Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 185 of 211
Found at i:54741374 original size:25 final size:25
Alignment explanation
Indices: 54741340--54741390 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
54741330 ATATTTATGG
54741340 AAAGTCAAAGATATGAGTATCAAAT
1 AAAGTCAAAGATATGAGTATCAAAT
*
54741365 AAAGTCAAAGATATGGGTATCAAAT
1 AAAGTCAAAGATATGAGTATCAAAT
54741390 A
1 A
54741391 TTGGAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAGTCAAAGATATGAGTATCAAAT
Found at i:54741401 original size:30 final size:30
Alignment explanation
Indices: 54741337--54741425 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
54741327 TCCATATTTA
*
54741337 TGGAAAGTCAAAGATATGAGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
54741364 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
54741392 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
54741423 TGG
1 TGG
54741426 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:54745561 original size:16 final size:18
Alignment explanation
Indices: 54745532--54745565 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54745522 TTTCTTGCTT
54745532 TATTTTATATGAACTTTG
1 TATTTTATATGAACTTTG
54745550 TATTTT-TA-GAACTTTG
1 TATTTTATATGAACTTTG
54745566 AAGTTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (18 bp):
TATTTTATATGAACTTTG
Found at i:54746342 original size:24 final size:24
Alignment explanation
Indices: 54746314--54746366 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
54746304 ATTAGTAGGT
*
54746314 TAAATAAACTAT-GCTAATAAATGC
1 TAAATAAACTATAG-TAATAAATAC
* *
54746338 TAAATATATTATAGTAATAAATAC
1 TAAATAAACTATAGTAATAAATAC
54746362 TAAAT
1 TAAAT
54746367 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATAGTAATAAATAC
Found at i:54770373 original size:102 final size:102
Alignment explanation
Indices: 54770197--54770427 Score: 381
Period size: 102 Copynumber: 2.3 Consensus size: 102
54770187 ATTGAATATA
54770197 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * *
54770262 GGTTGCTAAGTGCTGATTCCACCGTATTTTATATGTG
66 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
* * *
54770299 AAGGGGGTTGCTCAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCTCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
54770364 GGTTGCTAAGTGTTGATCCCACCATATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
*
54770401 AAAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
54770428 GAATCACTGG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 119 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
Found at i:54778993 original size:22 final size:22
Alignment explanation
Indices: 54778968--54779016 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54778958 TCCTTTATTC
54778968 ATCATCCCTCAAGAATCCCTTA
1 ATCATCCCTCAAGAATCCCTTA
* * *
54778990 ATCATTCTTCAAGGATCCCTTA
1 ATCATCCCTCAAGAATCCCTTA
*
54779012 TTCAT
1 ATCAT
54779017 TCTCATCACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (22 bp):
ATCATCCCTCAAGAATCCCTTA
Found at i:54779017 original size:22 final size:22
Alignment explanation
Indices: 54778976--54779019 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54778966 TCATCATCCC
54778976 TCAAGAATCCCTTAATCATTCT
1 TCAAGAATCCCTTAATCATTCT
* *
54778998 TCAAGGATCCCTTATTCATTCT
1 TCAAGAATCCCTTAATCATTCT
54779020 CATCACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (22 bp):
TCAAGAATCCCTTAATCATTCT
Found at i:54788571 original size:20 final size:20
Alignment explanation
Indices: 54788546--54788584 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54788536 TGTAATTACC
54788546 GGTTGTTCATCTAGATCACA
1 GGTTGTTCATCTAGATCACA
*
54788566 GGTTGTTCATCTCGATCAC
1 GGTTGTTCATCTAGATCAC
54788585 GGTAATGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (20 bp):
GGTTGTTCATCTAGATCACA
Found at i:54799334 original size:11 final size:11
Alignment explanation
Indices: 54799318--54799342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54799308 TGGTTGAGCC
54799318 CTTTCTGATAG
1 CTTTCTGATAG
54799329 CTTTCTGATAG
1 CTTTCTGATAG
54799340 CTT
1 CTT
54799343 GTCCCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (11 bp):
CTTTCTGATAG
Found at i:54827288 original size:27 final size:27
Alignment explanation
Indices: 54827250--54827305 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
54827240 ATCCACATAG
54827250 TCGTACAAATCTTGAAGATAGGTCAGT
1 TCGTACAAATCTTGAAGATAGGTCAGT
54827277 TCGTACAAATCTTGAAGATAGGTCAGT
1 TCGTACAAATCTTGAAGATAGGTCAGT
54827304 TC
1 TC
54827306 ATGTCCTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (27 bp):
TCGTACAAATCTTGAAGATAGGTCAGT
Found at i:54830677 original size:42 final size:42
Alignment explanation
Indices: 54830624--54830703 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
54830614 CTATCCATGC
54830624 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
1 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
* *
54830666 ATGTGTGTAACTTTTCATCTTCAAGTCTCTTCACTCTT
1 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTT
54830704 TTAACTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (42 bp):
ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
Found at i:54834896 original size:21 final size:22
Alignment explanation
Indices: 54834846--54834908 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
54834836 TCAATATTTG
54834846 GAGAAATAAAATA-AA-GAAAAT
1 GAGAAA-AAAATATAATGAAAAT
*
54834867 GATAAAAAAATATAATGAAAA-
1 GAGAAAAAAATATAATGAAAAT
*
54834888 GAGAAAAAAATTTATATGAAA
1 GAGAAAAAAATATA-ATGAAA
54834909 GAAATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.17
21 19 0.53
22 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (22 bp):
GAGAAAAAAATATAATGAAAAT
Found at i:54834909 original size:21 final size:20
Alignment explanation
Indices: 54834870--54834919 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
54834860 AGAAAATGAT
*
54834870 AAAAAAATATAATGAAAAGA
1 AAAAAAATTTAATGAAAAGA
54834890 GAAAAAAATTTATATG-AAAGA
1 -AAAAAAATTTA-ATGAAAAGA
*
54834911 AATAAAATT
1 AAAAAAATT
54834920 CCTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 15 0.58
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAAAAATTTAATGAAAAGA
Found at i:54834917 original size:22 final size:21
Alignment explanation
Indices: 54834853--54834917 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
54834843 TTGGAGAAAT
*
54834853 AAAATA-AA-GAAAATGATAAA
1 AAAATATAATGAAAA-GAAAAA
*
54834873 AAAATATAATGAAAAGAGAAA
1 AAAATATAATGAAAAGAAAAA
* *
54834894 AAAATTTATATG-AAAGAAATA
1 AAAATATA-ATGAAAAGAAAAA
54834915 AAA
1 AAA
54834918 TTCCTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 6 0.16
21 24 0.63
22 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (21 bp):
AAAATATAATGAAAAGAAAAA
Found at i:54835139 original size:42 final size:42
Alignment explanation
Indices: 54835086--54835169 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
54835076 CTATCCATGC
54835086 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
1 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
* *
54835128 ATGTGTGTAACTTTTCATCTTCAAGTCTCTTCACTCTTCATA
1 ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
54835170 TTCAAGTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (42 bp):
ATGTGTATAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
Found at i:54835173 original size:23 final size:23
Alignment explanation
Indices: 54835099--54835188 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
54835089 TGTATAACTT
54835099 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
54835122 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
*
54835141 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
*
54835164 TTCATATTCAAGTCTCTTCATTC
1 TTCATATTCAAGTCTCTTCACTC
54835187 TT
1 TT
54835189 TTAACTTTTC
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
22 4 0.08
23 33 0.66
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.47
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:54836443 original size:42 final size:42
Alignment explanation
Indices: 54836391--54836637 Score: 302
Period size: 42 Copynumber: 5.8 Consensus size: 42
54836381 CAAACATAAA
* * **
54836391 CGCCGCTAAAGACCATATTCTTTAGCGGCGTTTTTGTT-TGTG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TTCTAAG
*
54836433 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
* * * * *
54836475 TGCCTCTAAAGAGCATGTTCTTTAGCGGCATTTTTTTTCTATG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGC-GTTTTTTTCTAAG
* *
54836518 CGCCGCTAAAGAACATGGTT-TTTAACGGCGTTTTTTTCTAGG
1 CGCCGCTAAAGAACAT-GTTCTTTAGCGGCGTTTTTTTCTAAG
*
54836560 CGCCGCTAAAGAACATAG-TCTTTAGTGGCGTCTTTTTTCTAAG
1 CGCCGCTAAAGAACAT-GTTCTTTAGCGGCGT-TTTTTTCTAAG
*
54836603 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
54836638 ATACAAAAAC
Statistics
Matches: 178, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.02
42 103 0.58
43 69 0.39
44 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:54836547 original size:85 final size:85
Alignment explanation
Indices: 54836391--54836637 Score: 320
Period size: 85 Copynumber: 2.9 Consensus size: 85
54836381 CAAACATAAA
* * * * *
54836391 CGCCGCTAAAGACCATATTCTTTAGCGGCGTTTTTGTT-TGTGCGCCTCTAAAGAACATGTTCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTCTATGCGCCGCTAAAGAACATGTTCTT
54836455 TAGCGGCGTTTTTTTCTAAG
66 TAGCGGCGTTTTTTTCTAAG
* * * *
54836475 TGCCTCTAAAGAGCATGTTCTTTAGCGGCATTTTTTTTCTATGCGCCGCTAAAGAACATGGTT-T
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTCTATGCGCCGCTAAAGAACAT-GTTCT
* *
54836539 TTAACGGCGTTTTTTTCTAGG
65 TTAGCGGCGTTTTTTTCTAAG
* * *
54836560 CGCCGCTAAAGAACATAG-TCTTTAGTGGCGTCTTTTTTCTAAGCGCCGCTAAAGAACATGTTCT
1 CGCCGCTAAAGAACAT-GTTCTTTAGCGGCGTTTTTTTTCTATGCGCCGCTAAAGAACATGTTCT
*
54836624 TTAGCGGCGCTTTT
65 TTAGCGGCGTTTTT
54836638 ATACAAAAAC
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
84 35 0.25
85 101 0.72
86 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTCTATGCGCCGCTAAAGAACATGTTCTT
TAGCGGCGTTTTTTTCTAAG
Found at i:54837024 original size:21 final size:21
Alignment explanation
Indices: 54836956--54837026 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
54836946 TTTTGCTCTG
*
54836956 CTCTGCTTCTCTCGCTGT-AGC
1 CTCTGCTTCCCTCGCT-TCAGC
* *
54836977 CTCCGCTTCCCTTG-TTGCAGC
1 CTCTGCTTCCCTCGCTT-CAGC
* *
54836998 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTTCAGC
54837019 CTCTGCTT
1 CTCTGCTT
54837027 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 35 0.90
22 2 0.05
ACGTcount: A:0.03, C:0.44, G:0.18, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:54842624 original size:25 final size:23
Alignment explanation
Indices: 54842596--54842729 Score: 83
Period size: 25 Copynumber: 5.4 Consensus size: 23
54842586 CATGTAAGTA
*
54842596 ATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTTATGT-A-TAATGTATT
* *
54842621 ATGTAAGTTGTGTACTACAT-CATT
1 ATGTAAGTTATGTA-TA-ATGTATT
* *
54842645 ATGTGAGTTGTGTATAATGTATGTT
1 ATGTAAGTTATGTATAATGTA--TT
* *
54842670 AAG-AAGGTTATGTATAATGTAAGTA
1 ATGTAA-GTTATGTATAATGT-A-TT
*
54842695 ATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTTATGT-A-TAATGTATT
54842720 ATGTAAGTTA
1 ATGTAAGTTA
54842730 AGAAGGTTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 20 0.23
25 50 0.58
26 5 0.06
27 6 0.07
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAAGTTATGTATAATGTATT
Found at i:54842626 original size:34 final size:34
Alignment explanation
Indices: 54842587--54842727 Score: 105
Period size: 34 Copynumber: 4.2 Consensus size: 34
54842577 TGTATGCCAC
54842587 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
** ** * *
54842621 ATGTAAGTTGTGT-A-CTACATCA-TTATGTGAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * * * *
54842654 GTGT-A-TAATGTATGTTAAG-AAGGTTATGTATA
1 ATGTAAGTAATGTAAGCTATGTAA-GTAATGTATT
54842686 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
54842720 ATGTAAGT
1 ATGTAAGT
54842728 TAAGAAGGTT
Statistics
Matches: 77, Mismatches: 21, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
31 9 0.12
32 12 0.16
33 10 0.13
34 44 0.57
35 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (34 bp):
ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
Found at i:54842634 original size:16 final size:16
Alignment explanation
Indices: 54842587--54842628 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
54842577 TGTATGCCAC
*
54842587 ATGTAAGTAATGTAAGCT
1 ATGTAAGTAATGT-A-TT
54842605 ATGTAAGTAATGTATT
1 ATGTAAGTAATGTATT
54842621 ATGTAAGT
1 ATGTAAGT
54842629 TGTGTACTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (16 bp):
ATGTAAGTAATGTATT
Found at i:54842696 original size:9 final size:9
Alignment explanation
Indices: 54842686--54843531 Score: 855
Period size: 9 Copynumber: 94.2 Consensus size: 9
54842676 GTTATGTATA
*
54842686 ATGTAAGTA
1 ATGTAAGTT
*
54842695 ATGTAAGCT
1 ATGTAAGTT
*
54842704 ATGTAAGTA
1 ATGTAAGTT
54842713 ATGT-A-TT
1 ATGTAAGTT
54842720 ATGTAAGTT
1 ATGTAAGTT
*
54842729 AAG-AAGGTT
1 ATGTAA-GTT
*
54842738 ATGT-A-TA
1 ATGTAAGTT
54842745 ATGTAAGTT
1 ATGTAAGTT
*
54842754 ACT-TAATTT
1 A-TGTAAGTT
54842763 ATGTAAGTT
1 ATGTAAGTT
54842772 ATGTAAGTT
1 ATGTAAGTT
* *
54842781 ATTTAATTT
1 ATGTAAGTT
*
54842790 ATGTAAGCT
1 ATGTAAGTT
*
54842799 ATGTAATTT
1 ATGTAAGTT
54842808 ATGTAAGTT
1 ATGTAAGTT
54842817 ATGTAAGTT
1 ATGTAAGTT
54842826 ATGTAAGTT
1 ATGTAAGTT
*
54842835 ATTTAA-TT
1 ATGTAAGTT
*
54842843 AACT-TAATTT
1 -A-TGTAAGTT
54842853 ATGTAAGTT
1 ATGTAAGTT
*
54842862 ATGTAAGAT
1 ATGTAAGTT
*
54842871 ATTTAA-TT
1 ATGTAAGTT
54842879 AATGTAAGTT
1 -ATGTAAGTT
54842889 ATGTAAGTT
1 ATGTAAGTT
*
54842898 ACT-TAATTT
1 A-TGTAAGTT
54842907 ATGTAAGTT
1 ATGTAAGTT
54842916 ATGTAAGTT
1 ATGTAAGTT
* *
54842925 ATTTAATTT
1 ATGTAAGTT
54842934 ATGTAAGTT
1 ATGTAAGTT
54842943 ATGTTAAGTT
1 ATG-TAAGTT
* *
54842953 ATTTAATTT
1 ATGTAAGTT
*
54842962 ACT-TAATTT
1 A-TGTAAGTT
54842971 ATGTAAGTT
1 ATGTAAGTT
*
54842980 ATGTAAGAT
1 ATGTAAGTT
*
54842989 ATTTAAGTT
1 ATGTAAGTT
54842998 ATGTAAGTT
1 ATGTAAGTT
54843007 ATGTAAGTT
1 ATGTAAGTT
* *
54843016 ATTTAATTT
1 ATGTAAGTT
54843025 ATGTAAGTT
1 ATGTAAGTT
54843034 ATGTAAGTT
1 ATGTAAGTT
* *
54843043 ATTTAATTT
1 ATGTAAGTT
*
54843052 ACT-TAATTT
1 A-TGTAAGTT
54843061 ATGTAAGTT
1 ATGTAAGTT
54843070 ATGTAAGTT
1 ATGTAAGTT
* *
54843079 ATTTAATTT
1 ATGTAAGTT
54843088 ATGTAAGTT
1 ATGTAAGTT
54843097 ATGTAAGTT
1 ATGTAAGTT
54843106 ATGTTAAGTT
1 ATG-TAAGTT
* *
54843116 ATTTAATTT
1 ATGTAAGTT
*
54843125 ACT-TAATTT
1 A-TGTAAGTT
54843134 ATGTAAGTT
1 ATGTAAGTT
*
54843143 ATGTAAGAT
1 ATGTAAGTT
* *
54843152 ATTTAATTT
1 ATGTAAGTT
54843161 ATGTAAGTT
1 ATGTAAGTT
54843170 ATGTAAGTT
1 ATGTAAGTT
* *
54843179 ATTTAATTT
1 ATGTAAGTT
54843188 ATGTAAGTT
1 ATGTAAGTT
54843197 ATGTAAGTT
1 ATGTAAGTT
* *
54843206 ATTTAATTT
1 ATGTAAGTT
*
54843215 ACT-TAATTT
1 A-TGTAAGTT
54843224 ATGTAAGTT
1 ATGTAAGTT
54843233 ATGTAAGTT
1 ATGTAAGTT
* *
54843242 ATTTAATTT
1 ATGTAAGTT
*
54843251 ACT-TAATTT
1 A-TGTAAGTT
54843260 ATGTAAGTT
1 ATGTAAGTT
54843269 ATGTAAGTT
1 ATGTAAGTT
* *
54843278 ATTTAATTT
1 ATGTAAGTT
54843287 ATGTAAGTT
1 ATGTAAGTT
54843296 ATGTAAGTT
1 ATGTAAGTT
54843305 ATGTAAGTT
1 ATGTAAGTT
54843314 ATGTAAGTT
1 ATGTAAGTT
* *
54843323 ATTTAATTT
1 ATGTAAGTT
*
54843332 ACT-TAATTT
1 A-TGTAAGTT
54843341 ATGTAAGTT
1 ATGTAAGTT
*
54843350 ATGTAAGAT
1 ATGTAAGTT
* *
54843359 ATTTAATTT
1 ATGTAAGTT
54843368 ATGTAAGTT
1 ATGTAAGTT
54843377 ATGTAAGTT
1 ATGTAAGTT
54843386 ATGTAAGTT
1 ATGTAAGTT
* *
54843395 ATTTAATTT
1 ATGTAAGTT
*
54843404 ACT-TAATTT
1 A-TGTAAGTT
*
54843413 ATGTAAGTA
1 ATGTAAGTT
*
54843422 ATGTAAGAT
1 ATGTAAGTT
* *
54843431 ATTTAATTT
1 ATGTAAGTT
54843440 ATGTAAGTT
1 ATGTAAGTT
54843449 ATGTAAGTT
1 ATGTAAGTT
* *
54843458 ATTTAATTT
1 ATGTAAGTT
54843467 ATGTAAGTT
1 ATGTAAGTT
54843476 ATGTAAGTT
1 ATGTAAGTT
54843485 ATGTAAGTT
1 ATGTAAGTT
* *
54843494 ATTTAATTT
1 ATGTAAGTT
*
54843503 TTGTAAGTT
1 ATGTAAGTT
54843512 ATGTAA-TT
1 ATGTAAGTT
54843520 AATGTAAGTT
1 -ATGTAAGTT
54843530 AT
1 AT
54843532 TTAATTTGTG
Statistics
Matches: 701, Mismatches: 102, Indels: 68
0.80 0.12 0.08
Matches are distributed among these distances:
7 10 0.01
8 20 0.03
9 639 0.91
10 32 0.05
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:54842776 original size:59 final size:59
Alignment explanation
Indices: 54842643--54842898 Score: 187
Period size: 63 Copynumber: 4.2 Consensus size: 59
54842633 TACTACATCA
* * *
54842643 TTATGTGAGTTGTGTATAATGTATGTTAAGAAGGTTATGTATAATGTAAGTAATGTAAG
1 TTATGTAAGTTATGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAGTAATGTAAG
* * * * *
54842702 CTATGTAAGTAATGTATTATGTAAGTTAAGAAGGTTATGTATAATGTAAGTTACT-TAAT
1 TTATGTAAGTTATGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAG-TAATGTAAG
* * * * * * *
54842761 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAA-GCTATGTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TAATGTAAGTTAAG-AAGGTTATGT-A-TAATGTAAGTAATGTAAG
* * * * * *
54842824 TTATGTAAGTTATTTAATTAACT-TAATTTATGTAA-GTTATGTAAGATATTTAATTAATGTAAG
1 TTATGTAAGTTATGT-A-TAA-TGTAAGTTAAG-AAGGTTATGT-ATA-ATGTAAGTAATGTAAG
54842887 TTATGTAAGTTA
1 TTATGTAAGTTA
54842899 CTTAATTTAT
Statistics
Matches: 161, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
59 60 0.37
60 4 0.02
61 17 0.11
62 5 0.03
63 74 0.46
64 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.45
Consensus pattern (59 bp):
TTATGTAAGTTATGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAGTAATGTAAG
Found at i:54846608 original size:261 final size:261
Alignment explanation
Indices: 54846063--54846617 Score: 900
Period size: 261 Copynumber: 2.1 Consensus size: 261
54846053 AGAGTAAAAA
*** *
54846063 CGCCACTAATAACACGGACAAAACGGCATCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
1 CGCCACTAATAACAAAAACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
* *
54846128 TATCTAAAGCGCCACTAATAAAAATAGGAAACGGCGTCGTTTCCTCAGCTCGTAATAAATATTTG
66 TAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGTCGTTTCCTCAGCTCGTAATAAATATTTG
*
54846193 TGGCGTTTTTAAACTGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATTACAGTTAAA
131 TGGCGTTTTTAAACTACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATTACAGTTAAA
* *
54846258 GGAAATTTATGGCGTTTCTTCGTAAAACGCCGATAATATATCACCTTTAGCGGCGTTTTTCATAT
196 GGAAATTTATGGCGTTTCTTCGTAAAACGCCGATAAAATATCACCTTTAGCGGCGTTTTTCAAAT
54846323 G
261 G
* *
54846324 CGCCACTAATAACAAAGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTT
1 CGCCACTAATAACAAAAACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
54846389 TAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGTCGTTTCCTCAGCTCGTAATAAATATTTG
66 TAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGTCGTTTCCTCAGCTCGTAATAAATATTTG
* * *
54846454 TGGCGTTTTTAAA-TATGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTATTATAGTTAAA
131 TGGCGTTTTTAAACTACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATTACAGTTAAA
* * *
54846518 GGAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAAAATATCACTTTTAGCGGCGTTTTTCAAAT
196 GGAAATTTATGGCGTTTCTTCGTAAAACGCCGATAAAATATCACCTTTAGCGGCGTTTTTCAAAT
54846583 G
261 G
*
54846584 CGCCACTAA-AGGA-AAACAACAAAACGGCATCGTC
1 CGCCACTAATA--ACAAA-AACAAAACGGCACCGTC
54846618 TTTGTTACAG
Statistics
Matches: 273, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
259 1 0.00
260 120 0.44
261 152 0.56
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (261 bp):
CGCCACTAATAACAAAAACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
TAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGTCGTTTCCTCAGCTCGTAATAAATATTTG
TGGCGTTTTTAAACTACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATTACAGTTAAA
GGAAATTTATGGCGTTTCTTCGTAAAACGCCGATAAAATATCACCTTTAGCGGCGTTTTTCAAAT
G
Found at i:54846674 original size:115 final size:114
Alignment explanation
Indices: 54846455--54846692 Score: 354
Period size: 115 Copynumber: 2.1 Consensus size: 114
54846445 AAATATTTGT
* *
54846455 GGCGTTTTTAAATATGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTATTATAGTTAAAGG
1 GGCGTTTTTAAATACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTATTACAGTTAAAGG
* *
54846520 AAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAAAATATCACTTTTAGC
66 AAATTTGTGGCGTTTCTTCGTAAAACGCCGATAAAATATCACCTTTAGC
* * * *
54846569 GGCGTTTTTCAAATGCGCCACTAAAGGAAAACAACAAAACGGCATCGTCTTTGTTACAGTTAAAG
1 GGCGTTTTT-AAATACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTATTACAGTTAAAG
*
54846634 GAAATTTGCT-GCGTTTCTTCAG-AAAACGCCGATAATATATCACCTTTAGC
65 GAAATTTG-TGGCGTTTCTTC-GTAAAACGCCGATAAAATATCACCTTTAGC
54846684 GGCGTTTTT
1 GGCGTTTTT
54846693 TATGAAGCGC
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
114 9 0.08
115 101 0.90
116 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (114 bp):
GGCGTTTTTAAATACGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTATTACAGTTAAAGG
AAATTTGTGGCGTTTCTTCGTAAAACGCCGATAAAATATCACCTTTAGC
Found at i:54847175 original size:7 final size:7
Alignment explanation
Indices: 54847160--54847234 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
54847150 TCTTAAATCA
*
54847160 TAAATCC
1 TAAACCC
54847167 TAAACCC
1 TAAACCC
54847174 TAAA-CC
1 TAAACCC
*
54847180 TAAAACTC
1 T-AAACCC
*
54847188 TAAACTC
1 TAAACCC
*
54847195 TAAACTC
1 TAAACCC
*
54847202 TAAACCG
1 TAAACCC
54847209 TAAACCC
1 TAAACCC
* *
54847216 TAAATCG
1 TAAACCC
54847223 TAAA-CC
1 TAAACCC
54847229 TAAACC
1 TAAACC
54847235 ATATTTTCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
6 8 0.14
7 47 0.82
8 2 0.04
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:54847177 original size:21 final size:19
Alignment explanation
Indices: 54847153--54847234 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 19
54847143 CCATAAATCT
54847153 TAAATCATAAATCCTAAACCC
1 TAAATC-TAAA-CCTAAACCC
* *
54847174 TAAACCTAAAACTCTAAACTC
1 TAAATCT-AAAC-CTAAACCC
54847195 TAAACTCTAAACCGTAAACCC
1 TAAA-TCTAAACC-TAAACCC
54847216 TAAATCGTAAACCTAAACC
1 TAAATC-TAAACCTAAACC
54847235 ATATTTTCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 11 0.21
21 39 0.75
22 2 0.04
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.22
Consensus pattern (19 bp):
TAAATCTAAACCTAAACCC
Found at i:54847185 original size:14 final size:13
Alignment explanation
Indices: 54847160--54847234 Score: 71
Period size: 14 Copynumber: 5.5 Consensus size: 13
54847150 TCTTAAATCA
54847160 TAAATCCTAAACCC
1 TAAA-CCTAAACCC
*
54847174 TAAACCTAAAACTC
1 TAAACCT-AAACCC
*
54847188 TAAACTCTAAACTC
1 TAAAC-CTAAACCC
54847202 TAAACCGTAAACCC
1 TAAACC-TAAACCC
*
54847216 TAAATCGTAAA-CC
1 TAAA-CCTAAACCC
54847229 TAAACC
1 TAAACC
54847235 ATATTTTCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.02
13 10 0.19
14 39 0.74
15 3 0.06
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (13 bp):
TAAACCTAAACCC
Found at i:54847402 original size:20 final size:21
Alignment explanation
Indices: 54847366--54847413 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
54847356 TTCAATTTCC
54847366 AAACT-AAACCCTAAAACCCA
1 AAACTCAAACCCTAAAACCCA
* *
54847386 AAACTCAAA-CCTTAAACCCT
1 AAACTCAAACCCTAAAACCCA
54847406 AAACTCAA
1 AAACTCAA
54847414 TCTCTAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACTCAAACCCTAAAACCCA
Found at i:54847592 original size:22 final size:22
Alignment explanation
Indices: 54847564--54847605 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54847554 TGCGTTGAAA
**
54847564 CCCTAACTGTAACCCCTAAATC
1 CCCTAACCCTAACCCCTAAATC
54847586 CCCTAACCCTAACCCCTAAA
1 CCCTAACCCTAACCCCTAAA
54847606 GCATAACACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.45, G:0.02, T:0.19
Consensus pattern (22 bp):
CCCTAACCCTAACCCCTAAATC
Found at i:54848184 original size:41 final size:41
Alignment explanation
Indices: 54848138--54848246 Score: 182
Period size: 41 Copynumber: 2.7 Consensus size: 41
54848128 ATTTTTTTTT
* * * *
54848138 GCGGCGCTTCTCTAAAAACGCCGCTAAATCCCTAAACATTA
1 GCGGCGCTTTTGTCAAAGCGCCGCTAAATCCCTAAACATTA
54848179 GCGGCGCTTTTGTCAAAGCGCCGCTAAATCCCTAAACATTA
1 GCGGCGCTTTTGTCAAAGCGCCGCTAAATCCCTAAACATTA
54848220 GCGGCGCTTTTGTCAAAGCGCCGCTAA
1 GCGGCGCTTTTGTCAAAGCGCCGCTAA
54848247 TTCCACGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTGTCAAAGCGCCGCTAAATCCCTAAACATTA
Found at i:54848392 original size:72 final size:72
Alignment explanation
Indices: 54848264--54848413 Score: 176
Period size: 72 Copynumber: 2.1 Consensus size: 72
54848254 AAAGCTGAGA
* * * * ** * *
54848264 AAACGACACCGTTTGGCTTAGGGTTTTTAGTGGTGCTTCCCCAAAAGCGCCGCTAAAT-CCCAAA
1 AAACGGCACCGTTTGGCTTAGGATTATTAGTGGCGCTTAACCAAAAACGCCACTAAATCCCCAAA
54848328 AACTACGG
66 AACT-CGG
** *
54848336 AAACGGCACCGTTTGGCTTAGGATTATTAGTGGCGCTTAATTAAAAACGTCACTAAATCCCCAAA
1 AAACGGCACCGTTTGGCTTAGGATTATTAGTGGCGCTTAACCAAAAACGCCACTAAATCCCCAAA
*
54848401 ACCTCGG
66 AACTCGG
54848408 AAACGG
1 AAACGG
54848414 TGTCATTGGG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 56 0.86
73 9 0.14
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (72 bp):
AAACGGCACCGTTTGGCTTAGGATTATTAGTGGCGCTTAACCAAAAACGCCACTAAATCCCCAAA
AACTCGG
Found at i:54861347 original size:21 final size:21
Alignment explanation
Indices: 54861294--54861347 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
54861284 GAAGATTTGG
54861294 TTTTTTATTAGTATAACATAT
1 TTTTTTATTAGTATAACATAT
*
54861315 TTAGCATTTATTAGTATAA-ATAT
1 TT---TTTTATTAGTATAACATAT
54861338 CTTTTTTATT
1 -TTTTTTATT
54861348 TCTTTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
21 8 0.30
23 4 0.15
24 15 0.56
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTTATTAGTATAACATAT
Found at i:54866021 original size:18 final size:18
Alignment explanation
Indices: 54865998--54866033 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54865988 CATTTTAGGT
54865998 CCACACGGCATGAGACAC
1 CCACACGGCATGAGACAC
54866016 CCACACGGCATGAGACAC
1 CCACACGGCATGAGACAC
54866034 AAGCGTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.22, T:0.06
Consensus pattern (18 bp):
CCACACGGCATGAGACAC
Found at i:54866405 original size:30 final size:32
Alignment explanation
Indices: 54866346--54866405 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
54866336 ATATATTATA
* * *
54866346 ATATTATATCTTAATTATTAAGTATATATATT
1 ATATTATATATTAATTAATAAGTAAATATATT
54866378 ATATTATATATT-A-TAATAAGTAAATATA
1 ATATTATATATTAATTAATAAGTAAATATA
54866406 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 1 0.04
32 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
ATATTATATATTAATTAATAAGTAAATATATT
Found at i:54866405 original size:32 final size:33
Alignment explanation
Indices: 54866332--54866405 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 33
54866322 TTTAAAGTTA
* *
54866332 AAATATATATTATAATATTATATCTTAATTATT
1 AAATATATATTATAATATTATATCTTAATAAGT
*
54866365 AAGTATATATATTATATTA-TATAT-TATAATAAGT
1 AA--ATATATATTATAATATTATATCT-TAATAAGT
54866399 AAATATA
1 AAATATA
54866406 ATAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
32 5 0.14
33 3 0.09
34 13 0.37
35 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (33 bp):
AAATATATATTATAATATTATATCTTAATAAGT
Found at i:54869688 original size:30 final size:31
Alignment explanation
Indices: 54869652--54869712 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
54869642 TATCAGTACA
*
54869652 GTGTGGGCCTTAGCCCATTACAGTAA-CAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
*
54869682 GTGTGGGCCTTAGCCTAATACAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
54869713 ACAATGCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (31 bp):
GTGTGGGCCTTAGCCCAATACAGTAATCAGT
Found at i:54869985 original size:27 final size:27
Alignment explanation
Indices: 54869925--54870267 Score: 333
Period size: 27 Copynumber: 12.7 Consensus size: 27
54869915 GGAGTATAAA
* * *
54869925 AGTCATTTTACCCGATGGGGGGTATTTC
1 AGTCATTTTACCC-TTCGAGGGTATTTC
54869953 -GATCATTTTACCCTTCGAGGGTATTTC
1 AG-TCATTTTACCCTTCGAGGGTATTTC
54869980 AGTCA-TTTACCCTTCGAGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTC
* *
54870006 GGTCATTTTACCCTTTGAGGGTATTT-
1 AGTCATTTTACCCTTCGAGGGTATTTC
* * * *
54870032 TGATCATTTTTCCCTTCAAGGGGTATTTT
1 AG-TCATTTTACCCTTCGA-GGGTATTTC
*
54870061 GGTCATTTTACCCTTCG-GGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTC
* *
54870087 GGTCATTTTACCCTTTGAGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTC
* *
54870114 -GATCATTTTACCCTTTGGGGGTATTTC
1 AG-TCATTTTACCCTTCGAGGGTATTTC
54870141 AGTCATTTTACCCTTCGAGGGTATTT-
1 AGTCATTTTACCCTTCGAGGGTATTTC
*
54870167 GGATCATTTTACCCTTC-AGGGGTATTTC
1 AG-TCATTTTACCCTTCGA-GGGTATTTC
* * * *
54870195 AATTATTTTACCCTTTGGGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTC
* * * *
54870222 AGTTATTTTACCTTTTGAGAGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTC
* *
54870249 -GATCATTGTACTCTTCGAG
1 AG-TCATTTTACCCTTCGAG
54870268 TATATTACGA
Statistics
Matches: 269, Mismatches: 32, Indels: 29
0.82 0.10 0.09
Matches are distributed among these distances:
26 54 0.20
27 180 0.67
28 34 0.13
29 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (27 bp):
AGTCATTTTACCCTTCGAGGGTATTTC
Found at i:54870066 original size:81 final size:82
Alignment explanation
Indices: 54869926--54870255 Score: 404
Period size: 81 Copynumber: 4.1 Consensus size: 82
54869916 GAGTATAAAA
* * * *
54869926 GTCATTTTACCCGATGGGGGGTATTTCGATCATTTTACCCTTCGA-GGGTATTTCAGTCA-TTTA
1 GTCATTTTACCC-TTTGAGGGTATTTCGATCATTTTACCCTTCAAGGGGTATTTCAGTCATTTTA
54869989 CCCTTCGAGGGTATTTCG
65 CCCTTCGAGGGTATTTCG
* * **
54870007 GTCATTTTACCCTTTGAGGGTATTTTGATCATTTTTCCCTTCAAGGGGTATTTTGGTCATTTTAC
1 GTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCAAGGGGTATTTCAGTCATTTTAC
54870072 CCTTCG-GGGTATTTCG
66 CCTTCGAGGGTATTTCG
**
54870088 GTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTT-TGGGGGTATTTCAGTCATTTTAC
1 GTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCAAGGGGTATTTCAGTCATTTTAC
54870152 CCTTCGAGGGTATTT-G
66 CCTTCGAGGGTATTTCG
* * * ** *
54870168 GATCATTTTACCC-TTCAGGGGTATTTCAATTATTTTACCCTT-TGGGGGTATTTCAGTTATTTT
1 G-TCATTTTACCCTTTGA-GGGTATTTCGATCATTTTACCCTTCAAGGGGTATTTCAGTCATTTT
* * *
54870231 ACCTTTTGAGAGTATTTCG
64 ACCCTTCGAGGGTATTTCG
*
54870250 ATCATT
1 GTCATT
54870256 GTACTCTTCG
Statistics
Matches: 221, Mismatches: 22, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
80 56 0.25
81 153 0.69
82 12 0.05
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (82 bp):
GTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCAAGGGGTATTTCAGTCATTTTAC
CCTTCGAGGGTATTTCG
Found at i:54870265 original size:108 final size:106
Alignment explanation
Indices: 54869944--54870267 Score: 420
Period size: 108 Copynumber: 3.0 Consensus size: 106
54869934 ACCCGATGGG
* *
54869944 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAGTCA-TTTACCCTTCGAGGGTATTTCGG
1 GGGTATTTGGATCATTTTACCCTTCG-GGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTC-G
* * *
54870008 TCATTTTACCCTTTGAGGGTATTTTGATCATTTTTCCCTTCAA
64 TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCGA
*
54870051 GGGGTATTTTGG-TCATTTTACCCTTCGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCG
1 -GGGTA-TTTGGATCATTTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCG
*
54870115 ATCATTTTACCCTTTGGGGGTATTTC-AGTCATTTTACCCTTCGA
64 -TCATTTTACCCTTTGAGGGTATTTCGA-TCATTTTACCCTTCGA
* * *
54870159 GGGTATTTGGATCATTTTACCCTTCAGGGGTATTTCAATTATTTTACCCTTTGGGGGTATTTCAG
1 GGGTATTTGGATCATTTTACCCTTC-GGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTC-G
* * * * *
54870224 TTATTTTACCTTTTGAGAGTATTTCGATCATTGTACTCTTCGA
64 TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCGA
54870267 G
1 G
54870268 TATATTACGA
Statistics
Matches: 191, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
106 5 0.03
107 34 0.18
108 146 0.76
109 6 0.03
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (106 bp):
GGGTATTTGGATCATTTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCGTC
ATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCGA
Found at i:54877737 original size:38 final size:38
Alignment explanation
Indices: 54877695--54877773 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
54877685 GCAAGTAAGA
54877695 AATTTCTTATCAGTCGTTTCAATAATTAGCAAATGGTT
1 AATTTCTTATCAGTCGTTTCAATAATTAGCAAATGGTT
*
54877733 AATTTCTTGTCAGTCGTTTCAATAATTAGCAAATGGTT
1 AATTTCTTATCAGTCGTTTCAATAATTAGCAAATGGTT
54877771 AAT
1 AAT
54877774 GGTCATTCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (38 bp):
AATTTCTTATCAGTCGTTTCAATAATTAGCAAATGGTT
Found at i:54888122 original size:15 final size:15
Alignment explanation
Indices: 54888102--54888134 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54888092 TATTAAATAC
54888102 TATTATTGTTTA-TAT
1 TATTATT-TTTATTAT
54888117 TATTATTTTTATTAT
1 TATTATTTTTATTAT
54888132 TAT
1 TAT
54888135 ATTATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTTATTAT
Found at i:54889242 original size:37 final size:37
Alignment explanation
Indices: 54889161--54889243 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
54889151 ATATGTGTGG
* *
54889161 AATTGAATCGAATATTGACTTGAAAATGGAAAAGTGA
1 AATTGAATCGAATATCGACTTGAAAATGGAAAAATGA
* *
54889198 ATTTTGAATCGAAT-TGCGA-TTGAAAGTGGAAAAAATGA
1 A-ATTGAATCGAATAT-CGACTTGAAAATGG-AAAAATGA
54889236 AATTGAAT
1 AATTGAAT
54889244 TAAAATGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
37 17 0.45
38 21 0.55
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (37 bp):
AATTGAATCGAATATCGACTTGAAAATGGAAAAATGA
Found at i:54889372 original size:23 final size:23
Alignment explanation
Indices: 54889346--54889455 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
54889336 GCTTTGCCGG
54889346 TCAGGCACTTTATGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATA
*
54889369 TCAGGCACTTTATGTGCCGTATA
1 TCAGGCACTTTATGTGTCGTATA
54889392 TCAGGCACTTTATGTGTCG--TA
1 TCAGGCACTTTATGTGTCGTATA
**
54889413 TCAGGCAAC-TCGTGTGTCGT-T-
1 TCAGGC-ACTTTATGTGTCGTATA
54889434 TCAGGCAC-TTATGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATA
54889456 CTGATTAGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
20 11 0.14
21 23 0.30
22 3 0.04
23 40 0.52
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATA
Found at i:54889831 original size:3 final size:3
Alignment explanation
Indices: 54889823--54889849 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54889813 ATTATATTCC
54889823 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
54889850 GAGTTATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:54899999 original size:1 final size:1
Alignment explanation
Indices: 54899993--54900022 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
54899983 CTTTGGCTTC
*
54899993 TTTTTTTTTTTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54900023 AACTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:54901582 original size:12 final size:12
Alignment explanation
Indices: 54901565--54901591 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54901555 ATTTAACGTA
54901565 CAAGATGAAGTC
1 CAAGATGAAGTC
54901577 CAAGATGAAGTC
1 CAAGATGAAGTC
54901589 CAA
1 CAA
54901592 TGATATCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (12 bp):
CAAGATGAAGTC
Found at i:54902040 original size:15 final size:14
Alignment explanation
Indices: 54902010--54902055 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
54902000 AGTTATAACT
54902010 ATTTAAATAATATA
1 ATTTAAATAATATA
*
54902024 ATTTAAATAGTTATA
1 ATTTAAATA-ATATA
54902039 ATATTAAATAA-ATA
1 AT-TTAAATAATATA
54902053 ATT
1 ATT
54902056 ATGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 1 0.04
14 14 0.50
15 6 0.21
16 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTTAAATAATATA
Found at i:54910584 original size:18 final size:18
Alignment explanation
Indices: 54910558--54910645 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
54910548 CCAACTACTA
*
54910558 TATACGTGAACAGTACCG
1 TATACGTGAATAGTACCG
* *
54910576 TATATGTGAATAGTGCCG
1 TATACGTGAATAGTACCG
54910594 TATACGTGAATAGTACCG
1 TATACGTGAATAGTACCG
* *
54910612 TATACGTAAATAGTGCCG
1 TATACGTGAATAGTACCG
54910630 TATACGTGAATAGTAC
1 TATACGTGAATAGTAC
54910646 TGTAAACGGT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
TATACGTGAATAGTACCG
Found at i:54910609 original size:36 final size:36
Alignment explanation
Indices: 54910558--54910645 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
54910548 CCAACTACTA
* * *
54910558 TATACGTGAACAGTACCGTATATGTGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCG
54910594 TATACGTGAATAGTACCGTATACGTAAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCG
54910630 TATACGTGAATAGTAC
1 TATACGTGAATAGTAC
54910646 TGTAAACGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTAAATAGTGCCG
Found at i:54918624 original size:34 final size:34
Alignment explanation
Indices: 54918585--54918656 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
54918575 GGAAACATGA
54918585 AAATATACACACTTTTTCATACCCTTTTTAACTC
1 AAATATACACACTTTTTCATACCCTTTTTAACTC
*
54918619 AAATATACACACTTTTTCATGCCCTTTTTAACTC
1 AAATATACACACTTTTTCATACCCTTTTTAACTC
54918653 AAAT
1 AAAT
54918657 TCATGCAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.01, T:0.40
Consensus pattern (34 bp):
AAATATACACACTTTTTCATACCCTTTTTAACTC
Found at i:54919630 original size:5 final size:5
Alignment explanation
Indices: 54919620--54919645 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54919610 TCTAAGTTAA
54919620 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
54919646 CTTAGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:54928052 original size:26 final size:26
Alignment explanation
Indices: 54927976--54928052 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
54927966 ACACCAATAT
* *
54927976 CACAGCAAAGCTGCCAGTAATAATGA
1 CACAGCAAAGCTGCCAGTAATAGTAA
* *
54928002 CACAACAAAGCTGCCAGTAACAGTAA
1 CACAGCAAAGCTGCCAGTAATAGTAA
* *
54928028 CGCAGCAAGGCTGCCAGTAATAGTA
1 CACAGCAAAGCTGCCAGTAATAGTA
54928053 TATGTGGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.14
Consensus pattern (26 bp):
CACAGCAAAGCTGCCAGTAATAGTAA
Found at i:54928646 original size:27 final size:27
Alignment explanation
Indices: 54928227--54928655 Score: 463
Period size: 27 Copynumber: 15.9 Consensus size: 27
54928217 GAGTATAACA
* *
54928227 GTCATTTTACCCTAT-GGGGGTATTTTG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
54928254 GTCATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
54928281 GTCATTTTACCCTTTGAGGGTACTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
54928308 GTTATTTTACCATTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
54928335 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
54928362 GTAATTTTACCCTTTGAGGGTATTAT-A
1 GTCATTTTACCCTTCGAGGGTATT-TCG
* *
54928389 GTCATTTTACCTTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
54928416 GTCACTTTACCCTTC-AGGGGTATTTCG
1 GTCATTTTACCCTTCGA-GGGTATTTCG
* * ** *
54928443 ATCAATTT-CACCTTCGAGTATATTTCT
1 GTCATTTTAC-CCTTCGAGGGTATTTCG
* ** *
54928470 ATCATTTTACCCTTCGAGATTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
54928497 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
54928524 GTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * **
54928551 GTTATTTTACCCTTTGAGGCTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
54928578 GTCATTTTAACCTTCG-GGATTATTTCG
1 GTCATTTTACCCTTCGAGG-GTATTTCG
*
54928605 ATCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
54928632 GTTATTTTACCCTTCAAGGGTATT
1 GTCATTTTACCCTTCGAGGGTATT
54928656 ACGATTATTT
Statistics
Matches: 341, Mismatches: 52, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
26 6 0.02
27 330 0.97
28 5 0.01
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:54936289 original size:38 final size:38
Alignment explanation
Indices: 54936195--54936313 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 38
54936185 TCGAATGCAT
* * * *
54936195 ATATATA-TTATTCAAACACATATGCCAAAAGCAAACA-
1 ATATATACTTA-TCAACCACATATGCCGAATGCACACAC
* * * *
54936232 AT-TATACTTATCAACCACATGTGCCGACTGCACATAT
1 ATATATACTTATCAACCACATATGCCGAATGCACACAC
* *
54936269 ATATATACTTAT-AATTCACATATGTCGAATGCACACAC
1 ATATATACTTATCAA-CCACATATGCCGAATGCACACAC
54936307 ATATATA
1 ATATATA
54936314 TATCTAACAA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
36 23 0.35
37 9 0.14
38 33 0.51
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (38 bp):
ATATATACTTATCAACCACATATGCCGAATGCACACAC
Found at i:54936536 original size:41 final size:42
Alignment explanation
Indices: 54936481--54936602 Score: 194
Period size: 41 Copynumber: 3.0 Consensus size: 42
54936471 TTAATTAAAA
* *
54936481 CAGATTCACTGGCACTTAGCCTACTAGGCTTAAAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
*
54936523 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
*
54936564 CA-ATTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGA
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGA
54936603 ATTGATTCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 69 0.93
42 4 0.05
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (42 bp):
CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:54939813 original size:25 final size:25
Alignment explanation
Indices: 54939753--54939813 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
54939743 TTTCTAGAAG
* *
54939753 ATTTAGTTTTTTATTTGTATAATAT
1 ATTTAGTTATTTATTAGTATAATAT
*
54939778 ATTTAG-CATTTATTAGTATAAATAT
1 ATTTAGTTATTTATTAGTAT-AATAT
54939803 ATTT-GTTATTT
1 ATTTAGTTATTT
54939814 CTTTTCATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (25 bp):
ATTTAGTTATTTATTAGTATAATAT
Found at i:54940168 original size:14 final size:14
Alignment explanation
Indices: 54940149--54940193 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
54940139 TATTCTAAAA
54940149 ATGCTAAATATATT
1 ATGCTAAATATATT
54940163 ATGCT-AATA-A--
1 ATGCTAAATATATT
54940173 ATGCTAAATATATT
1 ATGCTAAATATATT
54940187 ATGCTAA
1 ATGCTAA
54940194 TAAATACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 2 0.07
13 4 0.15
14 12 0.44
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (14 bp):
ATGCTAAATATATT
Found at i:54940179 original size:24 final size:24
Alignment explanation
Indices: 54940131--54940205 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
54940121 AAGAAATAAC
* *
54940131 AAATATTTTATTCTAA-AAATGCT
1 AAATATATTATGCTAATAAATGCT
54940154 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
*
54940178 AAATATATTATGCTAATAAATACT
1 AAATATATTATGCTAATAAATGCT
54940202 AAAT
1 AAAT
54940206 CTTCTCGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 14 0.29
24 34 0.71
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:54960263 original size:37 final size:37
Alignment explanation
Indices: 54960213--54960293 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
54960203 TTCTCAAAAA
*
54960213 ACTTTCATCTAAATGGCCATATGCGTTCATGATTTTT
1 ACTTTCATCTAAATGGCCATATGAGTTCATGATTTTT
54960250 ACTTTCATCTAAATGGCCATATGAGTTCATGATTTTT
1 ACTTTCATCTAAATGGCCATATGAGTTCATGATTTTT
54960287 -CTTTCAT
1 ACTTTCAT
54960294 GTTGGTTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 7 0.16
37 36 0.84
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (37 bp):
ACTTTCATCTAAATGGCCATATGAGTTCATGATTTTT
Found at i:54978095 original size:18 final size:18
Alignment explanation
Indices: 54978062--54978096 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54978052 CTCTCTCCTT
*
54978062 GATTTTTTTAGGGTTTAG
1 GATTTTTTTAGAGTTTAG
*
54978080 GATTTTTTTTGAGTTTA
1 GATTTTTTTAGAGTTTA
54978097 AGGTTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (18 bp):
GATTTTTTTAGAGTTTAG
Found at i:54979440 original size:17 final size:17
Alignment explanation
Indices: 54979372--54979430 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
54979362 TAATCACATT
*
54979372 AATATTAAA-TTAATAA
1 AATATTAAATTTAATTA
54979388 AATATT--ATTTAGA-TA
1 AATATTAAATTTA-ATTA
*
54979403 AATATTAAATTTAATTT
1 AATATTAAATTTAATTA
54979420 AATATTAAATT
1 AATATTAAATT
54979431 CATTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 1 0.03
15 10 0.28
16 8 0.22
17 17 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTAAATTTAATTA
Found at i:54980099 original size:40 final size:40
Alignment explanation
Indices: 54980022--54980099 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
54980012 TAACTTATAT
**
54980022 ACTTATAATTAAATTAATTAATCAAAATTAATTAATTTAA
1 ACTTATAATTAAATTAATTAATCAAAATTAACAAATTTAA
* * *
54980062 ACTT-TAATTAACTTACCTTAATCAAGATTAACAAATTT
1 ACTTATAATTAAATTA-ATTAATCAAAATTAACAAATTT
54980100 GGCGGATTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 10 0.31
40 22 0.69
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (40 bp):
ACTTATAATTAAATTAATTAATCAAAATTAACAAATTTAA
Found at i:54980678 original size:23 final size:24
Alignment explanation
Indices: 54980651--54980708 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 24
54980641 TTAAATATAT
54980651 ATAAA-ATATATATTTGATTAAAA
1 ATAAATATATATATTTGATTAAAA
54980674 ATAAAAAATATATATATTTGATTAAAA
1 AT---AAATATATATATTTGATTAAAA
*
54980701 ATATATAT
1 ATAAATAT
54980709 TTAATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.07
24 5 0.17
26 3 0.10
27 20 0.67
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
ATAAATATATATATTTGATTAAAA
Found at i:54984984 original size:41 final size:41
Alignment explanation
Indices: 54984917--54985013 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
54984907 GGGTGCCAAT
** *
54984917 TTACTTCGG-TTTAACCGATGAGACACTGGATGCCAATTTA
1 TTACTTCGGATTTATTCAATGAGACACTGGATGCCAATTTA
* *
54984957 TTACTTCGGATTTATTCAATGAGACACTGGTTGTCAATTTA
1 TTACTTCGGATTTATTCAATGAGACACTGGATGCCAATTTA
* *
54984998 CTACTTC-GAATTATTC
1 TTACTTCGGATTTATTC
54985014 GATAAGGCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
40 17 0.35
41 32 0.65
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (41 bp):
TTACTTCGGATTTATTCAATGAGACACTGGATGCCAATTTA
Found at i:54985144 original size:16 final size:17
Alignment explanation
Indices: 54985113--54985156 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
54985103 AAATTTTTAT
*
54985113 AATTGATATTGAAATGG
1 AATTGATATAGAAATGG
*
54985130 CATTG-TATAGAAATGG
1 AATTGATATAGAAATGG
54985146 AATTGATATAG
1 AATTGATATAG
54985157 TGAATTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (17 bp):
AATTGATATAGAAATGG
Found at i:54996207 original size:25 final size:25
Alignment explanation
Indices: 54996154--54996208 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
54996144 AAAAAAGTTT
**
54996154 TGTGTGTTTATTTTTATTTAAATTT
1 TGTGTGTTTATTTTTATTTAAATAA
*
54996179 TGTGCTGTTTATTTTTATTT-GATAA
1 TGTG-TGTTTATTTTTATTTAAATAA
54996204 TGTGT
1 TGTGT
54996209 AATTGCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 10 0.38
26 15 0.58
ACGTcount: A:0.18, C:0.02, G:0.16, T:0.64
Consensus pattern (25 bp):
TGTGTGTTTATTTTTATTTAAATAA
Found at i:54999270 original size:92 final size:91
Alignment explanation
Indices: 54999113--54999321 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
54999103 TTGATTTTAG
* * *
54999113 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
54999178 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
54999205 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATTTAAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATAT-AACTATTAAATTA
54999269 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
54999297 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
54999322 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:54999434 original size:16 final size:16
Alignment explanation
Indices: 54999413--54999456 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
54999403 TTATTAAATT
*
54999413 ATATATTTTAATTATA
1 ATATATTTTAATAATA
54999429 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
54999444 AT-TATGTTTAATA
1 ATATAT-TTTAATA
54999457 TGATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:54999561 original size:156 final size:157
Alignment explanation
Indices: 54999388--54999703 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
54999378 ATAAGAATAT
* *
54999388 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAGTATGTTT
* *
54999453 -AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
54999517 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
54999544 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAGTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAGTATGTTT
54999609 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
54999674 TAATCATTTATCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
54999701 TAA
1 TAA
54999704 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 63 0.41
157 89 0.59
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAGTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:54999584 original size:18 final size:17
Alignment explanation
Indices: 54999556--54999590 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54999546 ATTATTAAGA
*
54999556 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54999573 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54999591 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54999847 original size:16 final size:16
Alignment explanation
Indices: 54999826--54999861 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
54999816 GATTTGCTAT
54999826 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54999842 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54999858 TACA
1 TACA
54999862 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55003045 original size:14 final size:15
Alignment explanation
Indices: 55003028--55003056 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55003018 TATTTTTTAC
55003028 TATTTAAT-TTTAAA
1 TATTTAATATTTAAA
55003042 TATTTAATATTTAAA
1 TATTTAATATTTAAA
55003057 GATGAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAATATTTAAA
Found at i:55005223 original size:52 final size:54
Alignment explanation
Indices: 55005151--55005256 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 54
55005141 ATTTTTAAAT
55005151 ATTTATAAGTAAAAGAAATTGAAACAATTTTAAGCATGGTTAGTATGCAAATTA
1 ATTTATAAGTAAAAGAAATTGAAACAATTTTAAGCATGGTTAGTATGCAAATTA
*
55005205 ATTTA-AAGT-AAAGAAATTGAAACAATTTTAATCATGGTTAGTATGCAAATTA
1 ATTTATAAGTAAAAGAAATTGAAACAATTTTAAGCATGGTTAGTATGCAAATTA
55005257 TCTAAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 42 0.82
53 4 0.08
54 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (54 bp):
ATTTATAAGTAAAAGAAATTGAAACAATTTTAAGCATGGTTAGTATGCAAATTA
Found at i:55006219 original size:31 final size:31
Alignment explanation
Indices: 55006168--55006237 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
55006158 CTTAACAGTC
* * *
55006168 CAGTGACT-TAATAAAAACTTTCTAATATTT
1 CAGTGACTAAAATAAAAACTTTCAAATAATT
*
55006198 CAGTGACTAAAATGAAAACTTTCAAATAATT
1 CAGTGACTAAAATAAAAACTTTCAAATAATT
*
55006229 CAGTAACTA
1 CAGTGACTA
55006238 TTTTGTAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (31 bp):
CAGTGACTAAAATAAAAACTTTCAAATAATT
Found at i:55012807 original size:21 final size:21
Alignment explanation
Indices: 55012769--55012817 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
55012759 ATCCGATATT
55012769 AATCTTTCAAATTAATTAGAC-
1 AATCTTTCAAATTAATTA-ACA
*
55012790 AATCTTTCATGATT-ATTAACA
1 AATCTTTCA-AATTAATTAACA
55012811 AATCTTT
1 AATCTTT
55012818 TGTTAAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (21 bp):
AATCTTTCAAATTAATTAACA
Found at i:55020470 original size:2 final size:2
Alignment explanation
Indices: 55020463--55020496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55020453 ATGAGGAGGA
55020463 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
55020497 GAATATTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55021229 original size:23 final size:24
Alignment explanation
Indices: 55021201--55021250 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
55021191 ATGAAAAGAT
*
55021201 TTGATG-AAAAGCTTAA-AAAGAAC
1 TTGATGCAAAA-CTTAATAAAAAAC
55021224 TTGATGCAAAACTTAATAAAAAAC
1 TTGATGCAAAACTTAATAAAAAAC
55021248 TTG
1 TTG
55021251 GTAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (24 bp):
TTGATGCAAAACTTAATAAAAAAC
Found at i:55023809 original size:21 final size:20
Alignment explanation
Indices: 55023784--55023826 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
55023774 TTTTATAAAG
55023784 GTTATATATATTACAATTTAT
1 GTTATATATATT-CAATTTAT
* * *
55023805 GTTATTTTTATTTAATTTAT
1 GTTATATATATTCAATTTAT
55023825 GT
1 GT
55023827 ATTATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
GTTATATATATTCAATTTAT
Found at i:55031869 original size:29 final size:29
Alignment explanation
Indices: 55031827--55031884 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
55031817 CTTTCATACA
*
55031827 AGAAGTTACTGTCGATTTGTATCAATGGC
1 AGAAGTTACCGTCGATTTGTATCAATGGC
55031856 AGAAGTTACCGTCGATTTGTATCAATGGC
1 AGAAGTTACCGTCGATTTGTATCAATGGC
55031885 TTATAGTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (29 bp):
AGAAGTTACCGTCGATTTGTATCAATGGC
Found at i:55034724 original size:18 final size:19
Alignment explanation
Indices: 55034679--55034726 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
55034669 TATTTGTTAC
55034679 ATAAATAAAAATGATTAAAT
1 ATAAAT-AAAATGATTAAAT
* *
55034699 AT-ATTAAAAT-TTTAAAT
1 ATAAATAAAATGATTAAAT
55034716 ATAAATAAAAT
1 ATAAATAAAAT
55034727 ACTGTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 2 0.08
20 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAATAAAATGATTAAAT
Found at i:55041960 original size:138 final size:138
Alignment explanation
Indices: 55041712--55041972 Score: 450
Period size: 138 Copynumber: 1.9 Consensus size: 138
55041702 ATTTTTGTTT
* * * *
55041712 TTGCTCTGCTTTTAGCCAAAATATAGGATATGAAATGTGTGGGGGTATTTTAGAACTATTACTTA
1 TTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAACTACTACTTA
* *
55041777 CATGTTTTTTATTTATAACAGGTAGAACACGAGTCTGATAGCATTTTGAATTGCATTTTTCTTTT
66 CATGTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTGCATTTTTCTTTT
55041842 TCTTTTTA
131 TCTTTTTA
* *
55041850 TTGCTCTGCTTTTAGCCAAAATATAGGGCATGAAATGTGTGGAGGTAATTTAGAGCTACTACTTA
1 TTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAACTACTACTTA
55041915 CATGTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTGCATTT
66 CATGTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTGCATTT
55041973 CCTTGGAACA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 115 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (138 bp):
TTGCTCTGCTTTTAGCCAAAATATAGGACATGAAATGTGTGGAGGTAATTTAGAACTACTACTTA
CATGTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTGCATTTTTCTTTT
TCTTTTTA
Found at i:55044461 original size:24 final size:24
Alignment explanation
Indices: 55044416--55044461 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
55044406 AGTTTATAAA
* * *
55044416 ATTTATAAAAATTTCTGTAAAAGT
1 ATTTATAAAAAGTACTGAAAAAGT
*
55044440 ATTTTTAAAAAGTACTGAAAAA
1 ATTTATAAAAAGTACTGAAAAA
55044462 TGCACCTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (24 bp):
ATTTATAAAAAGTACTGAAAAAGT
Found at i:55044651 original size:21 final size:20
Alignment explanation
Indices: 55044614--55044660 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 20
55044604 ATTTTAATAC
55044614 TTTTCTATAATTTTAAAT-TA
1 TTTT-TATAATTTTAAATATA
55044634 TTTTTATAATTTTCTAAATATA
1 TTTTTATAA-TTT-TAAATATA
55044656 TTTTT
1 TTTTT
55044661 TGAAATCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 5 0.21
22 7 0.29
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTTAAATATA
Found at i:55047370 original size:18 final size:18
Alignment explanation
Indices: 55047347--55047395 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
55047337 ATCAAATACT
*
55047347 AAATTAAATATTAAAATA
1 AAATTAAATACTAAAATA
* *
55047365 AAATTATATACTAAATTA
1 AAATTAAATACTAAAATA
55047383 AACATTAAA-ACTA
1 AA-ATTAAATACTA
55047396 GCTTATATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAATACTAAAATA
Found at i:55047526 original size:75 final size:75
Alignment explanation
Indices: 55047434--55047589 Score: 258
Period size: 75 Copynumber: 2.1 Consensus size: 75
55047424 TATTGAAAAT
*
55047434 TATTGATTAACTATTGCAGACATGTACATTTACACGCATGGTTTGAAACATTTGCTTTTCTTTGA
1 TATTGATTAACTATTGCAGACATGTACATTTACACGCATGGTTTGAAACATTTGCTTTTCTTTAA
*
55047499 AATGTTGTCG
66 AACGTTGTCG
* * *
55047509 TATTGATTTATTATTGCAGACATGTACATTTACACGCGTGGTTTGAAACATTTGCTTTTCTTTAA
1 TATTGATTAACTATTGCAGACATGTACATTTACACGCATGGTTTGAAACATTTGCTTTTCTTTAA
55047574 AACGTTGTCG
66 AACGTTGTCG
*
55047584 TTTTGA
1 TATTGA
55047590 GGCCCCTAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (75 bp):
TATTGATTAACTATTGCAGACATGTACATTTACACGCATGGTTTGAAACATTTGCTTTTCTTTAA
AACGTTGTCG
Found at i:55049989 original size:31 final size:31
Alignment explanation
Indices: 55049954--55050018 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
55049944 AAAAAAACTT
*
55049954 AATAGCCTAAAGACTTAAATAAAAACTTTTG
1 AATAGCCTAAAGACTTAAATAAAAACTTTCG
** * * *
55049985 AATAGTTTAATGGCTTAAATGAAAACTTTCG
1 AATAGCCTAAAGACTTAAATAAAAACTTTCG
55050016 AAT
1 AAT
55050019 GGTTCAGTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (31 bp):
AATAGCCTAAAGACTTAAATAAAAACTTTCG
Found at i:55052954 original size:43 final size:45
Alignment explanation
Indices: 55052868--55052993 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 45
55052858 AACTCGTACA
*
55052868 ATGCCAACGTCCCAGACGTGGTCTTACATG-TAATCACAT--ATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATAAATCG
**
55052911 ATGCC-ACTGTTTCAGACAG-GGTCTTACAC-ATAA-ACATAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGATAACACATAAATCG
55052954 ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACATA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACATA
55052994 TCGGAAATCC
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
41 4 0.06
42 3 0.04
43 50 0.72
44 7 0.10
45 5 0.07
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (45 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACATAAATCG
Found at i:55055559 original size:21 final size:22
Alignment explanation
Indices: 55055533--55055575 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55055523 TATATACATA
*
55055533 TATAAAA-AAAACTGTAAGTAT
1 TATAAAATAAAAATGTAAGTAT
55055554 TATAAAATAAAAATGTAAGTAT
1 TATAAAATAAAAATGTAAGTAT
55055576 GTGTATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
TATAAAATAAAAATGTAAGTAT
Found at i:55057636 original size:44 final size:45
Alignment explanation
Indices: 55057535--55058510 Score: 893
Period size: 44 Copynumber: 22.2 Consensus size: 45
55057525 CAGAGGTAAA
* * * * * *
55057535 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGACAAG
* *
55057581 ATCTGCAATCTTCAATCTACTTC-CTACCAATATAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55057625 ACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * *
55057669 ATTTGCTTTCTTCGATCCAC-TCCCTACCAATATAGGGAGACAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
55057713 ACCTGTTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55057757 ATCTGC-ATCTTGGATCCACTTC-CTATCAATATAGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * * *
55057800 ACCAGCCATCTTCGATCTACTTCAC-GCCAATACATGAAGATAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * *
55057844 ATCTTCTTTCTTTGATCTACTTCGCTACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
55057889 ATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * * *
55057932 ACCTGCTATCTTTGATCTACTTCAC-GCCAATACATGAAGATAAA
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
55057976 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55058021 ATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55058064 ATCTGCTA-CTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55058107 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55058152 ATCTAC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55058195 ATCTGCTATCCTCGATCTACTTCA-TGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
55058239 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55058284 ATCTG-TCATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGG
1 ATCTGCT-ATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55058328 ATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
55058372 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55058417 ATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
55058460 ATCTGCTATCCTTCGATCTACTTCAC--GCAATACATGAAGACAAG
1 ATCTGCTAT-CTTCGATCTACTTCACTACCAATATAGGAAGACAAG
55058504 ATCTGCT
1 ATCTGCT
55058511 TTAATGACTT
Statistics
Matches: 738, Mismatches: 168, Indels: 50
0.77 0.18 0.05
Matches are distributed among these distances:
42 1 0.00
43 158 0.21
44 423 0.57
45 135 0.18
46 21 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
Found at i:55057918 original size:132 final size:132
Alignment explanation
Indices: 55057535--55058512 Score: 1322
Period size: 132 Copynumber: 7.4 Consensus size: 132
55057525 CAGAGGTAAA
* * * * * ** *
55057535 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 ATCTGCTATCTTCGATCTACTTCAC-GCC-AATACATGAAGACAAGATCTGCTTTCTTCGATCTA
* * * * * * *
55057600 CTTC-CTACCAATATAGGAAGACAAGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
64 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAA
* *
55057663 GACAAG
127 GATAGG
* * * * * * * * * *
55057669 ATTTGCTTTCTTCGATCCAC-TCCCTACCAATATAGGGAGACAGGACCTG-TTATCTTCGATCTA
1 ATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT-TCTTCGATCTA
* * *** * *
55057732 CTTC-ACGCCAATACATGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGA
64 CTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGA
* *
55057796 CAAG
129 TAGG
* * * * * *
55057800 ACCAGCCATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTTCTTTCTTTGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
* * * * *
55057865 TCGCTACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATA
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
55057930 GG
131 GG
* * * * *
55057932 ACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGATAAAATCTGCTTTCTGCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
55057997 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
55058062 GG
131 GG
55058064 ATCTGCTA-CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
*
55058128 TCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGATA
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
55058193 GG
131 GG
* * *
55058195 ATCTGCTATCCTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
55058260 TCGCCACCAATATGGGAAGACAAGATCTGTCATCTTCGATCCACTTCCTACCAATATAGGAAGAT
66 TCGCCACCAATATGGGAAGACAAGATCTG-CATCTTCGATCCACTTCCTACCAATATAGGAAGAT
55058325 AGG
130 AGG
*
55058328 ATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
55058393 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
55058458 GG
131 GG
55058460 ATCTGCTATCCTTCGATCTACTTCACG-CAATACATGAAGACAAGATCTGCTTT
1 ATCTGCTAT-CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
55058513 AATGACTTCA
Statistics
Matches: 756, Mismatches: 80, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 199 0.26
132 390 0.52
133 151 0.20
134 15 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA
GG
Found at i:55070360 original size:21 final size:22
Alignment explanation
Indices: 55070334--55070376 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55070324 TATATACATA
*
55070334 TATAAAA-AAAACTGTAAGTAT
1 TATAAAATAAAAATGTAAGTAT
55070355 TATAAAATAAAAATGTAAGTAT
1 TATAAAATAAAAATGTAAGTAT
55070377 GTGCATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
TATAAAATAAAAATGTAAGTAT
Found at i:55076760 original size:22 final size:22
Alignment explanation
Indices: 55076709--55076764 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
55076699 TTTAAGCGGT
*
55076709 ATCGATACCATCTATGAGAATG
1 ATCGATACCATTTATGAGAATG
* *
55076731 ATCAATACCATTTATGAGAATT
1 ATCGATACCATTTATGAGAATG
55076753 A-CTGATACCATT
1 ATC-GATACCATT
55076765 AAATGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (22 bp):
ATCGATACCATTTATGAGAATG
Found at i:55080941 original size:15 final size:15
Alignment explanation
Indices: 55080923--55080955 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
55080913 ATTCCTTTAA
55080923 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
55080938 AAATTATTAAAAATT
1 AAATTATTAAAAATT
55080953 AAA
1 AAA
55080956 ATTTCATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:55085446 original size:26 final size:26
Alignment explanation
Indices: 55085416--55085471 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
55085406 GGAGCTCTTG
* *
55085416 ATTAAAGGCTCTTCGTGAGCTTCCTA
1 ATTAAAAGCTCTTCGTGAACTTCCTA
* *
55085442 ATTAAAAGTTCTTTGTGAACTTCCTA
1 ATTAAAAGCTCTTCGTGAACTTCCTA
55085468 ATTA
1 ATTA
55085472 TGGCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (26 bp):
ATTAAAAGCTCTTCGTGAACTTCCTA
Found at i:55090656 original size:18 final size:19
Alignment explanation
Indices: 55090620--55090657 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55090610 TGCAAATGTA
**
55090620 TCATTTCTCATTTTTATTT
1 TCATTTCTCATTTCCATTT
55090639 TCATTT-TCATTTCCATTT
1 TCATTTCTCATTTCCATTT
55090657 T
1 T
55090658 GAGAAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (19 bp):
TCATTTCTCATTTCCATTT
Found at i:55091446 original size:7 final size:7
Alignment explanation
Indices: 55091434--55091462 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55091424 GTTCAAAAAA
55091434 TATATAT
1 TATATAT
55091441 TATATAT
1 TATATAT
55091448 TATATAT
1 TATATAT
55091455 TATATAT
1 TATATAT
55091462 T
1 T
55091463 TCAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATATAT
Found at i:55094618 original size:23 final size:23
Alignment explanation
Indices: 55094587--55094637 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
55094577 ACCTACTTTT
* * *
55094587 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
55094610 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
55094633 TTACA
1 TTACA
55094638 TATACGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:55095736 original size:24 final size:24
Alignment explanation
Indices: 55095680--55095734 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
55095670 AATGTAAGTT
* *
55095680 AAAAATATGTTGATTTATTTTTGA
1 AAAAATTTATTGATTTATTTTTGA
* *
55095704 ATAAATTTATTGA-TTATTTTTTA
1 AAAAATTTATTGATTTATTTTTGA
55095727 AAAAATTT
1 AAAAATTT
55095735 TAAAACTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
AAAAATTTATTGATTTATTTTTGA
Found at i:55102729 original size:21 final size:22
Alignment explanation
Indices: 55102705--55102757 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
55102695 TGTTAGTAAA
*
55102705 TAATTTAAATT-TTAAAAAAAT
1 TAATTTAAATTATAAAAAAAAT
**
55102726 TAATAAAAATTATAAAAAAAAT
1 TAATTTAAATTATAAAAAAAAT
55102748 TAATTCTAAA
1 TAATT-TAAA
55102758 AATGATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 9 0.36
22 13 0.52
23 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATTTAAATTATAAAAAAAAT
Found at i:55102757 original size:25 final size:22
Alignment explanation
Indices: 55102718--55102765 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
55102708 TTTAAATTTT
*
55102718 AAAAAAATTAATAAAAATTATA
1 AAAAAAATTAATAAAAATGATA
55102740 AAAAAAATTAATTCTAAAAATGATA
1 AAAAAAATTAA---TAAAAATGATA
55102765 A
1 A
55102766 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
25 11 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAAATTAATAAAAATGATA
Found at i:55103362 original size:27 final size:27
Alignment explanation
Indices: 55103332--55103391 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
55103322 GGCCAATCAC
*
55103332 ATTGGCGGCACCAAAGGTGCCAAAGTG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
55103359 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
55103386 ATTGGC
1 ATTGGC
55103392 CTGACCGGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:55103805 original size:19 final size:19
Alignment explanation
Indices: 55103781--55103843 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
55103771 AAGCAATAGT
55103781 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
*** ** * *
55103800 TTATTACTTTTTAATAAAC
1 TTATTAAAGTAAAATAGAG
55103819 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
55103838 TTATTA
1 TTATTA
55103844 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (19 bp):
TTATTAAAGTAAAATAGAG
Found at i:55104558 original size:27 final size:27
Alignment explanation
Indices: 55104520--55104576 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
55104510 GTCCAATCAG
*
55104520 GCCAATCTCTTTGGCACCTTTGGTGCC
1 GCCAATCACTTTGGCACCTTTGGTGCC
55104547 GCCAATCACTTTGGCACCTTTGGTGCC
1 GCCAATCACTTTGGCACCTTTGGTGCC
55104574 GCC
1 GCC
55104577 CAATGTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.12, C:0.35, G:0.23, T:0.30
Consensus pattern (27 bp):
GCCAATCACTTTGGCACCTTTGGTGCC
Found at i:55104691 original size:27 final size:27
Alignment explanation
Indices: 55104637--55104700 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
55104627 TTTTTTTTGT
* ***
55104637 ATATTTTTGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGGATA
55104664 ATATTTTGGTAAATAAAAAAAAGGATA
1 ATATTTTGGTAAATAAAAAAAAGGATA
*
55104691 ACATTTTGGT
1 ATATTTTGGT
55104701 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAAGGATA
Found at i:55106459 original size:24 final size:24
Alignment explanation
Indices: 55106432--55106505 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
55106422 TGAAATAAAA
55106432 TAAAAATTATGATAATTATACATT
1 TAAAAATTATGATAATTATACATT
* *
55106456 TAAAAATAATTATAATT-TA-A--
1 TAAAAATTATGATAATTATACATT
* * *
55106476 TAGAAATTATGATAGTTACACATT
1 TAAAAATTATGATAATTATACATT
55106500 TAAAAA
1 TAAAAA
55106506 CAATTAGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 13 0.34
21 1 0.03
22 2 0.05
23 2 0.05
24 20 0.53
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (24 bp):
TAAAAATTATGATAATTATACATT
Found at i:55106486 original size:44 final size:44
Alignment explanation
Indices: 55106430--55106519 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
55106420 TTTGAAATAA
* * *
55106430 AATAAAAATTATGATAATTATACATTTAAAAATAATTATAATTT
1 AATAAAAATTATGATAATTACACATTTAAAAACAATTAGAATTT
* *
55106474 AATAGAAATTATGATAGTTACACATTTAAAAACAATTAGAATTT
1 AATAAAAATTATGATAATTACACATTTAAAAACAATTAGAATTT
55106518 AA
1 AA
55106520 ATTACAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (44 bp):
AATAAAAATTATGATAATTACACATTTAAAAACAATTAGAATTT
Found at i:55106844 original size:23 final size:23
Alignment explanation
Indices: 55106812--55106861 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
55106802 GAATAGGTTA
* *
55106812 AAAATGTTTTAATTAATATTATTTG
1 AAAAT-TTTCAATT-ATAATATTTG
*
55106837 AAAATTTTCTATTATAATATTTG
1 AAAATTTTCAATTATAATATTTG
55106860 AA
1 AA
55106862 TTGTTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 6 0.27
25 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (23 bp):
AAAATTTTCAATTATAATATTTG
Found at i:55115016 original size:62 final size:59
Alignment explanation
Indices: 55114939--55115084 Score: 152
Period size: 57 Copynumber: 2.4 Consensus size: 59
55114929 ACTGCCTGGG
*
55114939 CACACGCCTATGTCCATGCTCTTGTGGTCCTAAATCATAAAAAGTGAGTTACACGACCTAGA
1 CACACGCCCATGTCCATGCTC-TGTGGT--TAAATCATAAAAAGTGAGTTACACGACCTAGA
* * * * * * *
55115001 CACACGCCCATGTCCATGC-CCGT-GTTAAATCATAAATAGTGAGTTACATGGCTTGGG
1 CACACGCCCATGTCCATGCTCTGTGGTTAAATCATAAAAAGTGAGTTACACGACCTAGA
* *
55115058 TACACGCCCATGTCCTTGCTCGTGTGG
1 CACACGCCCATGTCCATGCTC-TGTGG
55115085 CTTACACGGC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
57 43 0.61
58 1 0.01
59 4 0.06
60 3 0.04
61 1 0.01
62 18 0.26
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (59 bp):
CACACGCCCATGTCCATGCTCTGTGGTTAAATCATAAAAAGTGAGTTACACGACCTAGA
Found at i:55116291 original size:9 final size:8
Alignment explanation
Indices: 55116251--55116361 Score: 73
Period size: 9 Copynumber: 12.6 Consensus size: 8
55116241 TATTAATATT
*
55116251 TAAAAATA
1 TAAAATTA
55116259 TGAAAATTGA
1 T-AAAATT-A
55116269 TATAAATATA
1 TA-AAAT-TA
55116279 TAAACATTA
1 TAAA-ATTA
55116288 TAAACATATTA
1 T-AA-A-ATTA
55116299 TAAATATTA
1 TAAA-ATTA
*
55116308 TAAAAATA
1 TAAAATTA
55116316 TAAAAATTA
1 T-AAAATTA
55116325 T-AAATTA
1 TAAAATTA
55116332 T-AAATTA
1 TAAAATTA
*
55116339 TAAAAAGTA
1 T-AAAATTA
55116348 TAAAATTAA
1 TAAAATT-A
55116357 TAAAA
1 TAAAA
55116362 CATATTGTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
7 14 0.16
8 10 0.12
9 40 0.47
10 15 0.17
11 7 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (8 bp):
TAAAATTA
Found at i:55116291 original size:17 final size:16
Alignment explanation
Indices: 55116269--55116360 Score: 80
Period size: 17 Copynumber: 5.4 Consensus size: 16
55116259 TGAAAATTGA
55116269 TATAAATATATAAACAT
1 TATAAATATATAAA-AT
55116286 TATAAACATATTATAAATAT
1 TAT-AA-ATA-TATAAA-AT
*
55116306 TATAAAAATATAAAAAT
1 TATAAATATAT-AAAAT
55116323 TATAAAT-TAT-AAAT
1 TATAAATATATAAAAT
*
55116337 TATAAAAAGTATAAAAT
1 TATAAATA-TATAAAAT
55116354 TAATAAA
1 T-ATAAA
55116361 ACATATTGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.16
16 6 0.10
17 19 0.30
18 12 0.19
19 5 0.08
20 11 0.17
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (16 bp):
TATAAATATATAAAAT
Found at i:55116302 original size:20 final size:17
Alignment explanation
Indices: 55116197--55116366 Score: 98
Period size: 20 Copynumber: 9.5 Consensus size: 17
55116187 GAAATAATTG
*
55116197 AAAAATCATAAAAATGAT
1 AAAAAT-ATAAAAATTAT
* *
55116215 TAAAATAAAAGAAATTAT
1 AAAAATATAA-AAATTAT
* *
55116233 CAAAAAAATATTAATATT-T
1 ---AAAAATATAAAAATTAT
*
55116252 AAAAATATGAAAATTGAT
1 AAAAATATAAAAATT-AT
*
55116270 ATAAATATATAAACATTAT
1 A-AAA-ATATAAAAATTAT
*
55116289 AAACATATTATAAATATTAT
1 AAA-A-A-TATAAAAATTAT
55116309 AAAAATATAAAAATTAT
1 AAAAATATAAAAATTAT
*
55116326 --AAAT-TATAAATTAT
1 AAAAATATAAAAATTAT
55116340 AAAAAGTAT-AAAATTAAT
1 AAAAA-TATAAAAATT-AT
55116358 AAAACATAT
1 AAAA-ATAT
55116367 TGTAATGGCC
Statistics
Matches: 121, Mismatches: 15, Indels: 32
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.07
15 4 0.03
16 16 0.13
17 20 0.17
18 26 0.21
19 12 0.10
20 27 0.22
21 7 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAAATATAAAAATTAT
Found at i:55116361 original size:17 final size:16
Alignment explanation
Indices: 55116236--55116366 Score: 97
Period size: 16 Copynumber: 7.5 Consensus size: 16
55116226 AAATTATCAA
*
55116236 AAAAATATTAATATT-T
1 AAAAATA-TAAAATTAT
55116252 AAAAATATGAAAATTGAT
1 AAAAATAT-AAAATT-AT
55116270 ATAAATATATAAACATTAT
1 A-AAA-ATATAAA-ATTAT
55116289 AAACATATTATAAATATTAT
1 AAA-A-A-TATAAA-ATTAT
55116309 AAAAATATAAAAATTAT
1 AAAAATAT-AAAATTAT
*
55116326 -AAATTAT-AAATTAT
1 AAAAATATAAAATTAT
55116340 AAAAAGTATAAAATTAAT
1 AAAAA-TATAAAATT-AT
55116358 AAAACATAT
1 AAAA-ATAT
55116367 TGTAATGGCC
Statistics
Matches: 97, Mismatches: 4, Indels: 26
0.76 0.03 0.20
Matches are distributed among these distances:
14 7 0.07
15 4 0.04
16 21 0.22
17 13 0.13
18 17 0.18
19 14 0.14
20 21 0.22
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAAATATAAAATTAT
Found at i:55116432 original size:22 final size:21
Alignment explanation
Indices: 55116401--55116442 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55116391 CCCAGTTTAC
55116401 AAATAAATTACAAACCAAAAAA
1 AAATAAATTA-AAACCAAAAAA
* *
55116423 AAATACATTAAACCCAAAAA
1 AAATAAATTAAAACCAAAAA
55116443 GCCTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (21 bp):
AAATAAATTAAAACCAAAAAA
Found at i:55118818 original size:20 final size:21
Alignment explanation
Indices: 55118790--55118871 Score: 93
Period size: 20 Copynumber: 4.1 Consensus size: 21
55118780 GTTTCGACAC
*
55118790 ATATTAAAAT-ATATAAAATT
1 ATATAAAAATCATATAAAATT
*
55118810 ATATAAAAATTAT-TAAAATT
1 ATATAAAAATCATATAAAATT
55118830 ATATAAAAATCATA-AAAATT
1 ATATAAAAATCATATAAAATT
* *
55118850 AT-T-AAAATGATATAAACTT
1 ATATAAAAATCATATAAAATT
55118869 ATA
1 ATA
55118872 CAAATTATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.15
19 8 0.15
20 36 0.67
21 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (21 bp):
ATATAAAAATCATATAAAATT
Found at i:55118824 original size:29 final size:29
Alignment explanation
Indices: 55118791--55118871 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
55118781 TTTCGACACA
55118791 TATTAAAATATATAAAATTATATAAAAAT
1 TATTAAAATATATAAAATTATATAAAAAT
55118820 TATTAAAATTATATAAAA--ATCATAAAAAT
1 TATTAAAA-TATATAAAATTAT-ATAAAAAT
*
55118849 TATTAAAATGATATAAACTTATA
1 TATTAAAAT-ATATAAAATTATA
55118872 CAAATTATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
28 3 0.07
29 31 0.67
30 10 0.22
31 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (29 bp):
TATTAAAATATATAAAATTATATAAAAAT
Found at i:55118846 original size:48 final size:48
Alignment explanation
Indices: 55118795--55118895 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
55118785 GACACATATT
* *
55118795 AAAA-TATATAAAATTATATAAAAATTATTA-AAATTATATAAAAATCATA
1 AAAATTAT-TAAAATGATAT-AAAATTA-TACAAATTATAAAAAAATCATA
*
55118844 AAAATTATTAAAATGATATAAACTTATACAAATTATAAAAAAATCATA
1 AAAATTATTAAAATGATATAAAATTATACAAATTATAAAAAAATCATA
55118892 AAAA
1 AAAA
55118896 CTTGAATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
47 2 0.04
48 28 0.60
49 14 0.30
50 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (48 bp):
AAAATTATTAAAATGATATAAAATTATACAAATTATAAAAAAATCATA
Found at i:55118895 original size:9 final size:9
Alignment explanation
Indices: 55118795--55118884 Score: 72
Period size: 10 Copynumber: 9.4 Consensus size: 9
55118785 GACACATATT
55118795 AAAATATATA
1 AAAAT-TATA
*
55118805 AAATTATATA
1 AAAAT-TATA
55118815 AAAATTATTA
1 AAAATTA-TA
*
55118825 AAATTATATA
1 AAAAT-TATA
*
55118835 AAAATCATA
1 AAAATTATA
*
55118844 AAAATTATT
1 AAAATTATA
*
55118853 AAAATGATA
1 AAAATTATA
*
55118862 TAAACTTATA
1 -AAAATTATA
*
55118872 CAAATTATA
1 AAAATTATA
55118881 AAAA
1 AAAA
55118885 AATCATAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
9 29 0.46
10 32 0.51
11 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:55119425 original size:22 final size:22
Alignment explanation
Indices: 55119400--55119441 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
55119390 CTTTACTAAA
55119400 TTTATAATATTT-ATAAGTTTTT
1 TTTATAAT-TTTAATAAGTTTTT
55119422 TTTATAATTTTAATAAGTTT
1 TTTATAATTTTAATAAGTTT
55119442 ATATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTATAATTTTAATAAGTTTTT
Done.