Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold639
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: 281924
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:166294 original size:16 final size:15
Alignment explanation
Indices: 166245--166306 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 15
166235 AAGTTAGGTA
166245 AAAAAGAAAGAAAGAAG
1 AAAAAGAAA-AAA-AAG
**
166262 ATGAAGAAGAAAGAAAG
1 AAAAAGAA-AAA-AAAG
166279 AAAAAGGAAAAAAAAG
1 AAAAA-GAAAAAAAAG
166295 AAAAAGAAAAAA
1 AAAAAGAAAAAA
166307 TATGAAATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.18
16 9 0.24
17 17 0.45
18 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:166294 original size:20 final size:23
Alignment explanation
Indices: 166244--166297 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
166234 AAAGTTAGGT
166244 AAAAAAGAAAGAAAGAAGATGAAG
1 AAAAAAGAAAGAAAGAAGA-GAAG
*
166268 AAGAAAGAAAGAAA-AAG-GAA-
1 AAAAAAGAAAGAAAGAAGAGAAG
166288 AAAAAAGAAA
1 AAAAAAGAAA
166298 AAGAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
23 3 0.11
24 13 0.46
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAGAAAGAAGAGAAG
Found at i:166313 original size:16 final size:15
Alignment explanation
Indices: 166251--166313 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
166241 GGTAAAAAAG
*
166251 AAAGAAAGAAGATGAA
1 AAAGAAA-AAAATGAA
* *
166267 GAAGAAAGAAA-GAA
1 AAAGAAAAAAATGAA
*
166281 AAAGGAAAAAAAAGAA
1 AAA-GAAAAAAATGAA
166297 AAAGAAAAAATATGAA
1 AAAGAAAAAA-ATGAA
166313 A
1 A
166314 TGGAGTGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.13
15 16 0.42
16 17 0.45
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (15 bp):
AAAGAAAAAAATGAA
Found at i:169024 original size:47 final size:47
Alignment explanation
Indices: 168886--169025 Score: 165
Period size: 47 Copynumber: 3.0 Consensus size: 47
168876 CGTTGCGACA
* * *
168886 AGGTTCTAATGCCAATATAGTCAAACGAGAGTGGAAAGAGTTTGACT
1 AGGTCCTAATGCCAATACAGTCAAACGAGAGTGAAAAGAGTTTGACT
* * * * *
168933 AGGTCTTAATGCCAATACAATCAAATGAG-GATGAGAAGAATTTGACT
1 AGGTCCTAATGCCAATACAGTCAAACGAGAG-TGAAAAGAGTTTGACT
* * *
168980 AGGTCCTAATGCCAATGCAGTCAAACAAGAGTAAAAAGAGTTTGAC
1 AGGTCCTAATGCCAATACAGTCAAACGAGAGTGAAAAGAGTTTGAC
169026 CAGATGCAGT
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
46 1 0.01
47 73 0.97
48 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (47 bp):
AGGTCCTAATGCCAATACAGTCAAACGAGAGTGAAAAGAGTTTGACT
Found at i:169244 original size:35 final size:35
Alignment explanation
Indices: 169013--169298 Score: 241
Period size: 35 Copynumber: 8.1 Consensus size: 35
169003 AACAAGAGTA
* * ** *
169013 AAAAGAGTTTGACCAGATGCAGTCAAACAATGATGG
1 AAAA-AGTTTGACTAGATACAACCAAACGATGATGG
** *
169049 AAAAAGTTTGACTAGATACAGTCAAACGATAATGG
1 AAAAAGTTTGACTAGATACAACCAAACGATGATGG
* * * *
169084 AAAAAGCTTGACTAGATATAGCCAAACTATGATGG
1 AAAAAGTTTGACTAGATACAACCAAACGATGATGG
* * ** *
169119 AAAGAAGTTTAACCAGATACAGTCAAACGATGGTGG
1 AAA-AAGTTTGACTAGATACAACCAAACGATGATGG
** * * * * *
169155 AAAGTGTTTAACCAGATACTATCAAATGATGATGG
1 AAAAAGTTTGACTAGATACAACCAAACGATGATGG
* *
169190 AAAGAGTTTGACCAGATACAACCAAACGATGATGG
1 AAAAAGTTTGACTAGATACAACCAAACGATGATGG
* * *
169225 AAAAAGTTTGACTAAATACAACTAAACGATAATGG
1 AAAAAGTTTGACTAGATACAACCAAACGATGATGG
* * *
169260 AAAAAAGTTTAACTAGATATAGA-CAAACGATGGTGG
1 -AAAAAGTTTGACTAGATACA-ACCAAACGATGATGG
169296 AAA
1 AAA
169299 GATTTGATTG
Statistics
Matches: 209, Mismatches: 38, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
35 149 0.71
36 59 0.28
37 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (35 bp):
AAAAAGTTTGACTAGATACAACCAAACGATGATGG
Found at i:169260 original size:141 final size:141
Alignment explanation
Indices: 169042--169299 Score: 372
Period size: 141 Copynumber: 1.8 Consensus size: 141
169032 CAGTCAAACA
* ** * * *
169042 ATGATGGAAAAAGTTTGACTAGATACAGTCAAACGATAATGGAAAAAGCTTGACTAGATATAGCC
1 ATGATGGAAAAAGTTTGACCAGATACAACCAAACGATAATGGAAAAAGCTTGACTAAATACAACC
* * * *
169107 AAACTATGATGGAAAGAAGTTTAACCAGATACAGTCAAACGATGGTGGAAAGTGTTTAACCAGAT
66 AAACGATAATGGAAAAAAGTTTAACCAGATACAGACAAACGATGGTGGAAAGTGTTTAACCAGAT
169172 ACTATCAAATG
131 ACTATCAAATG
* * * *
169183 ATGATGGAAAGAGTTTGACCAGATACAACCAAACGATGATGGAAAAAGTTTGACTAAATACAACT
1 ATGATGGAAAAAGTTTGACCAGATACAACCAAACGATAATGGAAAAAGCTTGACTAAATACAACC
* *
169248 AAACGATAATGGAAAAAAGTTTAACTAGATATAGACAAACGATGGTGGAAAG
66 AAACGATAATGGAAAAAAGTTTAACCAGATACAGACAAACGATGGTGGAAAG
169300 ATTTGATTGA
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
141 101 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (141 bp):
ATGATGGAAAAAGTTTGACCAGATACAACCAAACGATAATGGAAAAAGCTTGACTAAATACAACC
AAACGATAATGGAAAAAAGTTTAACCAGATACAGACAAACGATGGTGGAAAGTGTTTAACCAGAT
ACTATCAAATG
Found at i:169291 original size:71 final size:70
Alignment explanation
Indices: 169037--169298 Score: 249
Period size: 71 Copynumber: 3.7 Consensus size: 70
169027 AGATGCAGTC
* * * * * *
169037 AAACAATGATGGAAAAAGTTTGACTAGATACAGTCAAACGATAATGGAAAAAGCTTGACTAGATA
1 AAACGATGATGGAAAAAGTTTAACCAGATACAGACAAACGATGATGGAAAAAGTTTGACTAGATA
* * *
169102 TAGCC
66 CAACT
* * * ** * *
169107 AAACTATGATGGAAAGAAGTTTAACCAGATACAGTCAAACGATGGTGGAAAGTGTTTAACCAGAT
1 AAACGATGATGGAAA-AAGTTTAACCAGATACAGACAAACGATGATGGAAAAAGTTTGACTAGAT
*
169172 ACTA-T
65 ACAACT
* * * *
169177 CAAATGATGATGGAAAGAGTTTGACCAGATACA-ACCAAACGATGATGGAAAAAGTTTGACTAAA
1 -AAACGATGATGGAAAAAGTTTAACCAGATACAGA-CAAACGATGATGGAAAAAGTTTGACTAGA
169241 TACAACT
64 TACAACT
* * * *
169248 AAACGATAATGGAAAAAAGTTTAACTAGATATAGACAAACGATGGTGGAAA
1 AAACGATGATGG-AAAAAGTTTAACCAGATACAGACAAACGATGATGGAAA
169299 GATTTGATTG
Statistics
Matches: 153, Mismatches: 33, Indels: 11
0.78 0.17 0.06
Matches are distributed among these distances:
70 66 0.43
71 86 0.56
72 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (70 bp):
AAACGATGATGGAAAAAGTTTAACCAGATACAGACAAACGATGATGGAAAAAGTTTGACTAGATA
CAACT
Found at i:169297 original size:106 final size:106
Alignment explanation
Indices: 169035--169305 Score: 280
Period size: 106 Copynumber: 2.6 Consensus size: 106
169025 CCAGATGCAG
* * * * * * * *
169035 TCAAACAATGATGGAAAAAGTTTGACTAGATACAGTCAAACGATAATGGAAAAAGCTTGACTAGA
1 TCAAACGATAATGGAAAAAGTTTAACTAGATATAGTCAAACGATGATGGAAAGAGTTTGACCAGA
* * * * *
169100 TATAGCCAAACTATGATGGAAAGAAGTTTAACCAGATACAG
66 TACAACCAAACGATGATGGAAAGAAGTTTAACCAAATACAC
** ** * *
169141 TCAAACGATGGTGGAAAGTGTTTAACCAGATACTA-TCAAATGATGATGGAAAGAGTTTGACCAG
1 TCAAACGATAATGGAAAAAGTTTAACTAGATA-TAGTCAAACGATGATGGAAAGAGTTTGACCAG
* *
169205 ATACAACCAAACGATGATGGAAA-AAGTTTGACTAAATACAAC
65 ATACAACCAAACGATGATGGAAAGAAGTTTAACCAAATAC-AC
* *
169247 T-AAACGATAATGGAAAAAAGTTTAACTAGATATAGACAAACGATGGTGGAAAGA-TTTGA
1 TCAAACGATAATGG-AAAAAGTTTAACTAGATATAGTCAAACGATGATGGAAAGAGTTTGA
169306 TTGAGTATAA
Statistics
Matches: 134, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
105 30 0.22
106 103 0.77
107 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (106 bp):
TCAAACGATAATGGAAAAAGTTTAACTAGATATAGTCAAACGATGATGGAAAGAGTTTGACCAGA
TACAACCAAACGATGATGGAAAGAAGTTTAACCAAATACAC
Found at i:169810 original size:89 final size:90
Alignment explanation
Indices: 169482--169813 Score: 445
Period size: 90 Copynumber: 3.7 Consensus size: 90
169472 TCCTAGTCCT
* * * ** * * * *
169482 AAGAAAATCAAGCTTTGTGATGCATCAATATCAGCTAGTGG-TTGGGTGAAGGAGATATGATTGG
1 AAGAAAATCAGGCTTGGTGATGCATCAATACCATATAGTGGTTTGGATAAAGGGGATATGATT-A
* * * *
169546 GGAATATGTAGGTTGCACCTTGTCCC
65 AGAATGTGTAGGTTGTACCTTGCCCC
*
169572 AA-AGAAATCAGGCTTGGTGATGCATCAGTACCATATAGTGGTTTGGATAAAGGGGATATGATTA
1 AAGA-AAATCAGGCTTGGTGATGCATCAATACCATATAGTGGTTTGGATAAAGGGGATATGATTA
169636 AGAATGTGTAGGTTGTACCTTGCCCC
65 AGAATGTGTAGGTTGTACCTTGCCCC
* * *
169662 AAGGAAATCAGGCTTGGTGATACATGAATACCATATAGTGGTTTGGATAAAGGGGATATGATTAA
1 AAGAAAATCAGGCTTGGTGATGCATCAATACCATATAGTGGTTTGGATAAAGGGGATATGATTAA
*
169727 GAATGTGTAGGCTGTACCTTG-CCC
66 GAATGTGTAGGTTGTACCTTGCCCC
* *
169751 AAGAAAATCAGTCTTGGTGATGCATCAATACCATCTAGTGGTTTGGATAAAGGGGATATGATT
1 AAGAAAATCAGGCTTGGTGATGCATCAATACCATATAGTGGTTTGGATAAAGGGGATATGATT
169814 GGGAAATATA
Statistics
Matches: 215, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
89 62 0.29
90 135 0.63
91 18 0.08
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (90 bp):
AAGAAAATCAGGCTTGGTGATGCATCAATACCATATAGTGGTTTGGATAAAGGGGATATGATTAA
GAATGTGTAGGTTGTACCTTGCCCC
Found at i:173479 original size:52 final size:52
Alignment explanation
Indices: 173331--173459 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
173321 CGAAATATGA
* *
173331 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
173383 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
173435 AAATTTGCCTGCATGTATCAATACA
1 AAATTTGCCTGCATGTATCGATACA
173460 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:173486 original size:13 final size:13
Alignment explanation
Indices: 173468--173492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173458 CAAAGATCAG
173468 TGTATCGATACAA
1 TGTATCGATACAA
173481 TGTATCGATACA
1 TGTATCGATACA
173493 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:173559 original size:19 final size:19
Alignment explanation
Indices: 173535--173599 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
173525 TAGCTTACAT
173535 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
173554 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
173567 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
173586 TGTATCGATACAAA
1 TGTATCGATACAAA
173600 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:173571 original size:32 final size:32
Alignment explanation
Indices: 173530--173697 Score: 173
Period size: 32 Copynumber: 5.1 Consensus size: 32
173520 GGCAGTAGCT
173530 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
173562 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* * * *
173594 TACAAATCGT-T-GAAATTCAAAA-TT-TTTAATCGT
1 TAC--ATTGTATCG--ATACAAAACTTATGT-ATCGA
*
173627 TGGGACCTTGTATCGATACAAAACTTATGTATCGA
1 T---ACATTGTATCGATACAAAACTTATGTATCGA
*
173662 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
173694 TACA
1 TACA
173698 AATCGTTGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
32 70 0.63
33 8 0.07
34 20 0.18
35 8 0.07
36 5 0.05
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:173572 original size:13 final size:13
Alignment explanation
Indices: 173554--173578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173544 ACAAAACTTA
173554 TGTATCGATACAT
1 TGTATCGATACAT
173567 TGTATCGATACA
1 TGTATCGATACA
173579 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:173646 original size:100 final size:100
Alignment explanation
Indices: 173534--173746 Score: 426
Period size: 100 Copynumber: 2.1 Consensus size: 100
173524 GTAGCTTACA
173534 TTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTATGTATCGATACAA
1 TTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTATGTATCGATACAA
173599 ATCGTTGAAATTCAAAATTTTTAATCGTTGGGACC
66 ATCGTTGAAATTCAAAATTTTTAATCGTTGGGACC
173634 TTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTATGTATCGATACAA
1 TTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTATGTATCGATACAA
173699 ATCGTTGAAATTCAAAATTTTTAATCGTTGGGACC
66 ATCGTTGAAATTCAAAATTTTTAATCGTTGGGACC
173734 TTGTATCGATACA
1 TTGTATCGATACA
173747 TTCTAACAAT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 113 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (100 bp):
TTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTATGTATCGATACAA
ATCGTTGAAATTCAAAATTTTTAATCGTTGGGACC
Found at i:173659 original size:19 final size:19
Alignment explanation
Indices: 173635--173699 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
173625 GTTGGGACCT
173635 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
173654 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
173667 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
173686 TGTATCGATACAAA
1 TGTATCGATACAAA
173700 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:173672 original size:13 final size:13
Alignment explanation
Indices: 173654--173678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173644 ACAAAACTTA
173654 TGTATCGATACAT
1 TGTATCGATACAT
173667 TGTATCGATACA
1 TGTATCGATACA
173679 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:175283 original size:13 final size:13
Alignment explanation
Indices: 175265--175289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175255 CATAAAGTGT
175265 TGTATCGATACAA
1 TGTATCGATACAA
175278 TGTATCGATACA
1 TGTATCGATACA
175290 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:175287 original size:33 final size:33
Alignment explanation
Indices: 175245--175311 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
175235 TTCAACGATT
175245 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
175278 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
175311 T
1 T
175312 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:175441 original size:52 final size:52
Alignment explanation
Indices: 175385--175513 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
175375 CACGGATCTT
*
175385 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
* *
175437 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
*
175489 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
175514 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
Found at i:178629 original size:194 final size:193
Alignment explanation
Indices: 178300--178684 Score: 725
Period size: 194 Copynumber: 2.0 Consensus size: 193
178290 AAATGATCGG
178300 TGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCAT
1 TGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCAT
* * *
178365 CTACTGATCTTTCCCTTTTAATTAACACGCTTCCCATCATGCAATAGAAATCCCCAATCGCGAGG
66 CTACTGATCTTCCCCCTTTAATTAACACACTTCCCATCATGCAATAGAAATCCCCAATCGCGAGG
*
178430 GATATTTAAGTCGAGCGTGCCTCATTTGCCCTATCGCTGGGGTCGAGCGCACGTTACGACAGCT
131 GATA-TTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAGCT
178494 TGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCAT
1 TGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCAT
178559 CTACTGATCTTCCCCCTTTAATTAACACACTTCCCATCATGCAATAGAAATCCCCAATCGCGAGG
66 CTACTGATCTTCCCCCTTTAATTAACACACTTCCCATCATGCAATAGAAATCCCCAATCGCGAGG
178624 GATATTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAG
131 GATATTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAG
178685 AGTGTTTGAA
Statistics
Matches: 187, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
193 56 0.30
194 131 0.70
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (193 bp):
TGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCAT
CTACTGATCTTCCCCCTTTAATTAACACACTTCCCATCATGCAATAGAAATCCCCAATCGCGAGG
GATATTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAGCT
Found at i:182374 original size:156 final size:155
Alignment explanation
Indices: 182187--182870 Score: 644
Period size: 156 Copynumber: 4.4 Consensus size: 155
182177 GAAAACCAAG
* * * * *
182187 CCTATCTCTAAATGCCCACCTTCAACGTAAAAGAGGACCTGGTGATAACCTAGGACTAGATTTTA
1 CCTATC-CTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGATAACCTAGGACTAGATTTTA
* **
182252 TAAAATTACAAAAATACCCTTATAAGTATACCTTCAACATAAAAGTATCCCGGCAACCCTAAAGG
65 -AAAATTACAAAAATACCCTTATAAGTATACCTTCGACATAAAAGTATCCCGATAACCCTAAAGG
182317 ACTTAAAAAGGTTATAGCTGGGGTGAA
129 ACTTAAAAAGGTTATAGCTGGGGTGAA
* * * * * *
182344 CCTATCCTAAATACCCACCTTTAGCATAAAAGCGAACCTAGTGACAACCTAAGACTCGATTCTAA
1 CCTATCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGATAACCTAGGACTAGATT-TTA
* * ** * * * *
182409 AAAATTACAAAAATGCCCTTGTGGGCATACCTTCGACATGAAAGTATCCTGATAACCCTAAAAGA
65 AAAATTACAAAAATACCCTTATAAGTATACCTTCGACATAAAAGTATCCCGATAACCCTAAAGGA
* **
182474 CTTAAAAAGGTTATAAG-TAGGGACAA
130 CTTAAAAAGGTTAT-AGCTGGGGTGAA
* *** *
182500 CCTATCCTAAATACCCACC-TCCGACATAAAAGCGAACCCAATGATAACCTAGGACTCGATTTTA
1 CCTATCCTAAATACCCACCTTCAG-CATAAAAGCGAACCTGGTGATAACCTAGGACTAGATTTTA
** ** *
182564 AATAATTACAAAAATATCCC-TATGGGTATAGTTTCGACATGAAAGTATCCCGATAATCCC-AAA
65 AA-AATTACAAAAATA-CCCTTATAAGTATACCTTCGACATAAAAGTATCCCGATAA-CCCTAAA
*
182627 GTACTTAAAAAGGTTATAGCTGGGGTGAA
127 GGACTTAAAAAGGTTATAGCTGGGGTGAA
** * * *
182656 CCTATCCTAAATACCCACCTTTGGCATAAAAGCGAA-CTCGGTGATAGCCTAGGACTAGGTTATA
1 CCTATCCTAAATACCCACCTTCAGCATAAAAGCGAACCT-GGTGATAACCTAGGACTAGATTTTA
* * * * * * * * *
182720 GGAAAATTAAAAAAATGCCCCTA-AAGGATACCTTCGACGTAGAAGTGT-CCGATACCCCTCAAG
65 --AAAATTACAAAAATACCCTTATAAGTATACCTTCGACATAAAAGTATCCCGATAACCCTAAAG
* * *** *
182783 AACTTAAAAAGATTATAAAAGGGATGAA
128 GACTTAAAAAGGTTATAGCTGGGGTGAA
* * * *
182811 CCTATCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGATAACCTAGGACT
1 -C---CTATCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGATAACCTAGGACT
182871 CAGTTCTGAA
Statistics
Matches: 433, Mismatches: 76, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
154 3 0.01
155 40 0.09
156 308 0.71
157 31 0.07
158 2 0.00
159 48 0.11
160 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (155 bp):
CCTATCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGATAACCTAGGACTAGATTTTAA
AAATTACAAAAATACCCTTATAAGTATACCTTCGACATAAAAGTATCCCGATAACCCTAAAGGAC
TTAAAAAGGTTATAGCTGGGGTGAA
Found at i:184938 original size:166 final size:165
Alignment explanation
Indices: 184653--185191 Score: 568
Period size: 166 Copynumber: 3.3 Consensus size: 165
184643 ATAAGAGTTT
* * * * * *
184653 AATAAAAATATTAGATGAATTTTAAAAATTTTAAACTGAAG-AAAAT-CCACC-GAAATATTTAT
1 AATAATAATATTTGATGAATTTTAAAAATTATAAAC-AAAGAAAAATCCCACCAAAAATATTTAC
** * * *
184715 GGAATCGAAAACTC-GATTTTTCGAAAACAGGGGAATTTCAAAGAAAAAATTCAAAACTCATGAA
65 GGAATAAAAAAATCTG-TATTTCGAAAATA-GGGAATTTCAAAGAAAAAATTCAAAACTCATGAA
184779 AATAAATTAATTTTTCAAAACTAATTTAATATGAATTA
128 AATAAATTAATTTTTCAAAACTAATTTAATATGAATTA
* *
184817 AATAATAATATTTGATGAATTTTAAAAATTATAAACAAAGAAAAATCCCCCCAAAAACATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTATAAACAAAGAAAAATCCCACCAAAAATATTTACG
* * ** *
184882 GAATAAAAAATTCTGTATTTCAAAAATAGAGGAATTTTGAAGAAAAAATTCAAAACTCATAAAAA
66 GAATAAAAAAATCTGTATTTCGAAAATAG-GGAATTTCAAAGAAAAAATTCAAAACTCATGAAAA
* * *
184947 TAGATTAATTTTTTAAAACAAATTTAATATGAATTA
130 TAAATTAATTTTTCAAAACTAATTTAATATGAATTA
* * * *
184983 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAATACTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTATAAACAAAGAAAAATCCCACCAAAAATATTTACG
** * * ** * * ** * *
185048 GGTTAGAAAAAAT-TGTATTTTGAAAATATGGGAGTTTCCTATAAAAACTAAAAAATTTATGAAA
66 GAATA-AAAAAATCTGTATTTCGAAAATA-GGGAATTTCAAAGAAAAAATTCAAAACTCATGAAA
* * * * * *
185112 ATGAATGAATTATTGAAAAATGATTTAATATGAATTA
129 ATAAATTAATTTTTCAAAACTAATTTAATATGAATTA
* * *
185149 AATAATAATATTTGATGAA-TTTAAAAATTTTAATCAATGAAAA
1 AATAATAATATTTGATGAATTTTAAAAATTATAAACAAAGAAAA
185192 TCCTCCTAAG
Statistics
Matches: 314, Mismatches: 54, Indels: 13
0.82 0.14 0.03
Matches are distributed among these distances:
163 3 0.01
164 38 0.12
165 24 0.08
166 241 0.77
167 8 0.03
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.32
Consensus pattern (165 bp):
AATAATAATATTTGATGAATTTTAAAAATTATAAACAAAGAAAAATCCCACCAAAAATATTTACG
GAATAAAAAAATCTGTATTTCGAAAATAGGGAATTTCAAAGAAAAAATTCAAAACTCATGAAAAT
AAATTAATTTTTCAAAACTAATTTAATATGAATTA
Found at i:187147 original size:168 final size:167
Alignment explanation
Indices: 186950--187322 Score: 385
Period size: 168 Copynumber: 2.2 Consensus size: 167
186940 ATTTTCGTGG
* * *
186950 GTTTAAATTTTTTAAAAATTTATCAAATATTATTATTTAATT-ACTAATAAATCAATATTCAAAA
1 GTTTAAAATTTTT-AAAATTTATCAAATATTATTATTTAATTCAC-AATAAACCAATATTAAAAA
* * * * * *
187014 ATTCATTTAACTTCATGAGTTTT-TTTATTTTCTACTTGAAATTTTCC-ATGTTT-CTAAAATAT
64 ATTCATTCAACTTCAAGAGTTTTAATT-TTTTCT--TTGAAATTCTCCTAT-TTTACAAAAAAAT
* * * *
187076 AAAGTTTTTTACTCCATAAATGTTTTCTGGGGGATTTTTCTTG
125 AAAGTTTTCTACTCCATAAATGTTTTCTAGGAGATTTTTCTTA
** * * * * * *
187119 GTTTTTAATTTTTAAAATTTATCAAATATTATCACTTGATTCACATTAAACCAGTTTTAAAAAAT
1 GTTTAAAATTTTTAAAATTTATCAAATATTATTATTTAATTCACAATAAACCAATATTAAAAAAT
* ** * *
187184 TTATTCATTTTCAAGAGTTTTAAATTTTTTCTTTGAAATTCTCCTATTTTAGAAAAAAATAGAGT
66 TCATTCAACTTCAAGAGTTTT-AATTTTTTCTTTGAAATTCTCCTATTTTACAAAAAAATAAAGT
* *
187249 TTTCTACTCCATAAATGTTTTTTAGGAGATTTTTTTTA
130 TTTCTACTCCATAAATGTTTTCTAGGAGATTTTTCTTA
* *
187287 GTTTAAAATTTTTAAAATTCATCTAATATTATTATT
1 GTTTAAAATTTTTAAAATTTATCAAATATTATTATT
187323 AAACTCTCAT
Statistics
Matches: 165, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
167 14 0.08
168 131 0.79
169 18 0.11
170 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (167 bp):
GTTTAAAATTTTTAAAATTTATCAAATATTATTATTTAATTCACAATAAACCAATATTAAAAAAT
TCATTCAACTTCAAGAGTTTTAATTTTTTCTTTGAAATTCTCCTATTTTACAAAAAAATAAAGTT
TTCTACTCCATAAATGTTTTCTAGGAGATTTTTCTTA
Found at i:189588 original size:154 final size:153
Alignment explanation
Indices: 189164--189589 Score: 459
Period size: 154 Copynumber: 2.8 Consensus size: 153
189154 ATATTGAAGA
* * * *
189164 TATCCTCTAAAGGCATTTTCATAATTTTT-AAAACTAAGT-TATAAGTTGTCACC-GAGTCCGCT
1 TATCCCCTAAAGGCATCTTCATAATTTTTCAAAACCAACTCT-T-AGTTGTCACCAG-GTCCGCT
* * * ** * *
189226 TTTATGCCGAAGGTGAGAATTTAGGATAGGTTCACCCCATCCATAATCCTTTCTAAGTCTTTTAG
63 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTC-CTCCATTTATAATCCTTTTTAAGTCTTTTAA
*
189291 GGGTATCGAGTATTTCTACGTCGAAAG
127 GGGTATCGAGTACTTCTACGTCGAAAG
* * * ** *
189318 TATCCCCTAAAGGCATTTTCGTAATTTTCCAAAA-CAACTCTTTAGTTGTCATTAGGTTCGCTTT
1 TATCCCCTAAAGGCATCTTCATAATTTTTCAAAACCAACTC-TTAGTTGTCACCAGGTCCGCTTT
* * * * * *
189382 TATGCCGAATGTGGGTATTTAGGATAGTTTCATCTCTTTTAAAATCCATTTTAAGTCTTTTAAGG
65 TATGCCGAAGGTGGGTATTTAGGATAGGTTCCTC-CATTTATAATCCTTTTTAAGTCTTTTAAGG
*
189447 GTATCGGGTACTTCTACGTC-AAAGG
129 GTATCGAGTACTTCTACGTCGAAA-G
* * *
189472 TATCCCCTAAGGGTATCTTCATAATTTTTCAAAACCAACTCTTAGGTTGTCACCAGGTCCGTTTT
1 TATCCCCTAAAGGCATCTTCATAATTTTTCAAAACCAACTCTTA-GTTGTCACCAGGTCCGCTTT
* *
189537 TATGCCAAAGGTGGGTATTTGGGATAGGTTCGCTCCATTTATAAT-CTTTTTAA
65 TATGCCGAAGGTGGGTATTTAGGATAGGTTC-CTCCATTTATAATCCTTTTTAA
189590 TTCCTTTAGG
Statistics
Matches: 223, Mismatches: 40, Indels: 18
0.79 0.14 0.06
Matches are distributed among these distances:
153 4 0.02
154 153 0.69
155 63 0.28
156 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (153 bp):
TATCCCCTAAAGGCATCTTCATAATTTTTCAAAACCAACTCTTAGTTGTCACCAGGTCCGCTTTT
ATGCCGAAGGTGGGTATTTAGGATAGGTTCCTCCATTTATAATCCTTTTTAAGTCTTTTAAGGGT
ATCGAGTACTTCTACGTCGAAAG
Found at i:190123 original size:13 final size:13
Alignment explanation
Indices: 190105--190130 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190095 TACACCAAGT
190105 ATGTATCGATACA
1 ATGTATCGATACA
190118 ATGTATCGATACA
1 ATGTATCGATACA
190131 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:193834 original size:15 final size:15
Alignment explanation
Indices: 193814--193852 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
193804 TAAAAATGTC
*
193814 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
193829 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
193844 CCAAATGAA
1 CAAAATGAA
193853 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:195943 original size:13 final size:13
Alignment explanation
Indices: 195925--195950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
195915 ACATTTTTCT
195925 TTGTATCGATACA
1 TTGTATCGATACA
195938 TTGTATCGATACA
1 TTGTATCGATACA
195951 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:196114 original size:20 final size:20
Alignment explanation
Indices: 196071--196116 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
196061 AAATCTTTTG
196071 CAAAATACTTATTTTTCACTT
1 CAAAATACTTATTTTTCAC-T
*
196092 CAAATTACTTCATTTTTCA-T
1 CAAAATACTT-ATTTTTCACT
196112 CAAAA
1 CAAAA
196117 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (20 bp):
CAAAATACTTATTTTTCACT
Found at i:198512 original size:13 final size:13
Alignment explanation
Indices: 198494--198519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198484 TACACCAAGT
198494 ATGTATCGATACA
1 ATGTATCGATACA
198507 ATGTATCGATACA
1 ATGTATCGATACA
198520 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:200255 original size:154 final size:154
Alignment explanation
Indices: 199831--200256 Score: 479
Period size: 154 Copynumber: 2.8 Consensus size: 154
199821 ATATTGAAGA
* * * * * *
199831 TATCCTCTAGAGGCATTTTCATAATTTT-TAAAACTAAGT-TATAAGTTGTCACC-GAGTCCGCT
1 TATCCCCTAGAGGCATCTTCGTAATTTTCCAAAAC-AACTCT-TTAGTTGTCACCAG-GTCCGCT
* * * ** * *
199893 TTTATGCCGAAGGTGAGAATTTAGGATAGGTTCACCCCATCCATAATCCTTTCTAAGTCTTTTAG
63 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATAATCCTTTTTAAGTCTTTTAA
*
199958 GGGTATCGAGTATTTCTACGTCGAAAG
128 GGGTATCGAGTACTTCTACGTCGAAAG
* ** *
199985 TATCCCCTAGAGGCATTTTCGTAATTTTCCAAAACAACTCTTTAGTTGTCATTAGGTTCGCTTTT
1 TATCCCCTAGAGGCATCTTCGTAATTTTCCAAAACAACTCTTTAGTTGTCACCAGGTCCGCTTTT
* * * * *
200050 ATGCCGAAGGTGGGTATTTAGGATAGTTTCATCTCTTTTAAAATCCATTTTAAGTCTTTTAAGGG
66 ATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATAATCCTTTTTAAGTCTTTTAAGGG
*
200115 TATCGGGTACTTCTACGTC-AAAGG
131 TATCGAGTACTTCTACGTCGAAA-G
* *
200139 TATCCCCTA-AGGGTATCTTCGTAATTTTTCAAAACCAACTC-TTAGGTTGTCACCAGGTCCGCT
1 TATCCCCTAGA-GGCATCTTCGTAATTTTCCAAAA-CAACTCTTTA-GTTGTCACCAGGTCCGCT
* * *
200202 TTTATGCCAAAGGTGGGTATTTGGGATAGGTTCGTCCCATTTATAAT-CTTTTTAA
63 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATAATCCTTTTTAA
200257 TTCCTTTAGG
Statistics
Matches: 229, Mismatches: 36, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
153 4 0.02
154 157 0.69
155 68 0.30
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (154 bp):
TATCCCCTAGAGGCATCTTCGTAATTTTCCAAAACAACTCTTTAGTTGTCACCAGGTCCGCTTTT
ATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATAATCCTTTTTAAGTCTTTTAAGGG
TATCGAGTACTTCTACGTCGAAAG
Found at i:200791 original size:13 final size:13
Alignment explanation
Indices: 200773--200798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200763 TGCACCAAGT
200773 ATGTATCGATACA
1 ATGTATCGATACA
200786 ATGTATCGATACA
1 ATGTATCGATACA
200799 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:202052 original size:37 final size:37
Alignment explanation
Indices: 202011--202086 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
202001 TCACATAGAA
202011 TAATAAAATTATTTTATTAAATATTATCTATGGGGAT
1 TAATAAAATTATTTTATTAAATATTATCTATGGGGAT
202048 TAATAAAATTATTTTATTAAATATTATCTATGGGGAT
1 TAATAAAATTATTTTATTAAATATTATCTATGGGGAT
202085 TA
1 TA
202087 TAATTAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (37 bp):
TAATAAAATTATTTTATTAAATATTATCTATGGGGAT
Found at i:202927 original size:13 final size:13
Alignment explanation
Indices: 202909--202934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
202899 TACACAAAGT
202909 ATGTATCGATACA
1 ATGTATCGATACA
202922 ATGTATCGATACA
1 ATGTATCGATACA
202935 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:202932 original size:32 final size:33
Alignment explanation
Indices: 202891--202954 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
202881 TAGCCAAACT
**
202891 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
202923 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
202955 TTGGCTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:203455 original size:34 final size:35
Alignment explanation
Indices: 203392--203458 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
203382 CTAAGTGATT
203392 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
203428 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
203459 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:208154 original size:13 final size:13
Alignment explanation
Indices: 208136--208161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208126 TACACAAAGT
208136 ATGTATCGATACA
1 ATGTATCGATACA
208149 ATGTATCGATACA
1 ATGTATCGATACA
208162 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:208159 original size:32 final size:33
Alignment explanation
Indices: 208118--208181 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
208108 TAGCCAAACT
**
208118 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
208150 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
208182 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:208683 original size:34 final size:35
Alignment explanation
Indices: 208620--208686 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
208610 CTAAGTGATT
208620 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
208656 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
208687 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:211476 original size:33 final size:33
Alignment explanation
Indices: 211419--211484 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
211409 GCCAAGGAAA
*
211419 TGTATCGATACATTATTCAATGTATTGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
**
211452 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ATTCAATGTATCGATACAT
211485 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:215139 original size:17 final size:17
Alignment explanation
Indices: 215117--215155 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
215107 GAAACACAAA
215117 AAAAATGA-AAAAAAATG
1 AAAAATGAGAAAAAAA-G
215134 AAAAATGAGAAAAAAAG
1 AAAAATGAGAAAAAAAG
215151 AAAAA
1 AAAAA
215156 AAAAAGCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAATGAGAAAAAAAG
Found at i:215158 original size:9 final size:10
Alignment explanation
Indices: 215114--215158 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
215104 TAAGAAACAC
215114 AAAAAAAATG
1 AAAAAAAATG
215124 AAAAAAAATG
1 AAAAAAAATG
215134 ---AAAAATG
1 AAAAAAAATG
215141 AGAAAAAAA-G
1 A-AAAAAAATG
215151 AAAAAAAA
1 AAAAAAAA
215159 AAGCATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
7 7 0.23
9 7 0.23
10 12 0.39
11 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:216436 original size:20 final size:20
Alignment explanation
Indices: 216413--216485 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
216403 ACAATTCAAA
216413 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
216433 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
216454 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
216474 GTATCGATACAT
1 GTATCGATACAT
216486 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:216457 original size:21 final size:21
Alignment explanation
Indices: 216431--216506 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
216421 ACATGTTGCA
216431 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
216452 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
216472 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
216493 ATGTATCGATACAT
1 ATGTATCGATACAT
216507 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:216464 original size:41 final size:41
Alignment explanation
Indices: 216413--216506 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
216403 ACAATTCAAA
*
216413 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
216454 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
216495 GTATCGATACAT
1 GTATCGATACAT
216507 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:216563 original size:13 final size:13
Alignment explanation
Indices: 216545--216570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
216535 TACAGCAAGT
216545 ATGTATCGATACA
1 ATGTATCGATACA
216558 ATGTATCGATACA
1 ATGTATCGATACA
216571 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:220653 original size:15 final size:15
Alignment explanation
Indices: 220633--220663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
220623 TAAAAATGTC
*
220633 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
220648 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
220663 C
1 C
220664 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:222761 original size:13 final size:13
Alignment explanation
Indices: 222743--222780 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
222733 CATTTTTATT
222743 TGTATCGATACAA
1 TGTATCGATACAA
*
222756 TGTATCGATACAC
1 TGTATCGATACAA
222769 TGTATCGATACA
1 TGTATCGATACA
222781 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:225247 original size:20 final size:20
Alignment explanation
Indices: 225224--225296 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
225214 ACAATTCAAA
225224 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
225244 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
*
225265 GTATTGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
225285 GTATCGATACAT
1 GTATCGATACAT
225297 AAAAAAGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:225268 original size:21 final size:21
Alignment explanation
Indices: 225242--225317 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
225232 ACATGTTGCA
225242 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
* ****
225263 ATGTATTGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
225283 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
225304 ATGTATCGATACAT
1 ATGTATCGATACAT
225318 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:225280 original size:41 final size:41
Alignment explanation
Indices: 225224--225317 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
225214 ACAATTCAAA
*
225224 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
225265 GTATTGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
225306 GTATCGATACAT
1 GTATCGATACAT
225318 TTCTTGGCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:225374 original size:13 final size:13
Alignment explanation
Indices: 225356--225381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
225346 TACAGCAAGT
225356 ATGTATCGATACA
1 ATGTATCGATACA
225369 ATGTATCGATACA
1 ATGTATCGATACA
225382 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:226392 original size:20 final size:20
Alignment explanation
Indices: 226321--226392 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
226311 TGTTAATGAT
* * *
226321 TGCATTTGTATCATTTTACA
1 TGCATTTGCATCATTTAATA
*
226341 TGCATTTGCATTCATATAATA
1 TGCATTTGCA-TCATTTAATA
* *
226362 TTGGGATTTGCACCATTTAATA
1 -T-GCATTTGCATCATTTAATA
226384 TGCATTTGC
1 TGCATTTGC
226393 CACTTCACTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 16 0.39
21 8 0.20
22 9 0.22
23 8 0.20
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.44
Consensus pattern (20 bp):
TGCATTTGCATCATTTAATA
Found at i:226510 original size:32 final size:34
Alignment explanation
Indices: 226469--226532 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
226459 TTCATGTGCA
*
226469 TTTGCCATTTTAC-TGATACTT-GCATTTGCATCG
1 TTTGCCATTTTACATGACA-TTGGCATTTGCATCG
226502 TTTG-CATTTTACATGACATTGGCATTTGCAT
1 TTTGCCATTTTACATGACATTGGCATTTGCAT
226533 TATTCCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (34 bp):
TTTGCCATTTTACATGACATTGGCATTTGCATCG
Found at i:227149 original size:89 final size:89
Alignment explanation
Indices: 226932--227592 Score: 647
Period size: 89 Copynumber: 7.4 Consensus size: 89
226922 CTAATCATAT
* * * * *
226932 ACCACTAG-TGGTATTGATGCATCACCAAGCCTGATTTCCTTAGGGCAAGGTGTAGCCTACACAT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
** *
226996 TCTTAATCATATCCCT-TTTATCCAA
66 TCCCAATCATATCCCTCTTTCT-C-A
* * * * *
227021 ACCACTATATGGTATTGACGCATCACCATGCCTAATTTCCTTAAGGAAAGGTGCAGCCCATACAC
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
*
227086 TCCTAATCATATCCCTCTTTCTCA
66 TCCCAATCATATCCCTCTTTCTCA
* * ** * * *
227110 ACCACTAGATGGTACTGATGCATCACCCAGCCTGATTTCCTTGGGGCAAGGTGCAACTCATACGC
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
* * *
227175 TCCCAATCATATCTCTATTTTTCA
66 TCCCAATCATATCCCTCTTTCTCA
* * *
227199 ACCACTAGATGG-ATTGATGCATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCATACAT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
227263 TCCCAATCATATCCCTCTTTTCTCA
66 TCCCAATCATATCCCTC-TTTCTCA
* ** * *
227288 ACCACTAAATGGTATTGATATATCACCAAGCCTGATTTCCTTAGGGCAAGGTGTAG-CC-TACAC
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
*** *
227351 ATTTTAATCATATCCC-CTTTATCCAA
66 -TCCCAATCATATCCCTCTTTCT-C-A
* * * * * *
227377 ACCACTAGATAGCATTGATTCATCACCAAGCTTGATTTCCTT-AGGACAAGGTGCAGCCTACACA
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGG-CAAGGTGCAGCCCATACA
227441 CTCCCAATCATATCCCTCTTTCTCA
65 CTCCCAATCATATCCCTCTTTCTCA
** * *** * ** ** * *
227466 ACCACTAGATGGTATTGATATATCA-TAAAAATAATTTCCTTGGGGCAAAATGCAGCCCACACAT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
* *
227530 TCCCTAATCATATCTCCTGTATCT-A
66 TCCC-AATCATATC-CCTCTTTCTCA
**
227555 ACCACTAGATGGTATTGATGCATCATAAAGCCTGATTT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTT
227593 TCCTAGGGAA
Statistics
Matches: 469, Mismatches: 88, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
87 4 0.01
88 97 0.21
89 227 0.48
90 128 0.27
91 13 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (89 bp):
ACCACTAGATGGTATTGATGCATCACCAAGCCTGATTTCCTTAAGGCAAGGTGCAGCCCATACAC
TCCCAATCATATCCCTCTTTCTCA
Found at i:227415 original size:267 final size:267
Alignment explanation
Indices: 226932--227605 Score: 758
Period size: 267 Copynumber: 2.5 Consensus size: 267
226922 CTAATCATAT
* * *
226932 ACCACTAG-TGGTATTGATGCATCACCAAGCCTGATTTCCTT-AGGGCAAGGTGTAGCCTACACA
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTAATTTCCTTGA-GGCAAGGTGCAGCCCACACA
** * * * *
226995 TTCTTAATCATATCCCTTTTATC-CAAACCACTATATGGTATTGACGCATCACCATGCCTAATTT
65 TTCCCAATCATATCCCTTTT-TCTC-AACCACTAAATGGTATTGATGCATCACCAAGCCTGATTT
* * * *
227059 CCTTAAGGAAAGGTGCAGCCCATACACTCCTAATCATATCCCTCTTTCTCAACCACTAGATGGTA
128 CCTTAGGGAAAGGTGCAGCCCATACACTCCTAATCATATCCCTCTTTATCAACCACTAGATAGCA
* * * * *
227124 CTGATGCATCACCCAGCCTGATTTCCTTGGGGCAAGGTGCAA-CTCATACGCTCCCAATCATATC
193 CTGATGCATCACCAAGCCTGATTTCCTTAGGACAAGGTGCAACCT-ACACACTCCCAATCATATC
* *
227188 TCTATTTTTCA
257 CCTATTTCTCA
*
227199 ACCACTAGATGG-ATTGATGCATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCATACAT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCACACAT
**
227263 TCCCAATCATATCCCTCTTTTCTCAACCACTAAATGGTATTGATATATCACCAAGCCTGATTTCC
66 TCCCAATCATATCCCT-TTTTCTCAACCACTAAATGGTATTGATGCATCACCAAGCCTGATTTCC
* * **
227328 TTAGGGCAAGGTGTAG-CC-TACACATTTTAATCATATCCC-CTTTATCCAAACCACTAGATAGC
130 TTAGGGAAAGGTGCAGCCCATACAC-TCCTAATCATATCCCTCTTTAT-C-AACCACTAGATAGC
* * * *
227390 ATTGATTCATCACCAAGCTTGATTTCCTTAGGACAAGGTGCAGCCTACACACTCCCAATCATATC
192 ACTGATGCATCACCAAGCCTGATTTCCTTAGGACAAGGTGCAACCTACACACTCCCAATCATATC
*
227455 CCTCTTTCTCA
257 CCTATTTCTCA
** * *** * **
227466 ACCACTAGATGGTATTGATATATCA-TAAAAATAATTTCCTTGGGGCAAAATGCAGCCCACACAT
1 ACCACTAGATGGTATTGATGCATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCACACAT
* * * **
227530 TCCCTAATCATATCTCCTGTATCT-AACCACTAGATGGTATTGATGCATCATAAAGCCTGATTTT
66 TCCC-AATCATATC-CCTTTTTCTCAACCACTAAATGGTATTGATGCATCACCAAGCCTGA-TTT
227594 CC-TAGGGAAAGG
128 CCTTAGGGAAAGG
227606 ATATCTCGAC
Statistics
Matches: 345, Mismatches: 50, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
265 10 0.03
266 16 0.05
267 278 0.81
268 38 0.11
269 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (267 bp):
ACCACTAGATGGTATTGATGCATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCACACAT
TCCCAATCATATCCCTTTTTCTCAACCACTAAATGGTATTGATGCATCACCAAGCCTGATTTCCT
TAGGGAAAGGTGCAGCCCATACACTCCTAATCATATCCCTCTTTATCAACCACTAGATAGCACTG
ATGCATCACCAAGCCTGATTTCCTTAGGACAAGGTGCAACCTACACACTCCCAATCATATCCCTA
TTTCTCA
Found at i:227855 original size:36 final size:36
Alignment explanation
Indices: 227808--228317 Score: 470
Period size: 36 Copynumber: 14.4 Consensus size: 36
227798 TCTTTTATCT
* * *
227808 TTTGACTGTATCTAGTCAAACTTTTTTCCATCATCA
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
227844 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* * * *
227880 TTTGACTCTATCTGGTCAAAC-TCTCTCCACCATTG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
** *
227915 TTTGACTACATCTAGTCAAACTTCTTTCCATCATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
227951 TTTGACTGTATCTGGTCAAAC-TCTTTCCATCATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* * * **
227986 TTTGACTGTATCTTGTTAAA-TTC-TCCTCATCATTA
1 TTTGACTGTATCTGGTCAAACTTCTTTC-CATCATCG
* *
228021 TTTGACTGCATCTAGTCAAACTTCTTTCCATCATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* * *
228057 TTTGA-TCGTTTCTAGTCAAAC-TCTCTCCA-CTATCG
1 TTTGACT-GTATCTGGTCAAACTTCTTTCCATC-ATCG
** * *
228092 TTTGACTACATCTGGTCAAACTTTTTTCCATTATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* * *
228128 TTTGACTATATCTGGTCAAAC-TCTCTCCACCATCG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* * * * *
228163 TTTGACTGCATCTAGTCAAACTT-TTCTCTACCATCA
1 TTTGACTGTATCTGGTCAAACTTCTT-TCCATCATCG
* * * *
228199 TTTGA-TAATATCTGGTCAAACTTCGTTCCACCATTG
1 TTTGACT-GTATCTGGTCAAACTTCTTTCCATCATCG
* * * *
228235 TTTGATTGTATTTGATCAAACGTT-TTT-CATCATTG
1 TTTGACTGTATCTGGTCAAAC-TTCTTTCCATCATCG
* * *
228270 TTTGATTATATCTGGTCAAAC-TCTTTCCATCATAG
1 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
* *
228305 TTTAATTGTATCT
1 TTTGACTGTATCT
228318 ATTAGACTCC
Statistics
Matches: 390, Mismatches: 66, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
33 1 0.00
34 6 0.02
35 186 0.48
36 191 0.49
37 6 0.02
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
Found at i:227941 original size:71 final size:72
Alignment explanation
Indices: 227808--228307 Score: 449
Period size: 71 Copynumber: 7.0 Consensus size: 72
227798 TCTTTTATCT
* * * * *
227808 TTTGACTGTATCTAGTCAAACTTTTTTCCATCATCATTTGACTGTATCTGGTCAAACTTCTTTCC
1 TTTGACTCTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTCC
227873 ATCATCG
66 ATCATCG
* * * * *
227880 TTTGACTCTATCTGGTCAAAC-TCTCTCCACCATTGTTTGACTACATCTAGTCAAACTTCTTTCC
1 TTTGACTCTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTCC
227944 ATCATCG
66 ATCATCG
* * * * *
227951 TTTGACTGTATCTGGTCAAAC-TCTTTCCATCATCGTTTGACTGTATCTTGTTAAA-TTC-TCCT
1 TTTGACTCTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTC-
**
228013 CATCATTA
65 CATCATCG
* * *
228021 TTTGACTGC-ATCTAGTCAAACTTCTTTCCATCATCGTTTGATCGT-T-TCTAGTCAAAC-TCTC
1 TTTGACT-CTATCTGGTCAAACTTCTTTCCATCATCGTTTGA-C-TATATCTGGTCAAACTTCTT
228082 TCCA-CTATCG
63 TCCATC-ATCG
* * *
228092 TTTGACTAC-ATCTGGTCAAACTTTTTTCCATTATCGTTTGACTATATCTGGTCAAAC-TCTCTC
1 TTTGACT-CTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTC
*
228155 CACCATCG
65 CATCATCG
* * * * *
228163 TTTGACTGC-ATCTAGTCAAACTT-TTCTCTACCATCATTTGA-TAATATCTGGTCAAACTTCGT
1 TTTGACT-CTATCTGGTCAAACTTCTT-TCCATCATCGTTTGACT-ATATCTGGTCAAACTTCTT
* *
228225 TCCACCATTG
63 TCCATCATCG
* * * * * *
228235 TTTGATTGTATTTGATCAAACGTT-TTT-CATCATTGTTTGATTATATCTGGTCAAAC-TCTTTC
1 TTTGACTCTATCTGGTCAAAC-TTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTC
*
228297 CATCATAG
65 CATCATCG
228305 TTT
1 TTT
228308 AATTGTATCT
Statistics
Matches: 356, Mismatches: 55, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
69 3 0.01
70 47 0.13
71 250 0.70
72 51 0.14
73 5 0.01
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (72 bp):
TTTGACTCTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGGTCAAACTTCTTTCC
ATCATCG
Found at i:227997 original size:142 final size:141
Alignment explanation
Indices: 227808--228307 Score: 537
Period size: 142 Copynumber: 3.5 Consensus size: 141
227798 TCTTTTATCT
* * *
227808 TTTGACTGTATCTAGTCAAACTTTTTTCCATCATCATTTGACTGTATCTGGTCAAACTTCTTTCC
1 TTTGACTGTATCTGGTCAAACTTTTTTCCATCATCGTTTGACTATATCTGGTCAAAC-TCTTTCC
* *
227873 ATCATCGTTTGACT-CTATCTGGTCAAAC-TCTCTCCACCATTGTTTGACTACATCTAGTCAAAC
65 ATCATCGTTTGACTGC-ATCTAGTCAAACTTCTCTCCACCATCGTTTGA-TACATCTAGTCAAAC
227936 TTCTTTCCATCATCG
128 TTCTTTCCA-CATCG
* * * * * *
227951 TTTGACTGTATCTGGTCAAAC-TCTTTCCATCATCGTTTGACTGTATCTTGTTAAATTC-TCCTC
1 TTTGACTGTATCTGGTCAAACTTTTTTCCATCATCGTTTGACTATATCTGGTCAAACTCTTTC-C
** * * *
228014 ATCATTATTTGACTGCATCTAGTCAAACTTCTTTCCATCATCGTTTGAT-CGTTTCTAGTCAAAC
65 ATCATCGTTTGACTGCATCTAGTCAAACTTCTCTCCACCATCGTTTGATAC--ATCTAGTCAAAC
*
228078 -TCTCTCCACTATCG
128 TTCTTTCCAC-ATCG
** * *
228092 TTTGACTACATCTGGTCAAACTTTTTTCCATTATCGTTTGACTATATCTGGTCAAACTCTCTCCA
1 TTTGACTGTATCTGGTCAAACTTTTTTCCATCATCGTTTGACTATATCTGGTCAAACTCTTTCCA
* * * * * *
228157 CCATCGTTTGACTGCATCTAGTCAAACTTTTCTCTACCATCATTTGATAATATCTGGTCAAACTT
66 TCATCGTTTGACTGCATCTAGTCAAACTTCTCTCCACCATCGTTTGAT-ACATCTAGTCAAACTT
* *
228222 CGTTCCACCATTG
130 CTTTCCA-CATCG
* * * * * *
228235 TTTGATTGTATTTGATCAAACGTTTTT-CATCATTGTTTGATTATATCTGGTCAAACTCTTTCCA
1 TTTGACTGTATCTGGTCAAACTTTTTTCCATCATCGTTTGACTATATCTGGTCAAACTCTTTCCA
*
228299 TCATAGTTT
66 TCATCGTTT
228308 AATTGTATCT
Statistics
Matches: 294, Mismatches: 51, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
140 4 0.01
141 57 0.19
142 181 0.62
143 51 0.17
144 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (141 bp):
TTTGACTGTATCTGGTCAAACTTTTTTCCATCATCGTTTGACTATATCTGGTCAAACTCTTTCCA
TCATCGTTTGACTGCATCTAGTCAAACTTCTCTCCACCATCGTTTGATACATCTAGTCAAACTTC
TTTCCACATCG
Found at i:228142 original size:177 final size:177
Alignment explanation
Indices: 227836--228175 Score: 538
Period size: 177 Copynumber: 1.9 Consensus size: 177
227826 AACTTTTTTC
* * *
227836 CATCATCATTTGACTGTATCTGGTCAAACTTCTTTCCATCATCGTTTGACTCTATCTGGTCAAAC
1 CATCATCATTTGACTGCATCTAGTCAAACTTCTTTCCATCATCGTTTGACTCTATCTAGTCAAAC
* *
227901 TCTCTCCACCATTGTTTGACTACATCTAGTCAAACTTCTTTCCATCATCGTTTGACTGTATCTGG
66 TCTCTCCACCATCGTTTGACTACATCTAGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGG
* * *
227966 TCAAACTCTTTCCATCATCGTTTGACTGTATCTTGTTAAATTCTCCT
131 TCAAACTCTCTCCACCATCGTTTGACTGCATCTTGTTAAATTCTCCT
* *
228013 CATCATTATTTGACTGCATCTAGTCAAACTTCTTTCCATCATCGTTTGA-TCGTTTCTAGTCAAA
1 CATCATCATTTGACTGCATCTAGTCAAACTTCTTTCCATCATCGTTTGACTC-TATCTAGTCAAA
* * * *
228077 CTCTCTCCACTATCGTTTGACTACATCTGGTCAAACTTTTTTCCATTATCGTTTGACTATATCTG
65 CTCTCTCCACCATCGTTTGACTACATCTAGTCAAACTTCTTTCCATCATCGTTTGACTATATCTG
228142 GTCAAACTCTCTCCACCATCGTTTGACTGCATCT
130 GTCAAACTCTCTCCACCATCGTTTGACTGCATCT
228176 AGTCAAACTT
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
176 2 0.01
177 146 0.99
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (177 bp):
CATCATCATTTGACTGCATCTAGTCAAACTTCTTTCCATCATCGTTTGACTCTATCTAGTCAAAC
TCTCTCCACCATCGTTTGACTACATCTAGTCAAACTTCTTTCCATCATCGTTTGACTATATCTGG
TCAAACTCTCTCCACCATCGTTTGACTGCATCTTGTTAAATTCTCCT
Found at i:228276 original size:35 final size:35
Alignment explanation
Indices: 227808--228317 Score: 257
Period size: 35 Copynumber: 14.4 Consensus size: 35
227798 TCTTTTATCT
* * **
227808 TTTGACTGTATCT-AGTCAAACTTTTTTCCATCATCA
1 TTTGATTGTATCTGA-TCAAAC-TCTTTCCATCATTG
* * *
227844 TTTGACTGTATCTGGTCAAACTTCTTTCCATCATCG
1 TTTGATTGTATCTGATCAAAC-TCTTTCCATCATTG
* * * * *
227880 TTTGACTCTATCTGGTCAAACTCTCTCCACCATTG
1 TTTGATTGTATCTGATCAAACTCTTTCCATCATTG
* ** *
227915 TTTGACTACATCT-AGTCAAACTTCTTTCCATCATCG
1 TTTGATTGTATCTGA-TCAAAC-TCTTTCCATCATTG
* * *
227951 TTTGACTGTATCTGGTCAAACTCTTTCCATCATCG
1 TTTGATTGTATCTGATCAAACTCTTTCCATCATTG
* * * * *
227986 TTTGACTGTATCTTG-TTAAATTC-TCCTCATCATTA
1 TTTGATTGTATC-TGATCAAACTCTTTC-CATCATTG
* * *
228021 TTTGACTGCATCT-AGTCAAACTTCTTTCCATCATCG
1 TTTGATTGTATCTGA-TCAAAC-TCTTTCCATCATTG
* * * *
228057 TTTGATCGTTTCT-AGTCAAACTCTCTCCA-CTATCG
1 TTTGATTGTATCTGA-TCAAACTCTTTCCATC-ATTG
* ** * * * *
228092 TTTGACTACATCTGGTCAAACTTTTTTCCATTATCG
1 TTTGATTGTATCTGATCAAAC-TCTTTCCATCATTG
* * * * * *
228128 TTTGACTATATCTGGTCAAACTCTCTCCACCATCG
1 TTTGATTGTATCTGATCAAACTCTTTCCATCATTG
* * * **
228163 TTTGACTGCATCT-AGTCAAACT-TTTCTCTACCATCA
1 TTTGATTGTATCTGA-TCAAACTCTTTC-C-ATCATTG
** * * *
228199 TTTGATAATATCTGGTCAAACTTCGTTCCACCATTG
1 TTTGATTGTATCTGATCAAAC-TCTTTCCATCATTG
* *
228235 TTTGATTGTATTTGATCAAACGT-TTTTCATCATTG
1 TTTGATTGTATCTGATCAAAC-TCTTTCCATCATTG
* * *
228270 TTTGATTATATCTGGTCAAACTCTTTCCATCATAG
1 TTTGATTGTATCTGATCAAACTCTTTCCATCATTG
*
228305 TTTAATTGTATCT
1 TTTGATTGTATCT
228318 ATTAGACTCC
Statistics
Matches: 379, Mismatches: 74, Indels: 43
0.76 0.15 0.09
Matches are distributed among these distances:
34 8 0.02
35 183 0.48
36 181 0.48
37 4 0.01
38 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTGATTGTATCTGATCAAACTCTTTCCATCATTG
Found at i:228448 original size:41 final size:42
Alignment explanation
Indices: 228387--228577 Score: 121
Period size: 40 Copynumber: 4.7 Consensus size: 42
228377 CCACCCTTGC
* *
228387 TTGACTTTATCAG-TTTTGCCCTAGTCAACCCTTTCAATTTG
1 TTGACTTTATCAGATTATGCCCTAGTCAACCCTTTCAATTGG
* * * *
228428 TTGGCTTTATC-GATTATGCCCTAG-CCAGCTTTTCAATTGG
1 TTGACTTTATCAGATTATGCCCTAGTCAACCCTTTCAATTGG
** * * * *
228468 TTGACTCCATC-GGTTTTGCCCTGGTCAACAC-TTCTAATCT-G
1 TTGACTTTATCAGATTATGCCCTAGTCAACCCTTTC-AAT-TGG
** * * * * *
228509 TTGGTTTTATCAGTTTA-ACCCTGGCCAA-CTTTTCAATTGG
1 TTGACTTTATCAGATTATGCCCTAGTCAACCCTTTCAATTGG
*
228549 TTGACTTTATCGGATT-TGCCCTAGTCAAC
1 TTGACTTTATCAGATTATGCCCTAGTCAAC
228578 GTTTCTAACC
Statistics
Matches: 108, Mismatches: 33, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
39 1 0.01
40 58 0.54
41 45 0.42
42 4 0.04
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (42 bp):
TTGACTTTATCAGATTATGCCCTAGTCAACCCTTTCAATTGG
Found at i:228541 original size:81 final size:81
Alignment explanation
Indices: 228387--228992 Score: 426
Period size: 81 Copynumber: 7.4 Consensus size: 81
228377 CCACCCTTGC
* * *
228387 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTT-TCAATTTGTTGGCTTTATC-GATTATGCCCT
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCT-AATCTGTTGGCTTTATCAGTTTA-GCCCT
* *
228450 AGCCAGCTTTTCAATTGG
64 GGCCAACTTTTCAATTGG
** * * * *
228468 TTGACTCCATCGGTTTTGCCCTGGTCAACACTTCTAATCTGTTGGTTTTATCAGTTTAACCCTGG
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCTGTTGGCTTTATCAGTTTAGCCCTGG
228533 CCAACTTTTCAATTGG
66 CCAACTTTTCAATTGG
* ** * ** * * *
228549 TTGACTTTATCGGATTTGCCCTAGTCAACGTTTCTAACCCATTGGCTTTATCAATTTTGTCCTGG
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCTGTTGGCTTTATCAGTTTAGCCCTGG
* *
228614 CCAACCCTTTT-AAGTGT
66 CCAA--CTTTTCAATTGG
* * * * *
228631 TTCGACTTTATCAGTTTTGCCTTGGTTAACCCTTCTAA-CTCGTTGGCTTTATC-GGTTACGCCC
1 TT-GACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCT-GTTGGCTTTATCAGTTTA-GCCC
*
228694 TGGCCAACCTCTTT-AATTAG
63 TGGCCAA-CT-TTTCAATTGG
* ** * * * *
228714 TTGACTTTATCAGTTTTGCCCT-GATCGGCCTTTCTAATCTGTTGGTTTTATCAGTTTCGCCTTG
1 TTGACTTTATCGGTTTTGCCCTAG-TCAACCCTTCTAATCTGTTGGCTTTATCAGTTTAGCCCTG
** *
228778 GCTGACATTTCAATTGG
65 GCCAACTTTTCAATTGG
* * * * * * * * *
228795 TTGACTTTATCGATTTTGCCCTAGTTAACCCTTCTAACCCGTTGACTTTAT-TGATTTTGCCTTC
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCTGTTGGCTTTATCAG-TTTAGCCCTG
* *
228859 GCTAACCCTTTT-AATTAG
65 GCCAA--CTTTTCAATTGG
* * * * * * *
228877 TTGACTTTATCGGTATTGCCCTAGTCAACCTTTCTAA-CTCATTGGCTTTATCGGCTTCG-CTTG
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCT-GTTGGCTTTATCAGTTTAGCCCTG
* * *
228940 ACTAATCTTTT-AATTAG
65 GCCAA-CTTTTCAATTGG
* * * *
228957 TTGACTTTATCGGTTTGGCCTTGGTCAACCCATCTA
1 TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTA
228993 TTCGCTTGAC
Statistics
Matches: 416, Mismatches: 91, Indels: 37
0.76 0.17 0.07
Matches are distributed among these distances:
80 45 0.11
81 184 0.44
82 115 0.28
83 72 0.17
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (81 bp):
TTGACTTTATCGGTTTTGCCCTAGTCAACCCTTCTAATCTGTTGGCTTTATCAGTTTAGCCCTGG
CCAACTTTTCAATTGG
Found at i:228735 original size:41 final size:39
Alignment explanation
Indices: 228387--228909 Score: 201
Period size: 41 Copynumber: 12.8 Consensus size: 39
228377 CCACCCTTGC
* * *
228387 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTTTCAATTTG
1 TTGACTTTATCAGTTTTGCCCTGGCCAA-CCTTTTAA-TTG
* * * *
228428 TTGGCTTTATC-GATTATGCCCTAGCC-AGCTTTTCAATTGG
1 TTGACTTTATCAG-TTTTGCCCTGGCCAACCTTTT-AATT-G
** * * *
228468 TTGACTCCATCGGTTTTGCCCTGGTCAACACTTCTAATCTG
1 TTGACTTTATCAGTTTTGCCCTGGCCAAC-CTTTTAAT-TG
** **
228509 TTGGTTTTATCAGTTTAACCCTGGCCAA-CTTTTCAATTGG
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCTTTT-AATT-G
* * * * * ***
228549 TTGACTTTATCGGATTTGCCCTAGTCAACGTTTCTAACCCA
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCTTT-TAA-TTG
* * * *
228590 TTGGCTTTATCAATTTTGTCCTGGCCAACCCTTTTAAGTG
1 TTGACTTTATCAGTTTTGCCCTGGCCAA-CCTTTTAATTG
* ** * *
228630 TTTCGACTTTATCAGTTTTGCCTTGGTTAACCCTTCTAACTCG
1 -TT-GACTTTATCAGTTTTGCCCTGGCCAA-CCTTTTAA-TTG
* * **
228673 TTGGCTTTATCGGTTACGCCCTGGCCAACCTCTTTAATTAG
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCT-TTTAATT-G
** **
228714 TTGACTTTATCAGTTTTGCCCTGATCGGCCTTTCTAATCTG
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCTTT-TAAT-TG
** * * ** * *
228755 TTGGTTTTATCAGTTTCGCCTTGGCTGACATTTCAATTGG
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCTTTTAATT-G
* ** * **
228795 TTGACTTTATC-GATTTTGCCCTAGTTAACCCTTCTAACCCG
1 TTGACTTTATCAG-TTTTGCCCTGGCCAA-CCTTTTAA-TTG
* * * *
228836 TTGACTTTAT-TGATTTTGCCTTCGCTAACCCTTTTAATTAG
1 TTGACTTTATCAG-TTTTGCCCTGGCCAA-CCTTTTAATT-G
* * * *
228877 TTGACTTTATCGGTATTGCCCTAGTCAACCTTT
1 TTGACTTTATCAGTTTTGCCCTGGCCAACCTTT
228910 CTAACTCATT
Statistics
Matches: 350, Mismatches: 105, Indels: 55
0.69 0.21 0.11
Matches are distributed among these distances:
39 13 0.04
40 81 0.23
41 213 0.61
42 42 0.12
43 1 0.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (39 bp):
TTGACTTTATCAGTTTTGCCCTGGCCAACCTTTTAATTG
Found at i:228832 original size:246 final size:244
Alignment explanation
Indices: 228387--228972 Score: 675
Period size: 246 Copynumber: 2.4 Consensus size: 244
228377 CCACCCTTGC
* * * * *
228387 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTT-TCAATTTGTTGGCTTTATCGATTATGCCCTA
1 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCT-AACTCGTTGGCTTTATCGGTTACGCCCTG
* * ** *
228451 GCC-AGCTTTTCAATTGGTTGACTCCATCGGTTTTGCCCTGGTCAACACTTCTAATCTGTTGGTT
65 GCCAACCTTTT-AATTAGTTGACTTTATCGGTTTTGCCCTGATCAACACTTCTAATCTGTTGGTT
* **
228515 TTATCAGTTTAACCCTGGCCAACTTTTCAATTGGTTGACTTTATCGGATTTGCCCTAGTCAACGT
129 TTATCAGTTTAACCCTGGCCAACATTTCAATTGGTTGACTTTATCGGATTTGCCCTAGTCAACCC
* *
228580 TTCTAACCCATTGGCTTTATCAATTTTGTCC-TGGCCAACCCTTTTAAGT-G
194 TTCTAACCCATTGACTTTATCAATTTTG-CCTTCGCCAACCCTTTTAAGTAG
* * *
228630 TTTCGACTTTATCAGTTTTGCCTTGGTTAACCCTTCTAACTCGTTGGCTTTATCGGTTACGCCCT
1 -TT-GACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACTCGTTGGCTTTATCGGTTACGCCCT
* **
228695 GGCCAACCTCTTTAATTAGTTGACTTTATCAGTTTTGCCCTGATCGGC-CTTTCTAATCTGTTGG
64 GGCCAACCT-TTTAATTAGTTGACTTTATCGGTTTTGCCCTGATCAACAC-TTCTAATCTGTTGG
** * ** *
228759 TTTTATCAGTTTCGCCTTGGCTGACATTTCAATTGGTTGACTTTATC-GATTTTGCCCTAGTTAA
127 TTTTATCAGTTTAACCCTGGCCAACATTTCAATTGGTTGACTTTATCGGA-TTTGCCCTAGTCAA
* ** * *
228823 CCCTTCTAACCCGTTGACTTTATTGATTTTGCCTTCGCTAACCCTTTTAATTAG
191 CCCTTCTAACCCATTGACTTTATCAATTTTGCCTTCGCCAACCCTTTTAAGTAG
* * * * *
228877 TTGACTTTATCGGTATTGCCCTAGTCAACCTTTCTAACTCATTGGCTTTATCGGCTT-CG-CTTG
1 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACTCGTTGGCTTTATCGG-TTACGCCCTG
* * *
228940 ACTAATCTTTTAATTAGTTGACTTTATCGGTTT
65 GCCAACCTTTTAATTAGTTGACTTTATCGGTTT
228973 GGCCTTGGTC
Statistics
Matches: 289, Mismatches: 44, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
243 24 0.08
244 10 0.03
245 107 0.37
246 144 0.50
247 4 0.01
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (244 bp):
TTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACTCGTTGGCTTTATCGGTTACGCCCTGG
CCAACCTTTTAATTAGTTGACTTTATCGGTTTTGCCCTGATCAACACTTCTAATCTGTTGGTTTT
ATCAGTTTAACCCTGGCCAACATTTCAATTGGTTGACTTTATCGGATTTGCCCTAGTCAACCCTT
CTAACCCATTGACTTTATCAATTTTGCCTTCGCCAACCCTTTTAAGTAG
Found at i:228911 original size:163 final size:164
Alignment explanation
Indices: 228387--228928 Score: 415
Period size: 163 Copynumber: 3.3 Consensus size: 164
228377 CCACCCTTGC
* * **** * *
228387 TTGACTTTATCAGTTTTGCCCTAGTCAACCCTTTC-AATTTGTTGGCTTTATCGATTAT-GCCCT
1 TTGACTTTATCGGTATTGCCCTAGTCAA-CCTTTCTAACCCATTGGCTTTATCAATT-TCGTCCT
* * * * ** * * * * * * *
228450 AGCC-AGCTTTTCAATTGGTT-GACTCCATCGGTTTTGCCCTGGTCAACACTTCTAATCTGTTGG
64 GGCCAACCATTTCAAGTGGTTCGACTTTATCAGTTTTGCCCTAGTTAACCCTTCTAACCCGTTGA
* * * * *
228513 TTTTATCAGTTTA-ACCCTGGCCAA-CTTTTCAATTGG
129 CTTTATC-GATTACGCCCTCGCCAACCTTTT-AATTAG
* *
228549 TTGACTTTATCGG-ATTTGCCCTAGTCAACGTTTCTAACCCATTGGCTTTATCAATTTTGTCCTG
1 TTGACTTTATCGGTA-TTGCCCTAGTCAACCTTTCTAACCCATTGGCTTTATCAATTTCGTCCTG
* * * * * * *
228613 GCCAACCCTTTTAAGTGTTTCGACTTTATCAGTTTTGCCTTGGTTAACCCTTCTAACTCGTTGGC
65 GCCAACCATTTCAAGTGGTTCGACTTTATCAGTTTTGCCCTAGTTAACCCTTCTAACCCGTTGAC
* *
228678 TTTATCGGTTACGCCCTGGCCAACCTCTTTAATTAG
130 TTTATCGATTACGCCCTCGCCAACCT-TTTAATTAG
* * ** * ** * *
228714 TTGACTTTATCAGTTTTGCCCT-GATCGGCCTTTCTAATCTGTTGGTTTTATCAGTTTCG-CCTT
1 TTGACTTTATCGGTATTGCCCTAG-TCAACCTTTCTAACCCATTGGCTTTATCAATTTCGTCC-T
** *
228777 GGCTGA-CATTTCAATTGGTT-GACTTTATC-GATTTTGCCCTAGTTAACCCTTCTAACCCGTTG
64 GGCCAACCATTTCAAGTGGTTCGACTTTATCAG-TTTTGCCCTAGTTAACCCTTCTAACCCGTTG
* ** * *
228839 ACTTTATTGATTTTGCCTTCGCTAACCCTTTTAATTAG
128 ACTTTATCGATTACGCCCTCGCCAA-CCTTTTAATTAG
*
228877 TTGACTTTATCGGTATTGCCCTAGTCAACCTTTCTAACTCATTGGCTTTATC
1 TTGACTTTATCGGTATTGCCCTAGTCAACCTTTCTAACCCATTGGCTTTATC
228929 GGCTTCGCTT
Statistics
Matches: 301, Mismatches: 65, Indels: 27
0.77 0.17 0.07
Matches are distributed among these distances:
161 6 0.02
162 49 0.16
163 119 0.40
164 67 0.22
165 57 0.19
166 3 0.01
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (164 bp):
TTGACTTTATCGGTATTGCCCTAGTCAACCTTTCTAACCCATTGGCTTTATCAATTTCGTCCTGG
CCAACCATTTCAAGTGGTTCGACTTTATCAGTTTTGCCCTAGTTAACCCTTCTAACCCGTTGACT
TTATCGATTACGCCCTCGCCAACCTTTTAATTAG
Found at i:229252 original size:43 final size:41
Alignment explanation
Indices: 229205--229338 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 41
229195 TGTACCTGTT
*
229205 GGTTTAGTCCTAAGTAAATCTTTTCATCCTTTGTTGACTTATC
1 GGTTTAGTCCT-GGTAAATCTTTT-ATCCTTTGTTGACTTATC
* * * * * * *
229248 GGTTTAGCCCTGGTCAACCTTTTATCCCTTATTTACATATC
1 GGTTTAGTCCTGGTAAATCTTTTATCCTTTGTTGACTTATC
* * * * *
229289 GGCTCAGTCCTTGGTGAACTCCTTTATCCTTTGTTGATTTATC
1 GGTTTAGTCC-TGGT-AAATCTTTTATCCTTTGTTGACTTATC
229332 GGTTTAG
1 GGTTTAG
229339 CCTTGGTCAA
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
41 21 0.31
42 13 0.19
43 33 0.49
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (41 bp):
GGTTTAGTCCTGGTAAATCTTTTATCCTTTGTTGACTTATC
Found at i:229344 original size:42 final size:42
Alignment explanation
Indices: 229230--229350 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 42
229220 AAATCTTTTC
* *
229230 ATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCAAC-CTTTT
1 ATCCTTTGTTGACTTATCGGTTTAGCCTTGGTCAACTCCTTT
* * * * * * *
229271 ATCCCTTATTTACATATCGGCTCAGTCCTTGGTGAACTCCTTT
1 ATCCTTTGTTGACTTATCGGTTTAG-CCTTGGTCAACTCCTTT
*
229314 ATCCTTTGTTGATTTATCGGTTTAGCCTTGGTCAACT
1 ATCCTTTGTTGACTTATCGGTTTAGCCTTGGTCAACT
229351 TTTCATCTCT
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
41 19 0.31
42 20 0.33
43 22 0.36
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (42 bp):
ATCCTTTGTTGACTTATCGGTTTAGCCTTGGTCAACTCCTTT
Found at i:229517 original size:84 final size:84
Alignment explanation
Indices: 229217--229499 Score: 313
Period size: 84 Copynumber: 3.4 Consensus size: 84
229207 TTTAGTCCTA
* *
229217 AGTAAA-TCTTTTCATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCAACCTTTTATCCCTTATT
1 AGTAAACTCCTTT-ATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCAACCTTTCATCCCTTATT
* *
229281 TACATATCGGCTCAGTCCTTG
65 TACATATCAGCTCAGTCC-CG
* * * * *
229302 -GTGAACTCCTTTATCCTTTGTTGATTTATCGGTTTAGCCTTGGTCAACTTTTCATCTC-TATTT
1 AGTAAACTCCTTTATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCAACCTTTCATCCCTTATTT
* * *
229365 ACTTGTCAGCTCAGTCCCT
66 ACATATCAGCTCAGTCCCG
* * * * *
229384 AGTAAACTCCCTTA-CCTTTTATTGACTTATCGGTTCAACCCTGGTCAACCTTTCATCCCTTGTT
1 AGTAAACTCCTTTATCC-TTTGTTGACTTATCGGTTTAGCCCTGGTCAACCTTTCATCCCTTATT
* * *
229448 TACCTATCAACTTAGTCCCG
65 TACATATCAGCTCAGTCCCG
* *
229468 AGTAAATTTCTTTATCCTTTGTTGACTTATCG
1 AGTAAACTCCTTTATCCTTTGTTGACTTATCG
229500 ATTCTATCCC
Statistics
Matches: 162, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
82 2 0.01
83 65 0.40
84 88 0.54
85 7 0.04
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (84 bp):
AGTAAACTCCTTTATCCTTTGTTGACTTATCGGTTTAGCCCTGGTCAACCTTTCATCCCTTATTT
ACATATCAGCTCAGTCCCG
Found at i:230113 original size:20 final size:21
Alignment explanation
Indices: 230077--230116 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
230067 AATTTTTCTA
230077 TTTTTGAAAATATTTTGAAAT
1 TTTTTGAAAATATTTTGAAAT
230098 TTTTCTGAAAA-A-TTTGAAA
1 TTTT-TGAAAATATTTTGAAA
230117 AATTAGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (21 bp):
TTTTTGAAAATATTTTGAAAT
Found at i:230992 original size:164 final size:164
Alignment explanation
Indices: 230606--230993 Score: 392
Period size: 166 Copynumber: 2.3 Consensus size: 164
230596 AAATTACAAG
* * * * *
230606 GTTTTCTTCTCCGTAAATTTTTTCGGGAGGA-TTTTCATGGGTTTAAAATTTTTTTGAATTCTTT
1 GTTTTCTACTCCGTAAATGTTTTCGGGAGGATTTTTC-TTGGTTT-AAA--TTTTT-AATTCATC
* * * * **
230670 AAATATTATTATTTAATTACTATTAAAGTAATTTTCAAAAATTCATTTATCTTCATGAGTTTTTC
61 AAATATTATCACTTAATTACTATTAAAGTAATTTTCAAAAATTCATTCATCTTCATAAGTTTTGA
* * *
230735 ATTTTTTTCCTTGAAATTTTCCATGTTTCTGAAATACAGA
126 ATTTTTTT-CTTGAAATTTCCCATATTTCTGAAAAACAGA
* * *
230775 GTTTTCTACGCCGTAAATGTTTTCCGGG-GGATTTTTCATGGTTTTTAATTTTTAATTCATCAAA
1 GTTTTCTACTCCGTAAATGTTTT-CGGGAGGATTTTTCTTGG-TTTAAATTTTTAATTCATCAAA
* * * ** *
230839 TATTATCACTTGATTCAC-ATTAAATTAGTTTTGGAAAATTCATTCATTTTCATAAGTTTTGAAT
64 TATTATCACTTAATT-ACTATTAAAGTAATTTTCAAAAATTCATTCATCTTCATAAGTTTTGAAT
*
230903 TTTTTT-TTGAAA-TTCCCTTATTTC-GAAAAAAACAGA
128 TTTTTTCTTGAAATTTCCCATATTTCTG--AAAAACAGA
* *
230939 GTTTTCTACTCCATAAATGTTTTCGGGAAGATTTTTCTTGGTTTAAGATTTTTAA
1 GTTTTCTACTCCGTAAATGTTTTCGGGAGGATTTTTCTTGGTTTAA-ATTTTTAA
230994 AATTCATCTA
Statistics
Matches: 182, Mismatches: 29, Indels: 21
0.78 0.12 0.09
Matches are distributed among these distances:
162 1 0.01
163 17 0.09
164 54 0.30
166 64 0.35
167 7 0.04
169 27 0.15
170 12 0.07
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (164 bp):
GTTTTCTACTCCGTAAATGTTTTCGGGAGGATTTTTCTTGGTTTAAATTTTTAATTCATCAAATA
TTATCACTTAATTACTATTAAAGTAATTTTCAAAAATTCATTCATCTTCATAAGTTTTGAATTTT
TTTCTTGAAATTTCCCATATTTCTGAAAAACAGA
Found at i:233029 original size:155 final size:155
Alignment explanation
Indices: 232845--233269 Score: 516
Period size: 155 Copynumber: 2.7 Consensus size: 155
232835 TCGTAGGGGT
* * * * *
232845 ATTTTTGTAATTTTTTAAAA-TCAAGTCCTAGGTTGTCATCGGGTTCGATTTTGTGCCGAATGTG
1 ATTTTTGTAATTTTTTAAAACT-AACTCCTAGGTTGTCACCGGGTTCGCTTTTATGCCGAAAGTG
* * * * *
232909 GGTTTTTAGGATAGGTTCACCCCATATATAATCCTTTTTAAGTCTTTTAGGGATATTGGGTACTT
65 GGTATTTAGGATAGGTTCATCCCATATATAATCCTTTTTAAGTCCTTTAAGGATATCGGGTACTT
*
232974 TTACATTGAAGGTAACCCTTAAGGGC
130 TTACATTAAAGGTAACCCTTAAGGGC
* *
233000 ATTTTTGTAATTTTTTAAAACTAACTCCTAGGTTGTCACCGGGTTTGCTTTTATGTCGAAAGTGG
1 ATTTTTGTAATTTTTTAAAACTAACTCCTAGGTTGTCACCGGGTTCGCTTTTATGCCGAAAGTGG
* * * * * *
233065 GTATTTAGGATAGGTTCATCCCTTTTA-AAACCATTTCAAGGTCCTTTAAGGTTATCGGGTACTT
66 GTATTTAGGATAGGTTCATCCCATATATAATCCTTTTTAA-GTCCTTTAAGGATATCGGGTACTT
** *
233129 TTATGTTAAAGGTATCCCTTAAGGGC
130 TTACATTAAAGGTAACCCTTAAGGGC
* * ** *
233155 ATATTCGTAATTTTCCAAAACCAACTCCTAGGTTGTCACCGGGTTCGCTTTTATGCC-AAAGGTG
1 ATTTTTGTAATTTTTTAAAACTAACTCCTAGGTTGTCACCGGGTTCGCTTTTATGCCGAAA-GTG
* * * *
233219 AGTATTTAGGATAGGTTCATTCCATCTAT-ATTCTTTTTAAGTCCTTTAAGG
65 GGTATTTAGGATAGGTTCATCCCATATATAATCCTTTTTAAGTCCTTTAAGG
233270 TTACCAAGAT
Statistics
Matches: 229, Mismatches: 37, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
154 23 0.10
155 205 0.90
156 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (155 bp):
ATTTTTGTAATTTTTTAAAACTAACTCCTAGGTTGTCACCGGGTTCGCTTTTATGCCGAAAGTGG
GTATTTAGGATAGGTTCATCCCATATATAATCCTTTTTAAGTCCTTTAAGGATATCGGGTACTTT
TACATTAAAGGTAACCCTTAAGGGC
Found at i:235488 original size:20 final size:21
Alignment explanation
Indices: 235440--235490 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
235430 TTGAAAATAT
235440 TGTATCGATACAATAAGGTAA
1 TGTATCGATACAATAAGGTAA
*
235461 TGT-GCGATAC-ATAA-GTGAA
1 TGTATCGATACAATAAGGT-AA
235480 TGTATCGATAC
1 TGTATCGATAC
235491 GTGTTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 9 0.35
20 12 0.46
21 3 0.12
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAATAAGGTAA
Found at i:235670 original size:49 final size:49
Alignment explanation
Indices: 235611--235712 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
235601 AATGTATCAT
*
235611 ACATTCTTCAATGTATAGATACATCCAGTTAAATTTAAATATTTCGAGC
1 ACATTCTTCAATGTATAGATACATCCAGTTAAATTTAAACATTTCGAGC
235660 ACATTCTTCAATGTATAGATACATCCAGTTAAATTTAAACATTTCGAGC
1 ACATTCTTCAATGTATAGATACATCCAGTTAAATTTAAACATTTCGAGC
235709 -CATT
1 ACATT
235713 TTTAGCCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 4 0.08
49 48 0.92
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (49 bp):
ACATTCTTCAATGTATAGATACATCCAGTTAAATTTAAACATTTCGAGC
Found at i:237496 original size:33 final size:33
Alignment explanation
Indices: 237459--237525 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
237449 TTCAACGATT
237459 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
***
237492 TGTATCGATACATATTTTGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
237525 T
1 T
237526 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:237497 original size:13 final size:13
Alignment explanation
Indices: 237479--237503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
237469 CATAAAATGT
237479 TGTATCGATACAA
1 TGTATCGATACAA
237492 TGTATCGATACA
1 TGTATCGATACA
237504 TATTTTGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:237584 original size:13 final size:13
Alignment explanation
Indices: 237566--237590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
237556 ATTACTCAAA
237566 TGTATCGATACAT
1 TGTATCGATACAT
237579 TGTATCGATACA
1 TGTATCGATACA
237591 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:237692 original size:52 final size:52
Alignment explanation
Indices: 237599--237722 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
237589 CACTGATCTT
*
237599 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
237650 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
237702 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
237723 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:242548 original size:21 final size:23
Alignment explanation
Indices: 242515--242569 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
242505 CCATTTTGTC
**
242515 TTTTCTTAATTAATTC-TCTATT
1 TTTTCTTCTTTAATTCTTCTATT
*
242537 TTTTC-TCTTTAATTCTTCTTTT
1 TTTTCTTCTTTAATTCTTCTATT
242559 TTTTCTTCTTT
1 TTTTCTTCTTT
242570 GCTGACTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.29
22 15 0.54
23 5 0.18
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTCTTTAATTCTTCTATT
Found at i:244899 original size:20 final size:20
Alignment explanation
Indices: 244874--244929 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
244864 TTTTTACCCA
*
244874 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTATC
* *
244894 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTATC
244914 AATGTATCGATACATT
1 AATGTATCGATACATT
244930 CTGTCTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTATC
Found at i:250959 original size:155 final size:154
Alignment explanation
Indices: 250473--250959 Score: 509
Period size: 155 Copynumber: 3.2 Consensus size: 154
250463 TACATCAAAA
* * * *
250473 TCGATTCTATAAAATTTAC-CAAAAT-GCCTTCGGGTATACCTTCAACATGAAAGTATCTCGATA
1 TCGATTCTAAAAAAATTACACAAAATCCCCTTC-GGTATACCTTCAACATGAAAGTATCCCGATA
* * * * * * *
250536 GCCTTAAAGGGCACGAAAGGATTGTAAAAGGTCAAACCTATCCTATA-TGTACACCTTTGGCATA
65 ACCCTAAAGGACACGAAAAGATCGTAAAAGGGCAAACCTATCCTA-AGTGTAGACCTTTGGCATA
* * * *
250600 AAAGCGA-CTCGGTAACAACCTAGGAT
129 AAAGCGACCT-AGTGACTACCTAGGAC
* * * * * * * * ** ** *
250626 TTGATTGTAAAAAAATTACAAAAAATGCCATTGGGTTTATCTTTGATGTGAAAGTATCCTGATAA
1 TCGATTCTAAAAAAATTACACAAAATCCCCTTCGGTATACCTTCAACATGAAAGTATCCCGATAA
* * * **
250691 CCCTAAAGGATACGAAAAGATCGTAAAAAGGCAAACCTATCCTAAGTGTAGAACTTTGATATAAA
66 CCCTAAAGGACACGAAAAGATCGTAAAAGGGCAAACCTATCCTAAGTGTAGACCTTTGGCATAAA
*
250756 AGCGACCAAGTGACTACCTAGGAC
131 AGCGACCTAGTGACTACCTAGGAC
* * *
250780 TC-AGTTCTAGAAAAAATAAC-CAAAATACCCCTTCGGTATACCTTCAACATGAAAGCATCCCAA
1 TCGA-TTCTA-AAAAAATTACACAAAAT-CCCCTTCGGTATACCTTCAACATGAAAGTATCCCGA
* *
250843 TAACCCTAAAGGACACAAAAAGATCGTAAAAGGGCGAACCTATCCTAAGTGTAGACCTTTGGCAT
63 TAACCCTAAAGGACACGAAAAGATCGTAAAAGGGCAAACCTATCCTAAGTGTAGACCTTTGGCAT
250908 AAAAGCGACCTAGTGACTACCTAGGAC
128 AAAAGCGACCTAGTGACTACCTAGGAC
* *
250935 TCGATTCTAAGAAAATTCCACAAAA
1 TCGATTCTAAAAAAATTACACAAAA
250960 AATTTTATGA
Statistics
Matches: 265, Mismatches: 60, Indels: 16
0.78 0.18 0.05
Matches are distributed among these distances:
153 17 0.06
154 114 0.43
155 133 0.50
156 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (154 bp):
TCGATTCTAAAAAAATTACACAAAATCCCCTTCGGTATACCTTCAACATGAAAGTATCCCGATAA
CCCTAAAGGACACGAAAAGATCGTAAAAGGGCAAACCTATCCTAAGTGTAGACCTTTGGCATAAA
AGCGACCTAGTGACTACCTAGGAC
Found at i:257193 original size:11 final size:11
Alignment explanation
Indices: 257177--257204 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
257167 TGCATGTGTT
257177 TTCTTTCCAAA
1 TTCTTTCCAAA
257188 TTCTTTCCAAA
1 TTCTTTCCAAA
257199 TTCTTT
1 TTCTTT
257205 TCTTACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (11 bp):
TTCTTTCCAAA
Found at i:265376 original size:41 final size:43
Alignment explanation
Indices: 265302--265388 Score: 151
Period size: 41 Copynumber: 2.1 Consensus size: 43
265292 GGGTGCTAGA
265302 ATTGGCAGTTTCTTAATATACTACTTATGTTCCAAATATTTTT
1 ATTGGCAGTTTCTTAATATACTACTTATGTTCCAAATATTTTT
*
265345 ATTGGCAGTTTCTT-A-ATACTACTTGTGTTCCAAATATTTTT
1 ATTGGCAGTTTCTTAATATACTACTTATGTTCCAAATATTTTT
265386 ATT
1 ATT
265389 TGTTATCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 28 0.65
42 1 0.02
43 14 0.33
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.49
Consensus pattern (43 bp):
ATTGGCAGTTTCTTAATATACTACTTATGTTCCAAATATTTTT
Found at i:266339 original size:2 final size:2
Alignment explanation
Indices: 266332--266361 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
266322 CTATGGTTCG
266332 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
266362 CAACTCCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268079 original size:2 final size:2
Alignment explanation
Indices: 268074--268108 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
268064 AAAAAATAAC
268074 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
268109 TTTTACTAAA
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:268692 original size:134 final size:134
Alignment explanation
Indices: 268452--268720 Score: 432
Period size: 134 Copynumber: 2.0 Consensus size: 134
268442 ATTCAAAGTA
* * ** *
268452 AAAATATGTGATTTATCAATACATATACTATTAGTATCAATGTACAAGGTTGACTTAGGCTATAA
1 AAAATACGTGATGTATCAATACATATACTATTAGTATCAATACACAAGGTTGACTTAGGCTACAA
268517 AGGGTCAAAACCCTTGATTGTATCGATACACACCTAGATGTATCGATATATTTTG-TGTAGTATC
66 AGGGTCAAAACCCTTGATTGTATCGATACACACCTAGATGTATCGATATATTTTGCT-TAGTATC
268581 GATAC
130 GATAC
* *
268586 AAAATACGTGATGTATCAATACATATACTATTGGTATCAATACATAAGGTTGACTTAGGCTACAA
1 AAAATACGTGATGTATCAATACATATACTATTAGTATCAATACACAAGGTTGACTTAGGCTACAA
* * *
268651 AGGGTCTAAACCTTTGATTGTATCGATACACATCTAGATGTATCGATATATTTTGCTTAGTATCG
66 AGGGTCAAAACCCTTGATTGTATCGATACACACCTAGATGTATCGATATATTTTGCTTAGTATCG
268716 ATAC
131 ATAC
268720 A
1 A
268721 TAAAATTGGC
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
134 123 0.99
135 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (134 bp):
AAAATACGTGATGTATCAATACATATACTATTAGTATCAATACACAAGGTTGACTTAGGCTACAA
AGGGTCAAAACCCTTGATTGTATCGATACACACCTAGATGTATCGATATATTTTGCTTAGTATCG
ATAC
Found at i:268789 original size:24 final size:24
Alignment explanation
Indices: 268757--268880 Score: 104
Period size: 24 Copynumber: 5.2 Consensus size: 24
268747 TTTCACTGTT
* *
268757 TATCACTATTAATTACTGTTTATA
1 TATCACTATTAATCACTGTTCATA
* *
268781 TATCACTATTCATCACTGTTCATG
1 TATCACTATTAATCACTGTTCATA
* * * *
268805 TATCATTGTTCATCACTGTTCATG
1 TATCACTATTAATCACTGTTCATA
* * * *
268829 TATCACTGTTCATCACTATTCATG
1 TATCACTATTAATCACTGTTCATA
* * * *
268853 TATCACTGTTCATCAATGTTCATG
1 TATCACTATTAATCACTGTTCATA
268877 TATC
1 TATC
268881 GATATATGTG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 90 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (24 bp):
TATCACTATTAATCACTGTTCATA
Found at i:268814 original size:14 final size:14
Alignment explanation
Indices: 268792--268865 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
268782 ATCACTATTC
268792 ATCACTGTTCATGT
1 ATCACTGTTCATGT
*
268806 ATCATTGTTC----
1 ATCACTGTTCATGT
268816 ATCACTGTTCATGT
1 ATCACTGTTCATGT
268830 ATCACTGTTC----
1 ATCACTGTTCATGT
*
268840 ATCACTATTCATGT
1 ATCACTGTTCATGT
268854 ATCACTGTTCAT
1 ATCACTGTTCAT
268866 CAATGTTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
10 18 0.38
14 30 0.62
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (14 bp):
ATCACTGTTCATGT
Found at i:268823 original size:48 final size:48
Alignment explanation
Indices: 268757--268880 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 48
268747 TTTCACTGTT
* * * * *
268757 TATCACTATTAATTACTGTTTATATATCACTATTCATCACTGTTCATG
1 TATCACTGTTCATCACTGTTCATATATCACTATTCATCACTATTCATG
* * *
268805 TATCATTGTTCATCACTGTTCATGTATCACTGTTCATCACTATTCATG
1 TATCACTGTTCATCACTGTTCATATATCACTATTCATCACTATTCATG
* *
268853 TATCACTGTTCATCAATGTTCATGTATC
1 TATCACTGTTCATCACTGTTCATATATC
268881 GATATATGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (48 bp):
TATCACTGTTCATCACTGTTCATATATCACTATTCATCACTATTCATG
Found at i:269420 original size:32 final size:36
Alignment explanation
Indices: 269335--269407 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
269325 TTAAGTGATT
* **
269335 GAGAGGTTCTATCTTAACCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
269371 GAGAGGTTCTATCTTAGCCCGTG-AAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
269406 GA
1 GA
269408 TTTCTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 14 0.41
36 20 0.59
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
Found at i:269725 original size:18 final size:18
Alignment explanation
Indices: 269698--269732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
269688 AATAAAATAT
269698 ATGTAATAAAAATTATTA
1 ATGTAATAAAAATTATTA
* *
269716 ATGTATTAAAATTTATT
1 ATGTAATAAAAATTATT
269733 TAAATATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGTAATAAAAATTATTA
Found at i:274490 original size:20 final size:20
Alignment explanation
Indices: 274465--274541 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
274455 GTAAAAAGAC
*
274465 AGAATGCATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
274485 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
274505 TA-CATGTATCAATACATTGA
1 -AGAATGTATCGATACATTGA
*
274525 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
274542 CTAGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:274526 original size:91 final size:90
Alignment explanation
Indices: 274417--274591 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 90
274407 TTTTAACTAG
* * *
274417 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAGACAGAATGCATCGATACAT
1 ATGTATCAATACATTGAAAAATATATCGATACATCTAGGT-AAAAGACAGAATGCATCAATACAT
*
274482 TGAAGAATGTATCGATACATTCATAC
65 TGAAAAATGTATCGATACATTCATAC
* *
274508 ATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAGACAGAATGTATCAATACATT
1 ATGTATCAATACATTGAAAAATATATCGATACATCTAGGTAAAAGACAGAATGCATCAATACATT
274573 GAAAAATGTATCGATACAT
66 GAAAAATGTATCGATACAT
274592 CTAGGTAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 41 0.53
91 37 0.47
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (90 bp):
ATGTATCAATACATTGAAAAATATATCGATACATCTAGGTAAAAGACAGAATGCATCAATACATT
GAAAAATGTATCGATACATTCATAC
Found at i:274601 original size:24 final size:24
Alignment explanation
Indices: 274524--274605 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 24
274514 CAATACATTG
274524 AAAAATGTATCGATACATCTAGGT
1 AAAAATGTATCGATACATCTAGGT
*
274548 AAAAGACAGAATGTATCAATACAT-T--G-
1 ---A-A-A-AATGTATCGATACATCTAGGT
274574 AAAAATGTATCGATACATCTAGGT
1 AAAAATGTATCGATACATCTAGGT
274598 AAAAATGT
1 AAAAATGT
274606 GACTTTCCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
20 14 0.30
21 2 0.04
22 1 0.02
23 2 0.04
24 8 0.17
27 2 0.04
28 1 0.02
29 2 0.04
30 14 0.30
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAAATGTATCGATACATCTAGGT
Found at i:278051 original size:20 final size:20
Alignment explanation
Indices: 277989--278052 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
277979 CGAAATGAAG
*
277989 ATACATATCAAAATGTATCA
1 ATACATCTCAAAATGTATCA
*
278009 ATACAATACAT-AATATGT-T-A
1 ATAC-AT-C-TCAAAATGTATCA
278029 ATACATCTCAAAATGTATCA
1 ATACATCTCAAAATGTATCA
278049 ATAC
1 ATAC
278053 TCTAAGCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
17 1 0.03
18 7 0.20
19 3 0.09
20 14 0.40
21 3 0.09
22 6 0.17
23 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (20 bp):
ATACATCTCAAAATGTATCA
Found at i:279549 original size:35 final size:34
Alignment explanation
Indices: 279510--279628 Score: 123
Period size: 35 Copynumber: 3.4 Consensus size: 34
279500 GCTAGAAAAA
279510 AGAAAACAAGAAATGAAACAGCAATAGTAGAGAAG
1 AGAAAACAAGAAATGAAA-AGCAATAGTAGAGAAG
**
279545 AGAAAACAAGAAACAAAATAGCAATTA-TAGAGAAG
1 AGAAAACAAGAAATGAAA-AGCAA-TAGTAGAGAAG
* * * *
279580 AGAAAGCAGGAAATGATAAAGCAATAGGAGAAAAAG
1 AGAAAACAAGAAATGA-AAAGCAATAGTAG-AGAAG
*
279616 AGAAAGCAAGAAA
1 AGAAAACAAGAAA
279629 CAAAAACAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
34 2 0.03
35 48 0.69
36 20 0.29
ACGTcount: A:0.61, C:0.08, G:0.23, T:0.08
Consensus pattern (34 bp):
AGAAAACAAGAAATGAAAAGCAATAGTAGAGAAG
Found at i:279765 original size:22 final size:21
Alignment explanation
Indices: 279740--279791 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
279730 CAATAGCCGA
279740 CAACAATAAACACAACAAGAAG
1 CAACAATAAACACAACAA-AAG
* * *
279762 CAACAATAAGCACACCAATAG
1 CAACAATAAACACAACAAAAG
279783 CAACAATAA
1 CAACAATAA
279792 TAGCAAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.60, C:0.25, G:0.08, T:0.08
Consensus pattern (21 bp):
CAACAATAAACACAACAAAAG
Done.