Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008814.1 Hibiscus syriacus cultivar Beakdansim tig00111976_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1021170
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:272175 original size:131 final size:131
Alignment explanation
Indices: 271941--272208 Score: 333
Period size: 131 Copynumber: 2.0 Consensus size: 131
271931 TAATTACATG
* * *
271941 ACTATTTCGTCTCAAAATTCAATATTGATTCGAGTGAAAACGATAATAACTAATGATTTCCAATC
1 ACTATTTCGTCTCAAAAATCAATATTGATTCGAGAGAAAACGATAATAACGAATGATTTCCAATC
* * * *
272006 AAGAATAAATAAACTCTCATTAATTACAACAATCATTTATTACTCCAATCGAAATGAAGAGATGT
66 AAGAATAAATAAACTCTCATGAATTACAACAATCATTTATTACTCCAAACGAAATGAAAAGATAT
272071 C
131 C
* * * *
272072 ACTATTAT-GTCTTAAAAATCAATATTGATTCGAGAGAAAATGATAATATCGAATTATTTCCAAT
1 ACTATT-TCGTCTCAAAAATCAATATTGATTCGAGAGAAAACGATAATAACGAATGATTTCCAAT
* * * ** * *
272136 CGAGAATAAATGACCTCTCATGCCTTA-AAGCAGTCATTTATTACTCTAAACGAAATGAAAAGAT
65 CAAGAATAAATAAACTCTCATGAATTACAA-CAATCATTTATTACTCCAAACGAAATGAAAAGAT
*
272200 ATT
129 ATC
272203 ACTATT
1 ACTATT
272209 CTTAATATTG
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
130 2 0.02
131 113 0.97
132 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (131 bp):
ACTATTTCGTCTCAAAAATCAATATTGATTCGAGAGAAAACGATAATAACGAATGATTTCCAATC
AAGAATAAATAAACTCTCATGAATTACAACAATCATTTATTACTCCAAACGAAATGAAAAGATAT
C
Found at i:272691 original size:5 final size:5
Alignment explanation
Indices: 272681--272708 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
272671 GTAAAAATTG
272681 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
272709 ATAGGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:274223 original size:3 final size:3
Alignment explanation
Indices: 274209--274238 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
274199 AAAGGTATGC
274209 AAT AATT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
274239 AGTCGGGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:274876 original size:133 final size:134
Alignment explanation
Indices: 274435--274926 Score: 490
Period size: 133 Copynumber: 3.6 Consensus size: 134
274425 GAGATATGGG
* * *
274435 AATGTTGATTCATTCCAC-CGTTCTTCAGGGAAAATAGAATCAGGGCAGACTTGTTCCACTGTTC
1 AATGTTGATTCATTCCACTC-TTCTTCA-GGAAAATTGAATCAAGGCAGACTTGTTCCACTATTC
* * * * * * *
274499 CTCAGGGAAGTTCAAATCTGGAAAAATAGAGGGATCTGTACTGGTGCTTCTTAAGGAAAAAATCA
64 CTCAAGGAAGATCAAATCTGGAAAAA-AGAGGGATATGTTCTGCTGCTTCTTGAGG-GAAAATCA
274564 TATCTGGA
127 TATCTGGA
* * * * * *
274572 AATGTTGATTTATTCCACTATTATTCAAGGAAAATTGAATCGAGACAGACTTGTTCCACTGTTCC
1 AATGTTGATTCATTCCACTCTTCTTC-AGGAAAATTGAATCAAGGCAGACTTGTTCCACTATTCC
* *** * * *
274637 TCAAGGAAAAT-AAAAAAGGAAAAAATAGGGATATGTTCTGCTGCTTCTTGAAGGAAAATCAGAT
65 TCAAGGAAGATCAAATCTGGAAAAAAGAGGGATATGTTCTGCTGCTTCTTGAGGGAAAATCATAT
274701 CTGGA
130 CTGGA
* * * * * *
274706 AATGCTGATTCATTCCACTGTTCTTTATGGAAGATTGAATCAAGGCAGACTTGATCCACTATTCT
1 AATGTTGATTCATTCCACTCTTCTTCA-GGAAAATTGAATCAAGGCAGACTTGTTCCACTATTCC
* * **
274771 TTAGGGAAGATCAAATCTGGAAAAAA-A-GGATATGTTCCT-CCACTTCTTGAGGGAAAATCATA
65 TCAAGGAAGATCAAATCTGGAAAAAAGAGGGATATGTT-CTGCTGCTTCTTGAGGGAAAATCATA
*
274833 TCTAGA
129 TCTGGA
* * * ** * * *
274839 AATGTTGATTCGTTCCACTCTTCTTCAGGTGATATTGAATTGAGGAAGACTTGTTCCACTACTAC
1 AATGTTGATTCATTCCACTCTTCTTCAGG-AAAATTGAATCAAGGCAGACTTGTTCCACTATTCC
*
274904 TCAAGGAAGATCAAATCTAGAAA
65 TCAAGGAAGATCAAATCTGGAAA
274927 GAGATTATAT
Statistics
Matches: 290, Mismatches: 59, Indels: 16
0.79 0.16 0.04
Matches are distributed among these distances:
132 2 0.01
133 103 0.36
134 77 0.27
135 34 0.12
136 10 0.03
137 63 0.22
138 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (134 bp):
AATGTTGATTCATTCCACTCTTCTTCAGGAAAATTGAATCAAGGCAGACTTGTTCCACTATTCCT
CAAGGAAGATCAAATCTGGAAAAAAGAGGGATATGTTCTGCTGCTTCTTGAGGGAAAATCATATC
TGGA
Found at i:276258 original size:13 final size:13
Alignment explanation
Indices: 276242--276271 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
276232 TAAACCCTCA
276242 TTTTATTTATTCT
1 TTTTATTTATTCT
276255 TTTTATTTATTCT
1 TTTTATTTATTCT
276268 TTTT
1 TTTT
276272 TTCTTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTCT
Found at i:282830 original size:21 final size:19
Alignment explanation
Indices: 282792--282837 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
282782 AATTAATCCT
282792 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
282812 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
282833 A-TAAT
1 ACTAAT
282838 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:287432 original size:202 final size:203
Alignment explanation
Indices: 287032--287449 Score: 560
Period size: 203 Copynumber: 2.0 Consensus size: 203
287022 CGAACTTGTA
* *
287032 ATTTTCATTTACAAAGACAATTAATTAATTGACTATCTGCCTGACTCTCTAAAGAAAGTCCCCAG
1 ATTTTCATTTACAAAGACAATCAATTAATTGACTATCTGCCTGACTCTCTAAAAAAAGTCCCCAG
* * * *
287097 CGGAGTCGCCAAACTATTGAAACGATTTGTAGAAAGGTGGCCTCGTTTCAAAATAATTTGATGTC
66 CGGAGTCGCCAAACTATCGAAACGATTTGTAGAAAGATGGCCTCATTTCAAAATAATTTGATAT-
* * * * *
287162 CATTTAATGATGAAACGTGGTTCGAGGAGTCGGCACCAACCTTTGATTAGGGTGTGATTGGGCAC
130 CATTTAATGATAAAACGTGGTTCGACGAGTCGCCACCAACATTTGATTAGGGTGTGATTGGACAC
287227 CC-AAAAAT
195 CCAAAAAAT
* *
287235 ATTTTCATTTACAAAGATAATCAATTAATTGACTATC-GACCTGACTCTCTAAAAAAAGTCCCTA
1 ATTTTCATTTACAAAGACAATCAATTAATTGACTATCTG-CCTGACTCTCTAAAAAAAGTCCCCA
* * * * *
287299 GCGTAGTCGCCAAGCTGTCGAAACGGTTTTTCA-AAA-ATGG-CTCATTTCAAAAATAATTTGAT
65 GCGGAGTCGCCAAACTATCGAAACGATTTGT-AGAAAGATGGCCTCATTTC-AAAATAATTTGAT
287361 AT-ATGGTTAATGATAAAACGTGGTTCGACGAGTCGCCACCAACATTTGATTAGGGTGTGATTGG
128 ATCAT--TTAATGATAAAACGTGGTTCGACGAGTCGCCACCAACATTTGATTAGGGTGTGATTGG
287425 ACACCCAAAAAAAT
191 ACACCC-AAAAAAT
287439 ATTTATCATTT
1 ATTT-TCATTT
287450 TAAAAAATAT
Statistics
Matches: 189, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
200 2 0.01
201 7 0.04
202 77 0.41
203 86 0.46
204 11 0.06
205 6 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (203 bp):
ATTTTCATTTACAAAGACAATCAATTAATTGACTATCTGCCTGACTCTCTAAAAAAAGTCCCCAG
CGGAGTCGCCAAACTATCGAAACGATTTGTAGAAAGATGGCCTCATTTCAAAATAATTTGATATC
ATTTAATGATAAAACGTGGTTCGACGAGTCGCCACCAACATTTGATTAGGGTGTGATTGGACACC
CAAAAAAT
Found at i:288100 original size:132 final size:130
Alignment explanation
Indices: 287821--288165 Score: 467
Period size: 132 Copynumber: 2.6 Consensus size: 130
287811 ATAATTCTAA
* *
287821 GAGAGAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGAA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAA-AA
* ** * * * *
287886 GACATTTATTACTCCAATCGAAATGAAGATATATCACTACTTCGTCTTGAAATTCAATATTGATT
65 GTCATTTATTACTCCAATAAAAATGAAGAGATATCACTACTTCGTCTTAAAAATCAATAGTGATT
287951 C
130 C
* ** * * * *
287952 GAGTGAAAACGATAATATCTAACGATTTCCAATCGAGAATAAATGATCTTTCATACCTTACAATA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTA-AAAA
288017 GTCATTTATTACTCCAATAAAAAATGAAGAGATATCACTA-TTCCGTCTTAAAAATCAATAGTGA
65 GTCATTTATTACTCCAAT-AAAAATGAAGAGATATCACTACTT-CGTCTTAAAAATCAATAGTGA
288081 TTC
128 TTC
* *
288084 GAGAGAAAACGGTAATATCGAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAA-A
*
288149 GTCATTTATTACACCAA
65 GTCATTTATTACTCCAA
288166 CCGAAATGAA
Statistics
Matches: 184, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
131 74 0.40
132 110 0.60
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAAAG
TCATTTATTACTCCAATAAAAATGAAGAGATATCACTACTTCGTCTTAAAAATCAATAGTGATTC
Found at i:290003 original size:22 final size:23
Alignment explanation
Indices: 289974--290027 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
289964 ACTATTAGAA
*
289974 TATT-TAAATATTAA-AAGTTAT
1 TATTGTAAATATTAATAAATTAT
289995 TATTGTAAATATTAATAAATTAT
1 TATTGTAAATATTAATAAATTAT
290018 TA-TGTAAATA
1 TATTGTAAATA
290028 ATTATGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.13
22 18 0.60
23 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TATTGTAAATATTAATAAATTAT
Found at i:293926 original size:31 final size:31
Alignment explanation
Indices: 293891--293967 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
293881 AGCTTAAGGG
* *
293891 AGCTTAATGGAGCTAAAATATTAGTTGAATA
1 AGCTTAAGGGAGCTAAAATATTAGATGAATA
*
293922 AGCTTAAGGGAGCTCAAATATTAGATGAATA
1 AGCTTAAGGGAGCTAAAATATTAGATGAATA
293953 AGCTTAAGGGGAGCT
1 AGCTTAA-GGGAGCT
293968 GAACTTAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 35 0.83
32 7 0.17
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (31 bp):
AGCTTAAGGGAGCTAAAATATTAGATGAATA
Found at i:295339 original size:15 final size:15
Alignment explanation
Indices: 295316--295353 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
295306 AAAAAGTAAC
295316 GAAAAAATCAA-AAA
1 GAAAAAATCAACAAA
295330 GAAGAAAATCAACAAA
1 GAA-AAAATCAACAAA
295346 GAAAAAAT
1 GAAAAAAT
295354 TCATCATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.59
16 6 0.27
ACGTcount: A:0.74, C:0.08, G:0.11, T:0.08
Consensus pattern (15 bp):
GAAAAAATCAACAAA
Found at i:301462 original size:11 final size:12
Alignment explanation
Indices: 301446--301478 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
301436 AGAGATGTTA
301446 AAAGGTTGATT-
1 AAAGGTTGATTG
301457 AAAGGTTGATTG
1 AAAGGTTGATTG
301469 AAA-GTTGATT
1 AAAGGTTGATT
301479 TCATGCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (12 bp):
AAAGGTTGATTG
Found at i:301727 original size:537 final size:523
Alignment explanation
Indices: 300697--301761 Score: 1752
Period size: 537 Copynumber: 2.0 Consensus size: 523
300687 AATCTTGTTG
**
300697 GATTTCAAAGATCTGAAATCTAAGGGTTTATATTCATGATAGGATTCATGAAATTGATGATAAAT
1 GATTTCAAAGATCCCAAATCTAAGGGTTTATATTCATGATAGGATTCATGAAATTGATGATAAAT
*
300762 CTTGATGATTTAGAGGTTGTAGATTTATTTTCAAGCTGGATTTATGGTTAAAACATGTTCAATCT
66 CTTGATGATTTAGAGGTTGTAGATTCATTTTCAAGCTGGATTTATGGTTAAAACATGTTCAATCT
* * *
300827 TTCTAGAGATATTATGTAAAATTCGGCCAAATTATAAGTTGGAAAACTTTGTGTTCTGATGAAAG
131 TTCTAGAGATATTATGTAAAATTCGGCCAAATTATAAGTTGGAAAACTTTGTATTCTAATAAAAG
300892 TTGATTAAGGTTTGATTGCAGAGATGTTAAAAGGTTGATTGAAAGTTGACTTCATGCTTGAATCG
196 TTGATTAAGGTTTGATTGCAGAGATGTTAAAAGGTTGATTGAAAGTTGACTTCATGCTTGAATCG
*
300957 AATCAAAATCGAACAAAATCATGAAAACGTAGTTCTAAAGGATAAAATATTCGATCATGATGTAT
261 AATCAAAATCGAACAAAATCATGAAAACGTAGTTCTAAAGGATAAAATATTCGATCATGACGTAT
* * *
301022 CTAAGTGATAAATGGTGAAGAACCATTTTATGTAATTGGAAAGGTTGGTGCCAATGTTAAAAAGG
326 CTAAGTGATAAATGGTGAAGAACCATTTTATGTAAATGGAAAGGTTGGTGCCAATGCTAAAAAAG
* * * *
301087 AATTATTAAGTGTTAAATATTTGGTAGAAAATGAGTTCCAAGTATATTATGGGGTTGTTATGGGA
391 AATTATTAAGTGTTAAATATTTGGTAGAAAATGAGTTCAAAGTATATGATGGAGTTGTAATGGGA
* * *
301152 TGTGTTCATGTTAGTATAATACTAACATATGTATCGTTATGAATTTGTGATTTATACATATTGTG
456 TGTGTTCATGTTAGTACAATACTAACATATGAATCGTTATGAATTTGTGATTTATACAAATTGTG
301217 ATT
521 ATT
*
301220 GATTTCAAAGATCCCAAATCTAAGGGTTTATGTTCATGATAGGATTCATGAAATTGATGATAAAT
1 GATTTCAAAGATCCCAAATCTAAGGGTTTATATTCATGATAGGATTCATGAAATTGATGATAAAT
301285 CTTGATGATTTAGAGGTTGTAGATTCATTTTCAAGCTGGATTTATGGTTAAAACATGTTCAATCT
66 CTTGATGATTTAGAGGTTGTAGATTCATTTTCAAGCTGGATTTATGGTTAAAACATGTTCAATCT
* *
301350 TTCTATAGATTATTATGTAAAATTTGGCCAAATTATAAGTTGGAAAACTTTGTATTCTAATAAAA
131 TTCTAGAGA-TATTATGTAAAATTCGGCCAAATTATAAGTTGGAAAACTTTGTATTCTAATAAAA
* *
301415 GTTGATTAAGGATTTGATTGTAGAGATGTTAAAAGGTTGATTAAAGGTTGATTGAAAGTTGATTT
195 GTTGATTAAGG-TTTGATTGCAGAGA---T-----GTT-A--AAAGGTTGATTGAAAGTTGACTT
* * * *
301480 CATGCTTGAATTGAATCAAAATCGAGCAAAATCATGAAAACGTAGTTTTAAAGGATAAAGTATTC
248 CATGCTTGAATCGAATCAAAATCGAACAAAATCATGAAAACGTAGTTCTAAAGGATAAAATATTC
301545 GATCATGACGTATCTAAGTGATAAAATGGTGAAGAACCATTTTATGTAAATGGAAAGGTTGGTGC
313 GATCATGACGTATCTAAGTGAT-AAATGGTGAAGAACCATTTTATGTAAATGGAAAGGTTGGTGC
301610 CAATGCTAAAAAAGAATTATTAAGTGTTAAATATTTGGTAGAAAATGAGTTCAAAGTATATGATG
377 CAATGCTAAAAAAGAATTATTAAGTGTTAAATATTTGGTAGAAAATGAGTTCAAAGTATATGATG
*
301675 GAGTTGTAATGGGATGTGTTTATGTTAGTACAATACTAACATATGAATCGTTATGAATTTGTGAT
442 GAGTTGTAATGGGATGTGTTCATGTTAGTACAATACTAACATATGAATCGTTATGAATTTGTGAT
*
301740 TTGTACAAATTGTGATT
507 TTATACAAATTGTGATT
301757 GATTT
1 GATTT
301762 GTGATCGAAG
Statistics
Matches: 500, Mismatches: 28, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
523 134 0.27
524 62 0.12
525 13 0.03
528 1 0.00
533 3 0.01
534 1 0.00
536 104 0.21
537 182 0.36
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (523 bp):
GATTTCAAAGATCCCAAATCTAAGGGTTTATATTCATGATAGGATTCATGAAATTGATGATAAAT
CTTGATGATTTAGAGGTTGTAGATTCATTTTCAAGCTGGATTTATGGTTAAAACATGTTCAATCT
TTCTAGAGATATTATGTAAAATTCGGCCAAATTATAAGTTGGAAAACTTTGTATTCTAATAAAAG
TTGATTAAGGTTTGATTGCAGAGATGTTAAAAGGTTGATTGAAAGTTGACTTCATGCTTGAATCG
AATCAAAATCGAACAAAATCATGAAAACGTAGTTCTAAAGGATAAAATATTCGATCATGACGTAT
CTAAGTGATAAATGGTGAAGAACCATTTTATGTAAATGGAAAGGTTGGTGCCAATGCTAAAAAAG
AATTATTAAGTGTTAAATATTTGGTAGAAAATGAGTTCAAAGTATATGATGGAGTTGTAATGGGA
TGTGTTCATGTTAGTACAATACTAACATATGAATCGTTATGAATTTGTGATTTATACAAATTGTG
ATT
Found at i:302225 original size:40 final size:40
Alignment explanation
Indices: 302168--302329 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
302158 TAAAGGTTTA
* *
302168 TAATACACTTAGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
302208 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
302248 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
302288 TAATGCACTTCGGTGTATATAGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
302328 TA
1 TA
302330 GCACTACGGT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:302483 original size:44 final size:45
Alignment explanation
Indices: 302433--302520 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
302423 GGTAACCATG
302433 AAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGACAAGTATATTGGT
* * **
302477 AAAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTATATTGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGACAAGTATATTGG
302521 AAAGAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 24 0.62
45 15 0.38
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGACAAGTATATTGGT
Found at i:310960 original size:18 final size:19
Alignment explanation
Indices: 310937--310973 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
310927 TAAAATATAG
310937 TAAATCAGG-AATCATACT
1 TAAATCAGGAAATCATACT
310955 TAAATCAGGTAAATCATAC
1 TAAATCAGG-AAATCATAC
310974 GGTAGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAATCAGGAAATCATACT
Found at i:313329 original size:32 final size:31
Alignment explanation
Indices: 313293--313369 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
313283 CAGGGCCATG
* * *
313293 GGGCCTACCTAAGAACATATTTTAGGGCCGCA
1 GGGCCTACCTAAGAA-AGATCTCAGGGCCGCA
** *
313325 GGGCCTACCCGAGAAGGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAAGATCTCAGGGCCGCA
*
313356 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
313370 GTTACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAAGATCTCAGGGCCGCA
Found at i:315903 original size:19 final size:19
Alignment explanation
Indices: 315860--315905 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
315850 GTTAAAGTTC
*
315860 TGGTCAACAGTAGTCAACG
1 TGGTCAACAGCAGTCAACG
315879 TCGGTCAACA-CAGTCAACGG
1 T-GGTCAACAGCAGTCAAC-G
315899 TGGTCAA
1 TGGTCAA
315906 AAGGTCAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (19 bp):
TGGTCAACAGCAGTCAACG
Found at i:323091 original size:21 final size:21
Alignment explanation
Indices: 323050--323095 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
323040 ATGGAAAGAT
*
323050 AGAAGAAATGATTTAAGGAAA
1 AGAAGAAATGATATAAGGAAA
323071 AGAAGGAAATGATATAA-GAAA
1 AGAA-GAAATGATATAAGGAAA
323092 AGAA
1 AGAA
323096 AATGAAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (21 bp):
AGAAGAAATGATATAAGGAAA
Found at i:327166 original size:25 final size:22
Alignment explanation
Indices: 327146--327196 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
327136 GGAAAGATAG
*
327146 AAGAAATGATTTAAGGAAAAG-A
1 AAGAAATAATTTAA-GAAAAGAA
327168 AAGAAATAATTTAAGAAAAGAA
1 AAGAAATAATTTAAGAAAAGAA
327190 AATGAAA
1 AA-GAAA
327197 GCAAAGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.23
22 16 0.62
23 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (22 bp):
AAGAAATAATTTAAGAAAAGAA
Found at i:327185 original size:21 final size:22
Alignment explanation
Indices: 327146--327190 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
327136 GGAAAGATAG
*
327146 AAGAAATGATTTAAGGAAAAGA
1 AAGAAATAATTTAAGGAAAAGA
327168 AAGAAATAATTTAA-GAAAAGA
1 AAGAAATAATTTAAGGAAAAGA
327189 AA
1 AA
327191 ATGAAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (22 bp):
AAGAAATAATTTAAGGAAAAGA
Found at i:330620 original size:18 final size:19
Alignment explanation
Indices: 330597--330635 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
330587 TTTAAGTAGT
*
330597 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
330615 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
330634 AA
1 AA
330636 AAATAAAAGA
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:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:333272 original size:13 final size:12
Alignment explanation
Indices: 333253--333285 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
333243 AACATGCTCG
333253 ATAAAAATAAAA
1 ATAAAAATAAAA
333265 AGTAAAAATAAAA
1 A-TAAAAATAAAA
333278 ATAAAAAT
1 ATAAAAAT
333286 TTAACGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:333277 original size:5 final size:6
Alignment explanation
Indices: 333253--333285 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
333243 AACATGCTCG
333253 ATAAAA ATAAAA AGTAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA A-TAAAA ATAAAA ATAAAA AT
333286 TTAACGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:336157 original size:18 final size:18
Alignment explanation
Indices: 336134--336168 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
336124 TTTAAGTAGT
*
336134 AATAAAAACGATTAAATA
1 AATAAAAACAATTAAATA
*
336152 AATAAAAGCAATTAAAT
1 AATAAAAACAATTAAAT
336169 TAAAAAATAA
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:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
AATAAAAACAATTAAATA
Found at i:340913 original size:11 final size:11
Alignment explanation
Indices: 340897--340947 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
340887 GCCTTGTACT
340897 TTGTGAGCTGA
1 TTGTGAGCTGA
*
340908 TTGTGAGCTGCC
1 TTGTGAGCTG-A
340920 TTGT-A-CT--
1 TTGTGAGCTGA
340927 TTGTGAGCTGA
1 TTGTGAGCTGA
340938 TTGTGAGCTG
1 TTGTGAGCTG
340948 CATATGATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 4 0.12
8 1 0.03
9 2 0.06
10 2 0.06
11 21 0.62
12 4 0.12
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (11 bp):
TTGTGAGCTGA
Found at i:340918 original size:30 final size:30
Alignment explanation
Indices: 340882--340948 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
340872 AGTGTTCCAC
340882 GAGCTGCCTTGTACTTTGTGAGCTGATTGT
1 GAGCTGCCTTGTACTTTGTGAGCTGATTGT
340912 GAGCTGCCTTGTACTTTGTGAGCTGATTGT
1 GAGCTGCCTTGTACTTTGTGAGCTGATTGT
340942 GAGCTGC
1 GAGCTGC
340949 ATATGATGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.37
Consensus pattern (30 bp):
GAGCTGCCTTGTACTTTGTGAGCTGATTGT
Found at i:348915 original size:31 final size:31
Alignment explanation
Indices: 348880--348945 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
348870 CAAATGGTCA
*
348880 GGGACCATATTGTAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
* ** * *
348911 GGGACCATGTTGCAAATGGATTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
348942 GGGA
1 GGGA
348946 ATGTATTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGG
Found at i:355046 original size:20 final size:20
Alignment explanation
Indices: 355023--355061 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
355013 AGGGATTATT
*
355023 AGTGGTCTTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
355043 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
355062 TATTCAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:358256 original size:19 final size:19
Alignment explanation
Indices: 358232--358277 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
358222 TATGATTTCA
* *
358232 AAAATAAAAATTAGACTTT
1 AAAATAAAAAATAAACTTT
358251 AAAATAAAAAATAAACTTT
1 AAAATAAAAAATAAACTTT
*
358270 ATAATAAA
1 AAAATAAA
358278 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAAAAATAAACTTT
Found at i:367521 original size:31 final size:31
Alignment explanation
Indices: 367486--367551 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
367476 CAAATGGTCA
*
367486 GGGACCATATTGTAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
* ** * *
367517 GGGACCATGTTGCAAATGGATTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
367548 GGGA
1 GGGA
367552 ATGTATTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGG
Found at i:373597 original size:20 final size:20
Alignment explanation
Indices: 373574--373612 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
373564 AGGGATTATT
*
373574 AGTGGTCTTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
373594 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
373613 TATTCAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:376806 original size:19 final size:19
Alignment explanation
Indices: 376782--376827 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
376772 TATGATTTCA
* *
376782 AAAATAAAAATTAGACTTT
1 AAAATAAAAAATAAACTTT
376801 AAAATAAAAAATAAACTTT
1 AAAATAAAAAATAAACTTT
*
376820 ATAATAAA
1 AAAATAAA
376828 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAAAAATAAACTTT
Found at i:377966 original size:2 final size:2
Alignment explanation
Indices: 377959--377983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
377949 CAAAGCAAAT
377959 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 T
377984 GGATACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:384316 original size:12 final size:12
Alignment explanation
Indices: 384299--384326 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
384289 AACCGATTGC
384299 TAAAATCTTACA
1 TAAAATCTTACA
384311 TAAAATCTTACA
1 TAAAATCTTACA
384323 TAAA
1 TAAA
384327 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAATCTTACA
Found at i:386078 original size:31 final size:31
Alignment explanation
Indices: 386022--386087 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
386012 CAAATGGTCA
386022 GGGACCATATTGTAAACAGACTAAATGTTGG
1 GGGACCATATTGTAAACAGACTAAATGTTGG
* ** * *
386053 GGGACCATGTTGTAAATGGATTAAATGTTTG
1 GGGACCATATTGTAAACAGACTAAATGTTGG
386084 GGGA
1 GGGA
386088 ATGTATTGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (31 bp):
GGGACCATATTGTAAACAGACTAAATGTTGG
Found at i:391465 original size:21 final size:19
Alignment explanation
Indices: 391441--391487 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
391431 CCTATTATAC
391441 AAATAATAT-TATATGTGATAT
1 AAATAATATGT-TATG-G-TAT
*
391462 AAATTATATGTTATGGTAT
1 AAATAATATGTTATGGTAT
391481 AAATAAT
1 AAATAAT
391488 TATGAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 9 0.39
20 1 0.04
21 12 0.52
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
AAATAATATGTTATGGTAT
Found at i:392111 original size:20 final size:20
Alignment explanation
Indices: 392088--392126 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
392078 AGGGATTATT
*
392088 AGTGGTCTTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
392108 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
392127 TATTCAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:399719 original size:12 final size:12
Alignment explanation
Indices: 399702--399729 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
399692 AACCGATTGC
399702 TAAAATCTTACA
1 TAAAATCTTACA
399714 TAAAATCTTACA
1 TAAAATCTTACA
399726 TAAA
1 TAAA
399730 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAATCTTACA
Found at i:401466 original size:31 final size:31
Alignment explanation
Indices: 401431--401496 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
401421 CAAATGGTCA
*
401431 GGGACCATATTGTAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
* ** * *
401462 GGGACCATGTTGCAAATGGATTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
401493 GGGA
1 GGGA
401497 ATGTATTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGG
Found at i:415285 original size:19 final size:19
Alignment explanation
Indices: 415261--415306 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
415251 TATGATTTCA
* *
415261 AAAATAAAAATTAGACTTT
1 AAAATAAAAAATAAACTTT
415280 AAAATAAAAAATAAACTTT
1 AAAATAAAAAATAAACTTT
*
415299 ATAATAAA
1 AAAATAAA
415307 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAAAAATAAACTTT
Found at i:423918 original size:19 final size:20
Alignment explanation
Indices: 423894--423932 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
423884 ATAATCAAGT
*
423894 AAACTAAA-TAAATAAAATA
1 AAACTAAAGTAAAAAAAATA
423913 AAACTAAAGTAAAAAAAATA
1 AAACTAAAGTAAAAAAAATA
423933 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (20 bp):
AAACTAAAGTAAAAAAAATA
Found at i:426655 original size:27 final size:28
Alignment explanation
Indices: 426636--426696 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
426626 GTTGCTAAGG
426636 CAATTGAATC-ATTTTCAGTTGTAACGA
1 CAATTGAATCAATTTTCAGTTGTAACGA
*
426663 CAATTGAATCAATTTTCA-TTGTCACGA
1 CAATTGAATCAATTTTCAGTTGTAACGA
426690 CAATTGA
1 CAATTGA
426697 GTTGCCTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (28 bp):
CAATTGAATCAATTTTCAGTTGTAACGA
Found at i:431103 original size:25 final size:24
Alignment explanation
Indices: 431075--431124 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
431065 TATTCTAACC
431075 ATACATACAAAAATATGTAAT-GAAA
1 ATACAT-CAAAAA-ATGTAATCGAAA
*
431100 ATACATCAAAAAATTTAATCGAAA
1 ATACATCAAAAAATGTAATCGAAA
431124 A
1 A
431125 GATCCCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (24 bp):
ATACATCAAAAAATGTAATCGAAA
Found at i:435856 original size:54 final size:53
Alignment explanation
Indices: 435798--436106 Score: 372
Period size: 54 Copynumber: 5.8 Consensus size: 53
435788 TATACGATCA
* * * * *
435798 TTCATAAACATATTATGAGTTACGTGGGTTGCACACATAGTGCTGAAATTGTTG
1 TTCATCAACATATGATGAATT-CGTGAGTTGCACACATAGTGCTGAAATGGTTG
* ** * *
435852 TTCATCAACATATGATGAATTCTGTGAGTTTCACAC--AGTGCCAAAACGGTTA
1 TTCATCAACATATGATGAATTC-GTGAGTTGCACACATAGTGCTGAAATGGTTG
* * * *
435904 TTCATCAACATATGATTAACTTCGTGAGTTGCACACATAGTGCCGAAACGATTG
1 TTCATCAACATATGATGAA-TTCGTGAGTTGCACACATAGTGCTGAAATGGTTG
* *
435958 TTCATCAACATATGATGAATTCCGTGAGTTACACAAATAGTG-TCGAAATGGTTG
1 TTCATCAACATATGATGAATT-CGTGAGTTGCACACATAGTGCT-GAAATGGTTG
436012 TTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTGAAATGGTTG
1 TTCATCAACATATGATGAATT-CGTGAGTTGCACACATAGTGCTGAAATGGTTG
* *
436066 TTCATCAACATATGATGAATTCAGTGAGTTGTACGCATAGT
1 TTCATCAACATATGATGAATTC-GTGAGTTGCACACATAGT
436107 ACCCATACAG
Statistics
Matches: 222, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
52 41 0.18
53 7 0.03
54 173 0.78
55 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (53 bp):
TTCATCAACATATGATGAATTCGTGAGTTGCACACATAGTGCTGAAATGGTTG
Found at i:436097 original size:31 final size:31
Alignment explanation
Indices: 436008--436097 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 31
435998 TGTCGAAATG
*
436008 GTTGTTCATCAACATATGATGAATTCCGTGA
1 GTTGTTCATCAACATATGATGAATTCAGTGA
*
436039 GTTG--CA-C-ACATAGTGCTGAA---A-TG-
1 GTTGTTCATCAACATA-TGATGAATTCAGTGA
436062 GTTGTTCATCAACATATGATGAATTCAGTGA
1 GTTGTTCATCAACATATGATGAATTCAGTGA
436093 GTTGT
1 GTTGT
436098 ACGCATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 20
0.67 0.04 0.29
Matches are distributed among these distances:
23 4 0.09
24 2 0.04
25 2 0.04
26 7 0.15
27 10 0.22
28 7 0.15
29 3 0.07
30 2 0.04
31 9 0.20
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (31 bp):
GTTGTTCATCAACATATGATGAATTCAGTGA
Found at i:438260 original size:55 final size:55
Alignment explanation
Indices: 438185--438328 Score: 200
Period size: 55 Copynumber: 2.6 Consensus size: 55
438175 TAAGTGTGAA
* *
438185 AAAACTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTTTGTGTGC
1 AAAAC-TAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATATGTGC
** * *
438241 AAAACTAAGAAATTTATACTAAATATATGAATTTCTGTATGGGCACTATATGTGC
1 AAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATATGTGC
* *
438296 -GAACTTAGAAATCCATACTAAGTGTATGAATTT
1 AAAACTAAGAAATCCATACTAAGTGTATGAATTT
438329 ACATATAGGA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
54 27 0.36
55 44 0.58
56 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (55 bp):
AAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATATGTGC
Found at i:438660 original size:68 final size:68
Alignment explanation
Indices: 438548--438852 Score: 488
Period size: 68 Copynumber: 4.5 Consensus size: 68
438538 AAAGATTAGT
*
438548 AGGCCTAACTGTGCATTTGACAGAAATA-TGTCATTTATGTCAGTTAGATGAAAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAGAAA-AGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
438612 TTTG
65 TTTG
* * *
438616 AGGCCTAACTGTGCATTTGACAGAAAAGTTTCATATATGCCAGTTAGATGAAAGGCTAAGTGCCA
1 AGGCCTAACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
438681 TTG
66 TTG
* * *
438684 AGGCCTAACTATGCATTTGACA-AAAAGGTGTCATTTATGTCAGTTAGATGAAAGGCTAAATGCC
1 AGGCCTAACTGTGCATTTGACAGAAAA-GTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
*
438748 TTCG
65 TTTG
*
438752 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
438817 TTG
66 TTG
*
438820 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCA
1 AGGCCTAACTGTGCATTTGACAGAAAAGTGTCA
438853 GTTAGATGAA
Statistics
Matches: 218, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
67 5 0.02
68 210 0.96
69 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:439208 original size:81 final size:82
Alignment explanation
Indices: 438852--439197 Score: 420
Period size: 81 Copynumber: 4.3 Consensus size: 82
438842 GAAAGGTGTC
*
438852 AGTTAGATGAACGGTTAAATACTGTTGAGTAAAAG-ATAAATGGCCTAGCTGTGCATTTGACAGA
1 AGTTAGATGAACGGTTAAATACTGTTGAGTAAAAGAATAAATGGCCTAGCTGTGCATTTGACAAA
** *
438916 CTGGTGTCAATTATGCT
66 AAGGTGTCAATTATGCA
* * *
438933 AGTTAGATGAACGATTAAATACTGTTGAGTAAAATAAT-AATGGCCTAGCTGTGCATTTGGCAAA
1 AGTTAGATGAACGGTTAAATACTGTTGAGTAAAAGAATAAATGGCCTAGCTGTGCATTTGACAAA
438997 AAGGTGTCAATTATG-A
66 AAGGTGTCAATTATGCA
* * * * *
439013 CAGTTAGATGAACAGTTAAATA-TCGTTGAGTAAAAG-ATGAATGGTCTAGATGTGCATTTGGCA
1 -AGTTAGATGAACGGTTAAATACT-GTTGAGTAAAAGAATAAATGGCCTAGCTGTGCATTTGACA
439076 AAAAGGTGTCAATTATGCTA
64 AAAAGGTGTCAATTATGC-A
* * * * *
439096 A-TTGGATGAACGGTTAAACACTATTGAGTAAAAGAAT-AATGGACTAGCTGTGCATTTGATAGA
1 AGTTAGATGAACGGTTAAATACTGTTGAGTAAAAGAATAAATGGCCTAGCTGTGCATTTGACA-A
*
439159 AAA-GTGTCAAATATGCA
65 AAAGGTGTCAATTATGCA
* *
439176 AGTTAGATGAAAGGCTAAATAC
1 AGTTAGATGAACGGTTAAATAC
439198 CTTTGGGTAA
Statistics
Matches: 230, Mismatches: 25, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
80 5 0.02
81 214 0.93
82 10 0.04
83 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (82 bp):
AGTTAGATGAACGGTTAAATACTGTTGAGTAAAAGAATAAATGGCCTAGCTGTGCATTTGACAAA
AAGGTGTCAATTATGCA
Found at i:439326 original size:55 final size:55
Alignment explanation
Indices: 439258--439368 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
439248 ATATGAAGGG
*
439258 ATGTTGTATATATATAATGTACAACAATGCATAATTAGTATGAATGAATATTATA
1 ATGTTATATATATATAATGTACAACAATGCATAATTAGTATGAATGAATATTATA
* **
439313 ATGTTATATATATATAATGTACAATAATGCATAATTAGTATGAATGGGTATTATA
1 ATGTTATATATATATAATGTACAACAATGCATAATTAGTATGAATGAATATTATA
439368 A
1 A
439369 ACGAAATCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (55 bp):
ATGTTATATATATATAATGTACAACAATGCATAATTAGTATGAATGAATATTATA
Found at i:443142 original size:3 final size:3
Alignment explanation
Indices: 443134--443159 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
443124 TCTATAAAAA
443134 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
443160 ACCACATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:446047 original size:15 final size:15
Alignment explanation
Indices: 446027--446071 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
446017 CCATCAGTAG
446027 GTACCCAAAATAGGT
1 GTACCCAAAATAGGT
446042 GTACCCAAAATAGGT
1 GTACCCAAAATAGGT
*
446057 GTACCCAAAGTAGGT
1 GTACCCAAAATAGGT
446072 ACTCAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (15 bp):
GTACCCAAAATAGGT
Found at i:448703 original size:14 final size:13
Alignment explanation
Indices: 448683--448716 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
448673 TATTTTTTTT
448683 CAAAAAAAAAAGG
1 CAAAAAAAAAAGG
448696 CAAAAAAAAAAGG
1 CAAAAAAAAAAGG
448709 CAAAAAAA
1 CAAAAAAA
448717 CAAAAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGG
Found at i:456771 original size:11 final size:12
Alignment explanation
Indices: 456755--456796 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
456745 AAGTAAAATG
456755 AATAAAAT-AAA
1 AATAAAATAAAA
456766 AAT-AAATAAAA
1 AATAAAATAAAA
*
456777 AATAAAAGAAATA
1 AATAAAATAAA-A
456790 AATAAAA
1 AATAAAA
456797 AAGTTAGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 4 0.15
11 9 0.33
12 6 0.22
13 8 0.30
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:458043 original size:23 final size:23
Alignment explanation
Indices: 458011--458057 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
458001 ACCAAAAAAG
458011 AAAAATGAAAATAAATAGATATAT
1 AAAAATGAAAATAAATA-ATATAT
458035 AAAAA-GAAAATAAATAATATAT
1 AAAAATGAAAATAAATAATATAT
458057 A
1 A
458058 GTAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAAATGAAAATAAATAATATAT
Found at i:458056 original size:24 final size:25
Alignment explanation
Indices: 458011--458062 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
458001 ACCAAAAAAG
458011 AAAAATGAAAATAAATAGATATA-T
1 AAAAATGAAAATAAATAGATATAGT
*
458035 AAAAA-GAAAATAAATAATATATAGT
1 AAAAATGAAAATAAAT-AGATATAGT
458060 AAA
1 AAA
458063 TAATATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 10 0.40
24 11 0.44
25 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (25 bp):
AAAAATGAAAATAAATAGATATAGT
Found at i:458072 original size:7 final size:7
Alignment explanation
Indices: 458043--458099 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
458033 ATAAAAAGAA
*
458043 AATAAAT
1 AATATAT
458050 AATATAT
1 AATATAT
* *
458057 AGTAAAT
1 AATATAT
458064 AATATAT
1 AATATAT
458071 AATACTAT
1 AATA-TAT
*
458079 ACTATAT
1 AATATAT
458086 AATATAT
1 AATATAT
458093 AA-ATAT
1 AATATAT
458099 A
1 A
458100 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
6 5 0.12
7 31 0.74
8 6 0.14
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (7 bp):
AATATAT
Found at i:458087 original size:22 final size:21
Alignment explanation
Indices: 458043--458100 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
458033 ATAAAAAGAA
* *
458043 AATAAATAATATATAGTAAAT
1 AATATATAATATATACTAAAT
*
458064 AATATATAATACTATACTATAT
1 AATATATAATA-TATACTAAAT
458086 AATATATAAATATAT
1 AATATAT-AATATAT
458101 TTTTTAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.31
22 18 0.56
23 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
AATATATAATATATACTAAAT
Found at i:458138 original size:37 final size:37
Alignment explanation
Indices: 458097--458348 Score: 357
Period size: 37 Copynumber: 6.7 Consensus size: 37
458087 ATATATAAAT
**
458097 ATATTTTTTAAAACTATATCA-TATATATATTTTCAAA
1 ATATTTTCAAAAACTATAT-ATTATATATATTTTCAAA
*
458134 ATATTTTCAAAAACTATATATTATATATATATTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
* *
458171 ATGTTTTCAAAAACTATATATTATATATATTTCCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
458208 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAA
1 ATATTTTCAAAAACTATATATTATATATA--TTTTCAAA
*
458247 ATGTTTTCAAAAACTATATATTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
458284 ATATTTTTAAAAACTATATATTATATATATGTTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATA--TTTTCAAA
458323 AT-TTTAT-AAAAACTATATATTATATA
1 ATATTT-TCAAAAACTATATATTATATA
458349 CTATATATAT
Statistics
Matches: 196, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
36 1 0.01
37 128 0.65
38 22 0.11
39 45 0.23
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAAACTATATATTATATATATTTTCAAA
Found at i:458235 original size:76 final size:76
Alignment explanation
Indices: 458106--458348 Score: 397
Period size: 76 Copynumber: 3.2 Consensus size: 76
458096 TATATTTTTT
*
458106 AAAACTATATCA-TATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATA--TATTC
1 AAAACTATAT-ATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATGTTTTC
458168 AAAATGTTTTCA
65 AAAATGTTTTCA
* *
458180 AAAACTATATATTATATATATTTCCAAAATATTTTCAAAAACTATATATTATATATATGTTTTTA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATGTTTTCA
458245 AAATGTTTTCA
66 AAATGTTTTCA
*
458256 AAAACTATATATTATATATATTTTCAAAATATTTTTAAAAACTATATATTATATATATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATGTTTTCA
458321 AAAT-TTTAT-A
66 AAATGTTT-TCA
458331 AAAACTATATATTATATA
1 AAAACTATATATTATATA
458349 CTATATATAT
Statistics
Matches: 159, Mismatches: 6, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
73 1 0.01
74 54 0.34
75 22 0.14
76 82 0.52
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (76 bp):
AAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATGTTTTCA
AAATGTTTTCA
Found at i:467820 original size:20 final size:19
Alignment explanation
Indices: 467791--467842 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
467781 GATTTAGACC
467791 AAAA-AAAGAAAAACA-AAA
1 AAAATAAAGAAAAA-AGAAA
467809 ATAAATAAAGAAAGAAAGAAA
1 A-AAATAAAGAAA-AAAGAAA
467830 AAAATAAAGAAAA
1 AAAATAAAGAAAA
467843 TGAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 19 0.63
21 6 0.20
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.06
Consensus pattern (19 bp):
AAAATAAAGAAAAAAGAAA
Found at i:467850 original size:13 final size:12
Alignment explanation
Indices: 467791--467842 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
467781 GATTTAGACC
*
467791 AAAAAAAGAAA-
1 AAAAAAATAAAG
*
467802 AACAAAAATAAAT
1 AA-AAAAATAAAG
* *
467815 AAAGAAAGAAAG
1 AAAAAAATAAAG
467827 AAAAAAATAAAG
1 AAAAAAATAAAG
467839 AAAA
1 AAAA
467843 TGAATAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAAAATAAAG
Found at i:467872 original size:7 final size:7
Alignment explanation
Indices: 467846--467897 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
467836 AAGAAAATGA
*
467846 ATAAAAT
1 ATAATAT
* *
467853 ATAGTAA
1 ATAATAT
467860 ATAATAT
1 ATAATAT
467867 ATAATACT
1 ATAATA-T
*
467875 ATACTAT
1 ATAATAT
467882 ATAATAT
1 ATAATAT
467889 ATAA-AT
1 ATAATAT
467895 ATA
1 ATA
467898 TTTTTTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
6 5 0.14
7 26 0.70
8 6 0.16
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:467898 original size:15 final size:15
Alignment explanation
Indices: 467860--467897 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
467850 AATATAGTAA
467860 ATAATATATAATACT
1 ATAATATATAATACT
*
467875 ATACTATATAATA-T
1 ATAATATATAATACT
467889 ATAA-ATATA
1 ATAATATATA
467898 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.24
14 4 0.19
15 12 0.57
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATATATAATACT
Found at i:467929 original size:25 final size:25
Alignment explanation
Indices: 467884--467934 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
467874 TATACTATAT
* *
467884 AATATATAAATATATTTTTTTTAAA
1 AATATATAAATATATTATTTTCAAA
*
467909 AATATAT-AATTTATATATTTTCAAA
1 AATATATAAATATAT-TATTTTCAAA
467934 A
1 A
467935 TATTTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATATAAATATATTATTTTCAAA
Found at i:467934 original size:24 final size:25
Alignment explanation
Indices: 467884--467937 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
467874 TATACTATAT
* *
467884 AATATATAAATATATTTTTTTTAAA
1 AATATATAAATATATATATTTTAAA
* *
467909 AATATAT-AATTTATATATTTTCAA
1 AATATATAAATATATATATTTTAAA
467933 AATAT
1 AATAT
467938 TTTCAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATATAAATATATATATTTTAAA
Found at i:467963 original size:39 final size:38
Alignment explanation
Indices: 467901--468153 Score: 304
Period size: 37 Copynumber: 6.7 Consensus size: 38
467891 AAATATATTT
* *
467901 TTTTTAAAAA-TATATA-ATTTATATATTTTCAAAATA
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATA
* *
467937 TTTTCAAAATCTATATTATATATATATATTTT-AAAATG
1 TTTTCAAAAACTATA-TATATATATATATTTTCAAAATA
467975 TTTTCAAAAACTATATAT-TATATATATTTTCAAAATA
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATA
* * * *
468012 TTTTCAAAAATTATAT-TATATATATGTTTTTAAAATG
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATA
*
468049 TTTACAAAAACTATATAT-TATATATATTTTCAAAATA
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATA
* *
468086 TTTTTAAAAACTATATATTATATATATGTTTTCAAAAT-
1 TTTTCAAAAACTATATA-TATATATATATTTTCAAAATA
* *
468124 TTTATAAAAAACTATATATTATATTTATAT
1 TTT-TCAAAAACTATATA-TATATATATAT
468154 ACTAAATAAA
Statistics
Matches: 187, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
36 21 0.11
37 88 0.47
38 26 0.14
39 52 0.28
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (38 bp):
TTTTCAAAAACTATATATATATATATATTTTCAAAATA
Found at i:468240 original size:16 final size:16
Alignment explanation
Indices: 468219--468260 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
468209 CCCACCAAGA
*
468219 AAACATACATAAACAT
1 AAACATACATAAACAC
*
468235 AAACATACATCAACAC
1 AAACATACATAAACAC
*
468251 ATACATACAT
1 AAACATACAT
468261 GATACGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACATACATAAACAC
Found at i:472677 original size:2 final size:2
Alignment explanation
Indices: 472672--472708 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
472662 ATATTAATAA
472672 AT AT AT AT AT 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 AT AT AT AT AT A
472709 CAATGTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:473182 original size:33 final size:33
Alignment explanation
Indices: 473081--473182 Score: 152
Period size: 33 Copynumber: 3.1 Consensus size: 33
473071 AATGTTTCGG
* *
473081 TTTTAGTGTTTCAATAGGACTCAAATACGTTGG
1 TTTTAGTGTTTCAATAGGACTCAAATAAGTTGA
**
473114 TTGCAGTGTTTCAATAGGACTCAAATACA-TTGA
1 TTTTAGTGTTTCAATAGGACTCAAATA-AGTTGA
473147 TTTTAGTGTTTCAATAGGACTCAAATAAGTTGA
1 TTTTAGTGTTTCAATAGGACTCAAATAAGTTGA
473180 TTT
1 TTT
473183 ATTTTCTGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TTTTAGTGTTTCAATAGGACTCAAATAAGTTGA
Found at i:473247 original size:9 final size:9
Alignment explanation
Indices: 473230--473302 Score: 53
Period size: 10 Copynumber: 7.7 Consensus size: 9
473220 GGGGTCTGCA
473230 AAAAT-AAT
1 AAAATAAAT
473238 AAAATAAAT
1 AAAATAAAT
473247 AATAAT-AAT
1 AA-AATAAAT
473256 AATAATAATAAT
1 AA-AAT-A-AAT
473268 AATAATAAAT
1 AA-AATAAAT
473278 -AAATATAAT
1 AAAATA-AAT
*
473287 ATAATATAAT
1 AAAATA-AAT
473297 AAAATA
1 AAAATA
473303 CATTTGTAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
8 9 0.16
9 18 0.32
10 19 0.34
11 1 0.02
12 9 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATAAAT
Found at i:473250 original size:3 final size:3
Alignment explanation
Indices: 473232--473302 Score: 80
Period size: 3 Copynumber: 24.3 Consensus size: 3
473222 GGTCTGCAAA
473232 AAT AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
473278 AA- ATAT AAT -AT AAT -AT AAT AA- AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT A
473303 CATTTGTAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
2 9 0.15
3 44 0.73
4 7 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:482440 original size:26 final size:26
Alignment explanation
Indices: 482404--482461 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
482394 AGTTTATGCA
482404 ATTAGGTTGTCCCTTTGAATCTAGAT
1 ATTAGGTTGTCCCTTTGAATCTAGAT
482430 ATTAGGTTGTCCCTTTGAATCTAGAT
1 ATTAGGTTGTCCCTTTGAATCTAGAT
482456 ATTAGG
1 ATTAGG
482462 ATCTCCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (26 bp):
ATTAGGTTGTCCCTTTGAATCTAGAT
Found at i:484940 original size:57 final size:56
Alignment explanation
Indices: 484816--484946 Score: 158
Period size: 57 Copynumber: 2.3 Consensus size: 56
484806 CATAAAGGAT
* *
484816 AAAACTATTTTTTAATTACAATAAAGTACAAACTTTTATAAATTATAAAAAAATAC
1 AAAACTATTTATAAATTACAATAAAGTACAAACTTTTATAAATTATAAAAAAATAC
* ** * *
484872 ATATTTTTTTATAAATTACAATTAAGTATTC-AACTTTTATAAATTA-AAATAAAATAC
1 AAAACTATTTATAAATTACAATAAAGTA--CAAACTTTTATAAATTATAAA-AAAATAC
484929 AAAACTATTTATAAATTA
1 AAAACTATTTATAAATTA
484947 TGATAAAAGA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
56 24 0.39
57 36 0.59
58 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (56 bp):
AAAACTATTTATAAATTACAATAAAGTACAAACTTTTATAAATTATAAAAAAATAC
Found at i:484945 original size:29 final size:28
Alignment explanation
Indices: 484829--484946 Score: 96
Period size: 29 Copynumber: 4.2 Consensus size: 28
484819 ACTATTTTTT
* *
484829 AATTACAATAAAGTAC-AAACTTTTATA
1 AATTAAAATAAAATACAAAACTTTTATA
***
484856 AATTATAAA-AAAATACATATTTTTTTATA
1 AATTA-AAATAAAATACA-AAACTTTTATA
* * * ***
484885 AATTACAATTAAGTATTCAACTTTTATA
1 AATTAAAATAAAATACAAAACTTTTATA
484913 AATTAAAATAAAATACAAAACTATTTATA
1 AATTAAAATAAAATACAAAACT-TTTATA
484942 AATTA
1 AATTA
484947 TGATAAAAGA
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
27 11 0.17
28 27 0.41
29 28 0.42
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTAAAATAAAATACAAAACTTTTATA
Found at i:484966 original size:29 final size:29
Alignment explanation
Indices: 484903--484961 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
484893 TTAAGTATTC
*
484903 AACT-TTTATAAATTAAAATAAAATACAA
1 AACTATTTATAAATTAAAATAAAAAACAA
**
484931 AACTATTTATAAATTATGATAAAAGAACAA
1 AACTATTTATAAATTAAAATAAAA-AACAA
484961 A
1 A
484962 TTATTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 17 0.65
30 5 0.19
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTATTTATAAATTAAAATAAAAAACAA
Found at i:490775 original size:23 final size:24
Alignment explanation
Indices: 490722--490784 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 24
490712 AATTTTTCAT
*
490722 AAATTATTGGTTTAATTCAAACTTCA
1 AAATTATT--TTTAATTCAAACTCCA
490748 AAATTATTTTTAATT-AAACTCCA
1 AAATTATTTTTAATTCAAACTCCA
*
490771 TAATTGGATTTTTA
1 AAATT--ATTTTTA
490785 TTTTGATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 11 0.33
24 7 0.21
25 7 0.21
26 8 0.24
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (24 bp):
AAATTATTTTTAATTCAAACTCCA
Found at i:490980 original size:13 final size:13
Alignment explanation
Indices: 490962--490987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490952 TTATTTTAAG
490962 TTTTATTATTATT
1 TTTTATTATTATT
490975 TTTTATTATTATT
1 TTTTATTATTATT
490988 GAGATCAAAC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:492129 original size:21 final size:20
Alignment explanation
Indices: 492105--492173 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
492095 GCTAATTTAT
492105 AACGTCACTAATTTAAATCAA
1 AACGTCA-TAATTTAAATCAA
492126 AACGTCATAA--T-AAT-AA
1 AACGTCATAATTTAAATCAA
**
492142 ATTGTCACTAATTTAAATCAA
1 AACGTCA-TAATTTAAATCAA
*
492163 AGCGTCATAAT
1 AACGTCATAAT
492174 AATAAATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
16 7 0.18
17 6 0.15
18 1 0.03
19 1 0.03
20 10 0.26
21 14 0.36
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (20 bp):
AACGTCATAATTTAAATCAA
Found at i:492158 original size:37 final size:37
Alignment explanation
Indices: 492108--492190 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
492098 AATTTATAAC
492108 GTCACTAATTTAAATCAAAACGTCATAATAATAAATT
1 GTCACTAATTTAAATCAAAACGTCATAATAATAAATT
*
492145 GTCACTAATTTAAATCAAAGCGTCATAATAATAAATT
1 GTCACTAATTTAAATCAAAACGTCATAATAATAAATT
492182 GTCACTAAT
1 GTCACTAAT
492191 ACTTTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (37 bp):
GTCACTAATTTAAATCAAAACGTCATAATAATAAATT
Found at i:494541 original size:40 final size:39
Alignment explanation
Indices: 494495--494609 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 39
494485 TGCTTTTACA
*
494495 AAGAAAATAAGTTCAACGATTTATTTCCTTTTACAAAAC
1 AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAAAC
*
494534 AATGAAAATAAATACAACGATTTATTTCCTTTTACAAAA-
1 AA-GAAAATAAATTCAACGATTTATTTCCTTTTACAAAAC
* * * *
494573 TAGAAAATAAATTGATCAATTTATTTCCTTTTACAAA
1 AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAA
494610 CTATTATCAT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 31 0.46
39 3 0.04
40 34 0.50
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (39 bp):
AAGAAAATAAATTCAACGATTTATTTCCTTTTACAAAAC
Found at i:494595 original size:38 final size:37
Alignment explanation
Indices: 494479--494609 Score: 158
Period size: 38 Copynumber: 3.5 Consensus size: 37
494469 AATCCAACAG
* *
494479 TTTATTTGCTTTTAC--AAAGAAAATAAGTTCAACGA
1 TTTATTTCCTTTTACAAAAAGAAAATAAATTCAACGA
*
494514 TTTATTTCCTTTTACAAAACAATGAAAATAAATACAACGA
1 TTTATTTCCTTTTAC-AAA-AA-GAAAATAAATTCAACGA
* * *
494554 TTTATTTCCTTTTACAAAATAGAAAATAAATTGATCAA
1 TTTATTTCCTTTTACAAAA-AGAAAATAAATTCAACGA
494592 TTTATTTCCTTTTACAAA
1 TTTATTTCCTTTTACAAA
494610 CTATTATCAT
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
35 14 0.17
38 33 0.40
39 6 0.07
40 30 0.36
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (37 bp):
TTTATTTCCTTTTACAAAAAGAAAATAAATTCAACGA
Found at i:494736 original size:32 final size:32
Alignment explanation
Indices: 494700--494761 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
494690 ATTTATTTCC
** *
494700 TTTTACAAAATTGGAAAATAAATCCAAAATTT
1 TTTTACAAAATAAGAAAATAAATCAAAAATTT
*
494732 TTTTACGAAATAAGAAAATAAATCAAAAAT
1 TTTTACAAAATAAGAAAATAAATCAAAAAT
494762 ATTATTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (32 bp):
TTTTACAAAATAAGAAAATAAATCAAAAATTT
Found at i:494863 original size:40 final size:38
Alignment explanation
Indices: 494809--494943 Score: 155
Period size: 39 Copynumber: 3.4 Consensus size: 38
494799 CCAAGAAGAT
*
494809 AAATTCAATGATTTATTTCCTTTTACAAAATAGAAAAGC
1 AAATTCAACGATTTATTTCCTTTTACAAAATAGAAAA-C
* * *
494848 AAATTATAACGATTTATTT-CTTTTACAGAATAGGAAAC
1 AAATT-CAACGATTTATTTCCTTTTACAAAATAGAAAAC
* * *
494886 TAAATCCAACGATTTATTTCCTTTTTCAAAATAGGAAAAAT
1 -AAATTCAACGATTTATTTCCTTTTACAAAATA-G-AAAAC
494927 AAATTCAACGATTTATT
1 AAATTCAACGATTTATT
494944 AAACTAGGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
38 13 0.16
39 36 0.45
40 28 0.35
41 3 0.04
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (38 bp):
AAATTCAACGATTTATTTCCTTTTACAAAATAGAAAAC
Found at i:495030 original size:58 final size:58
Alignment explanation
Indices: 494959--495264 Score: 279
Period size: 58 Copynumber: 5.3 Consensus size: 58
494949 AGGAAAATAA
* * * * *
494959 AAATTCAATAATTTATTTTCTTTCTCAAA-ATGGAATAATTCAAGATTATCAAGAAAAT
1 AAATTCAACAATTTATTTT-TTTCTCAAAGTTAGAATCATTCAAGATTCTCAAGAAAAT
* * * *
495017 AAATTCAACAA--T-TTTTTATAT-AAATTTAGAATCATTCAAGATTCTCAAGGAAAT
1 AAATTCAACAATTTATTTTTTTCTCAAAGTTAGAATCATTCAAGATTCTCAAGAAAAT
* *
495071 AAATTAAACAATTTA-TTTTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAAT
1 AAATTCAACAATTTATTTTTTTC-T-CAAAGTTAGAATCATTCAAGATTCTCAAGAAAAT
** * *
495130 ATGTTCAAGAATTTATTTTTCTT-ACAAAGTTAGAATCA-TCTAAGATTCTCAAGAAAAT
1 AAATTCAACAATTTATTTTT-TTCTCAAAGTTAGAATCATTC-AAGATTCTCAAGAAAAT
* * * * * *
495188 AAGTTCAACAATTTATTTTCCTTAT-AAAGTTAGAATCATTTAAGATTCTTAAGGAAAT
1 AAATTCAACAATTTATTTT-TTTCTCAAAGTTAGAATCATTCAAGATTCTCAAGAAAAT
* **
495246 AAATTAAATGATTTATTTT
1 AAATTCAACAATTTATTTT
495265 CGTTACGAAG
Statistics
Matches: 206, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
53 3 0.01
54 37 0.18
55 4 0.02
56 7 0.03
57 3 0.01
58 102 0.50
59 44 0.21
60 4 0.02
61 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (58 bp):
AAATTCAACAATTTATTTTTTTCTCAAAGTTAGAATCATTCAAGATTCTCAAGAAAAT
Found at i:495117 original size:59 final size:59
Alignment explanation
Indices: 494991--495264 Score: 312
Period size: 58 Copynumber: 4.8 Consensus size: 59
494981 TCTCAAAATG
* * * * * *
494991 GAATAATTCAAGATTATCAAGAAAATAAATTCAAC-A---ATTTTTT-ATATAAATTTA
1 GAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTTCTTACAAAGTTA
*
495045 GAATCATTCAAGATTCTCAAGGAAATAAATTAAACAATTTATTTTTTCTTACAAAGTTA
1 GAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTTCTTACAAAGTTA
** *
495104 GAATCATTCAAGATTCTCAAGGAAATATGTTCAAGAATTTA-TTTTTCTTACAAAGTTA
1 GAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTTCTTACAAAGTTA
* * * *
495162 GAATCA-TCTAAGATTCTCAAGAAAATAAGTTCAACAATTTA-TTTTCCTTATAAAGTTA
1 GAATCATTC-AAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTTCTTACAAAGTTA
* * * **
495220 GAATCATTTAAGATTCTTAAGGAAATAAATTAAATGATTTATTTT
1 GAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTT
495265 CGTTACGAAG
Statistics
Matches: 189, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
54 31 0.16
55 1 0.01
57 2 0.01
58 106 0.56
59 49 0.26
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (59 bp):
GAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTTCTTACAAAGTTA
Found at i:495549 original size:45 final size:44
Alignment explanation
Indices: 495470--495624 Score: 139
Period size: 45 Copynumber: 3.5 Consensus size: 44
495460 AAAAAGAAAA
* * * *
495470 AATCCTTCGATTTTAATTTTCGCAATCCAGTAATTGAAATGAACT
1 AATCCTTTGATTTTAATTTTCGCAA-CCAATAATTAAAAGGAACT
* * *
495515 AATCGTTTGATTTTAATTTTTGCAACACATTAATTAAAAGGAACT
1 AATCCTTTGATTTTAATTTTCGCAAC-CAATAATTAAAAGGAACT
* * * * * * *
495560 TATCTTTTTAATTTACTTTTGGCAACTCAATAATCAAAAGGAACT
1 AATCCTTTGATTTTAATTTTCGCAAC-CAATAATTAAAAGGAACT
* *
495605 ACTCCTTTGATTTTACTTTT
1 AATCCTTTGATTTTAATTTT
495625 GATAACTCAA
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
44 1 0.01
45 88 0.99
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (44 bp):
AATCCTTTGATTTTAATTTTCGCAACCAATAATTAAAAGGAACT
Found at i:495625 original size:45 final size:44
Alignment explanation
Indices: 495510--495644 Score: 144
Period size: 45 Copynumber: 3.0 Consensus size: 44
495500 TAATTGAAAT
* * * * * *
495510 GAACTAATCGTTTGATTTTAATTTTTGCAACACATTAATTAAAAG
1 GAACT-ATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
* * *
495555 GAACTTATCTTTTTAATTTACTTTTGGCAACTCAATAATCAAAAG
1 GAAC-TATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
**
495600 GAACTACTCCTTTGATTTTACTTTTGATAACTCAATAATCAAAAG
1 GAACTA-TCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
495645 CTTTGGATTA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
44 2 0.03
45 72 0.96
46 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (44 bp):
GAACTATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
Found at i:500694 original size:17 final size:17
Alignment explanation
Indices: 500674--500723 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
500664 TTTAGGGAAG
500674 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
500691 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
500708 TAGTTCGTTTATTAAA
1 TAGTTCATTAATTAAA
500724 TTAACTCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:502229 original size:17 final size:17
Alignment explanation
Indices: 502197--502246 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
502187 TAAGAGTTAA
* *
502197 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
502214 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
502231 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
502247 CTTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:504553 original size:2 final size:2
Alignment explanation
Indices: 504546--504581 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
504536 ATAACTATGA
* *
504546 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504582 GTAACAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:506550 original size:24 final size:24
Alignment explanation
Indices: 506518--506571 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
506508 TTATTATTAT
*
506518 TAATAATAA-CAACAATACTTATAA
1 TAATAATAATCAA-AATAATTATAA
506542 TAATAATAATCAAAATAATTATAA
1 TAATAATAATCAAAATAATTATAA
*
506566 AAATAA
1 TAATAA
506572 ATATAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (24 bp):
TAATAATAATCAAAATAATTATAA
Found at i:506559 original size:18 final size:18
Alignment explanation
Indices: 506537--506578 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
506527 CAACAATACT
*
506537 TATAATAATAATAATCAAA
1 TATAATAATAAAAAT-AAA
*
506556 -ATAATTATAAAAATAAA
1 TATAATAATAAAAATAAA
506573 TATAAT
1 TATAAT
506579 GTTTTTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAATAATAAAAATAAA
Found at i:506877 original size:91 final size:91
Alignment explanation
Indices: 506704--506963 Score: 391
Period size: 91 Copynumber: 2.9 Consensus size: 91
506694 CGTTATTTGA
* *
506704 TTGAACAAGTTCTTCTCATTATGAACTTATTC-TCTCTTG-TGGATGAGTTCTTCTCT-CTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTTGTTGGATGAGTTCTTCT-TATTATGA
*
506766 ACTCTTTACTGGAAACACTGATGCAAGG
64 ACTCTTCACTGGAAACACTGATGCAAGG
*
506794 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCCTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTTATTATGAAC
* *
506859 TCTCCATTGGAAACACTGATGCAAGG
66 TCTTCACTGGAAACACTGATGCAAGG
* * *
506885 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT-TGTTGGATGAGTTCTTCTTATTATGAA
506950 CTCTTCACTGGAAA
65 CTCTTCACTGGAAA
506964 TGTTGATCCC
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
90 36 0.23
91 82 0.53
92 36 0.23
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTTATTATGAAC
TCTTCACTGGAAACACTGATGCAAGG
Found at i:507045 original size:136 final size:136
Alignment explanation
Indices: 506882--507240 Score: 592
Period size: 136 Copynumber: 2.6 Consensus size: 136
506872 CACTGATGCA
*
506882 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
*
506947 GAACTCTTCACTGGAAATGTTGATCCCTCAAGCAAGGTATCACTGATTCGAAATGCCATGAATTG
66 GAACTCTTCACTGGAAATGTTGATCCCTCAAGCAAGGTATCACTGATTCGAAATGCCATGAATCG
507012 AGTGAT
131 AGTGAT
* *
507018 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* ** * * *
507083 GAACTCTTCACTGGAAATATTGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGTCGTGAATCG
66 GAACTCTTCACTGGAAATGTTGATCCCTCAAGCAAGGTATCACTGATTCGAAATGCCATGAATCG
507148 AGTGAT
131 AGTGAT
* *
507154 AAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* *
507219 GAACTCTCCATTGGAAATGTTG
66 GAACTCTTCACTGGAAATGTTG
507241 GTTCACCTCC
Statistics
Matches: 206, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 206 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (136 bp):
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCTTCACTGGAAATGTTGATCCCTCAAGCAAGGTATCACTGATTCGAAATGCCATGAATCG
AGTGAT
Found at i:508130 original size:17 final size:15
Alignment explanation
Indices: 508109--508193 Score: 84
Period size: 15 Copynumber: 5.5 Consensus size: 15
508099 CAAACCCTCA
508109 TTTTTCTCTTTTCA-T
1 TTTTTCT-TTTTCATT
*
508124 TTCTT-TTTTTCATT
1 TTTTTCTTTTTCATT
508138 TTTTTCTTTTTCATT
1 TTTTTCTTTTTCATT
*
508153 TTTTTCATTTTTTCATC
1 TTTTTC--TTTTTCATT
* *
508170 TTTTTATTTGTTCCTT
1 TTTTTCTTT-TTCATT
508186 TTTTTCTT
1 TTTTTCTT
508194 CAAGCATAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
13 6 0.10
14 6 0.10
15 22 0.38
16 11 0.19
17 13 0.22
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTTTCATT
Found at i:508136 original size:27 final size:27
Alignment explanation
Indices: 508106--508157 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
508096 TCTCAAACCC
508106 TCATTTTTCTC-TTTTCATTTCTTTTTT
1 TCATTTTTCTCTTTTTCATTT-TTTTTT
*
508133 TCATTTTTTTCTTTTTCATTTTTTT
1 TCATTTTTCTCTTTTTCATTTTTTT
508158 CATTTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (27 bp):
TCATTTTTCTCTTTTTCATTTTTTTTT
Found at i:508141 original size:9 final size:9
Alignment explanation
Indices: 508123--508191 Score: 62
Period size: 9 Copynumber: 8.4 Consensus size: 9
508113 TCTCTTTTCA
508123 TTTC-TTTT
1 TTTCATTTT
508131 TTTCATTTT
1 TTTCATTTT
508140 TTTC---TT
1 TTTCATTTT
508146 TTTCATTTT
1 TTTCATTTT
508155 TTTCA-TTT
1 TTTCATTTT
*
508163 TTTCATCTT
1 TTTCATTTT
508172 TTT-A-TTT
1 TTTCATTTT
* *
508179 GTTCCTTTT
1 TTTCATTTT
508188 TTTC
1 TTTC
508192 TTCAAGCATA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
6 6 0.12
7 4 0.08
8 13 0.27
9 26 0.53
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTCATTTT
Found at i:514619 original size:24 final size:24
Alignment explanation
Indices: 514587--514640 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
514577 TTATTATTAT
*
514587 TAATAATAA-CAACAATACTTATAA
1 TAATAATAATCAA-AATAATTATAA
514611 TAATAATAATCAAAATAATTATAA
1 TAATAATAATCAAAATAATTATAA
514635 TAATAA
1 TAATAA
514641 ATATAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (24 bp):
TAATAATAATCAAAATAATTATAA
Found at i:514628 original size:18 final size:18
Alignment explanation
Indices: 514606--514647 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
514596 CAACAATACT
514606 TATAATAATAATAATCAAA
1 TATAATAATAATAAT-AAA
*
514625 -ATAATTATAATAATAAA
1 TATAATAATAATAATAAA
514642 TATAAT
1 TATAAT
514648 GTTTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAATAATAATAATAAA
Found at i:514960 original size:82 final size:82
Alignment explanation
Indices: 514798--515019 Score: 212
Period size: 82 Copynumber: 2.7 Consensus size: 82
514788 ACAAAGTAGT
* ** ** * *
514798 ACTTTAGCGGTGTTTTTATGCAAATACCGCAATA-GATCCATCTATAGTGGCATTTTTTCAATAA
1 ACTTTAGCAGTGTTTTTACACAAATGTCGCAATAGGGTTCATCTATAGTGGCA-TTTTTCAATAA
* ** * *
514862 ATGTTGCAAGATATTAGT
65 ACGCCGCAAGAGATTAGA
* ** * *
514880 ACTTTAGTAGTGTTTTTACATGAATGTCGTAATAGGGTTCATCTATAGCGGCATTTTTCAATAAA
1 ACTTTAGCAGTGTTTTTACACAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTTCAATAAA
* *
514945 CGCCGTAATAGATTAGA
66 CGCCGCAAGAGATTAGA
* * * * *
514962 ACTTTAGCGGTGTTTTTAGACAAATGTTGCAATAGGGTTCACCTATAGTGACATTTTT
1 ACTTTAGCAGTGTTTTTACACAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTT
515020 TTCTCACGAA
Statistics
Matches: 110, Mismatches: 29, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
82 95 0.86
83 15 0.14
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (82 bp):
ACTTTAGCAGTGTTTTTACACAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTTCAATAAA
CGCCGCAAGAGATTAGA
Found at i:516064 original size:18 final size:17
Alignment explanation
Indices: 516036--516072 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
516026 AGTGGTTTAG
516036 TTTGTTTGTTGTCTTAT
1 TTTGTTTGTTGTCTTAT
516053 TTTGTATTGTTGTCTTAT
1 TTTGT-TTGTTGTCTTAT
516071 TT
1 TT
516073 CATTTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTGTCTTAT
Found at i:518147 original size:193 final size:187
Alignment explanation
Indices: 517775--518200 Score: 548
Period size: 193 Copynumber: 2.2 Consensus size: 187
517765 TACAAATAAG
** * * * * * *
517775 TATCGATACATAACAATATAAAAGGTTGAAGTTTGACAAAGTCGGGTTCAATATGATAAAATCGG
1 TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGTTTCAATATGAAAAAACCGG
* * * * *
517840 TAAAGTGCCACCGTATATGTTGAAGGTATCGATACTGTAATAAGTATCATATTATCGATACTTTA
66 TAAAGAGCCACCGAATATGTTAAAAGTATCGATACTATAATAAGTATCATATTATCGATACTTTA
*
517905 GGAATTTAAAAGAATTGCAATAATAGCGCTATAAAGTATCGATACTTTATAAACACA
131 GGAATTTAAAAGAATTGCAAGAATAGCGCTATAAAGTATCGATACTTTATAAACACA
* * * *
517962 TATCGATACATAATAATATAAGAGGTAAAAATATGAGAAAATCGGTTTCATTATGAAAAAACCGG
1 TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGTTTCAATATGAAAAAACCGG
* *
518027 TAAAGATCTACCGAATATGTTAAAAGTATCGATACTTTAATAAGTATATGTATCATATTATCGAT
66 TAAAGAGCCACCGAATATGTTAAAAGTATCGATAC--T-ATAA-TA-A-GTATCATATTATCGAT
* **
518092 ACTTTAGGAATTTAAAAGAATTGCAAGAATCGCGCCTATAAA-TATCGATACTTTATAAACATG
125 ACTTTAGGAATTTAAAAGAATTGCAAGAATAGCG-CTATAAAGTATCGATACTTTATAAACACA
* * *
518155 TATCGATACATAACAATATAACATGTAAAAATATGACAAAACCGGT
1 TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGT
518201 AAAGCGCTAC
Statistics
Matches: 204, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
187 82 0.40
189 1 0.00
190 3 0.01
191 2 0.01
192 1 0.00
193 108 0.53
194 7 0.03
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (187 bp):
TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGTTTCAATATGAAAAAACCGG
TAAAGAGCCACCGAATATGTTAAAAGTATCGATACTATAATAAGTATCATATTATCGATACTTTA
GGAATTTAAAAGAATTGCAAGAATAGCGCTATAAAGTATCGATACTTTATAAACACA
Found at i:518902 original size:197 final size:197
Alignment explanation
Indices: 518567--518921 Score: 507
Period size: 197 Copynumber: 1.8 Consensus size: 197
518557 TAATTGAAAA
* * * * * *
518567 TAGGGTTTTATGTGTTTGGGGTTTTGAAGTAAATAAGCATTTGGTACCGATTACAGATAGAAAGT
1 TAGGGTTTTATGGGTTTGGGATTTCGAAGCAAAGAAGCATTTGGAACCGATTACAGATAGAAAGT
* * * * *
518632 GATATTCTAGGTAGATAACAAATATCGATACTTTTATAAAATATTATAGGTAGAAAATGATATTG
66 GATATTATAGGTAAAAAACAAATATCGATACTTGTAGAAAATATTATAGGTAGAAAATGATATTG
518697 TAGGTTGTATAAATGTACCGATACTTGTTGTATAGAGTATTCCCGTTCGTTTCAAGGAAAAATAG
131 TAGGTTGTATAAATGTACCGATACTTGTTGTATAGAGTATTCCCGTTCGTTTCAAGGAAAAATAG
518762 AT
196 AT
* * *
518764 TAGGG-TTTATGGGTTTGAGGATTTCGAAGCAAAGAAGGATTTGGAACCGATTAGAGTTAGAAAG
1 TAGGGTTTTATGGGTTTG-GGATTTCGAAGCAAAGAAGCATTTGGAACCGATTACAGATAGAAAG
* * * *
518828 TGATATTATAGGTAAAAAATAAATATTGATGCTTGTAGATAATATTATAGGTAGAAAATGATAAT
65 TGATATTATAGGTAAAAAACAAATATCGATACTTGTAGAAAATATTATAGGTAGAAAATGAT-AT
*
518893 T-TAGGTTGTATAAATGTATCGATACTTGT
129 TGTAGGTTGTATAAATGTACCGATACTTGT
518922 AGTAGTGGCC
Statistics
Matches: 137, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
196 11 0.08
197 123 0.90
198 3 0.02
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (197 bp):
TAGGGTTTTATGGGTTTGGGATTTCGAAGCAAAGAAGCATTTGGAACCGATTACAGATAGAAAGT
GATATTATAGGTAAAAAACAAATATCGATACTTGTAGAAAATATTATAGGTAGAAAATGATATTG
TAGGTTGTATAAATGTACCGATACTTGTTGTATAGAGTATTCCCGTTCGTTTCAAGGAAAAATAG
AT
Found at i:519306 original size:17 final size:17
Alignment explanation
Indices: 519284--519319 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
519274 ATGACTGAAT
519284 GCCAAAGGATGAAGGAA
1 GCCAAAGGATGAAGGAA
*
519301 GCCAAAGTATGAAGGAA
1 GCCAAAGGATGAAGGAA
519318 GC
1 GC
519320 TGGTAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.14, G:0.33, T:0.08
Consensus pattern (17 bp):
GCCAAAGGATGAAGGAA
Found at i:520238 original size:22 final size:23
Alignment explanation
Indices: 520190--520240 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
520180 TGTTGGGTTT
*
520190 TTATATAAAATGATAGCATACTTA
1 TTATATAAAATAATAGCATA-TTA
520214 TTATATAAAATAATA-CAT-TTAA
1 TTATATAAAATAATAGCATATT-A
520236 TTATA
1 TTATA
520241 AATGCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 6 0.24
23 3 0.12
24 14 0.56
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (23 bp):
TTATATAAAATAATAGCATATTA
Found at i:520760 original size:62 final size:65
Alignment explanation
Indices: 520662--520806 Score: 224
Period size: 62 Copynumber: 2.3 Consensus size: 65
520652 AATTGAGAGC
**
520662 CTTAAGGGGGAAGTGGGTGGAAAAATTGATGGAGTGGTGAAAGAAGTTGTGGAATTGAGGGGTGA
1 CTTAAGGGGGTGGTGGGTGGAAAAATT-ATGGAGTGGTGAAAGAAGTTGTGGAATTGAGGGGTGA
520727 A
65 A
520728 CTTAAGGGGGTGGTGGGTGG-AAAA-T-TGGAGTGGTGAAAGAAGTTGTGGAATTGAGGGGTGAA
1 CTTAAGGGGGTGGTGGGTGGAAAAATTATGGAGTGGTGAAAGAAGTTGTGGAATTGAGGGGTGAA
* *
520790 CTTAAAGGGGTGATGGG
1 CTTAAGGGGGTGGTGGG
520807 AGTGGTTGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
62 52 0.69
64 1 0.01
65 4 0.05
66 18 0.24
ACGTcount: A:0.29, C:0.02, G:0.46, T:0.23
Consensus pattern (65 bp):
CTTAAGGGGGTGGTGGGTGGAAAAATTATGGAGTGGTGAAAGAAGTTGTGGAATTGAGGGGTGAA
Found at i:525600 original size:12 final size:12
Alignment explanation
Indices: 525585--525610 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
525575 TTGGAGTTTG
525585 AATTTAAATTTC
1 AATTTAAATTTC
525597 AATTTAAATTTC
1 AATTTAAATTTC
525609 AA
1 AA
525611 CTCCACTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (12 bp):
AATTTAAATTTC
Found at i:528339 original size:57 final size:57
Alignment explanation
Indices: 528246--528385 Score: 228
Period size: 57 Copynumber: 2.5 Consensus size: 57
528236 TATGCATTTC
* * * *
528246 TTCGGGAAGATGATGACCTTGAAATGAACCTATTATAGGTTGAAAGTTCAATCTTTG
1 TTCGCGAAGATGATGACCTTGAAATGAACCTATTATAGGTCGAAAGTTAAATCTTAG
528303 TTCGCGAAGATGATGACCTTGAAAT-AGACCTATTATAGGTCGAAAGTTAAATCTTAG
1 TTCGCGAAGATGATGACCTTGAAATGA-ACCTATTATAGGTCGAAAGTTAAATCTTAG
528360 TTCGCGAAGATGATGACCTTGAAATG
1 TTCGCGAAGATGATGACCTTGAAATG
528386 GAGTCCGAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
56 1 0.01
57 76 0.99
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (57 bp):
TTCGCGAAGATGATGACCTTGAAATGAACCTATTATAGGTCGAAAGTTAAATCTTAG
Found at i:530780 original size:225 final size:223
Alignment explanation
Indices: 530340--531044 Score: 986
Period size: 225 Copynumber: 3.1 Consensus size: 223
530330 AACAAATAAT
* * ** *
530340 GTAATTAACCGAGTT-TGTTGTCGTC-ATATTCCTAAGGCTCCGTCAACTTAAATTTTGTTAACA
1 GTAATTAACCGA-TTATGTTATCGTCGA-ATTTCTAAGGCTCTATCAACTTAAATTTTGGTAACA
* *
530403 -TTTAGGTGTTACGTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
64 TTTTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTA
* * * * * *
530467 TCGTCGAATTTCTAAGGCCCCATCAGCTTTAATAATGCGCTACCTATTACGTTACATAAACCCTA
129 TCGTCGGATTTCCAAAG-CCCATCAGCTTTAA-AAAGCGCTACCTATTACGTTATATAAACGCTA
*
530532 TCTAATATGTTATTATACTTGATAATGTTTCCA
192 -CTAATATGTTATTATGCTTGATAATGTTTCCA
* *
530565 GTAATTAACTGGTTATGTTATCGTCGAATTTCTAAGGCTCTATCAACTTAAATTTTGGTAACATT
1 GTAATTAACCGATTATGTTATCGTCGAATTTCTAAGGCTCTATCAACTTAAATTTTGGTAACATT
* *
530630 TTAGATGTTACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
66 TTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
* *
530695 GTAGGATTTCCAAAGACCCATCAGCTTTAAAAAGACGCTATCTATTACGTTATATAAACGCTACT
131 GTCGGATTTCCAAAG-CCCATCAGCTTTAAAAAG-CGCTACCTATTACGTTATATAAACGCTACT
*
530760 AATATGTTATTACGCTTGATAATGTTTCCA
194 AATATGTTATTATGCTTGATAATGTTTCCA
* * * * *
530790 GTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTTTATCAGCTTAAACTCTGGTAACATT
1 GTAATTAACCGATTATGTTATCGTCGAATTTCTAAGGCTCTATCAACTTAAATTTTGGTAACATT
* * *
530855 TTAGGCGTTACCTAATATGTTGATAATACTAATAAAAAATTAAGAAATTAACCTATTTTGTTATC
66 TTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
* **
530920 TTCGGATTTCCAAAGCCCATCAGC-TTAAAAAGGCGCTACCTATTACGTTATATAAGTGCTACTA
131 GTCGGATTTCCAAAGCCCATCAGCTTTAAAAA-GCGCTACCTATTACGTTATATAAACGCTACTA
* *
530984 ATATGCTATTATGCTTGATAATGTTTACA
195 ATATGTTATTATGCTTGATAATGTTTCCA
* *
531013 GTAATTAACCGATTACGTTATCGTCGGATTTC
1 GTAATTAACCGATTATGTTATCGTCGAATTTC
531045 CAAAGCCCCA
Statistics
Matches: 432, Mismatches: 43, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
223 92 0.21
224 12 0.03
225 215 0.50
226 113 0.26
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (223 bp):
GTAATTAACCGATTATGTTATCGTCGAATTTCTAAGGCTCTATCAACTTAAATTTTGGTAACATT
TTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
GTCGGATTTCCAAAGCCCATCAGCTTTAAAAAGCGCTACCTATTACGTTATATAAACGCTACTAA
TATGTTATTATGCTTGATAATGTTTCCA
Found at i:531118 original size:117 final size:115
Alignment explanation
Indices: 530672--531154 Score: 468
Period size: 117 Copynumber: 4.2 Consensus size: 115
530662 TAACAAATTA
* * * * *
530672 AGTAATTAACCTATTTTGTTATCGTAGGATTTCCAAAGACCCATCAGCTTTAAAAAGACGCTATC
1 AGTAATTAACCGATTATGTTATCGTCGGATTTCCAAAG-CCCATCAGC-TTAAAAAGGCGCTACC
* * * *
530737 TATTACGTTATATAAACGCTACTAATATGTTATTACGCTTGATAATGTTTCC
64 TATTACGTTATATAAGCGCTACTAATATGCTATTATGCTTGATAATGTTTAC
* * ** * **
530789 AGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTTTATCAGCTT--AAA--CTCT-GGT
1 AGTAATTAACCGATTATGTTATCGTCGGATTTCCAAAGC-CCATCAGCTTAAAAAGGCGCTACCT
* * * * * * * ***
530849 A--ACATT-T-TAGGCGTTACCTAATATGTTGATAATAC-TAATAAAAAATTA-
65 ATTACGTTATATAAGCGCTA-CTAATATGCT-ATTATGCTTGAT-AATGTTTAC
* * * *
530897 AGAAATTAACCTATTTTGTTATCTTCGGATTTCCAAAGCCCATCAGCTTAAAAAGGCGCTACCTA
1 AGTAATTAACCGATTATGTTATCGTCGGATTTCCAAAGCCCATCAGCTTAAAAAGGCGCTACCTA
*
530962 TTACGTTATATAAGTGCTACTAATATGCTATTATGCTTGATAATGTTTAC
66 TTACGTTATATAAGCGCTACTAATATGCTATTATGCTTGATAATGTTTAC
*
531012 AGTAATTAACCGATTACGTTATCGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACC
1 AGTAATTAACCGATTATGTTATCGTCGGATTTCCAAAG-CCCATCAGC-TTAAAAAGGCGCTACC
* * * *
531077 TA-TACGTTATATAAGCGCTACCTAATATGTTATTGTTCTTGATAATGTTTCC
64 TATTACGTTATATAAGCGCTA-CTAATATGCTATTATGCTTGATAATGTTTAC
*
531129 AGTAATTAACCGGTTATGTTATCGTC
1 AGTAATTAACCGATTATGTTATCGTC
531155 TATATTTTTT
Statistics
Matches: 292, Mismatches: 56, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
107 14 0.05
108 47 0.16
109 15 0.05
111 5 0.02
112 5 0.02
114 17 0.06
115 46 0.16
116 35 0.12
117 108 0.37
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (115 bp):
AGTAATTAACCGATTATGTTATCGTCGGATTTCCAAAGCCCATCAGCTTAAAAAGGCGCTACCTA
TTACGTTATATAAGCGCTACTAATATGCTATTATGCTTGATAATGTTTAC
Found at i:531574 original size:26 final size:24
Alignment explanation
Indices: 531545--531598 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 24
531535 CGATTCATTG
531545 TCGACTTCGGCTCATCACAATTGATT
1 TCGACTTC--CTCATCACAATTGATT
531571 TCGA----CTCATCACAATTGATT
1 TCGACTTCCTCATCACAATTGATT
531591 TCGACTTC
1 TCGACTTC
531599 AATTCTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
20 20 0.83
26 4 0.17
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (24 bp):
TCGACTTCCTCATCACAATTGATT
Found at i:531578 original size:20 final size:20
Alignment explanation
Indices: 531550--531596 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
531540 CATTGTCGAC
*
531550 TTCGGCTCATCACAATTGAT
1 TTCGACTCATCACAATTGAT
531570 TTCGACTCATCACAATTGAT
1 TTCGACTCATCACAATTGAT
531590 TTCGACT
1 TTCGACT
531597 TCAATTCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCGACTCATCACAATTGAT
Found at i:535935 original size:18 final size:19
Alignment explanation
Indices: 535907--535942 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
535897 ACTGTACTTA
535907 ATAATTATTTTTATAATTT
1 ATAATTATTTTTATAATTT
*
535926 ATAA-TATTTTTTTAATT
1 ATAATTATTTTTATAATT
535943 AGAATATTAA
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:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAATTATTTTTATAATTT
Found at i:535948 original size:17 final size:18
Alignment explanation
Indices: 535912--535950 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
535902 ACTTAATAAT
*
535912 TATTTTTATAATTTATAA
1 TATTTTTATAATTTAGAA
*
535930 TATTTTTTTAA-TTAGAA
1 TATTTTTATAATTTAGAA
535947 TATT
1 TATT
535951 AATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTTTATAATTTAGAA
Found at i:545599 original size:24 final size:24
Alignment explanation
Indices: 545563--545609 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
545553 AAGAAATAAA
* *
545563 AACATAATTCATATCAGATATCAT
1 AACAAAATCCATATCAGATATCAT
545587 AACAAAATCCATATCAGATATCA
1 AACAAAATCCATATCAGATATCA
545610 GAATAGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (24 bp):
AACAAAATCCATATCAGATATCAT
Found at i:545626 original size:24 final size:24
Alignment explanation
Indices: 545575--545626 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
545565 CATAATTCAT
* *
545575 ATCAGATATCATAACAAAATCCAT
1 ATCAGATATCAGAACAAAATCCAG
* * *
545599 ATCAGATATCAGAATAGAATCCGG
1 ATCAGATATCAGAACAAAATCCAG
545623 ATCA
1 ATCA
545627 AAAATCATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAGATATCAGAACAAAATCCAG
Found at i:546257 original size:27 final size:28
Alignment explanation
Indices: 546201--546263 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
546191 AATTCTAGGG
* *
546201 TTTAGAGGTATTTTAGGCCATTTTACAC
1 TTTAGGGGTATTTTAGGCCATTTAACAC
*
546229 TTTAGGGGTATTTT-GGTCATTTAACAC
1 TTTAGGGGTATTTTAGGCCATTTAACAC
546256 TTTAGGGG
1 TTTAGGGG
546264 CATTATCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (28 bp):
TTTAGGGGTATTTTAGGCCATTTAACAC
Found at i:546277 original size:27 final size:27
Alignment explanation
Indices: 546220--546278 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
546210 ATTTTAGGCC
* * * ** *
546220 ATTTTACACTTTAGGGGTATTTTGGTC
1 ATTTAACACTTTAGGGGCATTATCATA
546247 ATTTAACACTTTAGGGGCATTATCATA
1 ATTTAACACTTTAGGGGCATTATCATA
546274 ATTTA
1 ATTTA
546279 TCCATGGCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (27 bp):
ATTTAACACTTTAGGGGCATTATCATA
Found at i:546837 original size:28 final size:27
Alignment explanation
Indices: 546799--546860 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
546789 TTTTGTCAAA
* *
546799 GTCAACACTGGTCAATGCCTGATCAATG
1 GTCAACACTGGTCAACG-CTGATCAACG
* *
546827 GTCAACGCTGGTCAACGCTGGTCAACG
1 GTCAACACTGGTCAACGCTGATCAACG
546854 GTCAACA
1 GTCAACA
546861 TGATCGGCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (27 bp):
GTCAACACTGGTCAACGCTGATCAACG
Done.