Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 6 of 33
Found at i:722049 original size:25 final size:26
Alignment explanation
Indices: 722022--722094 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
722012 TGTCAGTCTA
722022 AAAATATAATTTTAATTA-AA-TTTT
1 AAAATATAATTTTAATTATAATTTTT
722046 AAAAT-TAATATATTAATTATAATTTTTT
1 AAAATATAAT-T-TTAATTATAA-TTTTT
*
722074 AAAATATTATTTTAATTATAA
1 AAAATATAATTTTAATTATAA
722095 GATTAGATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
23 4 0.10
24 6 0.14
25 7 0.17
26 2 0.05
27 10 0.24
28 10 0.24
29 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAAATATAATTTTAATTATAATTTTT
Found at i:722080 original size:22 final size:21
Alignment explanation
Indices: 722050--722090 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
722040 AATTTTAAAA
*
722050 TTAATATATTAATTATAATTTT
1 TTAAAATATT-ATTATAATTTT
*
722072 TTAAAATATTATTTTAATT
1 TTAAAATATTATTATAATT
722091 ATAAGATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAAATATTATTATAATTTT
Found at i:725438 original size:1 final size:1
Alignment explanation
Indices: 725432--725463 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
725422 GCATTTTCGT
*
725432 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
725464 TGTTTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:727697 original size:2 final size:2
Alignment explanation
Indices: 727690--727719 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
727680 AATATAATTA
727690 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
727720 TGAAATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:728017 original size:27 final size:24
Alignment explanation
Indices: 727968--728045 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
727958 ATATTTGAAA
727968 TTATTAAATT-TAA-AATTAATTTT
1 TTATTAAATTATAATAATTAA-TTT
727991 TTATATAAATTATAAATAATTAA-TT
1 TTAT-TAAATTAT-AATAATTAATTT
728016 TTATTAAATTATAAT-ATTAAATTT
1 TTATTAAATTATAATAATT-AATTT
728040 TTATTA
1 TTATTA
728046 TTAATAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.06
23 9 0.18
24 22 0.45
25 7 0.14
26 2 0.04
27 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTAAATTATAATAATTAATTT
Found at i:729005 original size:2 final size:2
Alignment explanation
Indices: 728998--729024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
728988 TGTATTTCTT
728998 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
729025 TTCTGCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:729039 original size:6 final size:6
Alignment explanation
Indices: 728994--729051 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
728984 ATCGTGTATT
* * *
728994 TCTTTC TC--TC TCTCTC TCTCTC TCTCTC TCTTTC TGCTTTC TCTTTC
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC T-CTTTC TCTTTC
729041 -C-TTC TCTTTC T
1 TCTTTC TCTTTC T
729052 TTCTTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
4 7 0.15
5 2 0.04
6 31 0.67
7 6 0.13
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.59
Consensus pattern (6 bp):
TCTTTC
Found at i:729658 original size:45 final size:45
Alignment explanation
Indices: 729599--729698 Score: 177
Period size: 45 Copynumber: 2.3 Consensus size: 45
729589 CATTAATCTT
729599 AAATATT-TT-AACATTAAATTTATACATGTAATAAATGGTAAAG
1 AAATATTATTCAACATTAAATTTATACATGTAATAAATGGTAAAG
*
729642 AAATGTTATTCAACATTAAATTTATACATGTAATAAATGGTAAAG
1 AAATATTATTCAACATTAAATTTATACATGTAATAAATGGTAAAG
729687 AAATATTATTCA
1 AAATATTATTCA
729699 TACTTTATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 6 0.11
44 2 0.04
45 45 0.85
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (45 bp):
AAATATTATTCAACATTAAATTTATACATGTAATAAATGGTAAAG
Found at i:731409 original size:24 final size:24
Alignment explanation
Indices: 731360--731406 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
731350 TTTGGTAAGA
* *
731360 TTGATTTTTGTTTAATTTGATAAT
1 TTGATTTTTATTTAATTTAATAAT
*
731384 TTGATTTTTATTTTATATTAATA
1 TTGATTTTTATTTAAT-TTAATA
731407 TTTTTGCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (24 bp):
TTGATTTTTATTTAATTTAATAAT
Found at i:732860 original size:2 final size:2
Alignment explanation
Indices: 732853--732887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
732843 ATACTAATCC
732853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
732888 CTCCCCCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:733481 original size:64 final size:64
Alignment explanation
Indices: 733380--733499 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
733370 ATAACCTCGT
* *
733380 TAATTTTATCGAAGTATGTAAGCTTATCTGTTTAGATTCCGATAGGGGGGCCTTCCAAACCAAG
1 TAATTTTATCGAAGTATGTAAGCTTATCTGTTTAGATTCCGACAAGGGGGCCTTCCAAACCAAG
*
733444 TAATTTTATC-ACAGTATGTAAGCTTATCT-TTCTAGATTCTGACAAGGGGGCCTTCC
1 TAATTTTATCGA-AGTATGTAAGCTTATCTGTT-TAGATTCCGACAAGGGGGCCTTCC
733500 CCTTTGGCTG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
63 3 0.06
64 48 0.94
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
TAATTTTATCGAAGTATGTAAGCTTATCTGTTTAGATTCCGACAAGGGGGCCTTCCAAACCAAG
Found at i:733522 original size:156 final size:155
Alignment explanation
Indices: 733225--733525 Score: 487
Period size: 156 Copynumber: 1.9 Consensus size: 155
733215 TAAAACCAAA
*
733225 TAATTTAATCGAAGTATGTAAGCTCATCTATCTAGATTCCGATCGGGGTCCTTCCAAACCAAGTA
1 TAATTTAATCGAAGTATGTAAGCTCATCTATCTAGATTCCGATCGGGGGCCTTCCAAACCAAGTA
*
733290 ATTTTATCAAAGTATGTAAGCTTATCTTTCTAGATTCTGACAGGGGGGCCTTCCCCGTTTCGCTG
66 ATTTTATCAAAGTATGTAAGCTTATCTTTCTAGATTCTGACAAGGGGGCCTTCCCCGTTTCGCTG
733355 ACTGAGATTTTTTTTATAACCTCGT
131 ACTGAGATTTTTTTTATAACCTCGT
* * * * *
733380 TAATTTTATCGAAGTATGTAAGCTTATCTGTTTAGATTCCGATAGGGGGGCCTTCCAAACCAAGT
1 TAATTTAATCGAAGTATGTAAGCTCATCTATCTAGATTCCGAT-CGGGGGCCTTCCAAACCAAGT
* *
733445 AATTTTATCACAGTATGTAAGCTTATCTTTCTAGATTCTGACAAGGGGGCCTTCCCC-TTTGGCT
65 AATTTTATCAAAGTATGTAAGCTTATCTTTCTAGATTCTGACAAGGGGGCCTTCCCCGTTTCGCT
*
733509 GACTTGAGTTTTTTTTT
130 GAC-TGAGATTTTTTTT
733526 TTTTTTATAA
Statistics
Matches: 134, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
155 48 0.36
156 86 0.64
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (155 bp):
TAATTTAATCGAAGTATGTAAGCTCATCTATCTAGATTCCGATCGGGGGCCTTCCAAACCAAGTA
ATTTTATCAAAGTATGTAAGCTTATCTTTCTAGATTCTGACAAGGGGGCCTTCCCCGTTTCGCTG
ACTGAGATTTTTTTTATAACCTCGT
Found at i:734591 original size:2 final size:2
Alignment explanation
Indices: 734584--734618 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
734574 CAGATGATTC
734584 AT AT 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 AT AT A
734619 CACACACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:738826 original size:15 final size:16
Alignment explanation
Indices: 738811--738844 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
738801 TTATTATAAA
738811 TAAAAAAATTAAAAAT
1 TAAAAAAATTAAAAAT
*
738827 TAAAAAAA-TCAAAAT
1 TAAAAAAATTAAAAAT
738842 TAA
1 TAA
738845 TTTTTTTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAAAAAT
Found at i:738903 original size:2 final size:2
Alignment explanation
Indices: 738898--738930 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
738888 TAATTTTAAG
738898 AT 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 AT A
738931 ACCAAACAAA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:741830 original size:2 final size:2
Alignment explanation
Indices: 741823--741869 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
741813 ACAGAAACAC
741823 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
741865 AG AG A
1 AG AG A
741870 CCTTAAGCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:746407 original size:7 final size:7
Alignment explanation
Indices: 746395--746421 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
746385 GTATAAATTT
746395 TTTTTTA
1 TTTTTTA
746402 TTTTTTA
1 TTTTTTA
746409 TTTTTTA
1 TTTTTTA
746416 TTTTTT
1 TTTTTT
746422 TCCCTGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:746822 original size:27 final size:25
Alignment explanation
Indices: 746792--746860 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 25
746782 TGATAATATA
*
746792 TATATTAATTATATGTATATATTTTAT
1 TATATTAATTATATGTA-AAATTTT-T
*
746819 TATATTATAATTATATTTAAAATTTTT
1 TATA-T-TAATTATATGTAAAATTTTT
*
746846 TATATTTATATATAT
1 TATATTAAT-TATAT
746861 TTTAATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 3 0.08
26 6 0.17
27 9 0.25
28 7 0.19
29 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TATATTAATTATATGTAAAATTTTT
Found at i:746865 original size:27 final size:28
Alignment explanation
Indices: 746788--746851 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
746778 ATATTGATAA
* *
746788 TATATATATTAATTATATGTATATATTTTAT
1 TATAT-TA-TAATTATATTTA-AAATTTTAT
746819 TATATTATAATTATATTTAAAATTTT-T
1 TATATTATAATTATATTTAAAATTTTAT
746846 TATATT
1 TATATT
746852 TATATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.23
28 6 0.19
29 11 0.35
30 2 0.06
31 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TATATTATAATTATATTTAAAATTTTAT
Found at i:746934 original size:32 final size:32
Alignment explanation
Indices: 746847--746934 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
746837 AAAATTTTTT
* * * *
746847 ATATTTATATATATTTTAATATATTAATAATTA
1 ATATTTATATAAATTTTTATATAATATTAA-TA
746880 ATA-TTATAT-AATTTTTA-A-AATATTAA-A
1 ATATTTATATAAATTTTTATATAATATTAATA
746907 ATATTTATAATAAATTTTTATATAATAT
1 ATATTTAT-ATAAATTTTTATATAATAT
746935 GCAAATTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 8 0.17
30 9 0.20
31 7 0.15
32 11 0.24
33 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATTTATATAAATTTTTATATAATATTAATA
Found at i:747264 original size:17 final size:17
Alignment explanation
Indices: 747242--747294 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
747232 ATTATTTGAC
747242 ATATATATAATTATAAT
1 ATATATATAATTATAAT
* *
747259 ATATATTTTATTATTTAAT
1 ATATATATAATTA--TAAT
* *
747278 ATAAATATAATTTTAAT
1 ATATATATAATTATAAT
747295 TATTAATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 15 0.54
19 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATAATTATAAT
Found at i:747277 original size:25 final size:25
Alignment explanation
Indices: 747249--747302 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
747239 GACATATATA
747249 TAATTAT-AATATATATTTT-ATTATT
1 TAATTATAAATATA-ATTTTAATTA-T
747274 TAA-TATAAATATAATTTTAATTAT
1 TAATTATAAATATAATTTTAATTAT
747298 TAATT
1 TAATT
747303 TTACACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATTATAAATATAATTTTAATTAT
Found at i:747373 original size:17 final size:18
Alignment explanation
Indices: 747337--747377 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
747327 TATTTAATGA
747337 TATTTT-TTATTATAATT
1 TATTTTATTATTATAATT
*
747354 TATTTTATTATTATTA-T
1 TATTTTATTATTATAATT
747371 TATTTTA
1 TATTTTA
747378 ATCTCACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTATTATTATAATT
Found at i:747727 original size:3 final size:3
Alignment explanation
Indices: 747721--747752 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
747711 TGATGATCTT
747721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
747753 TTGTATAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:748107 original size:3 final size:3
Alignment explanation
Indices: 748099--748128 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
748089 ATTTTAAACC
748099 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
748129 TATTATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:748826 original size:18 final size:18
Alignment explanation
Indices: 748785--748852 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
748775 ATACATATCT
748785 TAAAA-TTTATAT-AATA
1 TAAAATTTTATATAAATA
748801 -AAAA--TTAT-TAATATA
1 TAAAATTTTATATAA-ATA
*
748816 TTAAATTTTATATAAATA
1 TAAAATTTTATATAAATA
*
748834 TAAAATATT-T-TAAATA
1 TAAAATTTTATATAAATA
748850 TAA
1 TAA
748853 TTATAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 7 0.16
16 12 0.28
17 1 0.02
18 14 0.33
19 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTATATAAATA
Found at i:748826 original size:32 final size:33
Alignment explanation
Indices: 748779--748879 Score: 95
Period size: 32 Copynumber: 3.1 Consensus size: 33
748769 CTATGAATAC
* *
748779 ATATCTTAAAATTTATATAATAAAAAT-TATTA
1 ATATATTAAATTTTATATAATAAAAATATATTA
*
748811 ATATATTAAATTTTATATAAATATAAAATATTTTA
1 ATATATTAAATTTTATAT-AATA-AAAATATATTA
* *
748846 A-ATA-T-AATTATAATATAAT-AAAATATATAA
1 ATATATTAAATT-TTATATAATAAAAATATATTA
748876 ATAT
1 ATAT
748880 GATCTGATGT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
30 10 0.17
31 2 0.03
32 23 0.40
33 10 0.17
34 8 0.14
35 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATATTAAATTTTATATAATAAAAATATATTA
Found at i:748840 original size:27 final size:30
Alignment explanation
Indices: 748810--748879 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 30
748800 AAAAATTATT
* *
748810 AATATATTAAATTTTA-TATAA-AT-ATAA
1 AATATATTAAATATAATTATAATATAATAA
*
748837 AATATTTTAAATATAATTATAATATAATAA
1 AATATATTAAATATAATTATAATATAATAA
748867 AATATA-TAAATAT
1 AATATATTAAATAT
748880 GATCTGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.36
28 5 0.14
29 9 0.25
30 9 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATATTAAATATAATTATAATATAATAA
Found at i:749450 original size:2 final size:2
Alignment explanation
Indices: 749437--749473 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
749427 TTTATTAGGA
*
749437 AT AT AA 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 AT AT AT A
749474 CATTTGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:751467 original size:19 final size:19
Alignment explanation
Indices: 751429--751467 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
751419 TAAATTTTAA
*
751429 TATTTTTATAATTTATTTT
1 TATTTTTATAATTTAATTT
751448 TATTTTTA-AATTATAATTT
1 TATTTTTATAATT-TAATTT
751467 T
1 T
751468 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTATAATTTAATTT
Found at i:754884 original size:35 final size:35
Alignment explanation
Indices: 754814--754894 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
754804 AGAGAACAAT
*
754814 GCCAAGCGATATTCTCTTATTTTAAACTCTATAAA
1 GCCAAGCAATATTCTCTTATTTTAAACTCTATAAA
* *
754849 GCCAAG-AATATTCTCTT-TTTTCCAACCTCTGTAAA
1 GCCAAGCAATATTCTCTTATTTT--AAACTCTATAAA
754884 GCCAAGCAATA
1 GCCAAGCAATA
754895 CCCAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 4 0.10
34 10 0.25
35 22 0.55
36 4 0.10
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (35 bp):
GCCAAGCAATATTCTCTTATTTTAAACTCTATAAA
Found at i:760521 original size:14 final size:14
Alignment explanation
Indices: 760502--760531 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
760492 ATCACATTTT
760502 TTAATTTTTTAAAA
1 TTAATTTTTTAAAA
*
760516 TTAATTTTTTATAA
1 TTAATTTTTTAAAA
760530 TT
1 TT
760532 TTAAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTAATTTTTTAAAA
Found at i:761672 original size:21 final size:21
Alignment explanation
Indices: 761648--761690 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
761638 GATTGTTATA
761648 CACGCAATAAATACATAAATT
1 CACGCAATAAATACATAAATT
761669 CACGCAATAAATACATAAATT
1 CACGCAATAAATACATAAATT
761690 C
1 C
761691 CATATGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (21 bp):
CACGCAATAAATACATAAATT
Found at i:762378 original size:2 final size:2
Alignment explanation
Indices: 762371--762406 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
762361 TGACGTTCTT
762371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
762407 AACATTACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:763198 original size:2 final size:2
Alignment explanation
Indices: 763191--763217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
763181 ACTGCATAAC
763191 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 A
763218 CTGAAATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:763856 original size:3 final size:3
Alignment explanation
Indices: 763848--763882 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
763838 GTAAAATCAA
763848 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
763883 AAGCTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:765353 original size:18 final size:17
Alignment explanation
Indices: 765319--765357 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
765309 ATTAAAATTA
765319 TATATAGATAATTAAGT
1 TATATAGATAATTAAGT
765336 GTATATA-ATAATTAAAGT
1 -TATATAGATAATT-AAGT
765354 TATA
1 TATA
765358 ATCATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TATATAGATAATTAAGT
Found at i:767552 original size:17 final size:18
Alignment explanation
Indices: 767526--767567 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
767516 TGTTTGTAGA
*
767526 ATTAAAAAAATTTTACGT
1 ATTAAAAAATTTTTACGT
767544 ATTAAAAAATTTTTACGT
1 ATTAAAAAATTTTTACGT
*
767562 GTTAAA
1 ATTAAA
767568 TCTTAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (18 bp):
ATTAAAAAATTTTTACGT
Found at i:768881 original size:19 final size:21
Alignment explanation
Indices: 768821--768881 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
768811 TTTTTTTATT
768821 TTAT-ATAA-TTTATT-ATAAA
1 TTATAATAATTTTATTAAT-AA
* *
768840 ATATAATAATTTTATTTATAA
1 TTATAATAATTTTATTAATAA
768861 TTATAA-AATTTT-TTAATAA
1 TTATAATAATTTTATTAATAA
768880 TT
1 TT
768882 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.31
20 10 0.28
21 13 0.36
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATAATAATTTTATTAATAA
Found at i:768881 original size:31 final size:32
Alignment explanation
Indices: 768841--768922 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
768831 TATTATAAAA
768841 TATAATAATTTTATTTATAA-TTATAAAATTT
1 TATAATAATTTTATTTATAATTTATAAAATTT
* **
768872 TTTAATAATTTT-TAAAATAATTTATAAAATTT
1 TATAATAATTTTAT-TTATAATTTATAAAATTT
*
768904 TATAA-ATTTTTATTTATAA
1 TATAATAATTTTATTTATAA
768923 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
30 1 0.02
31 24 0.59
32 16 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATAATAATTTTATTTATAATTTATAAAATTT
Found at i:768905 original size:10 final size:10
Alignment explanation
Indices: 768861--768916 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
768851 TTATTTATAA
768861 TTATAAAATT
1 TTATAAAATT
*
768871 TTTTAATAATT
1 TTATAA-AATT
768882 TT-TAAAATAAT
1 TTATAAAAT--T
768893 TTATAAAATT
1 TTATAAAATT
*
768903 TTATAAATTT
1 TTATAAAATT
768913 TTAT
1 TTAT
768917 TTATAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.08
10 22 0.55
11 9 0.22
12 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTATAAAATT
Found at i:768915 original size:20 final size:20
Alignment explanation
Indices: 768818--768916 Score: 62
Period size: 20 Copynumber: 4.8 Consensus size: 20
768808 TAATTTTTTT
768818 ATTTTATATAATTTATTATAAA
1 ATTTTATA-AATTT-TTATAAA
* * * *
768840 ATATAAT-AATTTTATTTATA
1 ATTTTATAAATTTT-TATAAA
*
768860 ATTATA-AAATTTTT-TAATA
1 ATTTTATAAATTTTTATAA-A
*
768879 ATTTT-TAAAATAATTTATAAA
1 ATTTTAT-AAAT-TTTTATAAA
768900 ATTTTATAAATTTTTAT
1 ATTTTATAAATTTTTAT
768917 TTATAAAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 18
0.67 0.13 0.21
Matches are distributed among these distances:
18 2 0.03
19 7 0.12
20 27 0.47
21 13 0.22
22 9 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTATAAATTTTTATAAA
Found at i:769105 original size:21 final size:20
Alignment explanation
Indices: 769055--769112 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
769045 ATTATAAAAT
**
769055 AATAATTATTTTATTATTTTA
1 AATAATTA-TTTAAAATTTTA
*
769076 TATATATTATTTAAAATTTTAA
1 AATA-ATTATTTAAAATTTT-A
*
769098 AATAATTAATTAAAA
1 AATAATTATTTAAAA
769113 AACAAAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATAATTATTTAAAATTTTA
Found at i:769704 original size:27 final size:27
Alignment explanation
Indices: 769674--769776 Score: 131
Period size: 27 Copynumber: 3.9 Consensus size: 27
769664 ATAAAAGTCA
*
769674 TTCTTTATGTTTATCAAAAATGGTGAT
1 TTCTTTATGTTTGTCAAAAATGGTGAT
* *
769701 TTCTTTGTGTTTGTAAAAAATGGTGAT
1 TTCTTTATGTTTGTCAAAAATGGTGAT
*
769728 TTCTTTTTGTTTGTCAAAAATGGTGA-
1 TTCTTTATGTTTGTCAAAAATGGTGAT
* *
769754 TT-TAT-TGTTTGTCAAAATTGGTG
1 TTCTTTATGTTTGTCAAAAATGGTG
769777 GCTAATTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
24 17 0.25
25 2 0.03
26 2 0.03
27 48 0.70
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (27 bp):
TTCTTTATGTTTGTCAAAAATGGTGAT
Found at i:774089 original size:27 final size:26
Alignment explanation
Indices: 774058--774151 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
774048 GAAGCCACCT
*
774058 TTTGTGTTTGTCAAAAATGGTGGTTCC
1 TTTGTGTTTGTCAAAAATAGTGGTT-C
* *
774085 TTTGTGTTTGTAAAAAATAGTGATTTC
1 TTTGTGTTTGTCAAAAATAGTG-GTTC
* *
774112 TTTTTATTTGTCAAAAATAGTGG--C
1 TTTGTGTTTGTCAAAAATAGTGGTTC
774136 -TTGTTGTTTGTCAAAA
1 TTTG-TGTTTGTCAAAA
774152 TTGGTGACTA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.04
24 12 0.21
27 40 0.71
28 2 0.04
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.47
Consensus pattern (26 bp):
TTTGTGTTTGTCAAAAATAGTGGTTC
Found at i:774890 original size:19 final size:19
Alignment explanation
Indices: 774866--774913 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
774856 AATTATTTAA
* *
774866 TTTAATTTAAATCATATTT
1 TTTAATTTAAATAATAATT
*
774885 TTTAA-TAAAATAATAATT
1 TTTAATTTAAATAATAATT
774903 TTT-ATTTAAAT
1 TTTAATTTAAAT
774914 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 1 0.04
18 18 0.75
19 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATTTAAATAATAATT
Found at i:775172 original size:18 final size:18
Alignment explanation
Indices: 775149--775197 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
775139 TAAATTTATT
775149 CACGTGTGGATTAACTGA
1 CACGTGTGGATTAACTGA
775167 CACGTGTGGATTAACTGA
1 CACGTGTGGATTAACTGA
*
775185 CACATGTGGATTA
1 CACGTGTGGATTA
775198 CTTGTCAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (18 bp):
CACGTGTGGATTAACTGA
Found at i:776184 original size:27 final size:29
Alignment explanation
Indices: 776125--776187 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
776115 AATTTTTATC
*
776125 ATATTTTTTATATATTATAATTAAATTTA
1 ATATATTTTATATATTATAATTAAATTTA
*
776154 ATATATTTTATAT-TTAT-A-TAAATTTTG
1 ATATATTTTATATATTATAATTAAA-TTTA
776181 ATATATT
1 ATATATT
776188 AATAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.13
27 11 0.35
28 4 0.13
29 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
ATATATTTTATATATTATAATTAAATTTA
Found at i:776192 original size:18 final size:16
Alignment explanation
Indices: 776149--776193 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
776139 TTATAATTAA
*
776149 ATTTAATATATTTTAT
1 ATTTAATAAATTTTAT
776165 ATTTATATAAATTTTGAT
1 ATTTA-ATAAATTTT-AT
776183 ATATTAATAAA
1 AT-TTAATAAA
776194 AATATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
18 9 0.36
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAATAAATTTTAT
Found at i:778364 original size:20 final size:20
Alignment explanation
Indices: 778318--778361 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
778308 TTCACATTCA
* *
778318 ATAAATTTAAATTTTTTATT
1 ATAATTTTAAATTTTTCATT
*
778338 TTAATTTTATAATTTTTCATT
1 ATAATTTTA-AATTTTTCATT
778359 ATA
1 ATA
778362 TTTACATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATAATTTTAAATTTTTCATT
Found at i:778519 original size:2 final size:2
Alignment explanation
Indices: 778512--778537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
778502 AAAACTTGAA
778512 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
778538 GGAAACGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:778981 original size:4 final size:4
Alignment explanation
Indices: 778972--779008 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
778962 TGGAGATTTC
778972 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
779009 AGTCCCTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:781100 original size:21 final size:21
Alignment explanation
Indices: 781076--781115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
781066 CTAATATACC
*
781076 TTTTT-TTTAATTATATATTA
1 TTTTTATTTTATTATATATTA
*
781096 TTTTTATTTTTTTATATATT
1 TTTTTATTTTATTATATATT
781116 GTATATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTTTATTATATATTA
Found at i:781167 original size:14 final size:13
Alignment explanation
Indices: 781131--781193 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 13
781121 TTTATATCAC
* *
781131 ATAAATAATACAT
1 ATAAATATTAAAT
*
781144 ATATATTATTACAAT
1 ATA-AATATTA-AAT
781159 ATAAATATTAAA-
1 ATAAATATTAAAT
*
781171 ATATATATTAAAT
1 ATAAATATTAAAT
781184 CATAAATATT
1 -ATAAATATT
781194 TTAAAACTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 11 0.28
13 5 0.12
14 19 0.47
15 5 0.12
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATATTAAAT
Found at i:781188 original size:26 final size:29
Alignment explanation
Indices: 781130--781193 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 29
781120 ATTTATATCA
* *
781130 CATAAATAATACATATATATTATTACAAT
1 CATAAATATTACAAATATATTATTACAAT
781159 -ATAAATATTA-AAATATA-TATTA-AAT
1 CATAAATATTACAAATATATTATTACAAT
781184 CATAAATATT
1 CATAAATATT
781194 TTAAAACTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.09
26 14 0.44
27 6 0.19
28 9 0.28
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (29 bp):
CATAAATATTACAAATATATTATTACAAT
Found at i:781304 original size:21 final size:20
Alignment explanation
Indices: 781275--781348 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
781265 TCTTAAACAT
*
781275 ATATTAATTAATTATTTATAA
1 ATATAAATTAATT-TTTATAA
**
781296 ATATAAATTAATTTAAATAAA
1 ATATAAATTAATTTTTAT-AA
* *
781317 ATTTAAAATTTATTTTT-TAA
1 ATAT-AAATTAATTTTTATAA
781337 AT-TAAATTAATT
1 ATATAAATTAATT
781349 AAATAATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.19
19 1 0.02
20 7 0.16
21 18 0.42
22 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATTAATTTTTATAA
Found at i:781305 original size:25 final size:24
Alignment explanation
Indices: 781259--781308 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
781249 AAAAATACTA
*
781259 TAATTATCTTAAACATATATTAAT
1 TAATTATCTTAAACATAAATTAAT
* *
781283 TAATTATTTATAAATATAAATTAAT
1 TAATTATCT-TAAACATAAATTAAT
781308 T
1 T
781309 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTATCTTAAACATAAATTAAT
Found at i:782738 original size:27 final size:26
Alignment explanation
Indices: 782708--782794 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
782698 ATGCCATGGT
782708 TGCTTTGTTGTCTGGTTATGATGTTGG
1 TGCTTTGTTGTCT-GTTATGATGTTGG
* * * *
782735 TGCTTCT-TTTTCCTGTATATGCTGTAGT
1 TGCTT-TGTTGT-CTGT-TATGATGTTGG
* *
782763 TACTTTGTTGTCCAGTTATGATGTTGG
1 TGCTTTGTTGT-CTGTTATGATGTTGG
782790 TGCTT
1 TGCTT
782795 CATTTTGATG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.10, C:0.13, G:0.25, T:0.52
Consensus pattern (26 bp):
TGCTTTGTTGTCTGTTATGATGTTGG
Found at i:782755 original size:28 final size:27
Alignment explanation
Indices: 782722--782800 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
782712 TTGTTGTCTG
*
782722 GTTATGATGTTGGTGCTTCTTTTTCCT
1 GTTATGATGTTGGTGCTTCTTTTTCCA
* * * * *
782749 GTATATGCTGTAGTTACTT-TGTTGTCCA
1 GT-TATGATGTTGGTGCTTCT-TTTTCCA
*
782777 GTTATGATGTTGGTGCTTCATTTT
1 GTTATGATGTTGGTGCTTCTTTTT
782801 GATGTGCTGC
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (27 bp):
GTTATGATGTTGGTGCTTCTTTTTCCA
Found at i:790250 original size:15 final size:15
Alignment explanation
Indices: 790230--790259 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
790220 ATAAAAACCT
790230 AATTAAAAATAAAAG
1 AATTAAAAATAAAAG
790245 AATTAAAAATAAAAG
1 AATTAAAAATAAAAG
790260 TGAGACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AATTAAAAATAAAAG
Found at i:791854 original size:22 final size:22
Alignment explanation
Indices: 791826--791868 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
791816 GTAATAGCCT
*
791826 TATAAAAATCGGGCACTATAAA
1 TATAAAAATCGGACACTATAAA
*
791848 TATAAAAATCGGACGCTATAA
1 TATAAAAATCGGACACTATAA
791869 TCAGTAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (22 bp):
TATAAAAATCGGACACTATAAA
Found at i:798166 original size:13 final size:13
Alignment explanation
Indices: 798150--798176 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
798140 AGGCATTTAA
798150 TCTAAATAAAGAC
1 TCTAAATAAAGAC
798163 TCTAAATAAAGAC
1 TCTAAATAAAGAC
798176 T
1 T
798177 TCAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (13 bp):
TCTAAATAAAGAC
Found at i:801703 original size:2 final size:2
Alignment explanation
Indices: 801696--801721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
801686 GTAATTTTGC
801696 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
801722 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:801726 original size:2 final size:2
Alignment explanation
Indices: 801721--801755 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
801711 TATATATATA
*
801721 TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
801756 TTTTAGCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:801992 original size:17 final size:19
Alignment explanation
Indices: 801960--801995 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
801950 AATAATGTAT
801960 TTTTATTTATATAAAAATA
1 TTTTATTTATATAAAAATA
801979 TTTT-TTTA-ATAAAAATA
1 TTTTATTTATATAAAAATA
801996 ATTAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATTTATATAAAAATA
Found at i:801993 original size:18 final size:20
Alignment explanation
Indices: 801957--801993 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
801947 GTTAATAATG
*
801957 TATTTTTATTTATATAAAAA
1 TATTTTTATTAATATAAAAA
801977 TATTTTT-TTAATA-AAAA
1 TATTTTTATTAATATAAAA
801994 TAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 5 0.31
20 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTATTAATATAAAAA
Found at i:803831 original size:24 final size:26
Alignment explanation
Indices: 803795--803847 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
803785 TTTAAATCGA
* *
803795 TTAAATTTAAATTAT-TATATATTTT
1 TTAAATTTAAATTATAAAAATATTTT
803820 TTAAATTT-AATTATAAAAATATTTT
1 TTAAATTTAAATTATAAAAATATTTT
803845 TTA
1 TTA
803848 TAAATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAAATTTAAATTATAAAAATATTTT
Found at i:804262 original size:2 final size:2
Alignment explanation
Indices: 804255--804293 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
804245 ACATATGTAA
* *
804255 AT AT AT AT CT AT -T AC 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
804294 GTTTGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:804839 original size:22 final size:20
Alignment explanation
Indices: 804813--804867 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 20
804803 TAAATTTATT
804813 TTAAATAATATTTTTAATAAAA
1 TTAAATAATATTTTT-AT-AAA
804835 TTAAA-AAT-TTTACTTATAAA
1 TTAAATAATATTT--TTATAAA
804855 TTAAATAA-ATTTT
1 TTAAATAATATTTT
804868 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 10 0.34
22 7 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATAATATTTTTATAAA
Found at i:804857 original size:20 final size:21
Alignment explanation
Indices: 804813--804872 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
804803 TAAATTTATT
*
804813 TTAAATAATATTTT-TAATAAAA
1 TTAAATAA-ATTTTATTAT-AAA
804835 TT-AA-AAATTTTACTTATAAA
1 TTAAATAAATTTTA-TTATAAA
804855 TTAAATAAATTTTATTAT
1 TTAAATAAATTTTATTAT
804873 TATTAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 11 0.33
22 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATAAATTTTATTATAAA
Found at i:804883 original size:21 final size:22
Alignment explanation
Indices: 804832--804872 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
804822 ATTTTTAATA
804832 AAATT-AA-AAATTTTACTTAT
1 AAATTAAATAAATTTTACTTAT
804852 AAATTAAATAAATTTTA-TTAT
1 AAATTAAATAAATTTTACTTAT
804873 TATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTAAATAAATTTTACTTAT
Found at i:807818 original size:33 final size:33
Alignment explanation
Indices: 807763--807828 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
807753 CTAATAGAAA
* *
807763 TCTTTGTTTCTGATTATCATACTCCGAGGTAAT
1 TCTTTGTTGCTGAATATCATACTCCGAGGTAAT
* * *
807796 TCTTTGTTGCTGAATGTTATACTCTGAGGTAAT
1 TCTTTGTTGCTGAATATCATACTCCGAGGTAAT
807829 GTGACAAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (33 bp):
TCTTTGTTGCTGAATATCATACTCCGAGGTAAT
Found at i:811959 original size:475 final size:475
Alignment explanation
Indices: 811069--812003 Score: 1870
Period size: 475 Copynumber: 2.0 Consensus size: 475
811059 TGTTTTTCTA
811069 CAGGTTTGGCAACCGTAATTGGGATAAAGTATGAGTCTCCAGGGGAAGCTGATGGTAGAAACCCT
1 CAGGTTTGGCAACCGTAATTGGGATAAAGTATGAGTCTCCAGGGGAAGCTGATGGTAGAAACCCT
811134 ACTCTCAAAGTGAAGTCTTTTGTAGGCGATGAGTACAAAGATCTAATTGAACAGGCTGCCAGGTT
66 ACTCTCAAAGTGAAGTCTTTTGTAGGCGATGAGTACAAAGATCTAATTGAACAGGCTGCCAGGTT
811199 TTGAGATGGCCGTGATTGCTGTTTCCGGACTGAGCATGAATCCGGATTGCGAATTGAGTTTTAGC
131 TTGAGATGGCCGTGATTGCTGTTTCCGGACTGAGCATGAATCCGGATTGCGAATTGAGTTTTAGC
811264 ATCCTTCGATGAACTGACCATTTGTTCACGGCTTCTCTTAGTATCGATTTATGTGATATGTTCTG
196 ATCCTTCGATGAACTGACCATTTGTTCACGGCTTCTCTTAGTATCGATTTATGTGATATGTTCTG
811329 CATTTGCTTGTGAACTTGTAGGGATATCTGTTGTGGATATAATCTTTACCCATGTGATTTTTTAC
261 CATTTGCTTGTGAACTTGTAGGGATATCTGTTGTGGATATAATCTTTACCCATGTGATTTTTTAC
811394 GGTATGATCATTAAGAATCAGGCTTAGATCGACTTAGATTACTAAAACTAATTTCAGGTTTGGTT
326 GGTATGATCATTAAGAATCAGGCTTAGATCGACTTAGATTACTAAAACTAATTTCAGGTTTGGTT
811459 TAATTCAGCGGAGTTTATCAGGTCAGTCAGATAAATAATTTGATCCGTAGACAAAATCTCATTTC
391 TAATTCAGCGGAGTTTATCAGGTCAGTCAGATAAATAATTTGATCCGTAGACAAAATCTCATTTC
811524 ACGGAGTTTATCAGGTCAGT
456 ACGGAGTTTATCAGGTCAGT
811544 CAGGTTTGGCAACCGTAATTGGGATAAAGTATGAGTCTCCAGGGGAAGCTGATGGTAGAAACCCT
1 CAGGTTTGGCAACCGTAATTGGGATAAAGTATGAGTCTCCAGGGGAAGCTGATGGTAGAAACCCT
811609 ACTCTCAAAGTGAAGTCTTTTGTAGGCGATGAGTACAAAGATCTAATTGAACAGGCTGCCAGGTT
66 ACTCTCAAAGTGAAGTCTTTTGTAGGCGATGAGTACAAAGATCTAATTGAACAGGCTGCCAGGTT
811674 TTGAGATGGCCGTGATTGCTGTTTCCGGACTGAGCATGAATCCGGATTGCGAATTGAGTTTTAGC
131 TTGAGATGGCCGTGATTGCTGTTTCCGGACTGAGCATGAATCCGGATTGCGAATTGAGTTTTAGC
811739 ATCCTTCGATGAACTGACCATTTGTTCACGGCTTCTCTTAGTATCGATTTATGTGATATGTTCTG
196 ATCCTTCGATGAACTGACCATTTGTTCACGGCTTCTCTTAGTATCGATTTATGTGATATGTTCTG
811804 CATTTGCTTGTGAACTTGTAGGGATATCTGTTGTGGATATAATCTTTACCCATGTGATTTTTTAC
261 CATTTGCTTGTGAACTTGTAGGGATATCTGTTGTGGATATAATCTTTACCCATGTGATTTTTTAC
811869 GGTATGATCATTAAGAATCAGGCTTAGATCGACTTAGATTACTAAAACTAATTTCAGGTTTGGTT
326 GGTATGATCATTAAGAATCAGGCTTAGATCGACTTAGATTACTAAAACTAATTTCAGGTTTGGTT
811934 TAATTCAGCGGAGTTTATCAGGTCAGTCAGATAAATAATTTGATCCGTAGACAAAATCTCATTTC
391 TAATTCAGCGGAGTTTATCAGGTCAGTCAGATAAATAATTTGATCCGTAGACAAAATCTCATTTC
811999 ACGGA
456 ACGGA
812004 AAATGAGTTC
Statistics
Matches: 460, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 460 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (475 bp):
CAGGTTTGGCAACCGTAATTGGGATAAAGTATGAGTCTCCAGGGGAAGCTGATGGTAGAAACCCT
ACTCTCAAAGTGAAGTCTTTTGTAGGCGATGAGTACAAAGATCTAATTGAACAGGCTGCCAGGTT
TTGAGATGGCCGTGATTGCTGTTTCCGGACTGAGCATGAATCCGGATTGCGAATTGAGTTTTAGC
ATCCTTCGATGAACTGACCATTTGTTCACGGCTTCTCTTAGTATCGATTTATGTGATATGTTCTG
CATTTGCTTGTGAACTTGTAGGGATATCTGTTGTGGATATAATCTTTACCCATGTGATTTTTTAC
GGTATGATCATTAAGAATCAGGCTTAGATCGACTTAGATTACTAAAACTAATTTCAGGTTTGGTT
TAATTCAGCGGAGTTTATCAGGTCAGTCAGATAAATAATTTGATCCGTAGACAAAATCTCATTTC
ACGGAGTTTATCAGGTCAGT
Found at i:812320 original size:34 final size:34
Alignment explanation
Indices: 812275--812348 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
812265 TAATGTATTA
* *
812275 ATTTTTGTTTGCATTACCCTCATCTTCTAGAAAC
1 ATTTTTCTTTGCATTACACTCATCTTCTAGAAAC
* *
812309 ATTTTTCTTTGCATTATACTCGTCTTCTAGAAAC
1 ATTTTTCTTTGCATTACACTCATCTTCTAGAAAC
*
812343 CTTTTT
1 ATTTTT
812349 GTTTTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (34 bp):
ATTTTTCTTTGCATTACACTCATCTTCTAGAAAC
Found at i:813080 original size:25 final size:24
Alignment explanation
Indices: 813046--813095 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
813036 ATTATATCTT
*
813046 TATCATATTTGTTAAAGTGTTAAAA
1 TATCATATTTGTTAAA-TATTAAAA
813071 TATCATATTTGTTAAATATTAAAA
1 TATCATATTTGTTAAATATTAAAA
813095 T
1 T
813096 TTTATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
TATCATATTTGTTAAATATTAAAA
Found at i:813196 original size:22 final size:21
Alignment explanation
Indices: 813164--813224 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
813154 ATCAAAAATT
* * *
813164 ATATAAATATAATATATTTTAA
1 ATATAATTATAATATA-ATAAA
813186 ATATAATTATAATATAATAAA
1 ATATAATTATAATATAATAAA
813207 ATAATAATTATAATATAA
1 AT-ATAATTATAATATAA
813225 ATGATATAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAATTATAATATAATAAA
Found at i:813199 original size:11 final size:11
Alignment explanation
Indices: 813164--813224 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
813154 ATCAAAAATT
*
813164 ATATAAATATA
1 ATATAATTATA
*
813175 ATAT-ATTTTAA
1 ATATAATTAT-A
813186 ATATAATTATA
1 ATATAATTATA
*
813197 ATATAA-TAAA
1 ATATAATTATA
813207 ATAATAATTATA
1 AT-ATAATTATA
813219 ATATAA
1 ATATAA
813225 ATGATATAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 8 0.20
11 24 0.59
12 9 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAATTATA
Found at i:813955 original size:2 final size:2
Alignment explanation
Indices: 813948--813983 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
813938 CGAGGTGAAA
813948 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
813984 GAGTAAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:814554 original size:27 final size:29
Alignment explanation
Indices: 814480--814560 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 29
814470 TCAAAAAAGT
*
814480 TTAACTATATAATATTTTTTTAAAATAAA
1 TTAATTATATAATATTTTTTTAAAATAAA
* * *
814509 TTAATTAGAT-ATGTATTTTT-AAATAAA
1 TTAATTATATAATATTTTTTTAAAATAAA
*
814536 TTAATTATATAATTTTTTTTTAAAA
1 TTAATTATATAATATTTTTTTAAAA
814561 AAAGAAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 16 0.37
28 16 0.37
29 11 0.26
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAATTATATAATATTTTTTTAAAATAAA
Found at i:816951 original size:3 final size:3
Alignment explanation
Indices: 816943--816988 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
816933 CAATTGAGAG
816943 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
816989 AAGGCTCTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:818910 original size:16 final size:16
Alignment explanation
Indices: 818889--818933 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
818879 TCTATTTATC
818889 TTATAAATTATATATT
1 TTATAAATTATATATT
*
818905 TTATAAATAAT-TATT
1 TTATAAATTATATATT
818920 TT-T-AA-TATATATT
1 TTATAAATTATATATT
818933 T
1 T
818934 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.08
13 7 0.27
14 1 0.04
15 6 0.23
16 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATAAATTATATATT
Found at i:819142 original size:2 final size:2
Alignment explanation
Indices: 819135--819160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
819125 CATCAAACAA
819135 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
819161 TGTTGCAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:821084 original size:8 final size:8
Alignment explanation
Indices: 821071--821121 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
821061 GTATCACATC
821071 TATATAAA
1 TATATAAA
821079 TATATAAA
1 TATATAAA
* *
821087 TTTTTAAA
1 TATATAAA
821095 TATAT-AA
1 TATATAAA
*
821102 TATAAAAA
1 TATATAAA
*
821110 AATATAAA
1 TATATAAA
821118 TATA
1 TATA
821122 ACATAAATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:821114 original size:17 final size:18
Alignment explanation
Indices: 821092--821133 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
821082 ATAAATTTTT
821092 AAATATATAATATAA-AA
1 AAATATATAATATAACAA
*
821109 AAATATA-AATATAACAT
1 AAATATATAATATAACAA
821126 AAATATAT
1 AAATATAT
821134 TAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAATATAACAA
Found at i:822104 original size:29 final size:29
Alignment explanation
Indices: 822063--822146 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
822053 ATGAAAATTG
* * * *
822063 ATAAAATTGAAAATACTATAATCAAATTTA
1 ATAAAATTAAAAATA-AATAATAAAAGTTA
*
822093 ATAAAATTAAAAATAAATGATAAAAGTTA
1 ATAAAATTAAAAATAAATAATAAAAGTTA
* *
822122 ACAAAATT-AAAATATAATGATAAAA
1 ATAAAATTAAAAATA-AATAATAAAA
822147 TTCAATGTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.13
29 27 0.57
30 14 0.30
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.29
Consensus pattern (29 bp):
ATAAAATTAAAAATAAATAATAAAAGTTA
Found at i:823846 original size:22 final size:21
Alignment explanation
Indices: 823803--823842 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
823793 AATAATTTTT
823803 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
823824 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
823843 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:823931 original size:24 final size:24
Alignment explanation
Indices: 823891--823948 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
823881 TACTTAAAGA
* *
823891 AAAATATGTTTGGATAAAAATAAAT
1 AAAATAT-TTTGAATAAAAAGAAAT
*
823916 AAAATATTTTGAATAAATAGAAAT
1 AAAATATTTTGAATAAAAAGAAAT
823940 AAAAT-TTTT
1 AAAATATTTT
823949 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 4 0.13
24 19 0.63
25 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (24 bp):
AAAATATTTTGAATAAAAAGAAAT
Found at i:824471 original size:104 final size:104
Alignment explanation
Indices: 824291--824491 Score: 402
Period size: 104 Copynumber: 1.9 Consensus size: 104
824281 AGAAAAAAGT
824291 AAGTCAGGTTCTTGCTGAGAATCCATTGAAATTTGAAAGCTATAGAGCTAAGCTAGTTAATGAAG
1 AAGTCAGGTTCTTGCTGAGAATCCATTGAAATTTGAAAGCTATAGAGCTAAGCTAGTTAATGAAG
824356 CAATACTAGCAACAAACAAGAAAATCCATTGAGCTTTCC
66 CAATACTAGCAACAAACAAGAAAATCCATTGAGCTTTCC
824395 AAGTCAGGTTCTTGCTGAGAATCCATTGAAATTTGAAAGCTATAGAGCTAAGCTAGTTAATGAAG
1 AAGTCAGGTTCTTGCTGAGAATCCATTGAAATTTGAAAGCTATAGAGCTAAGCTAGTTAATGAAG
824460 CAATACTAGCAACAAACAAGAAAATCCATTGA
66 CAATACTAGCAACAAACAAGAAAATCCATTGA
824492 ACTTGGAAAG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (104 bp):
AAGTCAGGTTCTTGCTGAGAATCCATTGAAATTTGAAAGCTATAGAGCTAAGCTAGTTAATGAAG
CAATACTAGCAACAAACAAGAAAATCCATTGAGCTTTCC
Found at i:827243 original size:10 final size:10
Alignment explanation
Indices: 827222--827252 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
827212 AGGAAGTGAG
827222 GAGAAA-AAA
1 GAGAAAGAAA
827231 GAGAAAGAAA
1 GAGAAAGAAA
827241 GAGAAAGAAA
1 GAGAAAGAAA
827251 GA
1 GA
827253 AAGAAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
GAGAAAGAAA
Found at i:827255 original size:18 final size:19
Alignment explanation
Indices: 827222--827259 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
827212 AGGAAGTGAG
827222 GAGAAAAAAGAGAAAGAAA
1 GAGAAAAAAGAGAAAGAAA
*
827241 GAGAAAGAA-AGAAAGAAA
1 GAGAAAAAAGAGAAAGAAA
827259 G
1 G
827260 GTTAGAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
GAGAAAAAAGAGAAAGAAA
Found at i:828488 original size:23 final size:23
Alignment explanation
Indices: 828447--828490 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
828437 AATATAAATA
*
828447 TATTTAATATATTTTTATATTCG
1 TATTTAATATATTTATATATTCG
828470 TATTTAATAT-TTTAATATATT
1 TATTTAATATATTT-ATATATT
828491 TAATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTTAATATATTTATATATTCG
Found at i:833854 original size:15 final size:16
Alignment explanation
Indices: 833824--833892 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 16
833814 AATAAGTTAT
*
833824 AATTTATAATTAAAAA
1 AATTAATAATTAAAAA
833840 AATTAATAA-TAAAAA
1 AATTAATAATTAAAAA
833855 ATATTATATATTATTATAATAA
1 A-ATTA-ATA--ATTA-AA-AA
**
833877 AATTTTTAATTAAAAA
1 AATTAATAATTAAAAA
833893 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
15 7 0.16
16 14 0.33
17 5 0.12
18 4 0.09
19 1 0.02
20 4 0.09
21 5 0.12
22 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATAATTAAAAA
Found at i:834369 original size:25 final size:25
Alignment explanation
Indices: 834341--834391 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
834331 TGTAAAATTT
* *
834341 TTTATTTTTATTTTTTAATTTTTAA
1 TTTATTTTTAATTTTTAATATTTAA
834366 TTTATTTTTAATTTTTAATATTTAA
1 TTTATTTTTAATTTTTAATATTTAA
834391 T
1 T
834392 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTATTTTTAATTTTTAATATTTAA
Found at i:834375 original size:18 final size:19
Alignment explanation
Indices: 834347--834384 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
834337 ATTTTTTATT
834347 TTTATTTTTTAATTTTTAA
1 TTTATTTTTTAATTTTTAA
834366 TTTA-TTTTTAATTTTTAA
1 TTTATTTTTTAATTTTTAA
834384 T
1 T
834385 ATTTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTTTTAATTTTTAA
Found at i:834382 original size:7 final size:7
Alignment explanation
Indices: 834336--834391 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
834326 TTTTCTGTAA
834336 AATTTTT
1 AATTTTT
*
834343 TATTTTT
1 AATTTTT
*
834350 ATTTTTT
1 AATTTTT
834357 AATTTTT
1 AATTTTT
834364 AA--TTT
1 AATTTTT
834369 -ATTTTT
1 AATTTTT
834375 AATTTTT
1 AATTTTT
*
834382 AATATTT
1 AATTTTT
834389 AAT
1 AAT
834392 ATAAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 3 0.07
7 34 0.83
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:842045 original size:4 final size:4
Alignment explanation
Indices: 842036--842060 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
842026 GTGCGGGTTG
842036 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
842061 TTGTTTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:848072 original size:3 final size:3
Alignment explanation
Indices: 848064--848126 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
848054 GAACATAGCT
*
848064 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
848112 TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
848127 CAACAACAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:849526 original size:2 final size:2
Alignment explanation
Indices: 849519--849551 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
849509 GGAAGCAATT
849519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
849552 CCAACTGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:849776 original size:20 final size:20
Alignment explanation
Indices: 849741--849780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
849731 TTTATTTATA
849741 TAATATTAAAATTTTAATTT
1 TAATATTAAAATTTTAATTT
849761 TAATAATTAAAA-TTTAATTT
1 TAAT-ATTAAAATTTTAATTT
849781 CAAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATATTAAAATTTTAATTT
Found at i:849786 original size:21 final size:21
Alignment explanation
Indices: 849745--849788 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
849735 TTTATATAAT
*
849745 ATTAAAATTTTAATTTTAATA
1 ATTAAAATTTTAATTTAAATA
849766 ATTAAAA-TTTAATTTCAAATA
1 ATTAAAATTTTAATTT-AAATA
849787 AT
1 AT
849789 ATCAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAAATTTTAATTTAAATA
Found at i:851149 original size:16 final size:17
Alignment explanation
Indices: 851128--851166 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
851118 AAATCATTTG
851128 TAATTAAT-AATAATAA
1 TAATTAATAAATAATAA
*
851144 TAATTAATAAATTATAA
1 TAATTAATAAATAATAA
851161 T-ATTAA
1 TAATTAA
851167 ATTATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAATAAATAATAA
Found at i:851963 original size:19 final size:21
Alignment explanation
Indices: 851926--851964 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
851916 TTTGAGTGAT
*
851926 ATAAAATATAATATGTATTTG
1 ATAAAATATAATATATATTTG
851947 ATAAAAT-T-ATATATATTT
1 ATAAAATATAATATATATTT
851965 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
ATAAAATATAATATATATTTG
Found at i:851969 original size:16 final size:16
Alignment explanation
Indices: 851948--851981 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
851938 ATGTATTTGA
851948 TAAAATTATATATATT
1 TAAAATTATATATATT
* *
851964 TAAAATTTTTTATATT
1 TAAAATTATATATATT
851980 TA
1 TA
851982 TATATTAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAATTATATATATT
Found at i:852021 original size:21 final size:22
Alignment explanation
Indices: 851975--852021 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
851965 AAAATTTTTT
*
851975 ATATTTATATATTAAAAATATT
1 ATATTTATATATTAAAAATATA
*
851997 ATATTCTATAT-TTAAATATA-A
1 ATATT-TATATATTAAAAATATA
852018 ATAT
1 ATAT
852022 AAATATAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTATATATTAAAAATATA
Found at i:854317 original size:24 final size:25
Alignment explanation
Indices: 854266--854323 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
854256 TGGGTGGCTA
*
854266 GTCAACAAAAGTCACCATTTGTGTTT
1 GTCAACAAAAGCCACCA-TTGTGTTT
854292 GTCAACAAAAGCCACCA-TGTGTTT
1 GTCAACAAAAGCCACCATTGTGTTT
854316 GTCAACAA
1 GTCAACAA
854324 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
26 16 0.52
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (25 bp):
GTCAACAAAAGCCACCATTGTGTTT
Found at i:854352 original size:27 final size:27
Alignment explanation
Indices: 854313--854378 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
854303 CCACCATGTG
*
854313 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
854340 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
854367 TTTGTCAAAAAT
1 TTTGTCAAAAAT
854379 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:854408 original size:24 final size:24
Alignment explanation
Indices: 854340--854409 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
854330 TTACTTTGTA
* *
854340 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
854367 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
854391 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
854410 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:854481 original size:20 final size:20
Alignment explanation
Indices: 854456--854496 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
854446 AAAAGGAGGC
*
854456 TCCCTCCTCCCTCTCAAGCA
1 TCCCTCATCCCTCTCAAGCA
854476 TCCCTCATCCCTCTCAAGCA
1 TCCCTCATCCCTCTCAAGCA
854496 T
1 T
854497 TCTCTCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.51, G:0.05, T:0.27
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGCA
Found at i:858926 original size:24 final size:25
Alignment explanation
Indices: 858875--858932 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
858865 TGGGTGGCTA
858875 GTCAACAAAAGCCACCATTTGTGTTT
1 GTCAACAAAAGCCACCA-TTGTGTTT
858901 GTCAACAAAAGCCACCA-TGTGTTT
1 GTCAACAAAAGCCACCATTGTGTTT
858925 GTCAACAA
1 GTCAACAA
858933 TGGTGGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 15 0.47
26 17 0.53
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
GTCAACAAAAGCCACCATTGTGTTT
Found at i:858961 original size:27 final size:27
Alignment explanation
Indices: 858922--858987 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
858912 CCACCATGTG
*
858922 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
858949 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
858976 TTTGTCAAAAAT
1 TTTGTCAAAAAT
858988 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:859017 original size:24 final size:24
Alignment explanation
Indices: 858949--859018 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
858939 TTACTTTGTA
* *
858949 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
858976 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
859000 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
859019 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:859090 original size:20 final size:20
Alignment explanation
Indices: 859065--859105 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
859055 AAAAGGAGGC
*
859065 TCCCTCCTCCCTCTCAAGCA
1 TCCCTCATCCCTCTCAAGCA
859085 TCCCTCATCCCTCTCAAGCA
1 TCCCTCATCCCTCTCAAGCA
859105 T
1 T
859106 TCTCTCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.51, G:0.05, T:0.27
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGCA
Found at i:861220 original size:23 final size:23
Alignment explanation
Indices: 861171--861220 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
861161 AATATAAATA
*
861171 TAAATTTAAATTAAAAGTCTATC
1 TAAATTTAAATTAAAAGTCAATC
861194 TAAATTTAAATTAAAAGTTCAAT-
1 TAAATTTAAATTAAAAG-TCAATC
861217 TAAA
1 TAAA
861221 ATAAAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAATTTAAATTAAAAGTCAATC
Found at i:862060 original size:2 final size:2
Alignment explanation
Indices: 862055--862090 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
862045 ACTTTTTTTG
862055 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
862091 TAAAGGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:868470 original size:2 final size:2
Alignment explanation
Indices: 868419--868450 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
868409 ATTTTCCTTC
868419 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
868451 TGCGGCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:880645 original size:19 final size:21
Alignment explanation
Indices: 880599--880646 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
880589 ATTAATTATA
*
880599 TTTTATATTTTATATTTTAAT
1 TTTTATATTATATATTTTAAT
**
880620 TAGTATATTAT-TA-TTTAAT
1 TTTTATATTATATATTTTAAT
880639 TTTTATAT
1 TTTTATAT
880647 AAAAAATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 12 0.55
20 2 0.09
21 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATATTATATATTTTAAT
Found at i:880696 original size:7 final size:7
Alignment explanation
Indices: 880674--880708 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
880664 ATAAAATTAT
880674 AATTATTA
1 AATT-TTA
880682 AA-TTTA
1 AATTTTA
880688 AATTTTA
1 AATTTTA
880695 AATTTTA
1 AATTTTA
880702 AATTTTA
1 AATTTTA
880709 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.19
7 19 0.73
8 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTTA
Found at i:880701 original size:14 final size:13
Alignment explanation
Indices: 880659--880708 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
880649 AAAATATAAT
*
880659 AATTTATAAAATTA
1 AATTT-TAAATTTA
880673 TAATTATTAAATTTA
1 -AATT-TTAAATTTA
880688 AATTTTAAATTTTA
1 AATTTTAAA-TTTA
880702 AATTTTA
1 AATTTTA
880709 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.16
14 15 0.47
15 11 0.34
16 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:881470 original size:13 final size:14
Alignment explanation
Indices: 881420--881473 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
881410 TTATATATTT
881420 ATATTTAAATAT--
1 ATATTTAAATATAA
* *
881432 ATA-TTAGATATAG
1 ATATTTAAATATAA
881445 AT-TTTAAATATAA
1 ATATTTAAATATAA
881458 ATATTTAAA-ATAA
1 ATATTTAAATATAA
881471 ATA
1 ATA
881474 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 7 0.20
12 3 0.09
13 19 0.54
14 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (14 bp):
ATATTTAAATATAA
Found at i:881487 original size:17 final size:19
Alignment explanation
Indices: 881449--881484 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
881439 ATATAGATTT
*
881449 TAAATATAAATATTTAAAA
1 TAAATATAAAAATTTAAAA
881468 TAAATA-AAAAATTTAAA
1 TAAATATAAAAATTTAAA
881485 TAACCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATATAAAAATTTAAAA
Done.