Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 51
Found at i:5443928 original size:17 final size:18
Alignment explanation
Indices: 5443908--5443949 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5443898 ACTACTTCCC
5443908 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5443925 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5443943 T-AATGAA
1 TAAATGAA
5443950 CAACACACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5444139 original size:25 final size:25
Alignment explanation
Indices: 5444111--5444167 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
5444101 AGTAAGGTAA
5444111 AACTCTCTTTGAATCATCCTTGGTG
1 AACTCTCTTTGAATCATCCTTGGTG
* *
5444136 AACTTATTTGTTTGAATCATCCTTGGTG
1 AAC---TCTCTTTGAATCATCCTTGGTG
5444164 AACT
1 AACT
5444168 TTTTTTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 4 0.15
28 23 0.85
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (25 bp):
AACTCTCTTTGAATCATCCTTGGTG
Found at i:5447604 original size:18 final size:18
Alignment explanation
Indices: 5447581--5447627 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5447571 TAGTTTGATT
5447581 AATGAAATAAAATTATTC
1 AATGAAATAAAATTATTC
**
5447599 AATGAAATAACTTTATTC
1 AATGAAATAAAATTATTC
*
5447617 AATGAACTAAA
1 AATGAAATAAA
5447628 TGCATGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (18 bp):
AATGAAATAAAATTATTC
Found at i:5449060 original size:21 final size:19
Alignment explanation
Indices: 5449036--5449080 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5449026 CTCAATTTCA
5449036 CTCTCAATTCTCTTTTTAATG
1 CTCTCAA-TCTCTTTTTAA-G
* *
5449057 CTCTCAATGTCTTTTTCAG
1 CTCTCAATCTCTTTTTAAG
5449076 CTCTC
1 CTCTC
5449081 GTTTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 9 0.41
21 7 0.32
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.49
Consensus pattern (19 bp):
CTCTCAATCTCTTTTTAAG
Found at i:5449078 original size:19 final size:20
Alignment explanation
Indices: 5449031--5449080 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5449021 ATGTGCTCAA
5449031 TTTCA-CTCTCAATTCTCTT
1 TTTCAGCTCTCAATTCTCTT
* *
5449050 TTTAATGCTCTCAA-TGTCTT
1 TTTCA-GCTCTCAATTCTCTT
5449070 TTTCAGCTCTC
1 TTTCAGCTCTC
5449081 GTTTCTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 9 0.35
21 7 0.27
ACGTcount: A:0.16, C:0.28, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTCAGCTCTCAATTCTCTT
Found at i:5451023 original size:29 final size:29
Alignment explanation
Indices: 5450981--5451065 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 29
5450971 ATGTTAGAAC
*
5450981 ATGGAACGCTATTAATAAAATAAATGAAA
1 ATGGAACACTATTAATAAAATAAATGAAA
* * *
5451010 ATGGAACACTATTAATATAAGT-TA-GAAC
1 ATGGAACACTATTAATA-AAATAAATGAAA
5451038 ATGGAACACTATTAATAAAATAAATGAA
1 ATGGAACACTATTAATAAAATAAATGAA
5451066 CCTAGAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.06
28 21 0.45
29 20 0.43
30 3 0.06
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (29 bp):
ATGGAACACTATTAATAAAATAAATGAAA
Found at i:5451502 original size:19 final size:19
Alignment explanation
Indices: 5451453--5451503 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
5451443 AATGTGCTCA
5451453 TTTTC-ACTCTCAATTCTC
1 TTTTCAACTCTCAATTCTC
*
5451471 TTTTTAATGCTCTCAATGTCT-
1 TTTTCAA--CTCTCAAT-TCTC
5451492 TTTTCAACTCTC
1 TTTTCAACTCTC
5451504 GTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
21 14 0.52
22 3 0.11
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTTCAACTCTCAATTCTC
Found at i:5453934 original size:18 final size:18
Alignment explanation
Indices: 5453890--5453937 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
5453880 GTTAGTTTGA
*
5453890 TCAATGAAATAACATTAT
1 TCAATGAACTAACATTAT
*
5453908 TCAATGAACTAACTTTAT
1 TCAATGAACTAACATTAT
5453926 TCAATGAACTAA
1 TCAATGAACTAA
5453938 ATGCATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (18 bp):
TCAATGAACTAACATTAT
Found at i:5457803 original size:18 final size:18
Alignment explanation
Indices: 5457780--5457820 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5457770 TAGTTTGATT
5457780 AATGAAATAA-TATTATTC
1 AATGAAATAACTA-TATTC
*
5457798 AATGAACTAACTATATTC
1 AATGAAATAACTATATTC
5457816 AATGA
1 AATGA
5457821 GCTAAATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (18 bp):
AATGAAATAACTATATTC
Found at i:5457901 original size:17 final size:18
Alignment explanation
Indices: 5457881--5457922 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5457871 ACTACTCTCC
5457881 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5457898 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5457916 T-AATGAA
1 TAAATGAA
5457923 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5461926 original size:19 final size:19
Alignment explanation
Indices: 5461877--5461926 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
5461867 AATGTGTTCA
5461877 TTTTCAA-TCTCAATTCTC
1 TTTTCAACTCTCAATTCTC
*
5461895 TTTTTAATGCTCTCAATGTCT-
1 TTTTCAA--CTCTCAAT-TCTC
5461916 TTTTCAACTCT
1 TTTTCAACTCT
5461927 TGTTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 6 0.23
19 4 0.15
21 13 0.50
22 3 0.12
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTCAACTCTCAATTCTC
Found at i:5462788 original size:13 final size:13
Alignment explanation
Indices: 5462754--5462778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5462744 CTTTTTAAAT
5462754 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
5462767 TTTTCTTTTTCT
1 TTTTCTTTTTCT
5462779 TTATTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTCTC
Found at i:5464342 original size:18 final size:18
Alignment explanation
Indices: 5464319--5464365 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5464309 TAGTTTGATT
*
5464319 AATGAAATAAAATTATTC
1 AATGAACTAAAATTATTC
**
5464337 AATGAACTAACTTTATTC
1 AATGAACTAAAATTATTC
5464355 AATGAACTAAA
1 AATGAACTAAA
5464366 TGCATGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (18 bp):
AATGAACTAAAATTATTC
Found at i:5473445 original size:19 final size:19
Alignment explanation
Indices: 5473421--5473485 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
5473411 GAAAAATCAG
5473421 AAAAGAAAGTGAAGCACTC
1 AAAAGAAAGTGAAGCACTC
* *
5473440 AAAAGAAA--GAA-AAATC
1 AAAAGAAAGTGAAGCACTC
5473456 AGAAAAGAAAGTGAAGCACTC
1 --AAAAGAAAGTGAAGCACTC
5473477 AAAAGAAAG
1 AAAAGAAAG
5473486 AAAAATCCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 8 0.22
19 17 0.46
20 3 0.08
21 3 0.08
ACGTcount: A:0.62, C:0.11, G:0.20, T:0.08
Consensus pattern (19 bp):
AAAAGAAAGTGAAGCACTC
Found at i:5473449 original size:37 final size:37
Alignment explanation
Indices: 5473404--5473492 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
5473394 AAAGTCAAAG
5473404 AAAA-AAAGAAAAATCAGAAAAGAAAGTGAAGCACTC
1 AAAAGAAAGAAAAATCAGAAAAGAAAGTGAAGCACTC
5473440 AAAAGAAAGAAAAATCAGAAAAGAAAGTGAAGCACTC
1 AAAAGAAAGAAAAATCAGAAAAGAAAGTGAAGCACTC
5473477 AAAAGAAAGAAAAATC
1 AAAAGAAAGAAAAATC
5473493 CAGCACTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.08
37 48 0.92
ACGTcount: A:0.65, C:0.10, G:0.17, T:0.08
Consensus pattern (37 bp):
AAAAGAAAGAAAAATCAGAAAAGAAAGTGAAGCACTC
Found at i:5473463 original size:18 final size:18
Alignment explanation
Indices: 5473402--5473466 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
5473392 GAAAAGTCAA
5473402 AGAAAA-AAAGAAAAATC
1 AGAAAAGAAAGAAAAATC
* *
5473419 AGAAAAGAAAGTGAAGCACTC
1 AGAAAAGAAA--GAA-AAATC
5473440 --AAAAGAAAGAAAAATC
1 AGAAAAGAAAGAAAAATC
5473456 AGAAAAGAAAG
1 AGAAAAGAAAG
5473467 TGAAGCACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 12 0.32
19 8 0.21
20 3 0.08
21 3 0.08
ACGTcount: A:0.68, C:0.08, G:0.18, T:0.06
Consensus pattern (18 bp):
AGAAAAGAAAGAAAAATC
Found at i:5473486 original size:23 final size:23
Alignment explanation
Indices: 5473459--5473512 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5473449 AAAAATCAGA
* *
5473459 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
5473482 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
5473506 -AAGAAAA
1 AAAGAAAA
5473513 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:5478225 original size:30 final size:31
Alignment explanation
Indices: 5478189--5478248 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5478179 CTTAGCTTTA
**
5478189 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
5478219 TATTATGTTTTCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5478249 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5479159 original size:19 final size:21
Alignment explanation
Indices: 5479135--5479186 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5479125 CGGCCAAGAG
*
5479135 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
5479154 CATGTATTTTAATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5479175 CATGTATTTTCA
1 CATGTATTTTCA
5479187 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5481167 original size:11 final size:11
Alignment explanation
Indices: 5481144--5481183 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
5481134 ATTTCAGTGC
5481144 AAAAAGAAGAGA
1 AAAAAGAA-AGA
5481156 AAAAAGAAAGA
1 AAAAAGAAAGA
*
5481167 AAAAATAAAGGA
1 AAAAAGAAA-GA
5481179 AAAAA
1 AAAAA
5481184 ATTCAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:5483576 original size:30 final size:31
Alignment explanation
Indices: 5483524--5483583 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5483514 GTTAGCTTTA
**
5483524 TATTATGTTTACATAAGTTTTAGAT-TCATT
1 TATTATGTTTACATAACATTTAGATATCATT
* *
5483554 TATTATGTTTCCATATCATTTAGATATCAT
1 TATTATGTTTACATAACATTTAGATATCAT
5483584 GGCAGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (31 bp):
TATTATGTTTACATAACATTTAGATATCATT
Found at i:5493488 original size:13 final size:12
Alignment explanation
Indices: 5493469--5493565 Score: 71
Period size: 13 Copynumber: 8.0 Consensus size: 12
5493459 ATATAGGCGT
5493469 GATATGGTGATG
1 GATATGGTGATG
5493481 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5493493 GATATAGG-CAT-
1 GATAT-GGTGATG
5493504 GATAATGGTGATG
1 GAT-ATGGTGATG
5493517 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5493529 GATATAGGCG-TG
1 GATAT-GGTGATG
5493541 G-TAATGGTGATG
1 GAT-ATGGTGATG
5493553 GACTATGGTGATG
1 GA-TATGGTGATG
5493566 ATACAGGCGT
Statistics
Matches: 69, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
11 20 0.29
12 18 0.26
13 28 0.41
14 3 0.04
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5493591 original size:36 final size:36
Alignment explanation
Indices: 5493451--5493590 Score: 219
Period size: 36 Copynumber: 3.9 Consensus size: 36
5493441 ATTTATAAGT
*
5493451 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
5493486 TGGTGATGATATAGGCATGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
5493522 TGGTGATGATATAGGCGTGGTAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
5493558 TGGTGATGATACAGGCGTGATAATGGTAATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
5493591 CAGATTGTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 19 0.20
36 77 0.80
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:5495335 original size:132 final size:133
Alignment explanation
Indices: 5495191--5495456 Score: 498
Period size: 132 Copynumber: 2.0 Consensus size: 133
5495181 TAATATGATT
5495191 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
1 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
* *
5495256 GCATGAATATCATATAACATGGTATTCATAAATGATAAATGG-AACATGTAATAATAATATCCTA
66 GCATCAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATATAATAATAATATCCTA
5495320 AGA
131 AGA
5495323 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
1 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
*
5495388 GCATCAATATCATATAACATGGTATTCATAAATTATAAATGGAAACATATAATAATAATATCCTA
66 GCATCAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATATAATAATAATATCCTA
5495453 AGA
131 AGA
5495456 A
1 A
5495457 ATGATATGTA
Statistics
Matches: 130, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
132 105 0.81
133 25 0.19
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (133 bp):
ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
GCATCAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATATAATAATAATATCCTA
AGA
Found at i:5497507 original size:5 final size:5
Alignment explanation
Indices: 5497497--5497527 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5497487 CTTCAACTTC
*
5497497 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
5497528 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:5499420 original size:133 final size:133
Alignment explanation
Indices: 5499182--5499444 Score: 499
Period size: 133 Copynumber: 2.0 Consensus size: 133
5499172 ATGATTATAT
*
5499182 GACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCAT
1 GACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTACATGTTGTATGCAT
5499247 GAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAA
66 GAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAA
5499312 TAA
131 TAA
5499315 GACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTACATGTTGTATGCAT
1 GACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTACATGTTGTATGCAT
* *
5499380 GAATATCATATAACATGGTATTTATAAATGATAAATGGAAACATTTAATAATAATATCCTAAGAA
66 GAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAA
5499445 ATGATATGTA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 127 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (133 bp):
GACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTACATGTTGTATGCAT
GAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAA
TAA
Found at i:5500420 original size:24 final size:21
Alignment explanation
Indices: 5500385--5500427 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
5500375 GGCTCATTCT
*
5500385 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
5500408 TTTGACATGTCAAAGGACAT
1 TTTGA-ATGTCAAAGGACAT
5500428 TTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 8 0.44
24 6 0.33
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:5501686 original size:5 final size:5
Alignment explanation
Indices: 5501676--5501706 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5501666 CTTCAACTTC
*
5501676 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
5501707 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:5503511 original size:133 final size:133
Alignment explanation
Indices: 5503273--5503538 Score: 496
Period size: 133 Copynumber: 2.0 Consensus size: 133
5503263 ATAATATGAT
5503273 TATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTA
1 TATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTA
* *
5503338 TGCATGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCT
66 TGAATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCT
5503403 AAG
131 AAG
*
5503406 TATAAGACTATCCTAATATGCTTATAACATTGTGTATTAATCATAAAGATAGGGTATATGTTGTA
1 TATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTA
*
5503471 TGAATGAATATCATATAAAATGGTATTCATAAATGATAAATGGATACATGTAATAATAATATCCT
66 TGAATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCT
5503536 AAG
131 AAG
5503539 AAATGATATG
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (133 bp):
TATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTA
TGAATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCT
AAG
Found at i:5509052 original size:18 final size:17
Alignment explanation
Indices: 5508999--5509055 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
5508989 TTAATAAATT
* *
5508999 AACTAGTTTGATGAATG
1 AACTAATTTGATTAATG
*
5509016 AACCAATTTGATTAATG
1 AACTAATTTGATTAATG
5509033 AACTAACTTT-ATTAAATG
1 AACTAA-TTTGATT-AATG
5509051 AACTA
1 AACTA
5509056 GATGCATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (17 bp):
AACTAATTTGATTAATG
Found at i:5513120 original size:24 final size:25
Alignment explanation
Indices: 5513085--5513139 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
5513075 ACTTGGAGCC
*
5513085 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
5513109 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
5513133 TCAAGTG
1 TCAAGTG
5513140 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:5514693 original size:19 final size:21
Alignment explanation
Indices: 5514669--5514720 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5514659 TGTACAAGAG
*
5514669 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
5514688 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5514709 CATGTATTTTCA
1 CATGTATTTTCA
5514721 AAGGGGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:5515705 original size:17 final size:18
Alignment explanation
Indices: 5515683--5515717 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5515673 ACATTTAAAT
5515683 CATTTCTTCTA-TCTTTC
1 CATTTCTTCTATTCTTTC
5515700 CATTTCTTCTATTCTTTC
1 CATTTCTTCTATTCTTTC
5515718 TACCCTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
CATTTCTTCTATTCTTTC
Found at i:5517600 original size:17 final size:18
Alignment explanation
Indices: 5517560--5517600 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
5517550 TATTTACTTA
*
5517560 TTTATGCACTATATATAT
1 TTTATGCACTATACATAT
5517578 TATTATGCACTATACAT-T
1 T-TTATGCACTATACATAT
5517596 TTTAT
1 TTTAT
5517601 ATTATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 14 0.67
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTATGCACTATACATAT
Found at i:5518919 original size:17 final size:17
Alignment explanation
Indices: 5518897--5518932 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5518887 AACTATATAA
*
5518897 TGCATATAATAATGATG
1 TGCATATAATAAAGATG
*
5518914 TGCATATTATAAAGATG
1 TGCATATAATAAAGATG
5518931 TG
1 TG
5518933 ACTATAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (17 bp):
TGCATATAATAAAGATG
Found at i:5519256 original size:162 final size:166
Alignment explanation
Indices: 5519075--5519400 Score: 606
Period size: 168 Copynumber: 2.0 Consensus size: 166
5519065 TAATGCAGTA
5519075 TCTAATGTGCAAATGTATGC-ATAATA-ATATA-TGCAT-AATAAGTAAATATAAGATAAAGTAT
1 TCTAATGTGCAAATGTATGCAATAATATATATAGTGCATAAATAAGTAAATATAAGATAAAGTAT
5519136 GGAAGAACTCCCTTAGAACCAGCTTTGAATAACTTCCATGGTGTGATCAAGTCTTGGAGAAAATT
66 GGAAGAACTCCCTTAGAACCAGCTTTGAATAACTTCCATGGTGTGATCAAGTCTTGGAGAAAATT
5519201 GGAGCTAGATAGGATCACATCATCCTCCCCTTATAG
131 GGAGCTAGATAGGATCACATCATCCTCCCCTTATAG
5519237 TCTAATGTGCAAATGTATGCATAATAATATATATAGTGCATAAATAAGTAAATATAAGATAAAGT
1 TCTAATGTGCAAATGTATGC--AATAATATATATAGTGCATAAATAAGTAAATATAAGATAAAGT
5519302 ATGGAAGAACTCCCTTAGAACCAGCTTTGAATAACTTCCATGGTGTGATCAAGTCTTGGAGAAAA
64 ATGGAAGAACTCCCTTAGAACCAGCTTTGAATAACTTCCATGGTGTGATCAAGTCTTGGAGAAAA
5519367 TTGGAGCTAGATAGGATCACATCATCCTCCCCTT
129 TTGGAGCTAGATAGGATCACATCATCCTCCCCTT
5519401 CTTTTGGGCG
Statistics
Matches: 158, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
162 20 0.13
165 6 0.04
166 5 0.03
167 5 0.03
168 122 0.77
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (166 bp):
TCTAATGTGCAAATGTATGCAATAATATATATAGTGCATAAATAAGTAAATATAAGATAAAGTAT
GGAAGAACTCCCTTAGAACCAGCTTTGAATAACTTCCATGGTGTGATCAAGTCTTGGAGAAAATT
GGAGCTAGATAGGATCACATCATCCTCCCCTTATAG
Found at i:5521460 original size:8 final size:8
Alignment explanation
Indices: 5521447--5521483 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
5521437 CTTGCTTTCT
5521447 CTTTTTTA
1 CTTTTTTA
5521455 C-TTTTTA
1 CTTTTTTA
5521462 CTTTTTT-
1 CTTTTTTA
*
5521469 CTTTTTTT
1 CTTTTTTA
5521477 CTTTTTT
1 CTTTTTT
5521484 TCTTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTA
Found at i:5521475 original size:7 final size:7
Alignment explanation
Indices: 5521446--5521517 Score: 56
Period size: 8 Copynumber: 9.7 Consensus size: 7
5521436 GCTTGCTTTC
5521446 TCTTTTT
1 TCTTTTT
5521453 TACTTTTT
1 T-CTTTTT
*
5521461 ACTTTTT
1 TCTTTTT
5521468 TCTTTTTT
1 TC-TTTTT
5521476 TCTTTTT
1 TCTTTTT
* *
5521483 T-TCTTC
1 TCTTTTT
5521489 TCTTTTT
1 TCTTTTT
5521496 CTCTTCTTT
1 -TCTT-TTT
*
5521505 TGTCTTTT
1 TCT-TTTT
5521513 TCTTT
1 TCTTT
5521518 CTTTTTACAC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
6 4 0.08
7 19 0.37
8 24 0.47
9 4 0.08
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (7 bp):
TCTTTTT
Found at i:5521475 original size:15 final size:15
Alignment explanation
Indices: 5521446--5521522 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
5521436 GCTTGCTTTC
5521446 TCTTTTTTAC-TTTTT
1 TCTTTTTT-CTTTTTT
*
5521461 ACTTTTTTCTTTTTT
1 TCTTTTTTCTTTTTT
* *
5521476 TC-TTTTT-TTCTTC
1 TCTTTTTTCTTTTTT
5521489 TCTTTTTCTCTTCTTTT
1 TCTTTTT-TCTT-TTTT
5521506 GTC-TTTTTCTTTCTTT
1 -TCTTTTTTCTTT-TTT
5521522 T
1 T
5521523 TACACTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 6 0.12
14 10 0.20
15 16 0.33
16 9 0.18
17 6 0.12
18 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (15 bp):
TCTTTTTTCTTTTTT
Found at i:5521495 original size:29 final size:28
Alignment explanation
Indices: 5521462--5521523 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
5521452 TTACTTTTTA
* *
5521462 CTTTTT-TCTTTTTTTCTTTTTTTCTTCT
1 CTTTTTCTCTTCTTTTCTCTTTTTCTT-T
*
5521490 CTTTTTCTCTTCTTTTGTCTTTTTCTTT
1 CTTTTTCTCTTCTTTTCTCTTTTTCTTT
5521518 CTTTTT
1 CTTTTT
5521524 ACACTCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (28 bp):
CTTTTTCTCTTCTTTTCTCTTTTTCTTT
Found at i:5521510 original size:18 final size:17
Alignment explanation
Indices: 5521489--5521522 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5521479 TTTTTTCTTC
5521489 TCTTTTTCTCTTCTTTTG
1 TCTTTTTCT-TTCTTTTG
5521507 TCTTTTTCTTTCTTTT
1 TCTTTTTCTTTCTTTT
5521523 TACACTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (17 bp):
TCTTTTTCTTTCTTTTG
Found at i:5521817 original size:19 final size:19
Alignment explanation
Indices: 5521789--5521833 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5521779 AGATAATAAT
5521789 ATAAGTAATGAAAAT-AAATA
1 ATAAG-AATG-AAATGAAATA
5521809 ATAAGAATGAAATGAAATA
1 ATAAGAATGAAATGAAATA
5521828 A-AAGAA
1 ATAAGAA
5521834 AGGATAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 10 0.42
20 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (19 bp):
ATAAGAATGAAATGAAATA
Found at i:5524276 original size:35 final size:36
Alignment explanation
Indices: 5524237--5524313 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
5524227 TTGGTGGTTA
*
5524237 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGAAAGATGGTGATGT
5524272 TATAGGCGTGAAAATGGTGATGAAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGAAAGATGGTGATGT
5524308 TATAGG
1 TATAGG
5524314 TAGTATCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 10 0.25
36 30 0.75
ACGTcount: A:0.31, C:0.03, G:0.38, T:0.29
Consensus pattern (36 bp):
TATAGGCGTGAAAATGGTGATGAAAGATGGTGATGT
Found at i:5524303 original size:13 final size:13
Alignment explanation
Indices: 5524249--5524306 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
5524239 TAGGCGTGAA
*
5524249 ATGGTGATGGAAG
1 ATGGTGATGAAAG
** *
5524262 ATGGTGATGTTAT
1 ATGGTGATGAAAG
*
5524275 A-GGCG-TGAAA-
1 ATGGTGATGAAAG
5524285 ATGGTGATGAAAG
1 ATGGTGATGAAAG
5524298 ATGGTGATG
1 ATGGTGATG
5524307 TTATAGGTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.17
12 8 0.23
13 20 0.57
ACGTcount: A:0.31, C:0.02, G:0.40, T:0.28
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:5530543 original size:38 final size:38
Alignment explanation
Indices: 5530501--5530575 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
5530491 ACATTCATCC
5530501 ATGAATGTTCACTTATTAAAGCTTGTATGTGTATCCTG
1 ATGAATGTTCACTTATTAAAGCTTGTATGTGTATCCTG
5530539 ATGAATGTTCACTTATTAAAGCTTGTATGTGTATCCT
1 ATGAATGTTCACTTATTAAAGCTTGTATGTGTATCCT
5530576 AGGAATACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (38 bp):
ATGAATGTTCACTTATTAAAGCTTGTATGTGTATCCTG
Found at i:5538155 original size:36 final size:36
Alignment explanation
Indices: 5538082--5538222 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
5538072 ATTTATAAGT
* *
5538082 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5538117 TGGTGATGATATAGGCGTGATAATAGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5538153 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5538189 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5538223 AGATTGTATC
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 20 0.20
36 78 0.80
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5538196 original size:13 final size:12
Alignment explanation
Indices: 5538100--5538221 Score: 55
Period size: 11 Copynumber: 10.2 Consensus size: 12
5538090 ATATAGGCGT
5538100 GATATGGTGATG
1 GATATGGTGATG
5538112 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5538124 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5538135 GATAATAGTGATG
1 GAT-ATGGTGATG
5538148 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5538160 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5538171 GATAATGGAGATG
1 GAT-ATGGTGATG
5538184 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5538196 GATATAGG-CAT-
1 GATAT-GGTGATG
5538207 GATAATGGTGATG
1 GAT-ATGGTGATG
5538220 GA
1 GA
5538222 CAGATTGTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 29
0.69 0.07 0.23
Matches are distributed among these distances:
11 30 0.35
12 24 0.28
13 30 0.35
14 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5543873 original size:13 final size:12
Alignment explanation
Indices: 5543855--5543951 Score: 53
Period size: 13 Copynumber: 8.0 Consensus size: 12
5543845 TATAGGCGCG
5543855 ATATGGTGATGGA
1 ATATGGTGAT-GA
5543868 ATATGGTGATGA
1 ATATGGTGATGA
*
5543880 TATAGGCGTGAT-A
1 -ATATG-GTGATGA
5543893 ATA--GTGATGGA
1 ATATGGTGAT-GA
*
5543904 CTATGGTGATG-
1 ATATGGTGATGA
5543915 ATATAGGTG-TG-
1 ATAT-GGTGATGA
*
5543926 ATAATGGAGATGGA
1 AT-ATGGTGAT-GA
*
5543940 CTATGGTGATGA
1 ATATGGTGATGA
5543952 TATAGGCGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
9 5 0.07
11 13 0.19
12 15 0.22
13 28 0.42
14 6 0.09
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:5543900 original size:23 final size:23
Alignment explanation
Indices: 5543868--5543973 Score: 60
Period size: 23 Copynumber: 4.5 Consensus size: 23
5543858 TGGTGATGGA
*
5543868 ATATGGTGATGATATAGGCG-TG
1 ATATAGTGATGATATAGGCGATG
*
5543890 ATAATAGTGATGGACTAT-GGTGATG
1 AT-ATAGTGAT-GA-TATAGGCGATG
*
5543915 ATATAGGTG-TGATA-ATGGAGATGG
1 ATATA-GTGATGATATA-GGCGAT-G
*
5543939 ACTATGGTGATGATATAGGCG-TG
1 A-TATAGTGATGATATAGGCGATG
*
5543962 ATAATGGTGATG
1 AT-ATAGTGATG
5543974 GACAGATTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.07
23 25 0.37
24 15 0.22
25 21 0.31
26 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
ATATAGTGATGATATAGGCGATG
Found at i:5543909 original size:36 final size:36
Alignment explanation
Indices: 5543836--5543976 Score: 221
Period size: 36 Copynumber: 3.9 Consensus size: 36
5543826 ATTTATAAGT
* * *
5543836 TGGTGATAATATAGGCGCGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5543871 TGGTGATGATATAGGCGTGATAATAGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
5543907 TGGTGATGATATAGGTGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5543943 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5543977 AGATTGTATC
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 19 0.20
36 77 0.80
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5546472 original size:12 final size:12
Alignment explanation
Indices: 5546455--5546496 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
5546445 TATTTTTTTC
5546455 AAAAAAACAGCA
1 AAAAAAACAGCA
5546467 AAAAAAACA--A
1 AAAAAAACAGCA
*
5546477 AAAAAAA-AGCC
1 AAAAAAACAGCA
5546488 AAAAAAACA
1 AAAAAAACA
5546497 AAAAAAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 1 0.04
10 8 0.31
11 7 0.27
12 10 0.38
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAACAGCA
Found at i:5546483 original size:22 final size:21
Alignment explanation
Indices: 5546455--5546503 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5546445 TATTTTTTTC
*
5546455 AAAAAAACAGCAAAAAAAACA
1 AAAAAAAAAGCAAAAAAAACA
*
5546476 AAAAAAAAAGCCAAAAAAACA
1 AAAAAAAAAGCAAAAAAAACA
5546497 AAAAAAA
1 AAAAAAA
5546504 GCCAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGCAAAAAAAACA
Found at i:5546509 original size:11 final size:11
Alignment explanation
Indices: 5546454--5546511 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
5546444 CTATTTTTTT
5546454 CAAAAAAACAG-
1 CAAAAAAA-AGC
5546465 CAAAAAAAA-C
1 CAAAAAAAAGC
*
5546475 AAAAAAAAAAGC
1 -CAAAAAAAAGC
5546487 C-AAAAAAA--
1 CAAAAAAAAGC
5546495 CAAAAAAAAGC
1 CAAAAAAAAGC
5546506 CAAAAA
1 CAAAAA
5546512 TTCAAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 1 0.03
9 7 0.18
10 8 0.21
11 22 0.56
12 1 0.03
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:5546510 original size:10 final size:10
Alignment explanation
Indices: 5546478--5546511 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5546468 AAAAAACAAA
5546478 AAAAAAAGCC
1 AAAAAAAGCC
*
5546488 AAAAAAA-CA
1 AAAAAAAGCC
5546497 AAAAAAAGCC
1 AAAAAAAGCC
5546507 AAAAA
1 AAAAA
5546512 TTCAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:5546520 original size:19 final size:19
Alignment explanation
Indices: 5546454--5546511 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
5546444 CTATTTTTTT
*
5546454 CAAAAAAACAGCAAAAAAAA
1 CAAAAAAA-AGCCAAAAAAA
5546474 CAAAAAAAAAAGCCAAAAAAA
1 C--AAAAAAAAGCCAAAAAAA
5546495 CAAAAAAAAGCCAAAAA
1 CAAAAAAAAGCCAAAAA
5546512 TTCAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 11 0.31
22 7 0.20
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAGCCAAAAAAA
Found at i:5557250 original size:13 final size:11
Alignment explanation
Indices: 5557209--5557293 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5557199 ACAATCTGTC
5557209 CATCACCATTAT
1 CATCACCA-TAT
*
5557221 CA-CGCCTATAT
1 CATCACC-ATAT
5557232 CATCACCATAGT
1 CATCACCATA-T
5557244 CCATCACCATTAT
1 -CATCACCA-TAT
*
5557257 CA-CGCCTATAT
1 CATCACC-ATAT
5557268 CATCACCATATT
1 CATCACCATA-T
5557280 CCATCACCATAT
1 -CATCACCATAT
5557292 CA
1 CA
5557294 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5557253 original size:36 final size:36
Alignment explanation
Indices: 5557206--5557310 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5557196 GATACAATCT
5557206 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5557242 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5557278 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5557311 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5558892 original size:106 final size:106
Alignment explanation
Indices: 5558707--5558919 Score: 381
Period size: 106 Copynumber: 2.0 Consensus size: 106
5558697 GTTCATAGAC
*
5558707 TATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGACCGGTCTC
1 TATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAACGGTCTC
* * *
5558772 AACTTGGCTTGAAATGAAATGTATTATGAGAAAATGATTCA
66 AACTTGGCTTGAAATAAAAGGTATTATGAGAAAACGATTCA
5558813 TATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAACGGTCTC
1 TATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAACGGTCTC
*
5558878 AACTTGGTTTGAAATAAAAGGTATTATGAGAAAACGATTCA
66 AACTTGGCTTGAAATAAAAGGTATTATGAGAAAACGATTCA
5558919 T
1 T
5558920 TCCTAATCAC
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (106 bp):
TATGCCTTAATATGGTGGGATCAACTTACCCTTAACCGAAGGAGGAATGGAGAACGAACGGTCTC
AACTTGGCTTGAAATAAAAGGTATTATGAGAAAACGATTCA
Found at i:5561856 original size:13 final size:11
Alignment explanation
Indices: 5561815--5561899 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5561805 ACAATATGTC
5561815 CATCACCATTAT
1 CATCACCA-TAT
*
5561827 CA-CGCCTATAT
1 CATCACC-ATAT
5561838 CATCACCATAGT
1 CATCACCATA-T
5561850 CCATCACCATTAT
1 -CATCACCA-TAT
*
5561863 CA-CGCCTATAT
1 CATCACC-ATAT
5561874 CATCACCATATT
1 CATCACCATA-T
5561886 CCATCACCATAT
1 -CATCACCATAT
5561898 CA
1 CA
5561900 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5561859 original size:36 final size:36
Alignment explanation
Indices: 5561812--5561916 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5561802 GATACAATAT
5561812 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5561848 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5561884 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5561917 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5563877 original size:11 final size:11
Alignment explanation
Indices: 5563857--5563897 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
5563847 TGCTGGAAAC
5563857 AAGATAAAAAT
1 AAGATAAAAAT
*
5563868 AAGATTAAAAT
1 AAGATAAAAAT
5563879 AAGATAAAGAA-
1 AAGATAAA-AAT
5563890 AAGATAAA
1 AAGATAAA
5563898 TGAATTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (11 bp):
AAGATAAAAAT
Found at i:5564306 original size:15 final size:17
Alignment explanation
Indices: 5564281--5564314 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5564271 TAAAGGTCCT
5564281 AAATAACTAAT-AAATA
1 AAATAACTAATAAAATA
5564297 AAATAA-TAATAAAATA
1 AAATAACTAATAAAATA
5564313 AA
1 AA
5564315 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAAATA
Found at i:5573841 original size:30 final size:30
Alignment explanation
Indices: 5573805--5573871 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
5573795 TTCATGAACC
5573805 TTAATGAATCTTGTACATTCATTCACATTG
1 TTAATGAATCTTGTACATTCATTCACATTG
5573835 TTAATGAATCTTGTACATTCATTCACATTG
1 TTAATGAATCTTGTACATTCATTCACATTG
5573865 TTAATGA
1 TTAATGA
5573872 TGCTTAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (30 bp):
TTAATGAATCTTGTACATTCATTCACATTG
Found at i:5575526 original size:13 final size:13
Alignment explanation
Indices: 5575508--5575572 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
5575498 TATAGGCATG
5575508 ATATGGTGATGGA
1 ATATGGTGATGGA
5575521 ATATGGTGAT-G-
1 ATATGGTGATGGA
*
5575532 ATATAGGCG-T-G-
1 ATAT-GGTGATGGA
5575543 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
* *
5575557 CTATGGTGATGAA
1 ATATGGTGATGGA
5575570 ATA
1 ATA
5575573 GGAGTGATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
11 11 0.26
12 7 0.17
13 23 0.55
14 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.34, T:0.31
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:5575562 original size:36 final size:36
Alignment explanation
Indices: 5575490--5575593 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
5575480 TTTATAAGTC
* * *
5575490 GGTGATAATATAGGCATGAT-ATGGTGATGGAATAT
1 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
5575525 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
1 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
* * *
5575561 GGTGATGAAATAGGAGTGATAATGGTGACGGAC
1 GGTGATGATATAGGCGTGATAATGGTGATGGAC
5575594 AGATTGTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 18 0.29
36 44 0.71
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.28
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
Found at i:5575981 original size:19 final size:20
Alignment explanation
Indices: 5575934--5575984 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5575924 GAAACCCCTT
**
5575934 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
5575954 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5575973 TGAAGATACATG
1 TGAAAATACATG
5575985 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5579467 original size:15 final size:15
Alignment explanation
Indices: 5579443--5579478 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5579433 TATGATAATT
*
5579443 AAGAAATGAAATGGA
1 AAGAATTGAAATGGA
5579458 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
5579473 TAGAAT
1 AAGAAT
5579479 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:5579657 original size:13 final size:12
Alignment explanation
Indices: 5579638--5579723 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
5579628 ATATAGGCGT
5579638 GATATGGTGATG
1 GATATGGTGATG
5579650 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5579662 GATATAGGCG-T-
1 GATAT-GGTGATG
5579673 GATAATGGTGATG
1 GAT-ATGGTGATG
5579686 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5579698 GATATAGG-CAT-
1 GATAT-GGTGATG
5579709 GATAATGGTGATG
1 GAT-ATGGTGATG
5579722 GA
1 GA
5579724 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5579693 original size:36 final size:36
Alignment explanation
Indices: 5579620--5579724 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5579610 ATTTATAAGT
* *
5579620 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5579655 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5579691 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5579725 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5588737 original size:30 final size:31
Alignment explanation
Indices: 5588698--5588757 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5588688 ACATGCTGCC
**
5588698 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
5588729 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
5588758 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:5589845 original size:20 final size:19
Alignment explanation
Indices: 5589820--5589860 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5589810 TCATGATATG
*
5589820 TAAATGATATGAAAACATAA
1 TAAATGA-ATCAAAACATAA
*
5589840 TAAATGAATCTAAACATAA
1 TAAATGAATCAAAACATAA
5589859 TA
1 TA
5589861 TAAAGCTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (19 bp):
TAAATGAATCAAAACATAA
Found at i:5591293 original size:22 final size:22
Alignment explanation
Indices: 5591268--5591309 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5591258 CAATTCATTT
5591268 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
5591290 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
5591310 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:5595882 original size:22 final size:21
Alignment explanation
Indices: 5595857--5595898 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5595847 CAATTCATTT
5595857 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTT-TTTTA
5595879 ATCTTATTTTTATCTTTTTT
1 ATCTTATTTTTATCTTTTTT
5595899 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (21 bp):
ATCTTATTTTTATCTTTTTTA
Found at i:5600625 original size:22 final size:23
Alignment explanation
Indices: 5600597--5600648 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
5600587 ATTTATAAGT
5600597 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
5600619 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
5600642 TGGTGAT
1 TGGTGAT
5600649 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:5600640 original size:36 final size:37
Alignment explanation
Indices: 5600599--5600714 Score: 143
Period size: 36 Copynumber: 3.2 Consensus size: 37
5600589 TTATAAGTTG
*
5600599 GTGATAATATAGGCGTGA-TATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
5600635 GTGAT-A-AT-GGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATAGGTG-T-GACTATGGTGATGATATAGGC
** *
5600671 GTGATAATGGAGATG-GACTATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
5600707 GTGATAAT
1 GTGATAAT
5600715 GGTGATGGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.04
34 3 0.04
35 3 0.04
36 57 0.81
37 1 0.01
39 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (37 bp):
GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
Found at i:5600715 original size:36 final size:36
Alignment explanation
Indices: 5600617--5600724 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
5600607 ATAGGCGTGA
5600617 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
5600653 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
5600689 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
5600725 AGATTGTATC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:5605167 original size:22 final size:23
Alignment explanation
Indices: 5605139--5605190 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
5605129 ATTTATAAGT
5605139 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
5605161 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
5605184 TGGTGAT
1 TGGTGAT
5605191 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:5605182 original size:36 final size:37
Alignment explanation
Indices: 5605141--5605256 Score: 143
Period size: 36 Copynumber: 3.2 Consensus size: 37
5605131 TTATAAGTTG
*
5605141 GTGATAATATAGGCGTGA-TATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
5605177 GTGAT-A-AT-GGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATAGGTG-T-GACTATGGTGATGATATAGGC
** *
5605213 GTGATAATGGAGATG-GACTATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
5605249 GTGATAAT
1 GTGATAAT
5605257 GGTGATTGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.04
34 3 0.04
35 3 0.04
36 57 0.81
37 1 0.01
39 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (37 bp):
GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
Found at i:5605257 original size:36 final size:36
Alignment explanation
Indices: 5605159--5605258 Score: 191
Period size: 36 Copynumber: 2.8 Consensus size: 36
5605149 ATAGGCGTGA
*
5605159 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
5605195 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
5605231 TATGGTGATGATATAGGCGTGATAATGG
1 TATGGTGATGATATAGGCGTGATAATGG
5605259 TGATTGACAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
Found at i:5610292 original size:36 final size:36
Alignment explanation
Indices: 5610209--5610346 Score: 172
Period size: 36 Copynumber: 3.9 Consensus size: 36
5610199 TATATGTATG
* * *
5610209 AAATGATGATAGAAGATGGTAATGA-TATAGGCGTG-
1 AAATGGTGATGGAAGATGGTGAT-ATTATAGGCGTGA
* * *
5610244 CAATGGTAATGGAAGATGGTGATATTATAGGCATGA
1 AAATGGTGATGGAAGATGGTGATATTATAGGCGTGA
* *
5610280 AAATGGTGATGGAAGATGATGATGTTATAGGCGTGA
1 AAATGGTGATGGAAGATGGTGATATTATAGGCGTGA
*
5610316 AAATGGTGATGGAAGATGGTGATGTTATAGG
1 AAATGGTGATGGAAGATGGTGATATTATAGG
5610347 TAGTACCTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 27 0.30
36 61 0.69
ACGTcount: A:0.36, C:0.03, G:0.34, T:0.28
Consensus pattern (36 bp):
AAATGGTGATGGAAGATGGTGATATTATAGGCGTGA
Found at i:5610334 original size:72 final size:71
Alignment explanation
Indices: 5610209--5610346 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 71
5610199 TATATGTATG
* *
5610209 AAATGATGATAGAAGATGGTAATGATATAGGCGTGCAATGGTAATGGAAGATGGTGATATTATAG
1 AAATGATGATAGAAGATGATAATGATATAGGCGTGAAATGGTAATGGAAGATGGTGATATTATAG
5610274 GCATGA
66 GCATGA
* * * * * *
5610280 AAATGGTGATGGAAGATGATGATGTTATAGGCGTGAAAATGGTGATGGAAGATGGTGATGTTATA
1 AAATGATGATAGAAGATGATAATGATATAGGCGTG-AAATGGTAATGGAAGATGGTGATATTATA
5610345 GG
65 GG
5610347 TAGTACCTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 30 0.52
72 28 0.48
ACGTcount: A:0.36, C:0.03, G:0.34, T:0.28
Consensus pattern (71 bp):
AAATGATGATAGAAGATGATAATGATATAGGCGTGAAATGGTAATGGAAGATGGTGATATTATAG
GCATGA
Found at i:5611475 original size:23 final size:23
Alignment explanation
Indices: 5611449--5611524 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
5611439 TTTAAAGATT
5611449 TAATTATGTAAATATGTGGTTCA
1 TAATTATGTAAATATGTGGTTCA
* * * * *
5611472 TAATAATAGCTAAGTATTTAAAGAT-A
1 TAATTAT-G-TAAATATGT--GGTTCA
5611498 TAATTATGTAAATATGTGGTTCA
1 TAATTATGTAAATATGTGGTTCA
5611521 TAAT
1 TAAT
5611525 AATAACTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 2 0.05
23 11 0.29
24 8 0.21
25 8 0.21
26 7 0.18
27 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (23 bp):
TAATTATGTAAATATGTGGTTCA
Found at i:5611483 original size:49 final size:49
Alignment explanation
Indices: 5611421--5611528 Score: 191
Period size: 49 Copynumber: 2.2 Consensus size: 49
5611411 CACAAGAAAG
*
5611421 CATAAT-ATAAGCTAAGTATTTAAAGATTTAATTATGTAAATATGTGGTT
1 CATAATAAT-AGCTAAGTATTTAAAGATATAATTATGTAAATATGTGGTT
5611470 CATAATAATAGCTAAGTATTTAAAGATATAATTATGTAAATATGTGGTT
1 CATAATAATAGCTAAGTATTTAAAGATATAATTATGTAAATATGTGGTT
5611519 CATAATAATA
1 CATAATAATA
5611529 ACTTCATACA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
49 55 0.96
50 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.39
Consensus pattern (49 bp):
CATAATAATAGCTAAGTATTTAAAGATATAATTATGTAAATATGTGGTT
Found at i:5617094 original size:16 final size:13
Alignment explanation
Indices: 5617054--5617087 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5617044 CCATTGCCAT
*
5617054 TTCATCATCATCC
1 TTCATCAACATCC
5617067 TTCATCAACATCC
1 TTCATCAACATCC
5617080 TTCATCAA
1 TTCATCAA
5617088 GACCATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (13 bp):
TTCATCAACATCC
Found at i:5617773 original size:22 final size:20
Alignment explanation
Indices: 5617732--5617781 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
5617722 AACACCATAT
5617732 TCATTTCATCATCAACACCA
1 TCATTTCATCATCAACACCA
*
5617752 TCATCTTCATCCATCAAGACCA
1 TCAT-TTCAT-CATCAACACCA
5617774 TCAATTTC
1 TC-ATTTC
5617782 GCAACCATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 15 0.58
23 2 0.08
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (20 bp):
TCATTTCATCATCAACACCA
Found at i:5622042 original size:13 final size:13
Alignment explanation
Indices: 5622024--5622064 Score: 68
Period size: 12 Copynumber: 3.3 Consensus size: 13
5622014 TTTCTTATCC
5622024 TTTCATTTCTTTA
1 TTTCATTTCTTTA
5622037 TTTCATTT-TTTA
1 TTTCATTTCTTTA
5622049 TTTCATTTC-TTA
1 TTTCATTTCTTTA
5622061 TTTC
1 TTTC
5622065 CAATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:5622273 original size:12 final size:13
Alignment explanation
Indices: 5622244--5622281 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5622234 CAAGTTCTAC
*
5622244 AAGAAAAAGAAAT
1 AAGAAAAAAAAAT
5622257 AAGAAAAAAAAAT
1 AAGAAAAAAAAAT
5622270 -AGAAAAGAAAAA
1 AAGAAAA-AAAAA
5622282 GACTCCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (13 bp):
AAGAAAAAAAAAT
Found at i:5633248 original size:9 final size:9
Alignment explanation
Indices: 5633216--5633275 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
5633206 ATTAGATTAC
*
5633216 AAAAAGAAA
1 AAAAAGAAG
*
5633225 AGAAAAG-AC
1 A-AAAAGAAG
*
5633234 AAAAAGTAG
1 AAAAAGAAG
5633243 AAAAAGAAG
1 AAAAAGAAG
5633252 AAAAAAAGAAG
1 --AAAAAGAAG
5633263 AAAAAGAAG
1 AAAAAGAAG
5633272 AAAA
1 AAAA
5633276 GTAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
8 5 0.11
9 25 0.57
10 5 0.11
11 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:5633255 original size:17 final size:18
Alignment explanation
Indices: 5633234--5633283 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
5633224 AAGAAAAGAC
5633234 AAAAAGTAGAAAAAGAAG
1 AAAAAGTAGAAAAAGAAG
*
5633252 AAAAAAAGAAGAAAAAGAAG
1 --AAAAAGTAGAAAAAGAAG
5633272 -AAAAGTA-AAAAA
1 AAAAAGTAGAAAAA
5633284 AAAGCAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.18
17 6 0.21
20 17 0.61
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAAAGTAGAAAAAGAAG
Found at i:5633284 original size:9 final size:8
Alignment explanation
Indices: 5633216--5633284 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 8
5633206 ATTAGATTAC
5633216 AAAAAGAAA
1 AAAAAG-AA
5633225 AGAAAAGACA
1 A-AAAAGA-A
5633235 AAAAGTAGAA
1 AAAA--AGAA
5633245 AAAGAAGAA
1 AAA-AAGAA
5633254 AAAAAGAA
1 AAAAAGAA
5633262 GAAAAAGAA
1 -AAAAAGAA
*
5633271 GAAAAGTAA
1 AAAAAG-AA
5633280 AAAAA
1 AAAAA
5633285 AAGCAAGCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 10 0.20
9 26 0.51
10 11 0.22
11 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5633286 original size:20 final size:20
Alignment explanation
Indices: 5633216--5633275 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
5633206 ATTAGATTAC
* *
5633216 AAAAAGAA-AAGAA-AAGAC
1 AAAAAGAAGAAAAAGAAGAA
*
5633234 AAAAAGTAGAAAAAGAAGAA
1 AAAAAGAAGAAAAAGAAGAA
5633254 AAAAAGAAGAAAAAGAAGAA
1 AAAAAGAAGAAAAAGAAGAA
5633274 AA
1 AA
5633276 GTAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 25 0.69
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAAAAAGAAGAA
Found at i:5640243 original size:21 final size:22
Alignment explanation
Indices: 5640202--5640243 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
5640192 CTCAGCTCCT
*
5640202 CAGCTACTCTCCTAGCTACTTC
1 CAGCTACTCTCCTAGCAACTTC
5640224 CAGCTA-TCT-CTAGTCAACTT
1 CAGCTACTCTCCTAG-CAACTT
5640244 TTCAACAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (22 bp):
CAGCTACTCTCCTAGCAACTTC
Found at i:5640320 original size:20 final size:20
Alignment explanation
Indices: 5640294--5640340 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
5640284 GCTACATGCT
5640294 AGCTCCTCCAGCTAAGTTGA
1 AGCTCCTCCAGCTAAGTTGA
*
5640314 AGTTCCTCCAGCTAAGTTGA
1 AGCTCCTCCAGCTAAGTTGA
5640334 AGCTCCT
1 AGCTCCT
5640341 TATGTGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (20 bp):
AGCTCCTCCAGCTAAGTTGA
Found at i:5643410 original size:19 final size:20
Alignment explanation
Indices: 5643386--5643428 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5643376 AGCATTTATC
*
5643386 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
5643405 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
5643425 TTCA
1 TTCA
5643429 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:5643968 original size:25 final size:25
Alignment explanation
Indices: 5643940--5644020 Score: 144
Period size: 25 Copynumber: 3.2 Consensus size: 25
5643930 TCTTTGATAA
* *
5643940 CATTTATATACATTTCAATTCTTAT
1 CATTTCTATCCATTTCAATTCTTAT
5643965 CATTTCTATCCATTTCAATTCTTAT
1 CATTTCTATCCATTTCAATTCTTAT
5643990 CATTTCTATCCATTTCAATTCTTAT
1 CATTTCTATCCATTTCAATTCTTAT
5644015 CATTTC
1 CATTTC
5644021 CTTTCTTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (25 bp):
CATTTCTATCCATTTCAATTCTTAT
Found at i:5643970 original size:15 final size:15
Alignment explanation
Indices: 5643950--5644020 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 15
5643940 CATTTATATA
5643950 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
*
5643965 CATTTCTA-TC----
1 CATTTCAATTCTTAT
5643975 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
*
5643990 CATTTCTA-TC----
1 CATTTCAATTCTTAT
5644000 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
5644015 CATTTC
1 CATTTC
5644021 CTTTCTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
14 4 0.10
15 20 0.48
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (15 bp):
CATTTCAATTCTTAT
Found at i:5644243 original size:6 final size:6
Alignment explanation
Indices: 5644232--5644265 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
5644222 GTGCTGTAAC
5644232 AAAAAG AAAAAG AAAGAAG AAAAA- AAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAA
5644266 GACTCCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5644253 original size:13 final size:11
Alignment explanation
Indices: 5644232--5644265 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
5644222 GTGCTGTAAC
5644232 AAAAAGAAAAA
1 AAAAAGAAAAA
5644243 GAAAGAAGAAAAA
1 -AAA-AAGAAAAA
5644256 AAAAAGAAAA
1 AAAAAGAAAA
5644266 GACTCCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 6 0.29
13 8 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:5644487 original size:16 final size:16
Alignment explanation
Indices: 5644453--5644501 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5644443 GTAAGTTATC
* * *
5644453 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
5644469 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
5644485 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
5644502 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:5648301 original size:13 final size:12
Alignment explanation
Indices: 5648282--5648405 Score: 59
Period size: 11 Copynumber: 10.3 Consensus size: 12
5648272 ATATAGGCGT
5648282 GATATGGTGATG
1 GATATGGTGATG
5648294 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5648306 GATATAGGCG-T-
1 GATAT-GGTGATG
5648317 GATAATGGTGATG
1 GAT-ATGGTGATG
5648330 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5648342 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5648353 GATAATGGAGATG
1 GAT-ATGGTGATG
*
5648366 GACTATAGTGAT-
1 GA-TATGGTGATG
*
5648378 GATATAGGCG-T-
1 GATAT-GGTGATG
5648389 GATAATGGTGATG
1 GAT-ATGGTGATG
5648402 GATA
1 GATA
5648406 GATTGTATCT
Statistics
Matches: 88, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
11 31 0.35
12 24 0.27
13 31 0.35
14 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5648326 original size:23 final size:23
Alignment explanation
Indices: 5648296--5648401 Score: 69
Period size: 23 Copynumber: 4.5 Consensus size: 23
5648286 TGGTGATGGA
5648296 ATATGGTGATGATATAGGCG-TG
1 ATATGGTGATGATATAGGCGATG
*
5648318 ATAATGGTGATGGACTAT-GGTGATG
1 AT-ATGGTGAT-GA-TATAGGCGATG
* *
5648343 ATATAGGCG-TGATA-ATGGAGATGG
1 ATAT-GGTGATGATATA-GGCGAT-G
*
5648367 ACTATAGTGATGATATAGGCG-TG
1 A-TATGGTGATGATATAGGCGATG
5648390 ATAATGGTGATG
1 AT-ATGGTGATG
5648402 GATAGATTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 23
0.68 0.07 0.24
Matches are distributed among these distances:
22 5 0.08
23 25 0.38
24 13 0.20
25 21 0.32
26 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (23 bp):
ATATGGTGATGATATAGGCGATG
Found at i:5648337 original size:36 final size:36
Alignment explanation
Indices: 5648264--5648403 Score: 237
Period size: 36 Copynumber: 3.9 Consensus size: 36
5648254 ATTTATAAGT
* *
5648264 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5648299 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5648335 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5648371 TAGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
5648404 TAGATTGTAT
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 20 0.20
36 79 0.80
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5652871 original size:15 final size:16
Alignment explanation
Indices: 5652844--5652880 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
5652834 CTTTATTATC
5652844 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
5652860 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
5652875 TTATTT
1 TTATTT
5652881 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:5653248 original size:11 final size:11
Alignment explanation
Indices: 5653232--5653280 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
5653222 TATTTTTTTC
5653232 AAAAAACAAAA
1 AAAAAACAAAA
5653243 AAAAAACAAAA
1 AAAAAACAAAA
**
5653254 AAAAGCCAAAA
1 AAAAAACAAAA
5653265 AAAAAACAAAA
1 AAAAAACAAAA
5653276 AAAAA
1 AAAAA
5653281 GCCAAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:5653269 original size:23 final size:23
Alignment explanation
Indices: 5653238--5653289 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
5653228 TTTCAAAAAA
5653238 CAAAAAAAAAAC-AAAAAAAAGC
1 CAAAAAAAAAACAAAAAAAAAGC
5653260 CAAAAAAAAAACAAAAAAAAAGC
1 CAAAAAAAAAACAAAAAAAAAGC
5653283 CAAAAAA
1 CAAAAAA
5653290 CCCAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAAACAAAAAAAAAGC
Found at i:5653287 original size:11 final size:11
Alignment explanation
Indices: 5653232--5653289 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
5653222 TATTTTTTTC
5653232 AAAAAA-CAAA
1 AAAAAACCAAA
*
5653242 AAAAAAACAAA
1 AAAAAACCAAA
*
5653253 AAAAAGCCAAA
1 AAAAAACCAAA
*
5653264 AAAAAAACAAA
1 AAAAAACCAAA
5653275 AAAAAAGCCAAA
1 AAAAAA-CCAAA
5653287 AAA
1 AAA
5653290 CCCAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
10 6 0.15
11 28 0.68
12 7 0.17
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAACCAAA
Found at i:5653289 original size:10 final size:10
Alignment explanation
Indices: 5653232--5653280 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
5653222 TATTTTTTTC
5653232 AAAAAACAAAA
1 AAAAAAC-AAA
5653243 AAAAAACAAA
1 AAAAAACAAA
*
5653253 AAAAAGCCAAAA
1 AAAAA-AC-AAA
5653265 AAAAAACAAA
1 AAAAAACAAA
5653275 AAAAAA
1 AAAAAA
5653281 GCCAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 17 0.50
11 9 0.26
12 8 0.24
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:5658216 original size:19 final size:19
Alignment explanation
Indices: 5658194--5658230 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5658184 TTCTCTTTTA
5658194 TTTTCTTCTTTCTTGTTGC
1 TTTTCTTCTTTCTTGTTGC
* *
5658213 TTTTTTTTTTTCTTGTTG
1 TTTTCTTCTTTCTTGTTG
5658231 TAGCACTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.76
Consensus pattern (19 bp):
TTTTCTTCTTTCTTGTTGC
Found at i:5658223 original size:26 final size:23
Alignment explanation
Indices: 5658174--5658226 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
5658164 GATGTAGGAG
5658174 TCTTTTTCTTTTCTCTTTTATTT
1 TCTTTTTCTTTTCTCTTTTATTT
* *
5658197 TCTTCTTTCTTGTTGCTTTTTTTTTT
1 TCTT-TTTCTT-TT-CTCTTTTATTT
5658223 TCTT
1 TCTT
5658227 GTTGTAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 6 0.24
25 2 0.08
26 13 0.52
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (23 bp):
TCTTTTTCTTTTCTCTTTTATTT
Found at i:5658643 original size:13 final size:12
Alignment explanation
Indices: 5658624--5658745 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 12
5658614 ATATAGGCGT
5658624 GATATGGTGATG
1 GATATGGTGATG
5658636 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5658648 GATATAGGCG-T-
1 GATAT-GGTGATG
5658659 GATAATGGTGATG
1 GAT-ATGGTGATG
5658672 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5658684 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5658695 GATAATGGAGATG
1 GAT-ATGGTGATG
5658708 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5658720 GATATAGGCG-T-
1 GATAT-GGTGATG
5658731 GATAATGGTGATG
1 GAT-ATGGTGATG
5658744 GA
1 GA
5658746 CAGATTGTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
11 31 0.35
12 24 0.27
13 31 0.35
14 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5658668 original size:23 final size:23
Alignment explanation
Indices: 5658638--5658743 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 23
5658628 TGGTGATGGA
5658638 ATATGGTGATGATATAGGCG-TG
1 ATATGGTGATGATATAGGCGATG
*
5658660 ATAATGGTGATGGACTAT-GGTGATG
1 AT-ATGGTGAT-GA-TATAGGCGATG
* *
5658685 ATATAGGCG-TGATA-ATGGAGATGG
1 ATAT-GGTGATGATATA-GGCGAT-G
5658709 ACTATGGTGATGATATAGGCG-TG
1 A-TATGGTGATGATATAGGCGATG
5658732 ATAATGGTGATG
1 AT-ATGGTGATG
5658744 GACAGATTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.07
23 26 0.39
24 14 0.21
25 21 0.31
26 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (23 bp):
ATATGGTGATGATATAGGCGATG
Found at i:5658679 original size:36 final size:36
Alignment explanation
Indices: 5658606--5658746 Score: 248
Period size: 36 Copynumber: 3.9 Consensus size: 36
5658596 AATTATAAGT
* *
5658606 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5658641 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5658677 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5658713 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5658747 AGATTGTATC
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.20
36 81 0.80
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5660749 original size:48 final size:46
Alignment explanation
Indices: 5660638--5660759 Score: 138
Period size: 48 Copynumber: 2.6 Consensus size: 46
5660628 GGTAACCATG
**
5660638 AAAATAAGCTTATGAGCTTACAGAATAATGGCAAGTATATTGAAAA
1 AAAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * **
5660684 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA
1 AAAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAA
*
5660732 AAAATAAGCTTATGAGCTTATGGGATAA
1 AAAATAAGCTTATGAGCTTATGGAATAA
5660760 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.03
46 23 0.36
48 25 0.39
49 14 0.22
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (46 bp):
AAAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:5667656 original size:21 final size:21
Alignment explanation
Indices: 5667632--5667697 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
5667622 TAATTTTTAT
5667632 GAATTTATATGTAAATTTTCG
1 GAATTTATATGTAAATTTTCG
5667653 GAATTTATATG-AAA--TT--
1 GAATTTATATGTAAATTTTCG
*
5667669 -AATTTTTAT-T-AATTTTCG
1 GAATTTATATGTAAATTTTCG
5667687 GAATTTATATG
1 GAATTTATATG
5667698 AACAGTAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
14 2 0.06
15 8 0.22
16 2 0.06
18 2 0.06
19 8 0.22
20 3 0.08
21 11 0.31
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (21 bp):
GAATTTATATGTAAATTTTCG
Found at i:5669324 original size:19 final size:20
Alignment explanation
Indices: 5669300--5669346 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5669290 CAAGAACATT
*
5669300 TATTTTCATT-AAAATTATG
1 TATTTTCATTAAAAATCATG
5669319 TATTTTCATTAAAAATCATG
1 TATTTTCATTAAAAATCATG
*
5669339 TGTTTTCA
1 TATTTTCA
5669347 AAGGAGTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (20 bp):
TATTTTCATTAAAAATCATG
Found at i:5673606 original size:22 final size:21
Alignment explanation
Indices: 5673571--5673612 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5673561 AAAAATAAAC
*
5673571 CTTACCAGTACACTCACAAAGT
1 CTTACAAGTACACTC-CAAAGT
*
5673593 CTTACAAGTTCACTCCAAAG
1 CTTACAAGTACACTCCAAAG
5673613 AAAAGATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.24
Consensus pattern (21 bp):
CTTACAAGTACACTCCAAAGT
Found at i:5675459 original size:13 final size:13
Alignment explanation
Indices: 5675443--5675480 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5675433 AGAAAAAATC
5675443 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
*
5675456 AGAAGAAAAGAAA
1 AGAAAAAAAGAAA
*
5675469 AGAAAAAGAGAA
1 AGAAAAAAAGAA
5675481 GTTCAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:5686572 original size:48 final size:48
Alignment explanation
Indices: 5686480--5686572 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 48
5686470 CATACTCCAA
* * * * *
5686480 TTTGCCTTTTCATCATGACTAGGAGGGTTGGTTAGAGCCATTATCGTG
1 TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACATTATCGTG
**
5686528 TTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACA-TTATC
5686573 CATCTATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
47 3 0.08
48 34 0.92
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (48 bp):
TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACATTATCGTG
Found at i:5687450 original size:18 final size:18
Alignment explanation
Indices: 5687429--5687489 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
5687419 TTTTGAATTC
5687429 TTTTTCTTTTCTTTTCTT
1 TTTTTCTTTTCTTTTCTT
*
5687447 TTTTTCTGATTGTTCTATTCTT
1 TTTTTC---TT-TTCTTTTCTT
*
5687469 TTTGTCTTTT-TCTTTCTT
1 TTTTTCTTTTCT-TTTCTT
5687487 TTT
1 TTT
5687490 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 16 0.46
19 2 0.06
21 2 0.06
22 14 0.40
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCTT
Found at i:5690547 original size:22 final size:24
Alignment explanation
Indices: 5690499--5690548 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
5690489 TTTTTTTTTC
**
5690499 TTTTGAGTGCTTTCAATTTCTTCT
1 TTTTGAGTGCTTTCAATTTCTGAT
*
5690523 TTTTGAGTGC-TTC-TTTTCTGAT
1 TTTTGAGTGCTTTCAATTTCTGAT
5690545 TTTT
1 TTTT
5690549 TTCTTGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (24 bp):
TTTTGAGTGCTTTCAATTTCTGAT
Done.