Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006573.1 Hibiscus syriacus cultivar Beakdansim tig00016106_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: 1218788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:465692 original size:4 final size:4
Alignment explanation
Indices: 465666--465731 Score: 51
Period size: 4 Copynumber: 14.8 Consensus size: 4
465656 TTATAAAATT
*
465666 ATAA ATAA AGAA ATAA AGTTAA ATAA ATAA ATAA AGTTAA ATAA ATTAA
1 ATAA ATAA ATAA ATAA A--TAA ATAA ATAA ATAA A--TAA ATAA A-TAA
*
465715 TTAA ATTAA ATTAA ATA
1 ATAA A-TAA A-TAA ATA
465732 CTATAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 32 0.62
5 12 0.23
6 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (4 bp):
ATAA
Found at i:465693 original size:14 final size:13
Alignment explanation
Indices: 465666--465731 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 13
465656 TTATAAAATT
*
465666 ATAAA-TAAAGAA
1 ATAAATTAAATAA
465678 ATAAAGTTAAATAA
1 ATAAA-TTAAATAA
465692 ATAAA-TAAAGTTAA
1 ATAAATTAAA--TAA
*
465706 ATAAATTAATTAA
1 ATAAATTAAATAA
465719 ATTAAATTAAATA
1 A-TAAATTAAATA
465732 CTATAATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 9 0.20
13 4 0.09
14 29 0.64
15 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (13 bp):
ATAAATTAAATAA
Found at i:465711 original size:18 final size:18
Alignment explanation
Indices: 465667--465731 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
465657 TATAAAATTA
*
465667 TAAATAAAGAAATAAAGT
1 TAAATAAATAAATAAAGT
465685 TAAATAAATAAATAAAGT
1 TAAATAAATAAATAAAGT
*
465703 TAAATAAATTAATTAAA-T
1 TAAATAAA-TAAATAAAGT
465721 TAAATTAAATA
1 TAAA-TAAATA
465732 CTATAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 32 0.74
19 11 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAATAAATAAATAAAGT
Found at i:465753 original size:26 final size:27
Alignment explanation
Indices: 465706--465768 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
465696 ATAAAGTTAA
465706 ATAAATTAATTAAATTAAATTAAATACT
1 ATAAATT-ATTAAATTAAATTAAATACT
* * * *
465734 AT-AATTATTATATTATATTACATATT
1 ATAAATTATTAAATTAAATTAAATACT
465760 ATAAATTAT
1 ATAAATTAT
465769 ACCTTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 18 0.60
27 10 0.33
28 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAATTATTAAATTAAATTAAATACT
Found at i:466757 original size:20 final size:21
Alignment explanation
Indices: 466729--466780 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
466719 AATAAACATT
*
466729 AATATTTATAATA-TTTAATA
1 AATAATTATAATATTTTAATA
*
466749 AATAATTATAATATTTTATTA
1 AATAATTATAATATTTTAATA
*
466770 AATAATAATAA
1 AATAATTATAA
466781 CAACATCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATTATAATATTTTAATA
Found at i:467442 original size:19 final size:19
Alignment explanation
Indices: 467418--467494 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
467408 CACGAACCAA
467418 TTCTCTTCTTCTTATTTCT
1 TTCTCTTCTTCTTATTTCT
*
467437 TTCTCTTTTCTCTTATTTCT
1 TTCTCTTCT-TCTTATTTCT
*
467457 TCCTCTT-TTC-T-TTTCT
1 TTCTCTTCTTCTTATTTCT
* *
467473 TTCT-TCTCCTCGTATTTCT
1 TTCTCT-TCTTCTTATTTCT
467492 TTC
1 TTC
467495 ACTCCCGGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.02
16 9 0.18
17 3 0.06
18 3 0.06
19 17 0.35
20 16 0.33
ACGTcount: A:0.04, C:0.29, G:0.01, T:0.66
Consensus pattern (19 bp):
TTCTCTTCTTCTTATTTCT
Found at i:467452 original size:20 final size:20
Alignment explanation
Indices: 467418--467477 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
467408 CACGAACCAA
*
467418 TTCTCTTCT-TCTTATTTCT
1 TTCTCTTTTCTCTTATTTCT
467437 TTCTCTTTTCTCTTATTTCT
1 TTCTCTTTTCTCTTATTTCT
* * *
467457 TCCTCTTTTCTTTTCTTTCT
1 TTCTCTTTTCTCTTATTTCT
467477 T
1 T
467478 CTCCTCGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 8 0.22
20 28 0.78
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTCTTTTCTCTTATTTCT
Found at i:467626 original size:23 final size:23
Alignment explanation
Indices: 467600--467650 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
467590 CCCACCATTA
*
467600 TTGCTCCATTATTGTTGCAATGC
1 TTGCACCATTATTGTTGCAATGC
* *
467623 TTGCAGCATTATTGTTGCCATGC
1 TTGCACCATTATTGTTGCAATGC
*
467646 ATGCA
1 TTGCA
467651 GATTCACGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (23 bp):
TTGCACCATTATTGTTGCAATGC
Found at i:467651 original size:23 final size:23
Alignment explanation
Indices: 467606--467651 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
467596 ATTATTGCTC
*
467606 CATTATTGTTGCAATGCTTGCAG
1 CATTATTGTTGCAATGCATGCAG
*
467629 CATTATTGTTGCCATGCATGCAG
1 CATTATTGTTGCAATGCATGCAG
467652 ATTCACGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (23 bp):
CATTATTGTTGCAATGCATGCAG
Found at i:468275 original size:2 final size:2
Alignment explanation
Indices: 468268--468295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
468258 AAATTTTGAA
468268 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
468296 GATTAAAAGG
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:478875 original size:54 final size:55
Alignment explanation
Indices: 478817--478942 Score: 166
Period size: 55 Copynumber: 2.3 Consensus size: 55
478807 GATGCATGAA
* * *
478817 ACTCGCACAATCTTCAACAAACGTCTCTGTT-CTCTA-TGCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAAACGTCTCTATTCCT-TATTGCTTCAAAGAGTATAAG
* * * *
478871 ACTCGAACAATCTTCAACAATCGTGTTTATTCCTTATTTCTTCAAAGAGTATAAG
1 ACTCGAACAATCTTCAACAAACGTCTCTATTCCTTATTGCTTCAAAGAGTATAAG
478926 ACTCGAACAATCTTCAA
1 ACTCGAACAATCTTCAA
478943 TAATCGGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
54 28 0.44
55 35 0.56
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAAACGTCTCTATTCCTTATTGCTTCAAAGAGTATAAG
Found at i:479082 original size:54 final size:54
Alignment explanation
Indices: 478947--480015 Score: 1202
Period size: 54 Copynumber: 19.7 Consensus size: 54
478937 CTTCAATAAT
* * *
478947 CGGGTCCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATAATCTTCTGCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * *
479002 CAGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGACATATTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* * * * * *
479056 CGAGTTCTCTCCCTTTTTC-TCTAGGGAGTATAGATCTTGGAAATTTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* *
479110 CGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTC-AAACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGGAA-ATCTTCTTCAAA
* * **
479164 CGGGTTCGCTTCGCTCTTTCTTCAGGGAGTATAGAACTCGAACAATTCTTCTGAAAA
1 CGGGTTCGC-TCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AA-TCTTCTTCAAA
*
479221 CGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GATAATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * *
479275 CGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACTTGGAAAT-TTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* * * **
479328 CGGGTTCGCTCCTTCTTTCATT-AAGGAGTATAGAACTCGAATAATCTTCTGAAAA
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
*
479383 CGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GATAATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * *
479437 CGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACTTGGAAAT-TTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* * * **
479490 CGGGTTCGCTCCTTCTTTCATT-AAGGAGTATAGAACTCGAATAATCTTCTGAAAA
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
*
479545 CGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GATAATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * * **
479599 CGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACTC-AAGAATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * * *
479653 CGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAA
1 CGGGTTCGC-TCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * *
479709 CAGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGGAAATTTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* * * **
479763 CGGGTTCGCTCCTTCTTTCATT-AGGAAGTATAGAACTC-AAGAATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * * *
479817 CGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAA
1 CGGGTTCGC-TCCCTCTTTCTTCAGGGAGTATAGAACTCGGA-AATCTTCTTCAAA
* * *
479873 CAGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGGAAATTTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* * * *
479927 CGGGTTCGCTCCTTCTTTCATT-AAGGAGTATAGAACTCGG--AT-ATCTTCATA
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
* *
479978 CGGGTTCGCTCCCTCTTTC-TCTAGGGATTATGGAACTC
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTC
480016 AAGTAATCTT
Statistics
Matches: 874, Mismatches: 113, Indels: 58
0.84 0.11 0.06
Matches are distributed among these distances:
49 1 0.00
51 38 0.04
52 2 0.00
53 87 0.10
54 397 0.45
55 258 0.30
56 72 0.08
57 19 0.02
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (54 bp):
CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGGAAATCTTCTTCAAA
Found at i:480455 original size:36 final size:36
Alignment explanation
Indices: 480397--480626 Score: 280
Period size: 36 Copynumber: 6.4 Consensus size: 36
480387 ACTCTTCTGA
* * * **
480397 GAAGGCTTAAAATGGATCTGCTTCACTACTTTTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTACTCTCCGGT
* *
480434 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
* * * *
480470 GAAGACTTATGATTGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
* * * *
480506 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
*
480542 GAAGGCTTCAGATGGTTTGCTTCACTACTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
* * *
480578 GAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
480614 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
480627 TGACTTGCTC
Statistics
Matches: 172, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
36 159 0.92
37 13 0.08
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGT
Found at i:480565 original size:108 final size:109
Alignment explanation
Indices: 480397--480635 Score: 315
Period size: 108 Copynumber: 2.2 Consensus size: 109
480387 ACTCTTCTGA
* * **
480397 GAAGGCTTAAAATGGA-TCTGCTTCACTACTT-TTTGGTGAAGACTTAAGATGGTTTGCTTCACT
1 GAAGGCTTAAGATTGACT-TGCTTCACTA-TTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACT
* * *
480460 ACTCTCTGGTGAAGACTTATGATTGTTTGCTTCACTAT-TCTCCGGT
64 ACTCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCCGGT
* * *
480506 GAAGGCTTCAGATTGA-TTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTAC
1 GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
* *
480570 TCTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
480614 GAAGGCTTAAGATTGACTTGCT
1 GAAGGCTTAAGATTGACTTGCT
480636 CCAATCTCAT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
107 3 0.03
108 92 0.81
109 19 0.17
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (109 bp):
GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
Found at i:482038 original size:125 final size:125
Alignment explanation
Indices: 481815--482193 Score: 519
Period size: 125 Copynumber: 3.0 Consensus size: 125
481805 ACTAATGTCG
* * * * *
481815 CAACATTATTTTATTCTGGTACGGGCCTTCAAAATGCCTCAAT-ATCTCAAATTATAAGGCTCAT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCAT
* * ** *
481879 TCTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCATCATGA-GGTGGGTTCAGTCGCGCCC
65 TCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGG-GGGTTCAGTCGTGCCC
*
481940 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
** * *
482005 CTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGTGCCC
66 CTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAGTCGTGCCC
** * * *
482065 CAACATTATCTTATAAAGGTACGGGTCTTCCAAAATACCCCAACACCTCAAATTGTAAGGCTCAT
1 CAACATTATCTTATACTGGTACGGGCCTT-CAAAATGCCCCATCACCTCAAATTGTAAGGCTCAT
* *
482130 TCTCAATGCCTTCTTCGTCTGGATCTTGTCATTTCAAAATGATGGGGGTTCAGTCATGCCC
65 TCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAGTCGTGCCC
482191 CAA
1 CAA
482194 TGTGGGTATT
Statistics
Matches: 225, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
124 3 0.01
125 129 0.57
126 93 0.41
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (125 bp):
CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
CTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAGTCGTGCCC
Found at i:482226 original size:126 final size:124
Alignment explanation
Indices: 481860--482193 Score: 393
Period size: 126 Copynumber: 2.7 Consensus size: 124
481850 GCCTCAATAT
* * * **
481860 CTCAAATTATAAGGCTCATTCTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCATCATGA-GGT
1 CTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGG-
* ** ** * * * *
481924 GGGTTCAGTCGCGCCCCAACATTATCTCATACTGGTACGGGCCT-TCAAAATGCCCCATCAC
65 GGGTTCAATCATGCCCCAACATTATCTCATA--GGTACCCGTCTGCCAAAATACCCCAACAC
** *
481985 CTCAAATTGTAAGGCTCATTCTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAAATGATGGG
1 CTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGG
* * ** *
482050 GGTTCAATCGTGCCCCAACATTATCTTATAAAGGTACGGGTCTTCCAAAATACCCCAACAC
66 GGTTCAATCATGCCCCAACATTATCTCAT--AGGTACCCGTCTGCCAAAATACCCCAACAC
*
482111 CTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCTGGATCTTGTCATTTCAAAATGATGGG
1 CTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGG
*
482176 GGTTCAGTCATGCCCCAA
66 GGTTCAATCATGCCCCAA
482194 TGTGGGTATT
Statistics
Matches: 185, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
125 91 0.49
126 93 0.50
127 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (124 bp):
CTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAAATGATGGG
GGTTCAATCATGCCCCAACATTATCTCATAGGTACCCGTCTGCCAAAATACCCCAACAC
Found at i:486119 original size:20 final size:21
Alignment explanation
Indices: 486094--486230 Score: 92
Period size: 21 Copynumber: 6.6 Consensus size: 21
486084 AATGTGAAGT
486094 GGTCTTCAT-GTCGTTATG-AA
1 GGTCTTC-TCGTCGTTATGAAA
486114 GGTCTTCTCGTCGTTATGAAA
1 GGTCTTCTCGTCGTTATGAAA
*
486135 GGTCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
* *
486156 GGCCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
486177 GG-CATTCTCGTC-TTGATG-AA
1 GGTC-TTCTCGTCGTT-ATGAAA
* * *
486197 TGACATTCTCGTC-TTGATGAAT
1 GGTC-TTCTCGTCGTT-ATGAAA
*
486219 GCTCTTCTCGTC
1 GGTCTTCTCGTC
486231 CTTGGTACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.20
21 79 0.77
22 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (21 bp):
GGTCTTCTCGTCGTTATGAAA
Found at i:486138 original size:21 final size:21
Alignment explanation
Indices: 486112--486230 Score: 127
Period size: 21 Copynumber: 5.7 Consensus size: 21
486102 TGTCGTTATG
486112 AAGGTCTTCTCGTCGTT-ATGA
1 AAGGTCTTCTCGTC-TTGATGA
486133 AAGGTCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
* *
486154 ATGGCCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
*
486175 ATGG-CATTCTCGTCTTGATG-
1 AAGGTC-TTCTCGTCTTGATGA
* *
486195 AATGACATTCTCGTCTTGATGA
1 AAGGTC-TTCTCGTCTTGATGA
* *
486217 ATGCTCTTCTCGTC
1 AAGGTCTTCTCGTC
486231 CTTGGTACAA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.06
21 79 0.92
22 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (21 bp):
AAGGTCTTCTCGTCTTGATGA
Found at i:492325 original size:21 final size:21
Alignment explanation
Indices: 492297--492348 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
492287 ACCGTGATTA
492297 CGGCCGTCGC-GAGCGCTATTG
1 CGGCCGTCGCGGA-CGCTATTG
*
492318 CGGTCGTCGCGGACGCTATTG
1 CGGCCGTCGCGGACGCTATTG
492339 CGGCCGTCGC
1 CGGCCGTCGC
492349 AGTTAACTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.08, C:0.35, G:0.38, T:0.19
Consensus pattern (21 bp):
CGGCCGTCGCGGACGCTATTG
Found at i:494406 original size:29 final size:29
Alignment explanation
Indices: 494334--494515 Score: 118
Period size: 29 Copynumber: 6.3 Consensus size: 29
494324 CGTTGATCGG
* * *
494334 GTGACATTTTGGTAATTATTTTGGAAATG
1 GTGATATTTTGGTAATTATTTTGAAAATA
* **
494363 GTGCT-TTTCTGGTAATTATTTTGAAAAGG
1 GTGATATTT-TGGTAATTATTTTGAAAATA
* * *
494392 GTGTTATTTTTGTAATT-TTTT-AAAAAA
1 GTGATATTTTGGTAATTATTTTGAAAATA
* * * ** * * *
494419 GTGACAATTTCGTAAAAAATTTAAAAAGA
1 GTGATATTTTGGTAATTATTTTGAAAATA
*
494448 GTGATATTTTAGTAATTATTTTGAAAATA
1 GTGATATTTTGGTAATTATTTTGAAAATA
* * * * *
494477 ATGCTATTTTGGTAATTAATTTCAAAATG
1 GTGATATTTTGGTAATTATTTTGAAAATA
*
494506 GTGCTATTTT
1 GTGATATTTT
494516 ATATTAAAAA
Statistics
Matches: 118, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
27 15 0.13
28 10 0.08
29 90 0.76
30 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTGAAAATA
Found at i:494514 original size:58 final size:57
Alignment explanation
Indices: 494333--494516 Score: 144
Period size: 58 Copynumber: 3.2 Consensus size: 57
494323 CCGTTGATCG
* * * ** * *
494333 GGTGACATTTTGGTAATTATTTTGGAAATGGTGCT-TTTCTGGTAATTATTTTGAAAAG
1 GGTGATATTTTAGTAATTATTTTGAAAATAATGCTATTT-TGGTAATTAATTT-AAAAA
* * * * **
494391 GGTGTTATTTTTGTAATT-TTTT-AAAA-AAGTGAC-AATTTCGTAAAAAATTTAAAAA
1 GGTGATATTTTAGTAATTATTTTGAAAATAA-TG-CTATTTTGGTAATTAATTTAAAAA
*
494446 GAGTGATATTTTAGTAATTATTTTGAAAATAATGCTATTTTGGTAATTAATTTCAAAAT
1 G-GTGATATTTTAGTAATTATTTTGAAAATAATGCTATTTTGGTAATTAATTT-AAAAA
*
494505 GGTGCTATTTTA
1 GGTGATATTTTA
494517 TATTAAAAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
55 5 0.05
56 29 0.30
57 12 0.12
58 44 0.45
59 7 0.07
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (57 bp):
GGTGATATTTTAGTAATTATTTTGAAAATAATGCTATTTTGGTAATTAATTTAAAAA
Found at i:495523 original size:42 final size:41
Alignment explanation
Indices: 495464--495626 Score: 245
Period size: 42 Copynumber: 3.9 Consensus size: 41
495454 GTATTACCAG
495464 GTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAA
1 GTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCCCAA
* *
495506 GTCCCTTTGCTGTGTGCGAAGGTAAGACTTACAGTTTACCAA
1 GTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCCCAA
* *
495548 GTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTAG
1 GTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCCCAA
*
495590 GTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 GTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
495627 TCCTAGACTC
Statistics
Matches: 112, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 4 0.04
42 108 0.96
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (41 bp):
GTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCCCAA
Found at i:511445 original size:29 final size:29
Alignment explanation
Indices: 511411--511569 Score: 128
Period size: 29 Copynumber: 5.6 Consensus size: 29
511401 TTTGGGAAAT
*
511411 GGTGCTATTCTGGTAATTATTTTGAAAAG
1 GGTGCTATTTTGGTAATTATTTTGAAAAG
* *
511440 GGTGCTATTTTTGTAATT-TTTTTAAAA-
1 GGTGCTATTTTGGTAATTATTTTGAAAAG
* ** * * *
511467 AGTGAC-AACTTCGTAA-AATTTTTAAAAG
1 GGTG-CTATTTTGGTAATTATTTTGAAAAG
* * * *
511495 AGTGATATTTTAGTAATTATTTTGAAAAT
1 GGTGCTATTTTGGTAATTATTTTGAAAAG
* * *
511524 GATGCTATTTTGGTAATTAATTTGAAAAT
1 GGTGCTATTTTGGTAATTATTTTGAAAAG
*
511553 GGTGCTATTTTCGTAAT
1 GGTGCTATTTTGGTAAT
511570 GTTAAAAAAA
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
27 19 0.18
28 20 0.19
29 64 0.62
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.45
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTATTTTGAAAAG
Found at i:511510 original size:28 final size:28
Alignment explanation
Indices: 511429--511510 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 28
511419 TCTGGTAATT
* * * * *
511429 ATTTTGAAAAGGGTGCTATTTTTGTAAT
1 ATTTTTAAAAGAGTGATATTTTAGTAAA
* * ** *
511457 TTTTTTAAAA-AGTGACAACTTCGTAAA
1 ATTTTTAAAAGAGTGATATTTTAGTAAA
511484 ATTTTTAAAAGAGTGATATTTTAGTAA
1 ATTTTTAAAAGAGTGATATTTTAGTAA
511511 TTATTTTGAA
Statistics
Matches: 39, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.43
Consensus pattern (28 bp):
ATTTTTAAAAGAGTGATATTTTAGTAAA
Found at i:512573 original size:42 final size:41
Alignment explanation
Indices: 512510--512714 Score: 259
Period size: 42 Copynumber: 4.8 Consensus size: 41
512500 GGATGTATTA
512510 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
* * *
512552 CCAAGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
512594 CCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
*
512636 CCAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTC
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTC
* * *
512679 CTAGG-CTCCTCTGCTTTGTGCACAGGCTAAGCCTTA
1 CCAGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTA
512715 TTGGTGTATA
Statistics
Matches: 146, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 110 0.75
43 21 0.14
44 11 0.08
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:515804 original size:61 final size:61
Alignment explanation
Indices: 515730--515854 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
515720 CATGCACCAA
515730 TGTCATGTGTATATGTATACACCACTATATATTATACTTCTTAATATATATGTATGTAATG
1 TGTCATGTGTATATGTATACACCACTATATATTATACTTCTTAATATATATGTATGTAATG
*
515791 TGTCATGTGTATATGTATACATCACTATATATTATACTTCTTAATATATATGTATGTAATG
1 TGTCATGTGTATATGTATACACCACTATATATTATACTTCTTAATATATATGTATGTAATG
515852 TGT
1 TGT
515855 TGCGTATATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (61 bp):
TGTCATGTGTATATGTATACACCACTATATATTATACTTCTTAATATATATGTATGTAATG
Found at i:521563 original size:691 final size:691
Alignment explanation
Indices: 520242--521627 Score: 2601
Period size: 691 Copynumber: 2.0 Consensus size: 691
520232 AGACTAAGTA
520242 AATGTCTTGGGCTTATTAAGGAATTTAAATAAACATAGGTGTTGTATTACCCTTAAAAGTAATGG
1 AATGTCTTGGGCTTATTAAGGAATTTAAATAAACATAGGTGTTGTATTACCCTTAAAAGTAATGG
* *
520307 AACACAATTTAAGTGAGTAGATAAACCCTAAAGCTATATCAATACCCGAATGTCATAAATATCAT
66 AACACAATTTAAGTGAGTAGATAAACCCTAAAACTATATCAATACCCGAATATCATAAATATCAT
* *
520372 TTGAATGCGTGTTAGTATTCACAAGTATGGATCGATGATAATTTTGGAAGTAATTGACTCAGCTC
131 TTGAATGCGTGTTAGTATTCACAAGTATGGATCGATGATAATTCTGGAAGTAATTGACTCAACTC
520437 AGCTCTAGAGCACATTCGATGCTAAGAAAGGGAAATTCGTGAGACAAATCAACCACGAATATCAG
196 AGCTCTAGAGCACATTCGATGCTAAGAAAGGGAAATTCGTGAGACAAATCAACCACGAATATCAG
* *
520502 ATTGACTAAATTGAACTAAAAGGTAGTACAATATGTATCTGAAATTCAGAAACATCTGAATTACT
261 ATTGACTAAATTGAACTAAAAGGTAGTACAATATGTATATGAAATTCAAAAACATCTGAATTACT
520567 CTGGAAAACTCTAAAGTAATCGGGATAGATTTGATTGCTAAATGAACTAAGTAACCTCAACGATT
326 CTGGAAAACTCTAAAGTAATCGGGATAGATTTGATTGCTAAATGAACTAAGTAACCTCAACGATT
520632 GAGGATTAAATAAGTGATTGGGTGAGTCTGGAAACACTGTTGAACTTACAAGATGAAATGTCTTT
391 GAGGATTAAATAAGTGATTGGGTGAGTCTGGAAACACTGTTGAACTTACAAGATGAAATGTCTTT
* *
520697 ACGGGTCATGAACCATGAATCAAGTACGTCTGTATTTCTTGATATTGTTGAAACGTGGAAATGAA
456 ACGAGTCATGAACCATGAATCAAGTACGTCTGTATTTCCTGATATTGTTGAAACGTGGAAATGAA
* *
520762 ATAAAGACCGTTGGAAGATCTATTCATCAACGATTACGAAGATGATTTATGGACAATAACTGTTA
521 ATAAAGACCGTTGGAAGATCTATTCATCAACGATTACGAACATGATTTATGGACAAGAACTGTTA
* *
520827 GTATTAAAGAATGAATACTGTGGAAGGGCATTGAATGGACTTGTCGACATGCGTTAGTTTAGGAG
586 GTATTAAAGAATGAATACTCTGGAAGGGCATTGAATGGACTTGTCGACATGCGTTAGTCTAGGAG
520892 TTATGTAACTCAATTTATTTGATAATCTAATTTATCAATAT
651 TTATGTAACTCAATTTATTTGATAATCTAATTTATCAATAT
520933 AATGTCTTGGGCTTATTAAGGAATTTAAATAAACATAGGTGTTGTATTACCCTTAAAAGTAATGG
1 AATGTCTTGGGCTTATTAAGGAATTTAAATAAACATAGGTGTTGTATTACCCTTAAAAGTAATGG
* * *
520998 AACATAATTTAAGTGAGTAGATAAACCCTAAAACTATGTCAATACCTGAATATCATAAATATCAT
66 AACACAATTTAAGTGAGTAGATAAACCCTAAAACTATATCAATACCCGAATATCATAAATATCAT
*
521063 TTGAATGCGTGTTAGTATTCACAAGTATGGATCGATGATAATTCTGGAAGTAATTGGCTCAACTC
131 TTGAATGCGTGTTAGTATTCACAAGTATGGATCGATGATAATTCTGGAAGTAATTGACTCAACTC
521128 AGCTCTAGAGCACATTCGATGCTAAGAAAGGGAAATTCGTGAGACAAATCAACCACGAATATCAG
196 AGCTCTAGAGCACATTCGATGCTAAGAAAGGGAAATTCGTGAGACAAATCAACCACGAATATCAG
*
521193 ATTTACTAAATTGAACTAAAAGGTAGTACAATATGTATATGAAATTCAAAAACATCTGAATTACT
261 ATTGACTAAATTGAACTAAAAGGTAGTACAATATGTATATGAAATTCAAAAACATCTGAATTACT
521258 CTGGAAAACTCTAAAGTAATCGGGATAGATTTGATTGCTAAATGAACTAAGTAACCTCAACGATT
326 CTGGAAAACTCTAAAGTAATCGGGATAGATTTGATTGCTAAATGAACTAAGTAACCTCAACGATT
521323 GAGGATTAAATAAGTGATTGGGTGAGTCTGGAAACACTGTTGAACTTACAAGATGAAATGTCTTT
391 GAGGATTAAATAAGTGATTGGGTGAGTCTGGAAACACTGTTGAACTTACAAGATGAAATGTCTTT
521388 ACGAGTCATGAACCATGAATCAAGTACGTCTGTATTTCCTGATATTGTTGAAACGTGGAAATGAA
456 ACGAGTCATGAACCATGAATCAAGTACGTCTGTATTTCCTGATATTGTTGAAACGTGGAAATGAA
521453 ATAAAGACCGTTGGAAGATCTATTCATCAACGATTACGAACATGATTTATGGACAAGAACTGTTA
521 ATAAAGACCGTTGGAAGATCTATTCATCAACGATTACGAACATGATTTATGGACAAGAACTGTTA
*
521518 GTATTAAAGAGTGAATACTCTGGAAGGGCATTGAATGGACTTGTCGACATGCGTTAGTCTAGGAG
586 GTATTAAAGAATGAATACTCTGGAAGGGCATTGAATGGACTTGTCGACATGCGTTAGTCTAGGAG
*
521583 TTATGTAACTCGATTTATTTGATAATCTAATTTATCAATAT
651 TTATGTAACTCAATTTATTTGATAATCTAATTTATCAATAT
521624 AATG
1 AATG
521628 GGTATATGTT
Statistics
Matches: 676, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
691 676 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (691 bp):
AATGTCTTGGGCTTATTAAGGAATTTAAATAAACATAGGTGTTGTATTACCCTTAAAAGTAATGG
AACACAATTTAAGTGAGTAGATAAACCCTAAAACTATATCAATACCCGAATATCATAAATATCAT
TTGAATGCGTGTTAGTATTCACAAGTATGGATCGATGATAATTCTGGAAGTAATTGACTCAACTC
AGCTCTAGAGCACATTCGATGCTAAGAAAGGGAAATTCGTGAGACAAATCAACCACGAATATCAG
ATTGACTAAATTGAACTAAAAGGTAGTACAATATGTATATGAAATTCAAAAACATCTGAATTACT
CTGGAAAACTCTAAAGTAATCGGGATAGATTTGATTGCTAAATGAACTAAGTAACCTCAACGATT
GAGGATTAAATAAGTGATTGGGTGAGTCTGGAAACACTGTTGAACTTACAAGATGAAATGTCTTT
ACGAGTCATGAACCATGAATCAAGTACGTCTGTATTTCCTGATATTGTTGAAACGTGGAAATGAA
ATAAAGACCGTTGGAAGATCTATTCATCAACGATTACGAACATGATTTATGGACAAGAACTGTTA
GTATTAAAGAATGAATACTCTGGAAGGGCATTGAATGGACTTGTCGACATGCGTTAGTCTAGGAG
TTATGTAACTCAATTTATTTGATAATCTAATTTATCAATAT
Found at i:522264 original size:32 final size:31
Alignment explanation
Indices: 522191--522311 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
522181 CTAATGTGAC
* * *
522191 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGATCAT
* * **
522222 TATCAGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGAT-CAT
* *
522254 TCTTAGGTAGGCCCCGTGGCCCTGAA-A-CTT
1 TCTTAGGTAGGCCCTGTGGCCCT-AAGATCAT
* * **
522284 TCTTGGGTAGGCTCTCAGGCCCTAAGAT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGAT
522312 GTTCCCTTAG
Statistics
Matches: 69, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
29 2 0.03
30 20 0.29
31 23 0.33
32 22 0.32
33 2 0.03
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGTGGCCCTAAGATCAT
Found at i:527855 original size:66 final size:66
Alignment explanation
Indices: 527773--527896 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 66
527763 TTAAATTCAG
* *
527773 ATTTTATCAGTTTTGGTGCAGAGGGAATCGATACCCCTTTAAAGGGGAACCGATTCCCATAATCA
1 ATTTTATCAGTTTTGGTGCAGAGGGAATCGATACCCCATTAAAGAGGAACCGATTCCCATAATCA
527838 T
66 T
*
527839 ATTTTATCAGTTTTGGTGCAGAGGGAATCGATACCCCATTGAAGAGGAACCGATTCCC
1 ATTTTATCAGTTTTGGTGCAGAGGGAATCGATACCCCATTAAAGAGGAACCGATTCCC
527897 CCCTGGGGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (66 bp):
ATTTTATCAGTTTTGGTGCAGAGGGAATCGATACCCCATTAAAGAGGAACCGATTCCCATAATCA
T
Found at i:528281 original size:10 final size:10
Alignment explanation
Indices: 528262--528292 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
528252 AGCACAAGAA
*
528262 TTTTTCAAAT
1 TTTTTGAAAT
528272 TTTTTGAAAT
1 TTTTTGAAAT
528282 TTTTTGAAAT
1 TTTTTGAAAT
528292 T
1 T
528293 AAAAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (10 bp):
TTTTTGAAAT
Found at i:530653 original size:21 final size:21
Alignment explanation
Indices: 530629--530678 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
530619 CTTAGGGAAT
*
530629 CGATTCCCAATGAGGGGTTAC
1 CGATTCCCAATGAGGGGGTAC
530650 CGATTCCCAATGAGGGGGTAC
1 CGATTCCCAATGAGGGGGTAC
530671 CGATTCCC
1 CGATTCCC
530679 CCCACACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (21 bp):
CGATTCCCAATGAGGGGGTAC
Found at i:542344 original size:3 final size:3
Alignment explanation
Indices: 542336--542464 Score: 258
Period size: 3 Copynumber: 43.0 Consensus size: 3
542326 GGTTAAAAGG
542336 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
542384 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
542432 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
542465 ACAGTACGTG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 126 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:542679 original size:2 final size:2
Alignment explanation
Indices: 542672--542699 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
542662 TGAATGATTA
542672 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
542700 TAAAATATAA
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:544036 original size:51 final size:51
Alignment explanation
Indices: 543960--544063 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
543950 AATATGCTTC
543960 ACCATTCCATGGCTTTATTATTCTAGAAAGTTTGTTCAGTTTTGCATCACG
1 ACCATTCCATGGCTTTATTATTCTAGAAAGTTTGTTCAGTTTTGCATCACG
544011 ACCATTCCATGGCTTTATTATTCTAGAAAGTTTGTTCAGTTTTGCATCACG
1 ACCATTCCATGGCTTTATTATTCTAGAAAGTTTGTTCAGTTTTGCATCACG
544062 AC
1 AC
544064 AAGCAATGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (51 bp):
ACCATTCCATGGCTTTATTATTCTAGAAAGTTTGTTCAGTTTTGCATCACG
Found at i:545515 original size:13 final size:13
Alignment explanation
Indices: 545497--545532 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
545487 ACCCGACCCA
*
545497 ACCCGACCCGTTT
1 ACCCGACCCGTTG
545510 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
545523 ACCGGACCCG
1 ACCCGACCCG
545533 ACCTGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:548101 original size:24 final size:24
Alignment explanation
Indices: 548028--548101 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
548018 TCGATTTGAA
*
548028 TTCTGATCTGATACTTGACATGGA-
1 TTCTGATCTGATACTTGACCT-GAT
*
548052 TTCTGATCTGTTACTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
*
548076 TTCTGATATGATACTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
548100 TT
1 TT
548102 ATGTTTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.04
24 43 0.96
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACCTGAT
Found at i:552782 original size:12 final size:12
Alignment explanation
Indices: 552745--552783 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
552735 ATATGATACT
552745 TGACATGGATTC
1 TGACATGGATTC
*
552757 TGATAT-GATATC
1 TGACATGGAT-TC
552769 TGACATGGATTC
1 TGACATGGATTC
552781 TGA
1 TGA
552784 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:552851 original size:24 final size:24
Alignment explanation
Indices: 552729--552844 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
552719 TTCGATTTGA
552729 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
552753 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
552777 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
552801 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
552824 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
552845 CTGATTTATT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:556436 original size:13 final size:14
Alignment explanation
Indices: 556414--556450 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
556404 GTCAAAGAAA
556414 GTCAACGGTCAACG
1 GTCAACGGTCAACG
556428 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
556441 GTCAACGGTC
1 GTCAACGGTC
556451 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:556462 original size:17 final size:17
Alignment explanation
Indices: 556440--556497 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
556430 CACGGTCAAC
556440 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
556457 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
556474 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
556491 GGTCAAC
1 GGTCAAC
556498 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:556467 original size:7 final size:7
Alignment explanation
Indices: 556414--556450 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
556404 GTCAAAGAAA
556414 GTCAACG
1 GTCAACG
556421 GTCAACG
1 GTCAACG
556428 GTC-ACG
1 GTCAACG
556434 GTCAACG
1 GTCAACG
556441 GTCAACG
1 GTCAACG
556448 GTC
1 GTC
556451 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:556515 original size:19 final size:19
Alignment explanation
Indices: 556491--556579 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
556481 AGTCGGGTCG
*
556491 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
556510 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
556529 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
556548 GGTCAAACCGGTTCAAAAC
1 GGTCAAACCGGTTCAGACC
556567 GGTCAAACCGGTT
1 GGTCAAACCGGTT
556580 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 1 0.02
19 64 0.98
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:556521 original size:9 final size:9
Alignment explanation
Indices: 556491--556578 Score: 95
Period size: 9 Copynumber: 9.3 Consensus size: 9
556481 AGTCGGGTCG
*
556491 GGTCAACCC
1 GGTCAAACC
*
556500 GGTTCAGACC
1 GG-TCAAACC
556510 GGTCAAACC
1 GGTCAAACC
*
556519 GGTTCAGACC
1 GG-TCAAACC
556529 GGTCAAACC
1 GGTCAAACC
*
556538 GGTTCGAACC
1 GG-TCAAACC
556548 GGTCAAACC
1 GGTCAAACC
*
556557 GGTTCAAAAC
1 GG-TCAAACC
556567 GGTCAAACC
1 GGTCAAACC
556576 GGT
1 GGT
556579 TTTCCAGCAG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
9 35 0.53
10 31 0.47
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:563754 original size:13 final size:14
Alignment explanation
Indices: 563732--563768 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
563722 GTCAAAGAAA
563732 GTCAACGGTCAACG
1 GTCAACGGTCAACG
563746 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
563759 GTCAACGGTC
1 GTCAACGGTC
563769 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:563780 original size:17 final size:17
Alignment explanation
Indices: 563758--563815 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
563748 CACGGTCAAC
563758 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
563775 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
563792 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
563809 GGTCAAC
1 GGTCAAC
563816 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:563785 original size:7 final size:7
Alignment explanation
Indices: 563732--563768 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
563722 GTCAAAGAAA
563732 GTCAACG
1 GTCAACG
563739 GTCAACG
1 GTCAACG
563746 GTC-ACG
1 GTCAACG
563752 GTCAACG
1 GTCAACG
563759 GTCAACG
1 GTCAACG
563766 GTC
1 GTC
563769 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:563833 original size:19 final size:19
Alignment explanation
Indices: 563809--563897 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
563799 AGTCGGGTCG
*
563809 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
563828 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
563847 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
563866 GGTCAAACCGGTTCAAAAC
1 GGTCAAACCGGTTCAGACC
563885 GGTCAAACCGGTT
1 GGTCAAACCGGTT
563898 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 1 0.02
19 64 0.98
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:563839 original size:9 final size:9
Alignment explanation
Indices: 563809--563896 Score: 95
Period size: 9 Copynumber: 9.3 Consensus size: 9
563799 AGTCGGGTCG
*
563809 GGTCAACCC
1 GGTCAAACC
*
563818 GGTTCAGACC
1 GG-TCAAACC
563828 GGTCAAACC
1 GGTCAAACC
*
563837 GGTTCAGACC
1 GG-TCAAACC
563847 GGTCAAACC
1 GGTCAAACC
*
563856 GGTTCGAACC
1 GG-TCAAACC
563866 GGTCAAACC
1 GGTCAAACC
*
563875 GGTTCAAAAC
1 GG-TCAAACC
563885 GGTCAAACC
1 GGTCAAACC
563894 GGT
1 GGT
563897 TTTCCAGCAG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
9 35 0.53
10 31 0.47
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:566506 original size:250 final size:250
Alignment explanation
Indices: 566065--566569 Score: 938
Period size: 250 Copynumber: 2.0 Consensus size: 250
566055 GTTGACTCTG
566065 AATGAGAGAATAACTTGAGAATTTGTTTTTAAATCGATAAATTACTGATTTGATTATTGGGATCC
1 AATGAGAGAATAACTTGAGAATTTGTTTTTAAATCGATAAATTACTGATTTGATTATTGGGATCC
*
566130 TACCTTTGTATGAAAAATTTCTGAAAATTTGTTAGCAACATTTGAAAAGACATTTAACCTGGAAA
66 TACCTTTGTATGAAAAATTTCTGAAAATTTGTTAGCAACATTTGAAAAGACATTTAACATGGAAA
566195 TTACCGAATTGAGTAAATACCTGAAGAATGAGTTATCGAAGGTGCTCTTTGGTCAGAATTGTTTG
131 TTACCGAATTGAGTAAATACCTGAAGAATGAGTTATCGAAGGTGCTCTTTGGTCAGAATTGTTTG
*
566260 AAAGGACTGAAGTAAGTGATAAGATTAAATTAAATAATAAGATCGAACGTAAGGA
196 AAAGGACTGAAGTAACTGATAAGATTAAATTAAATAATAAGATCGAACGTAAGGA
*
566315 AATGAGAGAATAACTTGAGAATTTGTTTTTAAATCGATAAATTACTGATTTGATTGTTGGGATCC
1 AATGAGAGAATAACTTGAGAATTTGTTTTTAAATCGATAAATTACTGATTTGATTATTGGGATCC
* * *
566380 TACCTTTTTATGAAAAATTTCTGAAAGTTTGTTAGTAACATTTGAAAAGACATTTAACATGGAAA
66 TACCTTTGTATGAAAAATTTCTGAAAATTTGTTAGCAACATTTGAAAAGACATTTAACATGGAAA
*
566445 TTACCGAATTGAGTAAATACCTGAAGAATGAGTTATCGAAGGTGCTCTTTGGTTAGAATTGTTTG
131 TTACCGAATTGAGTAAATACCTGAAGAATGAGTTATCGAAGGTGCTCTTTGGTCAGAATTGTTTG
*
566510 AAAGGACTGAAGTAACTGATAAGATTAAATTAAATAATAAGATCGGACGTAAGGA
196 AAAGGACTGAAGTAACTGATAAGATTAAATTAAATAATAAGATCGAACGTAAGGA
566565 AATGA
1 AATGA
566570 TGGAAATACA
Statistics
Matches: 247, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
250 247 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (250 bp):
AATGAGAGAATAACTTGAGAATTTGTTTTTAAATCGATAAATTACTGATTTGATTATTGGGATCC
TACCTTTGTATGAAAAATTTCTGAAAATTTGTTAGCAACATTTGAAAAGACATTTAACATGGAAA
TTACCGAATTGAGTAAATACCTGAAGAATGAGTTATCGAAGGTGCTCTTTGGTCAGAATTGTTTG
AAAGGACTGAAGTAACTGATAAGATTAAATTAAATAATAAGATCGAACGTAAGGA
Found at i:566709 original size:9 final size:9
Alignment explanation
Indices: 566695--566721 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
566685 AACGTTGAGC
566695 ACCAAAATG
1 ACCAAAATG
566704 ACCAAAATG
1 ACCAAAATG
566713 ACCAAAATG
1 ACCAAAATG
566722 CCTTTATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.11, T:0.11
Consensus pattern (9 bp):
ACCAAAATG
Found at i:579882 original size:45 final size:45
Alignment explanation
Indices: 579807--580536 Score: 938
Period size: 45 Copynumber: 16.2 Consensus size: 45
579797 TATACTTTAT
* * *
579807 TTTCATTTATGGCATCCTTTGATGCCGATAATGAACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * * *
579852 TTTTATTTATGGCATCATTTCATACTGATAATGCACCGTCATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
579897 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * * *
579942 TTTCATTTACGACGTCCTTTCATGTCAATAATGCGCCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
579987 TTTCATTTATGGCTTCCTTTCATGCCGATAATGCATCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* ** * *
580032 TTTCATTTATTGCATTTTTTCATACCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * *
580077 TTTCATTTACGGCATCCTTTCATGCCAATAATGCACTGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** * * *
580122 TTTCATTTATTACATCCTTTCATGTCAATAATGCACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* ** * * *
580167 TTTTATTTATCACACCCATTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
580212 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTCATGGA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
580257 TTTCATTTTTGGCATCCTTTCATGCTGATAATGCACCGTCATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** *
580302 TTTCATTTATTACATCCTTTCATGCTGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
580347 TTTCATTTATGACATCCTTTCATGCTGATAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
580392 TTTCATTTATGGCATCATTTCATGCCGATAATGCACTGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
580437 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATTCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
580482 TTTCATTTATGGCATCCTTTCATACCGATAATGCACTGTTATGCG
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
580527 TTTCATTTAT
1 TTTCATTTAT
580537 TTTAAAACAG
Statistics
Matches: 595, Mismatches: 90, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 595 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:586131 original size:22 final size:19
Alignment explanation
Indices: 586075--586131 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 19
586065 AACAATCGAC
586075 CGTTGACCTGCGTTGACCGA
1 CGTTGACC-GCGTTGACCGA
*
586095 CGTTGACCACTGTTGACCAGAA
1 CGTTGACCGC-GTTGACC-G-A
*
586117 CTTTGACCGGCGTTG
1 CGTTGACC-GCGTTG
586132 GCTGGGCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 15 0.50
21 1 0.03
22 12 0.40
23 1 0.03
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (19 bp):
CGTTGACCGCGTTGACCGA
Found at i:589835 original size:45 final size:45
Alignment explanation
Indices: 589771--590446 Score: 857
Period size: 45 Copynumber: 15.2 Consensus size: 45
589761 TATACTTTAT
* * *
589771 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTCATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * * *
589816 TTTCATTTATAGAATCCTTTCATGCTGATAATACACCCTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
589861 TTTCATTTATGGCATCATTTTATGCCGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
589906 TTTCGTTTATGGTATCTTTTCATGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
589951 TTTCATTTATGGCATCCTTTCATGCCAATAATGCACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * ** * *
589996 TTTCGTTTATGACATCCTTTAATATCGATAAAGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
590041 TTTCATTTATGGCATCCTCTCATGCCGATAAAGCACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** *
590086 TTTCATTTATGG--------CA-GCCGATAAAACACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
590122 TTTCATTTATGGCATCCTCTCATGGCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * *
590167 TTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATCATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
590212 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTCATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
*
590257 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATTCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
590302 TTTCATTTATGGCATCCTTTCATACCGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
590347 TTTCATTTATGTCATCCTTTCATGCTGATAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
590392 TTTCATTTATGACATCCTTTCATGCCGATAATGCATCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
*
590437 TTTTATTTAT
1 TTTCATTTAT
590447 TTTGAAACAA
Statistics
Matches: 548, Mismatches: 74, Indels: 18
0.86 0.12 0.03
Matches are distributed among these distances:
36 31 0.06
37 2 0.00
44 2 0.00
45 513 0.94
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:590104 original size:36 final size:36
Alignment explanation
Indices: 590064--590135 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
590054 ATCCTCTCAT
*
590064 GCCGATAAAGCA-CAGTTATGCATTTCATTTATGGCA
1 GCCGATAAAACACCA-TTATGCATTTCATTTATGGCA
590100 GCCGATAAAACACCATTATGCATTTCATTTATGGCA
1 GCCGATAAAACACCATTATGCATTTCATTTATGGCA
590136 TCCTCTCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 32 0.94
37 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (36 bp):
GCCGATAAAACACCATTATGCATTTCATTTATGGCA
Found at i:590346 original size:261 final size:261
Alignment explanation
Indices: 589842--590446 Score: 771
Period size: 261 Copynumber: 2.3 Consensus size: 261
589832 CTTTCATGCT
* * * *
589842 GATAATACACCCTTATACATTTCATTTATGGCATCATTTTATGCCGATAATGCACCATTATGCAT
1 GATAAAACACCATTATACATTTCATTTATGGCATCATCTCATGCCGATAATGCACCATTATGCAT
* * * * * * *
589907 TTCGTTTATGGTATCTTTTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
66 TTCATTTATGGCATCCTTTCATGCCAATAATGCACCATCATACATTTCATTTATGGCATCCTTTC
* * *
589972 ATGCCAATAATGCACAGTTATGCATTTCGTTTATGACATCCTTTAATATCGATAAAGCACCGTTA
131 ATGCCAATAATGCACAGTCATGCATTTCATTTATGACATCCTTTAATACCGATAAAGCACCGTTA
*
590037 TACATTTCATTTATGGCATCCTCTCATGCCGATAAAGCACAGTTATGCATTTCATTTATGGCAGC
196 TACATTTCATTTATGGCATCCTCTCATACCGATAAAGCACAGTTATGCATTTCATTTATGGCAGC
590102 C
261 C
* * * *
590103 GATAAAACACCATTATGCATTTCATTTATGGCATCCTCTCATGGCGATAATGCACCGTTATGCAT
1 GATAAAACACCATTATACATTTCATTTATGGCATCATCTCATGCCGATAATGCACCATTATGCAT
590168 TTCATTTATGGCATCCTTTCATGCCAATAATGCACCATCATACATTTCATTTATGGCATCCTTTC
66 TTCATTTATGGCATCCTTTCATGCCAATAATGCACCATCATACATTTCATTTATGGCATCCTTTC
* * * * * *
590233 ATGCCGATAATGCACTGTCATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTA
131 ATGCCAATAATGCACAGTCATGCATTTCATTTATGACATCCTTTAATACCGATAAAGCACCGTTA
* * *
590298 TTCATTTCATTTATGGCATCCTTTCATACCGATAATGCACCA-TTATGCATTTCATTTATGTCAT
196 TACATTTCATTTATGGCATCCTCTCATACCGATAAAGCA-CAGTTATGCATTTCATTTATG----
* *
590362 CCTTTCATGCT
256 ----GCA-GCC
** * * * * *
590373 GATAATGCACCGTTATACATTTCATTTATGACATCCTTTCATGCCGATAATGCATCATTATGCAT
1 GATAAAACACCATTATACATTTCATTTATGGCATCATCTCATGCCGATAATGCACCATTATGCAT
*
590438 TTTATTTAT
66 TTCATTTAT
590447 TTTGAAACAA
Statistics
Matches: 294, Mismatches: 40, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
261 224 0.76
262 2 0.01
269 2 0.01
270 66 0.22
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (261 bp):
GATAAAACACCATTATACATTTCATTTATGGCATCATCTCATGCCGATAATGCACCATTATGCAT
TTCATTTATGGCATCCTTTCATGCCAATAATGCACCATCATACATTTCATTTATGGCATCCTTTC
ATGCCAATAATGCACAGTCATGCATTTCATTTATGACATCCTTTAATACCGATAAAGCACCGTTA
TACATTTCATTTATGGCATCCTCTCATACCGATAAAGCACAGTTATGCATTTCATTTATGGCAGC
C
Found at i:594343 original size:13 final size:13
Alignment explanation
Indices: 594299--594343 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
594289 TATTTTCTAT
594299 ATTAATTATAATC
1 ATTAATTATAATC
*
594312 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
594327 -TTAATTATAATC
1 ATTAATTATAATC
594339 ATTAA
1 ATTAA
594344 ATAATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:594477 original size:2 final size:2
Alignment explanation
Indices: 594470--594512 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
594460 TAAAATTTTA
594470 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
594512 A
1 A
594513 AGATAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:594585 original size:2 final size:2
Alignment explanation
Indices: 594578--594608 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
594568 AAAATAAACC
594578 AT 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 A
594609 AGTGATAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:595144 original size:18 final size:18
Alignment explanation
Indices: 595121--595159 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
595111 TGATATATAT
595121 ATATATATATACACACAC
1 ATATATATATACACACAC
595139 ATATATATATACACACAC
1 ATATATATATACACACAC
595157 ATA
1 ATA
595160 CATACATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATATATATACACACAC
Found at i:595198 original size:19 final size:19
Alignment explanation
Indices: 595176--595219 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
595166 TGAATATATT
595176 CGTACATCATACAT-ATGTA
1 CGTACATCATAC-TCATGTA
595195 CGTACATCATACTCATGTA
1 CGTACATCATACTCATGTA
*
595214 CATACA
1 CGTACA
595220 CTTATGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (19 bp):
CGTACATCATACTCATGTA
Found at i:595385 original size:61 final size:61
Alignment explanation
Indices: 595311--595433 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
595301 TTTATATTAA
595311 ACTTATATACATACATCATACACTTATATACATACATCATACACTTATATACATAAATCAT
1 ACTTATATACATACATCATACACTTATATACATACATCATACACTTATATACATAAATCAT
*
595372 ACTTATATACATACATCATACACTTATATACATACATCATATACTTATATACATAAATCAT
1 ACTTATATACATACATCATACACTTATATACATACATCATACACTTATATACATAAATCAT
595433 A
1 A
595434 TATAAGTATA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (61 bp):
ACTTATATACATACATCATACACTTATATACATACATCATACACTTATATACATAAATCAT
Found at i:595435 original size:21 final size:21
Alignment explanation
Indices: 595311--595433 Score: 205
Period size: 21 Copynumber: 6.0 Consensus size: 21
595301 TTTATATTAA
595311 ACTTATATACATACATCATAC
1 ACTTATATACATACATCATAC
595332 ACTTATATACATACATCATAC
1 ACTTATATACATACATCATAC
*
595353 ACTTATATACATAAATCAT--
1 ACTTATATACATACATCATAC
595372 ACTTATATACATACATCATAC
1 ACTTATATACATACATCATAC
*
595393 ACTTATATACATACATCATAT
1 ACTTATATACATACATCATAC
*
595414 ACTTATATACATAAATCATA
1 ACTTATATACATACATCATA
595434 TATAAGTATA
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.19
21 78 0.81
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
ACTTATATACATACATCATAC
Found at i:595497 original size:2 final size:2
Alignment explanation
Indices: 595490--595564 Score: 67
Period size: 2 Copynumber: 41.0 Consensus size: 2
595480 ACTTATACTT
595490 TA TA TA TA TA TA CT- TA TA TA T- TA TA TA TA T- TA -A 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
* *
595529 TA -A TA TA T- TA T- TA AA TA TA TA TA TG TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
595565 AGTATAATGT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
1 8 0.13
2 51 0.85
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:595503 original size:21 final size:21
Alignment explanation
Indices: 595478--595564 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
595468 TATAGTTTAA
595478 ATACTTATACT-TTATATATAT
1 ATACTTATA-TATTATATATAT
595499 ATACTTATATATTATATATAT
1 ATACTTATATATTATATATAT
*
595520 -TA-ATATATA-TA-ATATAT
1 ATACTTATATATTATATATAT
* *
595537 -TA-TTAAATATATATATGTAT
1 ATACTTATATAT-TATATATAT
595557 ATA-TTATA
1 ATACTTATA
595565 AGTATAATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 13 0.23
18 2 0.04
19 8 0.14
20 8 0.14
21 25 0.45
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (21 bp):
ATACTTATATATTATATATAT
Found at i:595516 original size:19 final size:18
Alignment explanation
Indices: 595492--595564 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 18
595482 TTATACTTTA
595492 TATATATATACTTATATAT
1 TATATATATA-TTATATAT
*
595511 TATATATAT-TAATATA-
1 TATATATATATTATATAT
595527 TATA-ATATATTAT-TA-
1 TATATATATATTATATAT
*
595542 AATATATATATGTATATAT
1 TATATATATAT-TATATAT
595561 TATA
1 TATA
595565 AGTATAATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.20
16 13 0.29
17 9 0.20
18 2 0.04
19 12 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (18 bp):
TATATATATATTATATAT
Found at i:595527 original size:29 final size:29
Alignment explanation
Indices: 595490--595564 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
595480 ACTTATACTT
*
595490 TATATATATATACTTATA-TATTATATATA
1 TATATATATATA-TTATATTATTAAATATA
*
595519 T-TAATATATATAATATATTATTAAATATA
1 TAT-ATATATATATTATATTATTAAATATA
*
595548 TATATGTATATATTATA
1 TATATATATATATTATA
595565 AGTATAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.13
29 33 0.85
30 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TATATATATATATTATATTATTAAATATA
Found at i:595570 original size:21 final size:20
Alignment explanation
Indices: 595504--595550 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
595494 TATATATACT
595504 TATATATTATATA-TATTAA
1 TATATATTATATATTATTAA
*
595523 TATATATAATATATTATTAAA
1 TATATATTATATATTATT-AA
595544 TATATAT
1 TATATAT
595551 ATGTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 4 0.16
21 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATATTATATATTATTAA
Found at i:595706 original size:2 final size:2
Alignment explanation
Indices: 595695--595761 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
595685 ATTTTATTAT
595695 TA TA TA -A 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
595736 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
595762 ATTGTTTCAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:602216 original size:355 final size:354
Alignment explanation
Indices: 601642--602335 Score: 1219
Period size: 355 Copynumber: 2.0 Consensus size: 354
601632 AATCGTCAGT
* * * *
601642 ATTTTACATGTCTGATGTTATACAAATTTCCATTAACAACTGTCAGCTAGGGACAATAATTTTTA
1 ATTTTACATGTCTGATGTTATACAAATTGCAATTAACAACTGCCAGCTAGGGACAATAAATTTTA
*
601707 AATGATAAAAGGTAAGCGTGAGTAGTTACCCATGTTTTCTTTCACCCCATCATCACAAGCCGCCC
66 AATGATAAAAGGTAAACGTGAGTAGTTACCCATGTTTTCTTTCACCCCATCATCACAAGCCGCCC
*
601772 TCTTAAACCTATCACTACCATCCATTTAAATCATATGCATCCCTTCATCCTATCACTATACAACT
131 TCTTAAACCTATCACTACCATCCATTTAAATCATATACATCCCTTCATCCTATCACTATACAACT
601837 ATTTGTTTAAATTAAAAAATATTTTTTCCCATTTTCACATGCCACCACTAATACTCCCACCATCC
196 ATTTGTTTAAATTAAAAAATA-TTTTTCCCATTTTCACATGCCACCACTAATACTCCCACCATCC
* *
601902 TTAAAAGCTCACTTTATTTTTTCACCTACTCTTTTCACTTTCTTTTCAACTGTTTCCCTACCAAA
260 TTAAAAGCTCACTTTATTTTTTCACCTACCCTTTTCACTTTCTTTTCAACCGTTTCCCTACCAAA
601967 TCCTAAAACGTTTCTAATCGCTTGTAAATA
325 TCCTAAAACGTTTCTAATCGCTTGTAAATA
* *
601997 ATTTTGCATGTCTGATGTTATACTAATTGCAATTAACAACTGCCAGCTAGGGACAATAAATTTTA
1 ATTTTACATGTCTGATGTTATACAAATTGCAATTAACAACTGCCAGCTAGGGACAATAAATTTTA
*
602062 AATGATAAAAGGTAAACGTGAGCT-GTTACCCATGTTTTCTTTCACCCCATCATCACAAGCTGCC
66 AATGATAAAAGGTAAACGTGAG-TAGTTACCCATGTTTTCTTTCACCCCATCATCACAAGCCGCC
*
602126 CTCTTAAACCTATCACTACCATCCATTTAAATCATATACATCCCTTCATCCTATCGCTATACAAC
130 CTCTTAAACCTATCACTACCATCCATTTAAATCATATACATCCCTTCATCCTATCACTATACAAC
* *
602191 TATTTGTTTAAATTAAAAGATATTTTTCCTATTTTCACATGCCACCACTAATACTCCCACCATCC
195 TATTTGTTTAAATTAAAAAATATTTTTCCCATTTTCACATGCCACCACTAATACTCCCACCATCC
*
602256 TTAAAAGCTCACTTTATTTTTTCACCTTCCCTTTTCACTTTCTTTTCAACCGTTTCCCTACCAAA
260 TTAAAAGCTCACTTTATTTTTTCACCTACCCTTTTCACTTTCTTTTCAACCGTTTCCCTACCAAA
*
602321 TCCTAAAAGGTTTCT
325 TCCTAAAACGTTTCT
602336 GGTTGATTGT
Statistics
Matches: 322, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
354 118 0.37
355 203 0.63
356 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (354 bp):
ATTTTACATGTCTGATGTTATACAAATTGCAATTAACAACTGCCAGCTAGGGACAATAAATTTTA
AATGATAAAAGGTAAACGTGAGTAGTTACCCATGTTTTCTTTCACCCCATCATCACAAGCCGCCC
TCTTAAACCTATCACTACCATCCATTTAAATCATATACATCCCTTCATCCTATCACTATACAACT
ATTTGTTTAAATTAAAAAATATTTTTCCCATTTTCACATGCCACCACTAATACTCCCACCATCCT
TAAAAGCTCACTTTATTTTTTCACCTACCCTTTTCACTTTCTTTTCAACCGTTTCCCTACCAAAT
CCTAAAACGTTTCTAATCGCTTGTAAATA
Found at i:609495 original size:16 final size:17
Alignment explanation
Indices: 609463--609512 Score: 75
Period size: 16 Copynumber: 2.9 Consensus size: 17
609453 TATATATATT
609463 ATAAGAAGAAGAAAAAAC
1 ATAAGAAGAA-AAAAAAC
609481 ATAAGAA-AAAAAAAAC
1 ATAAGAAGAAAAAAAAC
*
609497 AGAAGAAGAAAAAAAA
1 ATAAGAAGAAAAAAAA
609513 TGAAAACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 13 0.43
17 10 0.33
18 7 0.23
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (17 bp):
ATAAGAAGAAAAAAAAC
Found at i:609523 original size:22 final size:22
Alignment explanation
Indices: 609492--609563 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
609482 TAAGAAAAAA
609492 AAAACAGAAGAAGAAAAAAAATG
1 AAAAC-GAAGAAGAAAAAAAATG
609515 AAAACGAAGAAGAAAAAAAATG
1 AAAACGAAGAAGAAAAAAAATG
* *
609537 AAAATG-AGAAAGAAAAGAAAAAG
1 AAAACGAAG-AAGAAAA-AAAATG
609560 AAAA
1 AAAA
609564 AAATTCACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.04
22 29 0.64
23 14 0.31
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAACGAAGAAGAAAAAAAATG
Found at i:609542 original size:6 final size:5
Alignment explanation
Indices: 609483--609563 Score: 53
Period size: 6 Copynumber: 15.4 Consensus size: 5
609473 GAAAAAACAT
*
609483 AAGAA AA-AA AA-AA CAGAA GAAGAA AA-AA AATGAA AACGAA GAAGAA
1 AAGAA AAGAA AAGAA AAGAA -AAGAA AAGAA AA-GAA AA-GAA -AAGAA
609529 AA-AA AATGAA AATGAGA AAGAA AAGAAA AAGAA AA
1 AAGAA AA-GAA AA-GA-A AAGAA AAG-AA AAGAA AA
609564 AAATTCACTT
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
4 15 0.23
5 16 0.25
6 28 0.44
7 5 0.08
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (5 bp):
AAGAA
Found at i:609564 original size:6 final size:6
Alignment explanation
Indices: 609465--609564 Score: 50
Period size: 6 Copynumber: 17.3 Consensus size: 6
609455 TATATATTAT
* * * *
609465 AAGAAG AAGAAA AA-ACAT AAGAAA AAAAAA ACAGAAG AAG-AA AA-AAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA
* * * * * *
609512 ATGAAA ACGAAG AAG-AA AA-AAA ATGAAA ATGAGA AAG-AA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
609557 AAGAAA AA
1 AAGAAA AA
609565 AATTCACTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
5 17 0.24
6 48 0.69
7 5 0.07
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:609565 original size:25 final size:25
Alignment explanation
Indices: 609497--609565 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 25
609487 AAAAAAAAAC
*
609497 AGAAGAAGAAAAAAAATGAAAACGA
1 AGAAGAAAAAAAAAAATGAAAACGA
609522 AGAAGAAAAAAAATGAAAATGAGAAA-GA
1 AGAAG-AAAAAAA--AAAATGA-AAACGA
609550 A-AAGAAAAAGAAAAAA
1 AGAAGAAAAA-AAAAAA
609566 ATTCACTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 9 0.24
26 11 0.29
27 5 0.13
28 10 0.26
29 3 0.08
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.04
Consensus pattern (25 bp):
AGAAGAAAAAAAAAAATGAAAACGA
Found at i:618888 original size:21 final size:21
Alignment explanation
Indices: 618845--618893 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
618835 ATAAACTCAG
* **
618845 TGCAAATGTGAAATGTAAAGA
1 TGCAAATGAGAAATACAAAGA
*
618866 TGCAAATGAGAAATACAAGGA
1 TGCAAATGAGAAATACAAAGA
*
618887 TGAAAAT
1 TGCAAAT
618894 TTAAATGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.20
Consensus pattern (21 bp):
TGCAAATGAGAAATACAAAGA
Found at i:626903 original size:48 final size:48
Alignment explanation
Indices: 626833--627010 Score: 187
Period size: 49 Copynumber: 3.7 Consensus size: 48
626823 ATGTTGATCA
* * * * *
626833 TCTGCAACCTTAAGATTTTCTTGAATAAAACTCAGGCTTATTTTATCG
1 TCTGCAATCTTAAAATTATCTTGAATAAATCTCAGGCTTCTTTTATCG
* * * *
626881 TCTGAAATCTTAAAATTATCTTGAATAAATCTCGGGCTTCTTTTCAACA
1 TCTGCAATCTTAAAATTATCTTGAATAAATCTCAGGCTTCTTTT-ATCG
* * * *
626930 TATGCAATTTTAAAATTATCTTGAATAAATGTCAGGCTTCTGTTGATCG
1 TCTGCAATCTTAAAATTATCTTGAATAAATCTCAGGCTTCT-TTTATCG
* *
626979 ACCT-CAATCTTAAGATTATCTTGAATAAATCT
1 -TCTGCAATCTTAAAATTATCTTGAATAAATCT
627011 TGGGTTTAGT
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
48 37 0.35
49 65 0.62
50 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (48 bp):
TCTGCAATCTTAAAATTATCTTGAATAAATCTCAGGCTTCTTTTATCG
Found at i:645672 original size:2 final size:2
Alignment explanation
Indices: 645665--645697 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
645655 AGTTTATGTT
645665 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
645698 TACATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:645706 original size:2 final size:2
Alignment explanation
Indices: 645701--645751 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
645691 ACACACATAC
645701 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
645743 AT AT AT AT A
1 AT AT AT AT A
645752 ACTGAAATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:657301 original size:21 final size:22
Alignment explanation
Indices: 657272--657313 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
657262 TTCCATAATC
* *
657272 AAATCCTAAATATA-TAAGCAA
1 AAATACTAAAAATACTAAGCAA
657293 AAATACTAAAAATACTAAGCA
1 AAATACTAAAAATACTAAGCA
657314 TTTTTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (22 bp):
AAATACTAAAAATACTAAGCAA
Found at i:659436 original size:15 final size:16
Alignment explanation
Indices: 659408--659438 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
659398 GTTAGTAATA
659408 ATATTAATAATAAAAT
1 ATATTAATAATAAAAT
659424 ATATTAA-AATAAAAT
1 ATATTAATAATAAAAT
659439 TAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATTAATAATAAAAT
Found at i:659868 original size:35 final size:35
Alignment explanation
Indices: 659829--659904 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
659819 TAAAATACTT
*
659829 TAATTTAGGGTTTTGAATGTAATTAAAGTATTTTG
1 TAATTTAGGGTTTAGAATGTAATTAAAGTATTTTG
* *
659864 TAATTTGGGGTTTAGAATGTAATTAAAGTGTTTTG
1 TAATTTAGGGTTTAGAATGTAATTAAAGTATTTTG
*
659899 GAATTT
1 TAATTT
659905 TGAACATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.47
Consensus pattern (35 bp):
TAATTTAGGGTTTAGAATGTAATTAAAGTATTTTG
Found at i:671249 original size:20 final size:20
Alignment explanation
Indices: 671177--671302 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
671167 AATTTCATTA
*
671177 GCATCCTTTCACGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* * *
671197 GCATCTTTTTATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
671222 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
671243 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
671268 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
671289 GCATCATTTCATGC
1 GCATCCTTTCATGC
671303 ATTTCATTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
20 37 0.44
21 9 0.11
22 2 0.02
24 2 0.02
25 9 0.11
26 25 0.30
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:671315 original size:46 final size:46
Alignment explanation
Indices: 671177--671315 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
671167 AATTTCATTA
* * *
671177 GCATCCTTTCACGCCTTAATGCATCTTTTTATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
* *
671223 ACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
671269 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
671315 G
1 G
671316 ATTCATTTTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
Found at i:675507 original size:33 final size:33
Alignment explanation
Indices: 675419--675509 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
675409 TATCATTTCA
** * * *
675419 CTAACAATTTATTCAAAAGGAAATCCTTTAGCT
1 CTAACAATTGGTTCTAAAGGAATTCCTCTAGCT
675452 CTAACAATTGGTTCTAAAGGAATTCCTCTAGCT
1 CTAACAATTGGTTCTAAAGGAATTCCTCTAGCT
675485 CTAACAATTGGTTCTAAAGGAATTC
1 CTAACAATTGGTTCTAAAGGAATTC
675510 TGACTAAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
CTAACAATTGGTTCTAAAGGAATTCCTCTAGCT
Found at i:681693 original size:34 final size:32
Alignment explanation
Indices: 681644--681711 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 32
681634 AAATTTTATA
681644 TTGAGTTGTTTTTAAGTTAGCATTAGATTCAT
1 TTGAGTTGTTTTTAAGTTAGCATTAGATTCAT
*
681676 TTGAGTTAGTGTTTTAAGTTAGCATTGGATTCAT
1 TTGAGTT-GT-TTTTAAGTTAGCATTAGATTCAT
681710 TT
1 TT
681712 ATGCAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 7 0.21
33 2 0.06
34 24 0.73
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.50
Consensus pattern (32 bp):
TTGAGTTGTTTTTAAGTTAGCATTAGATTCAT
Found at i:683225 original size:21 final size:21
Alignment explanation
Indices: 683201--683257 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
683191 CCCTTCATGC
* *
683201 AAAGGATCGATCTCTCTCCCT
1 AAAGGATCAATCCCTCTCCCT
683222 AAAGGATCAATCCCTCTCCCT
1 AAAGGATCAATCCCTCTCCCT
683243 AAAGGATCAATCCCT
1 AAAGGATCAATCCCT
683258 AACTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAGGATCAATCCCTCTCCCT
Found at i:710994 original size:6 final size:6
Alignment explanation
Indices: 710983--711009 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
710973 AAAACCCATA
710983 GGTCAT GGTCAT GGTCAT GGTCAT GGT
1 GGTCAT GGTCAT GGTCAT GGTCAT GGT
711010 ACAAGTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.37, T:0.33
Consensus pattern (6 bp):
GGTCAT
Found at i:720272 original size:89 final size:89
Alignment explanation
Indices: 720111--720286 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 89
720101 TAATCCTGAA
* *
720111 TATTTAATTACAATTAATTATAGATTAATTTAATTAATTTGAAATAATAAATCCCTAATATGATT
1 TATTAAATTACAATTAATTATAGATTAATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
720176 AGGGTAACTTGGATATAAAAGGAT
66 AGGGTAACTTGGATATAAAAGGAT
*
720200 TATTAAATTCCAATTAATTA-A-ATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGA
1 TATTAAATTACAATTAATTATAGAT-TA-ATTTAATTAATTTGAAATAATAAAACCCTAATATGA
*
720263 TTAGGGTAACTTGGCTATAAAAGG
64 TTAGGGTAACTTGGATATAAAAGG
720287 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
87 2 0.02
88 3 0.04
89 76 0.94
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTACAATTAATTATAGATTAATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:725876 original size:168 final size:169
Alignment explanation
Indices: 725595--725933 Score: 655
Period size: 168 Copynumber: 2.0 Consensus size: 169
725585 TACTCAAAAA
725595 AATGCTTTAGCTAAATCTCTCCATGATATGATATGGGATTTTGTTATCTGGTTGTACCACTTCCC
1 AATGCTTTAGCTAAATCTCTCCATGATATGATATGGGATTTTGTTATCTGGTTGTACCACTTCCC
725660 AGTAGATCCAAACAAGCTATCCTGGAAATAATGTATCATAATTTTCTCATTTTCAGTATAGCCAA
66 AGTAGATCCAAACAAGCTATCCTGGAAATAATGTATCATAATTTTCTCATTTTCAGTATAGCCAA
725725 CCATCCTTCTACAATACATGGTGAGGT-GGCAGATGGAT
131 CCATCCTTCTACAATACATGGTGAGGTGGGCAGATGGAT
725763 AATGCTTTAGCTAAATCTCTCCATGATATGATATGGGATTTTGTTATCTGGTTGTACCACTTCCC
1 AATGCTTTAGCTAAATCTCTCCATGATATGATATGGGATTTTGTTATCTGGTTGTACCACTTCCC
725828 AGTAGATCCAAACAAGCTATCCTGGAAATAATGTATCAATAA-TTTCTCATTTTCAGTATAGCCA
66 AGTAGATCCAAACAAGCTATCCTGGAAATAATGTATC-ATAATTTTCTCATTTTCAGTATAGCCA
725892 ACCATCCTTCTACAATACATGGTGAGGTGGGCAGATGGAT
130 ACCATCCTTCTACAATACATGGTGAGGTGGGCAGATGGAT
725932 AA
1 AA
725934 GTGGTCATAT
Statistics
Matches: 169, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
168 152 0.90
169 17 0.10
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (169 bp):
AATGCTTTAGCTAAATCTCTCCATGATATGATATGGGATTTTGTTATCTGGTTGTACCACTTCCC
AGTAGATCCAAACAAGCTATCCTGGAAATAATGTATCATAATTTTCTCATTTTCAGTATAGCCAA
CCATCCTTCTACAATACATGGTGAGGTGGGCAGATGGAT
Found at i:732588 original size:16 final size:16
Alignment explanation
Indices: 732564--732597 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
732554 GTGGGCCTTT
* *
732564 TGTTGTGGGCTTTGGG
1 TGTTATGGGCTTTCGG
732580 TGTTATGGGCTTTCGG
1 TGTTATGGGCTTTCGG
732596 TG
1 TG
732598 GCTGTAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.09, G:0.44, T:0.44
Consensus pattern (16 bp):
TGTTATGGGCTTTCGG
Found at i:733514 original size:30 final size:31
Alignment explanation
Indices: 733478--733537 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
733468 CTTAGCTTTA
733478 TATTATGTTTACATAT-ATTTTAGAT-TCATT
1 TATTATGTTTACATATCA-TTTAGATATCATT
*
733508 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
733538 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:734457 original size:19 final size:21
Alignment explanation
Indices: 734433--734484 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
734423 CGGCCAAGAG
*
734433 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
734452 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
734473 CATGTATTTTCA
1 CATGTATTTTCA
734485 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:736578 original size:24 final size:24
Alignment explanation
Indices: 736533--736579 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
736523 TTCCAATAGT
*
736533 TATGCCACTTGAAATTCAAAAAGA
1 TATGCCACTTGAAATGCAAAAAGA
* * *
736557 TATGTCACTTGAAGTGCCAAAAG
1 TATGCCACTTGAAATGCAAAAAG
736580 TTTATCATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
TATGCCACTTGAAATGCAAAAAGA
Found at i:737666 original size:31 final size:32
Alignment explanation
Indices: 737631--737691 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
737621 CTTAGCTTTA
**
737631 TATTATGTTTACATATGTTTTAGAT-TCATTT
1 TATTATGTTTACATATCATTTAGATATCATTT
*
737662 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
737692 GGTAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (32 bp):
TATTATGTTTACATATCATTTAGATATCATTT
Found at i:739887 original size:30 final size:31
Alignment explanation
Indices: 739829--739887 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
739819 GCATGATAAT
*
739829 TTTTTATATTTTATTTTTCCTCTTTTACTTC
1 TTTTTATATTTTATTTTTCCTCTATTACTTC
*
739860 TTTTTAT-TTTTGTTTTTCC-CTAATTACT
1 TTTTTATATTTTATTTTTCCTCT-ATTACT
739888 CAAACTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 16 0.64
31 7 0.28
ACGTcount: A:0.14, C:0.15, G:0.02, T:0.69
Consensus pattern (31 bp):
TTTTTATATTTTATTTTTCCTCTATTACTTC
Found at i:740842 original size:32 final size:33
Alignment explanation
Indices: 740785--740863 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
740775 AAATACAAAT
* * *
740785 ATGTAAATGCATAATGCAAAGATACATGTGTAA
1 ATGTAAATGCATAATGAAAAGATACAAGTGCAA
*
740818 ATGTAAATGTA-AATGAAAAGATACAAGTGCAA
1 ATGTAAATGCATAATGAAAAGATACAAGTGCAA
*
740850 ATGCAAAATGCATA
1 ATG-TAAATGCATA
740864 GATGTAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 21 0.55
33 16 0.42
34 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (33 bp):
ATGTAAATGCATAATGAAAAGATACAAGTGCAA
Found at i:743743 original size:37 final size:37
Alignment explanation
Indices: 743636--743743 Score: 96
Period size: 39 Copynumber: 2.8 Consensus size: 37
743626 AATTAATTTC
* **
743636 TAAATAATATATATAATAT-AAAAATAATATTAATGGTA
1 TAAA-AATATATATAATATAAAAAATAAAATTAA-GCAA
*
743674 TAAAAA-AGTATATAACATAATATAAATAAAAATTAA-CAA
1 TAAAAATA-TATATAATATAA-A-AAAT-AAAATTAAGCAA
743713 TAAAAATATATATAATATAAAAAGATAAAAT
1 TAAAAATATATATAATATAAAAA-ATAAAAT
743744 AAAAGAGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
36 1 0.02
37 18 0.31
38 8 0.14
39 19 0.33
40 5 0.09
41 7 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (37 bp):
TAAAAATATATATAATATAAAAAATAAAATTAAGCAA
Found at i:743744 original size:15 final size:16
Alignment explanation
Indices: 743712--743763 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
743702 AAAATTAACA
*
743712 ATAAAAATATATATAAT
1 ATAAAAAGATA-ATAAT
743729 ATAAAAAGATAA-AAT
1 ATAAAAAGATAATAAT
*
743744 A-AAAGAGATAATAAT
1 ATAAAAAGATAATAAT
743759 -TAAAA
1 ATAAAA
743764 GGGAAAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.30
15 10 0.33
16 1 0.03
17 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAAAAAGATAATAAT
Found at i:743745 original size:30 final size:31
Alignment explanation
Indices: 743693--743763 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
743683 ATATAACATA
* *
743693 ATATAA-ATAAAAATTAACAATAAAA-ATAT
1 ATATAATATAAAAAATAACAATAAAAGAGAT
743722 ATATAATATAAAAAGATAA-AATAAAAGAGAT
1 ATATAATATAAAAA-ATAACAATAAAAGAGAT
743753 A-ATAAT-TAAAA
1 ATATAATATAAAA
743764 GGGAAAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 11 0.30
30 19 0.51
31 7 0.19
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (31 bp):
ATATAATATAAAAAATAACAATAAAAGAGAT
Found at i:743922 original size:12 final size:11
Alignment explanation
Indices: 743905--743938 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
743895 GATCGAAACA
743905 AAAAATAAAATG
1 AAAAATAAAA-G
743917 AAAAATAAAAG
1 AAAAATAAAAG
743928 ATAAAATAAAA
1 A-AAAATAAAA
743939 AATTACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:743931 original size:19 final size:19
Alignment explanation
Indices: 743904--743941 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
743894 CGATCGAAAC
*
743904 AAAAAATAAAATGAAAAAT
1 AAAAAATAAAATAAAAAAT
*
743923 AAAAGATAAAATAAAAAAT
1 AAAAAATAAAATAAAAAAT
743942 TACCTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAAATAAAATAAAAAAT
Found at i:745308 original size:58 final size:59
Alignment explanation
Indices: 745245--745386 Score: 150
Period size: 58 Copynumber: 2.4 Consensus size: 59
745235 TATGACCAAT
* * *
745245 ATTTTAATTTGGTCCTTAAACTTTT-TAACGTTGAAATTTCATCCTTAAACTATGA-CTC
1 ATTTTAATTTGGTCCTTAAACTTTTGT-ACATTGAAATTTCATCCTCAAACCATGACCTC
* **
745303 ATTTTAAATTGGTCCTTAATA-TTTTGTACATTTCAATTTCATCCTCAAACCATGACCCTC
1 ATTTTAATTTGGTCCTTAA-ACTTTTGTACATTGAAATTTCATCCTCAAACCATGA-CCTC
*
745363 ATTCTT-ATTTAGTCC-TAAACTTTT
1 ATT-TTAATTTGGTCCTTAAACTTTT
745387 AAGTATTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
58 46 0.66
59 9 0.13
60 13 0.19
61 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (59 bp):
ATTTTAATTTGGTCCTTAAACTTTTGTACATTGAAATTTCATCCTCAAACCATGACCTC
Found at i:756549 original size:7 final size:7
Alignment explanation
Indices: 756537--756978 Score: 861
Period size: 7 Copynumber: 63.4 Consensus size: 7
756527 GTCAACTCGC
756537 TAATTGT
1 TAATTGT
756544 TAATTGT
1 TAATTGT
756551 TAATTGT
1 TAATTGT
756558 TAATTGT
1 TAATTGT
756565 TAATTGT
1 TAATTGT
756572 TAATTGT
1 TAATTGT
756579 TAATTGT
1 TAATTGT
756586 TAATTGT
1 TAATTGT
756593 TAATTGT
1 TAATTGT
756600 TAATTGT
1 TAATTGT
756607 TAATTGT
1 TAATTGT
756614 TAATTGT
1 TAATTGT
756621 TAATTGT
1 TAATTGT
756628 TAATTGT
1 TAATTGT
756635 TAATTGT
1 TAATTGT
756642 TAATTGT
1 TAATTGT
756649 TAA-TGT
1 TAATTGT
756655 TAATTGT
1 TAATTGT
756662 TAATTGT
1 TAATTGT
756669 TAATTGT
1 TAATTGT
756676 TAATTGT
1 TAATTGT
756683 TAATTGT
1 TAATTGT
756690 TAATTGT
1 TAATTGT
756697 TAATTGT
1 TAATTGT
756704 TAATTGT
1 TAATTGT
756711 TAATTGT
1 TAATTGT
756718 TAATTGT
1 TAATTGT
756725 TAATTGT
1 TAATTGT
756732 TAATTGT
1 TAATTGT
756739 TAATTGT
1 TAATTGT
756746 TAATTGT
1 TAATTGT
756753 TAATTGT
1 TAATTGT
756760 TAATTGT
1 TAATTGT
756767 TAATTGT
1 TAATTGT
756774 TAATTGT
1 TAATTGT
756781 TAATTGT
1 TAATTGT
756788 TAATTGT
1 TAATTGT
756795 TAATTG-
1 TAATTGT
756801 TAATTGT
1 TAATTGT
756808 TAATTGT
1 TAATTGT
756815 TAATTGT
1 TAATTGT
756822 TAATTGT
1 TAATTGT
756829 TAATTGT
1 TAATTGT
756836 TAATTGT
1 TAATTGT
756843 TAATTGT
1 TAATTGT
756850 TAATTGT
1 TAATTGT
756857 TAATTGT
1 TAATTGT
756864 TAATTGT
1 TAATTGT
756871 TAATTGT
1 TAATTGT
756878 TAATTGT
1 TAATTGT
756885 TAATTGT
1 TAATTGT
756892 TAATTGT
1 TAATTGT
756899 TAATTGT
1 TAATTGT
756906 TAATTGT
1 TAATTGT
756913 TAATTGT
1 TAATTGT
756920 TAATTGT
1 TAATTGT
756927 TAATTGT
1 TAATTGT
756934 TAATTGT
1 TAATTGT
*
756941 TAAATGT
1 TAATTGT
756948 TAATTGT
1 TAATTGT
756955 TAATTGT
1 TAATTGT
756962 TAATTGT
1 TAATTGT
756969 TAATTGT
1 TAATTGT
756976 TAA
1 TAA
756979 AATATATAAA
Statistics
Matches: 431, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
6 12 0.03
7 419 0.97
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
TAATTGT
Found at i:762259 original size:18 final size:18
Alignment explanation
Indices: 762236--762270 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
762226 TTTATTTTGG
762236 GTTGTTTTTCCTTTCTGA
1 GTTGTTTTTCCTTTCTGA
762254 GTTGTTTTTCCTTTCTG
1 GTTGTTTTTCCTTTCTG
762271 GGTTTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.17, G:0.17, T:0.63
Consensus pattern (18 bp):
GTTGTTTTTCCTTTCTGA
Found at i:762277 original size:15 final size:17
Alignment explanation
Indices: 762238--762279 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
762228 TATTTTGGGT
762238 TGTTTTTCCTTTCTGAG
1 TGTTTTTCCTTTCTGAG
*
762255 TTGTTTTTCCTTTCTGGG
1 -TGTTTTTCCTTTCTGAG
762273 T-TTTTTC
1 TGTTTTTC
762280 ATCTGAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
18 16 0.70
ACGTcount: A:0.02, C:0.17, G:0.17, T:0.64
Consensus pattern (17 bp):
TGTTTTTCCTTTCTGAG
Found at i:765343 original size:15 final size:16
Alignment explanation
Indices: 765308--765345 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
765298 GCTTCAAAAC
765308 AAATATATACTTCAATT
1 AAATATATACTTCAA-T
*
765325 AAATATATGCTTCAA-
1 AAATATATACTTCAAT
765340 AAATAT
1 AAATAT
765346 TATTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
17 14 0.70
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (16 bp):
AAATATATACTTCAAT
Found at i:771068 original size:46 final size:45
Alignment explanation
Indices: 771000--771112 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 45
770990 TATTCTTTAT
* * * * *
771000 TTTCATTGATAACATCCATTCAAG-CTTATAATGCACCATTATGACT
1 TTTCATTTATGACATCCTTTCAAGTCTT-TAATACACCATTAT-ACA
* * *
771046 TTTTATTTATGACATCCTTTCAAGTCTTTTATACACTATTATACA
1 TTTCATTTATGACATCCTTTCAAGTCTTTAATACACCATTATACA
*
771091 TTTCATTTATGGCATCCTTTCA
1 TTTCATTTATGACATCCTTTCA
771113 TGCCCATTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
45 22 0.39
46 31 0.55
47 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGACATCCTTTCAAGTCTTTAATACACCATTATACA
Found at i:771426 original size:29 final size:29
Alignment explanation
Indices: 771337--771416 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
771327 AATCCATTAT
*
771337 TCTTTTACTCAATAGTGTTTAATTGTTCA
1 TCTTTTACTCAACAGTGTTTAATTGTTCA
*
771366 TCTTTTACACAACAGTGTTTAATTGTTCA
1 TCTTTTACTCAACAGTGTTTAATTGTTCA
*
771395 TCTTTTACTCAACAGTCTTTAA
1 TCTTTTACTCAACAGTGTTTAA
771417 CCGTTAATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAATTGTTCA
Found at i:771691 original size:54 final size:54
Alignment explanation
Indices: 771632--771904 Score: 347
Period size: 54 Copynumber: 5.1 Consensus size: 54
771622 CACATACAGA
* ** * * *
771632 GCCTATACGG-TAGTTCATCAACTCATGATGAATTTCGTGGGTTACACACATCGT
1 GCCTGTACGGTTA-TTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
*
771686 GCCTATACGGTTATTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
1 GCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
* * * *
771740 GCATGTATGGCTATTCATCAACTCATGAT-AA-TTCGTGAAATGCACACTTAGT
1 GCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
* * * *
771792 ACCTGTACGATTATACATCAACTCATGATGAATTTCGTGGAATGCAAACTTAGT
1 GCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
* *
771846 GCATGTACGGTTATTCATCAACTCATGATGAA-ATCTGTGGAATGCACACTTAGT
1 GCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGAATGCACACTTAGT
771900 GCCTG
1 GCCTG
771905 ATTACTTCAG
Statistics
Matches: 190, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
52 43 0.23
53 6 0.03
54 139 0.73
55 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (54 bp):
GCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGAATGCACACTTAGT
Found at i:771818 original size:106 final size:107
Alignment explanation
Indices: 771637--771904 Score: 369
Period size: 106 Copynumber: 2.5 Consensus size: 107
771627 ACAGAGCCTA
** * * * * * *
771637 TACGG-TAGTTCATCAACTCATGATGAATTTCGTGGGTTACACACATCGTGCCTATACGGTTATT
1 TACGGCTA-TTCATCAACTCATGATGAA-TTCGTGGAATGCACACTTAGTGCCTGTACGATTATA
*
771701 CATCAACTCATGATGAATTTCGTGGAATGCACACTTAGTGCATG
64 CATCAACTCATGATGAATTTCGTGGAATGCAAACTTAGTGCATG
* * *
771745 TATGGCTATTCATCAACTCATGAT-AATTCGTGAAATGCACACTTAGTACCTGTACGATTATACA
1 TACGGCTATTCATCAACTCATGATGAATTCGTGGAATGCACACTTAGTGCCTGTACGATTATACA
771809 TCAACTCATGATGAATTTCGTGGAATGCAAACTTAGTGCATG
66 TCAACTCATGATGAATTTCGTGGAATGCAAACTTAGTGCATG
* *
771851 TACGGTTATTCATCAACTCATGATGAAATCTGTGGAATGCACACTTAGTGCCTG
1 TACGGCTATTCATCAACTCATGATGAATTC-GTGGAATGCACACTTAGTGCCTG
771905 ATTACTTCAG
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
106 91 0.65
107 6 0.04
108 41 0.29
109 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (107 bp):
TACGGCTATTCATCAACTCATGATGAATTCGTGGAATGCACACTTAGTGCCTGTACGATTATACA
TCAACTCATGATGAATTTCGTGGAATGCAAACTTAGTGCATG
Found at i:775734 original size:55 final size:55
Alignment explanation
Indices: 775521--776148 Score: 587
Period size: 55 Copynumber: 11.5 Consensus size: 55
775511 ATGATAAGTG
* *
775521 AGACTTGAAAAATCTTCAGA-AAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
1 AGACTCGAACAATCTTCA-ACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * * * *
775576 GGACTTGAAATAATATTCGAA-AAATGTGTCCACTCCCTATTCTTTCAGGGAGTATA
1 AGACTCG-AACAATCTTC-AACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * * * * * * *
775632 GGACTTGAAATAATCTTTAGA-AAATGGGTCTGCTCCTTATTCTTTCAGAGAGTATA
1 AGACTCG-AACAATCTTCA-ACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * ** *
775688 AGACTCAAACAATCTTCAACAACCGTGTCTACTCCCTATTCTTTCAGGAAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * *
775743 AGACTTGAACAATCTTCAGCAACCGTGTCTGCTCCCTATTCTTTCAGGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * *
775798 AGACTCGAACAATCTTCAACCAACGTGTCTGCTCCCTATTCGTTCATGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * *
775853 AGACTCGAACAATCTTCAATAAACGGGTCCGCCCCCTATTCGTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * * *
775907 AGAACTCGAACAATCTTTAATAAACGAGTTCGCTCCCTATTCGTTCAGGGAGTAT-
1 AG-ACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * * *
775962 AGAACTTGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAACAATCTTCA-ACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
* * * * *
776017 AGAACTCGAACAATCTTCAACAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
** * * *
776072 AGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
*
776128 GGACT----CAATCTTCAACAAACG
1 AGACTCGAACAATCTTCAACAAACG
776149 AGTTTGCTTC
Statistics
Matches: 501, Mismatches: 64, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
51 13 0.03
54 4 0.01
55 388 0.77
56 95 0.19
57 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (55 bp):
AGACTCGAACAATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGGGAGTATA
Found at i:776196 original size:37 final size:37
Alignment explanation
Indices: 776155--776256 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
776145 AACGAGTTTG
* *
776155 CTTCACCACTCTTCCGTGAAGGCTTAAGTTTGAATTT
1 CTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAATTA
776192 CTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAATTA
1 CTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAATTA
* *
776229 CTTCACTGCTCTTTCGTGAAGGCTTAAG
1 CTTCACTACTCTTCCGTGAAGGCTTAAG
776257 ATTAACTTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (37 bp):
CTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAATTA
Found at i:777556 original size:7 final size:7
Alignment explanation
Indices: 777540--777617 Score: 61
Period size: 7 Copynumber: 10.4 Consensus size: 7
777530 CCCCCTTTTA
777540 TTTC-TT
1 TTTCTTT
777546 TTTCTTT
1 TTTCTTT
777553 TTTCATCATT
1 TTTC-T--TT
*
777563 TTTCCTT
1 TTTCTTT
*
777570 TTTCCTT
1 TTTCTTT
777577 TTTCTATT
1 TTTCT-TT
777585 TTTCTTT
1 TTTCTTT
777592 TTTCCTTT
1 TTT-CTTT
777600 TTT-TTCT
1 TTTCTT-T
777607 TTTCATTT
1 TTTC-TTT
777615 TTT
1 TTT
777618 TCATCATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
6 6 0.10
7 28 0.46
8 19 0.31
9 2 0.03
10 6 0.10
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCTTT
Found at i:777564 original size:17 final size:16
Alignment explanation
Indices: 777544--777671 Score: 90
Period size: 17 Copynumber: 7.9 Consensus size: 16
777534 CTTTTATTTC
777544 TTTTTCTTTTTTCATCA
1 TTTTTCTTTTTTC-TCA
*
777561 TTTTTCCTTTTTC-C-
1 TTTTTCTTTTTTCTCA
777575 TTTTTCTATTTTTCT--
1 TTTTTCT-TTTTTCTCA
*
777590 TTTTTCCTTTTTTTTC-
1 TTTTT-CTTTTTTCTCA
777606 -TTTTCATTTTTT-TCA
1 TTTTTC-TTTTTTCTCA
777621 TCATTTTCATTTTTTCTCA
1 T--TTTTC-TTTTTTCTCA
* *
777640 TTTTACTTTTTTTATCA
1 TTTTTC-TTTTTTCTCA
777657 TTTTTCTTTTCTTCT
1 TTTTTCTTTT-TTCT
777672 TTTTCCATCT
Statistics
Matches: 92, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
14 9 0.10
15 28 0.30
16 6 0.07
17 33 0.36
18 12 0.13
19 4 0.04
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCA
Found at i:777588 original size:22 final size:24
Alignment explanation
Indices: 777543--777601 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
777533 CCTTTTATTT
*
777543 CTTTTTCTTTTTTCATCATTTTTC
1 CTTTTTCCTTTTTCATCATTTTTC
777567 CTTTTTCCTTTTTC-T-ATTTTTC
1 CTTTTTCCTTTTTCATCATTTTTC
*
777589 TTTTTTCCTTTTT
1 CTTTTTCCTTTTT
777602 TTTCTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 19 0.58
23 1 0.03
24 13 0.39
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
CTTTTTCCTTTTTCATCATTTTTC
Found at i:777615 original size:22 final size:22
Alignment explanation
Indices: 777540--777616 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
777530 CCCCCTTTTA
*
777540 TTTC-TTTTTCTTTTTTCATCATT
1 TTTCATTTTTCCTTTTTC-T-ATT
*
777563 TTTCCTTTTTCCTTTTTCTATT
1 TTTCATTTTTCCTTTTTCTATT
* *
777585 TTTCTTTTTTCCTTTTT-TTTCT
1 TTTCATTTTTCCTTTTTCTAT-T
777607 TTTCATTTTT
1 TTTCATTTTT
777617 TTCATCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.04
22 29 0.60
23 5 0.10
24 12 0.25
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCATTTTTCCTTTTTCTATT
Found at i:783877 original size:45 final size:47
Alignment explanation
Indices: 783804--783892 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
783794 TGCTTTGTTA
*
783804 TTCACAAAAAGAAATCCTAACCGTATGATATCTAATTCGCATGCTTG
1 TTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
* *
783851 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC
783893 ATTTATTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 27 0.69
46 8 0.21
47 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (47 bp):
TTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:787361 original size:28 final size:29
Alignment explanation
Indices: 787304--787367 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
787294 ATTTATACTT
* *
787304 ATATATATAATATGTATAATTATGATTAC-
1 ATATA-ATAATATGCATAATTATGAATACA
787333 ATATAATAATATGCATAATTA-GTAATACA
1 ATATAATAATATGCATAATTATG-AATACA
787362 ATATAA
1 ATATAA
787368 ACCTAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 19 0.61
29 11 0.35
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (29 bp):
ATATAATAATATGCATAATTATGAATACA
Found at i:790917 original size:2 final size:2
Alignment explanation
Indices: 790910--790935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
790900 ATTGTTGTAC
790910 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
790936 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:790940 original size:2 final size:2
Alignment explanation
Indices: 790935--790966 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
790925 ACACACACAC
790935 AT AT 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 AT AT
790967 CCCTTCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.