Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 15 of 228
Found at i:5248686 original size:5 final size:5
Alignment explanation
Indices: 5248676--5248708 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5248666 TGTGAAATTG
5248676 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
5248709 TGCTGGTGTT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:5270003 original size:32 final size:32
Alignment explanation
Indices: 5269962--5270025 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
5269952 GTACGTTTTC
5269962 TTTGCTATAAACAACCATTATCAGTAGAATCA
1 TTTGCTATAAACAACCATTATCAGTAGAATCA
5269994 TTTGCTATAAACAACCATTATCAGTAGAATCA
1 TTTGCTATAAACAACCATTATCAGTAGAATCA
5270026 ACAAATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (32 bp):
TTTGCTATAAACAACCATTATCAGTAGAATCA
Found at i:5285820 original size:18 final size:18
Alignment explanation
Indices: 5285797--5285832 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5285787 TACATGGATT
5285797 TTTTAATATCTATTTAAA
1 TTTTAATATCTATTTAAA
5285815 TTTTAATATCTATTTAAA
1 TTTTAATATCTATTTAAA
5285833 ATTGGTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATATCTATTTAAA
Found at i:5288673 original size:37 final size:36
Alignment explanation
Indices: 5288616--5288689 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 36
5288606 TGTTAATTTC
5288616 AAGACTTTGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTTGTAATGTTTTTAATTATGTAGTGATTCA
5288652 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTT-TGTAATGTTTTTAATTATGTAGTGATTCA
5288689 A
1 A
5288690 TTCGGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (36 bp):
AAGACTTTGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:5288679 original size:17 final size:17
Alignment explanation
Indices: 5288623--5288680 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
5288613 TTCAAGACTT
5288623 TGTAATGTTTTTAATTA
1 TGTAATGTTTTTAATTA
* ***
5288640 TGTAGTGATTCAAAGACTTA
1 TGTAATG-TTTTTA-A-TTA
5288660 TGTAATGTTTTTAATTA
1 TGTAATGTTTTTAATTA
5288677 TGTA
1 TGTA
5288681 GTGATTCAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 13 0.43
18 4 0.13
19 4 0.13
20 9 0.30
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (17 bp):
TGTAATGTTTTTAATTA
Found at i:5288702 original size:9 final size:9
Alignment explanation
Indices: 5288688--5288718 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5288678 GTAGTGATTC
*
5288688 AATTCGGGT
1 AATTCGGTT
5288697 AATTCGGTT
1 AATTCGGTT
5288706 AATTCGGTT
1 AATTCGGTT
5288715 AATT
1 AATT
5288719 TTTAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5291274 original size:8 final size:8
Alignment explanation
Indices: 5291261--5291288 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5291251 TTAATTTTTA
5291261 AAAAATAT
1 AAAAATAT
5291269 AAAAATAT
1 AAAAATAT
5291277 AAAAATAT
1 AAAAATAT
5291285 AAAA
1 AAAA
5291289 TTTTGAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:5303691 original size:19 final size:18
Alignment explanation
Indices: 5303655--5303705 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
5303645 AATTAATTTT
5303655 TAAAAATTTAAAAA-ATTA
1 TAAAAA-TTAAAAATATTA
5303673 TAAAAATTAAAAATCATTA
1 TAAAAATTAAAAAT-ATTA
*
5303692 -AAATCATTAAAAAT
1 TAAA-AATTAAAAAT
5303706 TATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
19 13 0.45
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATTAAAAATATTA
Found at i:5308749 original size:23 final size:22
Alignment explanation
Indices: 5308702--5308758 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5308692 AGACAAGTAC
*
5308702 AATACAATCAAAATATCTTATA
1 AATACAATCAAAATACCTTATA
*
5308724 AATACATATCCAAATAACCTTA-A
1 AATACA-ATCAAAAT-ACCTTATA
*
5308747 AATAGAATCAAA
1 AATACAATCAAA
5308759 GTAATACAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.38
23 13 0.45
24 5 0.17
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (22 bp):
AATACAATCAAAATACCTTATA
Found at i:5310962 original size:8 final size:8
Alignment explanation
Indices: 5310949--5310988 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
5310939 ATGATGAATG
5310949 AAAATGAA
1 AAAATGAA
5310957 AAAATG--
1 AAAATGAA
5310963 AAAATG-A
1 AAAATGAA
5310970 AAAATGAA
1 AAAATGAA
5310978 AAAATGAA
1 AAAATGAA
5310986 AAA
1 AAA
5310989 TAGAGAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.20
7 6 0.20
8 18 0.60
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:5310964 original size:14 final size:13
Alignment explanation
Indices: 5310945--5310989 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 13
5310935 AATGATGATG
5310945 AATGAAAATGAAAA
1 AATGAAAATG-AAA
5310959 AATGAAAATGAAA
1 AATGAAAATGAAA
5310972 AATGAAAAAATGAAA
1 AATG--AAAATGAAA
5310987 AAT
1 AAT
5310990 AGAGAGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.24
14 10 0.34
15 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (13 bp):
AATGAAAATGAAA
Found at i:5310973 original size:21 final size:20
Alignment explanation
Indices: 5310945--5310987 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
5310935 AATGATGATG
5310945 AATGAAAATGAAAAAATGAA
1 AATGAAAATGAAAAAATGAA
5310965 AATGAAAAATGAAAAAATGAA
1 AATG-AAAATGAAAAAATGAA
5310986 AA
1 AA
5310988 ATAGAGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (20 bp):
AATGAAAATGAAAAAATGAA
Found at i:5312315 original size:44 final size:42
Alignment explanation
Indices: 5312243--5312904 Score: 299
Period size: 44 Copynumber: 15.9 Consensus size: 42
5312233 AGAATTGCAG
*
5312243 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-TTAG-A
* * *
5312287 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATTAGA
* * * * * *
5312326 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATTAGA
* * *
5312367 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-TTAG-A
* * *
5312411 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATTAGA
* * * * * *
5312450 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATTAGA
* * *
5312491 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-TTAG-A
* ** ** *
5312535 ATCCTATCTCATTGAGATTACAGTGGAGTGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATTAGA
** ** ** * * *
5312574 ATCTTATCTCTTTGA-AGTTACAGCAGAGTGGATCGCATCA-A
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATTAGA
* * *
5312615 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-TTAG-A
* * * *
5312659 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AA--GGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATTAGA
* * * * * * *
5312698 ATTTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCA-A
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATTAGA
* * ** * *
5312739 GTCTTATCTCCTTGAGATTACAACGAAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-TTAG-A
* * * * * * * *
5312783 ATCCTATCTCCTTGAGATTACGGTAGAGCGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-GAAT-TAGA
* * * * *
5312827 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATTGTATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATTAGA
* * * * *
5312868 GTCTTATATCCCTGATG-TTGCAGTGGAACAGACTGAA
1 ATCTTATCTCCCTGA-GATTACAGTGGAGCAGATTGAA
5312905 AACGTAAATT
Statistics
Matches: 456, Mismatches: 125, Indels: 77
0.69 0.19 0.12
Matches are distributed among these distances:
38 4 0.01
39 104 0.23
40 11 0.02
41 133 0.29
42 17 0.04
43 11 0.02
44 172 0.38
45 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATTAGA
Found at i:5312387 original size:80 final size:81
Alignment explanation
Indices: 5312242--5312681 Score: 254
Period size: 80 Copynumber: 5.3 Consensus size: 81
5312232 AAGAATTGCA
* * * * * *
5312242 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGTA-TCAG--GTCTTATCTCCCTGAGATTA
*
5312307 CAGTGGAGCGGATTA-AAG
63 CAGTGGAGCAGATTAGAAG
* * *
5312325 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACA
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATCGTATCAGGTCTTATCTCCCTGAGATTACA
*
5312389 GCGGAGCAGATTGAAGATAG
65 GTGGAGCAGATT--AGA-AG
* * ** * * *
5312409 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGAT--TA-AAGGATCTTATCTCTCTGA-AGTTA
1 -GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGTATCAGG-TCTTATCTCCCTGAGA-TTA
* * **
5312470 CAGTAGAGTAGATCGTATCAG
63 CAGTGGAGCAGAT--TAGAAG
* * * * * **
5312491 G-TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AGTAATCCTATCTCATTGAGATT
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCG--TATCAG--GTCTTATCTCCCTGAGATT
**
5312554 ACAGTGGAGTGGATTA-AAG
62 ACAGTGGAGCAGATTAGAAG
** ** * *
5312573 GATCTTATCTCTTTGA-AGTTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGATTACA
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATCGTATCAGGTCTTATCTCCCTGAGATTACA
*
5312637 GCGGAGCAGATT-GAAG
65 GTGGAGCAGATTAGAAG
*
5312653 CTAGTAATCCTATCTCCCTGAGATTACAG
1 ---G--ATCTTATCTCCCTGAGATTACAG
5312682 TGGAGCGGAT
Statistics
Matches: 274, Mismatches: 54, Indels: 56
0.71 0.14 0.15
Matches are distributed among these distances:
80 89 0.32
81 2 0.01
82 16 0.06
83 89 0.32
84 5 0.02
85 70 0.26
86 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (81 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGATTAGAAG
Found at i:5312464 original size:124 final size:124
Alignment explanation
Indices: 5312244--5312882 Score: 1035
Period size: 124 Copynumber: 5.1 Consensus size: 124
5312234 GAATTGCAGA
*
5312244 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
5312309 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
5312368 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
5312433 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
**
5312492 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
* * * * * *
5312557 GTGGAGTGGATTAAAGGATCTTATCTCTTTGAAGTTACAGCAGAGTGGATCGCATCAAG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
*
5312616 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
* * *
5312681 GTGGAGCGGATTAAGGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAAG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
* * * * * *
5312740 TCTTATCTCCTTGAGATTACAACGAAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
* *
5312805 GTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGTATCAGG
66 GTGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
*
5312869 TCTTATATCCCTGA
1 TCTTATCTCCCTGA
5312883 TGTTGCAGTG
Statistics
Matches: 479, Mismatches: 31, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
124 422 0.88
125 1 0.00
129 56 0.12
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (124 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
Found at i:5312760 original size:80 final size:80
Alignment explanation
Indices: 5312415--5312760 Score: 233
Period size: 80 Copynumber: 4.2 Consensus size: 80
5312405 ATAGTAATCC
*
5312415 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGG-ATCTTATCTCTCTGA-AGTTACAGTAGAG
1 TATCTCCCTGAGATTACAGCGGAGCGGATT-AAGGAATCTTATCTCTCTGAGA-TTACAGTAGAG
*
5312478 TAGATCGTATCAGGTCT
64 TAGATCGTATCAAGTCT
* *
5312495 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCAT-TGAGATTACAGT
1 TATCTCCCTGAGATTACAGCGGAGCGGATT-AAG---G-AATCTTATCTC-TCTGAGATTACAGT
* *
5312559 GGAGTGGAT--TA--AAGGATCT
60 AGAGTAGATCGTATCAA-G-TCT
** * * ** ** * **
5312578 TATCTCTTTGA-AGTTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGATTACAGCGGA
1 TATCTCCCTGAGA-TTACAGCGGAGCGGAT-TAAGGAA-TCTTATCTCTCTGAGATTACAGTAGA
* * * * * *
5312642 GCAGATTGAAGCTAGTAATCC
63 GTAGATCGTATC-A--AGTCT
* * *
5312663 TATCTCCCTGAGATTACAGTGGAGCGGATTAAGGGATTTTATCTCTCTGA-AGTTACAGTAGAGT
1 TATCTCCCTGAGATTACAGCGGAGCGGATTAAGGAATCTTATCTCTCTGAGA-TTACAGTAGAGT
5312727 AGATCGTATCAAGTCT
65 AGATCGTATCAAGTCT
*
5312743 TATCTCCTTGAGATTACA
1 TATCTCCCTGAGATTACA
5312761 ACGAAGCAGA
Statistics
Matches: 199, Mismatches: 45, Indels: 44
0.69 0.16 0.15
Matches are distributed among these distances:
79 2 0.01
80 77 0.39
81 1 0.01
82 5 0.03
83 57 0.29
84 2 0.01
85 51 0.26
86 3 0.02
87 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (80 bp):
TATCTCCCTGAGATTACAGCGGAGCGGATTAAGGAATCTTATCTCTCTGAGATTACAGTAGAGTA
GATCGTATCAAGTCT
Found at i:5314461 original size:3 final size:3
Alignment explanation
Indices: 5314453--5314489 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
5314443 TATTTTAGTG
*
5314453 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
5314490 GTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5315294 original size:109 final size:109
Alignment explanation
Indices: 5314998--5315389 Score: 545
Period size: 109 Copynumber: 3.6 Consensus size: 109
5314988 TCAAAAAAGG
* * * * *
5314998 AAAATATTTCCAATTAAGGTAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAAAGTGCT
1 AAAA-ATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
* *
5315063 GGGTGTCGATTTTTCTCGTTCAACTAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * * *
5315108 AAAAAATTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAAGGTGCT
1 -AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
*
5315173 GGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
** * * *
5315218 AAAAATTTCAAAATAAGACAATGTTTTGCATTTGGGAAATTCGAG-GAACATGCTCTAAAGTGCT
1 AAAAATTTCAAAATAAGGTAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAAGTGCT
5315282 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * * * *
5315327 AAAATTTTCAAAATAAGGTAAAGTTTTGCGTTTGGAAATTCGAG-GAACAAGCCCTAATGTGCT
1 AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
5315390 AGGTTTTGAT
Statistics
Matches: 252, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
108 27 0.11
109 116 0.46
110 105 0.42
111 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:5325409 original size:10 final size:10
Alignment explanation
Indices: 5325379--5325414 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5325369 AATAAAGTAG
5325379 ATTATATATT
1 ATTATATATT
*
5325389 ATTTTTATATT
1 A-TTATATATT
5325400 ATTATATATT
1 ATTATATATT
5325410 ATTAT
1 ATTAT
5325415 TTTAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATATATT
Found at i:5325515 original size:56 final size:57
Alignment explanation
Indices: 5325404--5325536 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 57
5325394 TATATTATTA
* * *
5325404 TATATTATTATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
* *
5325462 TATATATT-TTTTATTAAATT-ATATTTAATAATAATTATGTTAA-AATATGATTAAAT
1 TATATATTATTTTATTAAATTCATA--TAAGAATAATTATATTAAGAATATGATTAAAT
*
5325518 TATTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
5325537 TAATCTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 3 0.05
56 29 0.45
57 23 0.35
58 10 0.15
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
Found at i:5325734 original size:45 final size:44
Alignment explanation
Indices: 5325646--5325738 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
5325636 AGTACAACAT
*
5325646 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
* *
5325690 CATTCCATTCAATCAAACA-ATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGCTCTATTC
5325735 CATT
1 CATT
5325739 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:5334774 original size:22 final size:22
Alignment explanation
Indices: 5334749--5334794 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5334739 AAGTTTATAC
5334749 ATAAAGATCTAAATAGCTAAAT
1 ATAAAGATCTAAATAGCTAAAT
5334771 ATAAAGATCTAAATAGCTAAAT
1 ATAAAGATCTAAATAGCTAAAT
5334793 AT
1 AT
5334795 GTCAGACCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (22 bp):
ATAAAGATCTAAATAGCTAAAT
Found at i:5335177 original size:6 final size:6
Alignment explanation
Indices: 5335145--5335195 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
5335135 GTCTACCTGC
5335145 AAAAT- AAAAT- AAAATA GAAGGAATA AAAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA -AA--AATA AAAATA AAAATA AAAATA AAAATA
5335193 AAA
1 AAA
5335196 TGTGTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 15 0.37
6 18 0.44
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:5345449 original size:20 final size:20
Alignment explanation
Indices: 5345393--5345457 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
5345383 TAAACATTTT
*
5345393 TAAATTTTAATT-AATTCAG
1 TAAATTTTAATTCAATTGAG
5345412 TAAATTTTATATTTCAATTGA-
1 TAAATTTTA-A-TTCAATTGAG
5345433 TAAACTTTTAATTCAATTGTAG
1 TAAA-TTTTAATTCAATTG-AG
5345455 TAA
1 TAA
5345458 TCATATTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 9 0.23
20 9 0.23
21 8 0.21
22 13 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TAAATTTTAATTCAATTGAG
Found at i:5350373 original size:10 final size:10
Alignment explanation
Indices: 5350358--5350382 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5350348 ACAAAAAATT
5350358 GAAAATCATA
1 GAAAATCATA
5350368 GAAAATCATA
1 GAAAATCATA
5350378 GAAAA
1 GAAAA
5350383 AAAACTCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (10 bp):
GAAAATCATA
Found at i:5352322 original size:31 final size:31
Alignment explanation
Indices: 5352282--5352344 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
5352272 ATTTTAGGCA
*
5352282 CTGTCGTTAACAACAATTTTTATTTTGGTCAC
1 CTGTCGTTAA-AACAATTTTCATTTTGGTCAC
** *
5352314 CTGT-GTTAATTCAATTTTCATTTTTGTCAC
1 CTGTCGTTAAAACAATTTTCATTTTGGTCAC
5352344 C
1 C
5352345 CAACCTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 18 0.67
31 5 0.19
32 4 0.15
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (31 bp):
CTGTCGTTAAAACAATTTTCATTTTGGTCAC
Found at i:5357237 original size:41 final size:41
Alignment explanation
Indices: 5357036--5357228 Score: 332
Period size: 41 Copynumber: 4.7 Consensus size: 41
5357026 TTAATTTAAA
*
5357036 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
5357078 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
5357119 CAAATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
5357160 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
5357201 CAGATCACCGGCACTTAGCCTGCTAGGC
1 CAGATCACCGGCACTTAGCCTGCTAGGC
5357229 GCTAAGCCTG
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 141 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:5363058 original size:11 final size:11
Alignment explanation
Indices: 5363042--5363066 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5363032 ATAAAATGAA
5363042 AAAAGTTGTTT
1 AAAAGTTGTTT
5363053 AAAAGTTGTTT
1 AAAAGTTGTTT
5363064 AAA
1 AAA
5363067 CTGCCCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (11 bp):
AAAAGTTGTTT
Found at i:5364752 original size:113 final size:114
Alignment explanation
Indices: 5364567--5365119 Score: 389
Period size: 114 Copynumber: 4.8 Consensus size: 114
5364557 AAATCTCAAG
* * *
5364567 ACCAACACGCAGCGTTCTGGTCTTGATGTAT-TTGGC-ATTAGTGGCGCTTACGAA-CAAACGCC
1 ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTGGCGCTTA-TAAGAAAACGCC
* * *
5364629 GGTAATGTATAGTATTAGCGGCGCTTAGAGG-AAGCGCCGCAAAAGAT-GTA
63 GCTAAAGTATAGTATTAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
*
5364679 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-AAGAAAACGCCGC
* ** * * *
5364744 TAATGTATAGTATTAGCGGCGCTCGGCGGCGCCGAGCGTTAAACGCCGCAAGACATCTTA
65 TAAAGTATAGTATTAGCGGCGCT--------TAGAG-G-TAAGCGCCGCAAAAGATCTTA
* * **
5364804 ATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGCG-TT-TAAGGAAAACGCCA
1 ACCAAAACGCAGCGT-TTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAA-GAAAACGCC-
* * * * * * *
5364867 G-TAAAGGATAGT-TATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTA
63 GCTAAAGTATAGTAT-TAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
* * * *
5364918 ACCAAAACGCAGAGTTTGGTCTTGAGGTGTATTAG-AATTAGTGGCGCTTGATGA-AAAACGCCG
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTT-ATAAGAAAACGCCG
* * *
5364981 CTAAAGTATA-TCATTAGCGGCG-TTTGTGG-AACGCGCCG-TAAAGTATCTTA
64 CTAAAGTATAGT-ATTAGCGGCGCTTAGAGGTAA-GCGCCGCAAAAG-ATCTTA
* * * ** * ** **
5365031 ACCAAAACACAGCTTTTAGTTCTTGATGTATACCGGAATTAGTGGCGCACATGGGAAAACGCCGC
1 ACCAAAACGCAGCGTTT-GGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAGAAAACGCCGC
* * *
5365096 TGAAGCATAGTATTAGTGGCGCTT
65 TAAAGTATAGTATTAGCGGCGCTT
5365120 TTACCGAAAC
Statistics
Matches: 353, Mismatches: 54, Indels: 65
0.75 0.11 0.14
Matches are distributed among these distances:
111 16 0.05
112 37 0.10
113 94 0.27
114 104 0.29
115 5 0.01
116 4 0.01
121 3 0.01
122 1 0.00
123 3 0.01
124 40 0.11
125 18 0.05
126 28 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (114 bp):
ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAGAAAACGCCGCT
AAAGTATAGTATTAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
Found at i:5366233 original size:7 final size:7
Alignment explanation
Indices: 5366217--5366263 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
5366207 TGTTCGAGGT
5366217 TTTGGGG
1 TTTGGGG
*
5366224 TTTAGGG
1 TTTGGGG
5366231 TTTGGGG
1 TTTGGGG
5366238 TTTGGGG
1 TTTGGGG
5366245 TTTGGGG
1 TTTGGGG
5366252 TTTGGGG
1 TTTGGGG
5366259 TTTGG
1 TTTGG
5366264 TTTTTGAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.53, T:0.45
Consensus pattern (7 bp):
TTTGGGG
Found at i:5366274 original size:21 final size:21
Alignment explanation
Indices: 5366217--5366275 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
5366207 TGTTCGAGGT
5366217 TTTGGGGTTT-AGGGTTTGGGG
1 TTTGGGGTTTGA-GGTTTGGGG
*
5366238 TTTGGGGTTTGGGGTTTGGGG
1 TTTGGGGTTTGAGGTTTGGGG
**
5366259 TTTGGTTTTTGAGGTTT
1 TTTGGGGTTTGAGGTTT
5366276 AAGGTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.49
Consensus pattern (21 bp):
TTTGGGGTTTGAGGTTTGGGG
Found at i:5368493 original size:16 final size:16
Alignment explanation
Indices: 5368472--5368507 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5368462 GTATTTATAA
*
5368472 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
5368488 TTATCGATTTACAATT
1 TTATCGATTTACAATT
5368504 TTAT
1 TTAT
5368508 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:5368657 original size:67 final size:67
Alignment explanation
Indices: 5368567--5368705 Score: 269
Period size: 67 Copynumber: 2.1 Consensus size: 67
5368557 ATTAATTGAC
*
5368567 TGAATGTCAATGAATTTTCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
5368632 AA
66 AA
5368634 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
5368699 AA
66 AA
5368701 TGAAT
1 TGAAT
5368706 TCTCAAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (67 bp):
TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:5368946 original size:17 final size:17
Alignment explanation
Indices: 5368924--5368958 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5368914 TACATGACTT
5368924 ACATATTACTTACTAAA
1 ACATATTACTTACTAAA
**
5368941 ACATATTTTTTACTAAA
1 ACATATTACTTACTAAA
5368958 A
1 A
5368959 TTTACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
ACATATTACTTACTAAA
Found at i:5368976 original size:13 final size:13
Alignment explanation
Indices: 5368960--5369018 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
5368950 TTACTAAAAT
*
5368960 TTACTTTAATATA
1 TTACTTAAATATA
*
5368973 TTACTTGAATATA
1 TTACTTAAATATA
5368986 TTACTTAAATA-A
1 TTACTTAAATATA
*
5368998 TTTACTTAAATACA
1 -TTACTTAAATATA
5369012 TTACTTA
1 TTACTTA
5369019 CTAAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:5369688 original size:9 final size:9
Alignment explanation
Indices: 5369676--5369906 Score: 171
Period size: 9 Copynumber: 26.4 Consensus size: 9
5369666 TAGTTACATA
*
5369676 ATAACTTAT
1 ATAACTTAC
5369685 ATAAACTTAC
1 AT-AACTTAC
*
5369695 ATAA-TACAC
1 ATAACT-TAC
*
5369704 ATTACTTAC
1 ATAACTTAC
* *
5369713 ATAGCATAC
1 ATAACTTAC
5369722 ATAACTTAC
1 ATAACTTAC
* *
5369731 ACAACTTAA
1 ATAACTTAC
5369740 ATAA--TAC
1 ATAACTTAC
5369747 ATAACTTAC
1 ATAACTTAC
5369756 ATAACTTAC
1 ATAACTTAC
*
5369765 ATAACCTAC
1 ATAACTTAC
*
5369774 ATAATACATA-
1 AT-A-ACTTAC
5369784 ATAACTTAC
1 ATAACTTAC
5369793 --AACTTAC
1 ATAACTTAC
*
5369800 ATAACATAC
1 ATAACTTAC
* **
5369809 ATTACTTTG
1 ATAACTTAC
5369818 ATAACTTAC
1 ATAACTTAC
5369827 ATAACTTAC
1 ATAACTTAC
5369836 ATAA--TAC
1 ATAACTTAC
* *
5369843 ACAACTTAA
1 ATAACTTAC
*
5369852 ATAGCTTAC
1 ATAACTTAC
*
5369861 TTAA--TAC
1 ATAACTTAC
5369868 ATAACTTAC
1 ATAACTTAC
5369877 ATAACTT--
1 ATAACTTAC
*
5369884 ATACACGTAC
1 ATA-ACTTAC
5369894 ATAACTTAC
1 ATAACTTAC
5369903 ATAA
1 ATAA
5369907 TTGACTTAAT
Statistics
Matches: 171, Mismatches: 34, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
7 28 0.16
8 8 0.05
9 116 0.68
10 15 0.09
11 4 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:5369752 original size:25 final size:25
Alignment explanation
Indices: 5369718--5369777 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 25
5369708 CTTACATAGC
5369718 ATACATAACTTACACAACTTAAATA
1 ATACATAACTTACACAACTTAAATA
* *
5369743 ATACATAACTTACATAACTTACATA
1 ATACATAACTTACACAACTTAAATA
5369768 ACCTACATAA
1 A--TACATAA
5369778 TACATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 24 0.77
27 7 0.23
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (25 bp):
ATACATAACTTACACAACTTAAATA
Found at i:5369757 original size:34 final size:34
Alignment explanation
Indices: 5369710--5369784 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
5369700 ACACATTACT
* *
5369710 TACATAGCATACATAACTTACACAACTTAAATAA
1 TACATAACATACATAACTTACACAACCTAAATAA
* * *
5369744 TACATAACTTACATAACTTACATAACCTACATAA
1 TACATAACATACATAACTTACACAACCTAAATAA
5369778 TACATAA
1 TACATAA
5369785 TAACTTACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.28
Consensus pattern (34 bp):
TACATAACATACATAACTTACACAACCTAAATAA
Found at i:5369803 original size:35 final size:36
Alignment explanation
Indices: 5369739--5369810 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
5369729 ACACAACTTA
*
5369739 AATAATACATAACTTACATAACTTACATAACCTACAT
1 AATAATACATAACTTACA-AACTTACATAACATACAT
5369776 AATACATA-ATAACTTAC-AACTTACATAACATACAT
1 AATA-ATACATAACTTACAAACTTACATAACATACAT
5369811 TACTTTGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 17 0.52
37 13 0.39
38 3 0.09
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (36 bp):
AATAATACATAACTTACAAACTTACATAACATACAT
Found at i:5369822 original size:62 final size:62
Alignment explanation
Indices: 5369717--5369884 Score: 179
Period size: 62 Copynumber: 2.7 Consensus size: 62
5369707 ACTTACATAG
5369717 CATACATAACTTACACAACTTAAATAATACATAACTTACATAACTTACATAACCTACATAATA
1 CATACATAACTTA-ACAACTTAAATAATACATAACTTACATAACTTACATAACCTACATAATA
* * ** *
5369780 CATA-ATAACTT-ACAACTTACATAACATACATTACTTTGATAACTTACATAACTTACATAATA
1 CATACATAACTTAACAACTTAAAT-A-ATACATAACTTACATAACTTACATAACCTACATAATA
**
5369842 C--AC--AACTTAA-ATAGCTTACTTAATACATAACTTACATAACTTA
1 CATACATAACTTAACA-A-CTTAAATAATACATAACTTACATAACTTA
5369885 TACACGTACA
Statistics
Matches: 90, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
59 24 0.27
60 14 0.16
61 7 0.08
62 41 0.46
63 4 0.04
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (62 bp):
CATACATAACTTAACAACTTAAATAATACATAACTTACATAACTTACATAACCTACATAATA
Found at i:5369825 original size:87 final size:86
Alignment explanation
Indices: 5369707--5369871 Score: 197
Period size: 87 Copynumber: 1.9 Consensus size: 86
5369697 AATACACATT
* * *
5369707 ACTTACATAGCATACATAACTTACACAACTTAAATAA-TACATAACTTACATAACTTACATAACC
1 ACTTACATAACATACATAACTTACACAACTTAAATAACTACATAA--TACACAACTTAAATAACC
5369771 TACATAATACATAATAACTTACA
64 TACATAATACATAATAACTTACA
* ** * * * *
5369794 ACTTACATAACATACATTACTTTGATAACTTACATAACTTACATAATACACAACTTAAATAGCTT
1 ACTTACATAACATACATAACTTACACAACTTAAATAAC-TACATAATACACAACTTAAATAACCT
*
5369859 ACTTAATACATAA
65 ACATAATACATAA
5369872 CTTACATAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 58 0.89
89 7 0.11
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (86 bp):
ACTTACATAACATACATAACTTACACAACTTAAATAACTACATAATACACAACTTAAATAACCTA
CATAATACATAATAACTTACA
Found at i:5369843 original size:34 final size:33
Alignment explanation
Indices: 5369722--5369907 Score: 149
Period size: 34 Copynumber: 5.7 Consensus size: 33
5369712 CATAGCATAC
* *
5369722 ATAACTTACACAACTTAAATAATACATAACTTA
1 ATAACTTACATAACTTACATAATACATAACTTA
*
5369755 CATAACTTACATAACCTACATAATAC---A--TA
1 -ATAACTTACATAACTTACATAATACATAACTTA
* *
5369784 ATAACTTAC--AACTTACATAACATACATTACTTTG
1 ATAACTTACATAACTTACAT-A-ATACATAAC-TTA
*
5369818 ATAACTTACATAACTTACATAATACACAACTTAA
1 ATAACTTACATAACTTACATAATACATAACTT-A
* *
5369852 ATAGCTTACTTAA--TACATAACTTACATAACTT-
1 ATAACTTACATAACTTACATAA--TACATAACTTA
*
5369884 ATACACGTACATAACTTACATAAT
1 ATA-ACTTACATAACTTACATAAT
5369908 TGACTTAATA
Statistics
Matches: 122, Mismatches: 14, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
26 8 0.07
27 1 0.01
28 13 0.11
29 2 0.02
31 2 0.02
32 10 0.08
33 10 0.08
34 59 0.48
35 8 0.07
36 9 0.07
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (33 bp):
ATAACTTACATAACTTACATAATACATAACTTA
Found at i:5369859 original size:25 final size:25
Alignment explanation
Indices: 5369744--5369919 Score: 106
Period size: 25 Copynumber: 6.8 Consensus size: 25
5369734 ACTTAAATAA
* *
5369744 TACATAACTTACATAACTTACATAACC
1 TACATAACTTACATAA--TACACAACT
5369771 TACATAA--TACATAATAACTTACAACT
1 TACATAACTTACATAAT-AC--ACAACT
* * ** *
5369797 TACATAACATACATTACTTTGATAACT
1 TACATAACTTACA-TA-ATACACAACT
5369824 TACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * * *
5369849 TAAATAGCTTACTTAATACATAACT
1 TACATAACTTACATAATACACAACT
* * * *
5369874 TACATAACTTATACACGTACATAACT
1 TACATAACTTACATA-ATACACAACT
*
5369900 TACATAA-TTGACTTAATACA
1 TACATAACTT-ACATAATACA
5369920 TAAATATATA
Statistics
Matches: 115, Mismatches: 25, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 50 0.43
26 31 0.27
27 24 0.21
28 4 0.03
29 2 0.02
30 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:5375447 original size:21 final size:21
Alignment explanation
Indices: 5375421--5375470 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5375411 CTACAACTTA
*
5375421 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
5375442 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
5375463 AAGCAGAG
1 AAGCAGAG
5375471 CAGGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:5375953 original size:42 final size:41
Alignment explanation
Indices: 5375864--5376000 Score: 222
Period size: 42 Copynumber: 3.3 Consensus size: 41
5375854 TAAGAATAAA
*
5375864 CGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCTTTTTTTCTAAG
*
5375904 CGTCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTTTCTAAG
*
5375946 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTTTCTAAG
5375988 CGCCGCTAAAGAA
1 CGCCGCTAAAGAA
5376001 TTCTTTAGCG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 27 0.30
42 63 0.70
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCTTTTTTTCTAAG
Found at i:5376138 original size:21 final size:21
Alignment explanation
Indices: 5376095--5376138 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5376085 TTAGTGGCGT
* *
5376095 TAAAAAGCGCCGCTAAAGGCC
1 TAAAAAACGCCGCTAAAGACC
*
5376116 TAAAAAACGCCGCTAGAGACC
1 TAAAAAACGCCGCTAAAGACC
5376137 TA
1 TA
5376139 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAGACC
Found at i:5377746 original size:16 final size:15
Alignment explanation
Indices: 5377698--5377748 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
5377688 AGCATCACCA
*
5377698 ATCCTTATCGCTGCCC
1 ATCC-TATCGCTCCCC
*
5377714 ATCC-ATTGCTCCCCC
1 ATCCTATCGCT-CCCC
5377729 ATCTCTATCGCTCCCC
1 ATC-CTATCGCTCCCC
5377745 ATCC
1 ATCC
5377749 CACTGCCCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 12 0.41
17 5 0.17
ACGTcount: A:0.14, C:0.49, G:0.08, T:0.29
Consensus pattern (15 bp):
ATCCTATCGCTCCCC
Found at i:5378452 original size:19 final size:21
Alignment explanation
Indices: 5378418--5378458 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
5378408 CTCCAAATCC
5378418 TAATTTAAAGATTATTATGAA
1 TAATTTAAAGATTATTATGAA
5378439 TAATTT-AA-ATTATTATGAA
1 TAATTTAAAGATTATTATGAA
5378458 T
1 T
5378459 TTGACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATTTAAAGATTATTATGAA
Found at i:5380389 original size:77 final size:77
Alignment explanation
Indices: 5380262--5380415 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
5380252 CATTATAAAG
*
5380262 CGCTGGATCAAAATTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
5380327 ATCATGTAACAT
66 ATCATGTAACAT
5380339 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
*
5380404 CTCATGTAACAT
66 ATCATGTAACAT
5380416 GAGGGGGCGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (77 bp):
CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
ATCATGTAACAT
Found at i:5388615 original size:78 final size:78
Alignment explanation
Indices: 5388486--5388636 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
5388476 GTCGTGACTT
* *
5388486 GTAGGATATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAAGTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
5388551 AACTATGCAACTC
66 AACTATGCAACTC
* *
5388564 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAATTCATTGAACTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
5388629 AACTATGC
66 AACTATGC
5388637 CAGGAGTACT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (78 bp):
GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
AACTATGCAACTC
Found at i:5391503 original size:14 final size:14
Alignment explanation
Indices: 5391486--5391513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5391476 ATCAATAGTC
5391486 AAAGCTTAATACGA
1 AAAGCTTAATACGA
5391500 AAAGCTTAATACGA
1 AAAGCTTAATACGA
5391514 GGATATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAGCTTAATACGA
Found at i:5394112 original size:18 final size:18
Alignment explanation
Indices: 5394091--5394141 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5394081 ACAATTTATA
*
5394091 TATATACATATATATTTT
1 TATATACATATATATTTC
*
5394109 TATATAC-TTTATAATTTC
1 TATATACATATAT-ATTTC
*
5394127 CATATACATATATAT
1 TATATACATATATAT
5394142 ACATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATACATATATATTTC
Found at i:5394125 original size:38 final size:39
Alignment explanation
Indices: 5394052--5394152 Score: 105
Period size: 40 Copynumber: 2.6 Consensus size: 39
5394042 TCATAATTCG
* * *
5394052 TATACACATATATTTTTTATATATATTTTACAATTT-ATA
1 TATATACATATATATTTT-TATATACTTTACAATTTCATA
*
5394091 TATATACATATATATTTTTATATACTTTATAATTTCCATA
1 TATATACATATATATTTTTATATACTTTACAATTT-CATA
* * * *
5394131 TACATATATATACATATTTATA
1 TATATACATATATATTTTTATA
5394153 CTTTTTTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
38 15 0.29
39 16 0.31
40 21 0.40
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (39 bp):
TATATACATATATATTTTTATATACTTTACAATTTCATA
Found at i:5395771 original size:24 final size:23
Alignment explanation
Indices: 5395743--5395822 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
5395733 TATGTTATAA
5395743 AAATATTATATTAATTATATATTT
1 AAAT-TTATATTAATTATATATTT
5395767 AAA--TA-A-TAATTATATATTT
1 AAATTTATATTAATTATATATTT
*
5395786 ATATTTATATTTATATT-TATATTT
1 AAATTTATA-TTA-ATTATATATTT
*
5395810 ATATTTATATTAA
1 AAATTTATATTAA
5395823 ATCACGAACC
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
19 15 0.31
20 1 0.02
21 4 0.08
22 2 0.04
23 3 0.06
24 21 0.43
25 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTATATTAATTATATATTT
Found at i:5395790 original size:6 final size:6
Alignment explanation
Indices: 5395779--5395820 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
5395769 ATAATAATTA
5395779 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
5395821 AAATCACGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:5396886 original size:50 final size:50
Alignment explanation
Indices: 5396823--5396930 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
5396813 CCGAAATGAT
* ** * *
5396823 ATTTTTTTTATGGCGCCTATCTGAGAGGCGCCAATGTTTATTTTGTATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
*
5396873 ATTTTTTTAATGGCGCCTATCTGATAGGCGCCAATGAATATTATATATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
5396923 ATTTTTTT
1 ATTTTTTT
5396931 TCTTTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (50 bp):
ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
Found at i:5400208 original size:18 final size:18
Alignment explanation
Indices: 5400187--5400242 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
5400177 AAGGCAACAT
5400187 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
* *
5400205 AAATTAAA-AGA-AAAAA
1 AAATTAAATTGATAAATA
5400221 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
5400239 AAAT
1 AAAT
5400243 GCCAACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.38
17 4 0.12
18 16 0.50
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATTAAATTGATAAATA
Found at i:5400590 original size:18 final size:18
Alignment explanation
Indices: 5400569--5400603 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5400559 TGCCTCCAGG
5400569 TCCGGCTCTAACTCTGGC
1 TCCGGCTCTAACTCTGGC
*
5400587 TCCGGCTCTAGCTCTGG
1 TCCGGCTCTAACTCTGG
5400604 GTCTGGTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.37, G:0.26, T:0.29
Consensus pattern (18 bp):
TCCGGCTCTAACTCTGGC
Found at i:5402247 original size:15 final size:15
Alignment explanation
Indices: 5402229--5402268 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 15
5402219 TAAAAATCAA
5402229 ATAAAATTACATTAT
1 ATAAAATTACATTAT
5402244 ATAAAAATTACATTAT
1 AT-AAAATTACATTAT
5402260 ATAAAATTA
1 ATAAAATTA
5402269 AATGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:5402588 original size:57 final size:57
Alignment explanation
Indices: 5402507--5402625 Score: 170
Period size: 56 Copynumber: 2.1 Consensus size: 57
5402497 TAATATTTAT
*
5402507 TTAAACAAAAAATATTTTTAATATAAAAAATTAATTCGCGCCTGTTAGATAGGCGCGA
1 TTAAACAAAAAATATTTTTAATAT-AAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
* * *
5402565 TTAAA-AAAACAAT-TTTTTAATATAAAACTTTATTCGCGTCTGTCAGATAGGCGCGA
1 TTAAACAAAA-AATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
5402621 TTAAA
1 TTAAA
5402626 TTTTTTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
56 34 0.61
57 14 0.25
58 8 0.14
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (57 bp):
TTAAACAAAAAATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
Found at i:5403024 original size:60 final size:60
Alignment explanation
Indices: 5402931--5403049 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
5402921 ATACTAAACT
* * * *
5402931 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAAATAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
*
5402991 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTA
5403050 TTAAAAGCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
Found at i:5403247 original size:17 final size:16
Alignment explanation
Indices: 5403217--5403250 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5403207 ACATTACCTT
5403217 TTTTTATTCTTTCTTC
1 TTTTTATTCTTTCTTC
*
5403233 TTTTTCTTCTCTTCTTC
1 TTTTTATTCT-TTCTTC
5403250 T
1 T
5403251 CCTTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTCTTTCTTC
Found at i:5406596 original size:42 final size:43
Alignment explanation
Indices: 5406489--5406647 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 43
5406479 TCTCGTACAT
* * * * *
5406489 TGCCAACGTCCCAGACGTGGTCTTACATG-TAT-TCAAATAACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAAT--CGA
* * * *
5406532 TGCCACTGTCCCAGACAGGGTCTTACACGAAAT-T-ATATACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAAT-CGA
* *
5406574 TGTCGATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCGA
1 TGCCAATGTCCCAAACATGGTCTTACACG-AAATCTCAAATCGA
*
5406618 TGCCAACGTCCCAAA-AGTGGTCTTACACGA
1 TGCCAATGTCCCAAACA-TGGTCTTACACGA
5406648 TATCACATAT
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.29
43 33 0.35
44 31 0.33
45 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAATCGA
Found at i:5407871 original size:16 final size:16
Alignment explanation
Indices: 5407834--5407873 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5407824 TTAATAAAAT
* *
5407834 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5407850 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5407866 TAAAATTA
1 TAAAATTA
5407874 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5407873 original size:22 final size:22
Alignment explanation
Indices: 5407802--5407858 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
5407792 AGGCCCGTTT
* * * *
5407802 TTAATTAAATTAAAATTATTTT
1 TTAATAAAATTAAAACTAATTG
5407824 TTAATAAAATTAAAACTAATTG
1 TTAATAAAATTAAAACTAATTG
*
5407846 TTATTAAAATTAA
1 TTAATAAAATTAA
5407859 TTGTTAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATAAAATTAAAACTAATTG
Found at i:5407905 original size:59 final size:67
Alignment explanation
Indices: 5407866--5408023 Score: 217
Period size: 59 Copynumber: 2.5 Consensus size: 67
5407856 TAATTGTTAG
5407866 TAAAATTATCAAATTATTAATTG-TTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
1 TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
5407930 AA
66 AA
*
5407932 TAAATTTATCAAATTATTAATTG--T-A---T--TAATTGTTGTAATAAAATCTAACATTTGATT
1 TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
*
5407989 AG
66 AA
*
5407991 TAAATTTATCAAATTATTAATTGTATTAATTGT
1 TAAAATTATCAAATTATTAATTG-ATTAATTGT
5408024 TGTAACAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
59 55 0.66
61 1 0.01
62 1 0.01
63 1 0.01
64 1 0.01
65 1 0.01
66 23 0.28
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (67 bp):
TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
AA
Found at i:5408024 original size:59 final size:59
Alignment explanation
Indices: 5407884--5408053 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
5407874 TCAAATTATT
* * *
5407884 AATTGTTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATTAATAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
5407943 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
5408002 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
5408054 ACAAACTTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 107 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:5409136 original size:43 final size:43
Alignment explanation
Indices: 5409075--5409275 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
5409065 ATGTTCCAAT
5409075 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
5409118 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGTTATTGG-
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
5409160 AGTCAATCTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 A-TCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* ***
5409204 ATCGATTTGAGATTTCGTGTAAAACCATAGCTAAACTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
** *
5409247 ATCGATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
5409276 GTTTGGGACA
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 126 0.91
44 12 0.09
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:5421901 original size:15 final size:17
Alignment explanation
Indices: 5421876--5421907 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5421866 AATTATTAAA
5421876 AAAACTTAT-AAATTTT
1 AAAACTTATAAAATTTT
5421892 AAAA-TTATAAAATTTT
1 AAAACTTATAAAATTTT
5421908 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAACTTATAAAATTTT
Found at i:5422051 original size:44 final size:46
Alignment explanation
Indices: 5422003--5422092 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 46
5421993 ATATTGTTAT
* *
5422003 TTTTAATAAAAATT-TTTGTAATTT-TGTAATTTTTAA-AACTTTTA
1 TTTT-ATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
* *
5422047 TTTTATAAAATTTGTTTATAATTTCTATGATTTTTAATAACTTTTA
1 TTTTATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
5422093 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 8 0.21
44 13 0.33
45 10 0.26
46 8 0.21
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.58
Consensus pattern (46 bp):
TTTTATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
Found at i:5431635 original size:16 final size:16
Alignment explanation
Indices: 5431606--5431656 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5431596 TTTTGGCATC
*
5431606 TAAAAATTTAAAACTTA
1 TAAAAATAT-AAACTTA
5431623 TAAAAATATAAAC-TA
1 TAAAAATATAAACTTA
* *
5431638 TTAAAATAATAAAATTA
1 TAAAAAT-ATAAACTTA
5431655 TA
1 TA
5431657 TTTTTACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.29
16 9 0.32
17 11 0.39
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATATAAACTTA
Found at i:5438108 original size:21 final size:21
Alignment explanation
Indices: 5438083--5438123 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5438073 ACAGAAAAAT
5438083 GTCATATCGTCAAAGAGGGAG
1 GTCATATCGTCAAAGAGGGAG
*
5438104 GTCATATTGTCAAAGAGGGA
1 GTCATATCGTCAAAGAGGGA
5438124 ATAATCGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (21 bp):
GTCATATCGTCAAAGAGGGAG
Found at i:5438782 original size:31 final size:30
Alignment explanation
Indices: 5438748--5438808 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
5438738 AAAAGTCTTT
5438748 TTTTTTTAA--ATTTACCGAAATGGGCCAC
1 TTTTTTTAATTATTTACCGAAATGGGCCAC
*
5438776 TTTTTTTAATTATTTACCGGAATGGGCCA-
1 TTTTTTTAATTATTTACCGAAATGGGCCAC
5438805 TTTT
1 TTTT
5438809 CCGTGAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.30
29 4 0.13
30 17 0.57
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (30 bp):
TTTTTTTAATTATTTACCGAAATGGGCCAC
Found at i:5439575 original size:29 final size:29
Alignment explanation
Indices: 5439512--5439568 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5439502 TTGAAAATAT
*
5439512 TAAAATTA-TTAAAATTATTTTTAAAAAA
1 TAAAAATATTTAAAATTATTTTTAAAAAA
5439540 TAAAAATATTTAAAATT-TTCTTTAAAAAA
1 TAAAAATATTTAAAATTATT-TTTAAAAAA
5439569 ATGAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATATTTAAAATTATTTTTAAAAAA
Found at i:5439629 original size:22 final size:22
Alignment explanation
Indices: 5439604--5439706 Score: 91
Period size: 22 Copynumber: 4.4 Consensus size: 22
5439594 TAATATGGAT
*
5439604 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGATTTTTGGAAGGAAA
5439626 TTGAGAGGA-TTTTGGAAGGAATTTGAGA
1 TTGAGA-GATTTTTGGAAGG-A----A-A
* *
5439654 GTTAAGAGAATTTTGGAAGGAAA
1 -TTGAGAGATTTTTGGAAGGAAA
*
5439677 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGATTTTTGGAAGGAAA
5439699 TTGAGAGA
1 TTGAGAGA
5439707 ATATTTGTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
22 44 0.64
23 4 0.06
24 1 0.01
27 1 0.01
28 4 0.06
29 15 0.22
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTGAGAGATTTTTGGAAGGAAA
Found at i:5439662 original size:51 final size:51
Alignment explanation
Indices: 5439607--5439705 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
5439597 TATGGATTTG
* * * *
5439607 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTA
5439658 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
5439706 AATATTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (51 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTA
Found at i:5439722 original size:24 final size:22
Alignment explanation
Indices: 5439658--5439713 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
5439648 TTGAGAGTTA
5439658 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
5439680 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
5439702 AGAGAATATTTG
1 AGAGAAT-TTTG
5439714 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:5440487 original size:26 final size:26
Alignment explanation
Indices: 5440458--5440510 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5440448 GATGACATGG
5440458 TACTTTTATAATTTATGTTTATTTAA
1 TACTTTTATAATTTATGTTTATTTAA
5440484 TACTTTTATAATTTATGTTTATTTAA
1 TACTTTTATAATTTATGTTTATTTAA
5440510 T
1 T
5440511 TAAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TACTTTTATAATTTATGTTTATTTAA
Found at i:5444432 original size:25 final size:26
Alignment explanation
Indices: 5444404--5444457 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
5444394 AGAGCTTGCA
*
5444404 TAATTATACATT-ATCAAAATTCATG
1 TAATTACACATTAATCAAAATTCATG
* *
5444429 TAATTACATATTAAATCAAAATTTATG
1 TAATTACACATT-AATCAAAATTCATG
5444456 TA
1 TA
5444458 CCCAAAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
27 14 0.58
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (26 bp):
TAATTACACATTAATCAAAATTCATG
Found at i:5446965 original size:7 final size:7
Alignment explanation
Indices: 5446953--5446977 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5446943 AAATAAATTA
5446953 ACTTTTC
1 ACTTTTC
5446960 ACTTTTC
1 ACTTTTC
5446967 ACTTTTC
1 ACTTTTC
5446974 ACTT
1 ACTT
5446978 GATGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
ACTTTTC
Found at i:5448541 original size:23 final size:23
Alignment explanation
Indices: 5448495--5448538 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5448485 CCAACTAAAC
*
5448495 TAAACCATAATATATATTTATTA
1 TAAACCATAATATAAATTTATTA
*
5448518 TAAATCATAATA-AAATTTATT
1 TAAACCATAATATAAATTTATT
5448539 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAACCATAATATAAATTTATTA
Found at i:5453311 original size:12 final size:14
Alignment explanation
Indices: 5453284--5453315 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
5453274 GTTTTGGAAG
5453284 AATAAAAGTCAAAA
1 AATAAAAGTCAAAA
5453298 AATAAAA-T-AAAA
1 AATAAAAGTCAAAA
5453310 AATAAA
1 AATAAA
5453316 GTAATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (14 bp):
AATAAAAGTCAAAA
Found at i:5456016 original size:36 final size:36
Alignment explanation
Indices: 5455951--5456549 Score: 550
Period size: 37 Copynumber: 16.4 Consensus size: 36
5455941 AAAAATGGAA
*
5455951 TACTGATTCTATTG-AAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
5455986 TACTGATACTATTGAAAGTGCTCAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * **
5456022 TACTGATCCTACTGAATGAGCTCAA-ATGAGCAATGCC
1 TACTGATTCTACTGAAAGTGCTCAACA--AGCAATATC
* * *
5456059 TATTGGTTCTACTGAAAGTGCTCAAACAAGCAATACC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* *
5456096 TACTGATACTACTGAAAGTGCTCAAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * * * *
5456133 TATTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * *
5456170 TACTTATTTTACTGAAAGTGCTCAAACGAGC---ATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * * *
5456204 TACTGATCCTACTAAAAGTGCTCAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* *
5456240 TACTGATTCTACTGAAAGTGCTAAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCT-CAACAAGCAATATC
* * *
5456277 TACT-AGTTCTATTGGAAGTGCTCAACGAGCAATATC
1 TACTGA-TTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
5456313 TATTGGTCCTACTGAAAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
5456349 TACTAATCCTACT-AAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAA-GTGCTC-AACAAGCAATATC
* *
5456386 TACTAATTCTACTG-AAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * *
5456422 TACTAATTCTACTGAAAGTGGTCAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
5456458 TACT-AGTCCTACTGAATGTGCTCAAACAAGTAATGTC
1 TACTGA-TTCTACTGAAAGTGCTC-AACAAGCAATATC
*
5456495 TACTGATTCTACTAAATAGTTGCTCAAACAAGCAATATC
1 TACTGATTCTACTGAA-AG-TGCTC-AACAAGCAATATC
*
5456534 TACTGATTTTACTGAA
1 TACTGATTCTACTGAA
5456550 TAGTTACTCA
Statistics
Matches: 474, Mismatches: 70, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.01
34 21 0.04
35 18 0.04
36 186 0.39
37 206 0.43
38 4 0.01
39 32 0.07
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (36 bp):
TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
Found at i:5456361 original size:109 final size:110
Alignment explanation
Indices: 5455964--5456549 Score: 686
Period size: 109 Copynumber: 5.4 Consensus size: 110
5455954 TGATTCTATT
* * *
5455964 GAAGTGCTC-AACAAGCAATATCTACTGATACTATTGAAAGTGCTCAATAAGCAATATCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
5456028 TCCTACTGAATGAGCTCAAATGAGCAATGCCTATTGGTTCTACTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * * *
5456073 AAAGTGCTCAAACAAGCAATACCTACTGATACTACTGAAAGTGCTCAAATAAGCAATATCTATTG
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTC-AACAAGCAATATCTACTG
*
5456138 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTACTTA-TTTTACTG
65 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTAC-TAGTTCTACTG
* * * * *
5456184 AAAGTGCTCAAACGAGC---ATCTACTGATCCTACTAAAAGTGCTCAACGAGCAATGTCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
5456246 TTCTACTGAAAGTGCTAAAACGAGCAATATCTACTAGTTCTATTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * *
5456291 GAAGTGCTC-AACGAGCAATATCTATTGGTCCTACTGAAAGTGCTCAACAAGCAATATCTACTAA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* *
5456355 TCCTACTAAATGTGCTCAAACGAGCAATGTCTACTAATTCTACT-
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * *
5456399 GAAGTGCTCAAACGAGCAATATCTACTAATTCTACTGAAAGTGGTCAACGAGCAATATCTACT-A
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * *
5456463 GTCCTACTGAATGTGCTCAAACAAGTAATGTCTACT-GATTCTACTA
66 -TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAG-TTCTACTG
* * **
5456509 AATAGTTGCTCAAACAAGCAATATCTACTGATTTTACTGAA
1 GA-AG-TGCTCAAACGAGCAATATCTACTGATACTACTGAA
5456550 TAGTTACTCA
Statistics
Matches: 412, Mismatches: 52, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
106 9 0.02
107 59 0.14
108 33 0.08
109 170 0.41
110 35 0.08
111 73 0.18
112 33 0.08
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (110 bp):
GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
Found at i:5456580 original size:39 final size:39
Alignment explanation
Indices: 5455968--5456629 Score: 273
Period size: 37 Copynumber: 17.9 Consensus size: 39
5455958 TCTATTGAAG
* * *
5455968 TGCTC-AACAAGCAATATCTACTGA-TACTATTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTA-TACTGAATAGT
* **
5456004 TGCTCAATA--AGCAATATCTACTGATCCTACTGAAT-G-
1 TGCTCAA-ACGAGCAATATCCACTGATTATACTGAATAGT
* * * * * *
5456040 AGCTCAAATGAGCAAT-GCCTATTGGTTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCC-ACTGATTATACTGAATAGT
*
5456077 TGCTCAAACAAGCAATA-CCTACTGA-TACTACTGAA-AG-
1 TGCTCAAACGAGCAATATCC-ACTGATTA-TACTGAATAGT
** * * **
5456114 TGCTCAAATAAGCAATATCTATTGATCCTACTGAAT-G-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * *
5456151 TGCTCAAACGAGCAATGTCTACTTATTTTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* ** *
5456188 TGCTCAAACGAGC---ATCTACTGATCCTACT-AAAAG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
5456222 TGCTC-AACGAGCAATGTCTACTGATTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * * *
5456258 TGCTAAAACGAGCAATATCTACT-AGTTCTATTGGA-AG-
1 TGCTCAAACGAGCAATATCCACTGA-TTATACTGAATAGT
* * * **
5456295 TGCTC-AACGAGCAATATCTATTGGTCCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * ** *
5456331 TGCTC-AACAAGCAATATCTACTAATCCTACTAAAT-G-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * *
5456367 TGCTCAAACGAGCAATGTCTACTAATTCTACTG-A-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
5456403 TGCTCAAACGAGCAATATCTACTAATTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * **
5456440 TGGTC-AACGAGCAATATCTACT-AGTCCTACTGAAT-G-
1 TGCTCAAACGAGCAATATCCACTGA-TTATACTGAATAGT
* * * * * *
5456476 TGCTCAAACAAGTAATGTCTACTGATTCTACTAAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
5456515 TGCTCAAACAAGCAATATCTACTGATTTTACTGAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * * *
5456554 TACTCAAACGAGAAATATCCATTGATTATAATGAAT-GCG
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAG-T
* *
5456593 TGCTCAAACGAGCATTATCCACTGATTATACTCAATA
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATA
5456630 AGATTTTCTG
Statistics
Matches: 513, Mismatches: 79, Indels: 64
0.78 0.12 0.10
Matches are distributed among these distances:
33 9 0.02
34 19 0.04
35 2 0.00
36 181 0.35
37 203 0.40
38 5 0.01
39 94 0.18
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (39 bp):
TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
Found at i:5459113 original size:5 final size:5
Alignment explanation
Indices: 5459103--5459173 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
5459093 GTGTTAAAAA
* *
5459103 ATATT ATATT ATAGTA ATGATT ATGTTTT ATATT ATATT ATCATT A-A-T
1 ATATT ATATT ATA-TT AT-ATT AT-AT-T ATATT ATATT AT-ATT ATATT
5459151 ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATAT
5459174 ACATAAAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
3 2 0.04
4 6 0.11
5 30 0.55
6 13 0.24
7 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:5459153 original size:19 final size:19
Alignment explanation
Indices: 5459131--5459173 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5459121 GATTATGTTT
5459131 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
5459150 TATATTATATTATATTATA
1 TATATTATATTATATTATA
5459169 TATAT
1 TATAT
5459174 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:5459157 original size:24 final size:23
Alignment explanation
Indices: 5459103--5459174 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
5459093 GTGTTAAAAA
* *
5459103 ATATTATATTATAGTAATGATTAT
1 ATATTATATTATA-TTATCATTAT
* *
5459127 GTTTTATATTATATTATCATTAAT
1 ATATTATATTATATTATCATT-AT
5459151 ATATTATATTATATTAT-A-TAT
1 ATATTATATTATATTATCATTAT
5459172 ATA
1 ATA
5459175 CATAAAACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 5 0.12
22 1 0.02
23 7 0.17
24 28 0.68
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATTATATTATATTATCATTAT
Found at i:5464134 original size:5 final size:5
Alignment explanation
Indices: 5464124--5464195 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
5464114 TGTTAAAAAA
* *
5464124 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
5464170 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
5464196 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:5464177 original size:19 final size:19
Alignment explanation
Indices: 5464153--5464195 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5464143 ATTATGTTTT
5464153 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
5464172 TATATTATATTATATTATA
1 TATATTATATTATATTATA
5464191 TATAT
1 TATAT
5464196 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:5469159 original size:5 final size:5
Alignment explanation
Indices: 5469149--5469220 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
5469139 TGTTAAAAAA
* *
5469149 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
5469195 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
5469221 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:5469202 original size:19 final size:19
Alignment explanation
Indices: 5469178--5469220 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5469168 ATTATGTTTT
5469178 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
5469197 TATATTATATTATATTATA
1 TATATTATATTATATTATA
5469216 TATAT
1 TATAT
5469221 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:5474181 original size:5 final size:5
Alignment explanation
Indices: 5474171--5474242 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
5474161 TGTTAAAAAA
* *
5474171 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
5474217 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
5474243 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:5474224 original size:19 final size:19
Alignment explanation
Indices: 5474200--5474242 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5474190 ATTATGTTTT
5474200 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
5474219 TATATTATATTATATTATA
1 TATATTATATTATATTATA
5474238 TATAT
1 TATAT
5474243 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:5478770 original size:21 final size:21
Alignment explanation
Indices: 5478744--5478784 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5478734 TTACAACCAA
* *
5478744 TACGAATAATAGTATAAAAAT
1 TACGAACAATAGTAAAAAAAT
*
5478765 TACGAACATTAGTAAAAAAA
1 TACGAACAATAGTAAAAAAA
5478785 ATTATTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (21 bp):
TACGAACAATAGTAAAAAAAT
Found at i:5479632 original size:31 final size:29
Alignment explanation
Indices: 5479574--5479636 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
5479564 AATTTTAACG
*
5479574 ATGAACAAAGAAAGAAATTAAGAACCAATA
1 ATGAACAAAGAAAGAAAATAAGAACCAA-A
5479604 ATGAACTAAAGAAAGAAAATAATG-ACCAAA
1 ATGAAC-AAAGAAAGAAAATAA-GAACCAAA
5479634 ATG
1 ATG
5479637 TGAATTAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 19 0.63
32 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (29 bp):
ATGAACAAAGAAAGAAAATAAGAACCAAA
Found at i:5480911 original size:59 final size:59
Alignment explanation
Indices: 5480819--5480939 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
5480809 ACTTAGGCCC
5480819 CAAAATGTTTCACAATATGCCACAACATACTTTTTAAATCAACTTCCTTTCACATCCAT
1 CAAAATGTTTCACAATATGCCACAACATACTTTTTAAATCAACTTCCTTTCACATCCAT
5480878 CAAAATGTTTCACAATATGCCACAACATACTTTTTAAATCAACTTCCTTTCACATCCAT
1 CAAAATGTTTCACAATATGCCACAACATACTTTTTAAATCAACTTCCTTTCACATCCAT
5480937 CAA
1 CAA
5480940 TCTTCTCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (59 bp):
CAAAATGTTTCACAATATGCCACAACATACTTTTTAAATCAACTTCCTTTCACATCCAT
Found at i:5497030 original size:105 final size:106
Alignment explanation
Indices: 5496854--5497053 Score: 384
Period size: 105 Copynumber: 1.9 Consensus size: 106
5496844 AAGCTTTAAG
*
5496854 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGTACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
5496919 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
5496960 AGGATATTTGGCTATTTAGTCGAACGAGAAATC-AAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
5497024 TTTTCCAAACGCGAAATATTGCCTTATTTA
66 TTTTCCAAACGCGAAATATTGCCTTATTTA
5497054 GAAAATTTTC
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 60 0.65
106 33 0.35
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (106 bp):
AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
Found at i:5497573 original size:38 final size:38
Alignment explanation
Indices: 5497514--5497619 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
5497504 TATTTTTAAG
*
5497514 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
5497551 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
5497589 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
5497620 TGTCACGGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:5498153 original size:48 final size:48
Alignment explanation
Indices: 5498080--5498173 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
5498070 AGGGAATTCT
* * *
5498080 GTTGAATCCTTTATTGTTGCGAGTTGAGATGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGATGACTTAAGCGTTTTTACG
* *
5498128 GTTGAATCCATTATTGGTG-GAAGTTGGGCTGACTTAAGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGAGATGACTTAAGCGTTTTTA
5498174 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGATGACTTAAGCGTTTTTACG
Found at i:5500670 original size:48 final size:48
Alignment explanation
Indices: 5500591--5500684 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
5500581 AGGGAATTCT
* *
5500591 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
5500639 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
5500685 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:5501088 original size:22 final size:23
Alignment explanation
Indices: 5501032--5501088 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
5501022 ATTTTAAAAT
5501032 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
5501055 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
5501076 AAAATATATAAAA
1 AAAATATATAAAA
5501089 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:5501819 original size:13 final size:13
Alignment explanation
Indices: 5501801--5501825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5501791 AAATGCGTAG
5501801 ATAAATAAATGAA
1 ATAAATAAATGAA
5501814 ATAAATAAATGA
1 ATAAATAAATGA
5501826 TAGATGATAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:5504498 original size:21 final size:20
Alignment explanation
Indices: 5504465--5504503 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5504455 TTGTGCAGCA
*
5504465 AGTTTTGCTGATGTTGCTTG
1 AGTTTTGCTGATGGTGCTTG
*
5504485 AGTTTCTGGTGATGGTGCT
1 AGTTT-TGCTGATGGTGCT
5504504 GATACCACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.46
Consensus pattern (20 bp):
AGTTTTGCTGATGGTGCTTG
Found at i:5506047 original size:30 final size:30
Alignment explanation
Indices: 5506011--5506069 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5506001 AGATATAAAA
*
5506011 TAACACAAACACAATATTAATATACAAATT
1 TAACACAAACAAAATATTAATATACAAATT
*
5506041 TAACACAAACAAAATGTTAATATACAAAT
1 TAACACAAACAAAATATTAATATACAAAT
5506070 CTAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
TAACACAAACAAAATATTAATATACAAATT
Found at i:5506829 original size:27 final size:29
Alignment explanation
Indices: 5506798--5506853 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
5506788 TCTCCTGCTA
*
5506798 GTTAGGGTTTT-GGGTTTTT-GGTTTAAG
1 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
5506825 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
1 GTTAGGGTTTTAGGATTTTTAGGTTTAAG
5506854 ATTTTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 11 0.42
28 7 0.27
29 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (29 bp):
GTTAGGGTTTTAGGATTTTTAGGTTTAAG
Found at i:5507085 original size:95 final size:96
Alignment explanation
Indices: 5506934--5507179 Score: 286
Period size: 96 Copynumber: 2.6 Consensus size: 96
5506924 TTCAAAATTG
* * *
5506934 GATTA-GGTTTCGTGTTTATGGTTTTTAAAGAAAAA-AATCAATTAAATT-AGGGTTAGGGTTAC
1 GATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAATAA--AA-TAAATTAAGGTTTAGGGTTAC
5506996 TTGAGTAAATTAATTA-AA-AAAAATAAAAAATCA
63 TTGAGTAAATTAATTATAATAAAAATAAAAAAT-A
* * *
5507029 TATTAGGGTTTAGTGTTAAGGGTTTTTAAGGAAAAATAAAATAAATTAAGGTTTAGGGTTACTTG
1 GATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAATAAAATAAATTAAGGTTTAGGGTTACTTG
***** *
5507094 AGTAAATTAATTATAATTTTTTTTAAAAATA
66 AGTAAATTAATTATAATAAAAATAAAAAATA
* *
5507125 GATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAACTCAAATAAATTACGGTTT
1 GATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAA-TAAAATAAATTAAGGTTT
5507180 GGAGTTTAGG
Statistics
Matches: 128, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
94 6 0.05
95 35 0.27
96 62 0.48
97 25 0.20
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38
Consensus pattern (96 bp):
GATTAGGGTTTAGTGTTTAGGGTTTTTAAAGAAAAATAAAATAAATTAAGGTTTAGGGTTACTTG
AGTAAATTAATTATAATAAAAATAAAAAATA
Found at i:5507454 original size:20 final size:20
Alignment explanation
Indices: 5507429--5507482 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5507419 CCTGATCAGT
*
5507429 AAACGACACATAAGTGCTTG
1 AAACGACACATAAGTGCCTG
* *
5507449 AAACGACACACGAGGTGCCTG
1 AAACGACACA-TAAGTGCCTG
*
5507470 ATACGACACATAA
1 AAACGACACATAA
5507483 AGTGTCTGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
AAACGACACATAAGTGCCTG
Found at i:5507491 original size:21 final size:19
Alignment explanation
Indices: 5507431--5507492 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 19
5507421 TGATCAGTAA
*
5507431 ACGACACATAAGTGCTTGAA
1 ACGACACATAAGTGC-TGAT
* *
5507451 ACGACACACGAGGTGCCTGAT
1 ACGACACA-TAAGTG-CTGAT
5507472 ACGACACATAAAGTGTCTGAT
1 ACGACACAT-AAGTG-CTGAT
5507493 CGGCAAAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 8 0.24
21 24 0.73
22 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (19 bp):
ACGACACATAAGTGCTGAT
Found at i:5508582 original size:12 final size:12
Alignment explanation
Indices: 5508565--5508596 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5508555 ATAATAATAT
5508565 AATATAATTTAC
1 AATATAATTTAC
5508577 AATATAATTTAC
1 AATATAATTTAC
5508589 AATATAAT
1 AATATAAT
5508597 AAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATAATTTAC
Found at i:5510535 original size:12 final size:11
Alignment explanation
Indices: 5510498--5510549 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
5510488 GCTTTTTTTA
*
5510498 AGAGGAATTTG
1 AGAGAAATTTG
*
5510509 AGATG-AATTTA
1 AGA-GAAATTTG
5510520 AGAGAATATTTG
1 AGAGAA-ATTTG
5510532 AGAGAAA-TTG
1 AGAGAAATTTG
5510542 AGAGAAAT
1 AGAGAAAT
5510550 GATTTAGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 11 0.31
11 13 0.37
12 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:5510972 original size:22 final size:23
Alignment explanation
Indices: 5510947--5510993 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5510937 TTAAAGCTTT
* *
5510947 TTTAAGAGGA-ATTTGAGAGGAA
1 TTTAAGAGAATATTTGAGAGAAA
5510969 TTTAAGAGAATATTTGAGAGAAA
1 TTTAAGAGAATATTTGAGAGAAA
5510992 TT
1 TT
5510994 GAGAGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.32
Consensus pattern (23 bp):
TTTAAGAGAATATTTGAGAGAAA
Found at i:5510987 original size:23 final size:22
Alignment explanation
Indices: 5510947--5511002 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5510937 TTAAAGCTTT
* *
5510947 TTTAAGAGGAATTTGAGAGGAA
1 TTTAAGAGAAATTTGAGAGAAA
5510969 TTTAAGAGAATATTTGAGAGAAA
1 TTTAAGAGAA-ATTTGAGAGAAA
*
5510992 -TTGAGAGAAAT
1 TTTAAGAGAAAT
5511003 GATTTAGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 17 0.57
23 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.29
Consensus pattern (22 bp):
TTTAAGAGAAATTTGAGAGAAA
Found at i:5510988 original size:12 final size:11
Alignment explanation
Indices: 5510951--5511002 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
5510941 AGCTTTTTTA
*
5510951 AGAGGAATTTG
1 AGAGAAATTTG
* *
5510962 AGAGGAATTTA
1 AGAGAAATTTG
5510973 AGAGAATATTTG
1 AGAGAA-ATTTG
5510985 AGAGAAA-TTG
1 AGAGAAATTTG
5510995 AGAGAAAT
1 AGAGAAAT
5511003 GATTTAGGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.28
11 16 0.44
12 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:5511049 original size:454 final size:450
Alignment explanation
Indices: 5510204--5511111 Score: 1676
Period size: 454 Copynumber: 2.0 Consensus size: 450
5510194 CGGTGATGGA
5510204 GGACCATGCATATTACGGATATAACATTGCAATATCCGATCTACAGACTTTTATAAGAAATAATA
1 GGACCATGCATATTACGGATATAACATTGCAATATCCGATCTACAGACTTTTATAAGAAATAATA
5510269 AAATAAAAATTATTTAAAATTACATAAATAAAAAAAATCTTAAATAATATTTAAAAATTAAATTT
66 AAATAAAAATTATTTAAAATTACATAAATAAAAAAAATCTTAAATAATATTTAAAAATTAAATTT
5510334 AACACTTACCATTTTCATTTGTTCGACTAATATGTGCTTGTTATCGAGACGAATTAATTCTCCGG
131 AACACTTACCATTTTCATTTGTTCGACTAATATGTGCTTGTTATCGAGACGAATTAATTCTCCGG
5510399 CCATTGCTAACATGAGCAAATTTTTATGATTTAAAAAAATCAAAAAAAAATAAAATTAAAGATTT
196 CCATTGCTAACATGAGCAAATTTTTATGATTTAAAAAAATC-AAAAAAAATAAAATTAAAGATTT
*
5510464 TTTTAAAATAATTAAAAAATTAAAGCTTTTTTTAAGAGGAATTTGAGATGAATTTAAGAGAATAT
260 TTTTAAAATAATTAAAAAATTAAAGCTTTTTTTAAGAGGAATTTGAGAGGAATTTAAGAGAATAT
5510529 TTGAGAGAAATTGAGAGAAATGATTTAGGTGTGAAAAAAATGAAATGGGGGTTTTTATAGTTTTT
325 TTGAGAGAAATTGAGAGAAATGATTTAGGTGTGAAAAAAATGAAATGGGGGTTTTTATAGTTTTT
*
5510594 TTTTTACCGTTGGGGGGGTTACCAACGGTCAAAAAAGTAACCGTTGCTACTGTTCACGTGCG
390 TTTTTACCGTT-GGGGGGTTACCAACGGTCAAAAAAGTAACCGTTGCTACTGTTCACGCGCG
*
5510656 GGACCATGTATATTACGGATATAACATTGCAATATCCGATCTACAGACTTTTATAAGAAATAATA
1 GGACCATGCATATTACGGATATAACATTGCAATATCCGATCTACAGACTTTTATAAGAAATAATA
*
5510721 AAATAAAAATTATTTAAAATTGCATAAATCAAAAAAAAATCTTAAATAATATTTAAAAATTAAAT
66 AAATAAAAATTATTTAAAATTACATAAAT--AAAAAAAATCTTAAATAATATTTAAAAATTAAAT
*
5510786 TTAACACTTACCATTTTCATTTGTTTGACTAATATGTGCTTGTTATCGAGACGAATTAATTCTCC
129 TTAACACTTACCATTTTCATTTGTTCGACTAATATGTGCTTGTTATCGAGACGAATTAATTCTCC
*
5510851 GGCCATTGCTAACATGAGCAAATTTTTATGATTTAAAAAAAATTC-AAAAAAATAAAATTAAAGC
194 GGCCATTGCTAACATGAGCAAATTTTTATGATTT-AAAAAAA-TCAAAAAAAATAAAATTAAAGA
5510915 TTTTTTTAAAATAATTAAAAAATTAAAGC-TTTTTTAAGAGGAATTTGAGAGGAATTTAAGAGAA
257 TTTTTTTAAAATAATTAAAAAATTAAAGCTTTTTTTAAGAGGAATTTGAGAGGAATTTAAGAGAA
5510979 TATTTGAGAGAAATTGAGAGAAATGATTTAGGTGTGAAAAAAATGAAATGGGGGTTTTTATAGTT
322 TATTTGAGAGAAATTGAGAGAAATGATTTAGGTGTGAAAAAAATGAAATGGGGGTTTTTATAG-T
*
5511044 TTTTTTTTTACCGTTGGGGGGTTACCAACGGTCAAAAAAGTAACCGTTGCTATTGTTCACGCGCG
386 TTTTTTTTTACCGTTGGGGGGTTACCAACGGTCAAAAAAGTAACCGTTGCTACTGTTCACGCGCG
5511109 GGA
1 GGA
5511112 AAATCGCTTC
Statistics
Matches: 444, Mismatches: 7, Indels: 9
0.97 0.02 0.02
Matches are distributed among these distances:
452 92 0.21
453 148 0.33
454 195 0.44
455 7 0.02
456 2 0.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (450 bp):
GGACCATGCATATTACGGATATAACATTGCAATATCCGATCTACAGACTTTTATAAGAAATAATA
AAATAAAAATTATTTAAAATTACATAAATAAAAAAAATCTTAAATAATATTTAAAAATTAAATTT
AACACTTACCATTTTCATTTGTTCGACTAATATGTGCTTGTTATCGAGACGAATTAATTCTCCGG
CCATTGCTAACATGAGCAAATTTTTATGATTTAAAAAAATCAAAAAAAATAAAATTAAAGATTTT
TTTAAAATAATTAAAAAATTAAAGCTTTTTTTAAGAGGAATTTGAGAGGAATTTAAGAGAATATT
TGAGAGAAATTGAGAGAAATGATTTAGGTGTGAAAAAAATGAAATGGGGGTTTTTATAGTTTTTT
TTTTACCGTTGGGGGGTTACCAACGGTCAAAAAAGTAACCGTTGCTACTGTTCACGCGCG
Found at i:5511326 original size:21 final size:21
Alignment explanation
Indices: 5511302--5511349 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5511292 AGGCTGAGAT
*
5511302 TATTTTGAGTGAT-TTTATAAA
1 TATTTTGA-TGATAATTATAAA
*
5511323 TATTTTGATTATAATTATAAA
1 TATTTTGATGATAATTATAAA
5511344 TATTTT
1 TATTTT
5511350 TAGGGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTTTGATGATAATTATAAA
Found at i:5511408 original size:31 final size:29
Alignment explanation
Indices: 5511373--5511438 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
5511363 CAAAATTATG
*
5511373 CATGAACTATGGTTTAATGTGCAATTGTATA
1 CATGAACTATGATTT--TGTGCAATTGTATA
* * *
5511404 CATGAATTTTGATTTTGTGCAATTTTATA
1 CATGAACTATGATTTTGTGCAATTGTATA
5511433 CATGAA
1 CATGAA
5511439 ATTTTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
31 12 0.39
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (29 bp):
CATGAACTATGATTTTGTGCAATTGTATA
Found at i:5511422 original size:29 final size:30
Alignment explanation
Indices: 5511390--5511448 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
5511380 TATGGTTTAA
5511390 TGTGCAATTGTATACATG-AATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
5511419 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
5511449 GATCAAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:5513483 original size:44 final size:45
Alignment explanation
Indices: 5513428--5513523 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 45
5513418 CAAGTATAAT
* *
5513428 ATTATAATACGGATTGTTCTAGTAATCATAAAGTA-TAACAAACA
1 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
*
5513472 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGATCAAACA
1 ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
5513517 ATTACAA
1 ATTACAA
5513524 GCACAAACAG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 34 0.71
45 14 0.29
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (45 bp):
ATTACAATACGGATTGTTCTAGTAATCATAAAGTAGGAACAAACA
Found at i:5517600 original size:57 final size:56
Alignment explanation
Indices: 5517484--5517618 Score: 155
Period size: 57 Copynumber: 2.3 Consensus size: 56
5517474 AATAAGATTA
* * *
5517484 TTAATAAAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAAT-AAAATAATATATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
5517542 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATATATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
5517599 TTACTAAAATCATAATATAA
1 TTAATAAAATAAT-ATATAA
5517619 AATACTATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 37 0.55
58 26 0.39
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATATATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Done.