Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 17 of 167
Found at i:5127369 original size:17 final size:20
Alignment explanation
Indices: 5127347--5127387 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
5127337 AAATATGAAA
5127347 TGAATTGAA-AAA-A-AAAT
1 TGAATTGAATAAAGATAAAT
5127364 TGAATTGAATAAAGATAAAT
1 TGAATTGAATAAAGATAAAT
5127384 TGAA
1 TGAA
5127388 ATGAGACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 1 0.05
20 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (20 bp):
TGAATTGAATAAAGATAAAT
Found at i:5127467 original size:5 final size:5
Alignment explanation
Indices: 5127457--5127495 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
5127447 AAAAATAATT
5127457 AATGA AATGA AATGA AATGTTA AATGA ATATGA AATGA A
1 AATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA A
5127496 TGATGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 21 0.68
6 5 0.16
7 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (5 bp):
AATGA
Found at i:5127501 original size:18 final size:19
Alignment explanation
Indices: 5127480--5127517 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5127470 GAAATGTTAA
5127480 ATGAATATGAAAT-GAATG
1 ATGAATATGAAATGGAATG
* *
5127498 ATGATTTTGAAATGGAATG
1 ATGAATATGAAATGGAATG
5127517 A
1 A
5127518 AAGTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (19 bp):
ATGAATATGAAATGGAATG
Found at i:5127579 original size:34 final size:32
Alignment explanation
Indices: 5127541--5127610 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
5127531 AATAAATTAT
* *
5127541 AAATTGAAATGGAAACAAAAACTGAAATGGAATA
1 AAATTGAAAT-GAAA-AAAAAATGAAATGGAAAA
*
5127575 AAATTGAAATGAAAAAAAAATTAAATGGAAAA
1 AAATTGAAATGAAAAAAAAATGAAATGGAAAA
5127607 AAAT
1 AAAT
5127611 AATTTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 19 0.58
33 4 0.12
34 10 0.30
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (32 bp):
AAATTGAAATGAAAAAAAAATGAAATGGAAAA
Found at i:5127582 original size:16 final size:16
Alignment explanation
Indices: 5127541--5127610 Score: 79
Period size: 16 Copynumber: 4.2 Consensus size: 16
5127531 AATAAATTAT
5127541 AAATTGAAATGGAAACAA
1 AAATTGAAATGG-AA-AA
* *
5127559 AAACTGAAATGGAATA
1 AAATTGAAATGGAAAA
*
5127575 AAATTGAAATGAAAAAA
1 AAATTGAAATG-GAAAA
5127592 AAATT-AAATGGAAAA
1 AAATTGAAATGGAAAA
5127607 AAAT
1 AAAT
5127611 AATTTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
15 8 0.18
16 16 0.36
17 10 0.22
18 11 0.24
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (16 bp):
AAATTGAAATGGAAAA
Found at i:5127614 original size:18 final size:17
Alignment explanation
Indices: 5127541--5127620 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
5127531 AATAAATTAT
5127541 AAATTGAAATGGAAACAAA
1 AAATT-AAATGGAAA-AAA
* * *
5127560 AACTGAAATGG--AATA
1 AAATTAAATGGAAAAAA
5127575 AAATTGAAAT-GAAAAAA
1 AAATT-AAATGGAAAAAA
5127592 AAATTAAATGGAAAAAA
1 AAATTAAATGGAAAAAA
5127609 ATAATTTAAATG
1 A-AA-TTAAATG
5127621 AAATGGAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.12
16 9 0.18
17 16 0.33
18 8 0.16
19 10 0.20
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.21
Consensus pattern (17 bp):
AAATTAAATGGAAAAAA
Found at i:5127617 original size:19 final size:18
Alignment explanation
Indices: 5127541--5127620 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 18
5127531 AATAAATTAT
* *
5127541 AAATTGAAATGGAAACAA
1 AAATTTAAATGGAAAAAA
* * *
5127559 AAACTGAAATGG--AATA
1 AAATTTAAATGGAAAAAA
*
5127575 AAATTGAAAT-GAAAAAA
1 AAATTTAAATGGAAAAAA
5127592 AAA-TTAAATGGAAAAAA
1 AAATTTAAATGGAAAAAA
5127609 ATAATTTAAATG
1 A-AATTTAAATG
5127621 AAATGGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 1 0.02
16 16 0.31
17 14 0.27
18 13 0.25
19 7 0.14
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.21
Consensus pattern (18 bp):
AAATTTAAATGGAAAAAA
Found at i:5127651 original size:5 final size:6
Alignment explanation
Indices: 5127616--5127648 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5127606 AAAATAATTT
5127616 AAAT-G AAATGG AAATGG AAATGG AAAT-G AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
5127649 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:5130395 original size:91 final size:89
Alignment explanation
Indices: 5130213--5130540 Score: 390
Period size: 91 Copynumber: 3.7 Consensus size: 89
5130203 AGTCTAGAAT
* * * * * * **
5130213 ATTAATACACAAAAATATAAAATTCAAAC-AAAAATAATGCACACTAAATTAAA-TTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
*
5130276 AACAAACTATAAACAGATAGGTAAA
66 AACAAACTACAAACAGAT-GGTAAA
*
5130301 ATTAATACACGAAAATTTTAAATTCAAACTGCATATAATACGGACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
5130366 AAACAAACTACAAACAGATGGATAAA
66 -AACAAACTACAAACAGATGG-TAAA
* * * * * * * ** * *
5130392 ATTAGTGCACCAAATTTTTAAAATTTAAACTATATATAACATAGACTAAATTGAATTTAAGCACC
1 ATTAATACACGAAAATTTT-AAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACC
5130457 CAACAAACTACAAACAGATGGGTAAA
65 CAACAAACTACAAACAGAT-GGTAAA
**
5130483 ATTAATACTTGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTA
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTA
5130541 TAAATACAAA
Statistics
Matches: 200, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
88 26 0.13
89 18 0.09
90 45 0.22
91 71 0.35
92 40 0.20
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (89 bp):
ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGTAAA
Found at i:5130878 original size:112 final size:112
Alignment explanation
Indices: 5130697--5130903 Score: 258
Period size: 112 Copynumber: 1.8 Consensus size: 112
5130687 GGTGGTATCA
* * * * * * * *
5130697 GCCATCAGTGTTCCAAAGTAAAAAAAAAATTGCATTTGGAGTCAAAAATGTACTTGGTGCCGGCT
1 GCCATCAGTGTCCCAAAATAAAAAAAAAAGTGCATTGGGAGTCAAAAATGTACCTGATGCCGACC
*
5130762 ATCTACTTGCCAGCA-CC-AATTTTTTTTTAAATGACATTGGTGCCG
66 ATCTACTAGCCAGCACCCAAATTTTTTTTTAAATGACATTGGTGCCG
* **
5130807 GCCATTAGTGTCCCAAAATAATAAAAAAAAGTG-ACTTGGGAGTCGAAATTTGTACCTGATGCCG
1 GCCATCAGTGTCCCAAAATAA-AAAAAAAAGTGCA-TTGGGAGTC-AAAAATGTACCTGATGCCG
5130871 ACCATCTACTAGCCAGCACCCAAATTTTTTTTT
63 ACCATCTACTAGCCAGCACCCAAATTTTTTTTT
5130904 TTAAATGTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
110 19 0.24
111 18 0.22
112 30 0.38
113 2 0.03
114 11 0.14
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (112 bp):
GCCATCAGTGTCCCAAAATAAAAAAAAAAGTGCATTGGGAGTCAAAAATGTACCTGATGCCGACC
ATCTACTAGCCAGCACCCAAATTTTTTTTTAAATGACATTGGTGCCG
Found at i:5140651 original size:23 final size:25
Alignment explanation
Indices: 5140606--5140652 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
5140596 CTTAAACATA
5140606 AAACAAATCAAACTCAAAATGATCT
1 AAACAAATCAAACTCAAAATGATCT
*
5140631 AAACAAAT-AATCT-AAAATGATC
1 AAACAAATCAAACTCAAAATGATC
5140653 CGAACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.57, C:0.17, G:0.04, T:0.21
Consensus pattern (25 bp):
AAACAAATCAAACTCAAAATGATCT
Found at i:5142633 original size:24 final size:24
Alignment explanation
Indices: 5142601--5142649 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5142591 CTTTCAAAGT
5142601 AATAGAATACTTTTGAGAGCATTA
1 AATAGAATACTTTTGAGAGCATTA
*
5142625 AATAGAATACTTTTGAGAGTATTA
1 AATAGAATACTTTTGAGAGCATTA
5142649 A
1 A
5142650 TTTAATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (24 bp):
AATAGAATACTTTTGAGAGCATTA
Found at i:5144418 original size:37 final size:37
Alignment explanation
Indices: 5144368--5144438 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5144358 AACATTGCAG
*
5144368 GTCAAAGAAAGAGTGCTCTTGTTGATATGAGGGCATC
1 GTCAAAGAAAGAGTGCTCTTGTTGATACGAGGGCATC
5144405 GTCAAAGAAAGAGTGCTCTTGTTGATACGAGGGC
1 GTCAAAGAAAGAGTGCTCTTGTTGATACGAGGGC
5144439 GTCAAATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (37 bp):
GTCAAAGAAAGAGTGCTCTTGTTGATACGAGGGCATC
Found at i:5145401 original size:21 final size:22
Alignment explanation
Indices: 5145355--5145403 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5145345 TATTGATAAG
**
5145355 AATTATATTAAATTTAATATTA
1 AATTATATTAAATTTAATAGAA
5145377 AATT-TATTAAA-TTAATAGAA
1 AATTATATTAAATTTAATAGAA
5145397 TAATTAT
1 -AATTAT
5145404 CTACAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTATATTAAATTTAATAGAA
Found at i:5157651 original size:3 final size:3
Alignment explanation
Indices: 5157645--5157677 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5157635 TTCATCATTG
*
5157645 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5157678 CCTTCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:5157682 original size:9 final size:9
Alignment explanation
Indices: 5157634--5157694 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
5157624 TCATCTTCAC
5157634 CTTCATCAT
1 CTTCATCAT
5157643 -TGTCATCAT
1 CT-TCATCAT
*
5157652 CATCATCAT
1 CTTCATCAT
*
5157661 CATCATCAT
1 CTTCATCAT
*
5157670 CTTCATCAC
1 CTTCATCAT
5157679 CTTCATTC-T
1 CTTCA-TCAT
5157688 CTTCATC
1 CTTCATC
5157695 TGTACTCTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
8 3 0.07
9 40 0.89
10 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.02, T:0.41
Consensus pattern (9 bp):
CTTCATCAT
Found at i:5162822 original size:59 final size:60
Alignment explanation
Indices: 5162751--5162865 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 60
5162741 ATCACTTTAA
* * *
5162751 TATTAAATTAATATAATATTTAT-T-ATGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCTAAT-ATAAATATTAAATTAAATTTAATATTAAATCT
*
5162810 TATTAAAATAATAGAATATTTATCTACAATATAAATATTAAATTTAATTTAATATT
1 TATTAAAATAATAGAATATTTATCT--AATATAAATATTAAATTAAATTTAATATT
5162866 TATCTTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
62 24 0.50
63 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (60 bp):
TATTAAAATAATAGAATATTTATCTAATATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:5162865 original size:17 final size:17
Alignment explanation
Indices: 5162843--5162900 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
5162833 CTACAATATA
5162843 AATATTAAATTTAATTT
1 AATATTAAATTTAATTT
*
5162860 AATATT-TATCTTAA--T
1 AATATTAAAT-TTAATTT
5162875 AATATTAAATTTAATTT
1 AATATTAAATTTAATTT
5162892 AATATTAAA
1 AATATTAAA
5162901 ATATTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 11 0.31
16 4 0.11
17 20 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTAAATTTAATTT
Found at i:5162913 original size:19 final size:18
Alignment explanation
Indices: 5162872--5162917 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
5162862 TATTTATCTT
5162872 AATAATATT-AAATTTAA
1 AATAATATTAAAATTTAA
**
5162889 TTTAATATTAAAATATTAA
1 AATAATATTAAAAT-TTAA
5162908 AATAATATTA
1 AATAATATTA
5162918 TTTTTGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATATTAAAATTTAA
Found at i:5167223 original size:133 final size:133
Alignment explanation
Indices: 5166971--5167290 Score: 509
Period size: 133 Copynumber: 2.4 Consensus size: 133
5166961 CTTCATAGCC
* * * * *
5166971 GATAAGACT-ACCATTCCTGATCTGCTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTCA
1 GATAAGACTCGCCATTTCTGATCTGCTCCATAGCTGATACATGGAGATAAGATCTATAATTTTCA
*
5167035 GTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTTCATAGCCGATACAT
66 GTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACAT
5167100 AAA
131 AAA
*
5167103 GATAAGACTCGCCATTTCTGATTTGCTCCATAGCTGATACATGGAGATAAGATCTATAATTTTCA
1 GATAAGACTCGCCATTTCTGATCTGCTCCATAGCTGATACATGGAGATAAGATCTATAATTTTCA
* *
5167168 GTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGTCGATACAT
66 GTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACAT
*
5167233 AGA
131 AAA
* *
5167236 GATAAGACTCGCCATTTCAGATCTGCTCCATAGCCT-ATACATGGAAATAAGATCT
1 GATAAGACTCGCCATTTCTGATCTGCTCCATAG-CTGATACATGGAGATAAGATCT
5167291 GGTATTTAGC
Statistics
Matches: 173, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
132 9 0.05
133 162 0.94
134 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (133 bp):
GATAAGACTCGCCATTTCTGATCTGCTCCATAGCTGATACATGGAGATAAGATCTATAATTTTCA
GTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACAT
AAA
Found at i:5167419 original size:266 final size:260
Alignment explanation
Indices: 5167185--5168090 Score: 1103
Period size: 266 Copynumber: 3.4 Consensus size: 260
5167175 TCCTGCAACT
* *
5167185 TCAG-GAAGATAAGACTTG-TGGCTAAAATCTGCTCCATAGTCGATACAT-AGAGATAAGACTCG
1 TCAGTGAAGATAAGGC-TGATGGCTAAAATCTGCTCCATAG-CGATACATGA-AGATAAGACTTG
* *
5167247 CC-ATTTCAGATCTGCTCCA-TAGCCT-ATACA-TGGAA-ATAAGATCTGGTATTTAGCCTGCTC
63 CCAATTT--GATCTGCTTCACT--CCTGCT-CAGT-GAAGATAAGATCTGGTATTTAGCCTGCTC
* *
5167307 CACTCCTGCTCAGTGAAGATAATGCTGATGATTGGAATCTGCTCCATCGTCGGTACGTGAAGATA
122 CACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTG-CGGTACGTGAAGATA
* * *
5167372 AGATTCTCCAAAGTTCGATTTGCTTCACTCCTGCTCAGTTAAGATAAGATCTAGTATTTAGCCTG
186 AGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTA-TATTTAGCCTG
5167437 CTCCACTCTTGC
250 CTCCACTC-TGC
* * *
5167449 TCAGTGAAGATAAGGCTGATGGCTGAAATCTACTCCATTACCGATACATGAAGATAAGACTTGCC
1 TCAGTGAAGATAAGGCTGATGGCTAAAATCTGCTCCA-TAGCGATACATGAAGATAAGACTTGCC
5167514 AAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCC
65 --AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCC
* * *
5167579 TGCTCAGTGAAGATAAGGCTGATGATTGGAATTTGCTCCATTACCGGTACGTGGAGATAAGATTC
128 TGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATT-GCGGTACGTGAAGATAAGATTC
* *
5167644 TCCAAATTTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCAC
192 TCCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCT-ATATTTAGCCTGCTCCAC
5167709 TCCTGC
256 T-CTGC
* *
5167715 TCAGTGAAAATAAGGCTGATGGCTAAAATCTGCTCCATTGCTGATACATGAAGATAAGACTTGCC
1 TCAGTGAAGATAAGGCTGATGGCTAAAATCTGCTCCATAGC-GATACATGAAGATAAGACTTGCC
5167780 AAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCC
65 --AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCC
* ** ** * *
5167845 TGCTCAGTGAAAATAAGGCTGATGGCTAAAATCTGCTCCATTGCTGATACATGAAGATAAGACTT
128 TGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGC-GGTACGTGAAGATAAGA-TT
* * * *
5167910 -GCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTACTC
191 CTCCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATC---TATATTTAGCCTGCTC
5167974 CACTCCTGC
253 CACT-CTGC
** ** * * *
5167983 TCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGA-TTCAC
1 TCAGTGAAGATAAGGCTGATGGCTAAAATCTGCTCCATAG-CGATACATGAAGATAAGACTT-GC
* * *
5168047 CAAAATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCT
64 C--AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCT
5168091 ACAATTTTAG
Statistics
Matches: 573, Mismatches: 47, Indels: 40
0.87 0.07 0.06
Matches are distributed among these distances:
264 6 0.01
265 58 0.10
266 383 0.67
267 6 0.01
268 118 0.21
269 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (260 bp):
TCAGTGAAGATAAGGCTGATGGCTAAAATCTGCTCCATAGCGATACATGAAGATAAGACTTGCCA
ATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTGC
TCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGCGGTACGTGAAGATAAGATTCTCCA
AAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTATATTTAGCCTGCTCCACTCTGC
Found at i:5167443 original size:133 final size:133
Alignment explanation
Indices: 5167282--5168090 Score: 1167
Period size: 133 Copynumber: 6.1 Consensus size: 133
5167272 ATACATGGAA
* * *
5167282 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAATGCTGATGATTGGAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
* * * * * * * *
5167347 GCTCCATCGTCGGTACGTGAAGATAAGA-TTCTCCAAAGTTCGATTTGCTTCACTCCTGCTCAGT
66 GCTCCATTGCCGATACATGAAGATAAGACTT-GCCAAAATTTGATCTGCTTCACTCCTGCTCAGT
*
5167411 TAAG
130 GAAG
* * *
5167415 ATAAGATCTAGTATTTAGCCTGCTCCACTCTTGCTCAGTGAAGATAAGGCTGATGGCTGAAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
* *
5167480 ACTCCATTACCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
66 GCTCCATTGCCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
5167545 AAG
131 AAG
* * *
5167548 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATTT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
* * * * *
5167613 GCTCCATTACCGGTACGTGGAGATAAGA-TT-CTCCAAATTTCGATCTGCTTCACTCCTGCTCAG
66 GCTCCATTGCCGATACATGAAGATAAGACTTGC-CAAAATTT-GATCTGCTTCACTCCTGCTCAG
5167676 TGAAG
129 TGAAG
* * *
5167681 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
*
5167746 GCTCCATTGCTGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
66 GCTCCATTGCCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
5167811 AAG
131 AAG
* * *
5167814 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
*
5167879 GCTCCATTGCTGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
66 GCTCCATTGCCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
5167944 AAG
131 AAG
* * *
5167947 ATAAGATCTGGTATGTTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAAT
1 ATAAGATCTGGTA--TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAAT
* * * *
5168012 CTGCTCCATTGCCGATACATGGAGATAAGA-TTCACCAAAATTTGATCTGCTCCGCTCCTGCTCA
64 CTGCTCCATTGCCGATACATGAAGATAAGACTT-GCCAAAATTTGATCTGCTTCACTCCTGCTCA
*
5168076 GCGAAG
128 GTGAAG
5168082 ATAAGATCT
1 ATAAGATCT
5168091 ACAATTTTAG
Statistics
Matches: 616, Mismatches: 52, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
131 1 0.00
132 9 0.01
133 478 0.78
134 13 0.02
135 115 0.19
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (133 bp):
ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAATCT
GCTCCATTGCCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
AAG
Found at i:5167712 original size:399 final size:400
Alignment explanation
Indices: 5167282--5168090 Score: 1284
Period size: 399 Copynumber: 2.0 Consensus size: 400
5167272 ATACATGGAA
* * * **
5167282 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAATGCTGATGATTGGAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGACTAAAATCT
* * * * *
5167347 GCTCCATCG-TCGGTACGTGAAGATAAGA-TTCTCCAAAGTTCGATTTGCTTCACTCCTGCTCAG
66 GCTCCATCGCT-GATACATGAAGATAAGACTT-GCCAAAATTCGATCTGCTTCACTCCTGCTCAG
* * * *
5167410 TTAAGATAAGATCTAGTATTTAGCCTGCTCCACTCTTGCTCAGTGAAGATAAGGCTGATGGCTGA
129 TGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAA
5167475 AATCTACTCCATTACCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCT
194 AATCTACTCCATTACCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCT
*
5167540 CAGTGAAGATAAGATCTGGTA-TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGA
259 CAGTGAAGATAAGATCTGGTAGTTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGCTGATGA
* * * * *
5167604 TTGGAATTTGCTCCATTACCGGTACGTGGAGATAAGATTCTCC-AAATTTCGATCTGCTTCACTC
324 TTGGAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCAAAATTT-GATCTGCTCCACTC
*
5167668 CTGCTCAGTGAAG
388 CTGCTCAGCGAAG
*
5167681 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAATCT
1 ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGACTAAAATCT
* *
5167746 GCTCCATTGCTGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTG
66 GCTCCATCGCTGATACATGAAGATAAGACTTGCCAAAATTCGATCTGCTTCACTCCTGCTCAGTG
*
5167811 AAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAA
131 AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAA
* * *
5167876 TCTGCTCCATTGCTGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCA
196 TCTACTCCATTACCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCA
5167941 GTGAAGATAAGATCTGGTATGTTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
261 GTGAAGATAAGATCTGGTA-GTTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
* *
5168006 TGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCGCTCCT
325 TGGAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCACTCCT
5168071 GCTCAGCGAAG
390 GCTCAGCGAAG
5168082 ATAAGATCT
1 ATAAGATCT
5168091 ACAATTTTAG
Statistics
Matches: 375, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
399 253 0.67
400 3 0.01
401 113 0.30
402 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (400 bp):
ATAAGATCTGGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGACTAAAATCT
GCTCCATCGCTGATACATGAAGATAAGACTTGCCAAAATTCGATCTGCTTCACTCCTGCTCAGTG
AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAA
TCTACTCCATTACCGATACATGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCA
GTGAAGATAAGATCTGGTAGTTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATT
GGAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCACTCCTG
CTCAGCGAAG
Found at i:5167772 original size:44 final size:43
Alignment explanation
Indices: 5167700--5167951 Score: 129
Period size: 44 Copynumber: 5.7 Consensus size: 43
5167690 GGTATTTAGC
* *
5167700 CTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAAT
1 CTGCTCCACTCCTGATCAGTGAAGATAAGGCT-ATGGCTAAAAT
* * * * *
5167744 CTGCTCCATTGCTGATACA-TGAAGATAAGACT-TGCCAAAATTTGAT
1 CTGCTCCACTCCTGAT-CAGTGAAGATAAGGCTATGGCTAAA----AT
* * * * * **
5167790 CTGCTTCACTCCTGCTCAGTGAAGATAA-GATCTGG-TATTTAGC
1 CTGCTCCACTCCTGATCAGTGAAGATAAGGCTATGGCTA--AAAT
* *
5167833 CTGCTCCACTCCTGCTCAGTGAAAATAAGGCTGATGGCTAAAAT
1 CTGCTCCACTCCTGATCAGTGAAGATAAGGCT-ATGGCTAAAAT
* * * * *
5167877 CTGCTCCATTGCTGATACA-TGAAGATAAGACT-TGCCAAAATTTGAT
1 CTGCTCCACTCCTGAT-CAGTGAAGATAAGGCTATGGCTAAA----AT
* *
5167923 CTGCTTCACTCCTGCTCAGTGAAGATAAG
1 CTGCTCCACTCCTGATCAGTGAAGATAAG
5167952 ATCTGGTATG
Statistics
Matches: 154, Mismatches: 36, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
42 12 0.08
43 26 0.17
44 51 0.33
45 13 0.08
46 51 0.33
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
CTGCTCCACTCCTGATCAGTGAAGATAAGGCTATGGCTAAAAT
Found at i:5169551 original size:6 final size:6
Alignment explanation
Indices: 5169542--5169582 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
5169532 GCCTCTCCAG
*
5169542 TTTCTT TTTC-T TTTCTT TTT-TT TTTATT TTTCTT TTT-TT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
5169583 GAAACTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:5169558 original size:11 final size:11
Alignment explanation
Indices: 5169542--5169582 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
5169532 GCCTCTCCAG
5169542 TTTCTTTTTCT
1 TTTCTTTTTCT
*
5169553 TTTCTTTTTTT
1 TTTCTTTTTCT
*
5169564 TTTATTTTTCT
1 TTTCTTTTTCT
5169575 TTT-TTTTT
1 TTTCTTTTT
5169583 GAAACTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 5 0.19
11 22 0.81
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:5170128 original size:27 final size:27
Alignment explanation
Indices: 5170076--5170129 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5170066 CTTTTTGTTG
* * *
5170076 TTTTTTTTTTGTTTTTTGCCTTCCTTT
1 TTTTTTTTTTCTTTTTGGCCTGCCTTT
5170103 TTTTGTTTTTTCTTTTTGGCC-GCCTTT
1 TTTT-TTTTTTCTTTTTGGCCTGCCTTT
5170130 GCTGTATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.00, C:0.17, G:0.11, T:0.72
Consensus pattern (27 bp):
TTTTTTTTTTCTTTTTGGCCTGCCTTT
Found at i:5174466 original size:27 final size:25
Alignment explanation
Indices: 5174436--5174488 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
5174426 TCACGCAAGA
*
5174436 AGAAAATGAAAGAATAATAACAAAATC
1 AGAAAAGGAAAGAA-AATAA-AAAATC
* *
5174463 AGAAAGGGAAAGAAACTAAAAAATC
1 AGAAAAGGAAAGAAAATAAAAAATC
5174488 A
1 A
5174489 CCTTTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.11
Consensus pattern (25 bp):
AGAAAAGGAAAGAAAATAAAAAATC
Found at i:5174833 original size:16 final size:16
Alignment explanation
Indices: 5174806--5174874 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
5174796 TTGGTTCGCT
*
5174806 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
*
5174822 GTACTGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
5174838 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
5174854 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
5174870 GTAAT
1 GTAAT
5174875 AGGTAATTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:5174911 original size:45 final size:44
Alignment explanation
Indices: 5174854--5174943 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 44
5174844 GAATAGATGC
5174854 GTAATGGAATAGAGGCGTAATAGGTAATTCTT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
5174899 GTAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAAT
5174943 G
1 G
5174944 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 6 0.14
44 17 0.39
45 21 0.48
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAAT
Found at i:5174945 original size:39 final size:43
Alignment explanation
Indices: 5174854--5174959 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 43
5174844 GAATAGATGC
5174854 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTGTTTGGTT--AT
5174899 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTT-TGTTTGGTTAT
*
5174939 G-AATGGAATAGAGGTGTAATA
1 GTAATGGAATAGAGGCGTAATA
5174960 ACATAAGGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
39 18 0.31
40 2 0.03
43 7 0.12
44 10 0.17
45 21 0.36
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (43 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTTGTTTGGTTAT
Found at i:5175112 original size:16 final size:15
Alignment explanation
Indices: 5175102--5175257 Score: 61
Period size: 17 Copynumber: 10.5 Consensus size: 15
5175092 CATAATTGTT
5175102 ATAAAATATAATTTA
1 ATAAAATATAATTTA
5175117 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
5175134 ATAAAAT-T--TTTA
1 ATAAAATATAATTTA
5175146 AT-AAATAT--TCTT-
1 ATAAAATATAAT-TTA
* * *
5175158 ATATGAAT-TTA-CTA
1 ATA-AAATATAATTTA
5175172 ATAAAATCATAATATATGA
1 ATAAAAT-ATAAT-T-T-A
5175191 TACTAAAATATAATTTA
1 -A-TAAAATATAATTTA
5175208 A-AATAAT-T-A-TT-
1 ATAA-AATATAATTTA
*
5175219 ATTAAATATAATTTA
1 ATAAAATATAATTTA
5175234 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
5175251 ATAAAAT
1 ATAAAAT
5175258 TGTTAATAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 50
0.66 0.04 0.30
Matches are distributed among these distances:
11 8 0.07
12 14 0.13
13 9 0.08
14 12 0.11
15 13 0.12
16 12 0.11
17 25 0.23
18 2 0.02
19 2 0.02
20 6 0.06
21 6 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:5175147 original size:17 final size:17
Alignment explanation
Indices: 5175107--5175140 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5175097 TTGTTATAAA
5175107 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5175124 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5175141 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5175264 original size:17 final size:17
Alignment explanation
Indices: 5175224--5175257 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5175214 TTATTATTAA
5175224 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5175241 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5175258 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5175293 original size:117 final size:116
Alignment explanation
Indices: 5175087--5175459 Score: 586
Period size: 117 Copynumber: 3.3 Consensus size: 116
5175077 TTAATCATAT
* * *
5175087 TTTAACATAATTGTTATAAAATATAATTTAATAAAATATATAATTTAATAAAATTTTTAATAAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAA-TTTTAATAAAT
*
5175152 ATTCTTATATGAATTTACTAATAAAATCATAATATATGATACTAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
5175204 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTGTTAATAAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATT-TTAATAAAT
5175269 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
*
5175321 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA--TT-CT---T
1 TTTAAAATAATTATTATTAAATATAATTTAATAA-AATATATAATTTAATAAAATTTTAATAAAT
5175380 ATTCTTATATGAATTTAC---TAAAATCATAATATATAATACTATAAAATATAA
65 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATAC--TAAAATATAA
5175431 TTT-AAATAATTATTATTAAATATAATTTA
1 TTTAAAATAATTATTATTAAATATAATTTA
5175460 TAATCTACTT
Statistics
Matches: 247, Mismatches: 5, Indels: 16
0.92 0.02 0.06
Matches are distributed among these distances:
108 21 0.09
109 26 0.11
110 13 0.05
111 19 0.08
114 1 0.00
115 2 0.01
116 2 0.01
117 144 0.58
118 19 0.08
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (116 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTTTAATAAATA
TTCTTATATGAATTTACTAATAAAATCATAATATATAATACTAAAATATAA
Found at i:5175329 original size:20 final size:21
Alignment explanation
Indices: 5175290--5175329 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5175280 AATTTACTAA
*
5175290 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
5175311 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
5175330 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:5175342 original size:26 final size:28
Alignment explanation
Indices: 5175297--5175376 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
5175287 TAATAAAATC
5175297 ATAATATATAATACTAAAATATAATTTAA-A
1 ATAATATATAAT--T-AAATATAATTTAATA
*
5175327 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
* *
5175354 ATAATATATAATTTAATAAAATT
1 ATAATATATAATTAAATATAATT
5175377 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 13 0.30
27 7 0.16
28 14 0.32
29 5 0.11
30 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:5175409 original size:44 final size:41
Alignment explanation
Indices: 5175191--5175409 Score: 131
Period size: 43 Copynumber: 5.3 Consensus size: 41
5175181 TAATATATGA
5175191 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * *
5175232 TAATAAAATATATAATTTAATAA-AATTGTTAATAAATAT--TCT
1 TACT-AAA-ATATAATTTAA-AATAATTATTATTAAATATAAT-T
* * * *
5175274 TA-T---AT-GAATTTACTAATAA-AATCA-TAATATATAA--
1 TACTAAAATATAATTTA-AAATAATTATTATTAA-ATATAATT
5175308 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * **
5175349 TAATAATAATATATAATTTAATAA-AATTCTTATTCTTATATGAATT
1 TACT-A-AA-ATATAATTTAA-AATAATTATTATT-AAATAT-AATT
5175395 TACTAAAATCATAAT
1 TACTAAAAT-ATAAT
5175410 ATATAATACT
Statistics
Matches: 136, Mismatches: 17, Indels: 47
0.68 0.09 0.23
Matches are distributed among these distances:
34 5 0.04
35 15 0.11
36 4 0.03
38 7 0.05
39 15 0.11
40 3 0.02
41 8 0.06
42 7 0.05
43 29 0.21
44 29 0.21
45 7 0.05
46 7 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (41 bp):
TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
Found at i:5175455 original size:32 final size:32
Alignment explanation
Indices: 5175419--5175482 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
5175409 TATATAATAC
*
5175419 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
5175451 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
5175483 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:5179291 original size:53 final size:54
Alignment explanation
Indices: 5179207--5179313 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 54
5179197 GCAGTGAATT
5179207 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
1 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
5179261 TCAAAAACCACAAC-AAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
1 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
5179314 GAATAGGTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.06
Consensus pattern (54 bp):
TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
Found at i:5182385 original size:67 final size:67
Alignment explanation
Indices: 5182306--5182448 Score: 277
Period size: 67 Copynumber: 2.1 Consensus size: 67
5182296 GTTGAATGAA
*
5182306 TTGAATCAGAACATACTTGAAATTGATAGAAATTGAAAACTAGGATAAAAATCAACAGCTAAATA
1 TTGAATCAGAACATACTTGAAATTGATAGAAATTGAAAACTAGGATAAAAATCAACAACTAAATA
5182371 TG
66 TG
5182373 TTGAATCAGAACATACTTGAAATTGATAGAAATTGAAAACTAGGATAAAAATCAACAACTAAATA
1 TTGAATCAGAACATACTTGAAATTGATAGAAATTGAAAACTAGGATAAAAATCAACAACTAAATA
5182438 TG
66 TG
5182440 TTGAATCAG
1 TTGAATCAG
5182449 TTTAATTTTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (67 bp):
TTGAATCAGAACATACTTGAAATTGATAGAAATTGAAAACTAGGATAAAAATCAACAACTAAATA
TG
Found at i:5185553 original size:53 final size:51
Alignment explanation
Indices: 5185410--5185558 Score: 132
Period size: 48 Copynumber: 2.9 Consensus size: 51
5185400 TATGTCATTG
* * * *
5185410 TATTTTTCTAATTAATTTAAA-TAAAATCAA-GAGATAAATAATAAAAATTTA
1 TATTTTTCTAATTAAATTAAATTAAATTAAATGATATAAATAAT--AAATTTA
** *
5185461 TATTATAACTAATTAAATTAAATT-AATTAAGTG--AT-AATAATAAA-TTA
1 TATT-TTTCTAATTAAATTAAATTAAATTAAATGATATAAATAATAAATTTA
5185508 TTATTTTCTCTAATTAAATTAAATTAAATTAATATGATATAAATAATAAAT
1 -TATTTT-TCTAATTAAATTAAATTAAATTAA-ATGATATAAATAATAAAT
5185559 AAAAGAGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
47 4 0.05
48 23 0.29
49 6 0.08
50 8 0.10
51 6 0.08
52 20 0.26
53 11 0.14
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (51 bp):
TATTTTTCTAATTAAATTAAATTAAATTAAATGATATAAATAATAAATTTA
Found at i:5188230 original size:19 final size:20
Alignment explanation
Indices: 5188206--5188249 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5188196 CCTAATTGAT
5188206 TATTTAA-TTATTTTATAAA
1 TATTTAATTTATTTTATAAA
* *
5188225 TATTTAATTTATTTTTTAAT
1 TATTTAATTTATTTTATAAA
5188245 TATTT
1 TATTT
5188250 TATAAGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTAATTTATTTTATAAA
Found at i:5188355 original size:25 final size:25
Alignment explanation
Indices: 5188292--5188374 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
5188282 AATTCTTTTA
*
5188292 AAAAAAT-TTAAAATTCTAATTTTT
1 AAAAAATATTAAAATTCTAATATTT
* *
5188316 AAAAAATATGAAAATTTTAATATTT
1 AAAAAATATTAAAATTCTAATATTT
5188341 -AAAAATATTATAAATTAGCCTAATATTAT
1 AAAAAATATTA-AAATT---CTAATATT-T
5188370 AAAAA
1 AAAAA
5188375 TTACTAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 16 0.34
25 19 0.40
28 7 0.15
29 1 0.02
30 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAAAATATTAAAATTCTAATATTT
Found at i:5197373 original size:40 final size:40
Alignment explanation
Indices: 5197321--5197399 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
5197311 GAAATGAATC
5197321 AATGAATGAATAGAGTTTAATTTATTTGAATGAAATATTT
1 AATGAATGAATAGAGTTTAATTTATTTGAATGAAATATTT
*
5197361 AATGAATGAATAGAGTTTAATTTGTTTGAATGAAATATT
1 AATGAATGAATAGAGTTTAATTTATTTGAATGAAATATT
5197400 ATGGAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (40 bp):
AATGAATGAATAGAGTTTAATTTATTTGAATGAAATATTT
Found at i:5197381 original size:18 final size:18
Alignment explanation
Indices: 5197321--5197381 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 18
5197311 GAAATGAATC
5197321 AATGAATGAATAGAGTTT
1 AATGAATGAATAGAGTTT
* * * *
5197339 AATTTATTTGAATGAAATATTT
1 AA-TGA-ATGAAT-AGA-GTTT
5197361 AATGAATGAATAGAGTTT
1 AATGAATGAATAGAGTTT
5197379 AAT
1 AAT
5197382 TTGTTTGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
18 8 0.26
19 4 0.13
20 10 0.32
21 4 0.13
22 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
AATGAATGAATAGAGTTT
Found at i:5197714 original size:75 final size:75
Alignment explanation
Indices: 5197559--5197703 Score: 195
Period size: 75 Copynumber: 1.9 Consensus size: 75
5197549 GTACATCCAG
* *
5197559 CTAGTGCTGGGCACACCATTATATTTGTCGGTTTATCCGACTAGCGTTAGCCGTAACCTTTGGCA
1 CTAGTGCTGGGCACACCATTATATTTGTCGATTTATCCGACTAGCGTTAGCCGCAACCTTTGGCA
* *
5197624 GTTTAGAGAA
66 GATTACAGAA
* * *
5197634 CTAGTGTTGGGCACACCATTATATTTGTCGATTTA-CCTGACTAGCGTTGAG-CGCAACTTTTGT
1 CTAGTGCTGGGCACACCATTATATTTGTCGATTTATCC-GACTAGCGTT-AGCCGCAACCTTTGG
5197697 CAGATTA
64 CAGATTA
5197704 TCTGCCTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
74 2 0.03
75 58 0.94
76 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (75 bp):
CTAGTGCTGGGCACACCATTATATTTGTCGATTTATCCGACTAGCGTTAGCCGCAACCTTTGGCA
GATTACAGAA
Found at i:5212207 original size:17 final size:15
Alignment explanation
Indices: 5212185--5212224 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
5212175 CTTAATATTT
5212185 AAGTAAATATATATATA
1 AAGTAAATATA-ATA-A
5212202 AAGTAAATATAATAA
1 AAGTAAATATAATAA
5212217 AA-TAAATA
1 AAGTAAATA
5212225 AGTAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 3 0.13
16 3 0.13
17 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
AAGTAAATATAATAA
Found at i:5212244 original size:4 final size:4
Alignment explanation
Indices: 5212232--5212310 Score: 51
Period size: 4 Copynumber: 20.0 Consensus size: 4
5212222 ATAAGTAAAT
* * *
5212232 GAAA TAAA GAAA GAAA GAAA GTAA -AAC GAAA G--A GAAA GGAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA
*
5212278 GAAA -ATAA AAAA GGGAAA GAAA GAAA G-AA GAAA
1 GAAA GA-AA GAAA --GAAA GAAA GAAA GAAA GAAA
5212311 CGCACAACCT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
2 2 0.03
3 5 0.08
4 44 0.75
5 5 0.08
6 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:5212299 original size:26 final size:28
Alignment explanation
Indices: 5212237--5212306 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
5212227 TAAATGAAAT
*
5212237 AAAGAAAGAAAGAAAGTAAAACGAAAGAG
1 AAAGAAAGAAAGAAAATAAAAC-AAAGAG
*
5212266 AAAGGAAAGAAAGAAAAT-AAA-AAAGGG
1 AAA-GAAAGAAAGAAAATAAAACAAAGAG
5212293 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
5212307 GAAACGCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 11 0.29
27 8 0.21
29 6 0.16
30 13 0.34
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.03
Consensus pattern (28 bp):
AAAGAAAGAAAGAAAATAAAACAAAGAG
Found at i:5216568 original size:3 final size:3
Alignment explanation
Indices: 5216560--5216698 Score: 79
Period size: 3 Copynumber: 45.0 Consensus size: 3
5216550 AGGTGTAAAT
* * * * *
5216560 ATA ATA ATA ATA AT- ATA TTG ATA ATAA ACA ATA ATA A-A AGGA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA
* * * * * *
5216605 AAA ATA ATA GTA ATA ATA AGA ATA TTTA ATA ATA GTA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
5216651 ATA AT- ATAA ATA ATA ATA TATA CATGA ATA ATA ATA AT- ATAA ATA
1 ATA ATA AT-A ATA ATA ATA -ATA -AT-A ATA ATA ATA ATA AT-A ATA
5216696 ATA
1 ATA
5216699 GAAAAAATAA
Statistics
Matches: 106, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
2 8 0.08
3 80 0.75
4 17 0.16
5 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5220706 original size:49 final size:48
Alignment explanation
Indices: 5220632--5220767 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 48
5220622 TATTCGGCCT
* * * *
5220632 AGCAACGCCATTATATGGCCTAACATTTTAGCCTGCACCATTAGGTCT
1 AGCAAGGCCATCATATGGCCCAACATTTTAGCCTGCACCATTAGGTCG
* * * * *
5220680 AGCAGGGTCATCCATATGGCCCAACA-TTCAGGCCTACACCATTTGGTCG
1 AGCAAGGCCAT-CATATGGCCCAACATTTTA-GCCTGCACCATTAGGTCG
* *
5220729 AGCAAGGCCATCATATGGCCCAAAATTTTTGCCTGCACC
1 AGCAAGGCCATCATATGGCCCAACATTTTAGCCTGCACC
5220768 GTTACCCATA
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
48 32 0.46
49 38 0.54
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (48 bp):
AGCAAGGCCATCATATGGCCCAACATTTTAGCCTGCACCATTAGGTCG
Found at i:5226669 original size:26 final size:26
Alignment explanation
Indices: 5226621--5226693 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
5226611 TTGTCACCCT
* *
5226621 AATTTTACCTC-AATAAAAATTTGAC
1 AATTTTACCCCTAATAAAATTTTGAC
5226646 AATTTTACCCCTAATAAAATTTTGAC
1 AATTTTACCCCTAATAAAATTTTGAC
* * *
5226672 GATTTTACCCTTGATAAAATTT
1 AATTTTACCCCTAATAAAATTT
5226694 CGAGAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 10 0.24
26 32 0.76
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (26 bp):
AATTTTACCCCTAATAAAATTTTGAC
Found at i:5230510 original size:13 final size:14
Alignment explanation
Indices: 5230494--5230522 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5230484 CACCTCTCTA
5230494 TTTTATCTTT-TAT
1 TTTTATCTTTATAT
5230507 TTTTATCTTTATAT
1 TTTTATCTTTATAT
5230521 TT
1 TT
5230523 CCCATGCATG
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:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATCTTTATAT
Found at i:5233002 original size:31 final size:31
Alignment explanation
Indices: 5232964--5233041 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
5232954 TTTTTCCTAA
* *
5232964 TTTGATACTTGAGTTTGGCTTCAATATTCAT
1 TTTGATACTTGAGTTTAGCTTCAATATTCAC
* *
5232995 TTTGATACTTGAGTTTAGCTTCAATTTTTAC
1 TTTGATACTTGAGTTTAGCTTCAATATTCAC
*
5233026 TTTGGTACTTGAGTTT
1 TTTGATACTTGAGTTT
5233042 TTTCAATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.51
Consensus pattern (31 bp):
TTTGATACTTGAGTTTAGCTTCAATATTCAC
Found at i:5236870 original size:28 final size:28
Alignment explanation
Indices: 5236839--5236895 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5236829 TTAAGACTCA
5236839 ATCAATAATAATAATAATTTA-AATATAT
1 ATCAAT-ATAATAATAATTTATAATATAT
* * *
5236867 ATCAATATTATTATATTTTATAATATAT
1 ATCAATATAATAATAATTTATAATATAT
5236895 A
1 A
5236896 AATTATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
ATCAATATAATAATAATTTATAATATAT
Found at i:5238365 original size:56 final size:57
Alignment explanation
Indices: 5238285--5238417 Score: 173
Period size: 56 Copynumber: 2.3 Consensus size: 57
5238275 AACTAATAAA
* * *
5238285 TTTAATATAATATATTTTTTAAAAGTTATATAGAATTTTTAAAT-TATTTTTATTAC
1 TTTAATATAATATATTTTTAAAAAGTTATATAAAAATTTTAAATGTATTTTTATTAC
* *
5238341 TTTAATATAGTAT-TTTTTAAAAAAGTTATATAAAAATTTTAAATGTATTTTTATTAT
1 TTTAATATAATATATTTTT-AAAAAGTTATATAAAAATTTTAAATGTATTTTTATTAC
5238398 TTTAAATATTAA-ATATTTTT
1 TTT-AATA-TAATATATTTTT
5238418 TATATTGTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
55 5 0.08
56 34 0.52
57 14 0.21
58 6 0.09
59 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (57 bp):
TTTAATATAATATATTTTTAAAAAGTTATATAAAAATTTTAAATGTATTTTTATTAC
Found at i:5238431 original size:27 final size:28
Alignment explanation
Indices: 5238366--5238431 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
5238356 TTTAAAAAAG
* * *
5238366 TTATATAAAAATTTTAAATGTATTTTTA
1 TTATTTAAAAATATTAAATATATTTTTA
*
5238394 TTATTT-TAAATATTAAATAT-TTTTTA
1 TTATTTAAAAATATTAAATATATTTTTA
5238420 -TATTGTAAAAAT
1 TTATT-TAAAAAT
5238432 TAAAATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.13
26 7 0.23
27 15 0.48
28 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
TTATTTAAAAATATTAAATATATTTTTA
Found at i:5238437 original size:26 final size:26
Alignment explanation
Indices: 5238379--5238435 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
5238369 TATAAAAATT
* * *
5238379 TTAAATGTATTTTTATTATTTTAAATA
1 TTAAATAT-TTTTTATTATTGTAAAAA
5238406 TTAAATATTTTTTA-TATTGTAAAAA
1 TTAAATATTTTTTATTATTGTAAAAA
5238431 TTAAA
1 TTAAA
5238436 ATTAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 14 0.52
26 6 0.22
27 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTAAATATTTTTTATTATTGTAAAAA
Found at i:5238496 original size:27 final size:32
Alignment explanation
Indices: 5238439--5238507 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 32
5238429 AATTAAAATT
*
5238439 AATTATATATAAATTAATAAAAATAATTTTTA
1 AATTATATTTAAATTAATAAAAATAATTTTTA
5238471 AATTA-ATTTAAA-TAAT-AAAA-AA-TTTTA
1 AATTATATTTAAATTAATAAAAATAATTTTTA
*
5238498 ATTTATATTT
1 AATTATATTT
5238508 CGTAAAACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 6 0.18
29 4 0.12
30 4 0.12
31 6 0.18
32 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTATATTTAAATTAATAAAAATAATTTTTA
Found at i:5244914 original size:7 final size:7
Alignment explanation
Indices: 5244883--5244907 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5244873 CGTCTCATTC
5244883 CTCTCTT
1 CTCTCTT
5244890 CTCTCTT
1 CTCTCTT
5244897 CTCTCTT
1 CTCTCTT
5244904 CTCT
1 CTCT
5244908 ACTCTCTTTT
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:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CTCTCTT
Found at i:5245662 original size:21 final size:21
Alignment explanation
Indices: 5245621--5245663 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5245611 ACATTATATT
* *
5245621 TTTATTAATATAAAATCTAAA
1 TTTATTAATAAAAAATATAAA
5245642 TTTATT-ATAAAAAGATATAAA
1 TTTATTAATAAAAA-ATATAAA
5245663 T
1 T
5245664 CTTAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTATTAATAAAAAATATAAA
Found at i:5246178 original size:22 final size:22
Alignment explanation
Indices: 5246153--5246210 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
5246143 CATGAAGCAA
5246153 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
5246175 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
* *
5246197 TCCCATACCTCCAC
1 CCCCATACCCCCAC
5246211 AGTCCTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.55, G:0.03, T:0.12
Consensus pattern (22 bp):
CCCCATACCCCCACTACAACAG
Found at i:5250117 original size:38 final size:38
Alignment explanation
Indices: 5250066--5250142 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5250056 TCTGATCTAA
5250066 AAGGGTTACCTCACTTGATACTATTGATCACAATGTAT
1 AAGGGTTACCTCACTTGATACTATTGATCACAATGTAT
5250104 AAGGGTTACCTCACTTGATACTATTGATCACAATGTAT
1 AAGGGTTACCTCACTTGATACTATTGATCACAATGTAT
5250142 A
1 A
5250143 GATCATGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (38 bp):
AAGGGTTACCTCACTTGATACTATTGATCACAATGTAT
Found at i:5252471 original size:14 final size:15
Alignment explanation
Indices: 5252452--5252484 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5252442 TTTAAAAGAG
*
5252452 AAATCAAA-TACAAA
1 AAATCAAACTAAAAA
5252466 AAATCAAACTAAAAA
1 AAATCAAACTAAAAA
5252481 AAAT
1 AAAT
5252485 GATGATTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATCAAACTAAAAA
Found at i:5253310 original size:24 final size:24
Alignment explanation
Indices: 5253283--5253328 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5253273 ATAGCAACCC
*
5253283 TTTATAGATTTTTTATCTTATTTA
1 TTTATAGATTTATTATCTTATTTA
**
5253307 TTTATTTATTTATTATCTTATT
1 TTTATAGATTTATTATCTTATT
5253329 ACCCTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATAGATTTATTATCTTATTTA
Found at i:5253315 original size:12 final size:13
Alignment explanation
Indices: 5253290--5253328 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
5253280 CCCTTTATAG
5253290 ATTT-TTTATCTT
1 ATTTATTTATCTT
5253302 ATTTATTTAT-TT
1 ATTTATTTATCTT
5253314 ATTTA-TTATCTT
1 ATTTATTTATCTT
5253326 ATT
1 ATT
5253329 ACCCTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.16
12 16 0.64
13 5 0.20
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTATCTT
Found at i:5253402 original size:3 final size:3
Alignment explanation
Indices: 5253394--5253433 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5253384 TTCTCACCAA
5253394 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5253434 TACTGTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5254518 original size:11 final size:11
Alignment explanation
Indices: 5254504--5254544 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5254494 TATTTTCTCC
5254504 CTATTTTGCTA
1 CTATTTTGCTA
*
5254515 CTATTTTACTA
1 CTATTTTGCTA
* *
5254526 TTATGTTGCTA
1 CTATTTTGCTA
5254537 CTATTTTG
1 CTATTTTG
5254545 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:5255202 original size:30 final size:30
Alignment explanation
Indices: 5255166--5255226 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5255156 ATTTTATTGT
*
5255166 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
5255196 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
5255226 T
1 T
5255227 TGTTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:5255346 original size:19 final size:18
Alignment explanation
Indices: 5255306--5255345 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5255296 GAAATATTTA
*
5255306 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTATAGTAT
5255324 TTTTGATGGTTTATA-TAT
1 TTTTGAT-GTTTATAGTAT
5255342 TTTT
1 TTTT
5255346 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
TTTTGATGTTTATAGTAT
Found at i:5255368 original size:12 final size:12
Alignment explanation
Indices: 5255347--5255380 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5255337 TATATTTTTT
*
5255347 AAAATTATATAA
1 AAAATAATATAA
5255359 AAAATAATATAA
1 AAAATAATATAA
*
5255371 AAATTAATAT
1 AAAATAATAT
5255381 GGGCGAGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:5260595 original size:78 final size:78
Alignment explanation
Indices: 5260466--5260695 Score: 381
Period size: 78 Copynumber: 2.9 Consensus size: 78
5260456 GGGTCACATC
* * * *
5260466 TCATGTAACTGCAGTGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCATGTCAAATCCTATCCACCTTAAGTTACCAT
*
5260531 AATGAATCATATA
66 AGTGAATCATATA
*
5260544 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCATGCCAAATCCTATCCACCTTAAGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCATGTCAAATCCTATCCACCTTAAGTTACCAT
5260609 AGTGAATCATATA
66 AGTGAATCATATA
*
5260622 TCATGTAACTGTAGCGAATCAGGATTACCTTTTC-TGGTCAAATCCTATCCGCCTTAAGTTACCA
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAT-GTCAAATCCTATCCACCTTAAGTTACCA
5260686 TAGTGAATCA
65 TAGTGAATCA
5260696 AGAATAAATC
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
77 1 0.01
78 142 0.99
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (78 bp):
TCATGTAACTGTAGCGAATCAGGATTACCTTTTCATGTCAAATCCTATCCACCTTAAGTTACCAT
AGTGAATCATATA
Found at i:5260724 original size:40 final size:40
Alignment explanation
Indices: 5260660--5260797 Score: 168
Period size: 40 Copynumber: 3.5 Consensus size: 40
5260650 CTTTTCTGGT
* * * *
5260660 CAAATCCTATCCGCCTTAAGTTACCATAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* *
5260700 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* ** **
5260740 CAAATCCTATCCACTTTGACGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
*
5260780 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
5260798 GATTCTCGAG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
Found at i:5266622 original size:46 final size:46
Alignment explanation
Indices: 5266570--5266794 Score: 306
Period size: 46 Copynumber: 4.9 Consensus size: 46
5266560 TTCTGAAATG
*
5266570 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGACATA
** * *
5266616 AAATGTGTAAGACCATGGTTGAAAGATACCGTGGCAACATGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGACATA
* * *
5266662 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAGCGTGACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGACATA
** * *
5266708 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
1 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGACATA
* * * *
5266754 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATG
5266795 TCAAAGATAA
Statistics
Matches: 159, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 159 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGACATA
Found at i:5267096 original size:16 final size:17
Alignment explanation
Indices: 5267075--5267107 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5267065 ATGATGGAGC
5267075 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
5267091 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
5267108 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:5268914 original size:9 final size:9
Alignment explanation
Indices: 5268870--5268913 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
5268860 TTTGAACAAA
5268870 AATTGAGA-
1 AATTGAGAG
5268878 AATTTGAGAG
1 AA-TTGAGAG
5268888 AATTGAGAG
1 AATTGAGAG
5268897 AATTGAGAG
1 AATTGAGAG
5268906 --TTGAGAG
1 AATTGAGAG
5268913 A
1 A
5268914 GAATAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.21
8 2 0.06
9 22 0.67
10 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (9 bp):
AATTGAGAG
Found at i:5269602 original size:6 final size:7
Alignment explanation
Indices: 5269576--5269613 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
5269566 TTAAAATTTC
5269576 AAAAAATT
1 AAAAAA-T
5269584 ACAAAAAT
1 A-AAAAAT
5269592 AAAAAAT
1 AAAAAAT
5269599 AAAAAAT
1 AAAAAAT
5269606 AAAAAAT
1 AAAAAAT
5269613 A
1 A
5269614 TCAATGCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 21 0.72
8 3 0.10
9 5 0.17
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:5271360 original size:2 final size:2
Alignment explanation
Indices: 5271353--5271384 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5271343 TCAGGTCTAT
5271353 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5271385 AAACATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5279325 original size:84 final size:86
Alignment explanation
Indices: 5279220--5279458 Score: 225
Period size: 88 Copynumber: 2.8 Consensus size: 86
5279210 AATTTTGCCA
* * * * * * *
5279220 AGGTTTTTTCAGCCTTCTCAATTATTTAATCTTACAAGTTAAAT-TCATTTTCT-CAAAAAT-GA
1 AGGTTGTTTCAGCATTTTCAATTATTTAATCTTAAAACTTAAATCTC-TTTTCTAAAAAAATAAA
* *
5279282 GTTGAGTTTCGAGATTTCTGT-G
65 G-AGAGCTTCGAGATTTCTGTCG
* * *
5279304 AGGTTGTTTCAGCATTTTCAATTATTTAATTTTAAAACTTGAATCTCTTTTTTGAAAAAAATACA
1 AGGTTGTTTCAGCATTTTCAATTATTTAATCTTAAAACTTAAATCTCTTTTCT-AAAAAAATA-A
5279369 AGAGAGCTTCGAGATTTCTGTCG
64 AGAGAGCTTCGAGATTTCTGTCG
* * * * * * * *
5279392 AGGTCGTTTTAGCATTTTTAATTATTTAATTTTAGAACTCAAATCTCTTTTTTGAAAAAATATAA
1 AGGTTGTTTCAGCATTTTCAATTATTTAATCTTAAAACTTAAATCTCTTTTCTAAAAAAATA-AA
5279457 GA
65 GA
5279459 AAGTTTCCTA
Statistics
Matches: 129, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
84 42 0.33
85 2 0.02
86 6 0.05
87 29 0.22
88 50 0.39
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (86 bp):
AGGTTGTTTCAGCATTTTCAATTATTTAATCTTAAAACTTAAATCTCTTTTCTAAAAAAATAAAG
AGAGCTTCGAGATTTCTGTCG
Found at i:5279415 original size:88 final size:87
Alignment explanation
Indices: 5279289--5279451 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 87
5279279 TGAGTTGAGT
* **
5279289 TTCGAGATTTCTGTGAGGTTGTTTCAGCATTTTCAATTATTTAATTTTAAAACTTGAATCTCTTT
1 TTCGAGATTTCTGTGAGGTCGTTTCAGCATTTTCAATTATTTAATTTTAAAACTCAAATCTCTTT
5279354 TTTGAAAAAAATACAAGAGAGC
66 TTTGAAAAAAATACAAGAGAGC
* * *
5279376 TTCGAGATTTCTGTCGAGGTCGTTTTAGCATTTTTAATTATTTAATTTTAGAACTCAAATCTCTT
1 TTCGAGATTTCTGT-GAGGTCGTTTCAGCATTTTCAATTATTTAATTTTAAAACTCAAATCTCTT
5279441 TTTTGAAAAAA
65 TTTTGAAAAAA
5279452 TATAAGAAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 14 0.20
88 55 0.80
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (87 bp):
TTCGAGATTTCTGTGAGGTCGTTTCAGCATTTTCAATTATTTAATTTTAAAACTCAAATCTCTTT
TTTGAAAAAAATACAAGAGAGC
Found at i:5281713 original size:25 final size:23
Alignment explanation
Indices: 5281662--5281714 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
5281652 TTTAAAATGT
* *
5281662 ATATACATGATATATATGAAAAT
1 ATATACATAATATATATGAAAAA
*
5281685 ATATACATAATATAGTTATTAAAAA
1 ATATACATAATATA--TATGAAAAA
5281710 ATATA
1 ATATA
5281715 TATATACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.52
25 12 0.48
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATACATAATATATATGAAAAA
Found at i:5282044 original size:3 final size:3
Alignment explanation
Indices: 5282036--5282069 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5282026 ACATTACTAT
5282036 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5282070 AGAAATGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5284771 original size:16 final size:16
Alignment explanation
Indices: 5284750--5284783 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5284740 ATGGGTTCGT
*
5284750 ATCATTTTAAGTTTAG
1 ATCATTTTAAGTATAG
5284766 ATCATTTTAAGTATAG
1 ATCATTTTAAGTATAG
5284782 AT
1 AT
5284784 GTTAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
ATCATTTTAAGTATAG
Found at i:5289434 original size:6 final size:7
Alignment explanation
Indices: 5289414--5289443 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
5289404 AAGGACTTGT
5289414 AAGAAAA
1 AAGAAAA
5289421 AAGAAAA
1 AAGAAAA
5289428 AAGAAAAA
1 AAG-AAAA
5289436 AAGAAAA
1 AAGAAAA
5289443 A
1 A
5289444 TTAAGGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:5292964 original size:17 final size:16
Alignment explanation
Indices: 5292923--5292967 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
5292913 ATTTTTTACA
5292923 ATAATTAATAT-AATTT
1 ATAA-TAATATAAATTT
5292939 -TAA-AATATAAATTAT
1 ATAATAATATAAATT-T
5292954 ATAATAATATAAAT
1 ATAATAATATAAAT
5292968 ACAATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.20
14 4 0.16
15 4 0.16
16 3 0.12
17 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATAATATAAATTT
Found at i:5296459 original size:7 final size:7
Alignment explanation
Indices: 5296425--5296462 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5296415 ACCTGAACTC
5296425 TAAACC-
1 TAAACCT
5296431 TAAA-CT
1 TAAACCT
*
5296437 TGAACCT
1 TAAACCT
5296444 TAAACCT
1 TAAACCT
5296451 TAAACCT
1 TAAACCT
5296458 TAAAC
1 TAAAC
5296463 TCTAAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.04
6 7 0.25
7 20 0.71
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:5296468 original size:14 final size:14
Alignment explanation
Indices: 5296420--5296468 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
5296410 TTGAAACCTG
5296420 AACTCTAAACC-TA
1 AACTCTAAACCTTA
*
5296433 AACT-TGAACCTTA
1 AACTCTAAACCTTA
5296446 AAC-CTTAAACCTTA
1 AACTC-TAAACCTTA
5296460 AACTCTAAA
1 AACTCTAAA
5296469 ACCAAACCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 5 0.17
13 9 0.30
14 15 0.50
15 1 0.03
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.27
Consensus pattern (14 bp):
AACTCTAAACCTTA
Found at i:5296741 original size:39 final size:39
Alignment explanation
Indices: 5296665--5296743 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
5296655 AATAAATATA
* *
5296665 ACTAGATAAATTAAAAATAATAAAAATTTAAACTCTATC
1 ACTAAATAAATTAAAAATAATAAAAATCTAAACTCTATC
**
5296704 ACTAAATAAA-TATAAAATAATAAAAATCTAATTTCTATC
1 ACTAAATAAATTA-AAAATAATAAAAATCTAAACTCTATC
5296743 A
1 A
5296744 ACTCTTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (39 bp):
ACTAAATAAATTAAAAATAATAAAAATCTAAACTCTATC
Found at i:5298811 original size:6 final size:6
Alignment explanation
Indices: 5298792--5298836 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5298782 TTTAAAAAAA
** *
5298792 ATAATT ATTAATT ATAATT ATAATT ATTTTT AAAATT ATAATT AT
1 ATAATT A-TAATT ATAATT ATAATT ATAATT ATAATT ATAATT AT
5298837 TTTTCAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATAATT
Found at i:5298852 original size:24 final size:23
Alignment explanation
Indices: 5298799--5298877 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 23
5298789 AAAATAATTA
5298799 TTAAT-TATAATTATAATTA-TT
1 TTAATATATAATTATAATTATTT
5298820 TT--TA-A-AATTATAATTATTT
1 TTAATATATAATTATAATTATTT
*
5298839 TTCAATATGTAATTATAATTATTT
1 TT-AATATATAATTATAATTATTT
*
5298863 TTAATGTATAATTAT
1 TTAATATATAATTAT
5298878 CACAACTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
18 11 0.23
19 6 0.12
21 2 0.04
22 2 0.04
23 11 0.23
24 16 0.33
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (23 bp):
TTAATATATAATTATAATTATTT
Found at i:5298854 original size:18 final size:18
Alignment explanation
Indices: 5298776--5298840 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
5298766 GCATTGCTTA
* **
5298776 AATTATTTTAAAAAAAAT
1 AATTATTTTTAAAATTAT
* *
5298794 AATTATTAATTATAATTAT
1 AATTATT-TTTAAAATTAT
5298813 AATTATTTTTAAAATTAT
1 AATTATTTTTAAAATTAT
5298831 AATTATTTTT
1 AATTATTTTT
5298841 CAATATGTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 26 0.67
19 13 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTATTTTTAAAATTAT
Found at i:5303276 original size:28 final size:29
Alignment explanation
Indices: 5303217--5303280 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
5303207 TTGAAATTTG
**
5303217 AAAAATAAAAAGGTTAAATTTCTAAAAAT
1 AAAAATAAAAAGACTAAATTTCTAAAAAT
* *
5303246 AAAAATATAAAGACTAAATTTC-AAATAT
1 AAAAATAAAAAGACTAAATTTCTAAAAAT
5303274 AAAAATA
1 AAAAATA
5303281 GTACAGGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAAATAAAAAGACTAAATTTCTAAAAAT
Found at i:5312587 original size:558 final size:558
Alignment explanation
Indices: 5311485--5312597 Score: 2023
Period size: 558 Copynumber: 2.0 Consensus size: 558
5311475 TCGAGCAATT
*
5311485 TGAAGGTATTTTTCATGTTTTTACTTAGTTTTAGTTCTTTGTTTTAATAAGTGAATTAGTGTGTT
1 TGAAGGTATTTTTCATGTTTTTACTTAGTTTTAGTTCTTTGCTTTAATAAGTGAATTAGTGTGTT
* * *
5311550 TTATACTATTTTTGAAACTCAAGTTGGTCAAGTGTGCCAAAGGAAACCTAATGGGTTGATTGAGT
66 TTACACTATTTTTGAAACCCAAGTTGGTCAAGTGCGCCAAAGGAAACCTAATGGGTTGATTGAGT
*
5311615 GTTGTAGGGGGTCGATGGCGGCCTAAACGTGAAGAAAACATCACTTAGAATAGGGGTATCGTGAT
131 GTTGTAGGGAGTCGATGGCGGCCTAAACGTGAAGAAAACATCACTTAGAATAGGGGTATCGTGAT
* * *
5311680 ATCGAAGCATAGAAGTCGTGATACCCCTAACAGACTGAAACGATGAGGATTAAGGCCATCTGCAG
196 ATCGAAGCAAAGAAGTCGTGATAACCCTAACAGACTGAAACGATGAGGATTAAGGCCATCTACAG
*
5311745 TGGTATTGCGATACTAGCCATGGGTATTGCAATACCCAACCTCCCAAGGCTCCCCCATTTCAAGA
261 TGGTATGGCGATACTAGCCATGGGTATTGCAATACCCAACCTCCCAAGGCTCCCCCATTTCAAGA
*
5311810 TTGTTGTGGGTATCTCGGTACCAGACCATGGTTATCACAATACCCCTAATGAGAGGAGACCAAAA
326 TTATTGTGGGTATCTCGGTACCAGACCATGGTTATCACAATACCCCTAATGAGAGGAGACCAAAA
5311875 AAAAAACTGATTGCAGGGGTAATCCTTGTACAACTTTAACATCAATCAAATTTAGACGTTGAGGG
391 AAAAAACTGATTGCAGGGGTAATCCTTGTACAACTTTAACATCAATCAAATTTAGACGTTGAGGG
* *
5311940 GCATTTTGGTCACAAAAATTAGGTTGTAATCAAATTAAACAGCCACTTGTGTCTGAGAATTGGAG
456 GCATTTTGGTCACAAAAATTAGGTTGTAATCAAATTAAAAAGCCACTTGTGTCTGAGAATTGAAG
5312005 GAAAAGCTTTTATTTAGGTTTTTTTTTCATATTTTTCA
521 GAAAAGCTTTTATTTAGGTTTTTTTTTCATATTTTTCA
5312043 TGAAGGTATTTTTCATGTTTTTACTTAGTTTTAGTTCTTTGCTTTAATAAGTGAATTAGTGTGTT
1 TGAAGGTATTTTTCATGTTTTTACTTAGTTTTAGTTCTTTGCTTTAATAAGTGAATTAGTGTGTT
*
5312108 TTACACTATTTTTGAGACCCAAGTTGGTCAAGTGCGCCAAAGGAAACCTAATGGGTTGATTGAGT
66 TTACACTATTTTTGAAACCCAAGTTGGTCAAGTGCGCCAAAGGAAACCTAATGGGTTGATTGAGT
*
5312173 GTTGTAGGGAGTCGATGGTGGCCTAAACGTGAAGAAAACATCACTTAGAATAGGGGTATCGTGAT
131 GTTGTAGGGAGTCGATGGCGGCCTAAACGTGAAGAAAACATCACTTAGAATAGGGGTATCGTGAT
* * * *
5312238 ATCGAAGCAAAGAAGTCGTGATAACCCTGACAGTGCTGAAGCGATGAGGATTAAGGCCATCTATA
196 ATCGAAGCAAAGAAGTCGTGATAACCCTAACAG-ACTGAAACGATGAGGATTAAGGCCATCTACA
5312303 GTGGTATGGCGATACTAGCCATGGGTATTGCAATACCCAACCTCCCAAGGCTCCCCCATTTCAAG
260 GTGGTATGGCGATACTAGCCATGGGTATTGCAATACCCAACCTCCCAAGGCTCCCCCATTTCAAG
5312368 ATTATTGTGGGTATCTCGGTACCAGACCATGGTTATCACAATACCCCTAATGAGAGGAGA-C-AA
325 ATTATTGTGGGTATCTCGGTACCAGACCATGGTTATCACAATACCCCTAATGAGAGGAGACCAAA
*
5312431 AAAAAAACTGATTGTAGGGGTAATCCTTGTACAACTTTAACATCAATCAAATTTAGACGTTGAGG
390 AAAAAAACTGATTGCAGGGGTAATCCTTGTACAACTTTAACATCAATCAAATTTAGACGTTGAGG
*
5312496 GGCATTTTGGTCACAAAAATTAGGTTGTAATCAAATTAAAAAGCTACTTGTGTCTGAGAATTGAA
455 GGCATTTTGGTCACAAAAATTAGGTTGTAATCAAATTAAAAAGCCACTTGTGTCTGAGAATTGAA
5312561 GGAAAAGCTTTTATTTAGGTTTTTTTTTCATATTTTT
520 GGAAAAGCTTTTATTTAGGTTTTTTTTTCATATTTTT
5312598 AGCTTAGGTT
Statistics
Matches: 534, Mismatches: 20, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
557 165 0.31
558 219 0.41
559 150 0.28
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (558 bp):
TGAAGGTATTTTTCATGTTTTTACTTAGTTTTAGTTCTTTGCTTTAATAAGTGAATTAGTGTGTT
TTACACTATTTTTGAAACCCAAGTTGGTCAAGTGCGCCAAAGGAAACCTAATGGGTTGATTGAGT
GTTGTAGGGAGTCGATGGCGGCCTAAACGTGAAGAAAACATCACTTAGAATAGGGGTATCGTGAT
ATCGAAGCAAAGAAGTCGTGATAACCCTAACAGACTGAAACGATGAGGATTAAGGCCATCTACAG
TGGTATGGCGATACTAGCCATGGGTATTGCAATACCCAACCTCCCAAGGCTCCCCCATTTCAAGA
TTATTGTGGGTATCTCGGTACCAGACCATGGTTATCACAATACCCCTAATGAGAGGAGACCAAAA
AAAAAACTGATTGCAGGGGTAATCCTTGTACAACTTTAACATCAATCAAATTTAGACGTTGAGGG
GCATTTTGGTCACAAAAATTAGGTTGTAATCAAATTAAAAAGCCACTTGTGTCTGAGAATTGAAG
GAAAAGCTTTTATTTAGGTTTTTTTTTCATATTTTTCA
Found at i:5314300 original size:21 final size:22
Alignment explanation
Indices: 5314259--5314306 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
5314249 ATAAAAATTC
5314259 AAAAA-ATAAAATATTTCTAAA
1 AAAAATATAAAATATTTCTAAA
*
5314280 AAAAATATAAAATGTTT-TAAA
1 AAAAATATAAAATATTTCTAAA
5314301 AAAAAT
1 AAAAAT
5314307 TACCTATGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATATAAAATATTTCTAAA
Found at i:5319610 original size:18 final size:18
Alignment explanation
Indices: 5319587--5319621 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5319577 TTCATTGCTT
*
5319587 TTCAAAAGCATTTCTGGC
1 TTCAAAAGCACTTCTGGC
5319605 TTCAAAAGCACTTCTGG
1 TTCAAAAGCACTTCTGG
5319622 AAGAAAAGCT
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:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (18 bp):
TTCAAAAGCACTTCTGGC
Found at i:5321469 original size:36 final size:36
Alignment explanation
Indices: 5321427--5321500 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
5321417 CCTACATCCT
* *
5321427 ATAGGCCAAATAGGCTGAATGCCTATGCTCCTATAC
1 ATAGGCCAAATAGGCCGAATGCCAATGCTCCTATAC
* * *
5321463 ATAGGCCAAGTAGGCCGAATGTCAATGCTCCTTTAC
1 ATAGGCCAAATAGGCCGAATGCCAATGCTCCTATAC
5321499 AT
1 AT
5321501 GAGCAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (36 bp):
ATAGGCCAAATAGGCCGAATGCCAATGCTCCTATAC
Found at i:5322398 original size:43 final size:43
Alignment explanation
Indices: 5322242--5322415 Score: 226
Period size: 42 Copynumber: 4.1 Consensus size: 43
5322232 GTTTATGTGA
* * *
5322242 AAAAACGCCGCTAAAGAACATGGCCTTTAGCAGTGCTTTC-CC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC
5322284 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTC-CC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC
* *
5322326 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTCTCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC
* ** * * * *
5322369 ACAGGCGCCGCTAAAAAACCTGACTTTTAGCGGCGCTTTTTCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC
5322412 AAAA
1 AAAA
5322416 CCCCACTAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 77 0.67
43 38 0.33
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC
Found at i:5323087 original size:23 final size:23
Alignment explanation
Indices: 5323061--5324043 Score: 373
Period size: 23 Copynumber: 43.0 Consensus size: 23
5323051 AACTAAACTA
* *
5323061 TTCAATTTGCAGTACTTAAAAAC
1 TTCAATTTGCAGCACTTAAACAC
* * *
5323084 TTCAATTTACAACATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* * *
5323107 TCCAATTTGTAGCACTTTTAACAC
1 TTCAATTTGCAGCAC-TTAAACAC
*
5323131 TTCAATTTGCAGCACTTTAACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * * *
5323153 TCTCAATTAACAACATTTATACTC
1 T-TCAATTTGCAGCACTTAAACAC
* * *
5323177 CTCAA-TTACAGCGA-TAAAACA-
1 TTCAATTTGCAGC-ACTTAAACAC
* * * *
5323198 TCTCAATGTCCGGCAAC-TGAACAC
1 T-TCAATTTGCAGC-ACTTAAACAC
* *
5323222 TTCGATTTGCAGTACTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* * *
5323245 TTCAATTTACAACATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
** *
5323268 TTCAATTTATAACA-TTCAAACAC
1 TTCAATTTGCAGCACTT-AAACAC
* *
5323291 TTCAATTTGCAGTACTTTAACAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5323314 TTCAATTTACAGCATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5323337 TTCAATTTGCATCACTTTAACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * *
5323359 TCTCAATTAACAACATTTATACAC
1 T-TCAATTTGCAGCACTTAAACAC
* * * *
5323383 CTCAA-TTACAGTGA-TAAAACA-
1 TTCAATTTGCAG-CACTTAAACAC
* *
5323404 TCTCAATGTCCAGCAAC-TAAACAC
1 T-TCAATTTGCAGC-ACTTAAACAC
*
5323428 TTCAATTTGCAGTACTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* * * *
5323451 TTCAATTTACAACATTTAAGCAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5323474 TTCAATTTACAACA-TCTAAACAC
1 TTCAATTTGCAGCACT-TAAACAC
* * *
5323497 TCCAATTTCCAGCACTTTAACAC
1 TTCAATTTGCAGCACTTAAACAC
*
5323520 TTCAATTTGCAGCACTTTAACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * *
5323542 TCTCAATTAACAACATTTATACAC
1 T-TCAATTTGCAGCACTTAAACAC
* * * *
5323566 CTCAA-TTACAGTGA-TAAAACA-
1 TTCAATTTGCAG-CACTTAAACAC
5323587 TCTCAA--T-CA--AC-TAAACAC
1 T-TCAATTTGCAGCACTTAAACAC
* *
5323605 TTCAATTTGCAGTACTTTAACAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5323628 TTCAATTTACAGCATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* * *
5323651 TTCAATTTGCTGTACTTTAACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * *
5323673 TCTCAATTAACAACATTTATACAC
1 T-TCAATTTGCAGCACTTAAACAC
* * *
5323697 CTCAA-TTGTAGCGA-TAAAACA-
1 TTCAATTTGCAGC-ACTTAAACAC
*
5323718 TCTCAATTTTCAGCAAC-TAAACAC
1 T-TCAATTTGCAGC-ACTTAAACAC
**
5323742 TTCAATTTGCAGCACTTTTACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * *
5323764 TCTCAATTAACAACATTTATACAC
1 T-TCAATTTGCAGCACTTAAACAC
* * *
5323788 CTCAA-TTGTAGCGA-TAAAACA-
1 TTCAATTTGCAGC-ACTTAAACAC
* * * *
5323809 TCCCCATGTCCAGCAAC-TAAACAC
1 T-TCAATTTGCAGC-ACTTAAACAC
*
5323833 TTCAATTTGCAGTACTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5323856 TTCAATTTGCAACATTTAAGCACTACAC
1 TTCAATTTGCAGCACTT-A--A--ACAC
*
5323884 TTCAATTTGCAGCACTTTAACA-
1 TTCAATTTGCAGCACTTAAACAC
** * * *
5323906 TCTCAATTAACAACATTTATACAC
1 T-TCAATTTGCAGCACTTAAACAC
* * * *
5323930 CTCAA-TTACAGCAATAAAACA-
1 TTCAATTTGCAGCACTTAAACAC
5323951 TCTCAATTTTGCAGCAAC-TAAACAC
1 T-TCAA-TTTGCAGC-ACTTAAACAC
* * *
5323976 TTCAAATTGCAGTATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* * *
5323999 TTCAATTTACAACATTTAAACAC
1 TTCAATTTGCAGCACTTAAACAC
* *
5324022 TTCAATTTACAGCATTTAAACA
1 TTCAATTTGCAGCACTTAAACA
5324044 ACAACAATCA
Statistics
Matches: 705, Mismatches: 192, Indels: 126
0.69 0.19 0.12
Matches are distributed among these distances:
17 10 0.01
18 1 0.00
19 1 0.00
20 4 0.01
21 1 0.00
22 96 0.14
23 526 0.75
24 43 0.06
25 3 0.00
26 1 0.00
28 19 0.03
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (23 bp):
TTCAATTTGCAGCACTTAAACAC
Found at i:5323634 original size:131 final size:133
Alignment explanation
Indices: 5323492--5323794 Score: 407
Period size: 131 Copynumber: 2.3 Consensus size: 133
5323482 ACAACATCTA
*
5323492 AACACTCCAATTTCCAGCACTTT-AACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAAC
1 AACACTCCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAAC
* *
5323556 ATTTATACACCTCAATTACAGTGATAAAACATCTCAA-T-CAACTAAACACTTCAATTTGCAGTA
65 ATTTATACACCTCAATTACAGCGATAAAACATCTCAATTACAACTAAACACTTCAATTTGCAGCA
5323619 CTTT
130 CTTT
* * *
5323623 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCTGTACTTTAACATCTCAATTAACAACA
1 AACACTCCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACA
**
5323688 TTTATACACCTCAATTGTAGCGATAAAACATCTCAATTTTCAGCAACTAAACACTTCAATTTGCA
66 TTTATACACCTCAATTACAGCGATAAAACATCTCAA--TT-A-CAACTAAACACTTCAATTTGCA
5323753 GCACTTT
127 GCACTTT
* * * * *
5323760 TACA-TCTCAATTAACAACATTTATACACCTCAATT
1 AACACTC-CAATTTACAGCATTTAAACACTTCAATT
5323795 GTAGCGATAA
Statistics
Matches: 150, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
130 3 0.02
131 90 0.60
134 1 0.01
136 1 0.01
137 55 0.37
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (133 bp):
AACACTCCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACA
TTTATACACCTCAATTACAGCGATAAAACATCTCAATTACAACTAAACACTTCAATTTGCAGCAC
TTT
Found at i:5323690 original size:46 final size:46
Alignment explanation
Indices: 5323237--5324043 Score: 536
Period size: 46 Copynumber: 17.7 Consensus size: 46
5323227 TTTGCAGTAC
* ** * *
5323237 TTAAACACTTCAATTTACAACATTTAAACA-CTTCAATTTATAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* * *
5323283 TCAAACACTTCAATTTGCAGTACTTTAACA-CTTCAATTTACAGCAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* *
5323329 TTAAACACTTCAATTTGCA-TCACTTTAACATCTCAATTAACAACAT
1 TTAAACACTTCAATTTGCAGT-ACTTAAACATCTCAATTTACAACAT
* * * * * * * *
5323375 TTATACACCTCAA-TTACAGTGA-TAAAACATCTCAATGTCCAGCAA
1 TTAAACACTTCAATTTGCAGT-ACTTAAACATCTCAATTTACAACAT
*
5323420 CTAAACACTTCAATTTGCAGTACTTAAACA-CTTCAATTTACAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* * * *
5323466 TTAAGCACTTCAATTTACA--ACATCTAAACA-CTCCAATTTCCAGCACT
1 TTAAACACTTCAATTTGCAGTAC-T-TAAACATCT-CAATTTACAACA-T
* * *
5323513 TT-AACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATCTCAATTTACAACAT
* * * *
5323558 TTATACACCTCAA-TTACAGTGA-TAAAACATCTCAA--T-CAAC--
1 TTAAACACTTCAATTTGCAGT-ACTTAAACATCTCAATTTACAACAT
* *
5323598 -TAAACACTTCAATTTGCAGTACTTTAACA-CTTCAATTTACAGCAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* * *
5323643 TTAAACACTTCAATTTGCTGTACTTTAACATCTCAATTAACAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATCTCAATTTACAACAT
* * * * * *
5323689 TTATACACCTCAATTGTAGC-G-A-TAAAACATCTCAATTTTCAGCAA
1 TTAAACACTTCAATT-T-GCAGTACTTAAACATCTCAATTTACAACAT
* * ** *
5323734 CTAAACACTTCAATTTGCAGCACTTTTACATCTCAATTAACAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATCTCAATTTACAACAT
* * * * * * * * *
5323780 TTATACACCTCAATTGTAGC-G-A-TAAAACATCCCCATGTCCAGCAA
1 TTAAACACTTCAATT-T-GCAGTACTTAAACATCTCAATTTACAACAT
* *
5323825 CTAAACACTTCAATTTGCAGTACTTAAACA-CTTCAATTTGCAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* * *
5323871 TTAAGCACTACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACAT
1 TT-A--A--ACACTTCAATTTGCAGTACTTAAACATCTCAATTTACAACAT
* * * * * * * * *
5323922 TTATACACCTCAA-TTACAGCAATAAAACATCTCAATTTTGCAGCAA
1 TTAAACACTTCAATTTGCAGTACTTAAACATCTCAA-TTTACAACAT
* * *
5323968 CTAAACACTTCAAATTGCAGTATTTAAACA-CTTCAATTTACAACAT
1 TTAAACACTTCAATTTGCAGTACTTAAACATC-TCAATTTACAACAT
* * *
5324014 TTAAACACTTCAATTTACAGCATTTAAACA
1 TTAAACACTTCAATTTGCAGTACTTAAACA
5324044 ACAACAATCA
Statistics
Matches: 588, Mismatches: 128, Indels: 90
0.73 0.16 0.11
Matches are distributed among these distances:
39 12 0.02
40 15 0.03
42 5 0.01
43 7 0.01
44 6 0.01
45 129 0.22
46 338 0.57
47 29 0.05
48 6 0.01
49 1 0.00
50 1 0.00
51 38 0.06
52 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (46 bp):
TTAAACACTTCAATTTGCAGTACTTAAACATCTCAATTTACAACAT
Found at i:5323739 original size:91 final size:91
Alignment explanation
Indices: 5323629--5323873 Score: 357
Period size: 91 Copynumber: 2.7 Consensus size: 91
5323619 CTTTAACACT
** *
5323629 TCAATTTACAGCATTTAAACACTTCAATTTGCTGTACTTTAACATCTCAATTAACAACATTTATA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGTACTTTAACATCTCAATTAACAACATTTATA
5323694 CACCTCAATTGTAGCGATAAAACATC
66 CACCTCAATTGTAGCGATAAAACATC
* * *
5323720 TCAATTTTCAGCAACTAAACACTTCAATTTGCAGCACTTTTACATCTCAATTAACAACATTTATA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGTACTTTAACATCTCAATTAACAACATTTATA
5323785 CACCTCAATTGTAGCGATAAAACATC
66 CACCTCAATTGTAGCGATAAAACATC
* * * * * **
5323811 CCCATGTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACA-CTTCAATTTGCAACATTTA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGTACTTTAACATC-TCAATTAACAACATTTA
5323874 AGCACTACAC
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
90 1 0.01
91 137 0.99
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (91 bp):
TCAATTTACAGCAACTAAACACTTCAATTTGCAGTACTTTAACATCTCAATTAACAACATTTATA
CACCTCAATTGTAGCGATAAAACATC
Found at i:5323908 original size:142 final size:143
Alignment explanation
Indices: 5323738--5324022 Score: 455
Period size: 142 Copynumber: 2.0 Consensus size: 143
5323728 CAGCAACTAA
* ** *
5323738 ACACTTCAATTTGCAGCACTTTTACATCTCAATTAACAACATTTATACACCTCAATTGTAGCGAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAAT
* * *
5323803 AAAACATCCCCA-TGTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTGCA
66 AAAACATCCCAATTGTCCAGCAACTAAACACTTCAAATTGCAGTACTTAAACACTTCAATTTACA
*
5323867 ACATTTAAGCACT
131 ACATTTAAACACT
5323880 ACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAAT
* * * *
5323945 AAAACATCTCAATTTTGCAGCAACTAAACACTTCAAATTGCAGTATTTAAACACTTCAATTTACA
66 AAAACATCCCAATTGTCCAGCAACTAAACACTTCAAATTGCAGTACTTAAACACTTCAATTTACA
5324010 ACATTTAAACACT
131 ACATTTAAACACT
5324023 TCAATTTACA
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 71 0.55
143 59 0.45
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (143 bp):
ACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAAT
AAAACATCCCAATTGTCCAGCAACTAAACACTTCAAATTGCAGTACTTAAACACTTCAATTTACA
ACATTTAAACACT
Found at i:5323958 original size:22 final size:23
Alignment explanation
Indices: 5323902--5323958 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
5323892 GCAGCACTTT
* *
5323902 AACATCTCAATTAACAACATTTA
1 AACATCTCAATTAACAACAATAA
* * *
5323925 TACACCTCAATT-ACAGCAATAA
1 AACATCTCAATTAACAACAATAA
5323947 AACATCTCAATT
1 AACATCTCAATT
5323959 TTGCAGCAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.28
Consensus pattern (23 bp):
AACATCTCAATTAACAACAATAA
Found at i:5324080 original size:7 final size:7
Alignment explanation
Indices: 5324068--5324124 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
5324058 TTAAATAAAA
5324068 GGTTTAG
1 GGTTTAG
5324075 GGTTTAG
1 GGTTTAG
*
5324082 GGTTTAA
1 GGTTTAG
*
5324089 GGTTTAA
1 GGTTTAG
*
5324096 GGTTTAA
1 GGTTTAG
5324103 GG-TT-G
1 GGTTTAG
5324108 GGTTTAG
1 GGTTTAG
5324115 GGTTTAG
1 GGTTTAG
5324122 GGT
1 GGT
5324125 AATGAGCAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 2 0.04
6 4 0.09
7 40 0.87
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:5326617 original size:41 final size:41
Alignment explanation
Indices: 5326546--5326642 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 41
5326536 TATAAAAATG
* * * * *
5326546 CCGCAAAAAACTGAACAATAGTAGCGTTTTTGGC-ACAAACA
1 CCGCTAAAAACTGATCAATAGGAGCATTTTTAGCTA-AAACA
*
5326587 CCGCTAAAAACTGATCAATAGCGA-CATTTTTAGCTAAAACG
1 CCGCTAAAAACTGATCAATAG-GAGCATTTTTAGCTAAAACA
*
5326628 CCACTAAAAACTGAT
1 CCGCTAAAAACTGAT
5326643 GAATGAGTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (41 bp):
CCGCTAAAAACTGATCAATAGGAGCATTTTTAGCTAAAACA
Found at i:5327046 original size:28 final size:28
Alignment explanation
Indices: 5327012--5327067 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5327002 TCTCTAAACC
5327012 CTTAAATCCT-AAACATTAAACCCTAAAT
1 CTTAAATCCTAAAACA-TAAACCCTAAAT
*
5327040 CTTAAATTCTAAAACATAAACCCTAAAT
1 CTTAAATCCTAAAACATAAACCCTAAAT
5327068 ACTAATCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (28 bp):
CTTAAATCCTAAAACATAAACCCTAAAT
Found at i:5327052 original size:21 final size:23
Alignment explanation
Indices: 5327004--5327045 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5326994 CATAACTTTC
5327004 TCTAAACCCTTAAATCCTAAACA
1 TCTAAACCCTTAAATCCTAAACA
*
5327027 T-TAAACCC-TAAATCTTAAA
1 TCTAAACCCTTAAATCCTAAA
5327046 TTCTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 7 0.39
23 1 0.06
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (23 bp):
TCTAAACCCTTAAATCCTAAACA
Found at i:5327066 original size:21 final size:21
Alignment explanation
Indices: 5327042--5327087 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5327032 CCCTAAATCT
*
5327042 TAAATTCTAAAACATAAACCC
1 TAAATACTAAAACATAAACCC
** *
5327063 TAAATACTAATCCATAAACTC
1 TAAATACTAAAACATAAACCC
5327084 TAAA
1 TAAA
5327088 ACCCTAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAATACTAAAACATAAACCC
Found at i:5327318 original size:36 final size:36
Alignment explanation
Indices: 5327239--5327319 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 36
5327229 GGTTTAAGGC
*
5327239 TTATGGTTTAAGGTTCAATGGTAGAATATATTTTAAGT
1 TTATGGTTTAAGGTTCAATGGT--AATATATGTTAAGT
* *
5327277 TTATGGTTTAGGGTTCAATGGT-ATAGTGTGTTAAGT
1 TTATGGTTTAAGGTTCAATGGTAATA-TATGTTAAGT
5327313 TTATGGT
1 TTATGGT
5327320 ATGGGCCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 3 0.08
36 15 0.38
38 21 0.54
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (36 bp):
TTATGGTTTAAGGTTCAATGGTAATATATGTTAAGT
Found at i:5334130 original size:40 final size:40
Alignment explanation
Indices: 5334070--5334180 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
5334060 CTCCAGAGGC
** * *
5334070 ATTAGCGGCATTTTTCTAAAAACACCACTAAAGATTGAGA
1 ATTAGCGGCGCTTTTGTAAAAACGCCACTAAAGATTGAGA
* * *
5334110 ATTAGCGGCGCTTTTGTAAAAATGCCGCAAAAGATTGAGA
1 ATTAGCGGCGCTTTTGTAAAAACGCCACTAAAGATTGAGA
* * *
5334150 TTTAACTGG-GCTTTTG-AAAAACGCCAATAAA
1 ATTAGC-GGCGCTTTTGTAAAAACGCCACTAAA
5334181 AGTCTAATTA
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
39 11 0.19
40 44 0.77
41 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTGTAAAAACGCCACTAAAGATTGAGA
Found at i:5336665 original size:46 final size:48
Alignment explanation
Indices: 5336614--5336744 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 48
5336604 ATGGTTGAGC
5336614 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACTAG
* * *
5336661 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTA-G
*
5336706 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5336745 GCGGGTTACA
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 28 0.40
48 2 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTAG
Found at i:5340621 original size:25 final size:25
Alignment explanation
Indices: 5340587--5340643 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
5340577 TCGTCAGCAA
* * *
5340587 CCCTCTGCTACATTTTCGCCGGCAT
1 CCCTTTGCTACATCTCCGCCGGCAT
*
5340612 CCCTTTGCTACATCTCCGTCGGCAT
1 CCCTTTGCTACATCTCCGCCGGCAT
5340637 CTCCTTT
1 C-CCTTT
5340644 CTGCCAACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.11, C:0.40, G:0.14, T:0.35
Consensus pattern (25 bp):
CCCTTTGCTACATCTCCGCCGGCAT
Found at i:5341229 original size:23 final size:23
Alignment explanation
Indices: 5341199--5341260 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5341189 AAAGTATTTG
5341199 GTTAAGAAAATTTATTTGATAAT
1 GTTAAGAAAATTTATTTGATAAT
*
5341222 GTTAAGAAAATTCATTTGATAAT
1 GTTAAGAAAATTTATTTGATAAT
**
5341245 AATAA-AAAATTTATTT
1 GTTAAGAAAATTTATTT
5341261 TTATTTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (23 bp):
GTTAAGAAAATTTATTTGATAAT
Found at i:5341955 original size:9 final size:9
Alignment explanation
Indices: 5341943--5342063 Score: 111
Period size: 9 Copynumber: 13.6 Consensus size: 9
5341933 TATATCATAT
5341943 CATAACTTA
1 CATAACTTA
*
5341952 CATAATTTA
1 CATAACTTA
5341961 CATAACTTA
1 CATAACTTA
*
5341970 TATAACTTA
1 CATAACTTA
* *
5341979 GATAA-ATA
1 CATAACTTA
*
5341987 TATAACTTA
1 CATAACTTA
5341996 CATAACTTA
1 CATAACTTA
* *
5342005 CACAA-ATA
1 CATAACTTA
* * *
5342013 TATATCATA
1 CATAACTTA
5342022 TCATAACTTA
1 -CATAACTTA
5342032 CATAACTTA
1 CATAACTTA
*
5342041 CAAAACTTA
1 CATAACTTA
*
5342050 CTTAACTTA
1 CATAACTTA
5342059 CATAA
1 CATAA
5342064 TACATAAATA
Statistics
Matches: 89, Mismatches: 20, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
8 10 0.11
9 73 0.82
10 6 0.07
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:5341990 original size:17 final size:17
Alignment explanation
Indices: 5341953--5342000 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5341943 CATAACTTAC
* *
5341953 ATAATTTACATAACTTAT
1 ATAACTTACATAA-ATAT
*
5341971 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
5341988 ATAACTTACATAA
1 ATAACTTACATAA
5342001 CTTACACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAACTTACATAAATAT
Found at i:5342133 original size:7 final size:7
Alignment explanation
Indices: 5342121--5342152 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
5342111 ACACCCATTA
5342121 GATACTT
1 GATACTT
5342128 GATACTT
1 GATACTT
5342135 GATACTT
1 GATACTT
5342142 GATACTT
1 GATACTT
5342149 GATA
1 GATA
5342153 TGTATTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (7 bp):
GATACTT
Found at i:5347823 original size:21 final size:21
Alignment explanation
Indices: 5347793--5347881 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
5347783 GTATTTAAGG
* *
5347793 GTTTAAGGGTTTAGTGTCTATA
1 GTTT-AGGGTTTAGGGTTTATA
5347815 GTTTAGGGTTTAGGGTTTATTA
1 GTTTAGGGTTTAGGGTTTA-TA
* *
5347837 -TTTAGGATTTAGGGTTTATG
1 GTTTAGGGTTTAGGGTTTATA
* * *
5347857 GTTTATGGTTTAAGGTTTAGA
1 GTTTAGGGTTTAGGGTTTATA
5347878 GTTT
1 GTTT
5347882 TATGATTTAG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 49 0.88
22 6 0.11
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.49
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTTTATA
Found at i:5347827 original size:7 final size:7
Alignment explanation
Indices: 5347790--5348024 Score: 73
Period size: 7 Copynumber: 33.0 Consensus size: 7
5347780 TTTGTATTTA
5347790 AGGGTTT
1 AGGGTTT
5347797 AAGGGTTT
1 -AGGGTTT
* *
5347805 AGTGTCT
1 AGGGTTT
**
5347812 ATAGTTT
1 AGGGTTT
5347819 AGGGTTT
1 AGGGTTT
5347826 AGGGTTT
1 AGGGTTT
***
5347833 ATTATTT
1 AGGGTTT
*
5347840 AGGATTT
1 AGGGTTT
5347847 AGGGTTT
1 AGGGTTT
*
5347854 ATGGTTT
1 AGGGTTT
*
5347861 ATGGTTT
1 AGGGTTT
*
5347868 AAGGTTT
1 AGGGTTT
*
5347875 AGAGTTTT
1 AG-GGTTT
* *
5347883 ATGATTT
1 AGGGTTT
*
5347890 AGGATTT
1 AGGGTTT
*
5347897 AGGATTT
1 AGGGTTT
* **
5347904 CGTATTT
1 AGGGTTT
*
5347911 AAGGGCTTA
1 -AGGG-TTT
5347920 AGGG-TT
1 AGGGTTT
*
5347926 AGTGATTT
1 AG-GGTTT
*
5347934 -GAGTTT
1 AGGGTTT
*
5347940 AAGGTTT
1 AGGGTTT
*
5347947 AAGGTTT
1 AGGGTTT
*
5347954 AGAGTTTT
1 AG-GGTTT
*
5347962 AGGATTT
1 AGGGTTT
*
5347969 AGGATTT
1 AGGGTTT
***
5347976 -TTATTT
1 AGGGTTT
5347982 AAGGGTTT
1 -AGGGTTT
*
5347990 AGTGATTT
1 AG-GGTTT
5347998 A-GGTTT
1 AGGGTTT
5348004 AGGGTTT
1 AGGGTTT
*
5348011 AAGGTTT
1 AGGGTTT
*
5348018 AGAGTTT
1 AGGGTTT
5348025 TAGGATTTAA
Statistics
Matches: 171, Mismatches: 45, Indels: 23
0.72 0.19 0.10
Matches are distributed among these distances:
6 15 0.09
7 121 0.71
8 33 0.19
9 2 0.01
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:5347911 original size:64 final size:63
Alignment explanation
Indices: 5347815--5348055 Score: 218
Period size: 64 Copynumber: 3.6 Consensus size: 63
5347805 AGTGTCTATA
* * ** *
5347815 GTTTAGGGTTTAGGGTTTATTATTTAGGATTT-AGGGTTTATGGTTTATGGTTTAAGGTTTAGAG
1 GTTTAGAGTTTAGGATTTAGGATTT-GTATTTAAGGGTTTATGGTTTATGGTTTAAGGTTTA-AG
* * *
5347879 TTTTATGA-TTTAGGATTTAGGATTTCGTATTTAAGGGCTTAAGGGTTAGTGATTTGAGTTTAAG
1 GTTTA-GAGTTTAGGATTTAGGATTT-GTATTTAAGGG-TTTATGGTT--T-A--TG-GTTTAAG
5347943 GTTTAAG
57 GTTTAAG
* * *
5347950 GTTTAGAGTTTTAGGATTTAGGATTTTTATTTAAGGGTTTAGTGATTTA-GGTTTAGGGTTTAAG
1 GTTTAGAG-TTTAGGATTTAGGATTTGTATTTAAGGGTTTA-TGGTTTATGGTTTAAGGTTTAAG
*
5348014 GTTTAGAGTTTTAGGATTTAAGATTTTGTATTTAAGGGTTTA
1 GTTTAGAG-TTTAGGATTTAGGA-TTTGTATTTAAGGGTTTA
5348056 AGGGAGTGTT
Statistics
Matches: 147, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
64 58 0.39
65 23 0.16
66 7 0.05
68 2 0.01
69 2 0.01
70 5 0.03
71 21 0.14
72 29 0.20
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.48
Consensus pattern (63 bp):
GTTTAGAGTTTAGGATTTAGGATTTGTATTTAAGGGTTTATGGTTTATGGTTTAAGGTTTAAG
Done.