Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold312
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: 931450
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 39452 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:308536 original size:42 final size:42
Alignment explanation
Indices: 308467--308552 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
308457 AATCATTTTA
* * *
308467 TTATTATTTTTGGACTCCAAGCACCCTTTGCGGGTTTTCACC
1 TTATTATTTTTGAACTCAAAGCACCCTTTACGGGTTTTCACC
* *
308509 TTATT-TTTTTAGAACTCAAAGCGCCCTTTATGGGTTTTCACC
1 TTATTATTTTT-GAACTCAAAGCACCCTTTACGGGTTTTCACC
308551 TT
1 TT
308553 GGTTCTCTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (42 bp):
TTATTATTTTTGAACTCAAAGCACCCTTTACGGGTTTTCACC
Found at i:318603 original size:15 final size:15
Alignment explanation
Indices: 318576--318623 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
318566 CATAAATATA
318576 AATAGAAAT-ATAAT
1 AATAGAAATAATAAT
* *
318590 AATAGTAATAATAAC
1 AATAGAAATAATAAT
318605 AATAGAAATAATAAT
1 AATAGAAATAATAAT
318620 AATA
1 AATA
318624 TCAAACCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (15 bp):
AATAGAAATAATAAT
Found at i:322505 original size:21 final size:22
Alignment explanation
Indices: 322480--322531 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
322470 GCTTCCCCTA
*
322480 GCCACG-CACGCCTCCGTACGT
1 GCCACGTCACGCCTCCGTACAT
*
322501 GCCACGTTCGCGCCTCCGTACAT
1 GCCACG-TCACGCCTCCGTACAT
322524 GCCACGTC
1 GCCACGTC
322532 CCTCGCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 6 0.22
22 2 0.07
23 19 0.70
ACGTcount: A:0.13, C:0.46, G:0.23, T:0.17
Consensus pattern (22 bp):
GCCACGTCACGCCTCCGTACAT
Found at i:323482 original size:28 final size:27
Alignment explanation
Indices: 323417--323482 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
323407 TATGAATTAT
** *
323417 TTTTTATATAATATATTTTTAATAACT
1 TTTTTATATAATATACGTTTAATAACA
*
323444 TTTATTTTATAATATACGTTTAA-AAGCCA
1 TTT-TTATATAATATACGTTTAATAA--CA
323473 TTTTTATATA
1 TTTTTATATA
323483 TTTCATCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.16
28 22 0.71
29 4 0.13
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTTTATATAATATACGTTTAATAACA
Found at i:325730 original size:25 final size:25
Alignment explanation
Indices: 325702--325754 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
325692 TTTAATAGGT
*
325702 TTTGTTTCATTATTATTTGTTATCA
1 TTTGTTTCATTATTATTTGATATCA
* * *
325727 TTTGTTTTATTTTTATTTGATATTA
1 TTTGTTTCATTATTATTTGATATCA
325752 TTT
1 TTT
325755 TATTTTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.70
Consensus pattern (25 bp):
TTTGTTTCATTATTATTTGATATCA
Found at i:326704 original size:17 final size:18
Alignment explanation
Indices: 326679--326712 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
326669 TTTTCTATTT
*
326679 AATTTTATT-TCATTTAA
1 AATTATATTATCATTTAA
326696 AATTATATTATCATTTA
1 AATTATATTATCATTTA
326713 TCAAATCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATATTATCATTTAA
Found at i:331582 original size:3 final size:3
Alignment explanation
Indices: 331574--331600 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
331564 GTTAAGAATG
331574 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
331601 ATTAATAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:334759 original size:28 final size:32
Alignment explanation
Indices: 334728--334787 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
334718 AATTGAGTAA
*
334728 TTAGGG-CT-AAAT-TGAAA-AAATAATATTT
1 TTAGGGACTAAAATGTGAAATAAATAAAATTT
334756 TTAGGGACTAAAATGTGAAATAAATAAAATTT
1 TTAGGGACTAAAATGTGAAATAAATAAAATTT
334788 GTGGACTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 6 0.22
29 2 0.07
30 4 0.15
31 5 0.19
32 10 0.37
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (32 bp):
TTAGGGACTAAAATGTGAAATAAATAAAATTT
Found at i:335351 original size:44 final size:43
Alignment explanation
Indices: 335298--335414 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
335288 TGTGTGTTAT
* * * *
335298 CGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTGTGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGT-AATTA
335342 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCAATATGTAATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAATATGTAATTA
* *
335385 CATGGAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
335415 TGTATGAGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
42 1 0.02
43 29 0.46
44 32 0.51
45 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTAATTA
Found at i:335404 original size:43 final size:44
Alignment explanation
Indices: 335303--335414 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 44
335293 GTTATCGTGT
* * * * * *
335303 AAGACCACGTTTGGGACGTTGGCATCGATTTGTGATTTACGTGT
1 AAGACCACGTCTGGGACGTTGGCATCAATATGTGAATTACATGG
335347 AAGACC-CTGTCTGGGACAG-TGGCATCAATATGT-AATTACATGG
1 AAGACCAC-GTCTGGGAC-GTTGGCATCAATATGTGAATTACATGG
335390 AAGACCACGTCTGGGACGTTGGCAT
1 AAGACCACGTCTGGGACGTTGGCAT
335415 TGTATGAGCT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
42 1 0.02
43 29 0.50
44 27 0.47
45 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (44 bp):
AAGACCACGTCTGGGACGTTGGCATCAATATGTGAATTACATGG
Found at i:337641 original size:30 final size:30
Alignment explanation
Indices: 337605--337665 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
337595 GAATTTCCTC
*
337605 AAGTTCCTAAATATATAATTTTCGATACTT
1 AAGTTCCTAAATATATAATTTTCAATACTT
337635 AAGTTCCTAAATATATAATTTTCAATACTT
1 AAGTTCCTAAATATATAATTTTCAATACTT
337665 A
1 A
337666 CCTGCAACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (30 bp):
AAGTTCCTAAATATATAATTTTCAATACTT
Found at i:350568 original size:23 final size:22
Alignment explanation
Indices: 350525--350582 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
350515 AAAGGGTATC
* *
350525 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
350546 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
350569 TGCATATCATATCT
1 TACAAATCATATCT
350583 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:351256 original size:40 final size:40
Alignment explanation
Indices: 351212--351290 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
351202 ACCTTTTCGA
*
351212 TAGATATTCATTTCGGATATATCCTTTTCAACATTTTCAT
1 TAGATATTCATTTCAGATATATCCTTTTCAACATTTTCAT
* * *
351252 TAGATATTCGTTTCAGATGTATCCTTTTCAACCTTTTCA
1 TAGATATTCATTTCAGATATATCCTTTTCAACATTTTCA
351291 AGAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (40 bp):
TAGATATTCATTTCAGATATATCCTTTTCAACATTTTCAT
Found at i:351392 original size:28 final size:28
Alignment explanation
Indices: 351360--351416 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
351350 TCAAGTGTAA
351360 TACCGTGGGGTATTTTGGTCTCGATCCT
1 TACCGTGGGGTATTTTGGTCTCGATCCT
351388 TACCGTGGGGTATTTTGGTCTCGATCCT
1 TACCGTGGGGTATTTTGGTCTCGATCCT
351416 T
1 T
351417 TCCTTTCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.11, C:0.21, G:0.28, T:0.40
Consensus pattern (28 bp):
TACCGTGGGGTATTTTGGTCTCGATCCT
Found at i:356514 original size:61 final size:62
Alignment explanation
Indices: 356397--356576 Score: 163
Period size: 61 Copynumber: 2.9 Consensus size: 62
356387 TTGGTCTAGT
*
356397 AATAAAATTAGCCCTCTAATGTTTACATATTCTATCAATTTTATCCTAAATATAAAAAATTC
1 AATAAAATTAGCCCTCTAATGTTTACAAATTCTATCAATTTTATCCTAAATATAAAAAATTC
* * * * * *
356459 AATAAATTTAGCCCTC-ATTGTTTACAAAATT-TTTC-ATTTTAGTTCTAATTCTAAAAAATTC
1 AATAAAATTAGCCCTCTAATGTTTAC-AAATTCTATCAATTTTA-TCCTAAATATAAAAAATTC
* ** ** * * *
356520 AATAAACTTTCCCCT-TAACATTTACAAAATCTATCAA-TTTAGTCCTAACTCTAAAAA
1 AATAAAATTAGCCCTCTAATGTTTACAAATTCTATCAATTTTA-TCCTAAATATAAAAA
356577 TAGAAAATAT
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
60 10 0.10
61 66 0.69
62 20 0.21
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (62 bp):
AATAAAATTAGCCCTCTAATGTTTACAAATTCTATCAATTTTATCCTAAATATAAAAAATTC
Found at i:363251 original size:18 final size:18
Alignment explanation
Indices: 363230--363264 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
363220 ATTTTGTAAT
363230 TAGTTTAAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
363248 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
363265 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:370153 original size:19 final size:19
Alignment explanation
Indices: 370131--370167 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
370121 AATAAGTGGG
370131 TGAATCATGAATAACTATC
1 TGAATCATGAATAACTATC
370150 TGAATCATGAATAACTAT
1 TGAATCATGAATAACTAT
370168 TGCTTGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (19 bp):
TGAATCATGAATAACTATC
Found at i:373261 original size:22 final size:22
Alignment explanation
Indices: 373233--373313 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
373223 ATTATGATGT
*
373233 ATGATAAATTTAAATAATATTA
1 ATGATAAATTTAAATAATACTA
*
373255 ATGAT-AATTTAAAATAATAGTA
1 ATGATAAATTT-AAATAATACTA
* * * *
373277 TATTATATATTAAAATAATGCTA
1 -ATGATAAATTTAAATAATACTA
373300 ATGATAAATTTAAA
1 ATGATAAATTTAAA
373314 ACATAGTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
21 5 0.11
22 26 0.55
23 13 0.28
24 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (22 bp):
ATGATAAATTTAAATAATACTA
Found at i:373263 original size:45 final size:45
Alignment explanation
Indices: 373214--373313 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
373204 CAAAATATAT
* * * *
373214 TAATTTTAAATTAT-GATGTATGATAAATTTAAATAATATTAATGA
1 TAATTTTAAATAATAG-TATATGATAAATTAAAATAATACTAATGA
* * * *
373259 TAATTTAAAATAATAGTATATTATATATTAAAATAATGCTAATGA
1 TAATTTTAAATAATAGTATATGATAAATTAAAATAATACTAATGA
*
373304 TAAATTTAAA
1 TAATTTTAAA
373314 ACATAGTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (45 bp):
TAATTTTAAATAATAGTATATGATAAATTAAAATAATACTAATGA
Found at i:373320 original size:45 final size:46
Alignment explanation
Indices: 373237--373346 Score: 122
Period size: 45 Copynumber: 2.4 Consensus size: 46
373227 TGATGTATGA
*
373237 TAAAT-TT-AAATAATATTAATGATAATTTAAAATAATAG-TATA-T
1 TAAATATTAAAATAATACTAATGATAATTTAAAATAATAGTTA-ACT
* * *
373280 TATATATTAAAATAATGCTAATGATAAATTTAAAA-CATAGTTAAGCT
1 TAAATATTAAAATAATACTAATGAT-AATTTAAAATAATAGTTAA-CT
373327 TAAATATTAAAATAATACTA
1 TAAATATTAAAATAATACTA
373347 TATTTAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
43 4 0.07
44 2 0.04
45 19 0.35
46 11 0.20
47 19 0.35
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (46 bp):
TAAATATTAAAATAATACTAATGATAATTTAAAATAATAGTTAACT
Found at i:374477 original size:16 final size:16
Alignment explanation
Indices: 374458--374506 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
374448 TTCGCTGTAT
*
374458 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
374474 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
374490 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
374506 T
1 T
374507 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:379187 original size:6 final size:6
Alignment explanation
Indices: 379176--379201 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
379166 TAGTTTGAAC
379176 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
379202 ATAATTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:383084 original size:51 final size:51
Alignment explanation
Indices: 383008--383367 Score: 320
Period size: 51 Copynumber: 7.4 Consensus size: 51
382998 CTCCAGGGAG
* * *
383008 ATAAGATTCGCTGCGTTCAACTTTAATCTGCTCTACTGCAATGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * * * *
383059 ATAAGACTCGCTACCTTCAGCTTTAA-----TCTACTGCGACGCCAGGGAG
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * * *
383105 ATAAGATTTGCTGCCTTCAGCTTTAATCTGCTCCACTGCAATGCTAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * * * *
383156 ATGAGATTCGCTGCCTTCAGCTTTAATCT--ACTAC-G--ACGCTAGGGAG
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * ** *
383202 ATAAGATTTGCTGTCTTTTGCTTTAATCTGCTCTACTGTAACGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * * *
383253 ATAAGACTCGCTGCCTTCAGCTTTAATCTG-----CTGCGACGCTAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
* * * *
383299 ATAAGACTCGCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCC-AGGAAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGG-AA
*
383350 ATAAGATTCGCTGTCTTC
1 ATAAGATTCGCTGCCTTC
383368 GATCTGCTCC
Statistics
Matches: 244, Mismatches: 49, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
46 112 0.46
48 5 0.02
49 4 0.02
50 2 0.01
51 121 0.50
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (51 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACGCCAAGGAA
Found at i:383109 original size:46 final size:46
Alignment explanation
Indices: 383039--383367 Score: 246
Period size: 46 Copynumber: 6.8 Consensus size: 46
383029 TTTAATCTGC
* *
383039 TCTACTGCAATGCCAAGGAAATAAGACTCGCTACCTTCAGCTTTAA
1 TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* * * * *
383085 TCTACTGCGACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAA
1 TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* * * *
383131 TCTGCTCCACTGCAATGCTAAGGAAATGAGATTCGCTGCCTTCAGCTTTAA
1 --T-CT--ACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* * * * * * * * **
383182 TCTACTACGACGCTAGGGAGATAAGATTTGCTGTCTTTTGCTTTAA
1 TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
*
383228 TCTGCTCTACTGTAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
1 -----TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* * * * *
383279 TCTGCTGCGACGCTAGGGAAATAAGACTCGCTGCCTTTAGCTTTAA
1 TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* *
383325 TCTGTTCCACTGCAACGCC-AGGAAAATAAGATTCGCTGTCTTC
1 TC---T--ACTGCAACGCCAAGG-AAATAAGACTCGCTGCCTTC
383368 GATCTGCTCC
Statistics
Matches: 219, Mismatches: 48, Indels: 27
0.74 0.16 0.09
Matches are distributed among these distances:
46 114 0.52
48 3 0.01
49 4 0.02
50 2 0.01
51 96 0.44
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (46 bp):
TCTACTGCAACGCCAAGGAAATAAGACTCGCTGCCTTCAGCTTTAA
Found at i:383167 original size:97 final size:97
Alignment explanation
Indices: 383000--383367 Score: 486
Period size: 97 Copynumber: 3.8 Consensus size: 97
382990 AATCTTAACT
* * * *
383000 CCAGGGAGATAAGATTCGCTGCGTTCAACTTTAATCTGCTCTACTGCAATGCCAAGGAAATAAGA
1 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGA
*
383065 CTCGCTACCTTCAGCTTTAATCTACTGCGACG
66 CTCGCTGCCTTCAGCTTTAATCTACTGCGACG
* * * *
383097 CCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGCTCCACTGCAATGCTAAGGAAATGAGA
1 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGA
* *
383162 TTCGCTGCCTTCAGCTTTAATCTACTACGACG
66 CTCGCTGCCTTCAGCTTTAATCTACTGCGACG
* * * ** * *
383194 CTAGGGAGATAAGATTTGCTGTCTTTTGCTTTAATCTGCTCTACTGTAACGCCAAGGAAATAAGA
1 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGA
*
383259 CTCGCTGCCTTCAGCTTTAATCTGCTGCGACG
66 CTCGCTGCCTTCAGCTTTAATCTACTGCGACG
* * * * *
383291 CTAGGGAAATAAGACTCGCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCC-AGGAAAATAAG
1 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGG-AAATAAG
* *
383355 ATTCGCTGTCTTC
65 ACTCGCTGCCTTC
383368 GATCTGCTCC
Statistics
Matches: 239, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 3 0.01
97 236 0.99
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (97 bp):
CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGA
CTCGCTGCCTTCAGCTTTAATCTACTGCGACG
Found at i:383336 original size:194 final size:194
Alignment explanation
Indices: 383002--383367 Score: 538
Period size: 194 Copynumber: 1.9 Consensus size: 194
382992 TCTTAACTCC
*
383002 AGGGAGATAAGATTCGCTGCGTTCAACTTTAATCTGCTCTACTGCAATGCCAAGGAAATAAGACT
1 AGGGAGATAAGATTCGCTGCGTTCAACTTTAATCTGCTCTACTGCAACGCCAAGGAAATAAGACT
* * *
383067 CGCTACCTTCAGCTTTAATCTACTGCGACGCCAGGGAGATAAGATTTGCTGCCTTCAGCTTTAAT
66 CGCTACCTTCAGCTTTAATCTACTGCGACGCCAGGGAAATAAGACTCGCTGCCTTCAGCTTTAAT
* *
383132 CTGCTCCACTGCAATGCTAAGG-AAATGAGATTCGCTGCCTTCAGCTTTAATCTACTACGACGCT
131 CTGCTCCACTGCAACGC-AAGGAAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTACGACGCT
* *** *
383196 AGGGAGATAAGATTTGCTGTC-TTTTGCTTTAATCTGCTCTACTGTAACGCCAAGGAAATAAGAC
1 AGGGAGATAAGATTCGCTG-CGTTCAACTTTAATCTGCTCTACTGCAACGCCAAGGAAATAAGAC
* * * *
383260 TCGCTGCCTTCAGCTTTAATCTGCTGCGACGCTAGGGAAATAAGACTCGCTGCCTTTAGCTTTAA
65 TCGCTACCTTCAGCTTTAATCTACTGCGACGCCAGGGAAATAAGACTCGCTGCCTTCAGCTTTAA
* * *
383325 TCTGTTCCACTGCAACGCCAGGAAAATAAGATTCGCTGTCTTC
130 TCTGCTCCACTGCAACGCAAGGAAAATAAGATTCGCTGCCTTC
383368 GATCTGCTCC
Statistics
Matches: 152, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
193 3 0.02
194 148 0.97
195 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (194 bp):
AGGGAGATAAGATTCGCTGCGTTCAACTTTAATCTGCTCTACTGCAACGCCAAGGAAATAAGACT
CGCTACCTTCAGCTTTAATCTACTGCGACGCCAGGGAAATAAGACTCGCTGCCTTCAGCTTTAAT
CTGCTCCACTGCAACGCAAGGAAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTACGACGCT
Found at i:383933 original size:173 final size:177
Alignment explanation
Indices: 383546--383985 Score: 647
Period size: 173 Copynumber: 2.5 Consensus size: 177
383536 AATCTTCAAC
* * * *
383546 CTACTCCACTGCAAACTTAAAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGG
1 CTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGG
* * *
383611 AAGACAAGATTTGCTATCTTCAGTATGCTCCACTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTC
66 AAGACAAGATCTGCTATCTTCAGTATGCTCCACTGC-AACTAAGGGAGATCAGGCTGGTGTCTTC
*
383676 GATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTCCAGT
130 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTCCAGT
* *
383724 CTACTCCGCTGCAAACTCAGAGAGGCAAGACTGGTGTCTTCAATCTGCTTCGCTGCCAATACAGG
1 CTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGG
* *
383789 AAGACAAGATCTGCTATCTTCAGTATTCT-C-C-GC-GCTAAGGGAGATCAGGCTGGTGTCTTCG
66 AAGACAAGATCTGCTATCTTCAGTATGCTCCACTGCAACTAAGGGAGATCAGGCTGGTGTCTTCG
*
383850 ATCTACTTCGTTGCCAATACAGGAAGACAAGATCTGTTATCTT-CAGT
131 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTAT-TTCCAGT
* * * * *
383897 CTGCTTCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGTTGCCAATACAGG
1 CTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGG
* *
383962 AAGACAATATCTGTTATCTTCAGT
66 AAGACAAGATCTGCTATCTTCAGT
383986 CTGAAAAGTG
Statistics
Matches: 239, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
173 147 0.62
174 2 0.01
175 2 0.01
176 1 0.00
177 1 0.00
178 86 0.36
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (177 bp):
CTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGG
AAGACAAGATCTGCTATCTTCAGTATGCTCCACTGCAACTAAGGGAGATCAGGCTGGTGTCTTCG
ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTCCAGT
Found at i:383986 original size:89 final size:89
Alignment explanation
Indices: 383549--383988 Score: 586
Period size: 89 Copynumber: 5.0 Consensus size: 89
383539 CTTCAACCTA
* * ** * *
383549 CTCCACTGCAAACTTAAAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
* * *
383614 ACAAGATTTGCTATCTTCAGTATG
66 ACAAGATCTGTTATCTTCAGTCTG
* *
383638 CTCCACTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
383703 ACAAGATCTGTTAT-TTCCAGTCTA
66 ACAAGATCTGTTATCTT-CAGTCTG
* * * *
383727 CTCCGCTGCAAACTCAGAGAGGCAAGACTGGTGTCTTCAATCTGCTTCGCTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
* * *
383792 ACAAGATCTGCTATCTTCAGTATT
66 ACAAGATCTGTTATCTTCAGTCTG
* ** * *
383816 CTCCGC-G----CTAAGGGAGATCAGGCTGGTGTCTTCGATCTACTTCGTTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
383876 ACAAGATCTGTTATCTTCAGTCTG
66 ACAAGATCTGTTATCTTCAGTCTG
* *
383900 CTTCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGTTGCCAATACAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
383965 ACAATATCTGTTATCTTCAGTCTG
66 ACAAGATCTGTTATCTTCAGTCTG
383989 AAAAGTGAAA
Statistics
Matches: 307, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
84 70 0.23
85 1 0.00
88 3 0.01
89 231 0.75
90 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (89 bp):
CTCCGCTGCAAACTCAGGGAGGCCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
ACAAGATCTGTTATCTTCAGTCTG
Found at i:384173 original size:21 final size:21
Alignment explanation
Indices: 384143--384201 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
384133 AAACAAATTG
* *
384143 TTGTTCTTTTTTACTGTTTTC
1 TTGTTATTTTTTACTATTTTC
*
384164 TTGTTATTTTTTACTATTTTA
1 TTGTTATTTTTTACTATTTTC
* *
384185 TTGCT-TTTTTTGCTATT
1 TTGTTATTTTTTACTATT
384202 GTTTTTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.71
Consensus pattern (21 bp):
TTGTTATTTTTTACTATTTTC
Found at i:397126 original size:24 final size:24
Alignment explanation
Indices: 397099--397145 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
397089 TTCATGTGAA
397099 CATAGACTCATTCAGCTT-TAATTT
1 CATA-ACTCATTCAGCTTCTAATTT
*
397123 CATATCTCATTCAGCTTCTAATT
1 CATAACTCATTCAGCTTCTAATT
397146 CAATTTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (24 bp):
CATAACTCATTCAGCTTCTAATTT
Found at i:399716 original size:80 final size:79
Alignment explanation
Indices: 399620--399769 Score: 219
Period size: 80 Copynumber: 1.9 Consensus size: 79
399610 CCTAAACTTA
* * *
399620 CTTGTGGAGTATAAAACCTTCACTGATAGTACACCAAATATTTTCTCATAATTTTAATATCATTA
1 CTTGTGGAGTATAAAACCTCCACCGATAGTACACCAAATATTTTCTCATAAGTTT-ATATCATTA
*
399685 ATCATACATGATGAG
65 AACATACATGATGAG
* * * *
399700 CTTGTGGAGTCTAAAACCTCCACCGATGGTGCACCAAATATTTTCTCATAAGTTTATATTATTAA
1 CTTGTGGAGTATAAAACCTCCACCGATAGTACACCAAATATTTTCTCATAAGTTTATATCATTAA
399765 ACATA
66 ACATA
399770 TATATTTACA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
79 13 0.21
80 49 0.79
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (79 bp):
CTTGTGGAGTATAAAACCTCCACCGATAGTACACCAAATATTTTCTCATAAGTTTATATCATTAA
ACATACATGATGAG
Found at i:399902 original size:18 final size:20
Alignment explanation
Indices: 399876--399916 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
399866 AATTTTAGCA
399876 TTAATAATAATTTTAA-ATT
1 TTAATAATAATTTTAATATT
*
399895 TTAA-AATATTTTTAATATT
1 TTAATAATAATTTTAATATT
399914 TTA
1 TTA
399917 TTTAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATAATAATTTTAATATT
Found at i:400660 original size:39 final size:40
Alignment explanation
Indices: 400603--400692 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 40
400593 AATTTATATC
* * * *
400603 TAATACAATATAATATTTATTATATTTA-GTTGCGTTTTT
1 TAATATAATAAAAGATTTATTATATTTAGGTAGCGTTTTT
**
400642 TAATATAATAAAAGATTTATTATATTTATGGTAGTTTTTTT
1 TAATATAATAAAAGATTTATTATATTTA-GGTAGCGTTTTT
400683 TAATATAATA
1 TAATATAATA
400693 TATTTTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 25 0.58
41 18 0.42
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (40 bp):
TAATATAATAAAAGATTTATTATATTTAGGTAGCGTTTTT
Found at i:411050 original size:5 final size:5
Alignment explanation
Indices: 411036--411065 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
411026 AGAACTTGAC
*
411036 CCCAA ACCAA CCCAA CCCAA CCCAA CCCAA
1 CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA
411066 GTTTATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.57, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAA
Found at i:418445 original size:7 final size:7
Alignment explanation
Indices: 418429--418491 Score: 92
Period size: 7 Copynumber: 8.9 Consensus size: 7
418419 AGGGATAGGC
418429 TTAGGGT
1 TTAGGGT
*
418436 TTAAGGT
1 TTAGGGT
418443 TTAGGGT
1 TTAGGGT
418450 TTAGGGTT
1 TTAGGG-T
418458 TTAGGG-
1 TTAGGGT
418464 TTAGGGTT
1 TTAGGG-T
418472 TTAGGGT
1 TTAGGGT
418479 TTAGGGT
1 TTAGGGT
418486 TTAGGG
1 TTAGGG
418492 AATGTCAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
6 6 0.12
7 32 0.63
8 13 0.25
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
TTAGGGT
Found at i:431394 original size:13 final size:13
Alignment explanation
Indices: 431378--431406 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
431368 ACTGGACTTT
431378 TTTACAAATAAAG
1 TTTACAAATAAAG
431391 TTTACAAATAAAG
1 TTTACAAATAAAG
431404 TTT
1 TTT
431407 TACTCTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (13 bp):
TTTACAAATAAAG
Found at i:434630 original size:23 final size:23
Alignment explanation
Indices: 434589--434632 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
434579 TAACCCTGAA
*
434589 GAAAACTAATATATCTAAAACTT
1 GAAAACTAATATATATAAAACTT
434612 GAAAACT-ATATATTATAAAAC
1 GAAAACTAATATA-TATAAAAC
434633 AAACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (23 bp):
GAAAACTAATATATATAAAACTT
Found at i:442817 original size:3 final size:3
Alignment explanation
Indices: 442809--442842 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
442799 ACACCTAACA
442809 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
442843 TGATACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:450739 original size:23 final size:23
Alignment explanation
Indices: 450709--450758 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
450699 AAACAGAGGG
450709 CAAAGGATCATAATTTAAAACAT
1 CAAAGGATCATAATTTAAAACAT
*
450732 CAAAGGATCATAGTTTAAAACAT
1 CAAAGGATCATAATTTAAAACAT
450755 CAAA
1 CAAA
450759 AACATTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (23 bp):
CAAAGGATCATAATTTAAAACAT
Found at i:451771 original size:29 final size:29
Alignment explanation
Indices: 451701--451771 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
451691 ATCTCTGCAG
*
451701 ATTTTTTTATTTTTTATTATTTTTAGTTT
1 ATTTATTTATTTTTTATTATTTTTAGTTT
* * *
451730 A-TAATTTGTTTTTT-TTTTGTTTTAGGTTT
1 ATTTATTTATTTTTTATTAT-TTTTA-GTTT
451759 ATTTATTTATTTT
1 ATTTATTTATTTT
451772 AATTTGGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 3 0.09
28 15 0.45
29 6 0.18
30 9 0.27
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (29 bp):
ATTTATTTATTTTTTATTATTTTTAGTTT
Found at i:451963 original size:18 final size:19
Alignment explanation
Indices: 451940--451983 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
451930 ATATACGATA
*
451940 ATAATATATTTAAATATAT
1 ATAATATATCTAAATATAT
*
451959 A-AATAT-TCTAAATTTAT
1 ATAATATATCTAAATATAT
451976 ATAATATA
1 ATAATATA
451984 AAATTCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATATATCTAAATATAT
Found at i:452180 original size:24 final size:24
Alignment explanation
Indices: 452128--452180 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
452118 CACGAAATTA
*
452128 AAATAAAAAAATAGTTTAAATTGT
1 AAATAAAAAAATAGTTTAAATGGT
*
452152 GAATAAAAGAAA-A-TTTAAATGGAT
1 AAATAAAA-AAATAGTTTAAATGG-T
452176 AAATA
1 AAATA
452181 CATCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 8 0.33
24 13 0.54
25 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATAAAAAAATAGTTTAAATGGT
Found at i:456750 original size:16 final size:16
Alignment explanation
Indices: 456717--456750 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
456707 TATTGTACAC
**
456717 ATATATATGTATTTGA
1 ATATATATGTATGCGA
456733 ATATATATGTATGCGA
1 ATATATATGTATGCGA
456749 AT
1 AT
456751 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:459379 original size:24 final size:24
Alignment explanation
Indices: 459253--459433 Score: 87
Period size: 25 Copynumber: 7.2 Consensus size: 24
459243 TCCTGATATT
*
459253 TGGCTCTCACGAGCTTCCCGTTAAA
1 TGGCTCTTACGAGCTTCCCGTT-AA
* * * *
459278 TGGTTCTTGCGAGTTTCCTGATTAA
1 TGGCTCTTACGAGCTTCCCG-TTAA
** *
459303 TGGCTCTCTTTTGAGCTTCCCGTTTA
1 TGG--CTCTTACGAGCTTCCCGTTAA
* * *
459329 TTGCTCTT-CGGAGCTTCCCAATAAA
1 TGGCTCTTAC-GAGCTTCCC-GTTAA
* *
459354 TGGCTCTTATGAGCTTTCCGTTAA
1 TGGCTCTTACGAGCTTCCCGTTAA
* * *
459378 TGGCTC-TCCGAATCTTCTCGTTACA
1 TGGCTCTTACG-AGCTTCCCGTTA-A
* ** *
459403 TAGCTCACATGAGCTTCCCGTTATA
1 TGGCTCTTACGAGCTTCCCGTTA-A
459428 TGGCTC
1 TGGCTC
459434 AAAAGAGCTT
Statistics
Matches: 113, Mismatches: 34, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
23 2 0.02
24 32 0.28
25 59 0.52
26 8 0.07
27 12 0.11
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (24 bp):
TGGCTCTTACGAGCTTCCCGTTAA
Found at i:459419 original size:25 final size:24
Alignment explanation
Indices: 459391--459458 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
459381 CTCTCCGAAT
* *
459391 CTTCTCGTTACATAGCTCACATGAG
1 CTTCTCGTTACAT-GCTCAAAAGAG
* *
459416 CTTCCCGTTATATGGCTCAAAAGAG
1 CTTCTCGTTACAT-GCTCAAAAGAG
459441 CTTCTCGATTACATGCTC
1 CTTCTCG-TTACATGCTC
459459 GTATGGCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
25 30 0.86
26 5 0.14
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (24 bp):
CTTCTCGTTACATGCTCAAAAGAG
Found at i:461992 original size:36 final size:36
Alignment explanation
Indices: 461952--462022 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
461942 TAAACTCTAT
* * *
461952 TCAGTTTAGCAGTCTTTTAGATCTATTCTAACTGAC
1 TCAGTTCAGCAGCCTTTCAGATCTATTCTAACTGAC
* *
461988 TCAGTTCAGCAGCCTTTCGGATCTATTCTGACTGA
1 TCAGTTCAGCAGCCTTTCAGATCTATTCTAACTGA
462023 GGCACTCCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (36 bp):
TCAGTTCAGCAGCCTTTCAGATCTATTCTAACTGAC
Found at i:464341 original size:12 final size:12
Alignment explanation
Indices: 464304--464354 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
464294 ATTAGAATCT
464304 TTACTTGCTT-C
1 TTACTTGCTTAC
* *
464315 TTTACTTACTCAC
1 -TTACTTGCTTAC
*
464328 TTACTTGTTTAC
1 TTACTTGCTTAC
464340 TTACTTGCTTAC
1 TTACTTGCTTAC
464352 TTA
1 TTA
464355 AATAACTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:464718 original size:56 final size:50
Alignment explanation
Indices: 464606--464748 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 50
464596 TTTCCTATAC
* * * *
464606 TGCCAATGCCATATCCCATACATGGTCTTACATGAGACCTCTTATCTCGG
1 TGCCAATGCCATATCCCAGACATGGTCTTATATGGGACCTCTTATCTCGA
*
464656 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATATCCCAGACATGGTCTTATATGGGACCTCT--T-ATCTC---GA
* *
464712 TGCCAATGCCATATCCCAGATATGTTCTTATATGGGA
1 TGCCAATGCCATATCCCAGACATGGTCTTATATGGGA
464749 TCTCATTCCT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
50 38 0.48
52 1 0.01
53 5 0.06
56 35 0.44
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATATCCCAGACATGGTCTTATATGGGACCTCTTATCTCGA
Found at i:472021 original size:15 final size:16
Alignment explanation
Indices: 471995--472025 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
471985 GAACCCATGA
471995 ACCAGTTTGGGCTGAG
1 ACCAGTTTGGGCTGAG
472011 ACCAG-TTGGGCTGAG
1 ACCAGTTTGGGCTGAG
472026 TTAGTGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (16 bp):
ACCAGTTTGGGCTGAG
Found at i:489040 original size:23 final size:23
Alignment explanation
Indices: 489014--489135 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
489004 ATAAGTGCCA
*
489014 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
** * *
489037 CACTGATACATAGCCGTAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
489060 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
489083 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
489106 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
489129 CACTGAT
1 CACTGAT
489136 CAATAACACT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:489379 original size:18 final size:17
Alignment explanation
Indices: 489353--489391 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
489343 ATTTTCCTTC
489353 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
489370 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
489388 CACA
1 CACA
489392 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:502182 original size:25 final size:25
Alignment explanation
Indices: 502148--502211 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
502138 ACGAGCTGTA
*
502148 AACGGTAAGCTCATCCAAGCTAAAT
1 AACGGGAAGCTCATCCAAGCTAAAT
* * * *
502173 AACGGGAAGCTCATGCGAGCTGAGT
1 AACGGGAAGCTCATCCAAGCTAAAT
*
502198 ATCGGGAAGCTCAT
1 AACGGGAAGCTCAT
502212 AAGAGCTGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (25 bp):
AACGGGAAGCTCATCCAAGCTAAAT
Found at i:503625 original size:25 final size:25
Alignment explanation
Indices: 503597--503662 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
503587 ACGCGAGAAC
503597 AATGCTCACACAAGCTGTGACGATA
1 AATGCTCACACAAGCTGTGACGATA
** *
503622 AATGCTCACATGAGCTGTGACTATA
1 AATGCTCACACAAGCTGTGACGATA
*
503647 AATGCTCACGCAAGCT
1 AATGCTCACACAAGCT
503663 ATGAAATGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (25 bp):
AATGCTCACACAAGCTGTGACGATA
Found at i:506893 original size:27 final size:26
Alignment explanation
Indices: 506854--506904 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
506844 TACAAGGACT
506854 TATGACATATTTTAATCTACTATAAAAA
1 TATGACATATTTTAAT-TA-TATAAAAA
506882 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
506905 TATGAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 10 0.43
28 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:510265 original size:27 final size:27
Alignment explanation
Indices: 510233--510286 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
510223 TCATATAATG
510233 GATTAGATCAAAATGTGAGAAAATCAT
1 GATTAGATCAAAATGTGAGAAAATCAT
*
510260 GATTAGATCAAAATGTGAGGAAATCAT
1 GATTAGATCAAAATGTGAGAAAATCAT
510287 ACCTTGCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.26
Consensus pattern (27 bp):
GATTAGATCAAAATGTGAGAAAATCAT
Found at i:510328 original size:17 final size:17
Alignment explanation
Indices: 510306--510338 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
510296 ATTAATTAAA
510306 ATATTT-ATTAATAATAG
1 ATATTTAATTAA-AATAG
510323 ATATTTAATTAAAATA
1 ATATTTAATTAAAATA
510339 TTAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTTAATTAAAATAG
Found at i:511939 original size:31 final size:31
Alignment explanation
Indices: 511904--511967 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
511894 AAATTAAAAG
511904 GTGAATGGAAATAGATATGAAATTTGAGTCC
1 GTGAATGGAAATAGATATGAAATTTGAGTCC
511935 GTGAATGGAAATAGATATGAAATTTGAGTCC
1 GTGAATGGAAATAGATATGAAATTTGAGTCC
511966 GT
1 GT
511968 CCTTCACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.30
Consensus pattern (31 bp):
GTGAATGGAAATAGATATGAAATTTGAGTCC
Found at i:515470 original size:7 final size:8
Alignment explanation
Indices: 515448--515477 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
515438 TTTAGCTTTG
515448 TATTGTTTT
1 TATT-TTTT
515457 TATTTTTT
1 TATTTTTT
515465 TATTTTTT
1 TATTTTTT
515473 TATTT
1 TATTT
515478 ATTTCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (8 bp):
TATTTTTT
Found at i:520832 original size:14 final size:14
Alignment explanation
Indices: 520809--520859 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
520799 AAGTTAAAGT
520809 AAAT-AATAATTTA
1 AAATAAATAATTTA
520822 AAATAAATAATTTA
1 AAATAAATAATTTA
* * * *
520836 TAA-GAACAATTCA
1 AAATAAATAATTTA
520849 AAATAAATAAT
1 AAATAAATAAT
520860 AAAAAGTTTC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (14 bp):
AAATAAATAATTTA
Found at i:520928 original size:25 final size:24
Alignment explanation
Indices: 520849--520962 Score: 122
Period size: 25 Copynumber: 4.6 Consensus size: 24
520839 GAACAATTCA
*
520849 AAATAAATAATAAAAAGTTTCAAAT
1 AAAT-AATAATAAAAAGTTTAAAAT
* * *
520874 AAACAATATGTAAAAACTTT-AAAT
1 AAATAATA-ATAAAAAGTTTAAAAT
520898 AAATAATAATAAAATAGTTTAAAAT
1 AAATAATAATAAAA-AGTTTAAAAT
**
520923 AAATAATATATAAAAAAACTTAAAAT
1 AAATAATA-AT-AAAAAGTTTAAAAT
520949 AAATAATAATAAAA
1 AAATAATAATAAAA
520963 GAGATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.07
24 23 0.30
25 26 0.34
26 18 0.24
27 4 0.05
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (24 bp):
AAATAATAATAAAAAGTTTAAAAT
Found at i:520949 original size:51 final size:51
Alignment explanation
Indices: 520813--520962 Score: 170
Period size: 48 Copynumber: 3.0 Consensus size: 51
520803 TAAAGTAAAT
* * *
520813 AATAATTTAAAATAAATAATTTATAAGAACAA-TTCAAAAT--A-AATAATAA
1 AATAGTTTAAAATAAATAATATATAA-AAAAACTT-AAAATAAATAATAATAA
* * * *
520862 AA-AGTTTCAAATAAACAATATGT--AAAAACTTTAAATAAATAATAATAA
1 AATAGTTTAAAATAAATAATATATAAAAAAACTTAAAATAAATAATAATAA
520910 AATAGTTTAAAATAAATAATATATAAAAAAACTTAAAATAAATAATAATAA
1 AATAGTTTAAAATAAATAATATATAAAAAAACTTAAAATAAATAATAATAA
520961 AA
1 AA
520963 GAGATTTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
45 8 0.10
46 2 0.02
47 1 0.01
48 26 0.31
49 20 0.24
51 26 0.31
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (51 bp):
AATAGTTTAAAATAAATAATATATAAAAAAACTTAAAATAAATAATAATAA
Found at i:520987 original size:51 final size:51
Alignment explanation
Indices: 520849--520965 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
520839 GAACAATTCA
* * ** *
520849 AAATAAATAATAAAA-AGTTTCAAATAAACAAT--ATGTAAAAACTTTAAAT
1 AAAT-AATAATAAAAGAGTTTAAAATAAATAATAAATAAAAAAACTTAAAAT
* *
520898 AAATAATAATAAAATAGTTTAAAATAAATAATATATAAAAAAACTTAAAAT
1 AAATAATAATAAAAGAGTTTAAAATAAATAATAAATAAAAAAACTTAAAAT
520949 AAATAATAATAAAAGAG
1 AAATAATAATAAAAGAG
520966 ATTTTTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
48 10 0.17
49 19 0.32
51 30 0.51
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.27
Consensus pattern (51 bp):
AAATAATAATAAAAGAGTTTAAAATAAATAATAAATAAAAAAACTTAAAAT
Found at i:528787 original size:86 final size:85
Alignment explanation
Indices: 528654--528813 Score: 191
Period size: 86 Copynumber: 1.9 Consensus size: 85
528644 CAATGCCAAC
* * * * *
528654 GTCCCAGACGTGGTCTTACATGTAATCAAATATTGATGCCACTGTCCCAGACAG-GATTTTACAC
1 GTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGAC-GTGATCTTACAC
528718 GAAATCATATACGATGCTGAT
65 GAAATCATATACGATGCTGAT
* *
528739 GTCCCAAACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGACGTGGTCTTAC
1 GTCCCAAACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTCCCAGACGTGATCTTAC
*
528802 ATGAAATCATAT
63 ACGAAATCATAT
528814 CTCAGAATCC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
85 21 0.33
86 38 0.60
87 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (85 bp):
GTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACGTGATCTTACACG
AAATCATATACGATGCTGAT
Found at i:536948 original size:30 final size:30
Alignment explanation
Indices: 536914--536974 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
536904 CAACTTCAAC
536914 AATTTCTTCTTTCATCTCATTTTTATAGTA
1 AATTTCTTCTTTCATCTCATTTTTATAGTA
* *
536944 AATTTCTTCTTTGATCTCATTTTTCTAGTA
1 AATTTCTTCTTTCATCTCATTTTTATAGTA
536974 A
1 A
536975 TGGCGGAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (30 bp):
AATTTCTTCTTTCATCTCATTTTTATAGTA
Found at i:544349 original size:41 final size:41
Alignment explanation
Indices: 544292--544480 Score: 324
Period size: 41 Copynumber: 4.6 Consensus size: 41
544282 TTAGCAACCC
* *
544292 TTCGGGGAATTTGCACTTAGCAACCCCTCTTTGATCAGTAA
1 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
544333 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
1 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
544374 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
1 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
* *
544415 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTTATCAGTGT
1 TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
* *
544456 TTCAGGGAATATGCACTTAGCAACC
1 TTCGGGGAATCTGCACTTAGCAACC
544481 GCTTACATTC
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 142 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (41 bp):
TTCGGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGA
Found at i:547339 original size:52 final size:52
Alignment explanation
Indices: 547275--547379 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
547265 TAATAATCTA
547275 AACAACATAATAATTAACT-ATTTAAAATAAAATAATTTAATAATATTTTCTT
1 AACAACATAATAATTAACTGA-TTAAAATAAAATAATTTAATAATATTTTCTT
* * *
547327 AACATCATAATAATTAACTGATTAAAATTAAATAATTTAATAATTTTTTCTT
1 AACAACATAATAATTAACTGATTAAAATAAAATAATTTAATAATATTTTCTT
547379 A
1 A
547380 CCATTTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 48 0.98
53 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.42
Consensus pattern (52 bp):
AACAACATAATAATTAACTGATTAAAATAAAATAATTTAATAATATTTTCTT
Found at i:554322 original size:17 final size:17
Alignment explanation
Indices: 554300--554333 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
554290 ACTTGATGAA
554300 TCGGATATTCAGACTGT
1 TCGGATATTCAGACTGT
554317 TCGGATATTCAGACTGT
1 TCGGATATTCAGACTGT
554334 ACTTAGACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (17 bp):
TCGGATATTCAGACTGT
Found at i:565641 original size:2 final size:2
Alignment explanation
Indices: 565634--565659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
565624 AGTGGCATTG
565634 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
565660 CATGAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:575152 original size:6 final size:6
Alignment explanation
Indices: 575141--575184 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
575131 TAGATATATA
*
575141 TATGTG TGTGTG TATGTG TATGTG TATGTG TATGTG TATGTG TA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TA
575185 GCCAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:577571 original size:1 final size:1
Alignment explanation
Indices: 577565--577590 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
577555 CATTCTCAGG
577565 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
577591 GGCATAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:593463 original size:24 final size:24
Alignment explanation
Indices: 593422--593468 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
593412 TGCTTCCTGA
*
593422 TTAATTTCTCTTCAGAGCTACCCG
1 TTAATTGCTCTTCAGAGCTACCCG
* *
593446 TTAATTGCTTTTCGGAGCTACCC
1 TTAATTGCTCTTCAGAGCTACCC
593469 ATTATAGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (24 bp):
TTAATTGCTCTTCAGAGCTACCCG
Found at i:597086 original size:28 final size:28
Alignment explanation
Indices: 597012--597091 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
597002 CTCTTTCCAC
597012 TATTTTAACATTTTTAATTTATCTCAACT
1 TATTTTAACA-TTTTAATTTATCTCAACT
* * *
597041 TATTTCAATATTGTTAATTTAT-TCAAATT
1 TATTTTAACATT-TTAATTTATCTC-AACT
*
597070 TATTTTAACCTTTTAATTTATC
1 TATTTTAACATTTTAATTTATC
597092 CATGTTATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 13 0.31
29 29 0.69
ACGTcount: A:0.31, C:0.11, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTTTAACATTTTAATTTATCTCAACT
Found at i:603746 original size:24 final size:24
Alignment explanation
Indices: 603719--603769 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
603709 TGCTTCCTGA
*
603719 TTAATTGCTCTTCGGAGCTACTCG
1 TTAATTGCTCTTCGGAGCTACCCG
*
603743 TTAATTGGTCTTCGGAGCTACCCG
1 TTAATTGCTCTTCGGAGCTACCCG
603767 TTA
1 TTA
603770 CGTGGTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (24 bp):
TTAATTGCTCTTCGGAGCTACCCG
Found at i:603775 original size:24 final size:24
Alignment explanation
Indices: 603727--603775 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
603717 GATTAATTGC
* *
603727 TCTTCGGAGCTACTCGTTAATTGG
1 TCTTCGGAGCTACCCGTTAAGTGG
*
603751 TCTTCGGAGCTACCCGTTACGTGG
1 TCTTCGGAGCTACCCGTTAAGTGG
603775 T
1 T
603776 TCACATGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (24 bp):
TCTTCGGAGCTACCCGTTAAGTGG
Found at i:604962 original size:73 final size:73
Alignment explanation
Indices: 604843--605033 Score: 301
Period size: 73 Copynumber: 2.6 Consensus size: 73
604833 TTCGGGTATT
* * * *
604843 TTCACACGGCCTGGCACACGGGCATGTGACTCGGCCGTGTGACCTCTGCACCTAATTAATGAAAA
1 TTCACACGGCCTAGCACACGGGCGTTTGACTTGGCCGTGTGACCTCTGCACCTAATTAATGAAAA
* *
604908 TTAATGTG
66 ATAATATG
*
604916 TTCACACAGCCTAGCACACGGGCGTTTGACTTGGCCGTGTGACCTCTGCACCTAATTAATGAAAA
1 TTCACACGGCCTAGCACACGGGCGTTTGACTTGGCCGTGTGACCTCTGCACCTAATTAATGAAAA
604981 ATAATATG
66 ATAATATG
* *
604989 TTCACACGGCCTAGTACACGGGCGTTTGTCTTGGCCGTGTGACCT
1 TTCACACGGCCTAGCACACGGGCGTTTGACTTGGCCGTGTGACCT
605034 AAGTTAGAGA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 108 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (73 bp):
TTCACACGGCCTAGCACACGGGCGTTTGACTTGGCCGTGTGACCTCTGCACCTAATTAATGAAAA
ATAATATG
Found at i:608397 original size:21 final size:21
Alignment explanation
Indices: 608344--608398 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
608334 CACGAAAGAG
*
608344 CACACGGGCAAGTGGAGTAGC
1 CACACGGGCATGTGGAGTAGC
608365 CACACGGGCATGTGG-GATAGC
1 CACACGGGCATGTGGAG-TAGC
*
608386 CACACGGCCATGT
1 CACACGGGCATGT
608399 CTGGAGCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.25, C:0.27, G:0.35, T:0.13
Consensus pattern (21 bp):
CACACGGGCATGTGGAGTAGC
Found at i:617899 original size:127 final size:127
Alignment explanation
Indices: 617673--617928 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 127
617663 GATCGGAATG
*
617673 TAGCTACACGATGCCGCTCACACAAGCTGATGAGTATCCGCAACAAATGTTGGAACTCAACCATC
1 TAGCTACACGATGCCGCTCACACAAGCTGACGAGTATCCGCAACAAATGTTGGAACTCAACCATC
617738 GGTAGGGCATTCAGGACCAGCACCCGAAACATGGTAACCCTAATGACATGTCATTTGTATCC
66 GGTAGGGCATTCAGGACCAGCACCCGAAACATGGTAACCCTAATGACATGTCATTTGTATCC
* *
617800 TAGCTACACGATGCCGCTCACACAATCTGACGAGTATCCGCAACAAATGTTGGAACTCAGCCATC
1 TAGCTACACGATGCCGCTCACACAAGCTGACGAGTATCCGCAACAAATGTTGGAACTCAACCATC
*
617865 GGTAGGGCATTCAGGACCAGTACCCGAAACATGGTAACCCTAATGACATGTCATTTGTATCC
66 GGTAGGGCATTCAGGACCAGCACCCGAAACATGGTAACCCTAATGACATGTCATTTGTATCC
617927 TA
1 TA
617929 TATATATTCC
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 125 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (127 bp):
TAGCTACACGATGCCGCTCACACAAGCTGACGAGTATCCGCAACAAATGTTGGAACTCAACCATC
GGTAGGGCATTCAGGACCAGCACCCGAAACATGGTAACCCTAATGACATGTCATTTGTATCC
Found at i:627095 original size:17 final size:17
Alignment explanation
Indices: 627069--627101 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
627059 GTGTCACCCA
627069 TTTGTGTTCTCTTCTTC
1 TTTGTGTTCTCTTCTTC
*
627086 TTTGTTTTCTCTTCTT
1 TTTGTGTTCTCTTCTT
627102 GTCGAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (17 bp):
TTTGTGTTCTCTTCTTC
Found at i:628317 original size:17 final size:17
Alignment explanation
Indices: 628295--628344 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
628285 TCTCAGATTT
*
628295 TGATACCCATAGCTTTC
1 TGATACCCATATCTTTC
628312 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
628329 TGATACCCATATCTTT
1 TGATACCCATATCTTT
628345 GACTTTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:632213 original size:28 final size:29
Alignment explanation
Indices: 632179--632267 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
632169 AATCATTATT
632179 TCTATTTTTATAACTTATATATGTA-ATCA
1 TCTATTTTTATAACTTATATATGTACAT-A
* **
632208 T-TATTTTCATAATCTATATATACATACATA
1 TCTATTTTTATAA-CT-TATATATGTACATA
*
632238 TCTATTCTTATAACTTATATATGTACATA
1 TCTATTTTTATAACTTATATATGTACATA
632267 T
1 T
632268 ATATACTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 10 0.20
29 16 0.33
30 12 0.24
31 11 0.22
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.49
Consensus pattern (29 bp):
TCTATTTTTATAACTTATATATGTACATA
Found at i:632258 original size:29 final size:29
Alignment explanation
Indices: 632179--632278 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
632169 AATCATTATT
*
632179 TCTATTTTTATAACTTATATATGTA-ATCA
1 TCTATTCTTATAACTTATATATGTACAT-A
**
632208 T-TATT-TTCATAATCTATATATACATACATA
1 TCTATTCTT-ATAA-CT-TATATATGTACATA
632238 TCTATTCTTATAACTTATATATGTACATA
1 TCTATTCTTATAACTTATATATGTACATA
* *
632267 TATATACTTATA
1 TCTATTCTTATA
632279 TTTTTTATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
27 2 0.03
28 8 0.14
29 25 0.42
30 12 0.20
31 10 0.17
32 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (29 bp):
TCTATTCTTATAACTTATATATGTACATA
Found at i:632287 original size:19 final size:18
Alignment explanation
Indices: 632265--632324 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
632255 TATATGTACA
632265 TATATATACTTATATTTTT
1 TATATATA-TTATATTTTT
* *
632284 TATACATATTTTATAATTTTA
1 TAT--ATATATTAT-ATTTTT
632305 TATATATATCTATATTTTT
1 TATATATAT-TATATTTTT
632324 T
1 T
632325 TCCATTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 14 0.42
20 7 0.21
21 12 0.36
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATATTATATTTTT
Found at i:632302 original size:21 final size:20
Alignment explanation
Indices: 632274--632322 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
632264 ATATATATAC
*
632274 TTATATTTTTTATACATATT
1 TTATATTTTATATACATATT
*
632294 TTATAATTTTATATATATA-T
1 TTAT-ATTTTATATACATATT
*
632314 CTATATTTT
1 TTATATTTT
632323 TTTCCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTTATATACATATT
Found at i:632319 original size:40 final size:39
Alignment explanation
Indices: 632263--632512 Score: 177
Period size: 38 Copynumber: 6.5 Consensus size: 39
632253 TATATATGTA
*
632263 CATATATATACTTATATTTTTTATACATATTTTATAATTT
1 CATATATATAC-TATATTTTTTATACATATTTTATAATTG
* * * *
632303 TATATATATATCTATATTTTTT-TCCAT-TTTTCGTAAATG
1 CATATATATA-CTATATTTTTTATACATATTTT-ATAATTG
* * *
632342 CAT-TA-ATAC-ATACTTATATATATATATTTTAT-A-TG
1 CATATATATACTATA-TTTTTTATACATATTTTATAATTG
*
632377 CATATATATACTTATATTTTTTATACATATTTTATAATTT
1 CATATATATAC-TATATTTTTTATACATATTTTATAATTG
* * * *
632417 TATATATATATCTATATTTTTT-TCCAT-TTTTCGTAAATG
1 CATATATATA-CTATATTTTTTATACATATTTT-ATAATTG
* * *
632456 CAT-TA-ATAC-ATACTTATATATATATATTTTAT-A-TG
1 CATATATATACTATA-TTTTTTATACATATTTTATAATTG
632491 CATATATATACTTATATTTTTT
1 CATATATATAC-TATATTTTTT
632513 TATGTTTATA
Statistics
Matches: 162, Mismatches: 28, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
35 16 0.10
36 16 0.10
37 22 0.14
38 40 0.25
39 27 0.17
40 39 0.24
41 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (39 bp):
CATATATATACTATATTTTTTATACATATTTTATAATTG
Found at i:632392 original size:25 final size:23
Alignment explanation
Indices: 632351--632433 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 23
632341 GCATTAATAC
*
632351 ATACTTATATATATATATTTTAT
1 ATACATATATATATATATTTTAT
* *
632374 ATGCATATATATACTTATATTTTTT
1 ATACATATATATA--TATATTTTAT
*
632399 ATACATAT-TTTATA-ATTTTAT
1 ATACATATATATATATATTTTAT
* *
632420 ATATATATCTATAT
1 ATACATATATATAT
632434 TTTTTTCCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 13 0.27
22 6 0.12
23 11 0.22
24 3 0.06
25 16 0.33
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (23 bp):
ATACATATATATATATATTTTAT
Found at i:632403 original size:114 final size:114
Alignment explanation
Indices: 632263--632512 Score: 500
Period size: 114 Copynumber: 2.2 Consensus size: 114
632253 TATATATGTA
632263 CATATATATACTTATATTTTTTATACATATTTTATAATTTTATATATATATCTATATTTTTTTCC
1 CATATATATACTTATATTTTTTATACATATTTTATAATTTTATATATATATCTATATTTTTTTCC
632328 ATTTTTCGTAAATGCATTAATACATACTTATATATATATATTTTATATG
66 ATTTTTCGTAAATGCATTAATACATACTTATATATATATATTTTATATG
632377 CATATATATACTTATATTTTTTATACATATTTTATAATTTTATATATATATCTATATTTTTTTCC
1 CATATATATACTTATATTTTTTATACATATTTTATAATTTTATATATATATCTATATTTTTTTCC
632442 ATTTTTCGTAAATGCATTAATACATACTTATATATATATATTTTATATG
66 ATTTTTCGTAAATGCATTAATACATACTTATATATATATATTTTATATG
632491 CATATATATACTTATATTTTTT
1 CATATATATACTTATATTTTTT
632513 TATGTTTATA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 136 1.00
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (114 bp):
CATATATATACTTATATTTTTTATACATATTTTATAATTTTATATATATATCTATATTTTTTTCC
ATTTTTCGTAAATGCATTAATACATACTTATATATATATATTTTATATG
Found at i:632406 original size:21 final size:20
Alignment explanation
Indices: 632382--632438 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
632372 ATATGCATAT
632382 ATATACTTATATTTTTTATAC
1 ATATA-TTATATTTTTTATAC
* * *
632403 ATATTTTATA-ATTTTATAT
1 ATATATTATATTTTTTATAC
632422 ATATATCTATATTTTTT
1 ATATAT-TATATTTTTT
632439 TCCATTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 12 0.41
20 9 0.31
21 8 0.28
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTATATTTTTTATAC
Found at i:632650 original size:9 final size:9
Alignment explanation
Indices: 632636--632668 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
632626 TGTTGATTTG
*
632636 TTATTTCAT
1 TTATTTTAT
632645 TTATTTTAT
1 TTATTTTAT
632654 TTATTTTAT
1 TTATTTTAT
632663 TT-TTTT
1 TTATTTT
632669 GCTATTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:637941 original size:52 final size:52
Alignment explanation
Indices: 637844--637965 Score: 167
Period size: 52 Copynumber: 2.3 Consensus size: 52
637834 ATCATAATTG
* * * *
637844 CACATAGTTCCACCCTTGTAGCCAACGCTACCTTCTTCACAAAAGTGGTCTT
1 CACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAAAGTGGCCTT
*
637896 CACATAGTACCACACTTGT-GACCAAAGCTATCTTTCTTCAC-AAAGTGGCCTT
1 CACATAGTACCACACTTGTAG-CCAAAGCTA-CCTTCTTCACAAAAGTGGCCTT
637948 CACATAGTACCACACTTG
1 CACATAGTACCACACTTG
637966 AGTCACTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 1 0.02
52 53 0.84
53 9 0.14
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (52 bp):
CACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAAAGTGGCCTT
Found at i:645406 original size:15 final size:15
Alignment explanation
Indices: 645381--645410 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
645371 TAATTGTATG
645381 AATGTTAATTAAATT
1 AATGTTAATTAAATT
645396 AATGTTAATTAAATT
1 AATGTTAATTAAATT
645411 GACTATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AATGTTAATTAAATT
Found at i:647467 original size:27 final size:27
Alignment explanation
Indices: 647433--647490 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
647423 ATATGGTGAG
*
647433 AAGT-GTACTATCTACACATATCACAA
1 AAGTCGTACTATCTACACAGATCACAA
*
647459 GAGTCGTACTATCTACACAGATCACAA
1 AAGTCGTACTATCTACACAGATCACAA
647486 AAGTC
1 AAGTC
647491 TCAAATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (27 bp):
AAGTCGTACTATCTACACAGATCACAA
Found at i:659618 original size:43 final size:43
Alignment explanation
Indices: 659564--659706 Score: 193
Period size: 43 Copynumber: 3.3 Consensus size: 43
659554 GTAGGAATGC
*
659564 TGTCGATATTAATTGCAGGGTGTTACAGTAAGACTGTATGAGG
1 TGTCTATATTAATTGCAGGGTGTTACAGTAAGACTGTATGAGG
*
659607 TGTCTATATTAATTGCAGGGTGTTACAGTAA-A-TATATGTTATGG
1 TGTCTATATTAATTGCAGGGTGTTACAGTAAGACTGTATG--A-GG
** *
659651 T-TCCCTTTTAATTGCAGGGTGTTACAGTAAGACTGTATGAGG
1 TGTCTATATTAATTGCAGGGTGTTACAGTAAGACTGTATGAGG
659693 TGTCTATATTAATT
1 TGTCTATATTAATT
659707 ATTTCAGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
41 5 0.06
42 4 0.05
43 67 0.79
44 4 0.05
45 5 0.06
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.38
Consensus pattern (43 bp):
TGTCTATATTAATTGCAGGGTGTTACAGTAAGACTGTATGAGG
Found at i:662467 original size:40 final size:39
Alignment explanation
Indices: 662398--662507 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 39
662388 AGATAGACTG
* * *
662398 AACACACCAGACATAAGCTTATAAGAGCTGATCCAACT-AA
1 AACACGCCA-ACAGAAGCTCATAAGAGCTGATCC-ACTCAA
* * * *
662438 AATACGCCAAACAGAAGCTCATAATAGCTGGTCCACTCGA
1 AACACGCC-AACAGAAGCTCATAAGAGCTGATCCACTCAA
662478 AACACGCCAACAGAAGCTCATAAGAGCTGA
1 AACACGCCAACAGAAGCTCATAAGAGCTGA
662508 ACAGAAACTC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 23 0.40
40 34 0.59
41 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.15
Consensus pattern (39 bp):
AACACGCCAACAGAAGCTCATAAGAGCTGATCCACTCAA
Found at i:662512 original size:21 final size:21
Alignment explanation
Indices: 662486--662528 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
662476 GAAACACGCC
*
662486 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
662507 AACAGAAACTCATAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
662528 A
1 A
662529 TCCACCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGCTG
Found at i:664242 original size:24 final size:25
Alignment explanation
Indices: 664196--664242 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
664186 TTGTCAACAT
* *
664196 TTTACTGGTAGTTTTAACTATATAC
1 TTTACTGGTAGGTTTAACCATATAC
664221 TTTACTGGT-GGTTTAACCATAT
1 TTTACTGGTAGGTTTAACCATAT
664243 CGAGCTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (25 bp):
TTTACTGGTAGGTTTAACCATATAC
Found at i:668430 original size:18 final size:19
Alignment explanation
Indices: 668407--668442 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
668397 GTTTTAGGGG
668407 TTTGGGGG-AAGTAAAAGT
1 TTTGGGGGAAAGTAAAAGT
668425 TTTGGGGGAAAGTAAAAG
1 TTTGGGGGAAAGTAAAAG
668443 GAAAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (19 bp):
TTTGGGGGAAAGTAAAAGT
Found at i:668499 original size:20 final size:19
Alignment explanation
Indices: 668453--668501 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
668443 GAAAAAATTG
*
668453 AAAGGTTTGGAGGGAAATA
1 AAAGTTTTGGAGGGAAATA
**
668472 AATTTTTTGGAGAGGAAATA
1 AAAGTTTTGGAG-GGAAATA
668492 AAAGTTTTGG
1 AAAGTTTTGG
668502 GAAAAAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (19 bp):
AAAGTTTTGGAGGGAAATA
Found at i:674660 original size:5 final size:5
Alignment explanation
Indices: 674650--674678 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
674640 TCCAATCCTA
674650 TCTTT TCTTT TCTTT TCTTT TCTTT TCTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTT
674679 CCCCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:680062 original size:85 final size:86
Alignment explanation
Indices: 679954--680153 Score: 289
Period size: 85 Copynumber: 2.3 Consensus size: 86
679944 TTTTAGAAAT
* * *
679954 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGACCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
680019 CTTTAGCGGCGCTTTT-GCAC
66 CTTTAGCGGCGCTTTTCCCAC
* *
680039 AAACGCCGCTATA-TCTCAAGACCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGA
1 AAACGCCGCTATAGAC-CAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCAAGA
680103 CCTTTAGCGGCGCTTTTCCCAC
65 CCTTTAGCGGCGCTTTTCCCAC
* * *
680125 AAACACCGCTATAAAACAA-ACCTTTAGCG
1 AAACGCCGCTATAGACCAAGACCTTTAGCG
680154 ATGCTTCTCG
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
84 1 0.01
85 84 0.82
86 18 0.17
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTATAGACCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCTTTTCCCAC
Found at i:680148 original size:42 final size:43
Alignment explanation
Indices: 679954--680153 Score: 287
Period size: 43 Copynumber: 4.7 Consensus size: 43
679944 TTTTAGAAAT
* *
679954 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
679997 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-GCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
** * *
680039 AAACGCCGCTATATCTCAAGACCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
680082 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
680125 AAACACCGCTATAAAACAA-ACCTTTAGCG
1 AAACGCCGCTATAGATCAAGACCTTTAGCG
680154 ATGCTTCTCG
Statistics
Matches: 141, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 47 0.33
43 94 0.67
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:683670 original size:21 final size:21
Alignment explanation
Indices: 683646--683699 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
683636 ACCCTAAACA
*
683646 CTAACTCTTAACCT-CTAACCC
1 CTAACTCCTAA-CTACTAACCC
*
683667 CTAACCCCTAACTACTAACCC
1 CTAACTCCTAACTACTAACCC
*
683688 CTAACTACTAAC
1 CTAACTCCTAAC
683700 CCTTAAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACTCCTAACTACTAACCC
Found at i:683671 original size:14 final size:14
Alignment explanation
Indices: 683667--683701 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
683657 CCTCTAACCC
683667 CTAACCCCTAACTA
1 CTAACCCCTAACTA
683681 CTAACCCCTAACTA
1 CTAACCCCTAACTA
683695 CTAACCC
1 CTAACCC
683702 TTAAACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (14 bp):
CTAACCCCTAACTA
Found at i:683677 original size:28 final size:28
Alignment explanation
Indices: 683637--683701 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
683627 AATTCTAAAA
* * *
683637 CCCTAAACACTAACT-CTTAACCTCTAAC
1 CCCTAACCCCTAACTAC-TAACCCCTAAC
683665 CCCTAACCCCTAACTACTAACCCCTAAC
1 CCCTAACCCCTAACTACTAACCCCTAAC
**
683693 TACTAACCC
1 CCCTAACCC
683702 TTAAACCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.22
Consensus pattern (28 bp):
CCCTAACCCCTAACTACTAACCCCTAAC
Found at i:683678 original size:7 final size:7
Alignment explanation
Indices: 683654--683692 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
683644 CACTAACTCT
*
683654 TAACCTC
1 TAACCCC
683661 TAACCCC
1 TAACCCC
683668 TAACCCC
1 TAACCCC
**
683675 TAACTAC
1 TAACCCC
683682 TAACCCC
1 TAACCCC
683689 TAAC
1 TAAC
683693 TACTAACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:683789 original size:14 final size:14
Alignment explanation
Indices: 683756--683792 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
683746 AAACCCTAAA
*
683756 CCCTAA-CCCGAAT
1 CCCTAACCCCGAAC
683769 CCCTAACCCCGAAC
1 CCCTAACCCCGAAC
683783 CCCTAACCCC
1 CCCTAACCCC
683793 TAAACTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.27, C:0.57, G:0.05, T:0.11
Consensus pattern (14 bp):
CCCTAACCCCGAAC
Found at i:683831 original size:88 final size:90
Alignment explanation
Indices: 683681--683851 Score: 274
Period size: 88 Copynumber: 1.9 Consensus size: 90
683671 CCCCTAACTA
* * *
683681 CTAACCCCTAACTACTAACCCTTAAACCTTATTTATAATATAAATTAAAAAACACTAATTAATCT
1 CTAACCCCGAACCACTAACCCCTAAACCTTATTTATAATATAAATTAAAAAACACTAATTAATCT
683746 AAACCCTAAACCCTAACCCGAATCC
66 AAACCCTAAACCCTAACCCGAATCC
* * *
683771 CTAACCCCGAACCCCTAACCCCTAAACTTTA-TT-TAATATAAATTAAAACACACTAATTAATCT
1 CTAACCCCGAACCACTAACCCCTAAACCTTATTTATAATATAAATTAAAAAACACTAATTAATCT
683834 AAACCCTAAACCCTAACC
66 AAACCCTAAACCCTAACC
683852 TAACACCAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
88 47 0.63
89 2 0.03
90 26 0.35
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (90 bp):
CTAACCCCGAACCACTAACCCCTAAACCTTATTTATAATATAAATTAAAAAACACTAATTAATCT
AAACCCTAAACCCTAACCCGAATCC
Found at i:683922 original size:14 final size:14
Alignment explanation
Indices: 683903--683936 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
683893 TCTAACCCCT
*
683903 AACCCTTAAATCAC
1 AACCCTTAAACCAC
*
683917 AACCCTTAAACCAG
1 AACCCTTAAACCAC
683931 AACCCT
1 AACCCT
683937 AATCCATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (14 bp):
AACCCTTAAACCAC
Found at i:688839 original size:14 final size:14
Alignment explanation
Indices: 688820--689030 Score: 79
Period size: 14 Copynumber: 14.9 Consensus size: 14
688810 TTGTATAAGC
* *
688820 CCCTAACCCCTAAA
1 CCCTAAACCATAAA
*
688834 CCCTAAATCATAAA
1 CCCTAAACCATAAA
* *
688848 ACATAAACCATAAA
1 CCCTAAACCATAAA
* *
688862 CCCTAAGCCCCT-AA
1 CCCTAA-ACCATAAA
*
688876 CCCTTAAACCTTAAA
1 CCC-TAAACCATAAA
* * *
688891 CCCCAACCCTTAAA
1 CCCTAAACCATAAA
* *
688905 CCATAAACCATAAT
1 CCCTAAACCATAAA
** * *
688919 CTATAATCCATAAT
1 CCCTAAACCATAAA
* *
688933 CTCTAAACCCATAAT
1 CCCTAAA-CCATAAA
* *
688948 CCATAAACCTTAAA
1 CCCTAAACCATAAA
* *
688962 --ATAGTAACTCCTAAA
1 CCCTA--AAC-CATAAA
* *
688977 TCCTAAACCCT-AA
1 CCCTAAACCATAAA
**
688990 CCCTAAACCATGTA
1 CCCTAAACCATAAA
*
689004 CCCTAAACTATAAA
1 CCCTAAACCATAAA
*
689018 CCCTAAACTATAA
1 CCCTAAACCATAA
689031 TAATAATTAA
Statistics
Matches: 152, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
12 3 0.02
13 11 0.07
14 105 0.69
15 31 0.20
17 2 0.01
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (14 bp):
CCCTAAACCATAAA
Found at i:688840 original size:7 final size:7
Alignment explanation
Indices: 688820--689025 Score: 62
Period size: 7 Copynumber: 29.1 Consensus size: 7
688810 TTGTATAAGC
*
688820 CCCTAAC
1 CCCTAAA
688827 CCCTAAA
1 CCCTAAA
688834 CCCTAAA
1 CCCTAAA
* *
688841 TCATAAA
1 CCCTAAA
* *
688848 ACATAAA
1 CCCTAAA
*
688855 CCATAAA
1 CCCTAAA
*
688862 CCCTAAGC
1 CCCTAA-A
688870 CCCT-AA
1 CCCTAAA
688876 CCCTTAAA
1 CCC-TAAA
*
688884 CCTTAAA
1 CCCTAAA
*
688891 CCC-CAA
1 CCCTAAA
688897 CCCTTAAA
1 CCC-TAAA
*
688905 CCATAAA
1 CCCTAAA
* *
688912 CCATAAT
1 CCCTAAA
** *
688919 CTATAAT
1 CCCTAAA
* *
688926 CCATAAT
1 CCCTAAA
*
688933 CTCTAAA
1 CCCTAAA
*
688940 CCCATAAT
1 CCC-TAAA
*
688948 CCATAAA
1 CCCTAAA
*
688955 CCTTAAA
1 CCCTAAA
*
688962 --ATAGTAA
1 CCCTA--AA
688969 CTCCTAAA
1 C-CCTAAA
*
688977 TCCTAAA
1 CCCTAAA
688984 CCCT-AA
1 CCCTAAA
688990 CCCTAAA
1 CCCTAAA
* **
688997 CCATGTA
1 CCCTAAA
689004 CCCTAAA
1 CCCTAAA
**
689011 CTATAAA
1 CCCTAAA
689018 CCCTAAA
1 CCCTAAA
689025 C
1 C
689026 TATAATAATA
Statistics
Matches: 149, Mismatches: 38, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
5 2 0.01
6 14 0.09
7 112 0.75
8 19 0.13
10 2 0.01
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:688900 original size:21 final size:22
Alignment explanation
Indices: 688869--688913 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
688859 AAACCCTAAG
*
688869 CCCCTAACCCTTAAACCTTAAA
1 CCCCTAACCCTTAAACCATAAA
688891 CCCC-AACCCTTAAACCATAAA
1 CCCCTAACCCTTAAACCATAAA
688912 CC
1 CC
688914 ATAATCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (22 bp):
CCCCTAACCCTTAAACCATAAA
Found at i:688905 original size:50 final size:50
Alignment explanation
Indices: 688815--688913 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
688805 ATTAATTGTA
* *
688815 TAAGCCCCTAACCCCTAAACCCTAAATCATAAAACATAAACCATAAACCC
1 TAAGCCCCTAACCCCTAAACCCTAAACCACAAAACATAAACCATAAACCC
* * * ** *
688865 TAAGCCCCTAACCCTTAAACCTTAAACCCCAACCCTTAAACCATAAACC
1 TAAGCCCCTAACCCCTAAACCCTAAACCACAAAACATAAACCATAAACC
688914 ATAATCTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.42, C:0.38, G:0.02, T:0.17
Consensus pattern (50 bp):
TAAGCCCCTAACCCCTAAACCCTAAACCACAAAACATAAACCATAAACCC
Found at i:689454 original size:40 final size:40
Alignment explanation
Indices: 689410--689496 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
689400 TTTTTTGCGC
* * *
689410 CGTTTTTCAAAAAGCGCCGCTAATGGTCAACCTATAGTGG
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGTGA
* * *
689450 CGTTTTTCAAAAAGCACTGCTAATGCTCGATCTATAGTGA
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGTGA
689490 CGTTTTT
1 CGTTTTT
689497 TTATCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGTGA
Found at i:690736 original size:11 final size:12
Alignment explanation
Indices: 690714--690757 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
690704 AACAAATCCT
690714 CTCTCAAATTTC
1 CTCTCAAATTTC
690726 CTCTC-AATTTC
1 CTCTCAAATTTC
690737 CT-TCCAAATTT-
1 CTCT-CAAATTTC
690748 CTCTCAAATT
1 CTCTCAAATT
690758 CATATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 17 0.59
12 11 0.38
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:692676 original size:18 final size:18
Alignment explanation
Indices: 692649--692688 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
692639 CAGGTTCGTT
* *
692649 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
692667 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
692685 TCCT
1 TCCT
692689 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:693292 original size:21 final size:21
Alignment explanation
Indices: 693268--693541 Score: 268
Period size: 22 Copynumber: 12.8 Consensus size: 21
693258 TAACCCTAAT
* *
693268 CCTAACTCTTAACTTAAAAAC
1 CCTAACCCTAAACTTAAAAAC
693289 CCTAACCCTTAAA-TTAAAAAC
1 CCTAACCC-TAAACTTAAAAAC
*
693310 CCTAAACCCTTAACTTAAAAAC
1 CCT-AACCCTAAACTTAAAAAC
*
693332 CCTAAACCCTAAACCTAAAAA-
1 CCT-AACCCTAAACTTAAAAAC
*
693353 CATAAACCCTAAACTTAAAAAC
1 CCT-AACCCTAAACTTAAAAAC
* *
693375 CCAAACCCTAAACCTAAAAAC
1 CCTAACCCTAAACTTAAAAAC
* * *
693396 CTTAAACTCTAAACTTAAAACC
1 CCT-AACCCTAAACTTAAAAAC
* * *
693418 CCAAACCCCAAACCT-AAAAC
1 CCTAACCCTAAACTTAAAAAC
*
693438 CCTAACCCTTAACTTAAAAAC
1 CCTAACCCTAAACTTAAAAAC
* *
693459 CACAAACCCTAAACCT-AAAAC
1 C-CTAACCCTAAACTTAAAAAC
693480 CCTAAACCCTAAACTTAAAAAC
1 CCT-AACCCTAAACTTAAAAAC
* *
693502 CACAAACCCTAAACCTAAAAAC
1 C-CTAACCCTAAACTTAAAAAC
*
693524 TCTAAACCCTAAACTTAA
1 CCT-AACCCTAAACTTAA
693542 TAAATTTTAA
Statistics
Matches: 207, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
20 16 0.08
21 91 0.44
22 99 0.48
23 1 0.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (21 bp):
CCTAACCCTAAACTTAAAAAC
Found at i:693317 original size:22 final size:22
Alignment explanation
Indices: 693278--693541 Score: 314
Period size: 21 Copynumber: 12.3 Consensus size: 22
693268 CCTAACTCTT
693278 AACTTAAAAACCCT-AACCCTTA
1 AACTTAAAAACCCTAAACCC-TA
*
693300 AA-TTAAAAACCCTAAACCCTT
1 AACTTAAAAACCCTAAACCCTA
693321 AACTTAAAAACCCTAAACCCTA
1 AACTTAAAAACCCTAAACCCTA
* *
693343 AACCTAAAAA-CATAAACCCTA
1 AACTTAAAAACCCTAAACCCTA
693364 AACTTAAAAACCC-AAACCCTA
1 AACTTAAAAACCCTAAACCCTA
* * *
693385 AACCTAAAAACCTTAAACTCTA
1 AACTTAAAAACCCTAAACCCTA
* *
693407 AACTT-AAAACCCCAAACCCCA
1 AACTTAAAAACCCTAAACCCTA
* *
693428 AACCT-AAAACCCT-AACCCTT
1 AACTTAAAAACCCTAAACCCTA
693448 AACTTAAAAACCAC-AAACCCTA
1 AACTTAAAAACC-CTAAACCCTA
*
693470 AACCT-AAAACCCTAAACCCTA
1 AACTTAAAAACCCTAAACCCTA
693491 AACTTAAAAACCAC-AAACCCTA
1 AACTTAAAAACC-CTAAACCCTA
* *
693513 AACCTAAAAACTCTAAACCCTA
1 AACTTAAAAACCCTAAACCCTA
693535 AACTTAA
1 AACTTAA
693542 TAAATTTTAA
Statistics
Matches: 206, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
20 10 0.05
21 100 0.49
22 95 0.46
23 1 0.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (22 bp):
AACTTAAAAACCCTAAACCCTA
Found at i:693318 original size:7 final size:7
Alignment explanation
Indices: 693306--693537 Score: 78
Period size: 7 Copynumber: 32.6 Consensus size: 7
693296 CTTAAATTAA
693306 AAACCCT
1 AAACCCT
693313 AAACCCT
1 AAACCCT
* *
693320 TAA-CTT
1 AAACCCT
693326 AAAAACCCT
1 --AAACCCT
693335 AAACCCT
1 AAACCCT
693342 AAA-CCT
1 AAACCCT
* *
693348 AAAAACAT
1 -AAACCCT
693356 AAACCCT
1 AAACCCT
*
693363 AAA-CTT
1 AAACCCT
693369 AAAAACCC-
1 --AAACCCT
693377 AAACCCT
1 AAACCCT
693384 AAA-CCT
1 AAACCCT
*
693390 AAAAACCTT
1 --AAACCCT
*
693399 AAACTCT
1 AAACCCT
*
693406 AAA-CTT
1 AAACCCT
*
693412 AAAACCCC
1 -AAACCCT
*
693420 AAACCCC
1 AAACCCT
693427 AAA-CCT
1 AAACCCT
693433 AAAACCCT
1 -AAACCCT
693441 -AACCCT
1 AAACCCT
* *
693447 TAA-CTT
1 AAACCCT
693453 AAAAACCAC-
1 --AAACC-CT
693462 AAACCCT
1 AAACCCT
693469 AAA-CCT
1 AAACCCT
693475 AAAACCCT
1 -AAACCCT
693483 AAACCCT
1 AAACCCT
*
693490 AAA-CTT
1 AAACCCT
693496 AAAAACCAC-
1 --AAACC-CT
693505 AAACCCT
1 AAACCCT
693512 AAA-CCT
1 AAACCCT
*
693518 AAAAACTCT
1 --AAACCCT
693527 AAACCCT
1 AAACCCT
693534 AAAC
1 AAAC
693538 TTAATAAATT
Statistics
Matches: 169, Mismatches: 24, Indels: 64
0.66 0.09 0.25
Matches are distributed among these distances:
6 37 0.22
7 98 0.58
8 25 0.15
9 9 0.05
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:693323 original size:43 final size:43
Alignment explanation
Indices: 693278--693541 Score: 367
Period size: 43 Copynumber: 6.2 Consensus size: 43
693268 CCTAACTCTT
* * *
693278 AACTTAAAAACCCTAACCCTTAAA-TTAAAAACCCTAAACCCTT
1 AACTTAAAAACCCAAACCC-TAAACCTAAAAACCCTAAACCCTA
*
693321 AACTTAAAAACCCTAAACCCTAAACCTAAAAA-CATAAACCCTA
1 AACTTAAAAACCC-AAACCCTAAACCTAAAAACCCTAAACCCTA
* *
693364 AACTTAAAAACCCAAACCCTAAACCTAAAAACCTTAAACTCTA
1 AACTTAAAAACCCAAACCCTAAACCTAAAAACCCTAAACCCTA
* * *
693407 AACTTAAAACCCCAAACCCCAAACCT-AAAACCCT-AACCCTT
1 AACTTAAAAACCCAAACCCTAAACCTAAAAACCCTAAACCCTA
693448 AACTTAAAAACCACAAACCCTAAACCT-AAAACCCTAAACCCTA
1 AACTTAAAAACC-CAAACCCTAAACCTAAAAACCCTAAACCCTA
*
693491 AACTTAAAAACCACAAACCCTAAACCTAAAAACTCTAAACCCTA
1 AACTTAAAAACC-CAAACCCTAAACCTAAAAACCCTAAACCCTA
693535 AACTTAA
1 AACTTAA
693542 TAAATTTTAA
Statistics
Matches: 200, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
41 16 0.08
42 46 0.23
43 105 0.52
44 33 0.17
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (43 bp):
AACTTAAAAACCCAAACCCTAAACCTAAAAACCCTAAACCCTA
Found at i:694074 original size:8 final size:9
Alignment explanation
Indices: 694051--694077 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
694041 TTACTTGACT
694051 TTAAAAATA
1 TTAAAAATA
694060 TTAAAAATA
1 TTAAAAATA
694069 TTAAAAATA
1 TTAAAAATA
694078 AGTAGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:696909 original size:7 final size:7
Alignment explanation
Indices: 696897--696922 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
696887 TTATATACAT
696897 GAAATGG
1 GAAATGG
696904 GAAATGG
1 GAAATGG
696911 GAAATGG
1 GAAATGG
696918 GAAAT
1 GAAAT
696923 AGATGTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (7 bp):
GAAATGG
Done.