Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004958.1 Hibiscus syriacus cultivar Beakdansim tig00011145_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: 107453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8800 original size:22 final size:22
Alignment explanation
Indices: 8775--8831 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
8765 TGAGAGAAAG
*
8775 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCATAATATAGAA
8797 GTATCGGTACCATAATATAGAA
1 GTATCGGTACCATAATATAGAA
*
8819 GTATCGATACCAT
1 GTATCGGTACCAT
8832 GGAAGGGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (22 bp):
GTATCGGTACCATAATATAGAA
Found at i:9303 original size:44 final size:44
Alignment explanation
Indices: 9253--9521 Score: 421
Period size: 44 Copynumber: 6.1 Consensus size: 44
9243 ACGAATCCAG
* *
9253 AAATGAAATGCATAATGGTACATTAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
* * *
9297 AAATGAAATGCATAATGGTACATTAAGGCATGACAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
*
9341 AAATGAAATGCATAACGGTGCATTAAGGCATGAAATGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
* *
9385 AAATGAAATGCATAACGGTGCATTAAGGCATGGAAGAATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
* *
9429 AAATAAAATGCATAACGATGCATTAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
* *
9473 AAATGAAATGCATAACGATGTATTAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATT-AAGGCATGAAAGGATGCCAT
9518 AAAT
1 AAAT
9522 AAAAGTATTG
Statistics
Matches: 210, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
44 186 0.89
45 24 0.11
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (44 bp):
AAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATGCCAT
Found at i:20822 original size:579 final size:579
Alignment explanation
Indices: 19724--20881 Score: 2289
Period size: 579 Copynumber: 2.0 Consensus size: 579
19714 CCAAAACCCT
19724 AAGAAATTCCCTACTATAAATACTGAAGGATACTCTACATTTTAAGAGAGCTTTTGGAGGGGTGA
1 AAGAAATTCCCTACTATAAATACTGAAGGATACTCTACATTTTAAGAGAGCTTTTGGAGGGGTGA
19789 CTTAAGAGAGAAGAGGAATGTGACTGCACAAAAAGTTCCCAATTTATTTTTGTGGTGTCCTCTAT
66 CTTAAGAGAGAAGAGGAATGTGACTGCACAAAAAGTTCCCAATTTATTTTTGTGGTGTCCTCTAT
19854 AGACGAGCTTTGAAGAGGTAGCAACTAAGACCTTGAAAGAGGCTAGCTTGTTATGTTGATTTGTG
131 AGACGAGCTTTGAAGAGGTAGCAACTAAGACCTTGAAAGAGGCTAGCTTGTTATGTTGATTTGTG
19919 GTTGTGGTTCTATATGGCATGAAAATAATCCTTTTGAGAGTTTTAATCTCCTCGTGCTTTCATTT
196 GTTGTGGTTCTATATGGCATGAAAATAATCCTTTTGAGAGTTTTAATCTCCTCGTGCTTTCATTT
19984 CTTTATTTTACATGGGTTTTTACTTAACATTGATGATGGATGGACTTAACCCCACCATAAACTAA
261 CTTTATTTTACATGGGTTTTTACTTAACATTGATGATGGATGGACTTAACCCCACCATAAACTAA
20049 CCTTATTTGATGTGAGTTTGTTATGAATGATTTTTCTTCTGTGTTAATGAATGGTTTAATGTTTT
326 CCTTATTTGATGTGAGTTTGTTATGAATGATTTTTCTTCTGTGTTAATGAATGGTTTAATGTTTT
20114 TATGTTTAAATTTATTTTGCTCATTATTTATATTTTAATTATTTAGTCTTGTAAGAGCCTTCGAG
391 TATGTTTAAATTTATTTTGCTCATTATTTATATTTTAATTATTTAGTCTTGTAAGAGCCTTCGAG
20179 AGTTAGTCGTGTTCTAAGTATGGATGCCTAATATCAAGAAAGTTATGCTAGATCGATGTGAGCAA
456 AGTTAGTCGTGTTCTAAGTATGGATGCCTAATATCAAGAAAGTTATGCTAGATCGATGTGAGCAA
*
20244 GGGAGATCAACTGAAATGGTGAGGTTCTAATCTACCTAAAAGATATAGAAAAGGTTTCA
521 GGGAGATCAACCGAAATGGTGAGGTTCTAATCTACCTAAAAGATATAGAAAAGGTTTCA
20303 AAGAAATTCCCTACTATAAATACTGAAGGATACTCTACATTTTAAGAGAGCTTTTGGAGGGGTGA
1 AAGAAATTCCCTACTATAAATACTGAAGGATACTCTACATTTTAAGAGAGCTTTTGGAGGGGTGA
20368 CTTAAGAGAGAAGAGGAATGTGACTGCACAAAAAGTTCCCAATTTATTTTTGTGGTGTCCTCTAT
66 CTTAAGAGAGAAGAGGAATGTGACTGCACAAAAAGTTCCCAATTTATTTTTGTGGTGTCCTCTAT
20433 AGACGAGCTTTGAAGAGGTAGCAACTAAGACCTTGAAAGAGGCTAGCTTGTTATGTTGATTTGTG
131 AGACGAGCTTTGAAGAGGTAGCAACTAAGACCTTGAAAGAGGCTAGCTTGTTATGTTGATTTGTG
*
20498 GTTGTGGTTCTATATGGCATGAAAATAATCCTTTTGAGAGTTTTAATCTCCTTGTGCTTTCATTT
196 GTTGTGGTTCTATATGGCATGAAAATAATCCTTTTGAGAGTTTTAATCTCCTCGTGCTTTCATTT
20563 CTTTATTTTACATGGGTTTTTACTTAACATTGATGATGGATGGACTTAACCCCACCATAAACTAA
261 CTTTATTTTACATGGGTTTTTACTTAACATTGATGATGGATGGACTTAACCCCACCATAAACTAA
20628 CCTTATTTGATGTGAGTTTGTTATGAATGATTTTTCTTCTGTGTTAATGAATGGTTTAATGTTTT
326 CCTTATTTGATGTGAGTTTGTTATGAATGATTTTTCTTCTGTGTTAATGAATGGTTTAATGTTTT
20693 TATGTTTAAATTTATTTTGCTCATTATTTATATTTTAATTATTTAGTCTTGTAAGAGCCTTCGAG
391 TATGTTTAAATTTATTTTGCTCATTATTTATATTTTAATTATTTAGTCTTGTAAGAGCCTTCGAG
*
20758 AGTTAGTCGTTTTCTAAGTATGGATGCCTAATATCAAGAAAGTTATGCTAGATCGATGTGAGCAA
456 AGTTAGTCGTGTTCTAAGTATGGATGCCTAATATCAAGAAAGTTATGCTAGATCGATGTGAGCAA
20823 GGGAGATCAACCGAAATGGTGAGGTTCTAATCTACCTAAAAGATATAGAAAAGGTTTCA
521 GGGAGATCAACCGAAATGGTGAGGTTCTAATCTACCTAAAAGATATAGAAAAGGTTTCA
20882 TCGACTAAAA
Statistics
Matches: 576, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
579 576 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (579 bp):
AAGAAATTCCCTACTATAAATACTGAAGGATACTCTACATTTTAAGAGAGCTTTTGGAGGGGTGA
CTTAAGAGAGAAGAGGAATGTGACTGCACAAAAAGTTCCCAATTTATTTTTGTGGTGTCCTCTAT
AGACGAGCTTTGAAGAGGTAGCAACTAAGACCTTGAAAGAGGCTAGCTTGTTATGTTGATTTGTG
GTTGTGGTTCTATATGGCATGAAAATAATCCTTTTGAGAGTTTTAATCTCCTCGTGCTTTCATTT
CTTTATTTTACATGGGTTTTTACTTAACATTGATGATGGATGGACTTAACCCCACCATAAACTAA
CCTTATTTGATGTGAGTTTGTTATGAATGATTTTTCTTCTGTGTTAATGAATGGTTTAATGTTTT
TATGTTTAAATTTATTTTGCTCATTATTTATATTTTAATTATTTAGTCTTGTAAGAGCCTTCGAG
AGTTAGTCGTGTTCTAAGTATGGATGCCTAATATCAAGAAAGTTATGCTAGATCGATGTGAGCAA
GGGAGATCAACCGAAATGGTGAGGTTCTAATCTACCTAAAAGATATAGAAAAGGTTTCA
Found at i:35609 original size:39 final size:39
Alignment explanation
Indices: 35564--35688 Score: 153
Period size: 39 Copynumber: 3.2 Consensus size: 39
35554 ATGCATATAT
* * *
35564 GTGCATATGGTGGGTACGACCTTTTGTGTAAGTACTTCA
1 GTGCATATGGTGGGAACGACCTTTTGTGTAAGCACTTCG
* *
35603 GTGCATATGGTGGGCACGA-CTTTATGTGTAAGCACTTTG
1 GTGCATATGGTGGGAACGACCTTT-TGTGTAAGCACTTCG
* * * *
35642 GTGCATATGGTTGGAACAACCTTATGTGTAAGCACTACG
1 GTGCATATGGTGGGAACGACCTTTTGTGTAAGCACTTCG
35681 GTGCATAT
1 GTGCATAT
35689 ATTTGATAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.05
39 67 0.91
40 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (39 bp):
GTGCATATGGTGGGAACGACCTTTTGTGTAAGCACTTCG
Found at i:37212 original size:20 final size:20
Alignment explanation
Indices: 37187--37238 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
37177 AGTTAAGGGA
37187 AGTATCGATACTCACTAGGT
1 AGTATCGATACTCACTAGGT
37207 AGTATCGATACTCACTAGGT
1 AGTATCGATACTCACTAGGT
37227 AGTATCGATACT
1 AGTATCGATACT
37239 ACCAGCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTCACTAGGT
Found at i:41551 original size:21 final size:21
Alignment explanation
Indices: 41508--41564 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
41498 TTTATCCAGT
* **
41508 AAAGGATTGATCCCTAGGGAA
1 AAAGGATCGATCCCTAGAAAA
*
41529 AAAGGATCGATCCCTCGAAAA
1 AAAGGATCGATCCCTAGAAAA
*
41550 AAAAGATCGATCCCT
1 AAAGGATCGATCCCT
41565 TCGATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (21 bp):
AAAGGATCGATCCCTAGAAAA
Found at i:42719 original size:38 final size:38
Alignment explanation
Indices: 42662--42782 Score: 179
Period size: 38 Copynumber: 3.2 Consensus size: 38
42652 TATGCACTGT
* *
42662 AGTGCTTACACAAAAGGTCGTGCCCACCATATGCACCGA
1 AGTGC-TACACATAAGGTCGTGCCCACCATATGCACCAA
* *
42701 AGTGCTACACATGAGGTCGTGCCCACCGTATGCACCAA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCAA
* *
42739 AGTGCTACGCATAAGGTCATGCCCACCATATGCACCAA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCAA
42777 AGTGCT
1 AGTGCT
42783 TAATCCATAC
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 69 0.93
39 5 0.07
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (38 bp):
AGTGCTACACATAAGGTCGTGCCCACCATATGCACCAA
Found at i:47993 original size:59 final size:59
Alignment explanation
Indices: 47925--48430 Score: 755
Period size: 59 Copynumber: 8.6 Consensus size: 59
47915 TTCCCATACA
* ** * * * *
47925 GAAACTCATACACTTAGTAT-AGATTTATGATCATTTTAGCACAC-AAGGTGTCCAATATG
1 GAAATTCATACACTTAGTATGA-ATTCCTTATCATGTTAGCACACGAA-GTGCCCTATATG
* * *
47984 GAAATTCATATAGTTAGTATGAATTCCTTATCATGTTAACACACGAAGTGCCCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
* *
48043 GAAATTAATACACTTAGTGTGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
*
48102 GAAATTCATACACTTAGAATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
* * * * *
48161 GAAATTCATACACTTAGTGTGAATTCCATATCATGTTAGCACACAAAATGCTCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
* * *
48220 GAAATTCATACACTTAGTATGAATTCCTTGTCATGTTAGTACACGAAGTACCCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
* * * *
48279 AAAATTCATACGCTTAGTGTGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATA
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
48338 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
1 GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
48397 GAAATTCATACACTTAGTATGAATTCCTTATCAT
1 GAAATTCATACACTTAGTATGAATTCCTTATCAT
48431 TTGGTAATCA
Statistics
Matches: 402, Mismatches: 43, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
59 399 0.99
60 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATG
Found at i:48918 original size:95 final size:95
Alignment explanation
Indices: 48750--48973 Score: 290
Period size: 95 Copynumber: 2.4 Consensus size: 95
48740 TCTGGTTCCT
* * * * *
48750 CAGTATCGATACTCC-CATCATGGTATCGATAGTACCCTACTATGGTATCGATACCCCTTTCCGA
1 CAGTATCGATAC-CCTTATCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTACGA
* *
48814 TATCGATACCGAAATTAGATTTGATCTAACC
65 TATCAATACCAAAATTAGATTTGATCTAACC
* *
48845 CAGTATCGATACCCTTATCATGGTATCGATACTACCATACTGTGGTACCGATACCCCTTTATGAT
1 CAGTATCGATACCCTTATCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTACGAT
* * *
48910 ATCAATACCAAAATTAGGTTTGATGTTACC
66 ATCAATACCAAAATTAGATTTGATCTAACC
** *
48940 TGGTATCGATACCCTTACCATGGTA-CGATACTAC
1 CAGTATCGATACCCTTATCATGGTATCGATACTAC
48974 TTCGTTCAGT
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
94 11 0.10
95 102 0.90
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (95 bp):
CAGTATCGATACCCTTATCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTACGAT
ATCAATACCAAAATTAGATTTGATCTAACC
Found at i:53744 original size:36 final size:37
Alignment explanation
Indices: 53665--53748 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
53655 TGGCAACCAA
*
53665 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
53702 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGAT-TTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
53738 -TGTTGAAAAAT
1 CT-TTGAAAAAT
53749 GATAATAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.02
36 12 0.28
37 30 0.70
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:55457 original size:23 final size:22
Alignment explanation
Indices: 55431--55492 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
55421 ACTAATGATC
55431 TATTTTAAAGTTAAATAAATAAT
1 TATTTTAAA-TTAAATAAATAAT
55454 TATTTTTAAA-TAAATTAAATAAT
1 TA-TTTTAAATTAAA-TAAATAAT
*
55477 AATTTTAAATTAAATA
1 TATTTTAAATTAAATA
55493 TTAAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 13 0.37
23 15 0.43
24 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTAAATTAAATAAATAAT
Found at i:55482 original size:22 final size:24
Alignment explanation
Indices: 55432--55491 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
55422 CTAATGATCT
55432 ATTTTAAAGTTAAA-TAAATAATTA
1 ATTTTAAA-TTAAATTAAATAATTA
*
55456 TTTTTAAA-TAAATTAAATAA-TA
1 ATTTTAAATTAAATTAAATAATTA
55478 ATTTTAAATTAAAT
1 ATTTTAAATTAAAT
55492 ATTAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 13 0.41
23 12 0.38
24 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTTAAATTAAATTAAATAATTA
Found at i:55501 original size:18 final size:18
Alignment explanation
Indices: 55464--55501 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55454 TATTTTTAAA
*
55464 TAAATTAAATAATAATTT
1 TAAATTAAATAATAAATT
*
55482 TAAATTAAATATTAAATT
1 TAAATTAAATAATAAATT
55500 TA
1 TA
55502 TGGTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAAATAATAAATT
Found at i:59613 original size:3 final size:3
Alignment explanation
Indices: 59605--59690 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
59595 GATTTTCATT
59605 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59653 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59691 TGGTATATAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:60074 original size:42 final size:42
Alignment explanation
Indices: 60011--60091 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
60001 ATGATGATCT
* *
60011 TGGACGAGCGAAATAATGATGTTGATCCAACTTCTTATGTGA
1 TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATGTGA
* *
60053 TGGATGAGCAAAATGATGATGTTGATCCAACTACTTATG
1 TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATG
60092 CAATGTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (42 bp):
TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATGTGA
Found at i:60381 original size:202 final size:202
Alignment explanation
Indices: 60102--60881 Score: 1030
Period size: 202 Copynumber: 3.9 Consensus size: 202
60092 CAATGTGATT
* * *
60102 GAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCAGATAAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTC
* * *
60167 ATTATGAACTCTCCACTAGAAATGTTGATCCTCC-CCTTTTTGTGATAGAATCGAACAAAGTGAT
66 ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCC-TTCTGTGATAGAATCGAACAAAGTGAT
* * * *
60231 CA-GC-AGATCCAACTTCATATTGGATGGATGAGCCAAGTATTAGTGTTGTTCTAACTCCTTATA
130 CATGCTA-ATCCAACTCCATA-TGGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATG
60294 TGATGGAAAC
193 TGATGGAAAC
* *
60304 GAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATCGGA-ATAGTTCTTCT
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATA-AGTTCTTCT
* * *
60368 CATTATTAACTCTCCACTGGAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGTGAT
65 CATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGAT
* * * * *
60433 TATGCTAATACAACTCCACATGGATGGATGAGCCAAGCATTTGTGTTGTTCCAACTCCTTATGTG
130 CATGCTAATCCAACTCCATATGGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
*
60498 ATAGAAAC
195 ATGGAAAC
* * * *
60506 AATCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGACTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTC
* * * * * *
60571 ATTATGAACTCTCCAATGGAAATGTTGATCCACCACTTTCTGTGATGGAATCAAACAAAGTGATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGATC
* * *
60636 ATGCTAATCCAACTCCCTATGCGATGTATGATCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
131 ATGCTAATCCAACTCCATATG-GATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
*
60701 ATGGAAAA
195 ATGGAAAC
* **
60709 TAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-AGTCGGACGAGTTCTTCT
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCA-TCGGATAAGTTCTTCT
* * *
60773 CATTATGAACCCTCCATTGGAAATGTTGATCCACCTCCTTCTGTGTTAGAATCGAACAAAGTGAT
65 CATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGAT
* * * ** * *
60838 GATGCTGATCTAACTCCATGCGCGATGGATGAGCAAAGTGTTTG
130 CATGCTAATCCAACTCCATATG-GATGGATGAGCCAAGTATTTG
60882 CACAAGTTCT
Statistics
Matches: 509, Mismatches: 62, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
201 1 0.00
202 297 0.58
203 210 0.41
204 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (202 bp):
GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGATC
ATGCTAATCCAACTCCATATGGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTGA
TGGAAAC
Found at i:60855 original size:405 final size:404
Alignment explanation
Indices: 60105--60843 Score: 1124
Period size: 405 Copynumber: 1.8 Consensus size: 404
60095 TGTGATTGAG
* *
60105 CTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCAGATAAGTTCTTCTCATT
1 CTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATAACTTCTTCTCATT
* * * * *
60170 ATGAACTCTCCACTAGAAATGTTGATCCTCCCCTTTTTGTGATAGAATCGAACAAAGTGATCAGC
66 ATGAACTCTCCAATAGAAATGTTGATCCACCACTTTCTGTGATAGAATCAAACAAAGTGATCAGC
* *
60235 AGATCCAACTTCATATTGGATGGATGAGCCAAGTATTAGTGTTGTTCTAACTCCTTATATGATGG
131 AGATCCAACTCCATATTGGATGGATGAGCCAAGTATTAGTGTTGTTCAAACTCCTTATATGATGG
* *
60300 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATCGGAATAGTTCT
196 AAAAGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATCGGAAGAGTTCT
* * * *
60365 TCTCATTATTAACTCTCCACTGGAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGT
261 TCTCATTATGAACCCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGT
*
60430 GATTATGCTAATACAACTCCACATGGATGGATGAGCCAAGCATTTGTGTTGTTCCAACTCCTTAT
326 GATGATGCTAATACAACTCCACATGGATGGATGAGCCAAGCATTTGTGTTGTTCCAACTCCTTAT
60495 GTGATAGAAACAAT
391 GTGATAGAAACAAT
* * *
60509 CTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGACTTCTTCTCATT
1 CTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATAACTTCTTCTCATT
* * *
60574 ATGAACTCTCCAATGGAAATGTTGATCCACCACTTTCTGTGATGGAATCAAACAAAGTGATGATG
66 ATGAACTCTCCAATAGAAATGTTGATCCACCACTTTCTGTGATAGAATCAAACAAAGTGATCA-G
* * * * *
60639 CTA-ATCCAACTCCCTA-TGCGATGTATGATCCAAGTATTTGTGTTGTTCAAACTCCTTATGTGA
130 C-AGATCCAACTCCATATTG-GATGGATGAGCCAAGTATTAGTGTTGTTCAAACTCCTTATATGA
* * * *
60702 TGGAAAATAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-AGTCGGACGAG
193 TGGAAAAGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCA-TCGGAAGAG
* *
60766 TTCTTCTCATTATGAACCCTCCATTGGAAATGTTGATCCACCTCCTTCTGTGTTAGAATCGAACA
257 TTCTTCTCATTATGAACCCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACA
60831 AAGTGATGATGCT
322 AAGTGATGATGCT
60844 GATCTAACTC
Statistics
Matches: 298, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
404 118 0.40
405 179 0.60
406 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (404 bp):
CTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATAACTTCTTCTCATT
ATGAACTCTCCAATAGAAATGTTGATCCACCACTTTCTGTGATAGAATCAAACAAAGTGATCAGC
AGATCCAACTCCATATTGGATGGATGAGCCAAGTATTAGTGTTGTTCAAACTCCTTATATGATGG
AAAAGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATCGGAAGAGTTCT
TCTCATTATGAACCCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGT
GATGATGCTAATACAACTCCACATGGATGGATGAGCCAAGCATTTGTGTTGTTCCAACTCCTTAT
GTGATAGAAACAAT
Found at i:61095 original size:117 final size:116
Alignment explanation
Indices: 60886--61157 Score: 402
Period size: 117 Copynumber: 2.3 Consensus size: 116
60876 TGTTTGCACA
* * * * * *
60886 AGTTCTCCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCCCCTTCTGTGATGTATCGAC
1 AGTTCTTCTCATTATGAAC-TCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGATGAATCAAC
* * **
60951 CAAAGGTTTAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATG
65 CAAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCAAATG
* *
61003 AGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGAT-GAATC-AA
61068 CC-AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCAAATG
64 CCAAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCAAATG
61120 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
61158 CTGGTTAATC
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
116 32 0.23
117 105 0.75
118 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGATGAATCAACC
AAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCAAATG
Found at i:62963 original size:20 final size:20
Alignment explanation
Indices: 62937--62991 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
62927 AAAACATTAT
62937 GCCCGAAGGACTTATGGATG
1 GCCCGAAGGACTTATGGATG
*
62957 TCCCGAAGGACTTATGGATG
1 GCCCGAAGGACTTATGGATG
*
62977 GCCCAAAGGACTTAT
1 GCCCGAAGGACTTAT
62992 CATCTTGCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (20 bp):
GCCCGAAGGACTTATGGATG
Found at i:63054 original size:242 final size:236
Alignment explanation
Indices: 62559--63227 Score: 617
Period size: 262 Copynumber: 2.7 Consensus size: 236
62549 TATGTTACGA
* * *
62559 GGCCTGAAAGACTTACTAAGTAAGTATTTTGGAAATCGTTTTCTTACTTTAAAAAAAATCAATTT
1 GGCCCGAAAGACTTACTAAGTAAGAACTTTGGAAATCGTTTTCTTACTTTAAAAAAAATCAATTT
*
62624 TCAGAAAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAA
66 TCAGAAAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCACGTGAAAA
* * * * * *
62689 CATCCTGCCTGAAGGTCTTATAGATAGCCCGAATGACTTATCATCTTGCTCGAAAAGCTTATAGA
131 CATCATGCCCGAAGGACTTATAGATAGCCCGAAGGACTTATCA-CTGGCTCCAAAAGCTTATAGA
* * * *
62754 TTACCCGAAGGATTTAGGCATCATGCTCGGAAGACTTACTGAT
195 TTACCCGAAAGATTTAGGCATCA-GCACGAAAGACTTACTCAT
* * *
62797 GGCCCGAATGACTTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAAAAAATTA
1 GGCCCGAAAGACTTACTAAGTAAG-AACTTTGGAAATCGTTTTCTTAC-TTT--AAAAAAAATCA
* *
62862 ATTTTCAGAAAATATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTGAAAATCACGTG
62 ATTTTCAGAAAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCACGTG
* *
62927 AAAACATTATGCCCGAAGGACTTATGGATGTCCCGAAGGACTTATGGATGGCCCAAAGGACTTAT
127 AAAACATCATGCCCGAAGGAC-T-T--A--T-----A-G----AT--A--GCCCGAAGGACTTAT
* * * * * * *
62992 CATCTTGCT-CGAAAGACTTATAGATCACACGAATGATTTAAGCATCATGCTCGAAAGACTTACT
172 CA-CTGGCTCCAAAAG-CTTATAGATTACCCGAAAGATTTAGGCATCA-GCACGAAAGACTTACT
*
63056 GAT
234 CAT
* * * *
63059 GGCCC-AAGGGACTTACTAAGTAAGAAACTTTGGGAATTGTTTTCTTACTTT--TAAAAATCAAT
1 GGCCCGAA-AGACTTACTAAGTAAG-AACTTTGGAAATCGTTTTCTTACTTTAAAAAAAATCAAT
* * * * * *
63121 TTCCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATAATGTGAA
64 TTTCAGAAAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCACGTGAA
* ** * ** *
63186 AACATCCTGCCTAAAGGTCTTACGGATGGCCCGAAGGACTTA
129 AACATCATGCCCGAAGGACTTATAGATAGCCCGAAGGACTTA
63228 CTAATCAAGA
Statistics
Matches: 364, Mismatches: 41, Indels: 53
0.79 0.09 0.12
Matches are distributed among these distances:
237 13 0.04
238 22 0.06
239 20 0.05
240 3 0.01
241 2 0.01
242 89 0.24
243 1 0.00
244 1 0.00
245 1 0.00
246 1 0.00
248 1 0.00
253 2 0.01
254 1 0.00
255 1 0.00
256 1 0.00
257 82 0.23
258 2 0.01
260 1 0.00
261 9 0.02
262 111 0.30
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (236 bp):
GGCCCGAAAGACTTACTAAGTAAGAACTTTGGAAATCGTTTTCTTACTTTAAAAAAAATCAATTT
TCAGAAAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCACGTGAAAA
CATCATGCCCGAAGGACTTATAGATAGCCCGAAGGACTTATCACTGGCTCCAAAAGCTTATAGAT
TACCCGAAAGATTTAGGCATCAGCACGAAAGACTTACTCAT
Found at i:63420 original size:59 final size:59
Alignment explanation
Indices: 63293--63451 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 59
63283 TAAGTAATCA
* * * * * * * *
63293 TCAAGAAAACTATGAAAATCAAACCTAGTTTCTTTTTAAAAAATTCTTTTGAAAACATCATG
1 TCAAGAAACCTCTAAAAATCAGACTTAGTTTC--TTT-AAAAATGCATTTGAAAACACCATG
* *
63355 TCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAATGCATTTGAAAATACCATG
1 TCAAGAAACCTCTAAAAATCAGACTTAGTTTCTTTAAAAATGCATTTGAAAACACCATG
*
63414 TCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAA
1 TCAAGAAACCTCTAAAAATCAGACTTAGTTTCTTTAAA
63452 GATATCATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 56 0.66
60 3 0.04
62 26 0.31
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (59 bp):
TCAAGAAACCTCTAAAAATCAGACTTAGTTTCTTTAAAAATGCATTTGAAAACACCATG
Found at i:73373 original size:400 final size:399
Alignment explanation
Indices: 72633--73437 Score: 1529
Period size: 400 Copynumber: 2.0 Consensus size: 399
72623 TGCGCCGACG
* *
72633 GCCCTAACAGGTACTCATGGCTCTCTTCGTGCCAAAATATTAATCTCGAATGATATCACTATTGT
1 GCCCTAAAAGGTACTCATGGCTCTCTTCATGCCAAAATATTAATCTCGAATGATATCACTATTGT
72698 GTCATTAATCAAAAATATTATCAAATAGCTTGAGGGCTTCTCTTCATGATCCCACAATTAGATGA
66 GTCATTAATCAAAAATATTATCAAATAGCTTGAGGGCTTCTCTTCATGATCCCACAATTAGATGA
72763 ACACTTAAGAAGTGATTAATTCTTCTAACAGAAATGTCTTGAATTTTTGCTTCGAGCTGAGATAT
131 ACACTTAAGAAGTGATTAATTCTTCTAACAGAAATGTCTTGAATTTTTGCTTCGAGCTGAGATAT
* *
72828 GTGCCCTTTCGACTAAGGCGATCGTATGCTTCTTGATGGGTTATCGACAACGTCACAAGGAAGTG
196 GTGCCCTTTCGACTAAGGCGATCGTATGCTTCTTAATGGGTTATCAACAACGTCACAAGGAAGTG
*
72893 TTAGAAGTTATATCCTCTAGTCTTTCTGATCTCTCAAACTATTGTGAAATATCTTCATTACTCTG
261 TTAGAAGTTATATCCTCCAGTCTTTCTGATCTCTCAAACTATTGTGAAATATCTTCATTACTCTG
72958 GTATCGCTTGTTTTTTTTTTCCCAATTGAGGTCGAATGAGCCTTACCAGCTTTATGGACCTTTTC
326 GTATCGCTTG-TTTTTTTTTCCCAATTGAGGTCGAATGAGCCTTACCAGCTTTATGGACCTTTTC
73023 ACTTGAGATT
390 ACTTGAGATT
73033 GCCCTAAAAGGTACTCATGGCTCTCTTCATGCCAAAATATTAATCTCGAATGATATCACTATTGT
1 GCCCTAAAAGGTACTCATGGCTCTCTTCATGCCAAAATATTAATCTCGAATGATATCACTATTGT
* *
73098 GTCATTAATCAACAATATTATCAAATAGCTTGAGGGCTTCTCTTCATGATCCCATAATTAGATGA
66 GTCATTAATCAAAAATATTATCAAATAGCTTGAGGGCTTCTCTTCATGATCCCACAATTAGATGA
73163 ACACTTAAGAAGTGATTAATTCTTCTAACAGAAATGTCTTGAATTTTTGCTTCGAGCTGAGATAT
131 ACACTTAAGAAGTGATTAATTCTTCTAACAGAAATGTCTTGAATTTTTGCTTCGAGCTGAGATAT
73228 GTGCCCTTTCGACTAAGGCGATCGTATGCTTCTTAATGGGTTATCAACAACGTCACAAGGAAGTG
196 GTGCCCTTTCGACTAAGGCGATCGTATGCTTCTTAATGGGTTATCAACAACGTCACAAGGAAGTG
73293 TTAGAAGTTATATCCTCCAGTCTTTCTGATCTCTCAAACTATTGTGAAATATCTTCATTACTCTG
261 TTAGAAGTTATATCCTCCAGTCTTTCTGATCTCTCAAACTATTGTGAAATATCTTCATTACTCTG
73358 GTATCGCTTGTTTTTTTTTCCCAATTGAGGTCGAATGAGCCTTACCAGCTTTATGGACCTTTTCA
326 GTATCGCTTGTTTTTTTTTCCCAATTGAGGTCGAATGAGCCTTACCAGCTTTATGGACCTTTTCA
73423 CTTGAGATT
391 CTTGAGATT
*
73432 GTCCTA
1 GCCCTA
73438 TTTGAAAATA
Statistics
Matches: 397, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
399 69 0.17
400 328 0.83
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (399 bp):
GCCCTAAAAGGTACTCATGGCTCTCTTCATGCCAAAATATTAATCTCGAATGATATCACTATTGT
GTCATTAATCAAAAATATTATCAAATAGCTTGAGGGCTTCTCTTCATGATCCCACAATTAGATGA
ACACTTAAGAAGTGATTAATTCTTCTAACAGAAATGTCTTGAATTTTTGCTTCGAGCTGAGATAT
GTGCCCTTTCGACTAAGGCGATCGTATGCTTCTTAATGGGTTATCAACAACGTCACAAGGAAGTG
TTAGAAGTTATATCCTCCAGTCTTTCTGATCTCTCAAACTATTGTGAAATATCTTCATTACTCTG
GTATCGCTTGTTTTTTTTTCCCAATTGAGGTCGAATGAGCCTTACCAGCTTTATGGACCTTTTCA
CTTGAGATT
Found at i:73705 original size:28 final size:28
Alignment explanation
Indices: 73672--73739 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
73662 GAAAAGTAGA
* * *
73672 GTGTTTCAGGTTAATTTGGGGAAGTAAT
1 GTGTTTCAGGTTAATTTAGAGAAGCAAT
* *
73700 GTGTTTCAGGTCAATTTAGAGAGGCAAT
1 GTGTTTCAGGTTAATTTAGAGAAGCAAT
73728 GTGTTTCAGGTT
1 GTGTTTCAGGTT
73740 GGCTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (28 bp):
GTGTTTCAGGTTAATTTAGAGAAGCAAT
Found at i:74505 original size:21 final size:21
Alignment explanation
Indices: 74481--74550 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
74471 ACTTTTTTTC
**
74481 CTTTTTTGGTTTCTTTTCTCT
1 CTTTTTTACTTTCTTTTCTCT
74502 CTTTTTTTACTTTCTTTTCT-T
1 C-TTTTTTACTTTCTTTTCTCT
* * *
74523 TTTATTTTTCTTTATTTTCTCT
1 CTT-TTTTACTTTCTTTTCTCT
74545 CTTTTT
1 CTTTTT
74551 ATGTTTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 2 0.05
21 19 0.47
22 19 0.47
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (21 bp):
CTTTTTTACTTTCTTTTCTCT
Found at i:74541 original size:26 final size:25
Alignment explanation
Indices: 74503--74559 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
74493 CTTTTCTCTC
*
74503 TTTTTTTACTTTCTTTTCTTTTTAT-
1 TTTTTTTACTTTC-TCTCTTTTTATG
*
74528 TTTTCTTTATTTTCTCTCTTTTTATG
1 TTTT-TTTACTTTCTCTCTTTTTATG
74554 TTTTTT
1 TTTTTT
74560 CTTCTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTTACTTTCTCTCTTTTTATG
Found at i:81079 original size:60 final size:60
Alignment explanation
Indices: 80984--81108 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
80974 GTTCCTAGAT
* * * ** * * * *
80984 TATGATCGTCATTTTAAATTGGTCTTTAATTTTTTGAATATTCAAATTTTATTCTTAAAC
1 TATGATCGTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCATCCTCAAAC
**
81044 TATGATAC-TCATTCTAAATTAGTCCTTAAACTTTTGAACATTGTAATTTCATCCTCAAAC
1 TATGAT-CGTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCATCCTCAAAC
81104 TATGA
1 TATGA
81109 CCCTCAATCT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 52 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (60 bp):
TATGATCGTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCATCCTCAAAC
Found at i:81857 original size:158 final size:158
Alignment explanation
Indices: 81622--81942 Score: 642
Period size: 158 Copynumber: 2.0 Consensus size: 158
81612 TCTAGTGCGG
81622 TTAAGATTTCGGACACTTCAATAATTAAATAAAATCACATATGTGTATGTATCCAAATAACTAAT
1 TTAAGATTTCGGACACTTCAATAATTAAATAAAATCACATATGTGTATGTATCCAAATAACTAAT
81687 TTCTAGCTGATGATGAACTGAATAGAAATAAAGGTGGGTGTGTTAGATTCTTTATTAGAGTTAGG
66 TTCTAGCTGATGATGAACTGAATAGAAATAAAGGTGGGTGTGTTAGATTCTTTATTAGAGTTAGG
81752 ATGTAAATCACAAACAGTGGTGGATGTA
131 ATGTAAATCACAAACAGTGGTGGATGTA
81780 TTAAGATTTCGGACACTTCAATAATTAAATAAAATCACATATGTGTATGTATCCAAATAACTAAT
1 TTAAGATTTCGGACACTTCAATAATTAAATAAAATCACATATGTGTATGTATCCAAATAACTAAT
81845 TTCTAGCTGATGATGAACTGAATAGAAATAAAGGTGGGTGTGTTAGATTCTTTATTAGAGTTAGG
66 TTCTAGCTGATGATGAACTGAATAGAAATAAAGGTGGGTGTGTTAGATTCTTTATTAGAGTTAGG
81910 ATGTAAATCACAAACAGTGGTGGATGTA
131 ATGTAAATCACAAACAGTGGTGGATGTA
81938 TTAAG
1 TTAAG
81943 CCTAAATTTC
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 163 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (158 bp):
TTAAGATTTCGGACACTTCAATAATTAAATAAAATCACATATGTGTATGTATCCAAATAACTAAT
TTCTAGCTGATGATGAACTGAATAGAAATAAAGGTGGGTGTGTTAGATTCTTTATTAGAGTTAGG
ATGTAAATCACAAACAGTGGTGGATGTA
Found at i:82810 original size:3 final size:3
Alignment explanation
Indices: 82790--82831 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
82780 TTATTGTATC
* * *
82790 ATA ATA AGA ATA ACA ATA ATA ATA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
82832 GAGATATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:82980 original size:20 final size:21
Alignment explanation
Indices: 82941--82980 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
82931 AGAATATTCA
*
82941 AAAATTAAATATCTAATTTTT
1 AAAATTAAATATCAAATTTTT
82962 AAAATTAAATAT-AAATTTT
1 AAAATTAAATATCAAATTTT
82981 AATTTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTAAATATCAAATTTTT
Found at i:83042 original size:2 final size:2
Alignment explanation
Indices: 83037--83084 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
83027 GTGTGTGTGT
83037 TA TA TA TA TA TA 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 TA TA TA TA TA TA
83079 TA TA TA
1 TA TA TA
83085 CCTAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84997 original size:3 final size:3
Alignment explanation
Indices: 84991--85070 Score: 96
Period size: 3 Copynumber: 28.0 Consensus size: 3
84981 TATAATAATA
*
84991 ATT ATT ATT ATT A-T ATT ATT A-A ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
85036 A-A ATT ATT ATT ATT ATT AAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
85071 TTACAGTTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 6 0.09
3 59 0.91
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:85025 original size:25 final size:25
Alignment explanation
Indices: 84977--85070 Score: 138
Period size: 25 Copynumber: 3.8 Consensus size: 25
84967 CTTATAAAAA
* *
84977 ATATTATAATAATAATTATTATTATT
1 ATATTATTA-AATTATTATTATTATT
85003 ATATTATTAAATTATTATTATTATT
1 ATATTATTAAATTATTATTATTATT
85028 ATATTATTAAATTATTATTATTATT
1 ATATTATTAAATTATTATTATTATT
85053 A-A-TATTAATATTATTATT
1 ATATTATTAA-ATTATTATT
85071 TTACAGTTAC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
23 6 0.09
24 10 0.15
25 41 0.63
26 8 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATTATTAAATTATTATTATTATT
Found at i:85262 original size:19 final size:19
Alignment explanation
Indices: 85238--85276 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
85228 ACAGCCCTCT
*
85238 ATCCCACCGACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
85257 ATCCCACCAACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
85276 A
1 A
85277 CTGAATGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.51, G:0.18, T:0.05
Consensus pattern (19 bp):
ATCCCACCAACGCCGAGCC
Found at i:86597 original size:2 final size:2
Alignment explanation
Indices: 86590--86615 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86580 TTTTATATTC
86590 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
86616 TACAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89800 original size:2 final size:2
Alignment explanation
Indices: 89790--89823 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
89780 CAACAAAAAA
89790 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89824 CAATAAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:91705 original size:18 final size:18
Alignment explanation
Indices: 91682--91762 Score: 119
Period size: 18 Copynumber: 4.5 Consensus size: 18
91672 TTCAGTTTTA
*
91682 AACCTAAAATATGGTTAT
1 AACCTAAAATATGGTTAC
91700 AACCTAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
*
91718 AACCTAAAAACAT-GTTAC
1 AACCT-AAAATATGGTTAC
*
91736 AACCCAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
91754 AACCTAAAA
1 AACCTAAAA
91763 ACAAGTTAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
17 6 0.11
18 44 0.79
19 6 0.11
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.25
Consensus pattern (18 bp):
AACCTAAAATATGGTTAC
Found at i:91770 original size:18 final size:18
Alignment explanation
Indices: 91713--91770 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
91703 CTAAAATATG
*
91713 GTTACAACCTAAAAACAT
1 GTTACAACCTAAAAACAA
* **
91731 GTTACAACCCAAAATA-TG
1 GTTACAACCTAAAA-ACAA
91749 GTTACAACCTAAAAACAA
1 GTTACAACCTAAAAACAA
91767 GTTA
1 GTTA
91771 AGTTGGTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.22
Consensus pattern (18 bp):
GTTACAACCTAAAAACAA
Found at i:102667 original size:24 final size:24
Alignment explanation
Indices: 102611--102668 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
102601 CACCGAAGTG
* *
102611 CCACGTAAAATTTGTCCTGAAGGA
1 CCACGTAGAATTTATCCTGAAGGA
*
102635 CCACATAGAATTTATCCTGAAGGA
1 CCACGTAGAATTTATCCTGAAGGA
**
102659 GTACGTAGAA
1 CCACGTAGAA
102669 ATGTCTCGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (24 bp):
CCACGTAGAATTTATCCTGAAGGA
Found at i:105580 original size:18 final size:19
Alignment explanation
Indices: 105526--105764 Score: 166
Period size: 18 Copynumber: 13.3 Consensus size: 19
105516 GGTTTTCAAT
*
105526 CTAAAAT-CTGGTTCACAAC
1 CTAAAATACAGGTT-ACAAC
* *
105545 CTAAAATTCAGTTTACAAC
1 CTAAAATACAGGTTACAAC
*
105564 CTAAAA-ACAGGTTACAAA
1 CTAAAATACAGGTTACAAC
105582 CTAAAA-ACTA-GTTA-AAC
1 CTAAAATAC-AGGTTACAAC
*
105599 CTAAAATA-TGGTTACAAC
1 CTAAAATACAGGTTACAAC
*
105617 CTAAAATA-TGGTTACAAC
1 CTAAAATACAGGTTACAAC
* * * *
105635 ATAAAA-AAATGTTAAAAC
1 CTAAAATACAGGTTACAAC
*
105653 CTAAAATA-TGGTTACAAC
1 CTAAAATACAGGTTACAAC
* * *
105671 CTAAAAAACATGTTACAAT
1 CTAAAATACAGGTTACAAC
**
105690 CTAAAATA-TTGTTAC-AC
1 CTAAAATACAGGTTACAAC
* *
105707 CT-TAA-ACATGTTACAAC
1 CTAAAATACAGGTTACAAC
* *
105724 CTAAAATA-TGGTAACAAC
1 CTAAAATACAGGTTACAAC
*
105742 CTAAAA-ACAAGTTACAAC
1 CTAAAATACAGGTTACAAC
105760 CTAAA
1 CTAAA
105765 TATGATTATT
Statistics
Matches: 176, Mismatches: 31, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
15 1 0.01
16 8 0.05
17 21 0.12
18 107 0.61
19 35 0.20
20 4 0.02
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (19 bp):
CTAAAATACAGGTTACAAC
Found at i:105654 original size:36 final size:36
Alignment explanation
Indices: 105540--105768 Score: 231
Period size: 36 Copynumber: 6.4 Consensus size: 36
105530 AATCTGGTTC
* * *
105540 ACAACCTAAAAT-TCAGTTTACAACCTAAAAACAGGTT
1 ACAACCTAAAATAT--GGTTACAACCTAAAAAAATGTT
* * *
105577 ACAAACTAAAA-ACTAGTTA-AACCT-AAAATATGGTT
1 ACAACCTAAAATA-TGGTTACAACCTAAAAAAAT-GTT
*
105612 ACAACCTAAAATATGGTTACAACATAAAAAAATGTT
1 ACAACCTAAAATATGGTTACAACCTAAAAAAATGTT
*
105648 AAAACCTAAAATATGGTTACAACCTAAAAAACATGTT
1 ACAACCTAAAATATGGTTACAACCTAAAAAA-ATGTT
* * * *
105685 ACAATCTAAAATATTGTTAC-ACCT-TAAACATGTT
1 ACAACCTAAAATATGGTTACAACCTAAAAAAATGTT
*
105719 ACAACCTAAAATATGGTAACAACCTAAAAACAA-GTT
1 ACAACCTAAAATATGGTTACAACCTAAAAA-AATGTT
105755 ACAACCT-AAATATG
1 ACAACCTAAAATATG
105769 ATTATTAACA
Statistics
Matches: 161, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
34 27 0.17
35 37 0.23
36 57 0.35
37 39 0.24
38 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.25
Consensus pattern (36 bp):
ACAACCTAAAATATGGTTACAACCTAAAAAAATGTT
Found at i:105785 original size:107 final size:108
Alignment explanation
Indices: 105557--105772 Score: 289
Period size: 107 Copynumber: 2.0 Consensus size: 108
105547 AAAATTCAGT
*
105557 TTACAACCT-AAAAACAGGTTACAAACTAAAAACTAGTTAAACCTAAAATATGGTTACAACCTAA
1 TTACAACCTAAAAAACAGGTTACAAACTAAAAACTAGTTAAACCTAAAACATGGTTACAACCTAA
* *
105621 AATATGGTTACAACATAAAAAAATGTTAAAACCTAAAATATGG
66 AATATGGTAACAACATAAAAAAATGTTAAAACCTAAAATATGA
* * * * *
105664 TTACAACCTAAAAAACATGTTACAATCTAAAATA-TTGTTACACCTTAAACAT-GTTACAACCTA
1 TTACAACCTAAAAAACAGGTTACAAACTAAAA-ACTAGTTAAACCTAAAACATGGTTACAACCTA
* *
105727 AAATATGGTAACAACCTAAAAACAA-GTTACAACCT-AAATATGA
65 AAATATGGTAACAACATAAAAA-AATGTTAAAACCTAAAATATGA
105770 TTA
1 TTA
105773 TTAACACAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
106 10 0.10
107 49 0.51
108 36 0.38
109 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.26
Consensus pattern (108 bp):
TTACAACCTAAAAAACAGGTTACAAACTAAAAACTAGTTAAACCTAAAACATGGTTACAACCTAA
AATATGGTAACAACATAAAAAAATGTTAAAACCTAAAATATGA
Done.