAGTTCG-GGGGT
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTT
* *
31664975 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGAGGTTT
* * * *
31665006 AAAATAGAATTTT--AGAAAGTTTGAGGGTT
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTT
*
31665035 -AAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGAGGTTT
**
31665065 AAAATGGAATTTT-G-GAAAGTTCG-GGGGT
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTT
31665093 AAAATGGTAATTTTTGGTGAAATCGAGGTTT
1 AAAATGG-AA-TTTTGGTGAAATCGAGGTTT
*
31665124 AAAATAGAATTTTGG
1 AAAATGGAATTTTGG
31665139 AAAGTTTGGG
Statistics
Matches: 184, Mismatches: 41, Indels: 53
0.66 0.15 0.19
Matches are distributed among these distances:
27 17 0.09
28 27 0.15
29 48 0.26
30 47 0.26
31 27 0.15
32 18 0.10
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCGAGGTTT
Found at i:31665167 original size:118 final size:117
Alignment explanation
Indices: 31664851--31665168 Score: 505
Period size: 118 Copynumber: 2.7 Consensus size: 117
31664841 TTTGGATACC
* * * *
31664851 CGGGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTG-AGGCTTCGAGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAG-TTTGAGG
*
31664914 GTAAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
65 GTAAATGGTAA-TTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
31664968 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGAGGG
31665033 TTAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
66 -TAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* * * *
31665086 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTTAAAATAGAATTTTGGAAAGTTTGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGAGGG
31665151 TAAAATGGTAATTTTTGG
66 T-AAATGGTAATTTTTGG
31665169 ACTGTTTGGG
Statistics
Matches: 188, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
117 17 0.09
118 159 0.85
119 12 0.06
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGAGGG
TAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:31665169 original size:30 final size:28
Alignment explanation
Indices: 31664938--31665165 Score: 144
Period size: 29 Copynumber: 7.8 Consensus size: 28
31664928 TTTGGTGAAA
*
31664938 TCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGT-AAAATGGAATTTTGGAAAGT
31664967 TCGGGGGTAAAATGGTAATTTTTGGTGAAA--
1 TCGGGGGTAAAATGG-AA-TTTT-G-GAAAGT
* * *
31664997 TCGGGGTTAAAAATAGAATTTTAGAAAGT
1 TCGGGGGT-AAAATGGAATTTTGGAAAGT
* * *
31665026 TTGAGGGTTAAATGGTAATTTTTGGTGAAA--
1 TCGGGGGTAAAATGG-AA-TTTT-G-GAAAGT
* *
31665056 TCGAGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGT-AAAATGGAATTTTGGAAAGT
31665085 TCGGGGGTAAAATGGTAATTTTTGGTGAAA--
1 TCGGGGGTAAAATGG-AA-TTTT-G-GAAAGT
** *
31665115 TCGAGGTTTAAAATAGAATTTTGGAAAGT
1 TCG-GGGGTAAAATGGAATTTTGGAAAGT
*
31665144 TTGGGGGTAAAATGGTAATTTT
1 TCGGGGGTAAAATGG-AATTTT
31665166 TGGACTGTTT
Statistics
Matches: 155, Mismatches: 22, Indels: 44
0.70 0.10 0.20
Matches are distributed among these distances:
27 12 0.08
28 30 0.19
29 44 0.28
30 34 0.22
31 23 0.15
32 12 0.08
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (28 bp):
TCGGGGGTAAAATGGAATTTTGGAAAGT
Found at i:31665529 original size:162 final size:161
Alignment explanation
Indices: 31665257--31665574 Score: 494
Period size: 162 Copynumber: 2.0 Consensus size: 161
31665247 GATTAAATTG
* * *
31665257 TAAATCTTGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGTTGATTTGGGATTAAATTAA
1 TAAACCTTAAAAAATTATTGGGCCAATTTCATAATTAAATAAAAGTTGATTTGGGATTAAATTAA
* *
31665322 AACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCT
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCTCT
31665387 GGTACAGTCAAACAGTCAAAGGACTAGTTTA
131 GGTACAGTCAAACAGTCAAAGGACTAGTTTA
**
31665418 TAAACCTTAAAAAATTATTGGGCCAATTTTGTAATTAAA-ATAAAGTTGATTTGGGGATTAAATT
1 TAAACCTTAAAAAATTATTGGGCCAATTTCATAATTAAATA-AAAGTTGATTT-GGGATTAAATT
*** * *
31665482 AAAACAAATTAAAAATGTCAGGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGCCT
64 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCT
*
31665547 CTGGTACAGTCAAATAGTCAAAGGACTA
129 CTGGTACAGTCAAACAGTCAAAGGACTA
31665575 AATTGAAAGC
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
160 1 0.01
161 45 0.32
162 96 0.68
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (161 bp):
TAAACCTTAAAAAATTATTGGGCCAATTTCATAATTAAATAAAAGTTGATTTGGGATTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCTCT
GGTACAGTCAAACAGTCAAAGGACTAGTTTA
Found at i:31666465 original size:3 final size:3
Alignment explanation
Indices: 31666451--31666503 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
31666441 CCTTCATTTT
*
31666451 TTA TTA TT- TTA TTA TCA TTA TTA TTTA TTCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA
31666497 TTTA TTA
1 -TTA TTA
31666504 CCATTAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 33 0.75
4 9 0.20
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31666473 original size:17 final size:17
Alignment explanation
Indices: 31666451--31666497 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 17
31666441 CCTTCATTTT
31666451 TTATTATTTTATTATCA
1 TTATTATTTTATTATCA
31666468 TTATTA-TTTA-T-TCA
1 TTATTATTTTATTATCA
31666482 TTATTATTATTATTAT
1 TTATTATT-TTATTAT
31666498 TTATTACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 7 0.27
17 7 0.27
18 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTATTTTATTATCA
Found at i:31666493 original size:23 final size:23
Alignment explanation
Indices: 31666459--31666502 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31666449 TTTTATTATT
31666459 TTATTATCATTATTATTTATTCA
1 TTATTATCATTATTATTTATTCA
*
31666482 TTATTATTATTATTATTTATT
1 TTATTATCATTATTATTTATT
31666503 ACCATTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTATCATTATTATTTATTCA
Found at i:31667226 original size:51 final size:51
Alignment explanation
Indices: 31667171--31667270 Score: 148
Period size: 52 Copynumber: 2.0 Consensus size: 51
31667161 GACTTTGGAC
* * *
31667171 TTTAATTTAAA-TTAATTTTAAATAAATTTAGATTCAAATTCAAATTTAAAG
1 TTTAATTTAAATTTAAATTTAAATAAATCTAAATTCAAA-TCAAATTTAAAG
*
31667222 TTTAATTTAAATTTAAATTTAAATAAATCTAAATTCATATCAAATTTAA
1 TTTAATTTAAATTTAAATTTAAATAAATCTAAATTCAAATCAAATTTAA
31667271 TTTTAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 21 0.48
52 23 0.52
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (51 bp):
TTTAATTTAAATTTAAATTTAAATAAATCTAAATTCAAATCAAATTTAAAG
Found at i:31667228 original size:18 final size:17
Alignment explanation
Indices: 31667171--31667276 Score: 67
Period size: 18 Copynumber: 6.3 Consensus size: 17
31667161 GACTTTGGAC
* *
31667171 TTTAATTTAAA-TTAAT
1 TTTAATTCAAATTTAAA
* *
31667187 TTTAAAT-AAATTTAGA
1 TTTAATTCAAATTTAAA
*
31667203 TTCAAATTCAAATTTAAA
1 TT-TAATTCAAATTTAAA
*
31667221 GTTTAATTTAAATTTAAA
1 -TTTAATTCAAATTTAAA
* *
31667239 TTTAAAT-AAATCTAAA
1 TTTAATTCAAATTTAAA
* *
31667255 -TTCATATCAAATTTAAT
1 TTTAAT-TCAAATTTAAA
31667272 TTTAA
1 TTTAA
31667277 AATAAATTAA
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
15 6 0.09
16 20 0.29
17 16 0.24
18 24 0.35
19 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAATTCAAATTTAAA
Found at i:31667234 original size:6 final size:6
Alignment explanation
Indices: 31667174--31667245 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
31667164 TTTGGACTTT
* * * *
31667174 AATTTA AA-TTA ATTTTA AA--TA AATTTA GATTCA AATTCA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
31667219 AAGTTT- AATTTA AATTTA AATTTA AAT
1 AA-TTTA AATTTA AATTTA AATTTA AAT
31667246 AAATCTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
4 4 0.07
5 7 0.13
6 41 0.75
7 3 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:31667258 original size:52 final size:50
Alignment explanation
Indices: 31667171--31667287 Score: 146
Period size: 52 Copynumber: 2.3 Consensus size: 50
31667161 GACTTTGGAC
* * *
31667171 TTTAATTTAAATTAATTTTAAATAAATTTAGATTCAAATTCAAATTTAAAG
1 TTTAATTTAAATTAAATTTAAATAAATCTAAATTCAAA-TCAAATTTAAAG
* *
31667222 TTTAATTTAAATTTAAATTTAAATAAATCTAAATTCATATCAAATTT-AAT
1 TTTAATTTAAA-TTAAATTTAAATAAATCTAAATTCAAATCAAATTTAAAG
**
31667272 TTTAAAATAAATTAAA
1 TTTAATTTAAATTAAA
31667288 AAAAAACCGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 5 0.09
50 11 0.19
51 19 0.33
52 23 0.40
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (50 bp):
TTTAATTTAAATTAAATTTAAATAAATCTAAATTCAAATCAAATTTAAAG
Found at i:31667794 original size:48 final size:48
Alignment explanation
Indices: 31667723--31667816 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
31667713 TAATGCCAAA
31667723 GAGGGAAGTGAATGGTCTTAAATTGCTTGTTTCTCCGCAAGCTACAAT
1 GAGGGAAGTGAATGGTCTTAAATTGCTTGTTTCTCCGCAAGCTACAAT
*
31667771 GAGGGAAGTGAATGGTCTTAAATTGCTTGTTTCTCTGCAAGCTACA
1 GAGGGAAGTGAATGGTCTTAAATTGCTTGTTTCTCCGCAAGCTACA
31667817 CTGTTGTACC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (48 bp):
GAGGGAAGTGAATGGTCTTAAATTGCTTGTTTCTCCGCAAGCTACAAT
Found at i:31668837 original size:16 final size:16
Alignment explanation
Indices: 31668800--31668837 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31668790 AGGTATAGTA
*
31668800 AAATATTAAAATAAAT
1 AAATATTAAAATAAAC
31668816 AAATATTAAAA-AAAC
1 AAATATTAAAATAAAC
31668831 AACATAT
1 AA-ATAT
31668838 GACAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATTAAAATAAAC
Found at i:31672737 original size:30 final size:33
Alignment explanation
Indices: 31672703--31672766 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 33
31672693 TTTTTGTAAC
31672703 TTTTAAAAAATTAA-AT-CAAATTT-TTATTAT
1 TTTTAAAAAATTAATATACAAATTTATTATTAT
* * *
31672733 TTTTAGAGAATTAATATACAATTTTATTATTAT
1 TTTTAAAAAATTAATATACAAATTTATTATTAT
31672766 T
1 T
31672767 AATTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.43
31 2 0.07
32 6 0.21
33 8 0.29
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (33 bp):
TTTTAAAAAATTAATATACAAATTTATTATTAT
Found at i:31672786 original size:22 final size:22
Alignment explanation
Indices: 31672742--31672787 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31672732 TTTTTAGAGA
*
31672742 ATTAATATACAATTTTATTATT
1 ATTAATATACAATTTTATAATT
*
31672764 ATTAATTTA-AATTTTATAAATT
1 ATTAATATACAATTTTAT-AATT
31672786 AT
1 AT
31672788 AAAAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAATATACAATTTTATAATT
Found at i:31673018 original size:21 final size:20
Alignment explanation
Indices: 31672992--31673030 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31672982 ATTGATTTAA
31672992 TTATTA-TTTACTATTTTATTT
1 TTATTAGTTTA-T-TTTTATTT
31673013 TTATTAGTTTATTTTTAT
1 TTATTAGTTTATTTTTAT
31673031 ATTATGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TTATTAGTTTATTTTTATTT
Found at i:31673023 original size:14 final size:14
Alignment explanation
Indices: 31672992--31673030 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
31672982 ATTGATTTAA
* *
31672992 TTATTATTTACTATT
1 TTATT-TTTATTAGT
31673007 TTATTTTTATTAGT
1 TTATTTTTATTAGT
31673021 TTATTTTTAT
1 TTATTTTTAT
31673031 ATTATGCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (14 bp):
TTATTTTTATTAGT
Found at i:31673035 original size:19 final size:20
Alignment explanation
Indices: 31672987--31673035 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
31672977 ACTAAATTGA
31672987 TTTA-ATTATTATTTACTAT
1 TTTATATTATTATTTACTAT
*
31673006 TTTATTTTTATTAGTTTA-T-T
1 TTTA-TATTATTA-TTTACTAT
31673026 TTTATATTAT
1 TTTATATTAT
31673036 GCTATGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 9 0.36
20 5 0.20
21 7 0.28
22 4 0.16
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTATATTATTATTTACTAT
Found at i:31673280 original size:26 final size:27
Alignment explanation
Indices: 31673251--31673303 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
31673241 AAAATTAATG
*
31673251 AATTATATGAAAAATTC-CCAACTTTA
1 AATTATAAGAAAAATTCACCAACTTTA
* *
31673277 AATTATAAGAAACATTCACCATCTTTA
1 AATTATAAGAAAAATTCACCAACTTTA
31673304 TTATACGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTATAAGAAAAATTCACCAACTTTA
Found at i:31676225 original size:2 final size:2
Alignment explanation
Indices: 31676218--31676260 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
31676208 TATAAATAAT
31676218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31676260 T
1 T
31676261 TTGTGGTGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31676491 original size:21 final size:17
Alignment explanation
Indices: 31676466--31676513 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 17
31676456 GTATTCAATT
31676466 TATATTATAAAATTTATTTAG
1 TATATTATAAAA---ATTT-G
31676487 TATATTATTAAAAATTTG
1 TATATTA-TAAAAATTTG
31676505 TATATTATA
1 TATATTATA
31676514 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
19 4 0.15
21 7 0.27
22 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TATATTATAAAAATTTG
Found at i:31676513 original size:23 final size:21
Alignment explanation
Indices: 31676465--31676521 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
31676455 TGTATTCAAT
*
31676465 TTATATTATAAAATTTATTTA
1 TTATATTATAAAATTTATATA
* *
31676486 GTATATTATTAAAAATTTGTATA
1 TTATATTA-T-AAAATTTATATA
*
31676509 TTATATTAAAAAA
1 TTATATTATAAAA
31676522 ATAAAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 11 0.38
22 1 0.03
23 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTATATTATAAAATTTATATA
Found at i:31676590 original size:17 final size:17
Alignment explanation
Indices: 31676545--31676604 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 17
31676535 ACTTTTAATA
* *
31676545 TAAATACAATATATT-T
1 TAAATATAAAATATTAT
31676561 T-AAT-TAAATATATTAT
1 TAAATATAAA-ATATTAT
31676577 TAAATATAAAATATTA-
1 TAAATATAAAATATTAT
*
31676593 TAAATCTAAAAT
1 TAAATATAAAAT
31676605 TTAAATATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.05
15 8 0.22
16 14 0.38
17 9 0.24
18 4 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAAAATATTAT
Found at i:31680456 original size:23 final size:23
Alignment explanation
Indices: 31680386--31680531 Score: 129
Period size: 23 Copynumber: 6.3 Consensus size: 23
31680376 ACGGAACAAG
* *
31680386 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
31680407 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
31680432 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
31680455 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
31680478 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
31680501 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
31680524 CAGAGAGC
1 CAGAGAGC
31680532 GCGCTAGTGT
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
21 15 0.15
23 68 0.66
24 1 0.01
25 13 0.13
26 6 0.06
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:31680505 original size:69 final size:66
Alignment explanation
Indices: 31680386--31680530 Score: 186
Period size: 69 Copynumber: 2.1 Consensus size: 66
31680376 ACGGAACAAG
*
31680386 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCAC-ACACAGTG
1 CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACGACAC-GTG
31680450 CTAAA
62 CTAAA
*
31680455 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACGAGACGTG
1 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACGACACGTG
31680519 CTAAA
62 CTAAA
31680524 CAGAGAG
1 CAGAGAG
31680531 CGCGCTAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
68 2 0.03
69 35 0.51
70 14 0.20
71 11 0.16
72 7 0.10
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.12
Consensus pattern (66 bp):
CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACGACACGTGCTAA
A
Found at i:31691822 original size:7 final size:7
Alignment explanation
Indices: 31691810--31691843 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31691800 ATATACTAAT
31691810 GAAAAGG
1 GAAAAGG
31691817 GAAAAGG
1 GAAAAGG
31691824 GAAAAGG
1 GAAAAGG
31691831 GAAAAGG
1 GAAAAGG
31691838 GAAAAG
1 GAAAAG
31691844 TCCTACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:31695081 original size:24 final size:24
Alignment explanation
Indices: 31695047--31695130 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
31695037 GAAGAATTTT
*
31695047 CTCCTAGGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
* *
31695071 CTTCAATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
31695095 CTCCTATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
31695119 CTCCTATGGGAG
1 CTCCTATGGGAG
31695131 ATTCAAATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.20
Consensus pattern (24 bp):
CTCCTATGGGAGCAAGAGGTGGTC
Found at i:31697470 original size:12 final size:12
Alignment explanation
Indices: 31697453--31697491 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31697443 TCTTTGAAAA
31697453 TATTTTAGTTTT
1 TATTTTAGTTTT
*
31697465 TATTTTATTTTAT
1 TATTTTAGTTT-T
*
31697478 TATTTAAGTTTT
1 TATTTTAGTTTT
31697490 TA
1 TA
31697492 ACTGAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (12 bp):
TATTTTAGTTTT
Found at i:31713613 original size:20 final size:20
Alignment explanation
Indices: 31713575--31713613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31713565 CAAATCTTTT
* *
31713575 AATATTTTATTATAGTATTA
1 AATATTTTATTAGAATATTA
31713595 AATATTTTATTAGAATATT
1 AATATTTTATTAGAATATT
31713614 GACCGTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AATATTTTATTAGAATATTA
Found at i:31718740 original size:16 final size:16
Alignment explanation
Indices: 31718702--31718741 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31718692 TATGATTCAT
31718702 ATAA-AAATTCAAAAA
1 ATAATAAATTCAAAAA
**
31718717 ATCGTAAATTCAAAAA
1 ATAATAAATTCAAAAA
31718733 ATAATAAAT
1 ATAATAAAT
31718742 AAAACTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (16 bp):
ATAATAAATTCAAAAA
Found at i:31720498 original size:51 final size:51
Alignment explanation
Indices: 31720372--31720560 Score: 191
Period size: 51 Copynumber: 3.6 Consensus size: 51
31720362 TTTCATTTAA
* ** * * *
31720372 TACTCACGATGACA-TATAGTCATCGGACCCCCTTGTTCCGTATAGAAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGA--CCTTTAATCCGTAAAG-GATTCATT
* * ** * *
31720426 TACTCACGATGGCACTGAGTCATCGGACCTTTAATTTGTCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
31720477 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
31720528 TTCTCACGATGACATTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
31720561 CGTTTATAGC
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
51 76 0.68
52 11 0.10
54 23 0.21
55 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:31725928 original size:3 final size:3
Alignment explanation
Indices: 31725920--31725956 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
31725910 TTTGGTTTGC
*
31725920 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31725957 AGAAAGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:31734814 original size:62 final size:61
Alignment explanation
Indices: 31734654--31735083 Score: 320
Period size: 62 Copynumber: 7.2 Consensus size: 61
31734644 AAAAAATTAT
* * * * * *
31734654 GTGTTGGCCA-CGCAATAGCCGACACCCCTTTTTTGTC-AGAAAAAAATTCAAA-ATTTTTG
1 GTGTTGGCCATC-AAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTTAAATTTTTTTG
* * * * *
31734713 AGTGTTTGCCATTAAATGGTCGA-AACCTCTTATTTCTCGAGAAAAAAATTTAAATTTTTTTG
1 -GTGTTGGCCATCAAATGGCCGACACCCCCTT-TTTCTCGAGAAAAAAATTTAAATTTTTTTG
* **
31734775 GTGTTGGTCATCAAATGATCGACACCCCCCTTTTTCTCGAG--AAAAA---AAA----TTT-
1 GTGTTGGCCATCAAATGGCCGACA-CCCCCTTTTTCTCGAGAAAAAAATTTAAATTTTTTTG
* * * * * * * *
31734827 GTGTTGGCCA-CGCAATGACCGACACTCCTTTTTTGTCAGAAAAAAAAATTTAAAATTTTTGG
1 GTGTTGGCCATC-AAATGGCCGACACCCCCTTTTTCTC-GAGAAAAAAATTTAAATTTTTTTG
* *
31734889 GTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAGAAAATTTAAATATTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAA-AAAATTTAAATTTTTTTG
* ** *** * *
31734951 GTATTGATCATTGCATGGCCGACACCCCC-TTTTCTGGAG-AAAAAATTCAAATTTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTTAAATTTTTTTG
* * * *
31735010 ATGTCGGCCATCAAATGGCCGACACTCCCTTTTTTTTTCGAG-AAAAAATTTGAAATTTTTTTG
1 GTGTTGGCCATCAAATGGCCGACAC-CCC-CTTTTTCTCGAGAAAAAAATTT-AAATTTTTTTG
31735073 GTGTTGGCCAT
1 GTGTTGGCCAT
31735084 TGCATGACAG
Statistics
Matches: 287, Mismatches: 59, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
51 11 0.04
52 21 0.07
53 3 0.01
54 5 0.02
57 6 0.02
59 38 0.13
60 31 0.11
61 47 0.16
62 99 0.34
63 26 0.09
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (61 bp):
GTGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTTAAATTTTTTTG
Found at i:31734981 original size:175 final size:173
Alignment explanation
Indices: 31734642--31734995 Score: 480
Period size: 175 Copynumber: 2.0 Consensus size: 173
31734632 GAATATGAAA
31734642 AAAAAAAATTATGTGTTGGCCACGCAATAGCCGACACCCCTTTTTTGTCAGAAAAAAATTCAAAA
1 AAAAAAAATTATGTGTTGGCCACGCAATAGCCGACACCCCTTTTTTGTCAGAAAAAAATTCAAAA
* * * * * *
31734707 TTTTTGAGTGTTTGCCATTAAATGGTCGAAACCTCTTATTTCTCGAGAAAAAAATTTAAATTTTT
66 TTTTTGAGTGTTGGCCATCAAATGGCCGAAACCCCCTATTTCTCGAGAAAAAAATTTAAATATTT
* * *
31734772 TTGGTGTTGGTCATCAAATGATCGACACCCCCCTTTTTCTCGAG
131 TTGGTATTGATCATCAAATGACCGACACCCCCC-TTTTCTCGAG
* *
31734816 AAAAAAAATT-TGTGTTGGCCACGCAAT-GACCGACACTCCTTTTTTGTCAGAAAAAAAAATTTA
1 AAAAAAAATTATGTGTTGGCCACGCAATAG-CCGACACCCCTTTTTTGTCAG--AAAAAAATTCA
* *
31734879 AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAGAAAATTTAAAT
63 AAATTTTTGAGTGTTGGCCATCAAATGGCCGAAACCCCCTATTTCTCGAGAAA-AAAATTTAAAT
*** * *
31734944 ATTTTTGGTATTGATCATTGCATGGCCGACA-CCCCCTTTTCTGGAG
127 ATTTTTGGTATTGATCATCAAATGACCGACACCCCCCTTTTCTCGAG
31734990 AAAAAA
1 AAAAAA
31734996 TTCAAATTTT
Statistics
Matches: 158, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
172 1 0.01
173 37 0.23
174 25 0.16
175 61 0.39
176 34 0.22
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (173 bp):
AAAAAAAATTATGTGTTGGCCACGCAATAGCCGACACCCCTTTTTTGTCAGAAAAAAATTCAAAA
TTTTTGAGTGTTGGCCATCAAATGGCCGAAACCCCCTATTTCTCGAGAAAAAAATTTAAATATTT
TTGGTATTGATCATCAAATGACCGACACCCCCCTTTTCTCGAG
Found at i:31735026 original size:121 final size:122
Alignment explanation
Indices: 31734869--31735089 Score: 295
Period size: 121 Copynumber: 1.8 Consensus size: 122
31734859 TTGTCAGAAA
* * *
31734869 AAAAAATTTAAAATTTTTGGGTGTTGGCCATCAAATGGCCGACAC-CCC-CTATTTCTCGAGAAA
1 AAAAAATTCAAAATTTTTGGATGTCGGCCATCAAATGGCCGACACTCCCTCTATTTCTCGAG-AA
*
31734932 GAAAATTT-AAATATTTTTGGTATTGATCATTGCATGGCCGACACCCCCTTTTCTGGAG
65 -AAAATTTGAAATATTTTTGGTATTGACCATTGCATGGCCGACACCCCCTTTTCTGGAG
* * * * *
31734990 AAAAAATTCAAATTTTTTTGATGTCGGCCATCAAATGGCCGACACTCCCTTTTTTTTTCGAGAAA
1 AAAAAATTCAAAATTTTTGGATGTCGGCCATCAAATGGCCGACACTCCCTCTATTTCTCGAGAAA
* * *
31735055 AAATTTGAAATTTTTTTGGTGTTGGCCATTGCATG
66 AAATTTGAAATATTTTTGGTATTGACCATTGCATG
31735090 ACAGTATATA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
121 47 0.55
122 29 0.34
123 9 0.11
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (122 bp):
AAAAAATTCAAAATTTTTGGATGTCGGCCATCAAATGGCCGACACTCCCTCTATTTCTCGAGAAA
AAATTTGAAATATTTTTGGTATTGACCATTGCATGGCCGACACCCCCTTTTCTGGAG
Found at i:31735517 original size:62 final size:62
Alignment explanation
Indices: 31735353--31735600 Score: 233
Period size: 59 Copynumber: 4.1 Consensus size: 62
31735343 AAAAAAAATT
* ** *
31735353 GAAATAGG-GGGTGTCGGTAATTTGATTG-CTAACATCAAAAAAATTTGAA-TTTTTTTCTCGA
1 GAAAAAGGAGGGTGTCGGCCATTTGA-TGACCAACA-CAAAAAAATTTGAATTTTTTTTCTCGA
*
31735414 GAAAAAAGGAGGGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTGAATTTTTTTTCTCGA
1 G-AAAAAGGAGGGTGTCGGCCATTTGATGACCAACACAAAAAAATTTGAATTTTTTTTCTCGA
* * *
31735477 G-AAAA-G-GGGTGTCGGCCATTTGATGACCAACACCAAAAAAAATT-AAATTTTTTTCTTGA
1 GAAAAAGGAGGGTGTCGGCCATTTGATGACCAACA-CAAAAAAATTTGAATTTTTTTTCTCGA
* * * *** ** * * *
31735536 -AAAAAGGAGGGTATTGACCATGCAATGGTCGACACCAAAAAATTTGAATTTTTTTTCTTGA
1 GAAAAAGGAGGGTGTCGGCCATTTGATGACCAACACAAAAAAATTTGAATTTTTTTTCTCGA
31735597 GAAA
1 GAAA
31735601 TGACCAACAC
Statistics
Matches: 157, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
59 42 0.27
60 21 0.13
61 36 0.23
62 25 0.16
63 33 0.21
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (62 bp):
GAAAAAGGAGGGTGTCGGCCATTTGATGACCAACACAAAAAAATTTGAATTTTTTTTCTCGA
Found at i:31735588 original size:120 final size:121
Alignment explanation
Indices: 31735360--31735600 Score: 297
Period size: 120 Copynumber: 2.0 Consensus size: 121
31735350 ATTGAAATAG
* * * * *
31735360 GGGGTGTCGGTAATTTGATTGCTAACATCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGGAG
1 GGGGTGTCGGCAATTTGATTGCCAACACCAAAAAAAATTAAATTTTTTTCTC-AGAAAAAAGGAG
* * ***
31735425 GGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTGAATTTTTTTTCTCGAGAAAA
65 GGTATCGACCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTTCTCGAGAAAA
* *
31735482 GGGGTGTCGGCCATTTGA-TGACCAACACCAAAAAAAATTAAATTTTTTTCT-TGAAAAAAGGAG
1 GGGGTGTCGGCAATTTGATTG-CCAACACCAAAAAAAATTAAATTTTTTTCTCAGAAAAAAGGAG
* * * * *
31735545 GGTATTGACCATGCAATGGTCGACACCAAAAAATTTGAATTTTTTTTCTTGAGAAA
65 GGTATCGACCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTTCTCGAGAAA
31735601 TGACCAACAC
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
120 57 0.56
121 2 0.02
122 42 0.42
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (121 bp):
GGGGTGTCGGCAATTTGATTGCCAACACCAAAAAAAATTAAATTTTTTTCTCAGAAAAAAGGAGG
GTATCGACCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTTCTCGAGAAAA
Found at i:31738346 original size:7 final size:7
Alignment explanation
Indices: 31738334--31738372 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
31738324 AGTAGATAAT
31738334 ATTTTAA
1 ATTTTAA
31738341 ATTTTAA
1 ATTTTAA
31738348 ATTTTAA
1 ATTTTAA
31738355 ATTTTAA
1 ATTTTAA
31738362 ATTTTAA
1 ATTTTAA
31738369 ATTT
1 ATTT
31738373 AATTATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:31739344 original size:13 final size:13
Alignment explanation
Indices: 31739322--31739374 Score: 90
Period size: 13 Copynumber: 4.2 Consensus size: 13
31739312 TTATATATGT
31739322 AAAGTGATAATTA
1 AAAGTGATAATTA
*
31739335 AAAATGATAATT-
1 AAAGTGATAATTA
31739347 AAAGTGATAATTA
1 AAAGTGATAATTA
31739360 AAAGTGATAATTA
1 AAAGTGATAATTA
31739373 AA
1 AA
31739375 TAAACGAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.30
13 26 0.70
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (13 bp):
AAAGTGATAATTA
Found at i:31739349 original size:25 final size:25
Alignment explanation
Indices: 31739321--31739374 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
31739311 CTTATATATG
31739321 TAAAGTGATAATTAAAAATGATAAT
1 TAAAGTGATAATTAAAAATGATAAT
*
31739346 TAAAGTGATAATTAAAAGTGATAAT
1 TAAAGTGATAATTAAAAATGATAAT
31739371 TAAA
1 TAAA
31739375 TAAACGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (25 bp):
TAAAGTGATAATTAAAAATGATAAT
Found at i:31745820 original size:16 final size:16
Alignment explanation
Indices: 31745801--31745853 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
31745791 TATATTTTTA
31745801 ATTTAATGTATTATTT
1 ATTTAATGTATTATTT
* *
31745817 ATTTATTTTATTATTT
1 ATTTAATGTATTATTT
31745833 -TTTACATGTAATTATCTT
1 ATTTA-ATGT-ATTAT-TT
31745851 ATT
1 ATT
31745854 GTGTTATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.14
16 16 0.55
17 5 0.17
18 2 0.07
19 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (16 bp):
ATTTAATGTATTATTT
Found at i:31768239 original size:24 final size:24
Alignment explanation
Indices: 31768189--31768235 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31768179 TACCTTTTTG
* *
31768189 TCTTTCTTTTGACTTTTACCTTTC
1 TCTTTCTTTTCACTTTTACATTTC
*
31768213 TCTTT-TTTTCACTTTTTCATTTC
1 TCTTTCTTTTCACTTTTACATTTC
31768236 CTCTCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (24 bp):
TCTTTCTTTTCACTTTTACATTTC
Found at i:31780755 original size:2 final size:2
Alignment explanation
Indices: 31780748--31780774 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31780738 GGACAGCAAC
31780748 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31780775 GTTCCAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31783990 original size:10 final size:10
Alignment explanation
Indices: 31783973--31784008 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
31783963 CTGCCCCTCT
31783973 CTCTCTCTCA
1 CTCTCTCTCA
*
31783983 CACTCTCTCA
1 CTCTCTCTCA
31783993 CTCTCTCTCA
1 CTCTCTCTCA
31784003 CTCTCT
1 CTCTCT
31784009 TAGTTTCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.11, C:0.50, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCTCTCA
Found at i:31794763 original size:23 final size:22
Alignment explanation
Indices: 31794736--31794787 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
31794726 ATATAAATTT
31794736 TAAATATTTTTAAGAAATTAAT-A
1 TAAATATTTTT--GAAATTAATAA
*
31794759 TAAATTATTTTTTAAATTAATAA
1 TAAA-TATTTTTGAAATTAATAA
31794782 TAAATA
1 TAAATA
31794788 AAATATTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATATTTTTGAAATTAATAA
Found at i:31804953 original size:228 final size:227
Alignment explanation
Indices: 31804547--31805208 Score: 731
Period size: 228 Copynumber: 2.9 Consensus size: 227
31804537 CTTTGAAGAA
* * * * *
31804547 GATGCAGATCTTTGTGAAAACCCTCACCGGCAAGACCATAACACTCGAGGTCGAAAGCTCCGACA
1 GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * *
31804612 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCCGACCAGCAGCGTCTC
66 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGG-AGGGATCCCACCTGACCAGCAGCGTCTC
* ** * * ** *
31804677 ATTTTCGCTGGCAAACAGCTCGAAGACGGTCGGACCCTT-GCCGATTATAACATCCAGAAAGAAT
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGA-CCTTGGCTGATTATAACATCCAGAAAGAAT
*
31804741 CCACCCTCCACCTCGTCTT-ACGCCTTCGAGG-GG
194 CCACCCTTCACCTCGTCTTGA-GCCTTCGAGGAGG
* * * *
31804774 GCATGCAAATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGAC
1 G-ATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGAC
* *
31804839 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAGGGCATCCCACCTGACCAACAGCGTTT
65 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAGGG-ATCCCACCTGACCAGCAGCGTCT
*
31804904 GATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCA-AAAGGAA
129 CATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAA-GAA
* * * *
31804968 TCCACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
193 TCCACCCTTCACCTCGTCTTGAGCCTTCGAGGAGG
* * * * * * * * * * *
31805003 GATGCAGATTTTTGTTAAGACTTTGACCGGCAAAACAATCACCTTGGAGGTTGAAAGCTCCGATA
1 GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * * * * * ** *
31805068 CCATTGACAATGTTAAGGCAAAGATTCAGGATAAGGAAGGAAT-CCACCTGATCAGCAAAGGCTC
66 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGG-AGGGATCCCACCTGACCAGCAGCGTCTC
* * * * *
31805132 ATCTTTGCCGGCAAACAATTGGAAGATGGGAGGACTTTGGCTGATTATAACATTCAGAAAGAGTC
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATC
*
31805197 TACCCTTCACCT
195 CACCCTTCACCT
31805209 TGTTCTTCGT
Statistics
Matches: 365, Mismatches: 62, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
227 93 0.25
228 265 0.73
229 7 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (227 bp):
GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAGGGATCCCACCTGACCAGCAGCGTCTCA
TCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCC
ACCCTTCACCTCGTCTTGAGCCTTCGAGGAGG
Found at i:31808879 original size:29 final size:32
Alignment explanation
Indices: 31808822--31808886 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
31808812 AATTCCCCAT
*
31808822 AATTTTATCGGCTCACTTTTTTATGTATA-TA
1 AATTTTATCGGCTCACTTTTTCATGTATATTA
* *
31808853 AATTTTAT-GGCTCTC-TTTTCCTGTATATTA
1 AATTTTATCGGCTCACTTTTTCATGTATATTA
31808883 AATT
1 AATT
31808887 ACTTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 12 0.40
31 8 0.27
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (32 bp):
AATTTTATCGGCTCACTTTTTCATGTATATTA
Found at i:31819153 original size:2 final size:2
Alignment explanation
Indices: 31819146--31819181 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31819136 CCCATAGATT
31819146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31819182 ATAAGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31819299 original size:144 final size:144
Alignment explanation
Indices: 31819039--31819308 Score: 540
Period size: 144 Copynumber: 1.9 Consensus size: 144
31819029 CTTGCCTACC
31819039 TAAGAATTTGTGTAATCAATGGATTAAGATGAACAGGAGAAAGTAGAGTTGGTTGCAATGCCACC
1 TAAGAATTTGTGTAATCAATGGATTAAGATGAACAGGAGAAAGTAGAGTTGGTTGCAATGCCACC
31819104 AATCTCATGAGCTTAATTTAGACATGTTGGAGCCCATAGATTTATATATATATATATATATATAT
66 AATCTCATGAGCTTAATTTAGACATGTTGGAGCCCATAGATTTATATATATATATATATATATAT
31819169 ATATATATATATAA
131 ATATATATATATAA
31819183 TAAGAATTTGTGTAATCAATGGATTAAGATGAACAGGAGAAAGTAGAGTTGGTTGCAATGCCACC
1 TAAGAATTTGTGTAATCAATGGATTAAGATGAACAGGAGAAAGTAGAGTTGGTTGCAATGCCACC
31819248 AATCTCATGAGCTTAATTTAGACATGTTGGAGCCCATAGATTTATATATATATATATATAT
66 AATCTCATGAGCTTAATTTAGACATGTTGGAGCCCATAGATTTATATATATATATATATAT
31819309 TTCACAATAG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 126 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (144 bp):
TAAGAATTTGTGTAATCAATGGATTAAGATGAACAGGAGAAAGTAGAGTTGGTTGCAATGCCACC
AATCTCATGAGCTTAATTTAGACATGTTGGAGCCCATAGATTTATATATATATATATATATATAT
ATATATATATATAA
Found at i:31829491 original size:23 final size:22
Alignment explanation
Indices: 31829465--31829517 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
31829455 TTTAGAAAGT
*
31829465 TATTTTTTATGAATAAATTATAA
1 TATTTTTTATGAAT-AAGTATAA
*
31829488 TATTTTTTTATGAATAAGTATAT
1 TA-TTTTTTATGAATAAGTATAA
31829511 TATTTTT
1 TATTTTT
31829518 ATAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 5 0.19
23 10 0.37
24 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TATTTTTTATGAATAAGTATAA
Found at i:31829494 original size:24 final size:23
Alignment explanation
Indices: 31829467--31829517 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31829457 TAGAAAGTTA
*
31829467 TTTTTTATGAATAAATTATAATAT
1 TTTTTTATGAAT-AAGTATAATAT
*
31829491 TTTTTTATGAATAAGTATATTAT
1 TTTTTTATGAATAAGTATAATAT
31829514 TTTT
1 TTTT
31829518 ATAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTTTTATGAATAAGTATAATAT
Found at i:31834759 original size:18 final size:18
Alignment explanation
Indices: 31834710--31834761 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
31834700 TTTACCTTTT
*
31834710 TTATTATTTATTTCATAATA
1 TTATT-TTTATTT-TTAATA
*
31834730 TT-TTTGTAATTTTTAATA
1 TTATTT-TTATTTTTAATA
31834748 TTATTTTTATTTTT
1 TTATTTTTATTTTT
31834762 CGGATGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 15 0.56
19 10 0.37
20 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTATTTTTAATA
Found at i:31835384 original size:13 final size:13
Alignment explanation
Indices: 31835366--31835390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31835356 TTTTTATATT
31835366 TTATATTATTAAA
1 TTATATTATTAAA
31835379 TTATATTATTAA
1 TTATATTATTAA
31835391 CTTTAATAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATTATTAAA
Found at i:31836702 original size:21 final size:21
Alignment explanation
Indices: 31836676--31836716 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31836666 TAATTAAATT
31836676 TAATTAATAATCT-ATATTAAA
1 TAATTAATAAT-TAATATTAAA
31836697 TAATTAATAATTAATATTAA
1 TAATTAATAATTAATATTAA
31836717 GTTAGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAATAATTAATATTAAA
Found at i:31846841 original size:14 final size:15
Alignment explanation
Indices: 31846822--31846850 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31846812 AAATATCTTA
31846822 AAATATA-TTATTTT
1 AAATATATTTATTTT
31846836 AAATATATTTATTTT
1 AAATATATTTATTTT
31846851 TGTCATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATATATTTATTTT
Found at i:31849333 original size:30 final size:29
Alignment explanation
Indices: 31849299--31849364 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
31849289 GTGATTTGTG
** *
31849299 AAAATTAAATTAAATCAAAATTTTATGTAT
1 AAAATTAAACAAAATCAAAA-TTCATGTAT
*
31849329 AAAATTACACAAAATCAAAATTCATGTAT
1 AAAATTAAACAAAATCAAAATTCATGTAT
*
31849358 AACATTA
1 AAAATTA
31849365 TACGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTAAACAAAATCAAAATTCATGTAT
Found at i:31851116 original size:27 final size:25
Alignment explanation
Indices: 31851086--31851184 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 25
31851076 TAGCGCGCTT
31851086 TTCGTTATTTTAGCACTGTGTGTGCTC
1 TTCGTTA--TTAGCACTGTGTGTGCTC
*
31851113 TTCGTTATTAGCACTTTGTGTGCTC
1 TTCGTTATTAGCACTGTGTGTGCTC
* * *
31851138 TCCG--AGTAGCACTTTGTGTGCTC
1 TTCGTTATTAGCACTGTGTGTGCTC
* * *
31851161 TCCG--AGTAGCACTTTGTGTGCTC
1 TTCGTTATTAGCACTGTGTGTGCTC
31851184 T
1 T
31851185 CTATTGCCTA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 42 0.61
25 20 0.29
27 7 0.10
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.42
Consensus pattern (25 bp):
TTCGTTATTAGCACTGTGTGTGCTC
Found at i:31851186 original size:25 final size:23
Alignment explanation
Indices: 31851096--31851185 Score: 135
Period size: 23 Copynumber: 3.8 Consensus size: 23
31851086 TTCGTTATTT
* * *
31851096 TAGCACTGTGTGTGCTCTTCGTTAT
1 TAGCACTTTGTGTGCTCTCCG--AG
31851121 TAGCACTTTGTGTGCTCTCCGAG
1 TAGCACTTTGTGTGCTCTCCGAG
31851144 TAGCACTTTGTGTGCTCTCCGAG
1 TAGCACTTTGTGTGCTCTCCGAG
31851167 TAGCACTTTGTGTGCTCTC
1 TAGCACTTTGTGTGCTCTC
31851186 TATTGCCTAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
23 43 0.69
25 19 0.31
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (23 bp):
TAGCACTTTGTGTGCTCTCCGAG
Found at i:31867451 original size:18 final size:18
Alignment explanation
Indices: 31867400--31867460 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
31867390 CTATAGATAG
*
31867400 ATATTTAATATTTTATTTT
1 ATATTTAATA-TTTATTCT
**
31867419 ATATAAAAT-TATTATTCT
1 ATATTTAATAT-TTATTCT
*
31867437 ATATTTAATATTTATCCT
1 ATATTTAATATTTATTCT
31867455 A-ATTTA
1 ATATTTA
31867461 GTTAAGACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.18
18 20 0.59
19 8 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTAATATTTATTCT
Found at i:31883676 original size:32 final size:32
Alignment explanation
Indices: 31883613--31883676 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
31883603 TCCCTAAACC
* * *
31883613 TTAATTTGATCAATTTTAGCCCTTTTTCTTTT
1 TTAAATTGATCAATTTTAGCCCTTGTGCTTTT
*
31883645 TTAAATTGATCGATTTTAG-CCTCTGTGCTTTT
1 TTAAATTGATCAATTTTAGCCCT-TGTGCTTTT
31883677 AAATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.55
Consensus pattern (32 bp):
TTAAATTGATCAATTTTAGCCCTTGTGCTTTT
Found at i:31886975 original size:8 final size:8
Alignment explanation
Indices: 31886954--31887004 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
31886944 TCTAATTTTT
*
31886954 TAAAATGA
1 TAAAATTA
31886962 TAAAAATTA
1 T-AAAATTA
*
31886971 TAAAAATA
1 TAAAATTA
31886979 TAAAA-TA
1 TAAAATTA
*
31886986 TTAAAATGA
1 -TAAAATTA
31886995 TAAAATTA
1 TAAAATTA
31887003 TA
1 TA
31887005 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 2 0.06
8 26 0.72
9 8 0.22
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (8 bp):
TAAAATTA
Found at i:31904344 original size:19 final size:21
Alignment explanation
Indices: 31904322--31904379 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
31904312 TTTTACATGA
31904322 TTTTCTATCTTTATTTTT-C-
1 TTTTCTATCTTTATTTTTACT
*
31904341 TTTTCTAT-TTTTTTTTTACT
1 TTTTCTATCTTTATTTTTACT
*
31904361 TTTTCTATCTCTTCTTTTT
1 TTTTCTATCT-TTATTTTT
31904380 TATAATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 8 0.24
21 1 0.03
22 7 0.21
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTATCTTTATTTTTACT
Found at i:31904349 original size:13 final size:12
Alignment explanation
Indices: 31904301--31904366 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 12
31904291 TTTTTAATTC
31904301 TTTTATTTTTCT
1 TTTTATTTTTCT
*
31904313 TTTACATGATTTTCT
1 TTT-TAT--TTTTCT
31904328 ATCTTTATTTTTCT
1 -T-TTTATTTTTCT
31904342 TTTCTATTTTT-T
1 TTT-TATTTTTCT
31904354 TTTTACTTTTTCT
1 TTTTA-TTTTTCT
31904367 ATCTCTTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
11 2 0.05
12 14 0.32
13 11 0.25
14 6 0.14
15 6 0.14
16 3 0.07
17 2 0.05
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTCT
Found at i:31907701 original size:22 final size:21
Alignment explanation
Indices: 31907665--31907733 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
31907655 CTATTAAAAA
*
31907665 AAAAAC-TAGGATTTTATAGAG
1 AAAAACTTAGGTTTTTATAG-G
*
31907686 AAATACTTAGGTTTTTATAGG
1 AAAAACTTAGGTTTTTATAGG
31907707 AAAAACTT-GAGTTTTTATAGG
1 AAAAACTTAG-GTTTTTATAGG
31907728 AAAAAC
1 AAAAAC
31907734 CAATTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 30 0.70
22 12 0.28
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (21 bp):
AAAAACTTAGGTTTTTATAGG
Found at i:31910134 original size:2 final size:2
Alignment explanation
Indices: 31910127--31910158 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31910117 ATTTTTATTA
31910127 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
31910159 TTAATGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31918258 original size:33 final size:33
Alignment explanation
Indices: 31918208--31918292 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
31918198 AAGTAATTTG
*
31918208 AAGTCTGA-AGTTCATGATAAAAGAAG-GACCTTC
1 AAGTCTGAGA-TTTATGATAAAAGAAGTGA-CTTC
*
31918241 AAGTCTGAGATTTATGATAAAAGAAGTGATTTC
1 AAGTCTGAGATTTATGATAAAAGAAGTGACTTC
* *
31918274 AAGTCTGAGGTTTTTGATA
1 AAGTCTGAGATTTATGATA
31918293 TGAGCTTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 43 0.93
34 3 0.07
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (33 bp):
AAGTCTGAGATTTATGATAAAAGAAGTGACTTC
Found at i:31929067 original size:41 final size:40
Alignment explanation
Indices: 31928972--31929070 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 40
31928962 AGCAATAAAG
* * *
31928972 TGACACCCAATGTCTCATCG-GCCTAGCCGAAGTAAAGTA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATA
* ** * *
31929011 -G-TACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAAT-A
31929050 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
31929071 CTCAATGTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
37 13 0.29
38 15 0.33
39 1 0.02
40 1 0.02
41 15 0.33
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.22
Consensus pattern (40 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATA
Found at i:31929522 original size:17 final size:18
Alignment explanation
Indices: 31929488--31929523 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31929478 TGAATTTCTA
*
31929488 TCCAATTTATTGCCTAAT
1 TCCAATTTAATGCCTAAT
31929506 TCCAATTTAAT-CCTAAT
1 TCCAATTTAATGCCTAAT
31929523 T
1 T
31929524 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
TCCAATTTAATGCCTAAT
Found at i:31942154 original size:50 final size:50
Alignment explanation
Indices: 31942096--31942197 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
31942086 TAGTGTTTGG
* *
31942096 AAAAATACTTAGTAATTAAATTTGGGTGTAATTAGAGTATTTACACAAAT
1 AAAAATACTTAGTAATTAAATTTGGGTATAATTAGAGTACTTACACAAAT
* *
31942146 AAAAATACTTAGTAATTGAATTTGGGTATAATTAGAGTACTTACGCAAAT
1 AAAAATACTTAGTAATTAAATTTGGGTATAATTAGAGTACTTACACAAAT
31942196 AA
1 AA
31942198 CTACACTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (50 bp):
AAAAATACTTAGTAATTAAATTTGGGTATAATTAGAGTACTTACACAAAT
Done.