Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold121
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: 1076282
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 28062 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:290980 original size:84 final size:84
Alignment explanation
Indices: 290729--290983 Score: 224
Period size: 84 Copynumber: 3.0 Consensus size: 84
290719 GCCTGTCAAT
* * * * ** * * * *
290729 TTTGACCCTAGAGACTGCCTCATCTCAAGTCTATTTATCGGCTTTGATCCTAGAGACTTTCATAC
1 TTTGACCCTGGAGACTACCCCACCTCAAGTCTACCTATCGACTTTGACCCAAGAGACTTTCTTAC
* * ** *
290794 C-CTCAGTTTGCTGGTCGAC
66 CTCT-AGTCTACCCGTCGGC
* * ***
290813 TTTGACCTTGGAGACTACCCCACCTCAAGTCTACCTATCGGCTTTGACCTTGGAGACTTTCTTAC
1 TTTGACCCTGGAGACTACCCCACCTCAAGTCTACCTATCGACTTTGACCCAAGAGACTTTCTTAC
* * **
290878 CTCTAGTTTGCCTATCGGC
66 CTCTAGTCTACCCGTCGGC
* * * * *
290897 TTTGACCCTGGAGATTACCTCACCTCAAGTCTACTTGTCGACTTTGACCCAAGAGACTTTTTTAC
1 TTTGACCCTGGAGACTACCCCACCTCAAGTCTACCTATCGACTTTGACCCAAGAGACTTTCTTAC
*
290962 CTCTTGTCTACCCGTCGGC
66 CTCTAGTCTACCCGTCGGC
290981 TTT
1 TTT
290984 AACTTGGAGA
Statistics
Matches: 140, Mismatches: 30, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
84 138 0.99
85 2 0.01
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (84 bp):
TTTGACCCTGGAGACTACCCCACCTCAAGTCTACCTATCGACTTTGACCCAAGAGACTTTCTTAC
CTCTAGTCTACCCGTCGGC
Found at i:291532 original size:6 final size:6
Alignment explanation
Indices: 291521--291563 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
291511 GAGTTATTTA
* *
291521 AAAAAT AAAAAT AAAAAA ATAAAAT AAAAAT AAATA- AAAAAT A
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT A
291564 TGCATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:291546 original size:19 final size:20
Alignment explanation
Indices: 291522--291559 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
291512 AGTTATTTAA
291522 AAAATAAAAATAAA-AAAAT
1 AAAATAAAAATAAATAAAAT
291541 AAAATAAAAATAAATAAAA
1 AAAATAAAAATAAATAAAA
291560 AATATGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAATAAAAATAAATAAAAT
Found at i:291593 original size:4 final size:4
Alignment explanation
Indices: 291576--291610 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
291566 CATGAAAAAA
*
291576 TAAT TAAA TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
291611 AAAAATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
TAAT
Found at i:292135 original size:44 final size:44
Alignment explanation
Indices: 292044--292140 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 44
292034 TGGCAACAGC
* ** *
292044 TGCTGCAATGAAGACATTAACGTGCTGTAATGAAGACATTAACG
1 TGCTGCAATGAAGACATTAACGTGCTGCAATGAAGACACCAAAG
292088 TGCTGCAATGAAGACATTAACGTGCTGCAATGAAGACACCAAAG
1 TGCTGCAATGAAGACATTAACGTGCTGCAATGAAGACACCAAAG
*
292132 TGCTACAAT
1 TGCTGCAAT
292141 CAACAAGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (44 bp):
TGCTGCAATGAAGACATTAACGTGCTGCAATGAAGACACCAAAG
Found at i:292140 original size:22 final size:22
Alignment explanation
Indices: 292044--292125 Score: 155
Period size: 22 Copynumber: 3.7 Consensus size: 22
292034 TGGCAACAGC
292044 TGCTGCAATGAAGACATTAACG
1 TGCTGCAATGAAGACATTAACG
*
292066 TGCTGTAATGAAGACATTAACG
1 TGCTGCAATGAAGACATTAACG
292088 TGCTGCAATGAAGACATTAACG
1 TGCTGCAATGAAGACATTAACG
292110 TGCTGCAATGAAGACA
1 TGCTGCAATGAAGACA
292126 CCAAAGTGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (22 bp):
TGCTGCAATGAAGACATTAACG
Found at i:296363 original size:2 final size:2
Alignment explanation
Indices: 296358--296405 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
296348 ATTCTATGTC
* *
296358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
296400 AT AT AT
1 AT AT AT
296406 TTCAGAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:296469 original size:2 final size:2
Alignment explanation
Indices: 296459--296497 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
296449 TTTTTATGTA
* *
296459 AT AT GT AT AT AT AT TT 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 AT A
296498 AAGAGTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:298472 original size:20 final size:19
Alignment explanation
Indices: 298436--298474 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
298426 TAAAATAAAT
* *
298436 AAAAATTACTTCAAAATAA
1 AAAAATTAATTAAAAATAA
298455 AAAAATTAATTAAGAAATAA
1 AAAAATTAATTAA-AAATAA
298475 TTTCATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATTAATTAAAAATAA
Found at i:301790 original size:9 final size:9
Alignment explanation
Indices: 301776--301805 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
301766 GCTGCCGAGC
301776 AGTCTTTCG
1 AGTCTTTCG
*
301785 AGTCTTTTG
1 AGTCTTTCG
301794 AGTCTTTCG
1 AGTCTTTCG
301803 AGT
1 AGT
301806 AGGCCTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (9 bp):
AGTCTTTCG
Found at i:308751 original size:20 final size:20
Alignment explanation
Indices: 308706--308751 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
308696 GTTAATAGCC
*
308706 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
308726 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
308747 CATGT
1 CATGT
308752 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:312361 original size:81 final size:81
Alignment explanation
Indices: 312226--312727 Score: 736
Period size: 81 Copynumber: 6.1 Consensus size: 81
312216 TCACTGTTCT
* * * *
312226 TTGATGGTGGCCTTGTTGAAGGAGGATGCACTGACATCGGTTTTGTTGGAATTGCTGGAATGGGA
1 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
312291 GATGCATTTAATGAGG
66 GATGCATTTAATGAGG
* *
312307 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTCGTTGGAATTGCTGGAATGGGA
1 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
312372 GATGCATTTAATGAGG
66 GATGCATTTAATGAGG
* * *
312388 ATGATGATGGCCTTATTGGAGGAGGATGCACTGGCATCGGTTTCGTTGGAACTGCTGGAATGGGA
1 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
*
312453 GATGCATATAATGAGG
66 GATGCATTTAATGAGG
*
312469 TTGATGATGGCCTTATTGGAGGAGGACGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
1 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
312534 GATGCATTTAATGAGG
66 GATGCATTTAATGAGG
*
312550 TTGATGATGGCCTTATTGGAGGAGGATGCTCTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
1 TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
* *
312615 GATCCATTGGAA-GAGG
66 GATGCATT-TAATGAGG
* * * * * * *
312631 TTGATGATGGCCTCATTGGGGGAGGAGGATGCACTGACGTTGGTCTTGATGGAATTGCTGGGATG
1 TTGATGATGGCCTTATT---GGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATG
*
312696 GGAGATCCATTTAATGATGAGG
63 GGAGATGCATTT-A--ATGAGG
312718 TTGATGATGG
1 TTGATGATGG
312728 ACTTGGAGGT
Statistics
Matches: 387, Mismatches: 26, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
81 320 0.83
82 2 0.01
84 50 0.13
86 1 0.00
87 14 0.04
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (81 bp):
TTGATGATGGCCTTATTGGAGGAGGATGCACTGACATCGGTTTTGTTGGAACTGCTGGAATGGGA
GATGCATTTAATGAGG
Found at i:313417 original size:13 final size:13
Alignment explanation
Indices: 313401--313461 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
313391 TTTAATATGT
313401 TATATAAATAAAA
1 TATATAAATAAAA
*
313414 TATA-AAATATAA
1 TATATAAATAAAA
*
313426 TA-ATAAAATTAAA
1 TATAT-AAATAAAA
*
313439 TAAATAAATATAAA
1 TATATAAATA-AAA
313453 TTATATAAA
1 -TATATAAA
313462 AATTATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 1 0.03
12 9 0.24
13 16 0.42
14 5 0.13
15 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATATAAATAAAA
Found at i:313423 original size:18 final size:18
Alignment explanation
Indices: 313402--313481 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
313392 TTAATATGTT
313402 ATATAAATAAAATATAAA
1 ATATAAATAAAATATAAA
313420 ATATAATAATAAAAT-T--A
1 ATAT-A-AATAAAATATAAA
313437 A-ATAAAT-AAATATAAA
1 ATATAAATAAAATATAAA
* *
313453 TTATATAA-AAATTATAAA
1 ATATA-AATAAAATATAAA
*
313471 AT-TATATAAAA
1 ATATAAATAAAA
313482 CAAAATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 19
0.67 0.07 0.26
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 1 0.02
16 4 0.08
17 10 0.21
18 15 0.31
19 2 0.04
20 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAATAAAATATAAA
Found at i:313453 original size:19 final size:18
Alignment explanation
Indices: 313404--313480 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 18
313394 AATATGTTAT
313404 ATAAATAAAATATAAAATATA
1 ATAAATAAAAT-T-AAATA-A
313425 AT-AATAAAATTAAATAA
1 ATAAATAAAATTAAATAA
*
313442 ATAAATATAAATTATATAA
1 ATAAATA-AAATTAAATAA
*
313461 A-AATTATAAAATTATATAA
1 ATAA--ATAAAATTAAATAA
313480 A
1 A
313481 ACAAAATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.06
18 11 0.22
19 24 0.47
20 11 0.22
21 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAAATTAAATAA
Found at i:313481 original size:19 final size:19
Alignment explanation
Indices: 313428--313481 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
313418 AAATATAATA
*
313428 ATAAAATTAAATAAATAAAT
1 ATAAAATTATATAAA-AAAT
*
313448 AT-AAATTATATAAAAATT
1 ATAAAATTATATAAAAAAT
313466 ATAAAATTATATAAAA
1 ATAAAATTATATAAAA
313482 CAAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 5 0.16
19 24 0.77
20 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATTATATAAAAAAT
Found at i:313522 original size:2 final size:2
Alignment explanation
Indices: 313515--313544 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
313505 TGAATGCTTC
313515 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
313545 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:313549 original size:2 final size:2
Alignment explanation
Indices: 313544--313568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
313534 TCTCTCTCTC
313544 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
313569 CACCTGGTAA
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:314302 original size:17 final size:17
Alignment explanation
Indices: 314277--314336 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
314267 ATAAATATAT
*
314277 TATAATTTATATAAAAA
1 TATAATTTAAATAAAAA
* *
314294 TATATTTTAAATATAAA
1 TATAATTTAAATAAAAA
314311 TATAA-TT-AAT--AAA
1 TATAATTTAAATAAAAA
*
314324 TATAATATAAATA
1 TATAATTTAAATA
314337 TTCAATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
15 6 0.17
16 2 0.06
17 18 0.51
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATTTAAATAAAAA
Found at i:314309 original size:19 final size:19
Alignment explanation
Indices: 314285--314328 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
314275 ATTATAATTT
*
314285 ATATAAAAATATATT-TTAA
1 ATATAAAAATA-ATTAATAA
*
314304 ATATAAATATAATTAATAA
1 ATATAAAAATAATTAATAA
314323 ATATAA
1 ATATAA
314329 TATAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAAAATAATTAATAA
Found at i:314322 original size:13 final size:11
Alignment explanation
Indices: 314303--314337 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
314293 ATATATTTTA
314303 AATATAAATAT
1 AATATAAATAT
314314 AATTAATAAATAT
1 AA-T-ATAAATAT
314327 AATATAAATAT
1 AATATAAATAT
314338 TCAATTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:314430 original size:2 final size:2
Alignment explanation
Indices: 314423--314467 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
314413 TGACAAATGC
314423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
314465 AT A
1 AT A
314468 GTTTATCCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:314659 original size:29 final size:28
Alignment explanation
Indices: 314627--314681 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
314617 TTATAATTTT
314627 ATTTAAATAAATTTTTATATTTTTATTAC
1 ATTTAAAT-AATTTTTATATTTTTATTAC
*
314656 ATTTAAATAATTTTTTTATTTTTATT
1 ATTTAAATAATTTTTATATTTTTATT
314682 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTAAATAATTTTTATATTTTTATTAC
Found at i:314683 original size:5 final size:6
Alignment explanation
Indices: 314668--314692 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
314658 TTAAATAATT
314668 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
314693 ACTTAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:314688 original size:29 final size:29
Alignment explanation
Indices: 314622--314688 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
314612 AAATTTTATA
314622 ATTTTATTTAAATAAATTTTTATATTTTT
1 ATTTTATTTAAATAAATTTTTATATTTTT
** *
314651 ATTACATTTAAAT-AATTTTTTTATTTTT
1 ATTTTATTTAAATAAATTTTTATATTTTT
314679 ATTTTTATTT
1 A-TTTTATTT
314689 TTATACTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTTTATTTAAATAAATTTTTATATTTTT
Found at i:314708 original size:37 final size:40
Alignment explanation
Indices: 314639--314724 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 40
314629 TTAAATAAAT
*
314639 TTTTATATTTTTATTACATTTAAATAATTTTTTTATTTTTA-
1 TTTT-TATTTTTATTACA-TTAAATAATTTTTTAATTTTTAC
314680 TTTTTATTTTTA-TAC-TTAAATGAA-TTTTTAATTTTTAC
1 TTTTTATTTTTATTACATTAAAT-AATTTTTTAATTTTTAC
314718 TTTTTAT
1 TTTTTAT
314725 CCAAATAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
37 18 0.43
38 9 0.21
39 3 0.07
40 8 0.19
41 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (40 bp):
TTTTTATTTTTATTACATTAAATAATTTTTTAATTTTTAC
Found at i:314829 original size:30 final size:29
Alignment explanation
Indices: 314790--314851 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
314780 TTATTTGATT
314790 TAAAAATTTATTTAAATATAAATAAAAAGA
1 TAAAAATTTATTTAAATAT-AATAAAAAGA
* * *
314820 TAAATATTTATTTAATTATAATAAAAATA
1 TAAAAATTTATTTAAATATAATAAAAAGA
314849 TAA
1 TAA
314852 GGATTTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAAATTTATTTAAATATAATAAAAAGA
Found at i:314857 original size:29 final size:30
Alignment explanation
Indices: 314790--314858 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
314780 TTATTTGATT
*
314790 TAAAAATTTATTTAAATATAAATAAAAAGA
1 TAAAGATTTATTTAAATATAAATAAAAAGA
* * *
314820 TAAATATTTATTTAATTAT-AATAAAAATA
1 TAAAGATTTATTTAAATATAAATAAAAAGA
*
314849 TAAGGATTTA
1 TAAAGATTTA
314859 AGTTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (30 bp):
TAAAGATTTATTTAAATATAAATAAAAAGA
Found at i:315917 original size:21 final size:21
Alignment explanation
Indices: 315884--315970 Score: 79
Period size: 22 Copynumber: 4.1 Consensus size: 21
315874 TCATGTCATT
* *
315884 ATTT-AAATAATAAATAAATA
1 ATTTAAAATTATAAATAAAAA
315904 ATTTAAAATTATAAAATAAAAA
1 ATTTAAAATTAT-AAATAAAAA
* *
315926 ATTTAAATTTTTAAA-AAAAA
1 ATTTAAAATTATAAATAAAAA
* *
315946 ATTAAAAATATGTATAATAAAAA
1 ATTTAAAAT-TATA-AATAAAAA
315969 AT
1 AT
315971 GAAAAAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.29
21 12 0.22
22 20 0.36
23 7 0.13
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (21 bp):
ATTTAAAATTATAAATAAAAA
Found at i:316472 original size:13 final size:14
Alignment explanation
Indices: 316456--316484 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
316446 CTGCTTTTCC
316456 TTCTTC-CTTTTTT
1 TTCTTCTCTTTTTT
316469 TTCTTCTCTTTTTT
1 TTCTTCTCTTTTTT
316483 TT
1 TT
316485 TTTCAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTCTCTTTTTT
Found at i:316512 original size:17 final size:16
Alignment explanation
Indices: 316480--316529 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
316470 TCTTCTCTTT
*
316480 TTTTTTTTCAGATTTA
1 TTTTTTTTCAAATTTA
316496 TTTTTTTTCAAATTTTA
1 TTTTTTTTCAAA-TTTA
* *
316513 TTATTTTACAAAATTTA
1 TTTTTTTTC-AAATTTA
316530 CATATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 11 0.38
17 15 0.52
18 3 0.10
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTTTTTCAAATTTA
Found at i:316519 original size:18 final size:17
Alignment explanation
Indices: 316482--316542 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
316472 TTCTCTTTTT
*
316482 TTTTTTCAGATTTATT-
1 TTTTTTCAAATTTATTA
316498 TTTTTTCAAATTTTATTA
1 TTTTTTCAAA-TTTATTA
* *
316516 -TTTTACAAAATTTACATA
1 TTTTTTC-AAATTTA-TTA
316534 TTTTTTCAA
1 TTTTTTCAA
316543 TTATTTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 9 0.25
17 15 0.42
18 7 0.19
19 5 0.14
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTTTTCAAATTTATTA
Found at i:316625 original size:9 final size:9
Alignment explanation
Indices: 316607--316668 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
316597 TTTTTTAGTA
316607 TTAT-ATTT
1 TTATAATTT
316615 TTATAATTT
1 TTATAATTT
* *
316624 TTGTATTTT
1 TTATAATTT
316633 TTA-AATTT
1 TTATAATTT
316641 TT-TATATTT
1 TTATA-ATTT
316650 TT-TGAATTT
1 TTAT-AATTT
*
316659 TTTTAATTT
1 TTATAATTT
316668 T
1 T
316669 AAAAATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
8 11 0.24
9 32 0.71
10 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (9 bp):
TTATAATTT
Found at i:316633 original size:18 final size:18
Alignment explanation
Indices: 316607--316690 Score: 77
Period size: 18 Copynumber: 4.6 Consensus size: 18
316597 TTTTTTAGTA
316607 TTATATTTTTATAATTTT
1 TTATATTTTTATAATTTT
316625 TGTAT-TTTTTA-AATTTT
1 T-TATATTTTTATAATTTT
316642 TTATATTTTT-TGAATTTT
1 TTATATTTTTAT-AATTTT
* *
316660 TT-TAATTTTAAAAATTATT
1 TTAT-ATTTTTATAATT-TT
316679 CTTATATTTTTA
1 -TTATATTTTTA
316691 ACTATATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
16 3 0.06
17 13 0.24
18 24 0.44
19 5 0.09
20 8 0.15
21 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATATTTTTATAATTTT
Found at i:316642 original size:27 final size:27
Alignment explanation
Indices: 316612--316668 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
316602 TAGTATTATA
*
316612 TTTTTATAATTTTTGTATTTTTTAAAT
1 TTTTTATAATTTTTGAATTTTTTAAAT
* *
316639 TTTTTATATTTTTTGAATTTTTTTAAT
1 TTTTTATAATTTTTGAATTTTTTAAAT
316666 TTT
1 TTT
316669 AAAAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTTTATAATTTTTGAATTTTTTAAAT
Found at i:316982 original size:22 final size:22
Alignment explanation
Indices: 316934--316975 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
316924 TTATATTACG
* *
316934 TAAATTTATTTATAAATTAAAA
1 TAAATTAATTTATAAATCAAAA
316956 TAAATTAATTT-TAAATCAAA
1 TAAATTAATTTATAAATCAAA
316976 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTAATTTATAAATCAAAA
Found at i:317216 original size:14 final size:15
Alignment explanation
Indices: 317191--317224 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
317181 AAAAGAGTGG
317191 GAAAAGGATGAAAGA
1 GAAAAGGATGAAAGA
*
317206 GAAAA-GATGAAAGT
1 GAAAAGGATGAAAGA
317220 GAAAA
1 GAAAA
317225 TTGGGTACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.09
Consensus pattern (15 bp):
GAAAAGGATGAAAGA
Found at i:317673 original size:7 final size:7
Alignment explanation
Indices: 317661--317685 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
317651 TGATATCCAA
317661 TAAATCT
1 TAAATCT
317668 TAAATCT
1 TAAATCT
317675 TAAATCT
1 TAAATCT
317682 TAAA
1 TAAA
317686 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATCT
Found at i:318487 original size:14 final size:14
Alignment explanation
Indices: 318464--318494 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
318454 TTTAATAATT
318464 ATAAAAATATTATA
1 ATAAAAATATTATA
*
318478 ATAAATATATTATA
1 ATAAAAATATTATA
318492 ATA
1 ATA
318495 TATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAAATATTATA
Found at i:318497 original size:24 final size:24
Alignment explanation
Indices: 318457--318538 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
318447 TGACACATTT
*
318457 AATA-ATTATAAAAATATTATAATA
1 AATATATTAT-AATATATTATAATA
*
318481 AATATATTATAATATATTAAAATA
1 AATATATTATAATATATTATAATA
*
318505 TAA-ATAATATAATATATT-TAATA
1 -AATATATTATAATATATTATAATA
* *
318528 TACATATTATA
1 AATATATTATA
318539 TTTATATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 1 0.02
23 11 0.22
24 30 0.61
25 7 0.14
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATATTATAATATATTATAATA
Found at i:318571 original size:8 final size:9
Alignment explanation
Indices: 318481--318581 Score: 56
Period size: 8 Copynumber: 11.8 Consensus size: 9
318471 TATTATAATA
318481 AATATATTAT
1 AATATATT-T
318491 AATATA-TT
1 AATATATTT
* *
318499 AAAATA-TA
1 AATATATTT
*
318507 AATA-ATAT
1 AATATATTT
318515 AATATATTT
1 AATATATTT
**
318524 AATATACAT
1 AATATATTT
*
318533 ATTATA-TT
1 AATATATTT
318541 --TATATTT
1 AATATATTT
*
318548 AAAAT-TTT
1 AATATATTT
318556 AATATATTT
1 AATATATTT
318565 AAT-TATTCT
1 AATATATT-T
318574 AAATATAT
1 -AATATAT
318582 ATATTTATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.06
7 3 0.04
8 26 0.37
9 25 0.36
10 9 0.13
11 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
AATATATTT
Found at i:320613 original size:26 final size:26
Alignment explanation
Indices: 320591--320651 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
320581 ATATTATTTG
320591 TTTTTAAAAAATATTAATTTTATTTAA
1 TTTTT-AAAAATATTAATTTTATTTAA
* * *
320618 TTTTTAATAATTTTATTTTTATTTAA
1 TTTTTAAAAATATTAATTTTATTTAA
*
320644 -ATTTAAAA
1 TTTTTAAAA
320652 TATAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 6 0.21
26 18 0.62
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTTAAAAATATTAATTTTATTTAA
Found at i:320749 original size:23 final size:22
Alignment explanation
Indices: 320722--320776 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
320712 TTATATGATA
*
320722 TAAATTAAAATAT-ATCTAATATG
1 TAAATTAAAAAATAAT-T-ATATG
*
320745 TAAATGAAAAAAATAATTATATG
1 TAAAT-TAAAAAATAATTATATG
320768 TAAATTAAA
1 TAAATTAAA
320777 CTGTATTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 15 0.56
24 7 0.26
25 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
TAAATTAAAAAATAATTATATG
Found at i:321331 original size:2 final size:2
Alignment explanation
Indices: 321324--321354 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
321314 ACCTTCTTCT
*
321324 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
321355 GTGTCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:321361 original size:14 final size:14
Alignment explanation
Indices: 321328--321362 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
321318 TCTTCTTCTC
*
321328 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTG
321342 TCTCTCTCTCTCTG
1 TCTCTCTCTCTCTG
*
321356 TGTCTCT
1 TCTCTCT
321363 TTTGGACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.40, G:0.06, T:0.54
Consensus pattern (14 bp):
TCTCTCTCTCTCTG
Found at i:327197 original size:12 final size:13
Alignment explanation
Indices: 327174--327202 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
327164 GAAAGTTTGA
327174 ATTTTAATATTTT
1 ATTTTAATATTTT
327187 ATTTT-ATATTTT
1 ATTTTAATATTTT
327199 ATTT
1 ATTT
327203 AATTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTAATATTTT
Found at i:329759 original size:20 final size:20
Alignment explanation
Indices: 329734--329779 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
329724 TTTATTAATT
329734 ATAAAC-GA-TAAATATAAATA
1 ATAAACAGACTAAA-ATAAA-A
329754 ATAAACAGACTAAAATAAAA
1 ATAAACAGACTAAAATAAAA
329774 ATAAAC
1 ATAAAC
329780 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (20 bp):
ATAAACAGACTAAAATAAAA
Found at i:330507 original size:23 final size:20
Alignment explanation
Indices: 330479--330532 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
330469 ACTTTATTTA
330479 ATTTTAATAAATAATATTTATAT
1 ATTTTAATAAA-AAT-TTTA-AT
*
330502 ATTTTAAATGAAAAGTTTTAAT
1 ATTTT-AAT-AAAAATTTTAAT
330524 ATTTTAATA
1 ATTTTAATA
330533 CTTTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 7 0.25
23 9 0.32
24 5 0.18
25 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTTTAATAAAAATTTTAAT
Found at i:332504 original size:26 final size:26
Alignment explanation
Indices: 332459--332508 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
332449 AATTTTTATA
332459 TATACATTTAATAAATAAAATTAATT
1 TATACATTTAATAAATAAAATTAATT
332485 TATACA-TTACATGAAA-AAAATTAA
1 TATACATTTA-AT-AAATAAAATTAA
332509 CTTTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.14
26 16 0.73
27 3 0.14
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (26 bp):
TATACATTTAATAAATAAAATTAATT
Found at i:333130 original size:21 final size:20
Alignment explanation
Indices: 333082--333132 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
333072 CGGATTACAT
333082 ATTTTATTTATTTTTAAATAA
1 ATTTT-TTTATTTTTAAATAA
* *
333103 ATATTTTTATTTTTTAAATGA
1 ATTTTTTTA-TTTTTAAATAA
*
333124 GTTTTTTTA
1 ATTTTTTTA
333133 ATGCATTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
ATTTTTTTATTTTTAAATAA
Found at i:333300 original size:14 final size:14
Alignment explanation
Indices: 333281--333310 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
333271 AAATATAATA
333281 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
*
333295 ATTTTTTAAAATAT
1 ATTTTTTAAAAAAT
333309 AT
1 AT
333311 GTATCATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTTAAAAAAT
Found at i:334369 original size:3 final size:3
Alignment explanation
Indices: 334361--334404 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
334351 CACACTAATA
334361 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
334405 ATTAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:336948 original size:20 final size:20
Alignment explanation
Indices: 336925--336962 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
336915 TTACTTAACA
336925 TTAAAATTATT-TTTAAATAC
1 TTAAAATT-TTGTTTAAATAC
336945 TTAAAATTTTGTTTAAAT
1 TTAAAATTTTGTTTAAAT
336963 GAATGTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAAATTTTGTTTAAATAC
Found at i:337133 original size:16 final size:16
Alignment explanation
Indices: 337112--337146 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
337102 ATTAATGTAG
*
337112 TAAAATCTTATAAATA
1 TAAAATATTATAAATA
*
337128 TAAAATATTTTAAATA
1 TAAAATATTATAAATA
337144 TAA
1 TAA
337147 TTATGACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATATTATAAATA
Found at i:340188 original size:84 final size:84
Alignment explanation
Indices: 339751--340342 Score: 675
Period size: 85 Copynumber: 7.0 Consensus size: 84
339741 TTCCTTCAGT
* * * * * * *
339751 CTGCTTCATTTAAAGTCTGCCTATCGACTTTAACCCT-GTGACTTTTTTACCCTTAGTCTGCCTG
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
339815 TCGGCTTTGACCCTGGAGA
66 TCGGCTTTGACCCTGGAGA
* * * * * * *
339834 CTGCCTCATCTAAGGTCTGCTTGTTGACTTTAACCCCAGAGACTTTCCTATCCTTCAGTCTGCCT
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCT
** * * *
339899 GTTAGCTTTAACCTTAGAGA
65 GTCGGCTTTGACCCTGGAGA
* * * * ** *
339919 CTGCTTCATCTAAAGTCTGCCTATCGGCTTTAACCCTGGAGACTTTCCTATCATTCAGTCTGCTT
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCT
* * *
339984 GTTGTCTTTGACCCTAGAGA
65 GTCGGCTTTGACCCTGGAGA
* * * * *
340004 CTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCCT
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCT
* *
340069 GTCGACTTTGACCCTAGAGA
65 GTCGGCTTTGACCCTGGAGA
* * * * *
340089 TTGCCTCATCCAAAGTCTG-CTCGTCGGCTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCT
1 CTGCCTCATCTAAAGTCTGCCT-GTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAGTCTGCCT
*
340153 GTCGGCTTTAACCCTGGAGA
65 GTCGGCTTTGACCCTGGAGA
* * * * * *
340173 CTGTCTCATCTAAAGTCTACTTCTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAATTTGCCTG
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
*
340238 TCAGCTTTGACCCTGGAGA
66 TCGGCTTTGACCCTGGAGA
* *
340257 CTGCCTCATCTAAAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
340322 TCGGCTTTGACCCTGGAGA
66 TCGGCTTTGACCCTGGAGA
340341 CT
1 CT
340343 TTTCTACCTT
Statistics
Matches: 435, Mismatches: 70, Indels: 7
0.85 0.14 0.01
Matches are distributed among these distances:
83 30 0.07
84 188 0.43
85 217 0.50
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (84 bp):
CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
TCGGCTTTGACCCTGGAGA
Found at i:340316 original size:42 final size:42
Alignment explanation
Indices: 339764--340377 Score: 363
Period size: 42 Copynumber: 14.6 Consensus size: 42
339754 CTTCATTTAA
* * * * * *
339764 AGTCTGCCTATCGACTTTAACCCT-GTGACTTTTTTACCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
** * *
339805 AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TGCCT-CATCTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTAC-CCTC
* * * * ** * *
339846 AGGTCTGCTTGTTGACTTTAACCCCAGAGACTTTCCTATCCTTC
1 A-GTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA-CCCTC
** * * * * * *
339890 AGTCTGCCTGTTAGCTTTAACCTTAGAGACTGCTTC-A-TCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCTACCCT-C
* * * **
339932 AGTCTGCCTATCGGCTTTAACCCTGGAGACTTTCCTATCATTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA-CCCTC
* * * * ** ** *
339975 AGTCTGCTTGTTGTCTTTGACCCTAGAGAC-TGCCT-CATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTAC-CCT-C
* *
340017 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA-CCCTC
* * ** * **
340060 AGTCTGCCTGTCGACTTTGACCCTAGAGA-TTGCCTCATCCAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCT-ACCCTC
*
340102 AGTCTG-CTCGTCGGCTTTGACCTTGGAGACTTTTCTACCCTC
1 AGTCTGCCT-GTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
* * * *
340144 AGTCTGCCTGTCGGCTTTAACCCTGGAGAC-TGTCT-CATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTAC-CCT-C
* * * * *
340186 AGTCTACTTCTCGGCTTTAACCCTAGAGACTTTTCTACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
* * * ** * *
340228 AATTTGCCTGTCAGCTTTGACCCTGGAGAC-TGCCT-CATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTAC-CCT-C
* *
340270 AGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTTCTACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
*
340312 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
* *
340354 AGACTGCCTATCGGCTTTGACCCT
1 AGTCTGCCTGTCGGCTTTGACCCT
340378 AAAGACTGCC
Statistics
Matches: 435, Mismatches: 110, Indels: 55
0.73 0.18 0.09
Matches are distributed among these distances:
40 4 0.01
41 44 0.10
42 275 0.63
43 102 0.23
44 8 0.02
45 2 0.00
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.34
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTC
Found at i:340361 original size:84 final size:84
Alignment explanation
Indices: 339761--340384 Score: 617
Period size: 84 Copynumber: 7.4 Consensus size: 84
339751 CTGCTTCATT
* * * * * *
339761 TAAAGTCTGCCTATCGACTTTAACCCT-GTGACTTTTTTACCCTTAGTCTGCCTGTCGGCTTTGA
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGA
*
339825 CCCTGGAGACTGCCTCATC
66 CCCTGGAGACTGCCTCACC
* * * * * * * * ** *
339844 TAAGGTCTGCTTGTTGACTTTAACCCCAGAGACTTTCCTATCCTTCAGTCTGCCTGTTAGCTTTA
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTG
* * * *
339909 ACCTTAGAGACTGCTTCATC
65 ACCCTGGAGACTGCCTCACC
* * * * ** * * *
339929 TAAAGTCTGCCTATCGGCTTTAACCCTGGAGACTTTCCTATCATTCAGTCTGCTTGTTGTCTTTG
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTG
* **
339994 ACCCTAGAGACTGCCTCATT
65 ACCCTGGAGACTGCCTCACC
* * * *
340014 TAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGACTTTG
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTG
* *
340079 ACCCTAGAGATTGCCTCATCC
65 ACCCTGGAGACTGCCTCA-CC
* * *
340100 -AAAGTCTG-CTCGTCGGCTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTA
1 TAAAGTCTGCCT-GTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTG
* *
340163 ACCCTGGAGACTGTCTCATC
65 ACCCTGGAGACTGCCTCACC
* * * * * * *
340183 TAAAGTCTACTTCTCGGCTTTAACCCTAGAGACTTTTCTACCCTCAATTTGCCTGTCAGCTTTGA
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGA
*
340248 CCCTGGAGACTGCCTCATC
66 CCCTGGAGACTGCCTCACC
*
340267 TAAAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGA
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGA
**
340332 CCCTGGAGACT-TTTCTACC
66 CCCTGGAGACTGCCTC-ACC
** * * *
340351 TTCAGACTGCCTATCGGCTTTGACCCTAAAGACT
1 TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACT
340385 GCCTTATCTA
Statistics
Matches: 457, Mismatches: 77, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
83 25 0.05
84 216 0.47
85 216 0.47
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.34
Consensus pattern (84 bp):
TAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGA
CCCTGGAGACTGCCTCACC
Found at i:340415 original size:126 final size:127
Alignment explanation
Indices: 339751--340459 Score: 455
Period size: 126 Copynumber: 5.6 Consensus size: 127
339741 TTCCTTCAGT
* * * * * * * *
339751 CTGCTTCATTTAAAGTCTGCCTATCGACTTTAACCCT-GTGACTTTTTTACCCTTAGTCTGCCTG
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTAAGTCTGCCTG
* * * * * * * * *
339815 TCGGCTTTGACCCTGGAGAC-TGCCTCAT-C-TAAGGTCTGCTTGTTGACTTTAACCCCAGAGA
66 TCGGCTTTGACCCTAGAGACTTTCCT-ATCCTTCA-GACTGCCTGTCGGCTTTGACCCTAGAGA
* ** ** * * * * *
339876 CTTTCCT-ATCCTTCAGTCTGCCTGTTAGCTTTAACCTTAGAGACTGCTTC-A-TCTAAAGTCTG
1 C-TGCCTCAT-CTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCTACCCT-AAGTCTG
* * * * * * * *
339938 CCTATCGGCTTTAACCCTGGAGACTTTCCTATCATTCAGTCTGCTTGTTGTCTTTGACCCTAGAG
62 CCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCTTCAGACTGCCTGTCGGCTTTGACCCTAGAG
340003 A
127 A
* * * *
340004 CTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCCT
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA-CCCTAAGTCTGCCT
* * ** * * *
340069 GTCGACTTTGACCCTAGAGA-TTGCCTCATCC-AAAGTCTG-CTCGTCGGCTTTGACCTTGGAGA
65 GTCGGCTTTGACCCTAGAGACTTTCCT-ATCCTTCAGACTGCCT-GTCGGCTTTGACCCTAGAGA
** * * * * * *
340131 CT-TTTCTACCCT-CAGTCTGCCTGTCGGCTTTAACCCTGGAGAC-TGTCT-CATCTAAAGTCTA
1 CTGCCTC-A-TCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTAC-CCT-AAGTCTG
* * * * * * * *
340192 CTTCTCGGCTTTAACCCTAGAGACTTTTCTA-CCCTCA-ATTTGCCTGTCAGCTTTGACCCTGGA
62 CCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCTTCAGA-CTGCCTGTCGGCTTTGACCCTAGA
340255 GA
126 GA
* * *
340257 CTGCCTCATCTAAAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTG
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTAAGTCTGCCTG
* * * *
340322 TCGGCTTTGACCCTGGAGACTTTTCTA-CCTTCAGACTGCCTATCGGCTTTGACCCTAAAGA
66 TCGGCTTTGACCCTAGAGACTTTCCTATCCTTCAGACTGCCTGTCGGCTTTGACCCTAGAGA
* * * * * * *
340383 CTGCCTTATCTAAAGTCTACCTATCGACTTTGATCCTGAAGACTTTT-TCACCCTTAAGTTTGCC
1 CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCT-ACCC-TAAGTCTGCC
*
340447 TGTTGGCTTTGAC
64 TGTCGGCTTTGAC
340460 TCGAGGACCT
Statistics
Matches: 451, Mismatches: 104, Indels: 56
0.74 0.17 0.09
Matches are distributed among these distances:
124 1 0.00
125 10 0.02
126 210 0.47
127 162 0.36
128 64 0.14
129 4 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (127 bp):
CTGCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTAAGTCTGCCTG
TCGGCTTTGACCCTAGAGACTTTCCTATCCTTCAGACTGCCTGTCGGCTTTGACCCTAGAGA
Found at i:341541 original size:20 final size:20
Alignment explanation
Indices: 341516--341722 Score: 161
Period size: 20 Copynumber: 10.8 Consensus size: 20
341506 GAAAGTTGTG
*
341516 AAAGCATGAAATGATGATAC
1 AAAGCATGAAATGATGATGC
* *
341536 AAAGCATGTAACG-TGGATGC
1 AAAGCATGAAATGAT-GATGC
*
341556 -AAGTATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* *
341575 AAAGCATG-AAGGTTG-TG-
1 AAAGCATGAAATGATGATGC
341592 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
341612 AAAGCATGTAACATG--GATGC
1 AAAGCATG-AA-ATGATGATGC
*
341632 -AAGTATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* *
341651 AAAGCATG-AAGGTTG-TG-
1 AAAGCATGAAATGATGATGC
**
341668 AAAATATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* *
341688 AAAGCATGTAACG-TGGATGC
1 AAAGCATGAAATGAT-GATGC
*
341708 -AAGTATGAAATGATG
1 AAAGCATGAAATGATG
341723 CAGTAAACAA
Statistics
Matches: 145, Mismatches: 26, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
17 17 0.12
18 16 0.11
19 51 0.35
20 56 0.39
21 2 0.01
22 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.23
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:341565 original size:39 final size:39
Alignment explanation
Indices: 341521--341722 Score: 286
Period size: 39 Copynumber: 5.3 Consensus size: 39
341511 TTGTGAAAGC
*
341521 ATGAAATGATGATACAAAGCATGTAACGTGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
* * * *
341560 ATGAAATGATGATGCAAAGCATG-AAGGTTG-TGAAAGC
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
*
341597 ATGAAATGATGATGCAAAGCATGTAACATGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
* * * *
341636 ATGAAATGATGATGCAAAGCATG-AAGGTTG-TGAAAAT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
341673 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
341712 ATGAAATGATG
1 ATGAAATGATG
341723 CAGTAAACAA
Statistics
Matches: 140, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
37 56 0.40
38 18 0.13
39 66 0.47
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.23
Consensus pattern (39 bp):
ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
Found at i:341592 original size:76 final size:76
Alignment explanation
Indices: 341504--341722 Score: 393
Period size: 76 Copynumber: 2.9 Consensus size: 76
341494 TGATAAATGA
* *
341504 ATGAAAGTTGTGAAAGCATGAAATGATGATACAAAGCATGTAACGTGGATGCAAGTATGAAATGA
1 ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGTATGAAATGA
341569 TGATGCAAAGC
66 TGATGCAAAGC
*
341580 ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGCATGTAACATGGATGCAAGTATGAAATGA
1 ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGTATGAAATGA
341645 TGATGCAAAGC
66 TGATGCAAAGC
**
341656 ATGAAGGTTGTGAAAATATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGTATGAAATGA
1 ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGTATGAAATGA
341721 TG
66 TG
341723 CAGTAAACAA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 137 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.23
Consensus pattern (76 bp):
ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGTATGAAATGA
TGATGCAAAGC
Found at i:342598 original size:20 final size:20
Alignment explanation
Indices: 342548--342598 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
342538 CTTTTGTTAG
*
342548 TTGATTTTTTTTATATATAT
1 TTGATTTTTTGTATATATAT
*
342568 TTG-TTTGTTTGTGTATAT-T
1 TTGATTT-TTTGTATATATAT
342587 TTGATTTATTTG
1 TTGATTT-TTTG
342599 AAAATCTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.69
Consensus pattern (20 bp):
TTGATTTTTTGTATATATAT
Found at i:345477 original size:23 final size:23
Alignment explanation
Indices: 345451--345495 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
345441 AATTTATCTT
*
345451 TAAAA-AATAAATAGATCATAAAA
1 TAAAATAA-AAATAGAACATAAAA
*
345474 TAAAATAAAAATATAACATAAA
1 TAAAATAAAAATAGAACATAAA
345496 GAGAAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAAATAAAAATAGAACATAAAA
Found at i:347273 original size:6 final size:7
Alignment explanation
Indices: 347226--347266 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
347216 ACAAGTTTAA
347226 TTCCTTT
1 TTCCTTT
347233 TTCCTTT
1 TTCCTTT
347240 TTCCTTT
1 TTCCTTT
347247 TTCCTTT
1 TTCCTTT
347254 TTCC-TT
1 TTCCTTT
347260 TTCCTTT
1 TTCCTTT
347267 CCTTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TTCCTTT
Found at i:348487 original size:23 final size:23
Alignment explanation
Indices: 348461--348538 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 23
348451 AATATATTTT
348461 AATAAATTAAAGATTATATTAAA
1 AATAAATTAAAGATTATATTAAA
* * *
348484 AATAAATTATCATGTTTCTATTAAA
1 AATAAATTA--AAGATTATATTAAA
348509 TAAT-AATTAAA-A-TATATTAAA
1 -AATAAATTAAAGATTATATTAAA
348530 AATAAATTA
1 AATAAATTA
348539 TTTAAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 3 0.07
21 13 0.29
23 10 0.22
25 16 0.36
26 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
AATAAATTAAAGATTATATTAAA
Found at i:348571 original size:14 final size:14
Alignment explanation
Indices: 348518--348575 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
348508 ATAATAATTA
348518 AAATATATTAAAAAT
1 AAATA-ATTAAAAAT
*
348533 AAATTATTTAAATAAAT
1 AAA-TAATT-AA-AAAT
348550 ATAA-AATTAAAAAT
1 A-AATAATTAAAAAT
348564 AAATAATTAAAA
1 AAATAATTAAAA
348576 CTTAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 13 0.36
15 7 0.19
16 7 0.19
17 5 0.14
18 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAATTAAAAAT
Found at i:349247 original size:21 final size:20
Alignment explanation
Indices: 349222--349271 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
349212 TTAAATAATA
* *
349222 ATTTTTTAACTATTATTTTTT
1 ATTTTTTAA-TATAAATTTTT
*
349243 ATTTTTGAATATAAATTTTT
1 ATTTTTTAATATAAATTTTT
349263 ATTTTTTAA
1 ATTTTTTAA
349272 AATGATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTTAATATAAATTTTT
Found at i:349681 original size:2 final size:2
Alignment explanation
Indices: 349674--349703 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
349664 CTAACTGTTC
349674 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
349704 AATCAATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:350478 original size:2 final size:2
Alignment explanation
Indices: 350421--350461 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
350411 TGTGTGTGTG
350421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
350462 GTACGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:350532 original size:14 final size:14
Alignment explanation
Indices: 350496--350535 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
350486 ACCCACACAC
350496 ATATATGTATATAT
1 ATATATGTATATAT
* * *
350510 TTGTGTGTATATAT
1 ATATATGTATATAT
350524 ATATATGTATAT
1 ATATATGTATAT
350536 GTTTTCATGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:350546 original size:28 final size:28
Alignment explanation
Indices: 350496--350550 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
350486 ACCCACACAC
*
350496 ATATATGTATATATTTGTGTGTATATAT
1 ATATATGTATATATTTGTATGTATATAT
*
350524 ATATATGTATATGTTT-TCATGTATATA
1 ATATATGTATATATTTGT-ATGTATATA
350551 GAGATGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.53
Consensus pattern (28 bp):
ATATATGTATATATTTGTATGTATATAT
Found at i:357790 original size:2 final size:2
Alignment explanation
Indices: 357783--357809 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
357773 TAGTCTTTTC
357783 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
357810 GTATGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:359360 original size:3 final size:3
Alignment explanation
Indices: 359352--359377 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
359342 TTGTAGATGT
359352 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
359378 GAAAAGAAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:360085 original size:44 final size:44
Alignment explanation
Indices: 360006--360092 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
359996 GAATAATTCG
*
360006 TAAATAAATTAATTAAAATTATTTATACTCATTTAATAAAATAAA
1 TAAATAAATTAAATAAAATTATTTATACTCATTTAA-AAAATAAA
360051 TAAATAAATATAAATAAAA-T-TTTA-AGCTCATTTAAAAAATAA
1 TAAATAAAT-TAAATAAAATTATTTATA-CTCATTTAAAAAATAA
360093 TTAATCTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
43 8 0.21
44 13 0.33
45 10 0.26
46 8 0.21
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (44 bp):
TAAATAAATTAAATAAAATTATTTATACTCATTTAAAAAATAAA
Found at i:360591 original size:24 final size:23
Alignment explanation
Indices: 360527--360597 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
360517 ACTTTGAACC
*
360527 AAATATTATTATTAATAAAAATATT
1 AAATATT-TTAAT-ATAAAAATATT
* *
360552 TAAT-TTTTAATTTAAAAATATT
1 AAATATTTTAATATAAAAATATT
*
360574 AAAATATTTTAATATAAAATTATT
1 -AAATATTTTAATATAAAAATATT
360598 TTAATAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 10 0.26
23 7 0.18
24 18 0.47
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTTTAATATAAAAATATT
Found at i:360597 original size:16 final size:16
Alignment explanation
Indices: 360568--360603 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
360558 TTAATTTAAA
360568 AATATTAAAATATTTT
1 AATATTAAAATATTTT
360584 AATA-TAAAATTATTTT
1 AATATTAAAA-TATTTT
360600 AATA
1 AATA
360604 ATATAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTAAAATATTTT
Found at i:360671 original size:22 final size:23
Alignment explanation
Indices: 360646--360692 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
360636 TAAACATACA
360646 TATTTA-TATTTTT-ATAATATAT
1 TATTTATTATTTTTAATAATA-AT
360668 TA-TTATTATTTTTAATAATAAT
1 TATTTATTATTTTTAATAATAAT
360690 TAT
1 TAT
360693 ATTAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.14
22 13 0.59
23 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTATTATTTTTAATAATAAT
Found at i:360691 original size:16 final size:16
Alignment explanation
Indices: 360672--360755 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
360662 ATATATTATT
360672 ATTATTTTTAATAATA
1 ATTATTTTTAATAATA
*
360688 ATTA-TATTAATAAT-
1 ATTATTTTTAATAATA
360702 -TTACTATTTTAATAA-A
1 ATTA-T-TTTTAATAATA
*
360718 ATTATTATTTAATATAAA
1 ATTATT-TTTAATA-ATA
360736 TATTATTATTTTAATAATA
1 -ATTA-T-TTTTAATAATA
360755 A
1 A
360756 ATTGTGACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
13 3 0.06
15 10 0.19
16 20 0.37
17 4 0.07
18 2 0.04
19 6 0.11
20 8 0.15
21 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTTTTAATAATA
Found at i:360742 original size:19 final size:21
Alignment explanation
Indices: 360711--360757 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
360701 TTTACTATTT
360711 TAATAAA-ATTATTA-TTTAA
1 TAATAAATATTATTATTTTAA
360730 T-ATAAATATTATTATTTTAA
1 TAATAAATATTATTATTTTAA
360750 TAATAAAT
1 TAATAAAT
360758 TGTGACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 6 0.24
21 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATAAATATTATTATTTTAA
Found at i:361215 original size:21 final size:20
Alignment explanation
Indices: 361168--361215 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
361158 CTAATTTATA
361168 TTAATATAACATAATTATTT
1 TTAATATAACATAATTATTT
* *
361188 TTAAATATTATATAATTAATTT
1 TT-AATATAACATAATT-ATTT
361210 TTAATA
1 TTAATA
361216 GATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATATAACATAATTATTT
Found at i:361678 original size:3 final size:3
Alignment explanation
Indices: 361670--361700 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
361660 TACATGCAAG
361670 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
361701 TCTGTCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:363221 original size:2 final size:2
Alignment explanation
Indices: 363214--363239 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
363204 TTCTGAATCC
363214 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
363240 GAAACATTCA
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):
TA
Found at i:364603 original size:3 final size:3
Alignment explanation
Indices: 364595--364620 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
364585 ATTATTCTTC
364595 CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CC
364621 ACAGATATAT
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:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:365227 original size:25 final size:26
Alignment explanation
Indices: 365193--365247 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
365183 ATCTAATTAA
365193 ATTTGAAATGAAAAT-TTTTAAAATT
1 ATTTGAAATGAAAATATTTTAAAATT
**
365218 CATTT-AAATGTTAATATTTTAAAATT
1 -ATTTGAAATGAAAATATTTTAAAATT
365244 ATTT
1 ATTT
365248 TGTTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTTGAAATGAAAATATTTTAAAATT
Found at i:365668 original size:22 final size:21
Alignment explanation
Indices: 365643--365685 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
365633 TGAAATATAT
365643 ATATATTACAAA-TAATATAAAA
1 ATATATTA-AAATTAA-ATAAAA
365665 ATATATTAAAATTAAATAAAA
1 ATATATTAAAATTAAATAAAA
365686 TAATAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATATTAAAATTAAATAAAA
Found at i:366410 original size:29 final size:30
Alignment explanation
Indices: 366348--366417 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
366338 TATAATTATT
* * * *
366348 AATTAATTTTATGTAAAAAATTATATTTTTA
1 AATT-ATTTTATATAAAAAAATATAATTTAA
366379 AATTATTTTATATAAAAAAATA-AATTTAA
1 AATTATTTTATATAAAAAAATATAATTTAA
*
366408 AATTTTTTTA
1 AATTATTTTA
366418 AATTGATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 14 0.41
30 16 0.47
31 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
AATTATTTTATATAAAAAAATATAATTTAA
Found at i:369614 original size:51 final size:51
Alignment explanation
Indices: 369546--369713 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
369536 TCGAAAATAA
* *
369546 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
* *** * * *
369597 CGGGGTTGGAGTATCCCCGATTA-AAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGA-G-AAATCAATATTTTGGAAATAAAGC
* *
369649 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
*
369700 CGAGGTTGGAGTAT
1 CGGGGTTGGAGTAT
369714 TCCCTCGGAA
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 1 0.01
51 53 0.56
52 40 0.42
53 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
Found at i:369734 original size:28 final size:26
Alignment explanation
Indices: 369703--369774 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
369693 ATAAAGTCGA
369703 GGTTGGAGTATTCCCTCG-GAAATAACGG
1 GGTTGGAGTA-TCCC-CGAG-AATAACGG
*
369731 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGA-GAATAACGG
*
369758 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
369775 TTGTGAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.05
27 27 0.68
28 11 0.28
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (26 bp):
GGTTGGAGTATCCCCGAGAATAACGG
Found at i:372331 original size:19 final size:18
Alignment explanation
Indices: 372307--372374 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
372297 CAGTAGCTAA
372307 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
372326 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
372341 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
372358 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
372375 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:372347 original size:13 final size:13
Alignment explanation
Indices: 372329--372353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372319 ACAATACTTA
372329 TGTATCGATACAT
1 TGTATCGATACAT
372342 TGTATCGATACA
1 TGTATCGATACA
372354 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:372351 original size:32 final size:32
Alignment explanation
Indices: 372310--372372 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
372300 TAGCTAATTA
*
372310 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
372342 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
372373 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:377931 original size:17 final size:17
Alignment explanation
Indices: 377909--377970 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
377899 CAATAATATT
*
377909 TAAATTTTTTATTTATA
1 TAAATTTTATATTTATA
377926 TAAATTTTAATATATTA-A
1 TAAATTTT-ATAT-TTATA
377944 T-AA-TTTATA-TTATA
1 TAAATTTTATATTTATA
377958 TAAATTTTTATAT
1 TAAA-TTTTATAT
377971 GATGTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 5 0.14
16 3 0.08
17 16 0.43
18 5 0.14
19 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTTTATATTTATA
Found at i:377990 original size:33 final size:32
Alignment explanation
Indices: 377920--377991 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
377910 AAATTTTTTA
*
377920 TTTATATAAATTTTAATATATTAATAATTTAT
1 TTTATATAAATTTTAATATATTAATAATTCAT
* * *
377952 ATTATATAAATTTTTATATGATGTTAT-ATTCAT
1 TTTATATAAATTTTAATAT-AT-TAATAATTCAT
377985 TTTATAT
1 TTTATAT
377992 TGCATAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 17 0.52
33 13 0.39
34 3 0.09
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (32 bp):
TTTATATAAATTTTAATATATTAATAATTCAT
Found at i:378024 original size:11 final size:11
Alignment explanation
Indices: 378008--378053 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
377998 ATGTATTAAT
378008 TATTTTATTTA
1 TATTTTATTTA
378019 TATTTTATTTA
1 TATTTTATTTA
378030 TATAATTATATTTA
1 TAT--TT-TATTTA
378044 -ATTTT-TTTA
1 TATTTTATTTA
378053 T
1 T
378054 GTCTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
9 4 0.13
10 1 0.03
11 16 0.52
13 4 0.13
14 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTATTTA
Found at i:379528 original size:2 final size:2
Alignment explanation
Indices: 379521--379558 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
379511 AAATAAAAGA
379521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
379559 TTGGGCGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380987 original size:100 final size:95
Alignment explanation
Indices: 380793--381036 Score: 278
Period size: 100 Copynumber: 2.5 Consensus size: 95
380783 TTTTTGGTTG
* * * * * *
380793 AAAAACAGGGTTTGAGTATTCC-CTCGAAAGAATGGGTTGAAGTATCCGGATGATGATAATTTAG
1 AAAAAAAGGGTTGGAGCA-TCCTCTCGAAAGAATGGGTTGGAGTATCCCGATGATGATAATTTAA
* ***
380857 GTAAAAATAAGATTTAAATCTTGTTTAGTTTTT
65 GCAAAAATAAGATTTAAATCTTGACAAG--TTT
380890 AAAAAAACGGGGTTGGAGCAT-CTCTTC-AGAAGAATGGGTTGGAGTATCCTCGATGATGATAAT
1 AAAAAAA--GGGTTGGAGCATCCTC-TCGA-AAGAATGGGTTGGAGTATCC-CGATGATGATAAT
380953 TTAAGCAAAAATAAGATTTAAATCTTGACAAGTTT
61 TTAAGCAAAAATAAGATTTAAATCTTGACAAGTTT
* *
380988 AAAAATAGGGTTGGAGTATCCTCTCGAAAGAATGGGGTTGGAGTATCCC
1 AAAAAAAGGGTTGGAGCATCCTCTCGAAAGAAT-GGGTTGGAGTATCCC
381037 CGTGAATAAC
Statistics
Matches: 126, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
96 20 0.16
97 25 0.20
98 12 0.10
99 30 0.24
100 39 0.31
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (95 bp):
AAAAAAAGGGTTGGAGCATCCTCTCGAAAGAATGGGTTGGAGTATCCCGATGATGATAATTTAAG
CAAAAATAAGATTTAAATCTTGACAAGTTT
Found at i:383339 original size:21 final size:20
Alignment explanation
Indices: 383315--383361 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
383305 TCCAAGATTG
383315 ATACATGCACTTAATGTATCA
1 ATACATGCACTT-ATGTATCA
** *
383336 ATACATTTACTTATGTATCG
1 ATACATGCACTTATGTATCA
383356 ATACAT
1 ATACAT
383362 TAACAGGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (20 bp):
ATACATGCACTTATGTATCA
Found at i:383353 original size:20 final size:21
Alignment explanation
Indices: 383323--383362 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
383313 TGATACATGC
383323 ACTTAATGTATCAATACATTT
1 ACTTAATGTATCAATACATTT
*
383344 ACTT-ATGTATCGATACATT
1 ACTTAATGTATCAATACATT
383363 AACAGGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (21 bp):
ACTTAATGTATCAATACATTT
Found at i:385061 original size:21 final size:21
Alignment explanation
Indices: 385035--385082 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
385025 CAAGACGGAG
*
385035 AATCTTGAGACTTGGAAGGCA
1 AATCTTGAGACCTGGAAGGCA
*
385056 AATCTTGAGGCCTGGAAGGCA
1 AATCTTGAGACCTGGAAGGCA
385077 AATCTT
1 AATCTT
385083 ACTAGGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (21 bp):
AATCTTGAGACCTGGAAGGCA
Found at i:386482 original size:15 final size:15
Alignment explanation
Indices: 386451--386510 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
386441 AAACAAAAAG
* *
386451 TTTTAAATTTATTAA
1 TTTTAAAATTATAAA
*
386466 TTTGAAAATTATAAA
1 TTTTAAAATTATAAA
*
386481 TTTTAAATTTA-AAA
1 TTTTAAAATTATAAA
386495 TTTTAAAATT-TAAA
1 TTTTAAAATTATAAA
386509 TT
1 TT
386511 CAAATCTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 17 0.45
15 21 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTAAAATTATAAA
Found at i:386487 original size:7 final size:7
Alignment explanation
Indices: 386451--386510 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
386441 AAACAAAAAG
386451 TTTTAAA
1 TTTTAAA
*
386458 TTTATTAA
1 TTT-TAAA
*
386466 TTTGAAAA
1 TTT-TAAA
*
386474 TTATAAA
1 TTTTAAA
386481 TTTTAAA
1 TTTTAAA
*
386488 TTTAAAA
1 TTTTAAA
386495 TTTTAAA
1 TTTTAAA
*
386502 ATTTAAA
1 TTTTAAA
386509 TT
1 TT
386511 CAAATCTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 31 0.76
8 10 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
TTTTAAA
Found at i:387153 original size:24 final size:23
Alignment explanation
Indices: 387097--387154 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
387087 ATAATATTTT
387097 TATTTAAAT-TTAATTATAAAAA
1 TATTTAAATATTAATTATAAAAA
*
387119 TATATAAATATTAA-TATAAAATAA
1 TATTTAAATATTAATTAT-AAA-AA
*
387143 TTTTTAAATATT
1 TATTTAAATATT
387155 TTAATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.37
23 7 0.23
24 12 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAATATTAATTATAAAAA
Found at i:387399 original size:2 final size:2
Alignment explanation
Indices: 387394--387435 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
387384 CTCTATATTC
*
387394 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
387436 GTATGTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388336 original size:50 final size:49
Alignment explanation
Indices: 388265--388365 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 49
388255 TCAACCATTT
388265 AAAAGAAGAGAAATTATTTCATCAATGCCGATTAGATCTAGCAAAATTA
1 AAAAGAAGAGAAATTATTTCATCAATGCCGATTAGATCTAGCAAAATTA
* *
388314 AAAAGGAAGAGAAATTATTTCATCAATGGCTATTAGATCTAGCAAAATTA
1 AAAA-GAAGAGAAATTATTTCATCAATGCCGATTAGATCTAGCAAAATTA
388364 AA
1 AA
388366 TATAATTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 4 0.08
50 45 0.92
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.27
Consensus pattern (49 bp):
AAAAGAAGAGAAATTATTTCATCAATGCCGATTAGATCTAGCAAAATTA
Found at i:388483 original size:27 final size:28
Alignment explanation
Indices: 388430--388486 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
388420 ATTAAAATCT
388430 ATGTAATATAAATTATTAAAATATTAAA
1 ATGTAATATAAATTATTAAAATATTAAA
*
388458 ATGT-ATATAAA-TA-TAAAATACTTTAA
1 ATGTAATATAAATTATTAAAATA-TTAAA
388484 ATG
1 ATG
388487 AGATAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
26 9 0.33
27 7 0.26
28 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
ATGTAATATAAATTATTAAAATATTAAA
Found at i:388492 original size:25 final size:27
Alignment explanation
Indices: 388437--388492 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
388427 TCTATGTAAT
*
388437 ATAAATTATTAAAATATTAAAATGTAT
1 ATAAATTATTAAAATATTAAAATGTAG
*
388464 ATAAA-TA-TAAAATACTTTAAATG-AG
1 ATAAATTATTAAAATA-TTAAAATGTAG
388489 ATAA
1 ATAA
388493 CAAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 12 0.46
26 9 0.35
27 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (27 bp):
ATAAATTATTAAAATATTAAAATGTAG
Found at i:389867 original size:2 final size:2
Alignment explanation
Indices: 389860--389896 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
389850 TTTAGTAATA
389860 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
389897 GAACTCCAAA
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:390401 original size:8 final size:8
Alignment explanation
Indices: 390390--390427 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
390380 ATAATTTAAA
390390 ATTAAAAT
1 ATTAAAAT
390398 ATTAAAAT
1 ATTAAAAT
390406 ATTAAAAT
1 ATTAAAAT
390414 -TTAAAAT
1 ATTAAAAT
390421 -TTAAAAT
1 ATTAAAAT
390428 TATTTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTAAAAT
Found at i:390419 original size:7 final size:7
Alignment explanation
Indices: 390382--390428 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
390372 ATAAAATCAT
390382 AATTTAA
1 AATTTAA
390389 AA-TTAA
1 AATTTAA
390395 AATATTAA
1 AAT-TTAA
390403 AATATTAA
1 AAT-TTAA
390411 AATTTAA
1 AATTTAA
390418 AATTTAA
1 AATTTAA
390425 AATT
1 AATT
390429 ATTTAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.16
7 17 0.45
8 15 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTTAA
Found at i:392637 original size:15 final size:16
Alignment explanation
Indices: 392610--392639 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
392600 ATTTAAATTA
392610 TTTATTATTATATTTT
1 TTTATTATTATATTTT
392626 TTTATT-TTATATTT
1 TTTATTATTATATTT
392640 ATGTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTATTATATTTT
Found at i:393439 original size:20 final size:20
Alignment explanation
Indices: 393410--393450 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
393400 TTTGAGCAGT
*
393410 TAAAATTATTATTTA-TTAAA
1 TAAAAATATT-TTTATTTAAA
393430 TAAAAATATTTTTATTTAAA
1 TAAAAATATTTTTATTTAAA
393450 T
1 T
393451 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTTTTATTTAAA
Found at i:393480 original size:19 final size:18
Alignment explanation
Indices: 393446--393486 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
393436 TATTTTTATT
393446 TAAATTTAATTAAAAATA
1 TAAATTTAATTAAAAATA
393464 TAAATATTAATATAAAATATA
1 TAAAT-TTAAT-TAAAA-ATA
393485 TA
1 TA
393487 TTTTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 5 0.25
21 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATTTAATTAAAAATA
Found at i:395246 original size:4 final size:4
Alignment explanation
Indices: 395237--395264 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
395227 AAAATCATGA
395237 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
395265 TTGAGCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:402080 original size:52 final size:52
Alignment explanation
Indices: 401932--402060 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
401922 CGAAATATGA
*
401932 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
401984 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
402036 AAATTTGCCTGCGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
402061 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:402087 original size:13 final size:13
Alignment explanation
Indices: 402069--402093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402059 CAAAGATCAG
402069 TGTATCGATACAA
1 TGTATCGATACAA
402082 TGTATCGATACA
1 TGTATCGATACA
402094 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:404056 original size:52 final size:52
Alignment explanation
Indices: 404033--404173 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 52
404023 TTGTTGATAG
* *
404033 TGATGATGCCATGGTGGTGATTAGAATCGGAGTGACTTGGCATCACTAATAA
1 TGATGATGCCATGGTGGTGATTAGAATCAGAGTGACTTGGTATCACTAATAA
* * *
404085 TGATGATGCCATGGTGGCGATTAGAATCAGAGTGACTTGGTATCACTGATGA
1 TGATGATGCCATGGTGGTGATTAGAATCAGAGTGACTTGGTATCACTAATAA
* * * *
404137 TGATGATACCATGGTGGCGATTATAATCGGAGTGACT
1 TGATGATGCCATGGTGGTGATTAGAATCAGAGTGACT
404174 GATAATGATG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (52 bp):
TGATGATGCCATGGTGGTGATTAGAATCAGAGTGACTTGGTATCACTAATAA
Found at i:404182 original size:42 final size:42
Alignment explanation
Indices: 404129--404215 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
404119 ACTTGGTATC
* * *
404129 ACTGATGATGATGATACCATGGTGGCGATTATAATCGGAGTG
1 ACTGATAATGATGACACCATGGTGGCGATTAGAATCGGAGTG
* *
404171 ACTGATAATGATGACACCATGGTGGCGATTAGAATTGGGGTG
1 ACTGATAATGATGACACCATGGTGGCGATTAGAATCGGAGTG
404213 ACT
1 ACT
404216 TGGTGTCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.28
Consensus pattern (42 bp):
ACTGATAATGATGACACCATGGTGGCGATTAGAATCGGAGTG
Found at i:410034 original size:31 final size:28
Alignment explanation
Indices: 409969--410030 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
409959 ACTTACTGGA
409969 AACAACTCACATGCTTTGACACAGTTCC
1 AACAACTCACATGCTTTGACACAGTTCC
*
409997 AACAACTCACATGCTTTGACATAGTTCC
1 AACAACTCACATGCTTTGACACAGTTCC
410025 AACAAC
1 AACAAC
410031 AACTAGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (28 bp):
AACAACTCACATGCTTTGACACAGTTCC
Found at i:412135 original size:21 final size:21
Alignment explanation
Indices: 412093--412132 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
412083 ATTGGACATG
412093 TTAAAATACATGGAACATGGC
1 TTAAAATACATGGAACATGGC
*
412114 TTAAAATCCAT-GAACATGG
1 TTAAAATACATGGAACATGG
412133 GCTGTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
TTAAAATACATGGAACATGGC
Found at i:413081 original size:52 final size:51
Alignment explanation
Indices: 413018--413198 Score: 199
Period size: 52 Copynumber: 3.5 Consensus size: 51
413008 GGATGTATCG
*
413018 ATACATTGAAGAATGTATCGATACATTTGGGTCAAAAACCAAGAATATATT
1 ATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCAAGAATATATT
* ** *
413069 AATACAATGAAGAATGTATCGATACATTTGGGTAAAAAATGTAA-AATATATCG
1 -ATACAATGAAGAATGTATCGATACATTTGGGTCAAAAA-CCAAGAATATAT-T
* * *
413122 ATACAATGAAGAATGTATTGATACATTTGGATC-AAAACC-AGAATGTATCT
1 ATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCAAGAATATAT-T
* * *
413172 ATGCAAT-AAAAATGTATCAATACATTT
1 ATACAATGAAGAATGTATCGATACATTT
413199 TCTTTCCAGA
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
49 18 0.16
50 13 0.12
51 4 0.04
52 73 0.66
53 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (51 bp):
ATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCAAGAATATATT
Done.