Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 16 of 136
Found at i:4947545 original size:37 final size:37
Alignment explanation
Indices: 4947489--4947565 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
4947479 AATGGTTTTA
4947489 AAATTATTAAAATTATTTTTTAAAATATAAAATTACT
1 AAATTATTAAAATTATTTTTTAAAATATAAAATTACT
* * *
4947526 AAATTATT-ATATTATTTTTTTGAAATATAAAATTATT
1 AAATTATTAAAATTA-TTTTTTAAAATATAAAATTACT
4947563 AAA
1 AAA
4947566 ATAGATCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 5 0.14
37 31 0.86
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
AAATTATTAAAATTATTTTTTAAAATATAAAATTACT
Found at i:4947970 original size:28 final size:30
Alignment explanation
Indices: 4947932--4948001 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
4947922 GGTGGTCGAA
*
4947932 TTTGGGGATTTTATG-TAAGG-TTTTTGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
4947960 TTTGGGGATTTT-TGTTTAGGATTTCTGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
4947989 TTTGGAGATTTTA
1 TTTGGGGATTTTA
4948002 GGGATTGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 16 0.44
29 18 0.50
ACGTcount: A:0.17, C:0.01, G:0.27, T:0.54
Consensus pattern (30 bp):
TTTGGGGATTTTATGTTAAGGATTTCTGAT
Found at i:4948317 original size:21 final size:19
Alignment explanation
Indices: 4948287--4948342 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
4948277 AATCTTCAAG
*
4948287 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4948306 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
4948327 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
4948343 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4948364 original size:23 final size:22
Alignment explanation
Indices: 4948287--4948365 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 22
4948277 AATCTTCAAG
* *
4948287 GATATACAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
4948309 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
4948327 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
4948349 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
4948366 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 11 0.23
22 8 0.17
23 12 0.25
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:4948730 original size:23 final size:22
Alignment explanation
Indices: 4948687--4948744 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
4948677 AAAGGGTATC
* *
4948687 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
4948708 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
4948731 TGCATATCATATCT
1 TACAAATCATATCT
4948745 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:4948760 original size:21 final size:21
Alignment explanation
Indices: 4948723--4948777 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
4948713 AATCATATCT
4948723 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
4948742 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
4948763 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
4948778 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 11 0.33
21 22 0.67
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:4949106 original size:29 final size:28
Alignment explanation
Indices: 4949064--4949133 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
4949054 AAGCAATCCC
* *
4949064 TAAAATCTCCAAAATCAGAAATCCTAAACA
1 TAAAATCCCCAAAATCA-AAAACCT-AACA
*
4949094 -AAAATCCCCAAAATCAAAAACCTTACA
1 TAAAATCCCCAAAATCAAAAACCTAACA
4949121 TAAAATCCCCAAA
1 TAAAATCCCCAAA
4949134 TTCGACCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 18 0.50
29 15 0.42
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.17
Consensus pattern (28 bp):
TAAAATCCCCAAAATCAAAAACCTAACA
Found at i:4949560 original size:37 final size:37
Alignment explanation
Indices: 4949500--4949576 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
4949490 AATGATCTAT
4949500 TTTAATAATTTTATATTTCAAAAAAATAA-TATAATAA
1 TTTAATAATTTTATATTTC-AAAAAATAATTATAATAA
* *
4949537 TTTAGTAATTTTATATATT-AAAAAATAATTTTAATAA
1 TTTAATAATTTTATAT-TTCAAAAAATAATTATAATAA
4949574 TTT
1 TTT
4949577 TAAAATCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 9 0.25
37 25 0.69
38 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
TTTAATAATTTTATATTTCAAAAAATAATTATAATAA
Found at i:4952190 original size:16 final size:16
Alignment explanation
Indices: 4952156--4952198 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4952146 AATTGAAATG
*
4952156 AATAT-ATATATGTGTA
1 AATATGATA-ATGTGCA
*
4952172 AATGTGATAATGTGCA
1 AATATGATAATGTGCA
4952188 AATATGATAAT
1 AATATGATAAT
4952199 TGGATATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.37
Consensus pattern (16 bp):
AATATGATAATGTGCA
Found at i:4955088 original size:27 final size:28
Alignment explanation
Indices: 4955058--4955112 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4955048 CAATAATACG
4955058 AGCAAGACTAAAGAT-AAG-ATAAATAAA
1 AGCAA-ACTAAAGATAAAGAATAAATAAA
**
4955085 AGCAAACTAATTATAAAGAATAAATAAA
1 AGCAAACTAAAGATAAAGAATAAATAAA
4955113 TAAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 8 0.33
28 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18
Consensus pattern (28 bp):
AGCAAACTAAAGATAAAGAATAAATAAA
Found at i:4963577 original size:27 final size:28
Alignment explanation
Indices: 4963547--4963601 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4963537 CAATAATACG
4963547 AGCAAGACTAAAGAT-AAG-ATAAATAAA
1 AGCAA-ACTAAAGATAAAGAATAAATAAA
**
4963574 AGCAAACTAATTATAAAGAATAAATAAA
1 AGCAAACTAAAGATAAAGAATAAATAAA
4963602 TAAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 8 0.33
28 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18
Consensus pattern (28 bp):
AGCAAACTAAAGATAAAGAATAAATAAA
Found at i:4965102 original size:19 final size:19
Alignment explanation
Indices: 4965056--4965102 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4965046 GTTTTTTATT
*
4965056 TTTATTTTTGGGCTTGTAA
1 TTTATTTTTGGACTTGTAA
*
4965075 TTTATTTTTTGGACTGTTTAA
1 TTTA-TTTTTGGACT-TGTAA
4965096 -TTATTTT
1 TTTATTTT
4965103 GGAATTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.64
Consensus pattern (19 bp):
TTTATTTTTGGACTTGTAA
Found at i:4965383 original size:25 final size:24
Alignment explanation
Indices: 4965355--4965408 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
4965345 GTTGAATAAT
* *
4965355 GGTAAGATCATACGAGCTGAGTATC
1 GGTAAGATCATAAGAGCTG-GAATC
* *
4965380 GGTAAGCTCATAAGAGTTGGAATC
1 GGTAAGATCATAAGAGCTGGAATC
4965404 GGTAA
1 GGTAA
4965409 CCCTAATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (24 bp):
GGTAAGATCATAAGAGCTGGAATC
Found at i:4966405 original size:9 final size:9
Alignment explanation
Indices: 4966391--4966417 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4966381 CTAATAGCAA
4966391 TTGACTTTT
1 TTGACTTTT
4966400 TTGACTTTT
1 TTGACTTTT
4966409 TTGACTTTT
1 TTGACTTTT
4966418 ATAATTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (9 bp):
TTGACTTTT
Found at i:4968200 original size:41 final size:42
Alignment explanation
Indices: 4968142--4968254 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 42
4968132 ATTTTTGAGG
* **
4968142 TATGATTTCGTGTAAGACCATATCTGGGGCATTGGCATCG-TA
1 TATGA-TTCGTGTAAGACCATATCTGGGACAGAGGCATCGATA
* *
4968184 TATGATTCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATA
1 TATGATTCGTGTAAGACCATATCTGGGACAGAGGCATCGATA
* * *
4968226 TGTGATAACATGTAAGACCATATCTGGGA
1 TATGAT-TCGTGTAAGACCATATCTGGGA
4968255 TATGGCATTG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 29 0.49
42 12 0.20
43 18 0.31
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (42 bp):
TATGATTCGTGTAAGACCATATCTGGGACAGAGGCATCGATA
Found at i:4970793 original size:13 final size:13
Alignment explanation
Indices: 4970775--4970802 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4970765 TGTCATTTTG
4970775 CTTGAAATGTTAC
1 CTTGAAATGTTAC
4970788 CTTGAAATGTTAC
1 CTTGAAATGTTAC
4970801 CT
1 CT
4970803 AAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (13 bp):
CTTGAAATGTTAC
Found at i:4975431 original size:26 final size:26
Alignment explanation
Indices: 4975402--4975451 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
4975392 TTTAAATTAA
*
4975402 ACTTTTCAAAAA-TACTTTTTCACAGC
1 ACTTTT-AAAAAGTACTTTTCCACAGC
4975428 ACTTTTAAAAAGTACTTTTCCACA
1 ACTTTTAAAAAGTACTTTTCCACA
4975452 ACTTGCGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (26 bp):
ACTTTTAAAAAGTACTTTTCCACAGC
Found at i:4976620 original size:29 final size:29
Alignment explanation
Indices: 4976578--4976638 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
4976568 GTCATCTAAT
*
4976578 TATGAAAAGTTACAAAATGATCACTTAAC
1 TATGAAAAGTTACAAAATGATCACTCAAC
4976607 TATGAAACA-TTACAAAATGATCACTCAAC
1 TATGAAA-AGTTACAAAATGATCACTCAAC
4976636 TAT
1 TAT
4976639 TTAATTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (29 bp):
TATGAAAAGTTACAAAATGATCACTCAAC
Found at i:4977955 original size:437 final size:438
Alignment explanation
Indices: 4977134--4978006 Score: 1739
Period size: 437 Copynumber: 2.0 Consensus size: 438
4977124 TTAAATTAGT
4977134 AAAGGTAAAATTGACTTTTGGCCCTCCTAAAATGATAAAAATTGATCTAATCCTTTAAAAACTAT
1 AAAGGTAAAATTGACTTTTGGCCCTCCTAAAATGATAAAAATTGATCTAATCCTTTAAAAACTAT
4977199 AAAGATAGAGTCTATTAAAATGGTGAAATTGTATTTTTATTATCGTTAAAATTACAATTTAATTT
66 AAAGATAGAGTCTATTAAAATGGTGAAATTGTATTTTTATTATCGTTAAAATTACAATTTAATTT
4977264 CGACCCCCCTCAAAAAATTTTCTGGCTTCCCCTTACTTATATATATATATATATATGTTTGTCAG
131 CGACCCCCCTCAAAAAATTTTCTGGCTTCCCCTTACTTATATATATATATATATATGTTTGTCAG
4977329 GTGAAGTTATGAGAGATTGTCATGTGTTACCACCAAATTGACTAGCAGTTTCATGTCAGTACAAA
196 GTGAAGTTATGAGAGATTGTCATGTGTTACCACCAAATTGACTAGCAGTTTCATGTCAGTACAAA
4977394 CTACCGGTGTTAATGCGGAGTACCAATCTGGTTGATGGAATATAAGTTTTGAGACTAACTAGACC
261 CTACCGGTGTTAATGCGGAGTACCAATCTGGTTGATGGAATATAAGTTTTGAGACTAACTAGACC
4977459 TAGAAAAACAATTTAGTGACCAGTTAGGTACAAATAGACAAGTTCAGGGGCTAAAGTATATATTA
326 TAGAAAAACAATTTAGTGACCAGTTAGGTACAAATAGACAAGTTCAGGGGCTAAAGTATATATTA
4977524 TCCCTATGGTTTATAAAAGATAAAAAGGTATATACTTTCACGAAAGTA
391 TCCCTATGGTTTATAAAAGATAAAAAGGTATATACTTTCACGAAAGTA
4977572 AAAGGT-AAATTGACTTTTGGCCCTCCTAAAATGATAAAAATTGATCTAATCCTTTAAAAACTAT
1 AAAGGTAAAATTGACTTTTGGCCCTCCTAAAATGATAAAAATTGATCTAATCCTTTAAAAACTAT
4977636 AAAGATAGAGTCTATTAAAATGGTGAAATTGTATTTTTATTATCGTTAAAATTACAATTTAATTT
66 AAAGATAGAGTCTATTAAAATGGTGAAATTGTATTTTTATTATCGTTAAAATTACAATTTAATTT
4977701 CGACCCCCCTCAAAAAATTTTCTGGCTTCCCCTTACTTATATATATATATATATATGTTTGTCAG
131 CGACCCCCCTCAAAAAATTTTCTGGCTTCCCCTTACTTATATATATATATATATATGTTTGTCAG
4977766 GTGAAGTTATGAGAGATTGTCATGTGTTACCACCAAATTGACTAGCAGTTTCATGTCAGTACAAA
196 GTGAAGTTATGAGAGATTGTCATGTGTTACCACCAAATTGACTAGCAGTTTCATGTCAGTACAAA
4977831 CTACCGGTGTTAATGCGGAGTACCAATCTGGTTGATGGAATATAAGTTTTGAGACTAACTAGACC
261 CTACCGGTGTTAATGCGGAGTACCAATCTGGTTGATGGAATATAAGTTTTGAGACTAACTAGACC
4977896 TAGAAAAACAATTTAGTGACCAGTTAGGTACAAATAGACAAGTTCAGGGGCTAAAGTATATATTA
326 TAGAAAAACAATTTAGTGACCAGTTAGGTACAAATAGACAAGTTCAGGGGCTAAAGTATATATTA
4977961 TCCCTATGGTTTATAAAAGATAAAAAGGTATATACTTTCACGAAAG
391 TCCCTATGGTTTATAAAAGATAAAAAGGTATATACTTTCACGAAAG
4978007 CAATCATCTA
Statistics
Matches: 435, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
437 429 0.99
438 6 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (438 bp):
AAAGGTAAAATTGACTTTTGGCCCTCCTAAAATGATAAAAATTGATCTAATCCTTTAAAAACTAT
AAAGATAGAGTCTATTAAAATGGTGAAATTGTATTTTTATTATCGTTAAAATTACAATTTAATTT
CGACCCCCCTCAAAAAATTTTCTGGCTTCCCCTTACTTATATATATATATATATATGTTTGTCAG
GTGAAGTTATGAGAGATTGTCATGTGTTACCACCAAATTGACTAGCAGTTTCATGTCAGTACAAA
CTACCGGTGTTAATGCGGAGTACCAATCTGGTTGATGGAATATAAGTTTTGAGACTAACTAGACC
TAGAAAAACAATTTAGTGACCAGTTAGGTACAAATAGACAAGTTCAGGGGCTAAAGTATATATTA
TCCCTATGGTTTATAAAAGATAAAAAGGTATATACTTTCACGAAAGTA
Found at i:4995162 original size:30 final size:31
Alignment explanation
Indices: 4995063--4995164 Score: 77
Period size: 34 Copynumber: 3.2 Consensus size: 31
4995053 AGTGATTATC
*
4995063 TTAATATTAAATTTAAT-TCAATATTTATCTT
1 TTAATATTAAATTTAATCT-AATATTTATATT
* * *
4995094 TTAGATA--AATATTATATTCTATTAATTTAATAGAT
1 TTA-ATATTAA-ATT-TAATCTAAT-ATTT-ATA-TT
4995129 TTAATATTAAATTTAATCTAATATTTAT-TT
1 TTAATATTAAATTTAATCTAATATTTATATT
4995159 TTAATA
1 TTAATA
4995165 GGTATTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
30 9 0.16
31 6 0.11
32 10 0.18
33 9 0.16
34 12 0.22
35 7 0.13
36 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (31 bp):
TTAATATTAAATTTAATCTAATATTTATATT
Found at i:4998115 original size:20 final size:20
Alignment explanation
Indices: 4998090--4998131 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4998080 CCCTCAAGAA
4998090 AAACCCTTATTGATTGACAT
1 AAACCCTTATTGATTGACAT
4998110 AAACCCTTATTGATTGACAT
1 AAACCCTTATTGATTGACAT
4998130 AA
1 AA
4998132 CTTAATTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (20 bp):
AAACCCTTATTGATTGACAT
Found at i:4999235 original size:157 final size:158
Alignment explanation
Indices: 4999035--4999350 Score: 625
Period size: 157 Copynumber: 2.0 Consensus size: 158
4999025 GAAAACTCCT
4999035 TCGAAGAGGATAAAAAACCATGAGCAAAGGAGGCTTCGACTTTTCACTAAATGAGTAAACAAACA
1 TCGAAGAGGATAAAAAACCATGAGCAAAGGAGGCTTCGACTTTTCACTAAATGAGTAAACAAACA
4999100 AGAGTACAATTTGTAGAAAATAAACTTAAATGTATTAAATGTACAAACCCAAACCCCGAAAACAA
66 AGAGTACAATTTGTAGAAAATAAACTTAAATGTATTAAATGTACAAACCCAAACCCCGAAAACAA
4999165 ATTCCTAACTTGGAAACAATATTCTCTC
131 ATTCCTAACTTGGAAACAATATTCTCTC
4999193 TCGAAGAGGAT-AAAAACCATGAGCAAAGGAGGCTTCGACTTTTCACTAAATGAGTAAACAAACA
1 TCGAAGAGGATAAAAAACCATGAGCAAAGGAGGCTTCGACTTTTCACTAAATGAGTAAACAAACA
4999257 AGAGTACAATTTGTAGAAAATAAACTTAAATGTATTAAATGTACAAACCCAAACCCCGAAAACAA
66 AGAGTACAATTTGTAGAAAATAAACTTAAATGTATTAAATGTACAAACCCAAACCCCGAAAACAA
4999322 ATTCCTAACTTGGAAACAATATTCTCTC
131 ATTCCTAACTTGGAAACAATATTCTCTC
4999350 T
1 T
4999351 ATAGTTACCA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 147 0.93
158 11 0.07
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (158 bp):
TCGAAGAGGATAAAAAACCATGAGCAAAGGAGGCTTCGACTTTTCACTAAATGAGTAAACAAACA
AGAGTACAATTTGTAGAAAATAAACTTAAATGTATTAAATGTACAAACCCAAACCCCGAAAACAA
ATTCCTAACTTGGAAACAATATTCTCTC
Found at i:5003895 original size:19 final size:19
Alignment explanation
Indices: 5003871--5003998 Score: 158
Period size: 19 Copynumber: 7.0 Consensus size: 19
5003861 NNNNNNNNNN
5003871 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
** * *
5003890 ATATCTAAGATTATATGTT
1 ATATCTAAGATTGCATATC
5003909 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
5003928 ATATCTAAGATTG-----C
1 ATATCTAAGATTGCATATC
** *
5003942 ATATCTAAGATTATATGTC
1 ATATCTAAGATTGCATATC
5003961 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
5003980 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
5003999 CCTGAAGATT
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
14 13 0.14
19 79 0.86
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (19 bp):
ATATCTAAGATTGCATATC
Found at i:5003946 original size:33 final size:33
Alignment explanation
Indices: 5003871--5003979 Score: 137
Period size: 33 Copynumber: 3.2 Consensus size: 33
5003861 NNNNNNNNNN
*
5003871 ATATCTAAGATTGCATATCATATCTAAGATTATATGTT
1 ATATCTAAGATTGCATATCATATCTAAG---AT-TG-C
5003909 ATATCTAAGATTGCATATCATATCTAAGATTGC
1 ATATCTAAGATTGCATATCATATCTAAGATTGC
** *
5003942 ATATCTAAGATTATATGTCATATCTAAGATTGC
1 ATATCTAAGATTGCATATCATATCTAAGATTGC
5003975 ATATC
1 ATATC
5003980 ATATCTAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
33 35 0.52
34 2 0.03
35 2 0.03
38 28 0.42
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (33 bp):
ATATCTAAGATTGCATATCATATCTAAGATTGC
Found at i:5003951 original size:52 final size:52
Alignment explanation
Indices: 5003889--5003998 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
5003879 GATTGCATAT
*
5003889 CATATCTAAGATTATATGTTATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCTAAGATTATATGTCATATCTAAGATTGCATATCATATCTAAGATTG
5003941 CATATCTAAGATTATATGTCATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCTAAGATTATATGTCATATCTAAGATTGCATATCATATCTAAGATTG
5003993 CATATC
1 CATATC
5003999 CCTGAAGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (52 bp):
CATATCTAAGATTATATGTCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:5003998 original size:14 final size:14
Alignment explanation
Indices: 5003927--5003979 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
5003917 GATTGCATAT
5003927 CATATCTAAGATTG
1 CATATCTAAGATTG
5003941 CATATCTAAGATTATATG
1 CATATCTAAG---AT-TG
5003959 TCATATCTAAGATTG
1 -CATATCTAAGATTG
5003974 CATATC
1 CATATC
5003980 ATATCTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 16 0.47
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.29
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (14 bp):
CATATCTAAGATTG
Found at i:5010059 original size:19 final size:19
Alignment explanation
Indices: 5010012--5010081 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
5010002 AAATTAAATC
*
5010012 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
5010032 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
5010054 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
5010073 TCTAAGATT
1 TCTAAGATT
5010082 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 27 0.61
22 7 0.16
23 10 0.23
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:5010675 original size:45 final size:45
Alignment explanation
Indices: 5010618--5010746 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 45
5010608 TTGTTTATTT
* * * *
5010618 AGTCTGCCCCACTACAATTTCAGGGGGATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
5010663 AGTCTGCTCCACTGCAGCTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
5010708 GGTCTGCTCCACTACAACTTCAGGGAGATAAGACCCGAT
1 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGAT
5010747 GCGATCTGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (45 bp):
AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:5012157 original size:44 final size:44
Alignment explanation
Indices: 5012109--5012208 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
5012099 CGCTGTTGCT
* *
5012109 CAGGGAGATAGGA-TTCACTATCTTCAACCTATTCCACTATTGAC
1 CAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTACTGAC
* *
5012153 CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTC
1 CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGAC
5012197 CAGGGAGATAGG
1 CAGGGAGATAGG
5012209 GCTGGGGTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 49 0.96
45 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGAC
Found at i:5012362 original size:88 final size:88
Alignment explanation
Indices: 5012219--5012609 Score: 611
Period size: 88 Copynumber: 4.4 Consensus size: 88
5012209 GCTGGGGTCA
* * *
5012219 TCGATTTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACTTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
5012284 CCAGAGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGTTGGTGTCT
* * *
5012307 TCGATCTACTTCACTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
5012372 CCAGGGAGGCAAGGTTAGTGTCT
66 CCAGGGAGGCAAGGTTGGTGTCT
* * *
5012395 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTGAACCTGCTCCACTATAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
**
5012460 CCAGGGATACAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGTTGGTGTCT
* * * *
5012483 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
5012548 CCAGGGAAGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGTTGGTGTCT
5012571 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
5012610 TTATCTTCAC
Statistics
Matches: 274, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 274 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGGGAGGCAAGGTTGGTGTCT
Found at i:5012599 original size:43 final size:44
Alignment explanation
Indices: 5012290--5012604 Score: 127
Period size: 44 Copynumber: 7.2 Consensus size: 44
5012280 CAACCCAGAG
* * *
5012290 AGGCAAGGCTGGTGTCTTCGATCTACTTCACTGTCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * ** * * * **** *
5012334 AGGCAAGATTTGCTATTTTTAACCTGCTCCGCT-ACAACCCAGGG
1 AGGCAAG-GTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
*
5012378 AGGCAAGGTTAGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * * * * * **** *
5012422 AGGCAAGATCTGCTAT-TTTGAACCTGCTCCACTAT-AACCCAGGG
1 AGGCAAGGT-TGGTGTCTTCG-ATCTGCTTCGCTGTCGGTGCAGGA
** *
5012466 ATACAAGGTTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * ** * * * ****
5012510 AGGCAAGATTTGCTATTTTTAACCTACTCCGCTG-CAACCCAGGGA
1 AGGCAAG-GTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCA-GGA
5012555 A-GCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
5012598 AGGCAAG
1 AGGCAAG
5012605 ATCTGTTATC
Statistics
Matches: 170, Mismatches: 91, Indels: 20
0.60 0.32 0.07
Matches are distributed among these distances:
43 50 0.29
44 73 0.43
45 47 0.28
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (44 bp):
AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
Found at i:5013965 original size:14 final size:15
Alignment explanation
Indices: 5013942--5013974 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5013932 ATCGACGCTT
5013942 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
5013956 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
5013971 TTCC
1 TTCC
5013975 TAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:5014852 original size:25 final size:26
Alignment explanation
Indices: 5014801--5014861 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5014791 AAGAAAATCC
* **
5014801 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
5014827 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
5014852 AAAATGAATG
1 AAAA-GAATG
5014862 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:5019768 original size:15 final size:14
Alignment explanation
Indices: 5019737--5019767 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5019727 AATTTTGGAC
*
5019737 TTTGTTTTATTATT
1 TTTGGTTTATTATT
5019751 TTTGGTTTATTATT
1 TTTGGTTTATTATT
5019765 TTT
1 TTT
5019768 TTATGAGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTGGTTTATTATT
Found at i:5019883 original size:51 final size:52
Alignment explanation
Indices: 5019815--5020002 Score: 190
Period size: 51 Copynumber: 3.7 Consensus size: 52
5019805 TTTCATGATA
* * *
5019815 CCGGTTCACATAGTAGCCTGCACACAGTACTACACATGTGGCCATCA-CTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGGCCATCAGCTAT
** *
5019866 CCAATACACGTAGTAGCCTGCACATAGTACTACACACGT-G--ATCGAAGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGGCCATC--AGCTAT
* * * * * *
5019917 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-T-ATCTTT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGGCCATCAGCTAT
**
5019967 TTGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACA
5020003 CGTGACTTTC
Statistics
Matches: 112, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
48 3 0.03
50 38 0.34
51 70 0.62
53 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (52 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGGCCATCAGCTAT
Found at i:5025811 original size:16 final size:16
Alignment explanation
Indices: 5025790--5025821 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5025780 GTTTTGTTGC
5025790 TAATTTTACTTTTTCA
1 TAATTTTACTTTTTCA
5025806 TAATTTTACTTTTTCA
1 TAATTTTACTTTTTCA
5025822 CTTTCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTACTTTTTCA
Found at i:5026114 original size:49 final size:51
Alignment explanation
Indices: 5026050--5026238 Score: 194
Period size: 49 Copynumber: 3.8 Consensus size: 51
5026040 CTAATTCACA
* *
5026050 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATCACTATCCGATACACG
1 TAGTAG-CTGCACATAGTACTACACACGTGACCCATCACTATCCGGTACACG
* * * ** *
5026101 TAGTAG-TGCACATAGTACTACACACGTGATCGA--AGCTATTCGGTATGCA
1 TAGTAGCTGCACATAGTACTACACACGTGACCCATCA-CTATCCGGTACACG
* *
5026150 TAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-T-TCCGGTACACG
1 TAGTAG-CTGCACATAGTACTACACACGTGACCCATCACTATCCGGTACACG
*
5026200 TAGTAGCCTGCACATAGTACTACACACGTGA-GCATCACT
1 TAGTAG-CTGCACATAGTACTACACACGTGACCCATCACT
5026239 TTCACTTTTA
Statistics
Matches: 113, Mismatches: 18, Indels: 15
0.77 0.12 0.10
Matches are distributed among these distances:
48 1 0.01
49 42 0.37
50 39 0.35
51 30 0.27
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (51 bp):
TAGTAGCTGCACATAGTACTACACACGTGACCCATCACTATCCGGTACACG
Found at i:5026254 original size:101 final size:100
Alignment explanation
Indices: 5026047--5026232 Score: 286
Period size: 100 Copynumber: 1.9 Consensus size: 100
5026037 ATACTAATTC
*
5026047 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGTGCAC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGTGCAC
* *
5026112 ATAGTACTACACACGTGATCGAAGCTATTCGGTAT
66 ATAGTACTACACACGTGAGCGAAGCTATTCCGTAT
* *
5026147 GCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-T-TCCGGTACACGTAGTAGCCTG
1 ACATAGTAGCCTGCACATAGTACTACACATGCGA-CCATCACTATCCGATACACGTAGTAG--TG
5026210 CACATAGTACTACACACGTGAGC
63 CACATAGTACTACACACGTGAGC
5026233 ATCACTTTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
99 16 0.20
100 33 0.42
101 30 0.38
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (100 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGTGCAC
ATAGTACTACACACGTGAGCGAAGCTATTCCGTAT
Found at i:5031207 original size:35 final size:35
Alignment explanation
Indices: 5031168--5031244 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
5031158 TATCACCTAA
* *
5031168 AAGGACCCGATAACCTTTTCCAT-AGTGTTGCCCCG
1 AAGGACCCGATAACCGTTTCC-TCAGTGTCGCCCCG
* * *
5031203 AAGGACCTGATAATCGTTTCCTCGGTGTCGCCCCG
1 AAGGACCCGATAACCGTTTCCTCAGTGTCGCCCCG
5031238 AAGGACC
1 AAGGACC
5031245 TGTCGAATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.23
Consensus pattern (35 bp):
AAGGACCCGATAACCGTTTCCTCAGTGTCGCCCCG
Found at i:5034836 original size:12 final size:12
Alignment explanation
Indices: 5034821--5034858 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
5034811 AAATTACAGT
5034821 AAAAATATTTTA
1 AAAAATATTTTA
*
5034833 AAAATTA-TTTA
1 AAAAATATTTTA
5034844 AAAAAT-TTTTA
1 AAAAATATTTTA
5034855 AAAA
1 AAAA
5034859 TAAATCTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAAATATTTTA
Found at i:5035858 original size:32 final size:34
Alignment explanation
Indices: 5035792--5035864 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 34
5035782 GAAGGTGAGT
*
5035792 AATCAAAACTTTTAGTTGATTTATTTTTTTGCTTC
1 AATC-AAACTTTTAGTTGATTTATTTTTTAGCTTC
* *
5035827 AATCAAATTTTTA-TTTATTTA-TTTTTAGCTTC
1 AATCAAACTTTTAGTTGATTTATTTTTTAGCTTC
5035859 AATCAA
1 AATCAA
5035865 GCATGGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 16 0.46
33 7 0.20
34 8 0.23
35 4 0.11
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.53
Consensus pattern (34 bp):
AATCAAACTTTTAGTTGATTTATTTTTTAGCTTC
Found at i:5042069 original size:74 final size:74
Alignment explanation
Indices: 5041976--5042121 Score: 184
Period size: 74 Copynumber: 2.0 Consensus size: 74
5041966 TTTAACATTG
* * ** * *
5041976 TTTTCTTACCAAATTAATATTTAAATACTATTTTGTATTTGTTTTTCAAATTAAAATAAAAATGT
1 TTTTCTTACCAAATCAATATTTAAATACTACTTTGTATTAATTTATCAAATTAAAATAAAAATAT
5042041 TACCAAACA
66 TACCAAACA
* * ** *
5042050 TTTTTTTATCAAATCAATATTTAGCTACTACTTTGTATTAATTTATCAAATTAAACTAAAAATAT
1 TTTTCTTACCAAATCAATATTTAAATACTACTTTGTATTAATTTATCAAATTAAAATAAAAATAT
*
5042115 TTCCAAA
66 TACCAAA
5042122 TTTATAAACT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (74 bp):
TTTTCTTACCAAATCAATATTTAAATACTACTTTGTATTAATTTATCAAATTAAAATAAAAATAT
TACCAAACA
Found at i:5043344 original size:264 final size:264
Alignment explanation
Indices: 5042874--5043405 Score: 1037
Period size: 264 Copynumber: 2.0 Consensus size: 264
5042864 TGCCTTTTTC
5042874 TATCACCAGAATGTTTGAAAATACAAAGAAGAAAAGGAAGAGTTTTGAGAGAAACAGAGTTTCGT
1 TATCACCAGAATGTTTGAAAATACAAAGAAGAAAAGGAAGAGTTTTGAGAGAAACAGAGTTTCGT
5042939 TAAGAGAAAAATATCAAAGAGTATTTTCTTGTGTAAAACCCTTCAGAAATCATGGTCTTTTATAG
66 TAAGAGAAAAATATCAAAGAGTATTTTCTTGTGTAAAACCCTTCAGAAATCATGGTCTTTTATAG
5043004 GCATGGAGAATGTTGAAATTTTGAAAAAAGTATCCACAAAATCTGCCATAATTTTAATCAAATCA
131 GCATGGAGAATGTTGAAATTTTGAAAAAAGTATCCACAAAATCTGCCATAATTTTAATCAAATCA
5043069 ATAAGGTAAGTATCCTTATATAAGCAGATTATGTTTGCTGAGGAAAATAAAAATCATGTTAGACT
196 ATAAGGTAAGTATCCTTATATAAGCAGATTATGTTTGCTGAGGAAAATAAAAATCATGTTAGACT
5043134 AAAA
261 AAAA
5043138 TATCACCAGAATGTTTGAAAATACAAAGAAGAAAAGGAAGAGTTTTGAGAGAAACAGAGTTTCGT
1 TATCACCAGAATGTTTGAAAATACAAAGAAGAAAAGGAAGAGTTTTGAGAGAAACAGAGTTTCGT
5043203 TAAGAGAAAAATATCAAAGAGTATTTTCTTGTGTAAAACCCTTCAGAAATCATGGTCTTTTATAG
66 TAAGAGAAAAATATCAAAGAGTATTTTCTTGTGTAAAACCCTTCAGAAATCATGGTCTTTTATAG
*
5043268 GCATGGAGAATGTTGAAATTTTGAAAAAAGTATCCACAAAATCTGCCATAATTTTAATCAATTCA
131 GCATGGAGAATGTTGAAATTTTGAAAAAAGTATCCACAAAATCTGCCATAATTTTAATCAAATCA
* *
5043333 ATAAGGTAAGTATCCTTATATAAGTAGATTATGTTTGCTGAGGAAAATAAAAATTATGTTAGACT
196 ATAAGGTAAGTATCCTTATATAAGCAGATTATGTTTGCTGAGGAAAATAAAAATCATGTTAGACT
5043398 AAAA
261 AAAA
5043402 TATC
1 TATC
5043406 CACAAGTCCT
Statistics
Matches: 265, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
264 265 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (264 bp):
TATCACCAGAATGTTTGAAAATACAAAGAAGAAAAGGAAGAGTTTTGAGAGAAACAGAGTTTCGT
TAAGAGAAAAATATCAAAGAGTATTTTCTTGTGTAAAACCCTTCAGAAATCATGGTCTTTTATAG
GCATGGAGAATGTTGAAATTTTGAAAAAAGTATCCACAAAATCTGCCATAATTTTAATCAAATCA
ATAAGGTAAGTATCCTTATATAAGCAGATTATGTTTGCTGAGGAAAATAAAAATCATGTTAGACT
AAAA
Found at i:5052870 original size:29 final size:29
Alignment explanation
Indices: 5052828--5052904 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
5052818 AATGTTCTTA
5052828 CGAGCACATA-AACGGGAAGCTCTCTTTAT
1 CGAGC-CATATAACGGGAAGCTCTCTTTAT
5052857 CGAGCCATATAACGGGAAGCTCTCTTTAT
1 CGAGCCATATAACGGGAAGCTCTCTTTAT
5052886 CGAGCCATATAACGGGAAG
1 CGAGCCATATAACGGGAAG
5052905 GTCATGTGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 4 0.09
29 43 0.91
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (29 bp):
CGAGCCATATAACGGGAAGCTCTCTTTAT
Found at i:5052940 original size:25 final size:26
Alignment explanation
Indices: 5052856--5052959 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 26
5052846 GCTCTCTTTA
* * *
5052856 TCGAGCCATATAACGGGAAGCTCTCTTTA
1 TCGAGTCATATAACGGGAAG--CTC-ATG
* *
5052885 TCGAGCCATATAACGGGAAGGTCATG
1 TCGAGTCATATAACGGGAAGCTCATG
*
5052911 T-GAGTCATATAATGGGAAGCTCAT-
1 TCGAGTCATATAACGGGAAGCTCATG
** *
5052935 TCGAGTTGTATAACGAGAAGCTCAT
1 TCGAGTCATATAACGGGAAGCTCAT
5052960 AAAAGCCGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.61
26 2 0.03
27 2 0.03
29 20 0.31
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (26 bp):
TCGAGTCATATAACGGGAAGCTCATG
Found at i:5053031 original size:25 final size:25
Alignment explanation
Indices: 5052968--5053041 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
5052958 ATAAAAGCCG
* ** * *
5052968 TAATCGGGAAGCTCAGGTGAGCTAA
1 TAATCGGGAAGCTCCGGAAAGCCAT
5052993 TAAT-GGGTAA-CTCCGGAAAGCCAT
1 TAATCGGG-AAGCTCCGGAAAGCCAT
5053017 TAATCGGGAAGCTCC-GAAGAGCCAT
1 TAATCGGGAAGCTCCGGAA-AGCCAT
5053042 ATATCAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 21 0.52
25 19 0.47
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.19
Consensus pattern (25 bp):
TAATCGGGAAGCTCCGGAAAGCCAT
Found at i:5053092 original size:24 final size:25
Alignment explanation
Indices: 5053019--5053123 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 25
5053009 AAAGCCATTA
*
5053019 ATCGGGAAGCTC-CGAAGAGCC-ATAT
1 ATCGGGAAGCTCATG-AGAGCCTA-AT
** * *
5053044 ATCAAGAAGCTCAAGAAAGCC-AAT
1 ATCGGGAAGCTCATGAGAGCCTAAT
*
5053068 ATCGGGATGCTCATGAGAG-CTAAT
1 ATCGGGAAGCTCATGAGAGCCTAAT
* * *
5053092 AACGGGAAGCTCGTGAGAGCCTATT
1 ATCGGGAAGCTCATGAGAGCCTAAT
5053117 ATCGGGA
1 ATCGGGA
5053124 CACTCATAAG
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.02
24 35 0.56
25 26 0.41
26 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCTAAT
Found at i:5064183 original size:17 final size:17
Alignment explanation
Indices: 5064161--5064199 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5064151 GGTTTCGTGG
*
5064161 CCACACAGGCGTCTGCC
1 CCACACAGGCATCTGCC
* *
5064178 CCACACGGGCATTTGCC
1 CCACACAGGCATCTGCC
5064195 CCACA
1 CCACA
5064200 TGGGCTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.46, G:0.21, T:0.13
Consensus pattern (17 bp):
CCACACAGGCATCTGCC
Found at i:5064204 original size:17 final size:17
Alignment explanation
Indices: 5064174--5064233 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
5064164 CACAGGCGTC
*
5064174 TGCCCCACACGGGCATT
1 TGCCCCACACGGGCATG
*
5064191 TGCCCCACATGGGC-TGG
1 TGCCCCACACGGGCAT-G
*
5064208 AGCCCCACACGGGCATG
1 TGCCCCACACGGGCATG
5064225 TGCCCCACA
1 TGCCCCACA
5064234 TGGGTGGCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 34 0.94
18 1 0.03
ACGTcount: A:0.18, C:0.42, G:0.27, T:0.13
Consensus pattern (17 bp):
TGCCCCACACGGGCATG
Found at i:5065984 original size:30 final size:30
Alignment explanation
Indices: 5065948--5066010 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5065938 TTTTCAGAAA
5065948 ACATGCCCGTGTGATCAGGCCGAGTGGTTC
1 ACATGCCCGTGTGATCAGGCCGAGTGGTTC
*
5065978 ACATGCCCGTGTGATCAGGCCGTGTGGTTC
1 ACATGCCCGTGTGATCAGGCCGAGTGGTTC
5066008 ACA
1 ACA
5066011 CGATCAAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (30 bp):
ACATGCCCGTGTGATCAGGCCGAGTGGTTC
Found at i:5070233 original size:25 final size:25
Alignment explanation
Indices: 5070202--5070344 Score: 102
Period size: 25 Copynumber: 5.8 Consensus size: 25
5070192 GCTCTCTCTC
5070202 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* *
5070227 GAGCCATGTAGCGGGAAGCTCAT-T
1 GAGCCATATAACGGGAAGCTCATGT
** * *
5070251 CGAGCTGTATAATGGAAAGCTCATAG-
1 -GAGCCATATAACGGGAAGCTCAT-GT
* * *
5070277 GAGCCATA-ATCGAGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGT
*
5070301 GAGCCA-ATAACGGGTAA-CTC-TGGA
1 GAGCCATATAACGGG-AAGCTCAT-GT
5070325 GAGCCAT-TAATCGGGAAGCT
1 GAGCCATATAA-CGGGAAGCT
5070345 TCGAATAGCC
Statistics
Matches: 91, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
23 3 0.03
24 36 0.40
25 52 0.57
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:5074488 original size:20 final size:20
Alignment explanation
Indices: 5074463--5074528 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
5074453 CACATATGTG
5074463 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCAGTA
** * * *
5074483 CCCCTGAATGCACAT-ATGTG
1 CCCCTGTTTGTACTTCA-GTA
* *
5074503 TCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCAGTA
5074523 CCCCTG
1 CCCCTG
5074529 AATGCATATA
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCAGTA
Found at i:5074502 original size:40 final size:40
Alignment explanation
Indices: 5074447--5074534 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 40
5074437 AATTATTGTA
5074447 TGAATGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
* *
5074487 TGAATGCACATATGTGTCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
5074527 TGAATGCA
1 TGAATGCA
5074535 TATACATGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (40 bp):
TGAATGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
Found at i:5086477 original size:12 final size:13
Alignment explanation
Indices: 5086457--5086492 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5086447 AAAATTCTCT
5086457 TTTCTTTTCTTTA
1 TTTCTTTTCTTTA
5086470 TTTC-TTTCTTTA
1 TTTCTTTTCTTTA
*
5086482 TTTTTTTTCTT
1 TTTCTTTTCTT
5086493 CAATTCAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTCTTTA
Found at i:5088113 original size:11 final size:11
Alignment explanation
Indices: 5088097--5088126 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5088087 TAAAAGATAA
5088097 GAATTTATTTT
1 GAATTTATTTT
5088108 GAATTTATTTT
1 GAATTTATTTT
*
5088119 GAAATTAT
1 GAATTTAT
5088127 AAAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (11 bp):
GAATTTATTTT
Found at i:5089870 original size:23 final size:23
Alignment explanation
Indices: 5089844--5089888 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5089834 AAGAGATTTG
* *
5089844 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
5089867 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
5089889 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:5090121 original size:19 final size:19
Alignment explanation
Indices: 5090068--5090178 Score: 159
Period size: 19 Copynumber: 5.6 Consensus size: 19
5090058 TACAAATTAA
*
5090068 ATATCTAAGATTACAAAATC
1 ATATCTAAGATTAC-ATATC
*
5090088 ATATCTTCCAAGATTGCATATC
1 ATATC-T--AAGATTACATATC
5090110 ATATCTAAGATTACATATC
1 ATATCTAAGATTACATATC
*
5090129 ATATCTAAGATTGCATATC
1 ATATCTAAGATTACATATC
5090148 ATATCTAAGATTACATATC
1 ATATCTAAGATTACATATC
5090167 ATATCTAAGATT
1 ATATCTAAGATT
5090179 GCATTTCCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
19 60 0.72
20 5 0.06
21 2 0.02
22 9 0.11
23 7 0.08
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATCTAAGATTACATATC
Found at i:5090148 original size:38 final size:38
Alignment explanation
Indices: 5090068--5090182 Score: 185
Period size: 38 Copynumber: 2.9 Consensus size: 38
5090058 TACAAATTAA
*
5090068 ATATCTAAGATTACAAAATCATATCTTCCAAGATTGCATATC
1 ATATCTAAGATTAC-ATATCATATC-T--AAGATTGCATATC
5090110 ATATCTAAGATTACATATCATATCTAAGATTGCATATC
1 ATATCTAAGATTACATATCATATCTAAGATTGCATATC
5090148 ATATCTAAGATTACATATCATATCTAAGATTGCAT
1 ATATCTAAGATTACATATCATATCTAAGATTGCAT
5090183 TTCCTTAAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 48 0.67
40 1 0.01
41 9 0.12
42 14 0.19
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (38 bp):
ATATCTAAGATTACATATCATATCTAAGATTGCATATC
Found at i:5093029 original size:18 final size:20
Alignment explanation
Indices: 5093006--5093046 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
5092996 AGTAAAAAAT
*
5093006 CATGTTTAG-GT-TCATTTG
1 CATGTTTAGTGTCACATTTG
5093024 CATGTTTAGTGTCACATTTG
1 CATGTTTAGTGTCACATTTG
5093044 CAT
1 CAT
5093047 ATATTAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (20 bp):
CATGTTTAGTGTCACATTTG
Found at i:5096435 original size:25 final size:26
Alignment explanation
Indices: 5096388--5096436 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5096378 GATAGGTTGA
**
5096388 ATATTTTATTATTATTTTATTATAAG
1 ATATTTTATTATTAAATTATTATAAG
*
5096414 ATATTTTA-TATTAAATTGTTATA
1 ATATTTTATTATTAAATTATTATA
5096437 TTTTATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATATTTTATTATTAAATTATTATAAG
Found at i:5097644 original size:16 final size:14
Alignment explanation
Indices: 5097613--5097652 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
5097603 ATTACTATAT
5097613 AATAAAATTATTTA
1 AATAAAATTATTTA
5097627 AATAAAATATATTTTA
1 AATAAAAT-TA-TTTA
*
5097643 AATTAAATTA
1 AATAAAATTA
5097653 AGTAATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAAAATTATTTA
Found at i:5100755 original size:69 final size:67
Alignment explanation
Indices: 5100660--5100793 Score: 182
Period size: 69 Copynumber: 2.0 Consensus size: 67
5100650 TGATTAAACT
*
5100660 TAATCACTTTAATATTAAATTGATAAAATACTTACCAAGATAAA-TATTAGAA-TAAATTTAATA
1 TAATCACTTTAATATTAAATTAATAAAATAC-TACCAAGA-AAATTATTA-AATTAAA-TTAATA
5100723 TTAAGA
62 TTAAGA
* **
5100729 TAATCACTTTAATGTTAAATTAATAAAATACTATTAAGAAAATTATTAAATTAAATTAATATTAA
1 TAATCACTTTAATATTAAATTAATAAAATACTACCAAGAAAATTATTAAATTAAATTAATATTAA
5100794 ATCTATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
67 15 0.25
68 15 0.25
69 29 0.49
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (67 bp):
TAATCACTTTAATATTAAATTAATAAAATACTACCAAGAAAATTATTAAATTAAATTAATATTAA
GA
Found at i:5104884 original size:24 final size:24
Alignment explanation
Indices: 5104852--5104898 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5104842 ACACACATCT
*
5104852 TTCCCATGACCCGAGTTCGCATTG
1 TTCCCATGACCCCAGTTCGCATTG
*
5104876 TTCCCATGACCCCAGTTTGCATT
1 TTCCCATGACCCCAGTTCGCATT
5104899 CTAGTTTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.32
Consensus pattern (24 bp):
TTCCCATGACCCCAGTTCGCATTG
Found at i:5106123 original size:175 final size:175
Alignment explanation
Indices: 5105832--5106183 Score: 659
Period size: 175 Copynumber: 2.0 Consensus size: 175
5105822 AGAGTAAAGA
* *
5105832 ATAGATAATACAAACAACAATAATACACGATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
1 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
5105897 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
66 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
5105962 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
131 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
*
5106007 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCGCGTC
1 ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
*
5106072 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGTAAGAG
66 ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
*
5106137 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATTTTTTTCC
131 ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
5106182 AT
1 AT
5106184 GTTGCATCAA
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 172 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (175 bp):
ATAGATAAAACAAACAACAATAATACACCATCTTTAGTCTCCAGATTAGCAACTCCAACCCCGTC
ACCATATTGGTACATGCATTGAGCCATCCTTGCTATGTTCAATGCAATATGTTTAAACGGAAGAG
ATAGGGAGGAGTGAGTCATTAAATATTCTTCATTCATCTTTTTCC
Found at i:5122319 original size:20 final size:20
Alignment explanation
Indices: 5122290--5122329 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5122280 AAGTGTGACT
*
5122290 GAGTTTGTGTCGAGAGTCAA
1 GAGTTGGTGTCGAGAGTCAA
*
5122310 GAGTTGGTGTTGAGAGTCAA
1 GAGTTGGTGTCGAGAGTCAA
5122330 CTTGACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (20 bp):
GAGTTGGTGTCGAGAGTCAA
Found at i:5132123 original size:12 final size:12
Alignment explanation
Indices: 5132105--5132172 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
5132095 GCTCACACGC
5132105 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
5132117 TCGTGTGCTAGG
1 CCGTGTGCTAGG
* *
5132129 CCGTGTGCCAAG
1 CCGTGTGCTAGG
* *
5132141 CCATGTGCCAGG
1 CCGTGTGCTAGG
*
5132153 CTGTGTGCTAGG
1 CCGTGTGCTAGG
5132165 CCGTGTGC
1 CCGTGTGC
5132173 AACCTTTTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.25
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:5133378 original size:39 final size:39
Alignment explanation
Indices: 5133324--5133401 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
5133314 CTCACATATA
5133324 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
1 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
5133363 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
1 ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
5133402 GCTCATACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (39 bp):
ATGTGCTAAACTGTAATCTATCAATTCCTGTACATGTAT
Found at i:5133439 original size:25 final size:25
Alignment explanation
Indices: 5133398--5133485 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
5133388 TCCTGTACAT
*
5133398 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTATAAATCG
* *
5133423 GTATGCTC-TCACTAGCTATAAATTG
1 GTATGCTCAT-ACGAGCTATAAATCG
* * *
5133448 GTAAGCTCATACAAGCT-GAAATCG
1 GTATGCTCATACGAGCTATAAATCG
* *
5133472 ATAAGCTCATACGA
1 GTATGCTCATACGA
5133486 CATGAAATCA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
24 18 0.35
25 33 0.63
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCG
Found at i:5137426 original size:22 final size:22
Alignment explanation
Indices: 5137392--5137447 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5137382 CCCCAACTAG
* *
5137392 AAGGGTGCA-GTACCTCTTGAAA
1 AAGGGTG-AGGTACCCCATGAAA
*
5137414 AAGGGTGAGGTACCCCATGAAT
1 AAGGGTGAGGTACCCCATGAAA
5137436 AA-GGTGAGGTAC
1 AAGGGTGAGGTAC
5137448 TTGGGTCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (22 bp):
AAGGGTGAGGTACCCCATGAAA
Found at i:5140080 original size:27 final size:27
Alignment explanation
Indices: 5140042--5140096 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5140032 GGAGAGTGAA
5140042 TGGCTGAAATTTATTTACTACTTTTAG
1 TGGCTGAAATTTATTTACTACTTTTAG
5140069 TGGCTGAAATTTATTTACTACTTTTAG
1 TGGCTGAAATTTATTTACTACTTTTAG
5140096 T
1 T
5140097 AGCCATTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (27 bp):
TGGCTGAAATTTATTTACTACTTTTAG
Found at i:5140167 original size:2 final size:2
Alignment explanation
Indices: 5140155--5140186 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
5140145 CATTCATTTC
5140155 CA CA CA TCA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA -CA CA CA CA CA CA CA CA CA CA CA CA C
5140187 TCTCTCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:5143796 original size:185 final size:185
Alignment explanation
Indices: 5143484--5143855 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 185
5143474 ATCATCCTAG
5143484 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
1 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
5143549 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
66 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
5143614 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
131 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
*
5143669 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACTATGAGA
1 GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
5143734 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
66 GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
5143799 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
131 TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
5143854 GA
1 GA
5143856 TGAGGACCCA
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 186 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (185 bp):
GAAAGTCTTTCCTAGCAACTTGAAGGACCTTTATTGATGTGCAGAAGGGCGAGCTTACCATGAGA
GTTCAGGATGATCAGGTAATTTTTAATGTTTTTAAGTCTATGCGATTTCCTGACACAGTTGATTA
TTGTTCTGCAGTATCTAAGTTAGAGGATTTAGCTCTAGAATGGGAACTCAACTCT
Found at i:5146994 original size:15 final size:16
Alignment explanation
Indices: 5146974--5147003 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5146964 TAACAAATAA
5146974 TATATAAT-TATATTT
1 TATATAATATATATTT
5146989 TATATAATATATATT
1 TATATAATATATATT
5147004 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:5147443 original size:238 final size:239
Alignment explanation
Indices: 5147013--5147490 Score: 949
Period size: 238 Copynumber: 2.0 Consensus size: 239
5147003 TAATTGTTAT
5147013 TAACCTTGTATAGGATTAGAATTATTTAATATTTTGTTAACATTTTATTTAAGAGTTTTATTTCT
1 TAACCTTGTATAGGATTAGAATTATTTAATATTTTGTTAACATTTTATTTAAGAGTTTTATTTCT
5147078 AATAAATAAGATAATATCAAGTAATATGTTAACATACTTTATATTATATACTAATTGATATTGTA
66 AATAAATAAGATAATATCAAGTAATATGTTAACATACTTTATATTATATACTAATTGATATTGTA
5147143 TTTAAGTAACATTAGGAGTTATAGTATTTTAATATTATTTGTTCTAAGAGTTTGAGTTAAATTCC
131 TTTAAGTAACATTAGGAGTTATAGTATTTTAATATTATTTGTTCTAAGAGTTTGAGTTAAATTCC
5147208 CCAATACTCACACTTTAAATACCTCATTCCCATGCACCTTTACC
196 CCAATACTCACACTTTAAATACCTCATTCCCATGCACCTTTACC
5147252 TAACCTTGTAT-GGATTAGAATTATTTAATATTTTGTTAACATTTTATTTAAGAGTTTTATTTCT
1 TAACCTTGTATAGGATTAGAATTATTTAATATTTTGTTAACATTTTATTTAAGAGTTTTATTTCT
5147316 AATAAATAAGATAATATCAAGTAATATGTTAACATACTTTATATTATATACTAATTGATATTGTA
66 AATAAATAAGATAATATCAAGTAATATGTTAACATACTTTATATTATATACTAATTGATATTGTA
5147381 TTTAAGTAACATTAGGAGTTATAGTATTTTAATATTATTTGTTCTAAGAGTTTGAGTTAAATTCC
131 TTTAAGTAACATTAGGAGTTATAGTATTTTAATATTATTTGTTCTAAGAGTTTGAGTTAAATTCC
5147446 CCAATACTCACACTTTAAATACCTCATTCCCATGCACCTTTACC
196 CCAATACTCACACTTTAAATACCTCATTCCCATGCACCTTTACC
5147490 T
1 T
5147491 TCATCATTCT
Statistics
Matches: 239, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
238 228 0.95
239 11 0.05
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (239 bp):
TAACCTTGTATAGGATTAGAATTATTTAATATTTTGTTAACATTTTATTTAAGAGTTTTATTTCT
AATAAATAAGATAATATCAAGTAATATGTTAACATACTTTATATTATATACTAATTGATATTGTA
TTTAAGTAACATTAGGAGTTATAGTATTTTAATATTATTTGTTCTAAGAGTTTGAGTTAAATTCC
CCAATACTCACACTTTAAATACCTCATTCCCATGCACCTTTACC
Found at i:5149021 original size:3 final size:3
Alignment explanation
Indices: 5149013--5149050 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5149003 TGAGGATCTC
*
5149013 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5149051 TCCCACAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5149791 original size:160 final size:161
Alignment explanation
Indices: 5149601--5149918 Score: 557
Period size: 161 Copynumber: 2.0 Consensus size: 161
5149591 AGTGTGGCAA
* *
5149601 TAGATATGTACATGCCTAGGATTGGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
1 TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
*
5149666 GACTCAC-TTTTTTTCTAGGGTCCTACCTGGTGTACAGTATCTATTAACTTCTATATTTTCATTC
66 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
*
5149730 TCTCTATTGTTTTTAATATTAGGGGCATGCC
131 TCTCTATTGTTTTTAATAGTAGGGGCATGCC
* * *
5149761 TAGATATGTACATGCCCGGGATTAGATTTGCCTTGGAAAAAGTTTATATTTAAGCTGTCAAACTT
1 TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
*
5149826 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTCACTTCTATATTTTCATTC
66 GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
5149891 TCTCTATTGTTTTTAATAGTAGGGGCAT
131 TCTCTATTGTTTTTAATAGTAGGGGCAT
5149919 TGTTCATCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
160 67 0.45
161 82 0.55
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (161 bp):
TAGATATGTACATGCCCAGGATTAGATTTGCCTTGGAAAAACTTGATATTTAAGCTGTCAAACTT
GACTCACTTTTTTTTCTAGGGTCCTACCTGGTGTACAATATCTATTAACTTCTATATTTTCATTC
TCTCTATTGTTTTTAATAGTAGGGGCATGCC
Found at i:5151878 original size:50 final size:49
Alignment explanation
Indices: 5151806--5151910 Score: 140
Period size: 50 Copynumber: 2.1 Consensus size: 49
5151796 CATTGAGATT
* *
5151806 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCT-GGACATGGCATGGGCACCGAG
* * *
5151856 ATGAGATGTCCC-TCGTAAGACCATGTCTGGAGATGGCATGGGCACCGAT
1 ATGAGAGGTCCCAT-GTAAGACCATGTCTGGACATGGCATGGGCACCGAG
5151905 ATGAGA
1 ATGAGA
5151911 ACCATGTTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 24 0.49
50 25 0.51
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGACATGGCATGGGCACCGAG
Found at i:5155211 original size:17 final size:18
Alignment explanation
Indices: 5155178--5155212 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5155168 GCTTGTTTGC
*
5155178 TTAAGTTGAAATGAATGA
1 TTAAGTTGAAATCAATGA
5155196 TTAAGTT-AAATCAATGA
1 TTAAGTTGAAATCAATGA
5155213 CCCTATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (18 bp):
TTAAGTTGAAATCAATGA
Found at i:5158687 original size:17 final size:18
Alignment explanation
Indices: 5158660--5158695 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5158650 AAATTTGAGA
*
5158660 ATTTATTTTGAATTTATT
1 ATTTATTTTGAAATTATT
5158678 ATTT-TTTTGAAATTATT
1 ATTTATTTTGAAATTATT
5158695 A
1 A
5158696 CAAAAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
ATTTATTTTGAAATTATT
Found at i:5161143 original size:50 final size:51
Alignment explanation
Indices: 5161058--5161156 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
5161048 AGCAGGTTGG
* * *
5161058 ACAAGTTAGAATCTATATAGAACTACTCCTCTTCTATTTGATATTGATTGC
1 ACAAGTTAGAATCTATATAGAACTAATCCTCTTCTATTTAAAATTGATTGC
* *
5161109 ACAAG-TAGAA-CTAGTATAGAACTAATCTTTTTCTATTTAAAATTGATT
1 ACAAGTTAGAATCTA-TATAGAACTAATCCTCTTCTATTTAAAATTGATT
5161157 AGAATAAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.07
50 34 0.81
51 5 0.12
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (51 bp):
ACAAGTTAGAATCTATATAGAACTAATCCTCTTCTATTTAAAATTGATTGC
Found at i:5165317 original size:20 final size:20
Alignment explanation
Indices: 5165288--5165336 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5165278 TGTTTAGGTT
*
5165288 CATTTGCATTTTTAGTGTCA
1 CATTTTCATTTTTAGTGTCA
5165308 CATTTTCATTTTTAGTGTCA
1 CATTTTCATTTTTAGTGTCA
*
5165328 TATTTTCAT
1 CATTTTCAT
5165337 ATATTAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.55
Consensus pattern (20 bp):
CATTTTCATTTTTAGTGTCA
Found at i:5174891 original size:13 final size:13
Alignment explanation
Indices: 5174873--5174897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5174863 GGGTTTTCTA
5174873 TGTGTTCAATTTG
1 TGTGTTCAATTTG
5174886 TGTGTTCAATTT
1 TGTGTTCAATTT
5174898 CTCAATTTCT
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:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (13 bp):
TGTGTTCAATTTG
Found at i:5180755 original size:20 final size:21
Alignment explanation
Indices: 5180725--5180764 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5180715 TCCTCTTTGG
*
5180725 AAGGTGGATATCATGATACCT
1 AAGGTGGATATCACGATACCT
5180746 AAGG-GGATATCACGATACC
1 AAGGTGGATATCACGATACC
5180765 ACTGAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
AAGGTGGATATCACGATACCT
Found at i:5184771 original size:20 final size:18
Alignment explanation
Indices: 5184721--5184772 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
5184711 TCTACAAGTA
5184721 AATATTAAATTAA-ATGT
1 AATATTAAATTAATATGT
*
5184738 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TGT
5184758 AATATTAAATTAATA
1 AATATTAAATTAATA
5184773 AAACACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATGT
Found at i:5184796 original size:24 final size:23
Alignment explanation
Indices: 5184765--5184814 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
5184755 TTTAATATTA
*
5184765 AATTAATA-AAACACTATTAAGAT
1 AATTAATATAAA-ACTATTAAAAT
*
5184788 AATTAAATATTAAACTATTAAAAT
1 AATT-AATATAAAACTATTAAAAT
5184812 AAT
1 AAT
5184815 ATTATTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTAATATAAAACTATTAAAAT
Found at i:5186407 original size:16 final size:16
Alignment explanation
Indices: 5186386--5186416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5186376 CTATGCATGT
*
5186386 AAAATATAAAAGATAA
1 AAAATACAAAAGATAA
5186402 AAAATACAAAAGATA
1 AAAATACAAAAGATA
5186417 TAATAGTGAA
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:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATACAAAAGATAA
Found at i:5203324 original size:27 final size:26
Alignment explanation
Indices: 5203287--5203351 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
5203277 AGTAGAGTTG
*
5203287 CCAGTACAGT-ATATGTGGCA-AAGCCA
1 CCAGAACAGTAAT-TGTGGCAGAA-CCA
5203313 CCAGCAACAGTAATTGTGGCAGAACCA
1 CCAG-AACAGTAATTGTGGCAGAACCA
5203340 CCAGAAGCAGTA
1 CCAGAA-CAGTA
5203352 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 6 0.18
27 24 0.71
28 4 0.12
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (26 bp):
CCAGAACAGTAATTGTGGCAGAACCA
Found at i:5203525 original size:28 final size:27
Alignment explanation
Indices: 5203481--5203575 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
5203471 TTCCCTAATG
*
5203481 GGGTATTAT-GGTAATTTTACCCATCGG
1 GGGTATT-TCGGTAATTTTACCCATCGA
*
5203508 GGGTATTTCAGGTAATTTTACTCATCGA
1 GGGTATTTC-GGTAATTTTACCCATCGA
*
5203536 GGGTATTTCGATAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCATCGA
*
5203563 GGGTATTGCGGTA
1 GGGTATTTCGGTA
5203576 CAGCTAACGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 34 0.57
28 25 0.42
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCATCGA
Found at i:5205603 original size:46 final size:48
Alignment explanation
Indices: 5205528--5205651 Score: 198
Period size: 46 Copynumber: 2.6 Consensus size: 48
5205518 AGATAATCAC
5205528 TTTAATATGAAATTAATAAAATACTATTAGGATAAGTATTTAAATTAA
1 TTTAATATGAAATTAATAAAATACTATTAGGATAAGTATTTAAATTAA
5205576 TTTAATA-GAAATTAAT-AAATACTATTAGGATAAGTATTTAAATTAA
1 TTTAATATGAAATTAATAAAATACTATTAGGATAAGTATTTAAATTAA
* * *
5205622 TTTAATATTAAATTTATTAAAATAATATTA
1 TTTAATATGAAA-TTAATAAAATACTATTA
5205652 TTTTTGAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
46 37 0.53
47 12 0.17
48 11 0.16
49 10 0.14
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (48 bp):
TTTAATATGAAATTAATAAAATACTATTAGGATAAGTATTTAAATTAA
Found at i:5205617 original size:23 final size:23
Alignment explanation
Indices: 5205546--5205618 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
5205536 GAAATTAATA
5205546 AAATACTATTAGGATAAGTATTT
1 AAATACTATTAGGATAAGTATTT
* *
5205569 AAATTAAT-TTA--AT-AGAAATTAAT
1 AAA-TACTATTAGGATAAG-TATT--T
5205592 AAATACTATTAGGATAAGTATTT
1 AAATACTATTAGGATAAGTATTT
5205615 AAAT
1 AAAT
5205619 TAATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
20 2 0.05
21 5 0.13
22 3 0.08
23 18 0.47
24 3 0.08
25 5 0.13
26 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (23 bp):
AAATACTATTAGGATAAGTATTT
Found at i:5208192 original size:35 final size:36
Alignment explanation
Indices: 5208137--5208207 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
5208127 CCATATTACT
5208137 CTTTTCAACCATAATCTTGAAAACTTTTTCTAAGAC
1 CTTTTCAACCATAATCTTGAAAACTTTTTCTAAGAC
5208173 CTTTTCAACC-TAATCTTGAAAACTTTTTCTAAGAC
1 CTTTTCAACCATAATCTTGAAAACTTTTTCTAAGAC
5208208 TCCCACTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (36 bp):
CTTTTCAACCATAATCTTGAAAACTTTTTCTAAGAC
Found at i:5214012 original size:27 final size:26
Alignment explanation
Indices: 5213948--5214132 Score: 212
Period size: 27 Copynumber: 7.0 Consensus size: 26
5213938 AGACCCCAAA
**
5213948 ATAGGGTAAAATGATTGAAATACACCT
1 ATAGGGTAAAATGACCGAAATAC-CCT
*
5213975 A-A-GGTAAAATGATCGAAATACGCCT
1 ATAGGGTAAAATGACCGAAATAC-CCT
* *
5214000 ATAAGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATA-CCCT
*
5214027 ATAGGGTAAAATGACCAAAATACCCT
1 ATAGGGTAAAATGACCGAAATACCCT
* *
5214053 CATAGGGTAAAACGACCGAAATACCCCC
1 -ATAGGGTAAAATGACCGAAATA-CCCT
*
5214081 ATAGGGTAAAATGAACGAAATACCCT
1 ATAGGGTAAAATGACCGAAATACCCT
*
5214107 CATAGGGTAAAATGACCAAAATACCC
1 -ATAGGGTAAAATGACCGAAATACCC
5214133 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
25 22 0.16
26 8 0.06
27 103 0.75
28 4 0.03
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (26 bp):
ATAGGGTAAAATGACCGAAATACCCT
Found at i:5214062 original size:54 final size:54
Alignment explanation
Indices: 5213948--5214132 Score: 250
Period size: 54 Copynumber: 3.5 Consensus size: 54
5213938 AGACCCCAAA
** * * *
5213948 ATAGGGTAAAATGATTGAAATA-CACC-TAAGGTAAAATGATCGAAATACGCCT-
1 ATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATAC-CCTC
* * *
5214000 ATAAGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCTC
*
5214054 ATAGGGTAAAACGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCTC
*
5214108 ATAGGGTAAAATGACCAAAATACCC
1 ATAGGGTAAAATGACCGAAATACCC
5214133 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
52 19 0.16
53 6 0.05
54 92 0.79
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (54 bp):
ATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCTC
Found at i:5214076 original size:81 final size:78
Alignment explanation
Indices: 5213948--5214132 Score: 244
Period size: 81 Copynumber: 2.3 Consensus size: 78
5213938 AGACCCCAAA
*** * * * *
5213948 ATAGGGTAAAATGATTGAAATACACCTAAGGTAAAATGATCGAAATACGCCTATAAGGTAAAATG
1 ATAGGGTAAAATGACCAAAATAC-CCTAAGGTAAAACGACCGAAATACCCCCATAAGGTAAAATG
*
5214013 ACCGAAATACCCCC
65 AACGAAATACCCCC
*
5214027 ATAGGGTAAAATGACCAAAATACCCTCATAGGGTAAAACGACCGAAATACCCCCATAGGGTAAAA
1 ATAGGGTAAAATGACCAAAATACCCT-A-A-GGTAAAACGACCGAAATACCCCCATAAGGTAAAA
*
5214092 TGAACGAAATACCCTC
63 TGAACGAAATACCCCC
5214108 ATAGGGTAAAATGACCAAAATACCC
1 ATAGGGTAAAATGACCAAAATACCC
5214133 NNNNNNNNNN
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 3 0.03
79 21 0.23
80 1 0.01
81 68 0.73
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (78 bp):
ATAGGGTAAAATGACCAAAATACCCTAAGGTAAAACGACCGAAATACCCCCATAAGGTAAAATGA
ACGAAATACCCCC
Found at i:5224718 original size:26 final size:26
Alignment explanation
Indices: 5224656--5224749 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
5224646 AGTATTGGTG
* **
5224656 GCTTTGCTACATATATTGTTACTGGCA
1 GCTTTGCTGCA-ATATCATTACTGGCA
* * *
5224683 ACTTTACTGCAATACTGA-TACTGGCA
1 GCTTTGCTGCAATA-TCATTACTGGCA
* *
5224709 GCTTCGCTGCGATATCATTACTGGCA
1 GCTTTGCTGCAATATCATTACTGGCA
*
5224735 GCTTTGCTGCGATAT
1 GCTTTGCTGCAATAT
5224750 TGGTGTGTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.04
26 43 0.80
27 9 0.17
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
GCTTTGCTGCAATATCATTACTGGCA
Found at i:5224887 original size:33 final size:33
Alignment explanation
Indices: 5224844--5224908 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5224834 TTGCATTATT
* *
5224844 GCACTATACTATTACTGTATTGGGCTAAGGCCC
1 GCACTATACTATTACTGAATAGGGCTAAGGCCC
* *
5224877 GCACTGTACTATTACTGAATAGGGCTCAGGCC
1 GCACTATACTATTACTGAATAGGGCTAAGGCC
5224909 TAGATTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (33 bp):
GCACTATACTATTACTGAATAGGGCTAAGGCCC
Found at i:5230732 original size:33 final size:33
Alignment explanation
Indices: 5230675--5230751 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
5230665 TGCATTATTG
* * * *
5230675 CACTATACTATTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
*
5230708 CACTGTACTGTTACTGAATAGGGCTTAGGCCCA
1 CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
*
5230741 GACTGTTACTG
1 CACTG-TACTG
5230752 CATGTTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (33 bp):
CACTGTACTGTTACTGAATAGGGCTAAGGCCCA
Found at i:5231233 original size:13 final size:14
Alignment explanation
Indices: 5231209--5231237 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5231199 ATCTCCTAAA
5231209 AATCTGGAAAACAT
1 AATCTGGAAAACAT
5231223 AATCT-GAAAACAT
1 AATCTGGAAAACAT
5231236 AA
1 AA
5231238 CTTGCACGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (14 bp):
AATCTGGAAAACAT
Found at i:5253908 original size:206 final size:207
Alignment explanation
Indices: 5253538--5253956 Score: 822
Period size: 206 Copynumber: 2.0 Consensus size: 207
5253528 AACTAATTCT
*
5253538 ATTTTATTTTATTTATTTTAATATTATATTATCCTATAAAAGAATTTATGTTTTAAATTTGATTT
1 ATTTAATTTTATTTATTTTAATATTATATTATCCTATAAAAGAATTTATGTTTTAAATTTGATTT
5253603 TGGTTTAGAATAAGGTGAAATGTTTAAAAATTAAGGATAAAATGTAGAATTTTATTTTTTTTATA
66 TGGTTTAGAATAAGGTGAAATGTTTAAAAATTAAGGATAAAATGTAGAATTTTATTTTTTTTATA
5253668 ATTTAAAATCTATATTTATCAAACAACCTAATTATATTCCATAATTAATTCTAAGTAATATGTCA
131 ATTTAAAATCTATATTTATCAAACAACCTAATTATATTCCATAATTAATTCTAAGTAATATGTCA
5253733 AACAATTTTATA
196 AACAATTTTATA
5253745 ATTTAATTTTATTTA-TTTAATATTATATTATCCTATAAAAGAATTTATGTTTTAAATTTGATTT
1 ATTTAATTTTATTTATTTTAATATTATATTATCCTATAAAAGAATTTATGTTTTAAATTTGATTT
5253809 TGGTTTAGAATAAGGTGAAATGTTTAAAAATTAAGGATAAAATGTAGAATTTTATTTTTTTTATA
66 TGGTTTAGAATAAGGTGAAATGTTTAAAAATTAAGGATAAAATGTAGAATTTTATTTTTTTTATA
5253874 ATTTAAAATCTATATTTATCAAACAACCTAATTATATTCCATAATTAATTCTAAGTAATATGTCA
131 ATTTAAAATCTATATTTATCAAACAACCTAATTATATTCCATAATTAATTCTAAGTAATATGTCA
5253939 AACAATTTTATA
196 AACAATTTTATA
5253951 ATTTAA
1 ATTTAA
5253957 ATTCAGTACT
Statistics
Matches: 211, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
206 197 0.93
207 14 0.07
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (207 bp):
ATTTAATTTTATTTATTTTAATATTATATTATCCTATAAAAGAATTTATGTTTTAAATTTGATTT
TGGTTTAGAATAAGGTGAAATGTTTAAAAATTAAGGATAAAATGTAGAATTTTATTTTTTTTATA
ATTTAAAATCTATATTTATCAAACAACCTAATTATATTCCATAATTAATTCTAAGTAATATGTCA
AACAATTTTATA
Found at i:5257950 original size:163 final size:162
Alignment explanation
Indices: 5257712--5258005 Score: 421
Period size: 163 Copynumber: 1.8 Consensus size: 162
5257702 TAATCCATAG
* * *
5257712 CAAGATCAACAAAAAAAATCATTGTCGATAAGCACCTCAAGACAAAAACACTGTCGTAAAAAAAG
1 CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACACTGTAGTAAAAAAAC
* **
5257777 ACCGCAAAGAACCTAGCTCACACTCCAAATTTAATCTTCTCTCTTCAGTTTCTACTAAGTCCTTA
66 ACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACT-AGTCCTTA
5257842 TTAAAAGTCTCTTAACATCTGTGTAATCGACAA
130 TTAAAAGTCTCTTAACATCTGTGTAATCGACAA
* * * *
5257875 CAAGATCAACAAAACAAACCATTGTTGATAAGCACCTCAAGAC-AAAGCACCT-TATTAAAAAAA
1 CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACA-CTGTAGTAAAAAAA
** * *
5257938 CCATTGCAAAGAACTTAGCTAACACTCCATATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTT
65 -CACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTT
5258003 ATT
129 ATT
5258006 GTAGTAGGGC
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
162 24 0.21
163 91 0.79
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (162 bp):
CAAGATCAACAAAAAAAACCATTGTCGATAAGCACCTCAAGACAAAAACACTGTAGTAAAAAAAC
ACCGCAAAGAACCTAGCTAACACTCCAAATTTAATCTTCTCTCTTCAAATTCTACTAGTCCTTAT
TAAAAGTCTCTTAACATCTGTGTAATCGACAA
Found at i:5271516 original size:51 final size:50
Alignment explanation
Indices: 5271392--5271576 Score: 167
Period size: 51 Copynumber: 3.7 Consensus size: 50
5271382 AAAGTGATGG
* * * * * * *
5271392 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAG-ATAGG
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAT-GA
* * *
5271442 TCGCATGTGTAGTACTATGTGCAGACTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * * *
5271493 TCACGTGTATAGTACTATATGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
*
5271544 TCACATGTTTAGTACTATGTGCAGGCTACTATG
1 TCACATGTATAGTACTATGTGCAGGCTACTATG
5271577 TGAACCGGTA
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 39 0.36
51 69 0.63
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACATGTATAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:5271653 original size:46 final size:43
Alignment explanation
Indices: 5271580--5271678 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
5271570 TACTATGTGA
*
5271580 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
5271623 ACCGGATATCATTTATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
5271669 ACCGTGTATC
1 ACCG-GTATC
5271679 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 26 0.54
47 4 0.08
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:5271823 original size:16 final size:16
Alignment explanation
Indices: 5271802--5271833 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5271792 TGATTGAAAG
*
5271802 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
5271818 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
5271834 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:5273258 original size:5 final size:5
Alignment explanation
Indices: 5273250--5273282 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5273240 TTGTTTTCTT
5273250 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
5273283 TATGCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:5283594 original size:33 final size:33
Alignment explanation
Indices: 5283552--5283619 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
5283542 TTCATTTTCG
5283552 ATACGCATTTATTGAAGAGAAGACATGATCGGT
1 ATACGCATTTATTGAAGAGAAGACATGATCGGT
5283585 ATACGCATTTATTGAAGAGAAGACATGATCGGT
1 ATACGCATTTATTGAAGAGAAGACATGATCGGT
5283618 AT
1 AT
5283620 GGTCTTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (33 bp):
ATACGCATTTATTGAAGAGAAGACATGATCGGT
Found at i:5284890 original size:13 final size:13
Alignment explanation
Indices: 5284872--5284898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5284862 ATATTTTTTT
5284872 TAAAAATAATATA
1 TAAAAATAATATA
5284885 TAAAAATAATATA
1 TAAAAATAATATA
5284898 T
1 T
5284899 GTATGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:5287291 original size:34 final size:34
Alignment explanation
Indices: 5287219--5287349 Score: 174
Period size: 34 Copynumber: 3.8 Consensus size: 34
5287209 AATTTTTGGT
*
5287219 TTAGGGTTTAGAGTTTTTTAAAAAAAATTAATTAAA
1 TTAGGGTTTAGAG-TTTTT-AAATAAATTAATTAAA
* * * *
5287255 TTAGGTTTTAGGGGTTTTAAATAAATAAATTAAA
1 TTAGGGTTTAGAGTTTTTAAATAAATTAATTAAA
5287289 TTAGGGTTTAGAGTTTTTAAGA-AAATTAATTAAA
1 TTAGGGTTTAGAGTTTTTAA-ATAAATTAATTAAA
*
5287323 TTAGGGTTTAGAGTTTTTAAATTAATT
1 TTAGGGTTTAGAGTTTTTAAATAAATT
5287350 TTGTTTTTAG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 1 0.01
34 66 0.80
35 5 0.06
36 11 0.13
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (34 bp):
TTAGGGTTTAGAGTTTTTAAATAAATTAATTAAA
Found at i:5287600 original size:125 final size:125
Alignment explanation
Indices: 5287464--5287798 Score: 483
Period size: 125 Copynumber: 2.7 Consensus size: 125
5287454 AAAGATAATT
* ** * *
5287464 TCAAAAACGCTTCATGCAGGATGCTTTGTCAGCAAAATTACTAAAAAAAGCTCCTAAGTGGACAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
*
5287529 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAATTGGTG
66 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
* * * * * *
5287589 TCAAAAACGCTTCAAGCAGCATGCACAGTCAACAAAAATACTGAAAAGAGCTCCCACGTGGACAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
* * *
5287654 TCTTTTTCTATAGTAGTTCCTAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATGGTG
66 TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
* *
5287714 TCAAAAATGCTTCAAGCAGGATACACTGTCAGCAAAATTGA-TGAAAAAAAGCTCCCACGTGGAC
1 TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACT-AAAAAAAGCTCCCACGTGGAC
*
5287778 GCTCTTTTTCTACAGTAGTTC
64 ACTCTTTTTCTACAGTAGTTC
5287799 TTATTTGGCC
Statistics
Matches: 183, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
125 144 0.79
126 39 0.21
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (125 bp):
TCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACAC
TCTTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACAATTATGAACAAATGGTG
Found at i:5291030 original size:34 final size:34
Alignment explanation
Indices: 5290986--5291076 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 34
5290976 TGTTTTTTTA
* *
5290986 AAAATTAATTAAATTAGGTTTTAGGGGTTTTAA-
1 AAAATTAATTAAATTAGGGTTTAGAGGTTTTAAG
* *
5291019 ATAAATAAATTAAATTAGGGTTTAGAGTTTTTAAG
1 A-AAATTAATTAAATTAGGGTTTAGAGGTTTTAAG
5291054 AAAATTAATTAAATTAGGGTTTA
1 AAAATTAATTAAATTAGGGTTTA
5291077 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
33 1 0.02
34 49 0.96
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (34 bp):
AAAATTAATTAAATTAGGGTTTAGAGGTTTTAAG
Found at i:5291278 original size:127 final size:127
Alignment explanation
Indices: 5291142--5291416 Score: 426
Period size: 127 Copynumber: 2.2 Consensus size: 127
5291132 ACAATAAGGA
* * * *
5291142 TTTTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAACAAATAGTATAA
1 TTTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGATCCTGAACAAAAAGTATAA
* * *
5291207 AAAATGCTTCAAGTAGGATGCATTGTCAGCAAAATTGATGAAAAAAGCTCCCACATGGACGC
66 AAAATACTTCAAGCAGGATGCATTGTCAACAAAATTGATGAAAAAAGCTCCCACATGGACGC
* * *
5291269 TTTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATCCTGAACAAAAAGTGTCA
1 TTTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGATCCTGAACAAAAAGTATAA
* *
5291334 AAAATACTTCAAGCAGGATGCATTGTCAACAAAATTGATGAAAAAAGCTCCCACGTGGGCGC
66 AAAATACTTCAAGCAGGATGCATTGTCAACAAAATTGATGAAAAAAGCTCCCACATGGACGC
*
5291396 -TCTTTTTCTACAGTAGTTCCT
1 TTTTTTTTCTACAGTAGTTCCT
5291417 ATTTGGCCTT
Statistics
Matches: 135, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
126 20 0.15
127 115 0.85
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (127 bp):
TTTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGATCCTGAACAAAAAGTATAA
AAAATACTTCAAGCAGGATGCATTGTCAACAAAATTGATGAAAAAAGCTCCCACATGGACGC
Found at i:5294909 original size:18 final size:18
Alignment explanation
Indices: 5294886--5294923 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5294876 GAAAAGGGAA
*
5294886 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
5294904 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
5294922 AC
1 AC
5294924 GCACCTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:5304205 original size:6 final size:6
Alignment explanation
Indices: 5304191--5304241 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
5304181 AAAAATTACA
5304191 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TCCTTCTA- TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T--TT-TAT TTTTAT TTTTAT
5304239 TTT
1 TTT
5304242 GCAGGTAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 12 0.29
6 24 0.59
8 3 0.07
9 2 0.05
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:5307017 original size:37 final size:37
Alignment explanation
Indices: 5306975--5307123 Score: 298
Period size: 37 Copynumber: 4.0 Consensus size: 37
5306965 ATTTTAGTGG
5306975 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
5307012 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
5307049 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
5307086 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
1 ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
5307123 A
1 A
5307124 GCTAGCCGCA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 112 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (37 bp):
ATAAACAACATGGATGTCGGCAAAATGCAACTTGTCA
Found at i:5311185 original size:19 final size:21
Alignment explanation
Indices: 5311145--5311185 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5311135 AATTTATGTC
5311145 AAATATTTATATTATTGAATT
1 AAATATTTATATTATTGAATT
*
5311166 AAAT-TTTATATT-TTGTATT
1 AAATATTTATATTATTGAATT
5311185 A
1 A
5311186 GTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
AAATATTTATATTATTGAATT
Found at i:5311681 original size:43 final size:43
Alignment explanation
Indices: 5311618--5311876 Score: 249
Period size: 42 Copynumber: 6.1 Consensus size: 43
5311608 CGCCGCTAAA
* * *
5311618 TTTTCCACATAAACGCCGCTATAGAACATGACCTTTAGCCGCGC
1 TTTTCC-CACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * *
5311662 TTTTCCCACAAACGTCGCTAAAGAACATGTCATTTAGCGGCGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * * * *
5311705 TTTT-CCACAAACCCCACCATAGAGCATGACCTTTAG-GAGCGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCG-GCGC
* *** * * * *
5311747 TTTT-CCACAAGCGCTATTATAGAGCATGACCTTTAGTGGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* * *
5311789 TTTTCCCACAAACGCTGCCAAAGAACATGA-CTTTAGCGGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
* *
5311831 -TTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCAGTGC
1 TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
5311873 TTTT
1 TTTT
5311877 AGTAAAAATG
Statistics
Matches: 180, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
41 28 0.16
42 88 0.49
43 58 0.32
44 6 0.03
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC
Found at i:5315563 original size:40 final size:40
Alignment explanation
Indices: 5315500--5315632 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 40
5315490 ATTTGGACAA
*
5315500 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTATAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGC-TTTATAG
** * * * *
5315541 -AAACGCCGCTAAAGGTCGAGCATTAGTGGCGCTTTCTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
* * *
5315580 AAAACGCCGCTAAAAAT-AA-TATTAGCGGCG-TTTTTCG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
5315617 AAAAGCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
5315633 GCCTAAGCCC
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
37 14 0.18
38 15 0.20
39 6 0.08
40 41 0.54
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATAG
Found at i:5315800 original size:40 final size:41
Alignment explanation
Indices: 5315660--5315820 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
5315650 TTCTAAGTTT
*
5315660 TGGGGCCTTTAGCGGCGTTTTAGAAC-AAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTG-ACGAAGCGCCGCTAATGC
* *
5315701 TGGGGCCTTTAGAGGCGTTTTTGAGGAAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
*
5315742 TGGGGCCTTTAGCGGCGTTTTTTACGAAGCGCCGCTAATGC
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
* **
5315783 T-CGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAAT
5315821 AATAATAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
40 34 0.31
41 75 0.69
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (41 bp):
TGGGGCCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGC
Found at i:5315955 original size:21 final size:20
Alignment explanation
Indices: 5315931--5315982 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
5315921 ATTTCGTTGT
*
5315931 ATTTATTATATATGATAACAA
1 ATTTATT-TAAATGATAACAA
5315952 ATTTACATTTAAATGATAACAA
1 ATTT--ATTTAAATGATAACAA
5315974 ATTATATTT
1 ATT-TATTT
5315983 TTTAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTATTTAAATGATAACAA
Found at i:5316513 original size:14 final size:13
Alignment explanation
Indices: 5316462--5316526 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
5316452 TATTAAATAA
5316462 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
*
5316476 GGGTTAGAGGTTAGG
1 GGTTTAG-GGTTA-G
* *
5316491 GGCTGAGGGTTATG
1 GGTTTAGGGTTA-G
5316505 GGTTTAGGGTTCAG
1 GGTTTAGGGTT-AG
5316519 GGTTTAGG
1 GGTTTAGG
5316527 ATTTAAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 34 0.81
15 7 0.17
ACGTcount: A:0.15, C:0.03, G:0.49, T:0.32
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:5316537 original size:15 final size:14
Alignment explanation
Indices: 5316462--5316537 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
5316452 TATTAAATAA
5316462 GGTTTAGGGGTT-AG
1 GGTTTA-GGGTTAAG
* *
5316476 GGGTTAGAGGTTAGG
1 GGTTTAG-GGTTAAG
* * *
5316491 GGCTGAGGGTTATG
1 GGTTTAGGGTTAAG
*
5316505 GGTTTAGGGTTCAG
1 GGTTTAGGGTTAAG
*
5316519 GGTTTAGGATTTAAG
1 GGTTTAGG-GTTAAG
5316534 GGTT
1 GGTT
5316538 AATGGTCGGG
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 1 0.02
14 33 0.69
15 14 0.29
ACGTcount: A:0.17, C:0.03, G:0.46, T:0.34
Consensus pattern (14 bp):
GGTTTAGGGTTAAG
Done.