Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000174.1 Hibiscus syriacus cultivar Beakdansim tig00000305_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 116205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3820 original size:22 final size:22
Alignment explanation
Indices: 3776--3820 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3766 TCAGAGAAAA
* * *
3776 ATAAAATAAAATTAAGCATTTG
1 ATAAAATAAAATAAAGAAATTG
*
3798 ATAAAATAAAATAAATAAATTG
1 ATAAAATAAAATAAAGAAATTG
3820 A
1 A
3821 ATGAAATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (22 bp):
ATAAAATAAAATAAAGAAATTG
Found at i:3828 original size:5 final size:5
Alignment explanation
Indices: 3820--3854 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3810 AAATAAATTG
*
3820 AATGA AATGA AATGA AATGA AAT-A AATTA AATGA A
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA A
3855 TAAGTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (5 bp):
AATGA
Found at i:3840 original size:19 final size:19
Alignment explanation
Indices: 3801--3854 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
3791 GCATTTGATA
3801 AAATAAAATAAAT-AAATTG
1 AAAT-AAATAAATGAAATTG
3820 -AATGAAATGAAATGAAA-TG
1 AAAT-AAAT-AAATGAAATTG
3839 AAATAAATTAAATGAA
1 AAATAAA-TAAATGAA
3855 TAAGTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 7 0.23
19 16 0.53
20 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AAATAAATAAATGAAATTG
Found at i:9063 original size:21 final size:21
Alignment explanation
Indices: 9039--9079 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9029 AGCGTTTGTG
9039 CGTGGATTCTTCGTGCTCGTA
1 CGTGGATTCTTCGTGCTCGTA
9060 CGTGGATTCTTCGTGCTCGT
1 CGTGGATTCTTCGTGCTCGT
9080 GCTTCGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.24, G:0.29, T:0.39
Consensus pattern (21 bp):
CGTGGATTCTTCGTGCTCGTA
Found at i:10133 original size:414 final size:414
Alignment explanation
Indices: 9329--10140 Score: 1371
Period size: 417 Copynumber: 2.0 Consensus size: 414
9319 TTGTTCCTGA
9329 ATGGTAGAGTTTGGATAGGGATTAAATTTAAGATTAAAAATAAATAAAAATATAAAAATAAAGGT
1 ATGGTAGAGTTTGGATAGGGATTAAATTTAAGATTAAAAATAAATAAAAATATAAAAATAAAGGT
* * *
9394 GATAAGAAAAAGATAAATAGGGGTTTTGGAAAAAGTGTTTCAAGATAAGATAAAGTCAAATAAAT
66 GATAAGAAAAAGATAAATAAGGGTTTTGGAAAAAATGTTTCAAGATAAGATAAAGTCAAATAAAA
9459 TAATAATAAATATAATAAAATAGAAATTAGAGTTTGAAAAGAAGACTTATTGTAAAAACTAGCCT
131 TAATAATAAATATAATAAAATAGAAATTAGAGTTTGAAAAGAAGACTTATTGTAAAAACTAGCCT
* *
9524 CAGGCTTTCAGTTTTTACTCAGTTTCCTCGGATCATCGAAATAGATCTTTACTTCAGGATTCACG
196 CAGGCTTTCAGCTTTTACTCAGTTTCCTCGGATCATCGAAATAGATCTTTACTCCAGGATTCACG
* *
9589 TCGGTTACTTGTCTACAACGACAAATCCTTGTGACTATGCTTTGTATACTGAATACCCAAGTGTA
261 TCCGTTACTTATCTACAACGACAAATCCTTGTGACTATGCTTTGTATACTGAATACCCAAGTGTA
*
9654 ATCTTTAATATCGATTTGTGAATTGATCTAAACAACAACAATATTGTAGATCTAAAAATGTTGAG
326 ATCTTTAATATCGATTTGTGAATTGATCTAAACAACAACAATATTGAAGATCTAAAAATGTTGAG
9719 GCTCGAAACGTTTGGATAGTGACT
391 GCTCGAAACGTTTGGATAGTGACT
*
9743 ATGGTAGAGTTTGGATATGGATTAAATTTAAGATTAAAAAATAAATAAAAATATAAAAATAAAAG
1 ATGGTAGAGTTTGGATAGGGATTAAATTTAAGATT-AAAAATAAATAAAAATATAAAAAT-AAAG
*
9808 GTGAGATAAGAAAAAGATAAATAAGGGTTTTGGAAAAAATGTTTCAAGATAAGATAAAGT-TAAT
64 GT--GATAAGAAAAAGATAAATAAGGGTTTTGGAAAAAATGTTTCAAGATAAGATAAAGTCAAAT
** * *
9872 AAAATAATAATAAATATAATAAAATATTAATTAGTGTTTGAAAAGAAGACTTGTTGTAAAAACTA
127 AAAATAATAATAAATATAATAAAATAGAAATTAGAGTTTGAAAAGAAGACTTATTGTAAAAACTA
*
9937 GCCTCAGGCTTTTAGCTTTTACTCAGTTTCCTCGGATCATCGAAATAGATCTTTACTCCAGGATT
192 GCCTCAGGCTTTCAGCTTTTACTCAGTTTCCTCGGATCATCGAAATAGATCTTTACTCCAGGATT
* * *
10002 TACG-CCGTTACTTATCTATAAGGA-AAATCCTTGTGACTATGCTTTGTATACT-AATACCCAAG
257 CACGTCCGTTACTTATCTACAACGACAAATCCTTGTGACTATGCTTTGTATACTGAATACCCAAG
* * *
10064 TGTAATCTTTAATATTGGTTTGTGAATTGATCTAAACAACAACAATGTTGAAGATCTAAAAATGT
322 TGTAATCTTTAATATCGATTTGTGAATTGATCTAAACAACAACAATATTGAAGATCTAAAAATGT
10129 TGAGGCTCGAAA
387 TGAGGCTCGAAA
10141 AGTTGTTGAC
Statistics
Matches: 373, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
414 117 0.31
415 52 0.14
416 22 0.06
417 128 0.34
418 54 0.14
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (414 bp):
ATGGTAGAGTTTGGATAGGGATTAAATTTAAGATTAAAAATAAATAAAAATATAAAAATAAAGGT
GATAAGAAAAAGATAAATAAGGGTTTTGGAAAAAATGTTTCAAGATAAGATAAAGTCAAATAAAA
TAATAATAAATATAATAAAATAGAAATTAGAGTTTGAAAAGAAGACTTATTGTAAAAACTAGCCT
CAGGCTTTCAGCTTTTACTCAGTTTCCTCGGATCATCGAAATAGATCTTTACTCCAGGATTCACG
TCCGTTACTTATCTACAACGACAAATCCTTGTGACTATGCTTTGTATACTGAATACCCAAGTGTA
ATCTTTAATATCGATTTGTGAATTGATCTAAACAACAACAATATTGAAGATCTAAAAATGTTGAG
GCTCGAAACGTTTGGATAGTGACT
Found at i:10504 original size:21 final size:24
Alignment explanation
Indices: 10478--10520 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
10468 ATATTTGAAA
10478 AAAACTT-AAAT-AAAA-AAAATG
1 AAAACTTGAAATGAAAAGAAAATG
10499 AAAACTTGAAATGAAAAGAAAA
1 AAAACTTGAAATGAAAAGAAAA
10521 GAGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 4 0.21
24 4 0.21
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (24 bp):
AAAACTTGAAATGAAAAGAAAATG
Found at i:19658 original size:3 final size:3
Alignment explanation
Indices: 19652--19685 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
19642 CATAATTTAT
19652 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19686 TATTTTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:19688 original size:12 final size:12
Alignment explanation
Indices: 19646--19691 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
19636 CAACAACATA
19646 ATTTA-TTTATT
1 ATTTATTTTATT
19657 A-TTATTATTATT
1 ATTTATT-TTATT
19669 ATTATTATTTTATT
1 A-T-TTATTTTATT
19683 ATTTATTTT
1 ATTTATTTT
19692 CTCTCACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.10
11 2 0.07
12 13 0.43
13 1 0.03
14 6 0.20
15 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:19756 original size:14 final size:15
Alignment explanation
Indices: 19732--19771 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
19722 TTTTAATGTA
19732 TTTTATATTTTTTT-C
1 TTTT-TATTTTTTTAC
19747 TTTTTATTTTTTTAC
1 TTTTTATTTTTTTAC
19762 TTTATTATTT
1 TTT-TTATTT
19772 CATAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.39
15 8 0.35
16 6 0.26
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTATTTTTTTAC
Found at i:19810 original size:21 final size:21
Alignment explanation
Indices: 19781--19820 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19771 TCATAAAATT
19781 TTTACTTGTTTATTTTATTTG
1 TTTACTTGTTTATTTTATTTG
*
19802 TTTATTTGTTTATTTTATT
1 TTTACTTGTTTATTTTATT
19821 ATTCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTACTTGTTTATTTTATTTG
Found at i:19885 original size:18 final size:19
Alignment explanation
Indices: 19837--19882 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
19827 TTTACTAAAT
*
19837 TTATTTATTTATATTTATTTA
1 TTATTTATTTTTA-TTA-TTA
19858 TCTATTTATTTTTATTATTA
1 T-TATTTATTTTTATTATTA
19878 TTATT
1 TTATT
19883 ATTATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 4 0.17
22 11 0.48
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTATTTTTATTATTA
Found at i:21780 original size:37 final size:37
Alignment explanation
Indices: 21730--21805 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
21720 TATTTTCATT
21730 TCTTTATATTCGCATTAACTAACAAAAGCATGTCTCC
1 TCTTTATATTCGCATTAACTAACAAAAGCATGTCTCC
21767 TCTTTATATTCGCATTAACTAACAAAAGCATGTCTCC
1 TCTTTATATTCGCATTAACTAACAAAAGCATGTCTCC
21804 TC
1 TC
21806 GAAAGGAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (37 bp):
TCTTTATATTCGCATTAACTAACAAAAGCATGTCTCC
Found at i:22790 original size:95 final size:97
Alignment explanation
Indices: 22627--22842 Score: 312
Period size: 95 Copynumber: 2.2 Consensus size: 97
22617 TGACAAACTT
* * *
22627 CCTCTAGAGCAATTGGTTAAACGCCTTGACTTTATAGATAAGATTCAGCTAGCCTGCTAAAGGTG
1 CCTCTAGAGCAATTGGTTAAACGCCTCGACTTTATAGATAAGATTCAGCTAGCCTGATAAAGGCG
*
22692 ATTATAATATACAATA-AA-G-CTTGAGTTGTC
66 ATTATAATAT-CAATACAATGAATTGAGTTGTC
* * * *
22722 CCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATTGATAATATTCAGCTAGCCTTATAAAGGCG
1 CCTCTAGAGCAATTGGTTAAACGCCTCGACTTTATAGATAAGATTCAGCTAGCCTGATAAAGGCG
*
22787 ATTATAATATCTATACAATGATATTGAGTTGTC
66 ATTATAATATCAATACAATGA-ATTGAGTTGTC
22820 CCTCTAGAGCAATTGGTTAAACG
1 CCTCTAGAGCAATTGGTTAAACG
22843 TGCCTACTTT
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
94 4 0.04
95 70 0.65
96 1 0.01
98 33 0.31
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (97 bp):
CCTCTAGAGCAATTGGTTAAACGCCTCGACTTTATAGATAAGATTCAGCTAGCCTGATAAAGGCG
ATTATAATATCAATACAATGAATTGAGTTGTC
Found at i:24321 original size:240 final size:240
Alignment explanation
Indices: 23882--24420 Score: 844
Period size: 240 Copynumber: 2.2 Consensus size: 240
23872 GACACCATTT
* *
23882 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAT
1 ACTCTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACGGCGAA
* * **
23947 GGGGCTTCCCAGTTTCATTTAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCAAAACA
66 GGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACAAAAAACA
*
24012 ATACAAGCTTGGATTTCAACTTCACGACGAAGGAAATTCAAGTCAAGGCTCAACTTCACAACAAA
131 ATACAAGCTTGGATTTCAACTTCACGACGAAGGAAATTCAAGTCAAGGCTCAACTTCAAAACAAA
*
24077 GGGGCTATCCACAATTTCAACTTCACGACGAAGGATATCGTGCTA
196 GGGGCCATCCACAATTTCAACTTCACGACGAAGGATATCGTGCTA
* * * * *
24122 ACTCTATATTGGATTTTAACTTCACGACGAATGATATCCAATTTAAAGCTCAACTTCACGGTGAA
1 ACTCTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACGGCGAA
*
24187 GGGGCTTTCCAATTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACAAAAAACA
66 GGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACAAAAAACA
* * * * *
24252 ATACAATCTTGGATTTCAACTTCACGACGGATGATATTCAAGTCAAGGCTCAACTTCAAAACGAA
131 ATACAAGCTTGGATTTCAACTTCACGACGAAGGAAATTCAAGTCAAGGCTCAACTTCAAAACAAA
*
24317 GGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCTA
196 GGGGCCATCCACAATTTCAACTTCACGACGAAGGATATCGTGCTA
* * * * * *
24362 ACGCAAGCTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCAC
1 ACTCTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCAC
24421 AACGAATGGG
Statistics
Matches: 270, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
240 270 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (240 bp):
ACTCTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACGGCGAA
GGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACAAAAAACA
ATACAAGCTTGGATTTCAACTTCACGACGAAGGAAATTCAAGTCAAGGCTCAACTTCAAAACAAA
GGGGCCATCCACAATTTCAACTTCACGACGAAGGATATCGTGCTA
Found at i:24413 original size:110 final size:110
Alignment explanation
Indices: 24259--24465 Score: 369
Period size: 110 Copynumber: 1.9 Consensus size: 110
24249 ACAATACAAT
* * *
24259 CTTGGATTTCAACTTCACGACGGATGATATTCAAGTCAAGGCTCAACTTCAAAACGAAGGGGCCA
1 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCAAAACGAAGGGGACA
24324 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCTAACGCAAG
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCTAACGCAAG
* *
24369 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGACA
1 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCAAAACGAAGGGGACA
24434 TCCACGATTTCAACTTCACGACGAAGGATATC
66 TCCACGATTTCAACTTCACGACGAAGGATATC
24466 TAATTCAAAG
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 92 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (110 bp):
CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCAAAACGAAGGGGACA
TCCACGATTTCAACTTCACGACGAAGGATATCGTGCTAACGCAAG
Found at i:24773 original size:124 final size:124
Alignment explanation
Indices: 24553--24784 Score: 340
Period size: 124 Copynumber: 1.9 Consensus size: 124
24543 TTGGACTCGA
* ** *
24553 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTCAGATTGGATTTCAACTTCACGACAAAAAATATCCAATTCAAAGCTCAAC
* ** * *
24618 TTCACAACGAATAGGTTATCCATGGTTTCAACTTCACGACGAAGAGAATTGTGCCCACC
66 TTCACAACGAAGAGGCCATCCACGATTTCAACTTCACGACGAAGAGAATTGTGCCCACC
*
24677 AGCAACATTCATCTTCAGATTGGATTTCAACTTTAC-AGCAAAAAATATCCAATTCAAAGCTCAA
1 AGCAACATTCATCTTCAGATTGGATTTCAACTTCACGA-CAAAAAATATCCAATTCAAAGCTCAA
* *
24741 CTTCACAACGAAGGGGCCCTCCACGATTTCAACTTCACGACGAA
65 CTTCACAACGAAGAGGCCATCCACGATTTCAACTTCACGACGAA
24785 TGATATCGTT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 1 0.01
124 94 0.99
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (124 bp):
AGCAACATTCATCTTCAGATTGGATTTCAACTTCACGACAAAAAATATCCAATTCAAAGCTCAAC
TTCACAACGAAGAGGCCATCCACGATTTCAACTTCACGACGAAGAGAATTGTGCCCACC
Found at i:24991 original size:84 final size:84
Alignment explanation
Indices: 24865--25141 Score: 340
Period size: 84 Copynumber: 3.3 Consensus size: 84
24855 TACAATATAG
* * * * * * * *
24865 CTCAAGGCAAAAAGGGCTATTTACCAACAAAAAACCTTCGAGTTTGACTACGCTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGATTACACTTAGCTCAAAGG
*
24930 CATATCATTTGTAGCATAA
66 CATATCATTTGCAGCATAA
* * * *
24949 CTCAAGGCTAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGATTACACTTAGCTCAAAGG
1 CTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGATTACACTTAGCTCAAAGG
* *
25014 CACATCATTTGCAGCATAG
66 CATATCATTTGCAGCATAA
* * *
25033 CTCAAGGCGACAAGGGCTATCTTCCAACAAAAGACCTTCGAGTTTGATTTA-ATTTAGCTCAAAG
1 CTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGA-TTACACTTAGCTCAAAG
*
25097 GCATATCCAATTTACAGCATAA
65 GCATAT-C-ATTTGCAGCATAA
*
25119 CTCAAGGCGAGAAGGGTTATCTG
1 CTCAAGGCGAGAAGGGCTATCTG
25142 TCAGTCAATA
Statistics
Matches: 163, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
84 128 0.79
85 4 0.02
86 31 0.19
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (84 bp):
CTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGATTACACTTAGCTCAAAGG
CATATCATTTGCAGCATAA
Found at i:25232 original size:169 final size:167
Alignment explanation
Indices: 24880--25233 Score: 362
Period size: 169 Copynumber: 2.1 Consensus size: 167
24870 GGCAAAAAGG
* **
24880 GCTAT-TTACCAACAAAAAACCTTCGAGTTTGACTACGCTCAGCTCAAAGGCATATCATTTGTAG
1 GCTATATT-CCAACAAAAAACCTTCGAGTTTGACTACACTCAGCTCAAAGGCATATCATTTACAG
*
24944 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGATTACACTTAGCTC
65 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGATTACACTTAGCTC
* * **
25009 AAAGGCACATCATTTGCAGCATAGCTCAAGGCGACAAGG
130 AAAGGCACA-CATTTACAGCATAACTCAAGGCGACAAAA
* * * * *
25048 GCTATCTTCCAACAAAAGACCTTCGAGTTTGATTTA-ATTTAGCTCAAAGGCATATCCAATTTAC
1 GCTATATTCCAACAAAAAACCTTCGAGTTTGA-CTACACTCAGCTCAAAGGCATAT-C-ATTTAC
* * * * *
25112 AGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AGTCAATACCTTCGAGTTCGATTTCA-TTCAG
63 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGATTACACTT-AG
* * * *
25175 CTCAAGAGTGTCA-A-ATTTACAGTATAACTTAAGTCGAGAAAA
127 CTCAA-AG-G-CACACATTTACAGCATAACTCAAGGCGACAAAA
*
25217 GTTATATGT-CAACAAAA
1 GCTATAT-TCCAACAAAA
25234 TTATTGAGTT
Statistics
Matches: 154, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
168 46 0.30
169 67 0.44
170 37 0.24
171 2 0.01
172 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (167 bp):
GCTATATTCCAACAAAAAACCTTCGAGTTTGACTACACTCAGCTCAAAGGCATATCATTTACAGC
ATAACTCAAGGCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGATTACACTTAGCTCA
AAGGCACACATTTACAGCATAACTCAAGGCGACAAAA
Found at i:26884 original size:20 final size:20
Alignment explanation
Indices: 26836--26877 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
26826 ATGTTCTTGC
26836 TTATTTCATT-TTATTATAAT
1 TTATTT-ATTATTATTATAAT
*
26856 TTATTTATTATTATTATTAT
1 TTATTTATTATTATTATAAT
26876 TT
1 TT
26878 TGTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTTATTATTATTATAAT
Found at i:26960 original size:15 final size:16
Alignment explanation
Indices: 26930--26971 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
26920 TCTTTTAACA
26930 TCTTTTTATATATTTT
1 TCTTTTTATATATTTT
26946 TCTTTTTATAT-TTTT
1 TCTTTTTATATATTTT
26961 TACTTTATTAT
1 T-CTTT-TTAT
26972 TTCATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.21
16 15 0.62
17 4 0.17
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTTTTATATATTTT
Found at i:26989 original size:8 final size:8
Alignment explanation
Indices: 26948--27031 Score: 55
Period size: 8 Copynumber: 10.4 Consensus size: 8
26938 TATATTTTTC
26948 TTTTTATAT
1 TTTTTAT-T
*
26957 TTTTTACT
1 TTTTTATT
*
26965 TTATTATT
1 TTTTTATT
** *
26973 TCATAATT
1 TTTTTATT
26981 TTTTTATT
1 TTTTTATT
*
26989 TGTTTATT
1 TTTTTATT
*
26997 TTATTATT
1 TTTTTATT
*
27005 TTATTT-GT
1 TT-TTTATT
27013 TTTTTATT
1 TTTTTATT
27021 ATTTTT-TT
1 -TTTTTATT
27029 TTT
1 TTT
27032 ACTAAATTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
7 6 0.10
8 39 0.67
9 13 0.22
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:27008 original size:21 final size:21
Alignment explanation
Indices: 26982--27032 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
26972 TTCATAATTT
26982 TTTTATTTGTTTATTTTATTA
1 TTTTATTTGTTTATTTTATTA
27003 TTTTATTTG-TT-TTTTATTA
1 TTTTATTTGTTTATTTTATTA
27022 TTTT-TTT-TTTA
1 TTTTATTTGTTTA
27033 CTAAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 2 0.07
21 9 0.32
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTATTTGTTTATTTTATTA
Found at i:27019 original size:16 final size:15
Alignment explanation
Indices: 26980--27069 Score: 65
Period size: 14 Copynumber: 5.7 Consensus size: 15
26970 ATTTCATAAT
*
26980 TTTTTTATTTGTTTA
1 TTTTTTATTTATTTA
*
26995 TTTTATTATTTTATTTG
1 TTTT-TTA-TTTATTTA
*
27012 TTTTTTA-TTATTTT
1 TTTTTTATTTATTTA
**
27026 TTTTTTACTAAATTTA
1 TTTTTTA-TTTATTTA
*
27042 TTTACCTTTATTTATCTA
1 TTT---TTTATTTATTTA
27060 TTTTTTATTT
1 TTTTTTATTT
27070 TCATTGTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 13 0.22
15 11 0.19
16 13 0.22
17 10 0.17
18 8 0.14
19 4 0.07
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTATTTATTTA
Found at i:27804 original size:35 final size:36
Alignment explanation
Indices: 27763--27831 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
27753 TCCATTCTCT
*
27763 TTATTTGGTTAATTTA-TTTATAAAATCTTGGCAAA
1 TTATTTGGTTAAATTATTTTATAAAATCTTGGCAAA
27798 TTATTTGGTTAAATTATTTTATAAAATCTTGGCA
1 TTATTTGGTTAAATTATTTTATAAAATCTTGGCA
27832 TAACGATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (36 bp):
TTATTTGGTTAAATTATTTTATAAAATCTTGGCAAA
Found at i:28670 original size:20 final size:20
Alignment explanation
Indices: 28645--28699 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
28635 TAATTAATCG
28645 TATTTTTATATTTAACTTAA
1 TATTTTTATATTTAACTTAA
*
28665 TATTTTTATATTTTAAATTTAA
1 TATTTTTATA-TTT-AACTTAA
*
28687 -ATATTTATATTTA
1 TATTTTTATATTTA
28700 GAAAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.42
21 11 0.35
22 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATATTTAACTTAA
Found at i:28679 original size:21 final size:22
Alignment explanation
Indices: 28645--28698 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
28635 TAATTAATCG
28645 TATTTTTATA-TTT-AACTTAA
1 TATTTTTATATTTTAAACTTAA
*
28665 TATTTTTATATTTTAAATTTAA
1 TATTTTTATATTTTAAACTTAA
*
28687 -ATATTTATATTT
1 TATTTTTATATTT
28699 AGAAAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 10 0.33
21 14 0.47
22 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATATTTTAAACTTAA
Found at i:30796 original size:16 final size:16
Alignment explanation
Indices: 30775--30810 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
30765 TTTGGGGTAA
30775 AGAAACGCTCAATGTC
1 AGAAACGCTCAATGTC
30791 AGAAACGCTCAATGTC
1 AGAAACGCTCAATGTC
30807 AGAA
1 AGAA
30811 CCGACAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAAACGCTCAATGTC
Found at i:31094 original size:11 final size:9
Alignment explanation
Indices: 31065--31114 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
31055 ATGCATTTGA
31065 TTTTTTCTT
1 TTTTTTCTT
31074 TTTTTTCTT
1 TTTTTTCTT
31083 TTTTGTTGCTT
1 TTTT-TT-CTT
* *
31094 TGTTTTCCAT
1 T-TTTTTCTT
31104 TTTTTTCTT
1 TTTTTTCTT
31113 TT
1 TT
31115 CTCCCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 21 0.62
10 5 0.15
11 5 0.15
12 3 0.09
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:34619 original size:13 final size:13
Alignment explanation
Indices: 34601--34641 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
34591 TCGATATTGA
*
34601 AAAATAAATGTTT
1 AAAATAAATATTT
*
34614 AAAATAATTTATTT
1 AAAATAA-ATATTT
34628 AAAATAAATATTT
1 AAAATAAATATTT
34641 A
1 A
34642 TTTACTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:36030 original size:3 final size:3
Alignment explanation
Indices: 36001--36083 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
35991 GGCCTGTTTG
* * *
36001 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
36048 TAA TTA TAA TTA TAA TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36084 AATGAGTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 60 0.91
4 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:36504 original size:36 final size:36
Alignment explanation
Indices: 36433--36561 Score: 199
Period size: 40 Copynumber: 3.5 Consensus size: 36
36423 GTTGAACAAA
*
36433 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
36467 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
36503 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAG
36543 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
36562 TCTCTGGAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
34 22 0.25
35 1 0.01
36 26 0.30
37 3 0.03
39 6 0.07
40 30 0.34
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.49
Consensus pattern (36 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
Found at i:37238 original size:113 final size:113
Alignment explanation
Indices: 36503--37238 Score: 1154
Period size: 113 Copynumber: 6.5 Consensus size: 113
36493 TTCAGATGAG
36503 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCT
* * *
36567 GGAAAAGTTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAG
65 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* * * *
36616 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTTATTATGAACT-TCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
* * *
36680 GAAAAGCTGATCCATCAAGTGATGGATCTGAGCAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* * *
36728 CTCTTCTCATTATGAACTTCTTCTTCCTACTTCAGATGAGTTCTTCTTATTATGAACT-TCTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TTCT
* * *
36792 GGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAG
65 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* *
36841 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
* * * *
36906 GAAAAGTTAATCCATCAAATGATGAATTTGAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
***
36954 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
* *
37019 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
37067 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
* * *
37132 GAAAAGCTAATCCATCAAATGATGAATTTGAGCAAAAGATTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
37180 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
37239 GAACTGGTTA
Statistics
Matches: 581, Mismatches: 40, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
112 105 0.18
113 475 0.82
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:38432 original size:94 final size:92
Alignment explanation
Indices: 38151--38517 Score: 554
Period size: 94 Copynumber: 4.0 Consensus size: 92
38141 CTATGAGCAA
* * * * *
38151 ATTCATTTTTCAATATCTCATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAA-ATTTAATGATTGGTT-TTTGGGTTCATACCAAACCAGATCAGATAACTCAA
38216 AGAACACTTCCAGAAGATGCTATTAACAC
64 AGAACACTTCCAGAAGATGCTATTAACAC
38245 ATTCATCTTTCAAATTTAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTTCAAATTTAATGATTGGTTTTT-GGGTTCATACCAAACCAGATCAGATAACTCAAA
38310 GAACACTTCCAGAAGATGCTATTAACAC
65 GAACACTTCCAGAAGATGCTATTAACAC
38338 ATTCATCTTTCAAATTTAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAATTTAATGATTGG-TTTTT-GGGTTCATACCAAACCAGATCAGATAACTCAA
38403 AGAACACTTCCAGAAGATGCTATTAACAC
64 AGAACACTTCCAGAAGATGCTATTAACAC
*
38432 ATTCATCTTTCAAATTCAATGATTGG----T---TT--TACCAAACCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATTTAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
38488 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATTAACAC
38515 ATT
1 ATT
38518 GCATTTGTTC
Statistics
Matches: 263, Mismatches: 8, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
83 55 0.21
85 2 0.01
89 1 0.00
92 2 0.01
93 99 0.38
94 104 0.40
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (92 bp):
ATTCATCTTTCAAATTTAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTAACAC
Found at i:39895 original size:8 final size:8
Alignment explanation
Indices: 39882--39944 Score: 72
Period size: 8 Copynumber: 7.4 Consensus size: 8
39872 CCTTGACCCC
39882 CTTTTTTT
1 CTTTTTTT
39890 CTTTTTCTTT
1 C-TTTT-TTT
39900 CTTTTTTT
1 CTTTTTTT
39908 CTTTTCTTTT
1 C-TTT-TTTT
39918 CTTTTTTT
1 CTTTTTTT
*
39926 CTTTCTTT
1 CTTTTTTT
*
39934 CTTTTTCT
1 CTTTTTTT
39942 CTT
1 CTT
39945 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 25 0.52
9 14 0.29
10 9 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTT
Found at i:39902 original size:4 final size:4
Alignment explanation
Indices: 39893--39937 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
39883 TTTTTTTCTT
* *
39893 TTTC TTTC TTTT TTTC TTTTC TTTTC TTTT TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC -TTTC -TTTC TTTC TTTC TTTC TTTC TTT
39938 TTCTCTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
4 27 0.75
5 9 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:39903 original size:18 final size:17
Alignment explanation
Indices: 39882--39944 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 17
39872 CCTTGACCCC
39882 CTTTTTTTCTTTTTCTTT
1 CTTTTTTTC-TTTTCTTT
39900 CTTTTTTTCTTTTCTTTT
1 CTTTTTTTCTTTTC-TTT
39918 CTTTTTTTC-TTTCTTT
1 CTTTTTTTCTTTTCTTT
*
39934 CTTTTTCTCTT
1 CTTTTTTTCTT
39945 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
16 11 0.26
17 10 0.24
18 21 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTTTTCTTTTCTTT
Found at i:39908 original size:12 final size:11
Alignment explanation
Indices: 39885--39944 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
39875 TGACCCCCTT
39885 TTTTTCTTTTTC
1 TTTTT-TTTTTC
39897 TTTCTTTTTTTC
1 TTT-TTTTTTTC
*
39909 -TTTTCTTTTC
1 TTTTTTTTTTC
39919 TTTTTTTCTTTC
1 TTTTTTT-TTTC
*
39931 TTTCTTTTTCTC
1 TTT-TTTTTTTC
39943 TT
1 TT
39945 CAAGCATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.17
11 7 0.17
12 21 0.51
13 6 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:39913 original size:13 final size:13
Alignment explanation
Indices: 39891--39938 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
39881 CCTTTTTTTC
39891 TTTTTC-TTTCTT
1 TTTTTCTTTTCTT
39903 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
39916 TTCTTT-TTTTCTT
1 TT-TTTCTTTTCTT
*
39929 TCTTTCTTTT
1 TTTTTCTTTT
39939 TCTCTTCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 9 0.28
13 20 0.62
14 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:39939 original size:22 final size:23
Alignment explanation
Indices: 39882--39941 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
39872 CCTTGACCCC
*
39882 CTTTTTTTCTTTTTCTTTCTTTT
1 CTTTCTTTCTTTTTCTTTCTTTT
39905 -TTTCTTT-TCTTTTCTTT-TTTT
1 CTTTCTTTCT-TTTTCTTTCTTTT
39926 CTTTCTTTCTTTTTCT
1 CTTTCTTTCTTTTTCT
39942 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 5 0.15
22 27 0.82
23 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
CTTTCTTTCTTTTTCTTTCTTTT
Found at i:46988 original size:15 final size:15
Alignment explanation
Indices: 46965--46996 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46955 TGAAATGAAT
46965 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
46980 AATGCATGTATGCAA
1 AATGAATGTATGCAA
46995 AA
1 AA
46997 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:50375 original size:27 final size:28
Alignment explanation
Indices: 50339--50394 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
50329 AAAAAAAGAA
50339 TTATAAATTAAATATATGA-AATTT-TAAT
1 TTATAAATT-AATATA-GACAATTTATAAT
50367 TTAT-AATTAATATAGACAATTTATAAT
1 TTATAAATTAATATAGACAATTTATAAT
50394 T
1 T
50395 GATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.08
26 11 0.42
27 9 0.35
28 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (28 bp):
TTATAAATTAATATAGACAATTTATAAT
Found at i:51001 original size:13 final size:13
Alignment explanation
Indices: 50983--51023 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
50973 TCGATATTGA
*
50983 AAAATAAATGTTT
1 AAAATAAATATTT
*
50996 AAAATAATTTATTT
1 AAAATAA-ATATTT
51010 AAAATAAATATTT
1 AAAATAAATATTT
51023 A
1 A
51024 TTTACTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:51992 original size:15 final size:15
Alignment explanation
Indices: 51972--52007 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
51962 TGATCGATCT
51972 TTTCTTTTCTTGTTG
1 TTTCTTTTCTTGTTG
* *
51987 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTGTTG
52002 TTTCTT
1 TTTCTT
52008 CGTTTGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTCTTTTCTTGTTG
Found at i:52435 original size:3 final size:3
Alignment explanation
Indices: 52406--52482 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
52396 GGCCTGTTTG
* * * *
52406 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
52453 TAA TTA TAA TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52483 AATGAGTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:60588 original size:15 final size:15
Alignment explanation
Indices: 60568--60597 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60558 TATTCTATAG
60568 TCAAAGATGAACAAA
1 TCAAAGATGAACAAA
60583 TCAAAGATGAACAAA
1 TCAAAGATGAACAAA
60598 CTTGGCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
TCAAAGATGAACAAA
Found at i:61195 original size:27 final size:26
Alignment explanation
Indices: 61164--61215 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
61154 TTTTAATTTC
61164 GAGGGCCACATATACTTCAAAAAAAAT
1 GAGGGCCACAT-TACTTCAAAAAAAAT
* *
61191 GAGGGCCACATTATTTTAAAAAAAA
1 GAGGGCCACATTACTTCAAAAAAAA
61216 AATAATACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.21
Consensus pattern (26 bp):
GAGGGCCACATTACTTCAAAAAAAAT
Found at i:61216 original size:27 final size:27
Alignment explanation
Indices: 61164--61216 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
61154 TTTTAATTTC
*
61164 GAGGGCCACATATACTTCAAAAAAAAT
1 GAGGGCCACATATACTTAAAAAAAAAT
*
61191 GAGGGCCACAT-TATTTTAAAAAAAAA
1 GAGGGCCACATATA-CTTAAAAAAAAA
61217 ATAATACAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (27 bp):
GAGGGCCACATATACTTAAAAAAAAAT
Found at i:61379 original size:2 final size:2
Alignment explanation
Indices: 61372--61400 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61362 TAGGTGTAAT
61372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61401 GAAGAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61501 original size:13 final size:11
Alignment explanation
Indices: 61473--61525 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
61463 CATTCGTCAG
*
61473 TATTTTT-TAT
1 TATTTTTATTT
61483 TATTTTTATATT
1 TATTTTTAT-TT
61495 ATATTTTTATTT
1 -TATTTTTATTT
*
61507 TACTTTTATTTT
1 TATTTTTA-TTT
61519 TATTTTT
1 TATTTTT
61526 TAATAACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 8 0.22
12 12 0.33
13 9 0.25
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:61505 original size:6 final size:6
Alignment explanation
Indices: 61482--61525 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
61472 GTATTTTTTA
* *
61482 TTATTT TTATATT ATATTT TTA-TT TTACTT TTATTT TTATTT TT
1 TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATTT TT
61526 TAATAACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.15
6 23 0.70
7 5 0.15
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:67480 original size:14 final size:14
Alignment explanation
Indices: 67461--67549 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
67451 CTCGAGTACA
67461 TATTTAATCATAAT
1 TATTTAATCATAAT
*
67475 TATTTAAAT-TTAAT
1 TATTT-AATCATAAT
*
67489 TATTTAA-CTTTAAT
1 TATTTAATC-ATAAT
*
67503 GATTT-A--ATAAT
1 TATTTAATCATAAT
*
67514 TATTTAA-CTTAAT
1 TATTTAATCATAAT
* *
67527 GATTTAATAATAAT
1 TATTTAATCATAAT
67541 TACTTTAAT
1 TA-TTTAAT
67550 GATTTAACTT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
11 8 0.14
12 1 0.02
13 13 0.22
14 28 0.47
15 9 0.15
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTTAATCATAAT
Found at i:67552 original size:23 final size:23
Alignment explanation
Indices: 67462--67704 Score: 196
Period size: 23 Copynumber: 10.3 Consensus size: 23
67452 TCGAGTACAT
*
67462 ATTTAATCATAATTA-TTTAA--
1 ATTTAATAATAATTACTTTAATG
*
67482 ATTTAAT--TATTTAACTTTAATG
1 ATTTAATAATAATT-ACTTTAATG
*
67504 ATTTAATAATTATTTAAC-TTAATG
1 ATTTAATAA-TAATT-ACTTTAATG
67528 ATTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
* * *
67551 ATTTAACT-TTAATGA-TTTAATA
1 ATTTAA-TAATAATTACTTTAATG
* * *
67573 ATAATTACTTTAATGATTTAATTTTAATG
1 AT--TTA--ATAAT-AATT-ACTTTAATG
67602 ATTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
*
67625 ATTTAATTTTAATGATTTAACTTTAATG
1 ATTTAA---TAAT-AATT-ACTTTAATG
*
67653 CTTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
67676 ATTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
67699 ATTTAA
1 ATTTAA
67705 CTTTAATGCT
Statistics
Matches: 184, Mismatches: 17, Indels: 41
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.02
19 1 0.01
20 12 0.07
22 17 0.09
23 72 0.39
24 25 0.14
25 17 0.09
26 5 0.03
27 8 0.04
28 15 0.08
29 8 0.04
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (23 bp):
ATTTAATAATAATTACTTTAATG
Found at i:67567 original size:37 final size:37
Alignment explanation
Indices: 67510--67848 Score: 443
Period size: 37 Copynumber: 9.0 Consensus size: 37
67500 AATGATTTAA
*
67510 TAATTATTTAAC-TTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
67546 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
67583 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* * *
67620 TAATGATTTAATTTTAATGATTTAACT-TTAA-TGCTT
1 TAATGATTTAACTTTAATGATTTAA-TAATAATTACTT
*
67656 TAATAATAATT-ACTTTAATGATTTAATAATAATTACTT
1 TAATGAT--TTAACTTTAATGATTTAATAATAATTACTT
*
67694 TAATGATTTAACTTTAATGCTTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
67731 TAATGATTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
* * *
67770 TAATGATTTGATTTTAATAATTTAATAATAATTACTTAATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAC-----TT
* *
67812 TAATGATTTAAATTTAATTATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
67849 GACTTTAATG
Statistics
Matches: 271, Mismatches: 18, Indels: 27
0.86 0.06 0.09
Matches are distributed among these distances:
36 24 0.09
37 166 0.61
38 13 0.05
39 34 0.13
42 34 0.13
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (37 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTT
Found at i:67623 original size:9 final size:8
Alignment explanation
Indices: 67471--67837 Score: 70
Period size: 8 Copynumber: 49.5 Consensus size: 8
67461 TATTTAATCA
67471 TAATTATT
1 TAATTATT
67479 TAA--ATT
1 TAATTATT
67485 TAATTATT
1 TAATTATT
*
67493 TAA--CTT
1 TAATTATT
*
67499 TAATGATT
1 TAATTATT
*
67507 TAA-TAAT
1 TAATTATT
* *
67514 TATTTAACT
1 TAATT-ATT
*
67523 TAATGATT
1 TAATTATT
*
67531 TAA-TA-A
1 TAATTATT
67537 TAATTACTT
1 TAATTA-TT
*
67546 TAATGATT
1 TAATTATT
*
67554 TAA--CTT
1 TAATTATT
*
67560 TAATGATT
1 TAATTATT
*
67568 TAA-TA-A
1 TAATTATT
67574 TAATTACTT
1 TAATTA-TT
*
67583 TAATGATT
1 TAATTATT
67591 TAA-T-TT
1 TAATTATT
*
67597 TAATGATT
1 TAATTATT
*
67605 TAA-TA-A
1 TAATTATT
67611 TAATTACTT
1 TAATTA-TT
*
67620 TAATGATT
1 TAATTATT
67628 TAA-T-TT
1 TAATTATT
*
67634 TAATGATT
1 TAATTATT
*
67642 TAA--CTT
1 TAATTATT
**
67648 TAATGCTT
1 TAATTATT
*
67656 TAA-TA-A
1 TAATTATT
67662 TAATTACTT
1 TAATTA-TT
*
67671 TAATGATT
1 TAATTATT
*
67679 TAA-TA-A
1 TAATTATT
67685 TAATTACTT
1 TAATTA-TT
*
67694 TAATGATT
1 TAATTATT
*
67702 TAA--CTT
1 TAATTATT
**
67708 TAATGCTT
1 TAATTATT
*
67716 TAA-TA-A
1 TAATTATT
67722 TAATTACTT
1 TAATTA-TT
*
67731 TAATGATT
1 TAATTATT
*
67739 TAATGATT
1 TAATTATT
*
67747 TAATGATT
1 TAATTATT
*
67755 TAA-TA-A
1 TAATTATT
67761 TAATTACTT
1 TAATTA-TT
*
67770 TAATGATT
1 TAATTATT
*
67778 TGA-T-TT
1 TAATTATT
*
67784 TAATAATT
1 TAATTATT
*
67792 TAA-TA-A
1 TAATTATT
*
67798 TAATTACT
1 TAATTATT
67806 TAA-T-TT
1 TAATTATT
*
67812 TAATGATT
1 TAATTATT
67820 TAA--ATT
1 TAATTATT
67826 TAATTATT
1 TAATTATT
67834 TAAT
1 TAAT
67838 AATAATTACT
Statistics
Matches: 258, Mismatches: 56, Indels: 90
0.64 0.14 0.22
Matches are distributed among these distances:
6 74 0.29
7 27 0.10
8 117 0.45
9 40 0.16
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (8 bp):
TAATTATT
Found at i:67711 original size:23 final size:23
Alignment explanation
Indices: 67556--67750 Score: 133
Period size: 23 Copynumber: 8.7 Consensus size: 23
67546 TAATGATTTA
*
67556 ACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAATATTAATT
* *
67579 ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGATTTAATATTAATT
* * *
67602 A-TTTAATAATAATTACT-TTAATG
1 ACTTTAATGAT--TTAATATTAATT
*
67625 A-TTTAAT--TTTAATGATT--TA
1 ACTTTAATGATTTAAT-ATTAATT
* *
67644 ACTTTAATGCTTTAATAATAATT
1 ACTTTAATGATTTAATATTAATT
*
67667 ACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAATATTAATT
67690 ACTTTAATGATTTAACT-TTAA-T
1 ACTTTAATGATTTAA-TATTAATT
* * * *
67712 GCTTTAATAATAATTACT-TTAATG
1 ACTTTAATGAT--TTAATATTAATT
67736 A-TTTAATGATTTAAT
1 ACTTTAATGATTTAAT
67751 GATTTAATAA
Statistics
Matches: 141, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.04
20 6 0.04
21 9 0.06
22 24 0.17
23 88 0.62
24 8 0.06
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (23 bp):
ACTTTAATGATTTAATATTAATT
Found at i:67787 original size:23 final size:22
Alignment explanation
Indices: 67737--67837 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 22
67727 ACTTTAATGA
*
67737 TTTAATGATTTAATGATTTAAT
1 TTTAATTATTTAATGATTTAAT
** *
67759 AATAATTACTTTAATGATTTGAT
1 TTTAATTA-TTTAATGATTTAAT
* *
67782 TTTAATAATTTAAT-A-ATAAT
1 TTTAATTATTTAATGATTTAAT
*
67802 TACTTAA-T-TTTAATGATTTAAA
1 T--TTAATTATTTAATGATTTAAT
67824 TTTAATTATTTAAT
1 TTTAATTATTTAAT
67838 AATAATTACT
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
20 14 0.23
21 3 0.05
22 25 0.42
23 18 0.30
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTAATTATTTAATGATTTAAT
Found at i:67869 original size:14 final size:13
Alignment explanation
Indices: 67471--67879 Score: 216
Period size: 14 Copynumber: 31.9 Consensus size: 13
67461 TATTTAATCA
*
67471 TAATTATTTAAATT
1 TAATGATTT-AATT
*
67485 TAATTATTTAACTT
1 TAATGATTTAA-TT
67499 TAATGATTTAA--
1 TAATGATTTAATT
* *
67510 TAATTATTTAACT
1 TAATGATTTAATT
67523 TAATGATTTAA--
1 TAATGATTTAATT
* *
67534 TAAT-AATTACTT
1 TAATGATTTAATT
67546 TAATGATTTAACTT
1 TAATGATTTAA-TT
67560 TAATGATTTAA--
1 TAATGATTTAATT
* *
67571 TAAT-AATTACTT
1 TAATGATTTAATT
67583 TAATGATTTAATTT
1 TAATGATTTAA-TT
67597 TAATGATTTAA--
1 TAATGATTTAATT
* *
67608 TAAT-AATTACTT
1 TAATGATTTAATT
67620 TAATGATTTAATTT
1 TAATGATTTAA-TT
67634 TAATGATTTAACTT
1 TAATGATTTAA-TT
*
67648 TAATGCTTTAA--
1 TAATGATTTAATT
* *
67659 TAAT-AATTACTT
1 TAATGATTTAATT
67671 TAATGATTTAA--
1 TAATGATTTAATT
* *
67682 TAAT-AATTACTT
1 TAATGATTTAATT
67694 TAATGATTTAACTT
1 TAATGATTTAA-TT
*
67708 TAATGCTTTAA--
1 TAATGATTTAATT
* *
67719 TAAT-AATTACTT
1 TAATGATTTAATT
67731 TAATGATTTAATGATT
1 TAATGATTT-A--ATT
67747 TAATGATTTAA--
1 TAATGATTTAATT
* *
67758 TAAT-AATTACTT
1 TAATGATTTAATT
*
67770 TAATGATTTGATTT
1 TAATGATTT-AATT
* *
67784 TAATAATTTAATAA
1 TAATGATTTAAT-T
* *
67798 TAATTACTTAATTT
1 TAATGATTTAA-TT
67812 TAATGATTTAAATT
1 TAATGATTT-AATT
* *
67826 TAATTATTTAATAA
1 TAATGATTTAAT-T
* * *
67840 TAATTACTTGACTT
1 TAATGA-TTTAATT
67854 TAATGATTTATATT
1 TAATGATTTA-ATT
* *
67868 TACTGATATAAT
1 TAATGATTTAAT
67880 AATAGTAAAT
Statistics
Matches: 303, Mismatches: 54, Indels: 77
0.70 0.12 0.18
Matches are distributed among these distances:
10 26 0.09
11 38 0.13
12 28 0.09
13 49 0.16
14 143 0.47
15 8 0.03
16 11 0.04
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (13 bp):
TAATGATTTAATT
Found at i:70389 original size:173 final size:173
Alignment explanation
Indices: 70095--70454 Score: 596
Period size: 173 Copynumber: 2.1 Consensus size: 173
70085 CATCAAATAT
* *
70095 AAAATGATCCCTAATTACTATTTACTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTACTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
70160 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
*
70225 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
**
70268 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAACTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTACTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
70332 TTATAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
70397 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
70441 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
70455 AACTTTACAA
Statistics
Matches: 174, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
172 1 0.01
173 173 0.99
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTACTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:70753 original size:41 final size:41
Alignment explanation
Indices: 70696--70779 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
70686 TCCCTCTCAG
*
70696 GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCTCGA
1 GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCGA
70737 GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCGA
1 GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCGA
70778 GC
1 GC
70780 AGTCTCTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (41 bp):
GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCGA
Found at i:70950 original size:23 final size:23
Alignment explanation
Indices: 70924--70967 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
70914 AATTGCATGC
70924 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
70947 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
70968 CCCCTGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:71099 original size:34 final size:34
Alignment explanation
Indices: 71044--71128 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
71034 CATGCACAGC
* *
71044 ACTGAAGACGCTGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
* *
71078 ACTGAAGATGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
71112 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
71129 ATCAATCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
Found at i:71217 original size:30 final size:30
Alignment explanation
Indices: 71181--71237 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
71171 AAATTGCGTT
*
71181 AAAGACGCCGAGATATCCA-GCCTTCCATGC
1 AAAGACGCCGAGAGATCCACG-CTTCCATGC
71211 AAAGACGCCGAGAGATCCACGCTTCCA
1 AAAGACGCCGAGAGATCCACGCTTCCA
71238 CATCTGCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.14
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCACGCTTCCATGC
Found at i:72161 original size:12 final size:12
Alignment explanation
Indices: 72130--72161 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
72120 GACATTCACG
72130 AATATATTT-TT
1 AATATATTTATT
72141 AAT-TATTTATT
1 AATATATTTATT
72152 AATATATTTA
1 AATATATTTA
72162 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 8 0.42
12 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AATATATTTATT
Found at i:72346 original size:10 final size:10
Alignment explanation
Indices: 72318--72390 Score: 67
Period size: 10 Copynumber: 7.2 Consensus size: 10
72308 AATTTATTTT
72318 TAAATAAATA
1 TAAATAAATA
*
72328 TAAATTAAACA
1 TAAA-TAAATA
72339 TAAATAAATA
1 TAAATAAATA
*
72349 TAAAATTAA-A
1 T-AAATAAATA
72359 TAAATAAATA
1 TAAATAAATA
* *
72369 TATATATATA
1 TAAATAAATA
* *
72379 TATATATATA
1 TAAATAAATA
72389 TA
1 TA
72391 TATGTATTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
9 6 0.11
10 33 0.61
11 15 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAATAAATA
Found at i:72358 original size:16 final size:16
Alignment explanation
Indices: 72327--72364 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
72317 TTAAATAAAT
72327 ATAAAT-TAAACATAA
1 ATAAATATAAACATAA
72342 ATAAATATAAA-ATTAA
1 ATAAATATAAACA-TAA
72358 ATAAATA
1 ATAAATA
72365 AATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATATAAACATAA
Found at i:72373 original size:2 final size:2
Alignment explanation
Indices: 72366--72393 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72356 AAATAAATAA
72366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72394 GTATTCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73040 original size:23 final size:24
Alignment explanation
Indices: 72985--73041 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
72975 AAACCATAAG
* *
72985 AAACATGCCACAAGAGCAGAGAAA
1 AAACATGTCATAAGAGCAGAGAAA
*
73009 AAACGTGTCATAAGAGCAGAG-AA
1 AAACATGTCATAAGAGCAGAGAAA
*
73032 AAGCATGTCA
1 AAACATGTCA
73042 CAAATACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.49, C:0.18, G:0.23, T:0.11
Consensus pattern (24 bp):
AAACATGTCATAAGAGCAGAGAAA
Found at i:73382 original size:2 final size:2
Alignment explanation
Indices: 73377--73432 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
73367 TAATTCATTT
73377 TA TA TA TA -A T- TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73416 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
73433 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94971 original size:22 final size:21
Alignment explanation
Indices: 94930--94971 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
94920 TTCTAACTTT
*
94930 TAAATCATGATTTTCTTTTTC
1 TAAATCATGATTTTCATTTTC
*
94951 TAAATCATTGATTTTGATTTT
1 TAAATCA-TGATTTTCATTTT
94972 TGAAATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (21 bp):
TAAATCATGATTTTCATTTTC
Found at i:94977 original size:22 final size:19
Alignment explanation
Indices: 94927--94978 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
94917 AATTTCTAAC
*
94927 TTTTAAATCATGATTTTCTT
1 TTTTAAATCATGATTTT-AT
94947 TTTCTAAATCATTGATTTTGAT
1 TTT-TAAATCA-TGATTTT-AT
94969 TTTTGAAATC
1 TTTT-AAATC
94979 TTAAAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 8 0.30
22 16 0.59
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTTAAATCATGATTTTAT
Found at i:97876 original size:49 final size:49
Alignment explanation
Indices: 97795--98106 Score: 367
Period size: 49 Copynumber: 6.4 Consensus size: 49
97785 GAGGTGGAGC
* ** *
97795 ATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATG
1 ATTTAGCATGTCTGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
* * *
97844 ATGTAGCATTTATGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
1 ATTTAGCATGTCTGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
* * *
97893 ATTTAGCATGTCTGACGTCTTTGTGA-TGATAGTGCTACTATTAATGATG
1 ATTTAGCATGTCTGACGTCTTTGTGACAG-TGGTACTACTATTAATGATG
* * * * *
97942 ATTTAGCACGTCTGACGTTTTTATGACAATGGTGCTACTATTAATGATG
1 ATTTAGCATGTCTGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
* * * * ** * *
97991 ATTTAACAAGTCTAATGTCTTTGTGATGGTGGTACTACTATTAAGGACG
1 ATTTAGCATGTCTGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
* *
98040 ATTTAGCACGTCTGACGTCTTTGTAAC-GATGGTACTACTATTAATGATG
1 ATTTAGCATGTCTGACGTCTTTGTGACAG-TGGTACTACTATTAATGATG
98089 ATTTAGCATGTCTGACGT
1 ATTTAGCATGTCTGACGT
98107 TACTTATATA
Statistics
Matches: 220, Mismatches: 40, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
48 2 0.01
49 218 0.99
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (49 bp):
ATTTAGCATGTCTGACGTCTTTGTGACAGTGGTACTACTATTAATGATG
Found at i:97969 original size:98 final size:98
Alignment explanation
Indices: 97795--98106 Score: 437
Period size: 98 Copynumber: 3.2 Consensus size: 98
97785 GAGGTGGAGC
* * ** *
97795 ATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATGTAGCATTTATGAC
1 ATTTAGCATGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGAC
97860 GTCTTTGTGACAGTGGTACTACTATTAATGATG
66 GTCTTTGTGACAGTGGTACTACTATTAATGATG
* *
97893 ATTTAGCATGTCTGACGTCTTTGTGATGATAGTGCTACTATTAATGATGATTTAGCACGTCTGAC
1 ATTTAGCATGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGAC
* * * *
97958 GTTTTTATGACAATGGTGCTACTATTAATGATG
66 GTCTTTGTGACAGTGGTACTACTATTAATGATG
* * * * * * *
97991 ATTTAACAAGTCTAATGTCTTTGTGATGGTGGTACTACTATTAAGGACGATTTAGCACGTCTGAC
1 ATTTAGCATGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGAC
*
98056 GTCTTTGTAAC-GATGGTACTACTATTAATGATG
66 GTCTTTGTGACAG-TGGTACTACTATTAATGATG
98089 ATTTAGCATGTCTGACGT
1 ATTTAGCATGTCTGACGT
98107 TACTTATATA
Statistics
Matches: 184, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
98 184 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (98 bp):
ATTTAGCATGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGAC
GTCTTTGTGACAGTGGTACTACTATTAATGATG
Found at i:98062 original size:147 final size:147
Alignment explanation
Indices: 97795--98125 Score: 428
Period size: 147 Copynumber: 2.2 Consensus size: 147
97785 GAGGTGGAGC
* * *** * ** *
97795 ATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAATGATGATGTAGCATTTATGAC
1 ATTTAGCACGTCTGACGTTTTTATGACAATGGTGCTACTATTAATGATGATGTAACAAGTATAAC
* * * * *
97860 GTCTTTGTGACAGTGGTACTACTATTAATGATGATTTAGCATGTCTGACGTCTTTGTGATGATAG
66 GTCTTTGTGACAGTGGTACTACTATTAAGGACGATTTAGCACGTCTGACGTCTTTGTAACGATAG
*
97925 TGCTACTATTAATGATG
131 TACTACTATTAATGATG
* * *
97942 ATTTAGCACGTCTGACGTTTTTATGACAATGGTGCTACTATTAATGATGATTTAACAAGTCTAAT
1 ATTTAGCACGTCTGACGTTTTTATGACAATGGTGCTACTATTAATGATGATGTAACAAGTATAAC
** *
98007 GTCTTTGTGATGGTGGTACTACTATTAAGGACGATTTAGCACGTCTGACGTCTTTGTAACGATGG
66 GTCTTTGTGACAGTGGTACTACTATTAAGGACGATTTAGCACGTCTGACGTCTTTGTAACGATAG
98072 TACTACTATTAATGATG
131 TACTACTATTAATGATG
* *
98089 ATTTAGCATGTCTGACGTTACTTATATAACAATGGTG
1 ATTTAGCACGTCTGACGTT--TT-TATGACAATGGTG
98126 TTGTTTATTT
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
147 144 0.91
149 2 0.01
150 12 0.08
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (147 bp):
ATTTAGCACGTCTGACGTTTTTATGACAATGGTGCTACTATTAATGATGATGTAACAAGTATAAC
GTCTTTGTGACAGTGGTACTACTATTAAGGACGATTTAGCACGTCTGACGTCTTTGTAACGATAG
TACTACTATTAATGATG
Found at i:101143 original size:23 final size:23
Alignment explanation
Indices: 101099--101150 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
101089 AATTAAATAT
101099 ATATTTTAAGAAATAATATTAAA
1 ATATTTTAAGAAATAATATTAAA
*
101122 TTATTTTAA-AAATTAA-ATTTAAA
1 ATATTTTAAGAAA-TAATA-TTAAA
101145 ATATTT
1 ATATTT
101151 ATTTATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTTTAAGAAATAATATTAAA
Found at i:112119 original size:2 final size:2
Alignment explanation
Indices: 112112--112141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
112102 AAGATGATGT
112112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112142 CTAACACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115478 original size:16 final size:16
Alignment explanation
Indices: 115457--115487 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
115447 TTATCTAACC
115457 TGTTTTCAACCTGACT
1 TGTTTTCAACCTGACT
115473 TGTTTTCAACCTGAC
1 TGTTTTCAACCTGAC
115488 CTGTAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACCTGACT
Found at i:115542 original size:16 final size:16
Alignment explanation
Indices: 115523--115553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115513 ACATGATCTG
*
115523 ATATTTACCTGACTTT
1 ATATTTAACTGACTTT
115539 ATATTTAACTGACTT
1 ATATTTAACTGACTT
115554 GACATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATTTAACTGACTTT
Found at i:115674 original size:20 final size:20
Alignment explanation
Indices: 115646--115684 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
115636 TACTATGATT
* *
115646 AATTTTTAAATATTATAATA
1 AATTATTAAATATGATAATA
*
115666 AATTATTAATTATGATAAT
1 AATTATTAAATATGATAAT
115685 TAATAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATTATTAAATATGATAATA
Done.