Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold253
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: 843195
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 44520 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:354458 original size:51 final size:51
Alignment explanation
Indices: 354403--354502 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
354393 AAATATTTAA
*
354403 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * * * * *
354454 AAATATGAATTTGAGTGAAATTTGGAAGGAATTTGAGAGCAATTTGAGA
1 AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
354503 GGAAATTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:354497 original size:11 final size:11
Alignment explanation
Indices: 354460--354537 Score: 77
Period size: 11 Copynumber: 7.0 Consensus size: 11
354450 GATTAAATAT
*
354460 GAATTTGAGTG
1 GAATTTGAGAG
*
354471 AAATTTG-GAAG
1 GAATTTGAG-AG
354482 GAATTTGAGAG
1 GAATTTGAGAG
*
354493 CAATTTGAGAG
1 GAATTTGAGAG
*
354504 GAAATTGAGAG
1 GAATTTGAGAG
*
354515 GAAATTGAGAG
1 GAATTTGAGAG
*
354526 AAAATTTGAGAG
1 -GAATTTGAGAG
354538 AGGATTAGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
10 1 0.02
11 45 0.80
12 10 0.18
ACGTcount: A:0.41, C:0.01, G:0.32, T:0.26
Consensus pattern (11 bp):
GAATTTGAGAG
Found at i:355801 original size:16 final size:14
Alignment explanation
Indices: 355780--355813 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
355770 AATACTTTGC
355780 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
355796 TTATAAATTTTATA
1 TTATAAATTTTATA
355810 TTAT
1 TTAT
355814 TTTTAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:359063 original size:28 final size:28
Alignment explanation
Indices: 359023--359080 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
359013 CTCTAGAGGG
359023 ATAAAACGTGTTTAAGTTTGGAATATCA
1 ATAAAACGTGTTTAAGTTTGGAATATCA
359051 ATAAAACGTGTTTAAGTTTGGAATATCA
1 ATAAAACGTGTTTAAGTTTGGAATATCA
359079 AT
1 AT
359081 TAATTTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (28 bp):
ATAAAACGTGTTTAAGTTTGGAATATCA
Found at i:359508 original size:67 final size:67
Alignment explanation
Indices: 359435--359573 Score: 251
Period size: 67 Copynumber: 2.1 Consensus size: 67
359425 GAAGTAAAAC
359435 AAAATTTGTCAATAATTGTTAAAAATAGAAGGATGATAATGACAATATATCACAAAGAAAAGAAA
1 AAAATTTGTCAATAATTGTTAAAAATAGAAGGATGATAATGACAATATATCACAAAGAAAAGAAA
359500 GA
66 GA
* * *
359502 AAAATTTGTCAATAATTGTTAAAAATAGAATGTTGATAATGATAATATATCACAAAGAAAAGAAA
1 AAAATTTGTCAATAATTGTTAAAAATAGAAGGATGATAATGACAATATATCACAAAGAAAAGAAA
359567 GA
66 GA
359569 AAAAT
1 AAAAT
359574 AGAACACACA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (67 bp):
AAAATTTGTCAATAATTGTTAAAAATAGAAGGATGATAATGACAATATATCACAAAGAAAAGAAA
GA
Found at i:367829 original size:21 final size:21
Alignment explanation
Indices: 367803--367859 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
367793 TTCTCATTTT
367803 CAACAACTTCTTCTTCT-TCAG
1 CAACAACTTCTTCTTCTGT-AG
* *
367824 CAACAACTTCCTCATCTGTAG
1 CAACAACTTCTTCTTCTGTAG
*
367845 CAGCAACTTCCTTCT
1 CAACAACTT-CTTCT
367860 CAACAACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.25, C:0.35, G:0.07, T:0.33
Consensus pattern (21 bp):
CAACAACTTCTTCTTCTGTAG
Found at i:382661 original size:126 final size:126
Alignment explanation
Indices: 382436--382690 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 126
382426 TAATGATTGT
*
382436 CAATTGAACATGGGATGGTAAAGCTCCTAGGATCTTTTAATTTCGGGGCAACTTGTTTGTCAAAA
1 CAATTAAACATGGGATGGTAAAGCTCCTAGGATCTTTTAATTTCGGGGCAACTTGTTTGTCAAAA
382501 AAGCACTACAGCCTTCTGTGAGTGCAATAGTTTCAATATCAGTAAGCTTCTTCTTCATGGA
66 AAGCACTACAGCCTTCTGTGAGTGCAATAGTTTCAATATCAGTAAGCTTCTTCTTCATGGA
*
382562 CAATTAAACATGGGATGGTAAAGCTCTTAGGATCTTTTAATTTCGGGGCAACTTGTTTGTCAAAA
1 CAATTAAACATGGGATGGTAAAGCTCCTAGGATCTTTTAATTTCGGGGCAACTTGTTTGTCAAAA
*
382627 CAGCACTACAGCCTTCTGTGAGTGCAATAGTTTCAATATCAGTAAGCTTCTTCTTCATGGA
66 AAGCACTACAGCCTTCTGTGAGTGCAATAGTTTCAATATCAGTAAGCTTCTTCTTCATGGA
382688 CAA
1 CAA
382691 GAGGTCTTTC
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (126 bp):
CAATTAAACATGGGATGGTAAAGCTCCTAGGATCTTTTAATTTCGGGGCAACTTGTTTGTCAAAA
AAGCACTACAGCCTTCTGTGAGTGCAATAGTTTCAATATCAGTAAGCTTCTTCTTCATGGA
Found at i:387926 original size:21 final size:21
Alignment explanation
Indices: 387888--387927 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
387878 CTTGCAATTC
* *
387888 AAAATTTTCAACTCTTTTCCT
1 AAAATTTCCAAATCTTTTCCT
*
387909 AAAATTTCCAAATGTTTTC
1 AAAATTTCCAAATCTTTTC
387928 GATTTAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (21 bp):
AAAATTTCCAAATCTTTTCCT
Found at i:394223 original size:20 final size:20
Alignment explanation
Indices: 394159--394237 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
394149 TTTGGGTGGA
* *
394159 TTAGCTCTTACGAGCTTTTG
1 TTAGCTCTCACGAGCTTCTG
*
394179 TTTAGCT-T-TCGAGCTTCT-
1 -TTAGCTCTCACGAGCTTCTG
394197 TTCAGCTCTCACGAGCTTCTG
1 TT-AGCTCTCACGAGCTTCTG
*
394218 TTAGCTTTCA--AGCTTCTG
1 TTAGCTCTCACGAGCTTCTG
394236 TT
1 TT
394238 TGTTATTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.04
18 14 0.28
19 9 0.18
20 17 0.34
21 8 0.16
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (20 bp):
TTAGCTCTCACGAGCTTCTG
Found at i:394232 original size:38 final size:39
Alignment explanation
Indices: 394161--394234 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
394151 TGGGTGGATT
* * *
394161 AGCTCTTACGAGCTTTTGTTTAGCTTTCGAGCTTCTTTC
1 AGCTCTCACGAGCTTCTGTTTAGCTTTCAAGCTTCTTTC
394200 AGCTCTCACGAGCTTCTG-TTAGCTTTCAAGCTTCT
1 AGCTCTCACGAGCTTCTGTTTAGCTTTCAAGCTTCT
394235 GTTTGTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 16 0.50
39 16 0.50
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.42
Consensus pattern (39 bp):
AGCTCTCACGAGCTTCTGTTTAGCTTTCAAGCTTCTTTC
Found at i:394233 original size:18 final size:18
Alignment explanation
Indices: 394180--394237 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
394170 GAGCTTTTGT
*
394180 TTAGCTTTCGAGCTTCT-
1 TTAGCTTTCAAGCTTCTG
*
394197 TTCAGCTCTCACGAGCTTCTG
1 TT-AGCTTTCA--AGCTTCTG
394218 TTAGCTTTCAAGCTTCTG
1 TTAGCTTTCAAGCTTCTG
394236 TT
1 TT
394238 TGTTATTAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.06
18 16 0.47
20 14 0.41
21 2 0.06
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (18 bp):
TTAGCTTTCAAGCTTCTG
Found at i:402223 original size:26 final size:26
Alignment explanation
Indices: 402151--402216 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
402141 TTTATACATT
*
402151 TCACACGAGCTGTGAAATGGGCCTAC
1 TCACACGAGCTGTGAAATGGGCATAC
* *
402177 TCACACGAGCTATGAAATGGGTATAC
1 TCACACGAGCTGTGAAATGGGCATAC
402203 TCACACGAGCTGTG
1 TCACACGAGCTGTG
402217 GATTGGGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATGGGCATAC
Found at i:408580 original size:13 final size:13
Alignment explanation
Indices: 408562--408633 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
408552 TAATTATTTC
*
408562 CATATAACTGATT
1 CATATAACTAATT
*
408575 CATATAA-TCATT
1 CATATAACTAATT
* *
408587 CAGTATAAATATTT
1 CA-TATAACTAATT
*
408601 CCATATAACCAATT
1 -CATATAACTAATT
*
408615 CATATAACCAATT
1 CATATAACTAATT
408628 CATATA
1 CATATA
408634 TTCATTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.12
13 31 0.62
14 11 0.22
15 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (13 bp):
CATATAACTAATT
Found at i:408581 original size:40 final size:40
Alignment explanation
Indices: 408520--408621 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
408510 TACATAATTA
* * * *
408520 TCCATATAAACATTTCGTATAAACACCTT-A-TATAATTATT
1 TCCATATAACCAATTCATATAAACA--TTCAGTATAAATATT
** *
408560 TCCATATAACTGATTCATATAATCATTCAGTATAAATATT
1 TCCATATAACCAATTCATATAAACATTCAGTATAAATATT
408600 TCCATATAACCAATTCATATAA
1 TCCATATAACCAATTCATATAA
408622 CCAATTCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 48 0.94
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (40 bp):
TCCATATAACCAATTCATATAAACATTCAGTATAAATATT
Found at i:408647 original size:53 final size:52
Alignment explanation
Indices: 408562--408672 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 52
408552 TAATTATTTC
** *
408562 CATATAACTGATTCATATAATCATTCAGTATAAATATTTCCATATAACCAATT
1 CATATAACCAATTCATATAATCATTCAGTATAAACATTTCCA-ATAACCAATT
* * * * *
408615 CATATAACCAATTCATATATTCATTTTA-TATAACCATTTCGAATAACCATTT
1 CATATAACCAATTCATATAATCA-TTCAGTATAAACATTTCCAATAACCAATT
408667 CATATA
1 CATATA
408673 CAAAATTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
52 15 0.31
53 31 0.63
54 3 0.06
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.39
Consensus pattern (52 bp):
CATATAACCAATTCATATAATCATTCAGTATAAACATTTCCAATAACCAATT
Found at i:408652 original size:13 final size:13
Alignment explanation
Indices: 408573--408672 Score: 87
Period size: 13 Copynumber: 7.6 Consensus size: 13
408563 ATATAACTGA
*
408573 TTCATATAATCA-
1 TTCATATAACCAT
**
408585 TTCAGTATAAATAT
1 TTCA-TATAACCAT
*
408599 TTCCATATAACCAA
1 TT-CATATAACCAT
*
408613 TTCATATAACCAA
1 TTCATATAACCAT
**
408626 TTCATATATTCAT
1 TTCATATAACCAT
*
408639 TTTATATAACCAT
1 TTCATATAACCAT
408652 TTCGA-ATAACCAT
1 TTC-ATATAACCAT
408665 TTCATATA
1 TTCATATA
408673 CAAAATTTAC
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.07
13 53 0.75
14 11 0.15
15 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:408665 original size:26 final size:26
Alignment explanation
Indices: 408522--408672 Score: 83
Period size: 26 Copynumber: 5.7 Consensus size: 26
408512 CATAATTATC
* * * *
408522 CATATAAACATTTCGTATAAACACCTT
1 CATATAACCATTTCATATAACCA-ATT
** **
408549 -ATATAATTATTTCCATATAACTGATT
1 CATATAACCATTT-CATATAACCAATT
* ** *
408575 CATATAATCA-TTCAGTATAAATATTT
1 CATATAACCATTTCA-TATAACCAATT
*
408601 CCATATAACCAATTCATATAACCAATT
1 -CATATAACCATTTCATATAACCAATT
** * *
408628 CATATATTCATTTTATATAACCATTT
1 CATATAACCATTTCATATAACCAATT
408654 CGA-ATAACCATTTCATATA
1 C-ATATAACCATTTCATATA
408673 CAAAATTTAC
Statistics
Matches: 95, Mismatches: 23, Indels: 13
0.73 0.18 0.10
Matches are distributed among these distances:
25 2 0.02
26 57 0.60
27 32 0.34
28 4 0.04
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (26 bp):
CATATAACCATTTCATATAACCAATT
Found at i:410353 original size:27 final size:27
Alignment explanation
Indices: 410314--410380 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
410304 GCACACTAGA
* *
410314 AAATGGAAACCTTTTTGGCAATCTATG
1 AAATGGAAGCCTTTTTGGAAATCTATG
*
410341 AAATGGAAGCCTTTTTGGAAATCTATT
1 AAATGGAAGCCTTTTTGGAAATCTATG
*
410368 ATAATAGAAGCCT
1 A-AATGGAAGCCT
410381 CTATGGTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (27 bp):
AAATGGAAGCCTTTTTGGAAATCTATG
Found at i:410579 original size:29 final size:29
Alignment explanation
Indices: 410499--410569 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
410489 TATTCTTGGT
* * *
410499 GAACTATGAAGGAGTAG--TATACATGGC
1 GAACTCTGAAGGAATAGTATATATATGGC
410526 GAACTCTGAAGGAATAGTATATATATGGC
1 GAACTCTGAAGGAATAGTATATATATGGC
410555 GAACTCTGAAGGAAT
1 GAACTCTGAAGGAAT
410570 GGTAAGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 15 0.38
29 24 0.62
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (29 bp):
GAACTCTGAAGGAATAGTATATATATGGC
Found at i:413944 original size:61 final size:61
Alignment explanation
Indices: 413846--413962 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
413836 AATGAATTTA
* *
413846 ATATTAAATTAAATTTAATATTTATCTAGATAGTATTTTATTAATGTAATATTAATATGAG
1 ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAG
*
413907 ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAAT
1 ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAAT
413963 GTGATTAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (61 bp):
ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAG
Found at i:414023 original size:97 final size:96
Alignment explanation
Indices: 413907--414095 Score: 290
Period size: 97 Copynumber: 2.0 Consensus size: 96
413897 TTAATATGAG
* * *
413907 ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAATGTGATTAAT
1 ATATTAAATTTAATATAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAGTAAT
*
413972 TAT-ACTCCTAGTTGAACTCTCTCTAAAATTTA
66 T-TCAATCCTAGTTGAACTCTCTC-AAAATTTA
* * *
414004 ATATTAAATTTAATATAATATTTATCTTGATTATATTTTATTAATTTAATATTAATATGAGTAAT
1 ATATTAAATTTAATATAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAGTAAT
414069 TTCAATCCTAGTTGAACTCTCTCAAAA
66 TTCAATCCTAGTTGAACTCTCTCAAAA
414096 CTCTCCTTAT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
96 5 0.06
97 79 0.94
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (96 bp):
ATATTAAATTTAATATAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAGTAAT
TTCAATCCTAGTTGAACTCTCTCAAAATTTA
Found at i:416406 original size:19 final size:19
Alignment explanation
Indices: 416370--416412 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
416360 GTTTTATTAA
*
416370 TATTTTTATATTTACCTAT
1 TATTTTTATAATTACCTAT
416389 TATTATTTATAATT-CCTAT
1 TATT-TTTATAATTACCTAT
416408 TATTT
1 TATTT
416413 GAGAACTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTATAATTACCTAT
Found at i:422306 original size:8 final size:8
Alignment explanation
Indices: 422295--422336 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
422285 AATTAATTAT
*
422295 ATAATTGA
1 ATAATTGG
422303 ATAATTGG
1 ATAATTGG
*
422311 ATAAAT--
1 ATAATTGG
422317 ATAATTGG
1 ATAATTGG
422325 ATAATTGG
1 ATAATTGG
422333 ATAA
1 ATAA
422337 CTAACTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
8 24 0.83
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (8 bp):
ATAATTGG
Found at i:422318 original size:22 final size:22
Alignment explanation
Indices: 422293--422336 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
422283 TTAATTAATT
422293 ATATAATTGAATAATTGGATAA
1 ATATAATTGAATAATTGGATAA
*
422315 ATATAATTGGATAATTGGATAA
1 ATATAATTGAATAATTGGATAA
422337 CTAACTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (22 bp):
ATATAATTGAATAATTGGATAA
Found at i:427239 original size:26 final size:26
Alignment explanation
Indices: 427195--427247 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
427185 TTGAATAAAA
*
427195 AGGGGTTGCTAGGTACTGATTCCCCG
1 AGGGGTTGCTAAGTACTGATTCCCCG
* *
427221 AGGGGTTTCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTACTGATTCCCCG
427247 A
1 A
427248 ATTATTGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTACTGATTCCCCG
Found at i:427320 original size:43 final size:44
Alignment explanation
Indices: 427260--427498 Score: 226
Period size: 43 Copynumber: 5.6 Consensus size: 44
427250 TATTGACTCT
* *
427260 AAAGGTGGTTGCTAAGTGCTGATCCCACCATATTTTTAATTGTG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCATATATTTAATTGTG
* * *
427304 AAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGAA-TAT-
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCATAT-ATTTAATTGTG
* * * *
427345 AAAGGTGGTTGCTATGTGCTGAATCCACAATATTTTTAATTGTG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCATATATTTAATTGTG
* * * * * *
427389 AATGG-GGTTGCTAAGTGTTGATTCC-CCGTATCACTGAA-TAT-
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCATAT-ATTTAATTGTG
* **
427430 AAAGGTGGTTGCTAAGTGCTGATTCCACCAAATCCTTAATTGTG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCATATATTTAATTGTG
*
427474 AAAGG-GGTTGCTATGTGCTGATTCC
1 AAAGGTGGTTGCTAAGTGCTGATTCC
427499 CCGTATCACT
Statistics
Matches: 155, Mismatches: 30, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
41 9 0.06
42 58 0.37
43 74 0.48
44 14 0.09
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (44 bp):
AAAGGTGGTTGCTAAGTGCTGATTCCACCATATATTTAATTGTG
Found at i:427364 original size:85 final size:84
Alignment explanation
Indices: 427221--427541 Score: 437
Period size: 85 Copynumber: 3.8 Consensus size: 84
427211 TGATTCCCCG
* * * * * *
427221 AGGGGTTTCTAAGTGCTGATTCCCCGAATTATTGACTCTAAAGGTGGTTGCTAAGTGCTGATCCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGAT-CC
427286 ACCATATTTTTAATTGTGAA
65 ACCATATTTTTAATTGTGAA
* *
427306 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAATATAAAGGTGGTTGCTATGTGCTGAATCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTG-ATCC
*
427371 ACAATATTTTTAATTGTGAA
65 ACCATATTTTTAATTGTGAA
* *
427391 TGGGGTTGCTAAGTGTTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGA-TCC
* **
427456 ACCAAATCCTTAATTGTGAA
65 ACCATATTTTTAATTGTGAA
* * * *
427476 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTATA-GTGGTTGCTAAGTGTTGAATCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTG-ATCC
427540 AC
65 AC
427542 TGAGTAACGG
Statistics
Matches: 212, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
84 22 0.10
85 188 0.89
86 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (84 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATCCA
CCATATTTTTAATTGTGAA
Found at i:430175 original size:20 final size:20
Alignment explanation
Indices: 430130--430180 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
430120 TATAATATTA
* *
430130 ATATTATATCAGTAATAGAG
1 ATATTGTATCAGTAATAAAG
430150 ATATTGTATCAGTAATAAAG
1 ATATTGTATCAGTAATAAAG
*
430170 ATATTGAATCA
1 ATATTGTATCA
430181 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATTGTATCAGTAATAAAG
Found at i:433635 original size:17 final size:17
Alignment explanation
Indices: 433589--433638 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
433579 TTTTTTAAAT
433589 AATTATTGAATTATTTGA
1 AATTATTGAATTATTT-A
*
433607 AA--ATT--TTTATTTA
1 AATTATTGAATTATTTA
433620 AATTATTGAATTATTTA
1 AATTATTGAATTATTTA
433637 AA
1 AA
433639 AATTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 3 0.12
14 6 0.23
15 3 0.12
16 3 0.12
17 9 0.35
18 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTATTGAATTATTTA
Found at i:433647 original size:30 final size:31
Alignment explanation
Indices: 433589--433654 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
433579 TTTTTTAAAT
*
433589 AATTATTGAATTATTTGAAAATTTTTATTTA
1 AATTATTGAATTATTTGAAAAATTTTATTTA
433620 AATTATTGAATTATTT-AAAAATTTTATTTA
1 AATTATTGAATTATTTGAAAAATTTTATTTA
433650 AATTA
1 AATTA
433655 ATATGTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (31 bp):
AATTATTGAATTATTTGAAAAATTTTATTTA
Found at i:434735 original size:19 final size:19
Alignment explanation
Indices: 434704--434759 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
434694 ACTTGTTTTA
434704 AAACAATTTTAACTTGATTG
1 AAAC-ATTTTAACTTGATTG
**
434724 AAA-ATGTTTAACTCAATTG
1 AAACAT-TTTAACTTGATTG
434743 AAATCATTTTAACTTGA
1 AAA-CATTTTAACTTGA
434760 CTTTATACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 11 0.38
21 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (19 bp):
AAACATTTTAACTTGATTG
Found at i:436349 original size:18 final size:18
Alignment explanation
Indices: 436314--436366 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
436304 TAATCGATTC
* *
436314 GATCGGTTCAATTAGTTT
1 GATCGGTACAATTGGTTT
*
436332 GATTGGTACAATTGGTTT
1 GATCGGTACAATTGGTTT
* *
436350 GATCGGTCCATTTGGTT
1 GATCGGTACAATTGGTT
436367 CTATTAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (18 bp):
GATCGGTACAATTGGTTT
Found at i:440870 original size:42 final size:42
Alignment explanation
Indices: 440783--440928 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
440773 CTTTCAATTT
* ** * *
440783 AGCTCTTATGAGCTTCTGTTCAACTCAAATGAGTTTTCGTCC
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTCGTTC
* * *
440825 AGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTC
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTCGTTC
* ** * *
440867 AGCTCTTATTAGCTTCCATTCAACCCTTATGGGTTTTTGTTT
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTCGTTC
* *
440909 AGCACTTATGTGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
440929 TAGCGTTCAA
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTCGTTC
Found at i:440916 original size:21 final size:21
Alignment explanation
Indices: 440892--440932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
440882 CCATTCAACC
* *
440892 CTTATGGGTTTTTGTTTAGCA
1 CTTATGGGCTTCTGTTTAGCA
*
440913 CTTATGTGCTTCTGTTTAGC
1 CTTATGGGCTTCTGTTTAGC
440933 GTTCAAGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.51
Consensus pattern (21 bp):
CTTATGGGCTTCTGTTTAGCA
Found at i:448609 original size:21 final size:21
Alignment explanation
Indices: 448585--448692 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 21
448575 CGTGTTTACT
* *
448585 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
448606 TTCTGTTCAACTCATATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
448627 TTCCGTTCAGCTCTTTTGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * * *
448648 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
*
448669 TTCAGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
448690 TTC
1 TTC
448693 CATTCAACCT
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:448707 original size:42 final size:42
Alignment explanation
Indices: 448584--448745 Score: 148
Period size: 42 Copynumber: 3.9 Consensus size: 42
448574 TCGTGTTTAC
* * * *
448584 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAA-CTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCT-TTATGGG
* * * *
448626 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCTTTATGGG
* **
448668 TTTCAGTTCAGCTCTTATGAGCTTCCATTCAACCTTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCTTTATGGG
* * * * *
448710 ATTCTGTTTAGCACTTATGTA-CTTTTGTTCAGCCTT
1 TTTCTGTTCAGCTCTTATG-AGCTTCTGTTCAACCTT
448746 CAGGCTTTTG
Statistics
Matches: 96, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 94 0.98
43 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCTTTATGGG
Found at i:452476 original size:14 final size:14
Alignment explanation
Indices: 452457--452486 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
452447 AATGTTACAA
452457 ATATATAAATATGG
1 ATATATAAATATGG
*
452471 ATATATAAATGTGG
1 ATATATAAATATGG
452485 AT
1 AT
452487 GTCTATATTT
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:0.17, T:0.37
Consensus pattern (14 bp):
ATATATAAATATGG
Found at i:454155 original size:51 final size:50
Alignment explanation
Indices: 454023--454210 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 50
454013 TGTCATCTGA
* * *
454023 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAGCTTTCCAG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGCTATCCGG
* *
454073 TTCACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGGCCATCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAA-GCTATCCGG
* * * ** *
454124 TACACTTAGTAGCCTGCACATAGTACTACACATGTGACCATTATTTAT-CGA
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCA--AGCTATCCGG
* *
454175 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
454211 TTCATAGGTA
Statistics
Matches: 119, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
50 39 0.33
51 77 0.65
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAGCTATCCGG
Found at i:458044 original size:23 final size:23
Alignment explanation
Indices: 458010--458060 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
458000 GTGACGAAGT
*
458010 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
458033 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
458056 AGTAA
1 TGTAA
458061 GAAAATAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:458538 original size:15 final size:15
Alignment explanation
Indices: 458518--458548 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
458508 TTTATTAATA
*
458518 TTTTAATTTGATTTT
1 TTTTAATTTAATTTT
458533 TTTTAATTTAATTTT
1 TTTTAATTTAATTTT
458548 T
1 T
458549 AAATGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTAATTTAATTTT
Found at i:463160 original size:30 final size:30
Alignment explanation
Indices: 463114--463171 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
463104 TCCGAGCTTT
463114 GGGGAAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGAAAAAGTGTAATTATGTAAAAGTTTA
* * * *
463144 GGGGCAAAATTGTAATTTTGTCAAAGTT
1 GGGGAAAAAGTGTAATTATGTAAAAGTT
463172 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGGAAAAAGTGTAATTATGTAAAAGTTTA
Found at i:466573 original size:50 final size:50
Alignment explanation
Indices: 466406--466592 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 50
466396 ATCGATGAAT
* *
466406 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAA-ACTTGGTC
* * * *
466457 ACATGTGTAGTACTAAGTGAAGGCTACTATGTATACCG-AAAAGCTTTGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAA-C-TTGGTC
* * *
466508 ACGTGTGTAGTACTATGTGAAGGTTACTACATGGACCGTAAAACTTGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGTC
* *
466558 ACGTGTGTGGTACTATGTGAAGGCTATTACGTGTA
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
466593 TCGAATGATA
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 36 0.32
51 70 0.61
52 4 0.04
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (50 bp):
ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGTC
Found at i:468933 original size:27 final size:27
Alignment explanation
Indices: 468903--468958 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
468893 GATATAAGAT
468903 TATTTTATTCAAATGATTCAAAATCCC
1 TATTTTATTCAAATGATTCAAAATCCC
468930 TATTTTATTCAAATGATTCAAAATCCC
1 TATTTTATTCAAATGATTCAAAATCCC
468957 TA
1 TA
468959 ATAGTCGGTT
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:0.38, C:0.18, G:0.04, T:0.41
Consensus pattern (27 bp):
TATTTTATTCAAATGATTCAAAATCCC
Found at i:469991 original size:20 final size:20
Alignment explanation
Indices: 469952--469991 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
469942 ATTTATAAAT
* **
469952 AAATTAAAAATATTTTTTTA
1 AAATTAAAAAAATTGATTTA
469972 AAATTAAAAAAATTGATTTA
1 AAATTAAAAAAATTGATTTA
469992 GTTGAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATTAAAAAAATTGATTTA
Found at i:475545 original size:16 final size:15
Alignment explanation
Indices: 475524--475554 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
475514 TTTCTTAGAT
475524 TATATAATATGTAATA
1 TATATAATAT-TAATA
475540 TATATAATATTAATA
1 TATATAATATTAATA
475555 AAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TATATAATATTAATA
Found at i:478477 original size:38 final size:37
Alignment explanation
Indices: 478407--478479 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
478397 CTTTCATAAT
*
478407 TTCACTTTTTCACTTTCAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCACAATTCAATTCAAAA
478444 TTCACTTTTCCA-TTTCTAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCACTTTC-AA-TCACA-ATTCAATTCAA
478480 TTCCACAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.42
Consensus pattern (37 bp):
TTCACTTTTCCACTTTCAATCACAATTCAATTCAAAA
Found at i:478677 original size:14 final size:14
Alignment explanation
Indices: 478654--478686 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
478644 TCGGTTCACG
*
478654 TAGTAGCCTGCACA
1 TAGTAACCTGCACA
478668 TAGTAACCTGCACA
1 TAGTAACCTGCACA
478682 TAGTA
1 TAGTA
478687 CTACACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (14 bp):
TAGTAACCTGCACA
Found at i:478744 original size:51 final size:49
Alignment explanation
Indices: 478676--478850 Score: 163
Period size: 51 Copynumber: 3.5 Consensus size: 49
478666 CATAGTAACC
*
478676 TGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCG
1 TGCACATAGTACTACACATGTGACCA-TACCATCCG-TACACGTAGTAGCA
* * * * * * * *
478727 TGCGCATAGTACTACACACGTGATCGAAACTATCCGGTACGCATAGTAGCT
1 TGCACATAGTACTACACATGTGA-CCATACCATCC-GTACACGTAGTAGCA
* * * *
478778 TGCTCATAGTACTACACATGCGACC-TATCATTCCTGTACACGTAGTAGAA
1 TGCACATAGTACTACACATGTGACCATACCA-TCC-GTACACGTAGTAGCA
*
478828 TACACATAGTACTACACATGTGA
1 TGCACATAGTACTACACATGTGA
478851 ACATCACTTT
Statistics
Matches: 98, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
49 2 0.02
50 35 0.36
51 58 0.59
52 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (49 bp):
TGCACATAGTACTACACATGTGACCATACCATCCGTACACGTAGTAGCA
Found at i:478842 original size:101 final size:101
Alignment explanation
Indices: 478666--478850 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 101
478656 GTAGCCTGCA
* ** * *
478666 CATAGTAACCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCGTGCG
1 CATAGTAACCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGAATACA
478731 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
478768 CATAGTAGCTTGCTCATAGTACTACACATGCGACC-TATCATTCCTG-TACACGTAGTAGAATAC
1 CATAGTAACCTGCACATAGTACTACACATGCGACCATACCA-TCC-GATACACGTAGTAGAATAC
*
478831 ACATAGTACTACACATGTGA
64 ACATAGTACTACACACGTGA
478851 ACATCACTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
100 4 0.06
101 35 0.49
102 32 0.45
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAACCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGAATACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:480201 original size:167 final size:167
Alignment explanation
Indices: 479925--480260 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
479915 AAACCACTAT
479925 TTTAGCTAGCCCCAAGTTTGGGCTGTTACATTCCATATGCTTTGGCAGTTGGAAGACTTATGTAT
1 TTTAGCTAGCCCCAAGTTTGGGCTGTTACATTCCATATGCTTTGGCAGTTGGAAGACTTATGTAT
479990 GCGATGCTTTACACACGTACAAATATTTGTTTTGCAGTGGGAATGGTTAGTCAATATAAAGCGAA
66 GCGATGCTTTACACACGTACAAATATTTGTTTTGCAGTGGGAATGGTTAGTCAATATAAAGCGAA
480055 TCTTGGTCTTAGGCATTAGCAAGCTATAAAGCATATA
131 TCTTGGTCTTAGGCATTAGCAAGCTATAAAGCATATA
480092 TTTAGCTAGCCCCAAGTTTGGGCTGTTACATTCCATATGCTTTGGCAGTTGGAAGACTTATGTAT
1 TTTAGCTAGCCCCAAGTTTGGGCTGTTACATTCCATATGCTTTGGCAGTTGGAAGACTTATGTAT
480157 GCGATGCTTTACACACGTACAAATATTTGTTTTGCAGTGGGAATGGTTAGTCAATATAAAGCGAA
66 GCGATGCTTTACACACGTACAAATATTTGTTTTGCAGTGGGAATGGTTAGTCAATATAAAGCGAA
480222 TCTTGGTCTTAGGCATTAGCAAGCTATAAAGCATATA
131 TCTTGGTCTTAGGCATTAGCAAGCTATAAAGCATATA
480259 TT
1 TT
480261 AAGGTATCTT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (167 bp):
TTTAGCTAGCCCCAAGTTTGGGCTGTTACATTCCATATGCTTTGGCAGTTGGAAGACTTATGTAT
GCGATGCTTTACACACGTACAAATATTTGTTTTGCAGTGGGAATGGTTAGTCAATATAAAGCGAA
TCTTGGTCTTAGGCATTAGCAAGCTATAAAGCATATA
Found at i:480708 original size:157 final size:156
Alignment explanation
Indices: 480408--480720 Score: 509
Period size: 157 Copynumber: 2.0 Consensus size: 156
480398 TGGCGTAGCC
*
480408 ATAGCATGGAGAAGTGTAAAACAAACTTGCACTGCTGACTCTACTATGGAGGCCAAGTATGTGGT
1 ATAGCATGGAGAAGTGTAAAACAAACTTGCACTACTGACTCTACTATGGAGGCCAAGTATGTGGT
* * * *
480473 TGTTTTTGAGACAACGAAAGAAGCAATTTGGTTTCGAAATTTCTTAACTGATCTTGAAGTCATTC
66 TGCTTTTGAGACAACGAAAGAAGCAATTTGGCTTCGAAAGTTCTTAACTAATCTTGAAGTCATTC
*
480538 CTGATATGAAAAAAAAGCTATAACACT
131 CTGATATG-AAAAAAAGATATAACACT
* *
480565 ATAGTATGGATAAGTGTAAAACAAACTTGCACTACTGACTCTACTATGGAGGCCAAGTATGTGGT
1 ATAGCATGGAGAAGTGTAAAACAAACTTGCACTACTGACTCTACTATGGAGGCCAAGTATGTGGT
* *
480630 TGCTTTTGAGACAATGAATGAAGCAATTTGGCTTCGAAAGTTCTTAACTAATCTTGAAGTCATTC
66 TGCTTTTGAGACAACGAAAGAAGCAATTTGGCTTCGAAAGTTCTTAACTAATCTTGAAGTCATTC
* *
480695 CTGGTATGGAAAAAAGATATAACACT
131 CTGATATGAAAAAAAGATATAACACT
480721 TTATTGTGAT
Statistics
Matches: 144, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
156 16 0.11
157 128 0.89
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (156 bp):
ATAGCATGGAGAAGTGTAAAACAAACTTGCACTACTGACTCTACTATGGAGGCCAAGTATGTGGT
TGCTTTTGAGACAACGAAAGAAGCAATTTGGCTTCGAAAGTTCTTAACTAATCTTGAAGTCATTC
CTGATATGAAAAAAAGATATAACACT
Found at i:493321 original size:13 final size:14
Alignment explanation
Indices: 493300--493350 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
493290 ACTAACCAGT
*
493300 TAACTTTTACTG-A
1 TAACATTTACTGAA
493313 TAACATTTAACTGTAA
1 TAACATTT-ACTG-AA
493329 TAACATTTAACTGTAA
1 TAACATTT-ACTG-AA
493345 TAACAT
1 TAACAT
493351 AAAACCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
16 23 0.68
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (14 bp):
TAACATTTACTGAA
Found at i:493333 original size:16 final size:16
Alignment explanation
Indices: 493312--493350 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
493302 ACTTTTACTG
493312 ATAACATTTAACTGTA
1 ATAACATTTAACTGTA
493328 ATAACATTTAACTGTA
1 ATAACATTTAACTGTA
493344 ATAACAT
1 ATAACAT
493351 AAAACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (16 bp):
ATAACATTTAACTGTA
Found at i:494963 original size:24 final size:23
Alignment explanation
Indices: 494932--494982 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
494922 AGCTGTGTAC
*
494932 TTGTGAAGTTGTAGGTTTTACCT
1 TTGTGAAGTTATAGGTTTTACCT
494955 TTGTAGAAGTTATAGGTTTTACCT
1 TTGT-GAAGTTATAGGTTTTACCT
494979 TTGT
1 TTGT
494983 TTGAAGATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.49
Consensus pattern (23 bp):
TTGTGAAGTTATAGGTTTTACCT
Found at i:500176 original size:50 final size:50
Alignment explanation
Indices: 500097--500194 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
500087 ACCTTATTCT
* *
500097 AATCAATGTCAAATAGAATGAGAGAAGTTCTATA-TGAATTCTACTTGTAC
1 AATCAATATCAAATAGAATGAGAGAAGTTCTATACAG-ATTCTACTTGTAC
*
500147 AATCAATATCAAATAGAA-GAAGAGTAGTTCTATACAGATTCTACTTGT
1 AATCAATATCAAATAGAATG-AGAGAAGTTCTATACAGATTCTACTTGT
500195 CCAGCCTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 1 0.02
50 41 0.95
51 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (50 bp):
AATCAATATCAAATAGAATGAGAGAAGTTCTATACAGATTCTACTTGTAC
Found at i:502213 original size:263 final size:263
Alignment explanation
Indices: 501734--502245 Score: 776
Period size: 263 Copynumber: 1.9 Consensus size: 263
501724 GCCACTCAAA
501734 TGTTAATATGCAGTAGAGCTAACATATATGTCGTACTGTGCAGTAAACCGCTATACAGACGTATT
1 TGTTAATATGCAGTAGAGCTAACATATATGTCGTACTGTGCAGTAAACCGCTATACAGACGTATT
* *
501799 GCAGTTGAAACTGCCAAAACAAATCAGACTCCCTTCTCTTCGCAACCCAACCTAAAAAGGTTAAT
66 GCAGTTGAAACTGCCAAAACAAATCAGACTCCCTTCTCTTCGCAACCCAACCCAAAAAGATTAAT
* * * * * *
501864 GCATATGCAAAAATGCACACTATACATTATTAGTCACACTAACATAGAAGCTCGTAAGCAGTTAG
131 GCATATGCAAAAATACACACCATACATTATCAGTCACACTAACATAGAAGCTCGTAAACAGTCAA
* * *
501929 TCAATTACAGAATCGATGTACACT-GTTTCCAGACAACCACAAACCAGATAAACATAATCGATGT
196 TCAATGACAGAATCAATGTACA-TAGTTTCCAGACAACCACAAACAAGATAAACATAATCGATGT
501993 ACAC
260 ACAC
*
501997 TGTTAATATGCTGTAGAGCTAACATATATGTCGTACTGTGCAGTAAACCGCTATACAGACGTATT
1 TGTTAATATGCAGTAGAGCTAACATATATGTCGTACTGTGCAGTAAACCGCTATACAGACGTATT
* * * * * *
502062 GTAGTTGAAATTGCCAAAACAGATCAGACTCCCTTCTCTTTGCAACCTAACCCAAAGAGATTAAT
66 GCAGTTGAAACTGCCAAAACAAATCAGACTCCCTTCTCTTCGCAACCCAACCCAAAAAGATTAAT
* *
502127 GCATGTGCAAAAATACACACCATACATTATCAGTCATAC-AGACATAGAAGCTCGTAAACAGTCA
131 GCATATGCAAAAATACACACCATACATTATCAGTCACACTA-ACATAGAAGCTCGTAAACAGTCA
* * * *
502191 ATTAATGATAGAATCAATGTACATAGTTTCCAGACAATCACACACAAGATAAACA
195 ATCAATGACAGAATCAATGTACATAGTTTCCAGACAACCACAAACAAGATAAACA
502246 GAATAGAAAG
Statistics
Matches: 223, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
262 2 0.01
263 221 0.99
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (263 bp):
TGTTAATATGCAGTAGAGCTAACATATATGTCGTACTGTGCAGTAAACCGCTATACAGACGTATT
GCAGTTGAAACTGCCAAAACAAATCAGACTCCCTTCTCTTCGCAACCCAACCCAAAAAGATTAAT
GCATATGCAAAAATACACACCATACATTATCAGTCACACTAACATAGAAGCTCGTAAACAGTCAA
TCAATGACAGAATCAATGTACATAGTTTCCAGACAACCACAAACAAGATAAACATAATCGATGTA
CAC
Found at i:502456 original size:15 final size:17
Alignment explanation
Indices: 502436--502467 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
502426 ACACAAGATC
502436 ACAAACA-AGT-CAAAA
1 ACAAACACAGTACAAAA
502451 ACAAACACAGTACAAAA
1 ACAAACACAGTACAAAA
502468 GTTGGCGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAACACAGTACAAAA
Found at i:520389 original size:13 final size:14
Alignment explanation
Indices: 520370--520407 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
520360 CAATGGCATA
520370 GAAATAATATAAAC
1 GAAATAATATAAAC
520384 -AAATAA-ATAAAC
1 GAAATAATATAAAC
520396 GAAATGAATATA
1 GAAAT-AATATA
520408 CATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:524647 original size:13 final size:13
Alignment explanation
Indices: 524629--524687 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
524619 CTCAATTTTT
*
524629 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
524642 TCAAAAACACTTC
1 TCAAAAGCACTTC
* * *
524655 TTAAAAACACTTT
1 TCAAAAGCACTTC
524668 TCAAAAGCACTTC
1 TCAAAAGCACTTC
524681 TCAAAAG
1 TCAAAAG
524688 TAATGAAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:527256 original size:18 final size:18
Alignment explanation
Indices: 527229--527267 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
527219 AGGAATAGGA
*
527229 AATTTCATTAGGTTAATT
1 AATTTAATTAGGTTAATT
*
527247 AATTTAATTAGTTTAATT
1 AATTTAATTAGGTTAATT
527265 AAT
1 AAT
527268 ATTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
AATTTAATTAGGTTAATT
Found at i:527652 original size:21 final size:22
Alignment explanation
Indices: 527616--527657 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
527606 ACGAGCTAGA
*
527616 TAGTGTTCTAACTTTTAATTTT
1 TAGTGTGCTAACTTTTAATTTT
*
527638 TAGTGTGCT-ACTTTTTATTT
1 TAGTGTGCTAACTTTTAATTT
527658 GTTTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.60
Consensus pattern (22 bp):
TAGTGTGCTAACTTTTAATTTT
Found at i:534827 original size:44 final size:44
Alignment explanation
Indices: 534772--534865 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
534762 CTTTGTGATG
* * *
534772 TATTTTGATTTGGGC-TTTATGGCATTCTGTTATCCTTTGTGGCA
1 TATTTTAATTT-GGCTTTTATGGCATTCTATTAGCCTTTGTGGCA
* *
534816 TATTTTAATTTGGCTTTTGTGGCATTCTATTAGCCTTTGTGGCT
1 TATTTTAATTTGGCTTTTATGGCATTCTATTAGCCTTTGTGGCA
534860 TATTTT
1 TATTTT
534866 GTATGTTGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.14, C:0.13, G:0.20, T:0.53
Consensus pattern (44 bp):
TATTTTAATTTGGCTTTTATGGCATTCTATTAGCCTTTGTGGCA
Found at i:536451 original size:25 final size:25
Alignment explanation
Indices: 536417--536465 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
536407 GTAAACTTGA
*
536417 AAATTCTCTAGAAAGCCTTTGTGGT
1 AAATTCTCTAAAAAGCCTTTGTGGT
*
536442 AAATTCTCTAAAAAGCTTTTGTGG
1 AAATTCTCTAAAAAGCCTTTGTGG
536466 CGTATCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (25 bp):
AAATTCTCTAAAAAGCCTTTGTGGT
Found at i:536542 original size:25 final size:24
Alignment explanation
Indices: 536514--536592 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 24
536504 AAGTCTTTAC
536514 GGCATATCATTTGAAAAGCCTTTGT
1 GGCATATC-TTTGAAAAGCCTTTGT
*
536539 GGCA-AGTTCTCTAGAAAAGCCTTTGT
1 GGCATA--TCT-TTGAAAAGCCTTTGT
536565 GGC-TAATCTTGTGAAAAGCCTTTGT
1 GGCAT-ATCTT-TGAAAAGCCTTTGT
536590 GGC
1 GGC
536593 GTGTTATCTG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
24 2 0.04
25 24 0.52
26 19 0.41
27 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
GGCATATCTTTGAAAAGCCTTTGT
Found at i:536559 original size:26 final size:25
Alignment explanation
Indices: 536526--536592 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 25
536516 CATATCATTT
536526 GAAAAGCCTTTGTGGC-AAGTTCTCT-A
1 GAAAAGCCTTTGTGGCTAA--TCT-TGA
*
536552 GAAAAGCCTTTGTGGCTAATCTTGT
1 GAAAAGCCTTTGTGGCTAATCTTGA
536577 GAAAAGCCTTTGTGGC
1 GAAAAGCCTTTGTGGC
536593 GTGTTATCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
24 1 0.03
25 19 0.50
26 16 0.42
27 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (25 bp):
GAAAAGCCTTTGTGGCTAATCTTGA
Found at i:536588 original size:51 final size:51
Alignment explanation
Indices: 536428--536592 Score: 169
Period size: 50 Copynumber: 3.3 Consensus size: 51
536418 AATTCTCTAG
* * * *
536428 AAAGCCTTTGTGGTAAATTCTCTA-AAAAGCTTTTGTGGCGT-ATCATTTGG
1 AAAGCCTTTGTGGCAAGTTCTCTAGAAAAGCCTTTGTGGC-TAATCATTTGA
* * ** * **
536478 AAAGCCTTTATAGTGAGTTCTCTAG-AAAGTCTTTACGGC-ATATCATTTGA
1 AAAGCCTTTGTGGCAAGTTCTCTAGAAAAGCCTTTGTGGCTA-ATCATTTGA
536528 AAAGCCTTTGTGGCAAGTTCTCTAGAAAAGCCTTTGTGGCTAATC-TTGTGA
1 AAAGCCTTTGTGGCAAGTTCTCTAGAAAAGCCTTTGTGGCTAATCATT-TGA
536579 AAAGCCTTTGTGGC
1 AAAGCCTTTGTGGC
536593 GTGTTATCTG
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
50 61 0.66
51 31 0.33
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (51 bp):
AAAGCCTTTGTGGCAAGTTCTCTAGAAAAGCCTTTGTGGCTAATCATTTGA
Found at i:539506 original size:22 final size:22
Alignment explanation
Indices: 539478--539522 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
539468 ATTATGATGA
539478 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
539500 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
539522 T
1 T
539523 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:539733 original size:16 final size:16
Alignment explanation
Indices: 539712--539742 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
539702 GGGATTTTCT
539712 TTTTGACTTTGGATTG
1 TTTTGACTTTGGATTG
*
539728 TTTTGATTTTGGATT
1 TTTTGACTTTGGATT
539743 TTTCTACAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.23, T:0.61
Consensus pattern (16 bp):
TTTTGACTTTGGATTG
Found at i:541764 original size:15 final size:16
Alignment explanation
Indices: 541729--541766 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
541719 CTTATGTGAT
*
541729 ACATGTGATGATTTAA
1 ACATGTGATGACTTAA
*
541745 GCATGTGA-GACTTAA
1 ACATGTGATGACTTAA
541760 ACATGTG
1 ACATGTG
541767 TCTGTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (16 bp):
ACATGTGATGACTTAA
Found at i:542035 original size:47 final size:48
Alignment explanation
Indices: 541982--542072 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
541972 TTATCTGCGA
* *
541982 TTATGTGGTCG-TTATCGGCAAATATGTGGTGGTTTGTCCACAATGTG
1 TTATGTGGTCGTTTATCGGCAAATATGTGGTGGCTTGTCAACAATGTG
**
542029 TTATGTGGTCGTTTATCGGCATTTATGTGGTGGCTTGTCAACAA
1 TTATGTGGTCGTTTATCGGCAAATATGTGGTGGCTTGTCAACAA
542073 ATGGTGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 11 0.28
48 28 0.72
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.40
Consensus pattern (48 bp):
TTATGTGGTCGTTTATCGGCAAATATGTGGTGGCTTGTCAACAATGTG
Found at i:545851 original size:11 final size:10
Alignment explanation
Indices: 545835--545867 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
545825 ATGTAATTAA
545835 TTTCTTTTTCT
1 TTTCTTTTT-T
545846 TTTCTTTTTT
1 TTTCTTTTTT
545856 TTT-TTTTTT
1 TTTCTTTTTT
545865 TTT
1 TTT
545868 GTGCAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:546129 original size:29 final size:28
Alignment explanation
Indices: 546097--546162 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
546087 AGCTTGAACT
* * *
546097 TATTATTTATTTAATATTAACTTTTAAAA
1 TATTATTTAATAAATATTAA-ATTTAAAA
*
546126 TATTCTATTAATAAATATTAAATTTAAAA
1 TATTAT-TTAATAAATATTAAATTTAAAA
*
546155 TATAATTT
1 TATTATTT
546163 GTTAAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 12 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTATTTAATAAATATTAAATTTAAAA
Found at i:555326 original size:20 final size:20
Alignment explanation
Indices: 555301--555342 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
555291 GATAGTTTTG
*
555301 TTATTTTGGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
555321 TTATTTTAGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
555341 TT
1 TT
555343 TCTCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTATTTTAGTTATTTTTATT
Found at i:556122 original size:20 final size:19
Alignment explanation
Indices: 556082--556124 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
556072 TATACATACT
*
556082 CTTTCTATTTTTATTTTTA
1 CTTTCTATTTTTATTTATA
556101 CTTTCCTATTTTT-TTATATA
1 CTTT-CTATTTTTATT-TATA
556121 CTTT
1 CTTT
556125 ATACTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTCTATTTTTATTTATA
Found at i:556251 original size:19 final size:20
Alignment explanation
Indices: 556204--556252 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
556194 AAAAAAATCA
*
556204 TTATAAATATTTTATTATAT
1 TTATAAATATTCTATTATAT
*
556224 TT-TACATATTCTATTAT-T
1 TTATAAATATTCTATTATAT
*
556242 TTATATATATT
1 TTATAAATATT
556253 GCACCTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 20 0.80
20 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATAAATATTCTATTATAT
Found at i:558475 original size:13 final size:13
Alignment explanation
Indices: 558457--558482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
558447 AAAGAAATTT
558457 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
558470 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
558483 AAATTGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:558552 original size:19 final size:19
Alignment explanation
Indices: 558512--558553 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
558502 GTCTCTTTTC
* *
558512 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
558531 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
558550 GCAT
1 GCAT
558554 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:560454 original size:20 final size:20
Alignment explanation
Indices: 560425--560465 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
560415 GCAAATGTTC
560425 TTTCACTCTTTACGATTTTT
1 TTTCACTCTTTACGATTTTT
* **
560445 TTTCATTCTTTTGGATTTTT
1 TTTCACTCTTTACGATTTTT
560465 T
1 T
560466 CGGCCAAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTCACTCTTTACGATTTTT
Found at i:562246 original size:44 final size:44
Alignment explanation
Indices: 562181--562762 Score: 516
Period size: 44 Copynumber: 13.1 Consensus size: 44
562171 GTGGCGAAAC
* * * *
562181 AGATCGAAGAAAGCGGATCTTGTTTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
** *** * * **
562225 AGATCAAAGGTAACAGATCTTGTCTTCCCATACTGGTGGCGAAAC
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* * *
562270 AGATCGAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* * *** * * * *
562314 AGATCAAATATAACAGATCTTGTCTTCCCATAGTGGTGCGAAAT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* * * *
562358 AGATCGAAGAAAGCAGATCTTGTCTTTATGTACTGGTGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* *** * * *
562402 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAAT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* * * * * * *
562447 AGATCGAATAAAGCGGATTTTGTCTTCATGTACTTGCGTGAAGA
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* *** * *
562491 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* * *
562536 AGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCATGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
*** * *
562580 AGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* *
562625 AGATCGAAGAAAACAGATCTTGCCTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* *** * *
562669 AGATCAAAGAAAATAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* *
562714 GGATAAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
562758 AGATC
1 AGATC
562763 NNNNNNNNGG
Statistics
Matches: 406, Mismatches: 127, Indels: 10
0.75 0.23 0.02
Matches are distributed among these distances:
44 236 0.58
45 170 0.42
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
Found at i:562298 original size:89 final size:89
Alignment explanation
Indices: 562147--562762 Score: 955
Period size: 89 Copynumber: 6.9 Consensus size: 89
562137 GTGGAGTAGC
* * *
562147 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGAAAGCGGATCTTGTTTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
562212 ACTGGCGTGAAGTAGATCAAAGGT
66 ACTGGCGTGAAGTAGATCAAAGAT
*
562236 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGAAAGCAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* *
562301 ACTAGCGTGAAGTAGATCAAATAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* *
562325 AACAGATCTTGTCTTCCCATAGTGGT-GCGAAATAGATCGAAGAAAGCAGATCTTGTCTTTATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
562389 ACTGGTGTGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* * *
562413 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAATAAAGCGGATTTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* *
562478 ACTTGCGTGAAGAAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* **
562502 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* *
562567 ACTGGCATGAAGTAGATCAAAGAA
66 ACTGGCGTGAAGTAGATCAAAGAT
* * *
562591 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGCCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
562656 ACTGGCGTGAAGTAGATCAAAGAA
66 ACTGGCGTGAAGTAGATCAAAGAT
* * * ** *
562680 AATAGATCTTGTCTTCCCATACTGGTGGCGAAGTGGATAAAAGAAAACAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
562745 ACTGGCGTGAAGTAGATC
66 ACTGGCGTGAAGTAGATC
562763 NNNNNNNNGG
Statistics
Matches: 489, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
88 82 0.17
89 407 0.83
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AACAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGT
ACTGGCGTGAAGTAGATCAAAGAT
Found at i:562879 original size:44 final size:44
Alignment explanation
Indices: 562820--563156 Score: 213
Period size: 44 Copynumber: 7.7 Consensus size: 44
562810 GCCAGTAATT
* *
562820 TTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATC
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
* * ** * *
562864 TTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGGCGGATT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
* * * * * *
562908 TTACCTCTCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC
1 TTATCTCCCT-AGG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATC
* * * * *
562953 -TATCTCTCTGGGTAGCAGTGGAATAGATCGAAGATTACAGATC
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
* * * ** *
562996 TTATCTCCCTATGCAGTAGTGGAGTAGATCGAAGATGGCAGATT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
* * * * * *
563040 TTACCTCGCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC
1 TTATCTCCCT-AGG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATC
* * * *
563085 -TATCTCCCTGGGCAACAGCGGAATAGATTGAAGATTACAGATC
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
* *
563128 TTATCTCCCTAGGCAGTAGTGGGGTAGAT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGAT
563157 CGAATATGGT
Statistics
Matches: 214, Mismatches: 63, Indels: 32
0.69 0.20 0.10
Matches are distributed among these distances:
41 6 0.03
42 5 0.02
43 38 0.18
44 123 0.57
45 37 0.17
46 3 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATC
Found at i:563012 original size:132 final size:132
Alignment explanation
Indices: 562772--563196 Score: 697
Period size: 132 Copynumber: 3.2 Consensus size: 132
562762 CNNNNNNNNG
* *
562772 GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAGGCCAGTAATTTTATCTCCCTGGGCAGC
1 GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
562837 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG
66 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG
*
562902 CG
131 CA
* *
562904 GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGGGTAGC
1 GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
* *
562969 AGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTATGCAGTAGTGGAGTAGATCGAAGATGG
66 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG
563034 CA
131 CA
* *
563036 GATTTTACCTCGCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAC
1 GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
* * *
563101 AGCGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGGGTAGATCGAATATGG
66 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG
*
563166 TA
131 CA
* * * *
563168 GATTTTATCTCCCTGAAGTTGCAGTGGAG
1 GATTTTACCTCTCTGAGGTTACAGTGGAG
563197 CAAACAGAAG
Statistics
Matches: 272, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 272 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (132 bp):
GATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG
CA
Found at i:563896 original size:20 final size:20
Alignment explanation
Indices: 563871--563912 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
563861 GATAGTTTTG
*
563871 TTATTTTGGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
563891 TTATTTTAGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
563911 TT
1 TT
563913 TCTCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTATTTTAGTTATTTTTATT
Found at i:564689 original size:20 final size:19
Alignment explanation
Indices: 564649--564691 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
564639 TATACATACT
*
564649 CTTTCTATTTTTATTTTTA
1 CTTTCTATTTTTATTTATA
564668 CTTTCCTATTTTT-TTATATA
1 CTTT-CTATTTTTATT-TATA
564688 CTTT
1 CTTT
564692 ATACTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTCTATTTTTATTTATA
Found at i:564805 original size:17 final size:17
Alignment explanation
Indices: 564779--564816 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
564769 ATCATTGTAA
*
564779 ATATTTTATTATTTTAC
1 ATATTCTATTATTTTAC
*
564796 ATATTCTATTATTTTAT
1 ATATTCTATTATTTTAC
564813 ATAT
1 ATAT
564817 ATTGCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTCTATTATTTTAC
Found at i:568006 original size:23 final size:24
Alignment explanation
Indices: 567950--568012 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
567940 GACAATTTGC
* *
567950 CGTCAATTCATCCTTTACATTTTT
1 CGTCAATTCATCCTTTACATATCT
*
567974 CATCAATTCATCCTTTACATATCT
1 CGTCAATTCATCCTTTACATATCT
567998 -GTCAATTCATCCTTT
1 CGTCAATTCATCCTTT
568013 CCTAATAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (24 bp):
CGTCAATTCATCCTTTACATATCT
Found at i:569070 original size:192 final size:193
Alignment explanation
Indices: 568730--569117 Score: 769
Period size: 192 Copynumber: 2.0 Consensus size: 193
568720 AAGGCAAGAA
568730 TTAAACTCACTTGAAGTAAAAATATGAAAAACCAGCTTTAGAAGCTCTCCTATGGCTATTTTTGG
1 TTAAACTCACTTGAAGTAAAAATATGAAAAACCAGCTTTAGAAGCTCTCCTATGGCTATTTTTGG
568795 CTGAAGATTGATGAAGAAATGTCTAAATTTTCAATTTAGTCTTTGTTTTAAATTTTTATCTTAAT
66 CTGAAGATTGATGAAGAAATGTCTAAATTTTCAATTTAGTCTTTGTTTTAAATTTTTATCTTAAT
568860 TCCCAAATGACCATTTTGCCCCATAAGTCATAAAATTTCAATATTTTCTCTACACATGCCGTT
131 TCCCAAATGACCATTTTGCCCCATAAGTCATAAAATTTCAATATTTTCTCTACACATGCCGTT
568923 TTAAACTCACTT-AAGTAAAAATATGAAAAACCAGCTTTAGAAGCTCTCCTATGGCTATTTTTGG
1 TTAAACTCACTTGAAGTAAAAATATGAAAAACCAGCTTTAGAAGCTCTCCTATGGCTATTTTTGG
568987 CTGAAGATTGATGAAGAAATGTCTAAATTTTCAATTTAGTCTTTGTTTTAAATTTTTATCTTAAT
66 CTGAAGATTGATGAAGAAATGTCTAAATTTTCAATTTAGTCTTTGTTTTAAATTTTTATCTTAAT
569052 TCCCAAATGACCATTTTGCCCCATAAGTCATAAAATTTCAATATTTTCTCTACACATGCCGTT
131 TCCCAAATGACCATTTTGCCCCATAAGTCATAAAATTTCAATATTTTCTCTACACATGCCGTT
569115 TTA
1 TTA
569118 GCATTCTAAT
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
192 183 0.94
193 12 0.06
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (193 bp):
TTAAACTCACTTGAAGTAAAAATATGAAAAACCAGCTTTAGAAGCTCTCCTATGGCTATTTTTGG
CTGAAGATTGATGAAGAAATGTCTAAATTTTCAATTTAGTCTTTGTTTTAAATTTTTATCTTAAT
TCCCAAATGACCATTTTGCCCCATAAGTCATAAAATTTCAATATTTTCTCTACACATGCCGTT
Found at i:575922 original size:24 final size:23
Alignment explanation
Indices: 575837--575945 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
575827 ACAATTTGCC
* *
575837 GTCAATTCATCCTTTACATTACC
1 GTCAATTCATCCTTTACATTTCT
*
575860 GTCAATTCATCCTTTA-ATTTTTT
1 GTCAATTCATCCTTTACA-TTTCT
* * * *
575883 CGTCAGTTCCTTCTTTACATTTTTT
1 -GTCAATTCATCCTTTACA-TTTCT
575908 GTCAATTCATCCTTTACATTTCT
1 GTCAATTCATCCTTTACATTTCT
*
575931 ATCAATTCATCCTTT
1 GTCAATTCATCCTTT
575946 CCCAATAACG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
22 1 0.01
23 36 0.50
24 28 0.39
25 7 0.10
ACGTcount: A:0.21, C:0.25, G:0.05, T:0.50
Consensus pattern (23 bp):
GTCAATTCATCCTTTACATTTCT
Found at i:586532 original size:21 final size:21
Alignment explanation
Indices: 586506--586548 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
586496 AATGGGGAGA
586506 ATAAATTGCCTTACCTTAACT
1 ATAAATTGCCTTACCTTAACT
586527 ATAAATTGCCTTACCTTAACT
1 ATAAATTGCCTTACCTTAACT
586548 A
1 A
586549 ACACTGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAATTGCCTTACCTTAACT
Found at i:588018 original size:6 final size:6
Alignment explanation
Indices: 588007--588035 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
587997 TAGGTTTCAA
588007 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
588036 ATTTTACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:596812 original size:27 final size:27
Alignment explanation
Indices: 596782--597047 Score: 116
Period size: 27 Copynumber: 9.9 Consensus size: 27
596772 GGGTAAAACA
*
596782 GTCATTTTATCCTATAG-GGGTATTTTG
1 GTCATTTTACCCT-TAGAGGGTATTTTG
*
596809 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTAGAGGGTATTTTG
* * * *
596836 GTAATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTAGAGGGTATTTTG
* * * * * **
596863 ATAATCTTACGCATCAG-GGGTATTTCA
1 GTCATTTTAC-CCTTAGAGGGTATTTTG
* * **
596890 GTAATTCTACCCATTAG-GGGTATTTCA
1 GTCATTTTACCC-TTAGAGGGTATTTTG
* * *
596917 GTAATTTTA-CCTATCGGGGGTATTTCT-
1 GTCATTTTACCCT-TAGAGGGTATTT-TG
* * * *
596944 GTAATTTTACCCATCGAGGGTA-TTCG
1 GTCATTTTACCCTTAGAGGGTATTTTG
* * * *
596970 GTAATTTTACCCCTCGGGGGTATTTTG
1 GTCATTTTACCCTTAGAGGGTATTTTG
* *
596997 GTTATTTTA-CCTTCAG-GGGTATTTTA
1 GTCATTTTACCCTT-AGAGGGTATTTTG
* * * *
597023 GTCAGTTTACCATTCGGGGGTATTT
1 GTCATTTTACCCTTAGAGGGTATTT
597048 CGGTATAGTT
Statistics
Matches: 193, Mismatches: 34, Indels: 24
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 49 0.25
27 139 0.72
28 4 0.02
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTTAGAGGGTATTTTG
Found at i:596857 original size:54 final size:55
Alignment explanation
Indices: 596797--597052 Score: 240
Period size: 54 Copynumber: 4.8 Consensus size: 55
596787 TTTATCCTAT
* * *
596797 AGGGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTTGGTAATTTTACCCATCG
1 AGGGGTATTTCGGTAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCG
* * * * * ** * *
596852 A-GGGTATTTCGATAATCTTACGCATCAGGGGTATTTCAGTAATTCTACCCAT-T
1 AGGGGTATTTCGGTAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCG
*
596905 AGGGGTATTTCAGTAATTTTA-CCTATCGGGGGTATTTCT-GTAATTTTACCCATCG
1 AGGGGTATTTCGGTAATTTTACCCT-TCGGGGGTATTT-TGGTAATTTTACCCATCG
* * *
596960 A-GGGTA-TTCGGTAATTTTACCCCTCGGGGGTATTTTGGTTATTTTA-CCTTC-
1 AGGGGTATTTCGGTAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCG
** * * * *
597011 AGGGGTATTTTAGTCAGTTTACCATTCGGGGGTATTTCGGTA
1 AGGGGTATTTCGGTAATTTTACCCTTCGGGGGTATTTTGGTA
597053 TAGTTAACGA
Statistics
Matches: 160, Mismatches: 33, Indels: 18
0.76 0.16 0.09
Matches are distributed among these distances:
51 1 0.01
52 10 0.06
53 60 0.38
54 87 0.54
55 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.40
Consensus pattern (55 bp):
AGGGGTATTTCGGTAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCG
Found at i:596921 original size:81 final size:80
Alignment explanation
Indices: 596826--596981 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 80
596816 TACCCTTCGA
** *
596826 GGGTATTTTGGTAATTTTACCCATCGAGGGTATTTC-GATAATCTTACGCATC-AGGGGTATTTC
1 GGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCTG-TAATCTTACCCATCGA-GGGTA-TTC
596889 AGTAATTCTACCCATTAG
63 AGTAATTCTACCCATTAG
* * * *
596907 GGGTATTTCAGTAATTTTACCTATCGGGGGTATTTCTGTAATTTTACCCATCGAGGGTATTCGGT
1 GGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCTGTAATCTTACCCATCGAGGGTATTCAGT
*
596972 AATTTTACCC
66 AATTCTACCC
596982 CTCGGGGGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
80 14 0.22
81 49 0.75
82 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (80 bp):
GGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCTGTAATCTTACCCATCGAGGGTATTCAGT
AATTCTACCCATTAG
Found at i:597304 original size:19 final size:19
Alignment explanation
Indices: 597269--597306 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
597259 GTATGGAGCC
*
597269 CACGAGCCCATTGGGCCCA
1 CACGAGCCCATTCGGCCCA
597288 CACGA-CCCATTTCGGCCCA
1 CACGAGCCCA-TTCGGCCCA
597307 ACAAGGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCGGCCCA
Found at i:601740 original size:50 final size:50
Alignment explanation
Indices: 601632--601862 Score: 214
Period size: 50 Copynumber: 4.5 Consensus size: 50
601622 ATGTCAAAGT
* ** * * * *
601632 CATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTAC--TGTCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAATGC
* * * ** *
601681 CATATCCCAGATATGGTATTACATGGGAGTTCTCATATCGGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
** * *
601731 CATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
*
601781 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGGATGCCAATGA
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC----GG-TGCCAATGC
*
601837 CATGCCCCAGACATGGTCTTACATGG
1 CATGTCCCAGACATGGTCTTACATGG
601863 TATCTCTTTA
Statistics
Matches: 147, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 29 0.20
50 81 0.55
51 2 0.01
55 2 0.01
56 32 0.22
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
Found at i:608071 original size:50 final size:50
Alignment explanation
Indices: 607971--608116 Score: 148
Period size: 50 Copynumber: 2.9 Consensus size: 50
607961 TTTCTTGTAC
* * * * **
607971 TGCCAATGCCATATCCCATATATGGTCTTACGTGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATATCGG
* ** * *
608021 TTCCCGTGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATATCGG
* * ** *
608071 TGCCAACGCCATGTCCCAGTCATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATA
608117 ACCTCAATGA
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATATCGG
Found at i:619747 original size:44 final size:44
Alignment explanation
Indices: 619662--619752 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
619652 TTCTATGGTG
*
619662 TATTTTGGGCATCGAGGGCTCGTATTAGGAACAATACGCATGAT
1 TATTTTGGGCATCGAGGGCTCGTATTAGGAACAACACGCATGAT
* *
619706 TATTTTGGGCATCGAGGGCTCGTATTAGGAACAACATGCATGGT
1 TATTTTGGGCATCGAGGGCTCGTATTAGGAACAACACGCATGAT
619750 TAT
1 TAT
619753 GATTGGTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (44 bp):
TATTTTGGGCATCGAGGGCTCGTATTAGGAACAACACGCATGAT
Found at i:623510 original size:15 final size:15
Alignment explanation
Indices: 623487--623516 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
623477 TTGTATGAGC
*
623487 AAATTTTGGTATGAA
1 AAATCTTGGTATGAA
623502 AAATCTTGGTATGAA
1 AAATCTTGGTATGAA
623517 TGGTAATGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
AAATCTTGGTATGAA
Found at i:626323 original size:42 final size:41
Alignment explanation
Indices: 626187--626419 Score: 234
Period size: 42 Copynumber: 5.6 Consensus size: 41
626177 GTTACACGGT
* * *
626187 GGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATACGG
1 GGAATCAGCACTTAGCAACC-CCTTTATAATCAATGATTCGG
** * * *
626228 GGAATCAGCAAATAGCAACCCGTTTCACAATCAATGATACGG
1 GGAATCAGCACTTAGCAACCCCTTT-ATAATCAATGATTCGG
* * *
626270 TGGAATCAGCACTTAGCAACCACCTTTATAATTAATAATTCAG
1 -GGAATCAGCACTTAGCAACC-CCTTTATAATCAATGATTCGG
* *
626313 GGAATCAGCACTTAGCAACCCCTTTCTTGATCAATGATTCGG
1 GGAATCAGCACTTAGCAACCCCTTT-ATAATCAATGATTCGG
* * * * * *
626355 GGAATCTGCACTTAGCAGCCCCTTTTTGATCAGTGATTTGG
1 GGAATCAGCACTTAGCAACCCCTTTATAATCAATGATTCGG
*
626396 GGAATCTGCACTTAGCAACCCCTT
1 GGAATCAGCACTTAGCAACCCCTT
626420 ACATTCAAAG
Statistics
Matches: 163, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 62 0.38
42 67 0.41
43 29 0.18
44 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTATAATCAATGATTCGG
Found at i:626359 original size:84 final size:84
Alignment explanation
Indices: 626182--626419 Score: 275
Period size: 84 Copynumber: 2.8 Consensus size: 84
626172 CAACCGTTAC
* **
626182 ACGGTGGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATACGGGGAATCAGCAAATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATT-AGTGATTCGGGGAATCAGCACTTAGCAA
*
626246 CCCGTTTCACAATCAATGAT
65 CCCCTTTCACAATCAATGAT
* * *
626266 ACGGTGGAATCAGCACTTAGCAACCACCTTTATAATTAATAATTCAGGGAATCAGCACTTAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTAT-ATTAGTGATTCGGGGAATCAGCACTTAGCAA
***
626331 CCCCTTTCTTGATCAATGAT
65 CCCCTTTCACAATCAATGAT
* * * * * * *
626351 TCGG-GGAATCTGCACTTAGCAGCC-CCTTTTTGATCAGTGATTTGGGGAATCTGCACTTAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTAT-ATTAGTGATTCGGGGAATCAGCACTTAGCAA
626414 CCCCTT
65 CCCCTT
626420 ACATTCAAAG
Statistics
Matches: 131, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
83 37 0.28
84 46 0.35
85 45 0.34
86 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (84 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTAGTGATTCGGGGAATCAGCACTTAGCAAC
CCCTTTCACAATCAATGAT
Found at i:629615 original size:29 final size:29
Alignment explanation
Indices: 629216--629656 Score: 412
Period size: 29 Copynumber: 15.4 Consensus size: 29
629206 TATAAGTGAC
*
629216 CCTTTGTGGCTATCTC--TAAAAGGAA-G
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
** *
629242 CCTTTGCAG-TGATCTTTGTTAAATGGAA-G
1 CCTTTGTGGCT-ATCTCTGTTAAA-GGAATG
*
629271 CCTTTGTGGCGATCTCTGTTAAATGGAA-G
1 CCTTTGTGGCTATCTCTGTTAAA-GGAATG
* *
629300 CCTTTGTGGCTATCTCTATTATAA-GAAAG
1 CCTTTGTGGCTATCTCTGTTA-AAGGAATG
629329 CCTTTGTGGCTATCTCTGTTAAAAGGATAT-
1 CCTTTGTGGCTATCTCTGTT-AAAGGA-ATG
* * *
629359 -CTTTGTGTCTATCTTTGTTAAAAGG-ATA
1 CCTTTGTGGCTATCTCTGTT-AAAGGAATG
* *
629387 CCTTTGTGGCTATCTTTGTTAAAAGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
*
629416 CCTTTGTGGCTATCTTTGTTAAAGGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
* * *
629445 TCTTTGTGGTTATCTCTGTTAAAGGAATA
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
629474 CCTTTGTGGCTATCTCTGTTAAAGGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
* * * *
629503 TCTTTATGGCTATCTCAGTTAAAAGG-ATT
1 CCTTTGTGGCTATCTCTGTT-AAAGGAATG
* * *
629532 TCTTTCTGGCTATCTCTATTAAAGGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
* *
629561 CC-TAGTGGCAAT-TCTGTTAAAGGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
*
629588 CCTTTGTGGTTATCTCTGTTAAAGGAATG
1 CCTTTGTGGCTATCTCTGTTAAAGGAATG
* *
629617 TCC--TGTGGCAAAT-TATGTTAAAGGAATG
1 -CCTTTGTGGC-TATCTCTGTTAAAGGAATG
*
629645 TC-TTGTGGCTAT
1 CCTTTGTGGCTAT
629657 TCATTGGTGT
Statistics
Matches: 349, Mismatches: 46, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.00
26 11 0.03
27 21 0.06
28 55 0.16
29 248 0.71
30 12 0.03
31 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (29 bp):
CCTTTGTGGCTATCTCTGTTAAAGGAATG
Found at i:630295 original size:68 final size:68
Alignment explanation
Indices: 630103--630286 Score: 251
Period size: 68 Copynumber: 2.7 Consensus size: 68
630093 AGTCCTCCAG
* ** * *
630103 GATAGTAAAAATGACATCATAATGTGTAAGACTGTAGCCGGGCTATGGCAACATATGAAGTCCGT
1 GATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGA
*
630168 CAG
66 CAA
* * * * *
630171 GACAGTAAACATGACATCATAATGTGTAAGACCATAGTTGGTCTATGACAACATATGCAGTCCGA
1 GATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGA
630236 CAA
66 CAA
* *
630239 GATAGTAAACATGGCATCATAATGTGTAAGACCATAACTGGGCTATGG
1 GATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGG
630287 TCGTATATGA
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 99 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (68 bp):
GATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGA
CAA
Found at i:630311 original size:68 final size:67
Alignment explanation
Indices: 630101--630312 Score: 223
Period size: 68 Copynumber: 3.1 Consensus size: 67
630091 GAAGTCCTCC
* ** *
630101 AGGATAGTAAAAATGACATCATAATGTGTAAGACTGTAGCCGGGCTATGGCAACATATGAAGTC-
1 AGGATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCA
630165 CGT
66 C-T
* * * * *
630168 CAGGACAGTAAACATGACATCATAATGTGTAAGACCATAGTTGGTCTATGACAACATATGCAGTC
1 -AGGATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGT-
630233 CGAC-
64 C-ACT
* * * **
630237 AAGATAGTAAACATGGCATCATAATGTGTAAGACCATAACTGGGCTATGGTC-GTATATGAAGTC
1 AGGATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGG-CAACATATGAAGTC
630301 TACT
65 -ACT
630305 AGGATAGT
1 AGGATAGT
630313 GAACTAGGAC
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
67 3 0.03
68 112 0.95
69 2 0.02
71 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (67 bp):
AGGATAGTAAACATGACATCATAATGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCA
CT
Found at i:630754 original size:19 final size:19
Alignment explanation
Indices: 630730--630767 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
630720 ACGTAGGAGT
630730 ATGAGCTGAAGCTAGATGG
1 ATGAGCTGAAGCTAGATGG
630749 ATGAGCTGAAGCTAGATGG
1 ATGAGCTGAAGCTAGATGG
630768 GGTCAAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.37, T:0.21
Consensus pattern (19 bp):
ATGAGCTGAAGCTAGATGG
Found at i:631372 original size:24 final size:24
Alignment explanation
Indices: 631344--631392 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
631334 AATAAGTCAG
631344 GTTAGAAATTTTGTTAAGTTATTC
1 GTTAGAAATTTTGTTAAGTTATTC
631368 GTTAGAAATTTTGTTAAGTTATTC
1 GTTAGAAATTTTGTTAAGTTATTC
631392 G
1 G
631393 AGTTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (24 bp):
GTTAGAAATTTTGTTAAGTTATTC
Found at i:632840 original size:16 final size:15
Alignment explanation
Indices: 632810--632847 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
632800 TTATTTATTA
632810 AATTAA-TTTTAATT
1 AATTAATTTTTAATT
632824 AATTAATTTTCTAATT
1 AATTAATTTT-TAATT
*
632840 AAATAATT
1 AATTAATT
632848 CTCTCAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTAATTTTTAATT
Found at i:640103 original size:11 final size:11
Alignment explanation
Indices: 640087--640112 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
640077 CTCCAATATT
640087 CTCTCAAATTC
1 CTCTCAAATTC
640098 CTCTCAAATTC
1 CTCTCAAATTC
640109 CTCT
1 CTCT
640113 TAAAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:640155 original size:30 final size:30
Alignment explanation
Indices: 640112--640173 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
640102 CAAATTCCTC
640112 TTAAAAAAACTTTAA-TTTTTTTAATTATT
1 TTAAAAAAACTTTAATTTTTTTTAATTATT
*
640141 TTAAAAAAAGCTTTAATTTTTTTTAATTTTT
1 TTAAAAAAA-CTTTAATTTTTTTTAATTATT
640172 TT
1 TT
640174 TAAATCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 9 0.30
30 6 0.20
31 15 0.50
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (30 bp):
TTAAAAAAACTTTAATTTTTTTTAATTATT
Found at i:640172 original size:9 final size:10
Alignment explanation
Indices: 640152--640176 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
640142 TAAAAAAAGC
640152 TTTAATTTTT
1 TTTAATTTTT
640162 TTTAATTTTT
1 TTTAATTTTT
640172 TTTAA
1 TTTAA
640177 ATCATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:641326 original size:7 final size:7
Alignment explanation
Indices: 641314--641339 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
641304 TAATCGATTG
641314 GTATTTA
1 GTATTTA
641321 GTATTTA
1 GTATTTA
641328 GTATTTA
1 GTATTTA
641335 GTATT
1 GTATT
641340 ATGTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:641888 original size:30 final size:30
Alignment explanation
Indices: 641839--641904 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
641829 GGAGACGACG
*
641839 CAGGCCTATCAAAATCACCCGAC-C-GATCAC
1 CAGGCCTAGCAAAATCACCC-ACACAG-TCAC
641869 CAGGCCTAGCAACAA-CACCCACACAGTCAC
1 CAGGCCTAGCAA-AATCACCCACACAGTCAC
641899 CAGGCC
1 CAGGCC
641905 CAACACTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 2 0.06
30 27 0.84
31 3 0.09
ACGTcount: A:0.33, C:0.42, G:0.15, T:0.09
Consensus pattern (30 bp):
CAGGCCTAGCAAAATCACCCACACAGTCAC
Found at i:642269 original size:21 final size:21
Alignment explanation
Indices: 642242--642289 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
642232 CCAACACCGA
* **
642242 CAACCAGATTCCTTATCGGAG
1 CAACCAGAATCCCCATCGGAG
*
642263 GAACCAGAATCCCCATCGGAG
1 CAACCAGAATCCCCATCGGAG
642284 CAACCA
1 CAACCA
642290 CAACCCCCGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (21 bp):
CAACCAGAATCCCCATCGGAG
Found at i:642297 original size:21 final size:21
Alignment explanation
Indices: 642256--642297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
642246 CAGATTCCTT
* * *
642256 ATCGGAGGAACCAGAATCCCC
1 ATCGGAGCAACCACAACCCCC
642277 ATCGGAGCAACCACAACCCCC
1 ATCGGAGCAACCACAACCCCC
642298 GCCAGAAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.40, G:0.19, T:0.07
Consensus pattern (21 bp):
ATCGGAGCAACCACAACCCCC
Found at i:645834 original size:126 final size:126
Alignment explanation
Indices: 645521--645937 Score: 667
Period size: 126 Copynumber: 3.3 Consensus size: 126
645511 TTAGGCCAAA
* * *
645521 CAGGAAGCCACTGT-GCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTACTATCAAAG
1 CAGG-AGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAAAG
* *
645585 CATCCTGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTA-TTTTT
65 CATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
** * * *
645646 CAGGAGCTACTGTAGCAAAAGCGTGTCCATGTGGGAGCTTCATTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAAAGC
*
645711 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTTAGAAACGTCTACTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
*
645772 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAAAGC
* *
645837 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* *
645898 TAGGAGCTACTGTAGCAAAAGAGCATCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTT
645938 TTTTAAATTA
Statistics
Matches: 269, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
124 8 0.03
125 100 0.37
126 161 0.60
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:646512 original size:125 final size:125
Alignment explanation
Indices: 646289--646581 Score: 428
Period size: 125 Copynumber: 2.3 Consensus size: 125
646279 TTAGGCCAAA
* * * *
646289 CAGGAGCCACTGTAGCAAAAGCGCATCCACGTGGGAGC-TTCTTTCAGTACTTTTACTATCAAAG
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACG-GGGAGCGAT-TTTCAGTACTTTTACTAACAAAG
* * *
646353 CATCCTGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTT
64 CATCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTACTCAAAATTATTTTTT
* *
646415 CAGGAGCTATTGTAGCAAAAGCGCGTCCACGAGGGAGCGATTTT-AGTACTTTTACTAACAATGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACG-GGGAGCGATTTTCAGTACTTTTACTAACAAAGC
* *
646479 ATCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACGTCTACTTAAAATTATTTTTT
65 ATCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTACTCAAAATTATTTTTT
* *
646540 CAAGAGCTACTGTAGCAAAAGCGCGTCCACGTGGAGCGATTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGGGGAGCGATTT
646582 CCTTAAAAAA
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
124 10 0.07
125 103 0.68
126 37 0.25
127 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (125 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGGGGAGCGATTTTCAGTACTTTTACTAACAAAGCA
TCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTACTCAAAATTATTTTTT
Found at i:648426 original size:64 final size:64
Alignment explanation
Indices: 648352--648480 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
648342 AAATAAGTTA
* * *
648352 ACAAAAAGAAAATGTTTGTCAACTGAATTGAATCGGATATAAATTGAGTTAATGTTTTATGTTT
1 ACAAAAAGAAAATATTTATCAACTGAATTGAATCAGATATAAATTGAGTTAATGTTTTATGTTT
* *
648416 ACAAAAAGAAAATATTTATCAATTGAATTGAATCAGATTTAAATTGAGTTAATGTTTTATGTTT
1 ACAAAAAGAAAATATTTATCAACTGAATTGAATCAGATATAAATTGAGTTAATGTTTTATGTTT
648480 A
1 A
648481 TTTAAAGTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (64 bp):
ACAAAAAGAAAATATTTATCAACTGAATTGAATCAGATATAAATTGAGTTAATGTTTTATGTTT
Found at i:658959 original size:21 final size:21
Alignment explanation
Indices: 658933--658972 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
658923 CACATACATA
658933 CATTTGTCTAACTTCATTTAT
1 CATTTGTCTAACTTCATTTAT
658954 CATTTGTCTAACTTCATTT
1 CATTTGTCTAACTTCATTT
658973 GTCTAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.53
Consensus pattern (21 bp):
CATTTGTCTAACTTCATTTAT
Found at i:658970 original size:14 final size:14
Alignment explanation
Indices: 658953--658979 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
658943 ACTTCATTTA
658953 TCATTTGTCTAACT
1 TCATTTGTCTAACT
658967 TCATTTGTCTAAC
1 TCATTTGTCTAAC
658980 AAACCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TCATTTGTCTAACT
Found at i:661283 original size:46 final size:46
Alignment explanation
Indices: 661216--661348 Score: 160
Period size: 46 Copynumber: 2.9 Consensus size: 46
661206 TGTTCTTGCC
* * *
661216 TAGGTTCCCAGCTCCTGCATATGTTGCGGGCTGGAGAATACGAATT
1 TAGGTTCCCAACTCCTTCATATGTTGCGGACTGGAGAATACGAATT
* * * *
661262 TAGGTTCCCAACTTCTTCATATGTTGTGGATTGGAGAATACGGATT
1 TAGGTTCCCAACTCCTTCATATGTTGCGGACTGGAGAATACGAATT
** *
661308 TAGGTTTTCAACTCCTTCATATATTGCGGA-TAGGAGAATAC
1 TAGGTTCCCAACTCCTTCATATGTTGCGGACT-GGAGAATAC
661349 ATAATATTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 1 0.01
46 73 0.99
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (46 bp):
TAGGTTCCCAACTCCTTCATATGTTGCGGACTGGAGAATACGAATT
Found at i:667926 original size:23 final size:23
Alignment explanation
Indices: 667898--667951 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
667888 CAGTGTTATT
667898 TATCAGTGGTAGCTTCGGCTACA
1 TATCAGTGGTAGCTTCGGCTACA
*
667921 TTTCAGTGGTAGCTTCGGCTACA
1 TATCAGTGGTAGCTTCGGCTACA
667944 TATCAGTG
1 TATCAGTG
667952 TGGCATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
TATCAGTGGTAGCTTCGGCTACA
Done.