Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 3 of 20
Found at i:861617 original size:27 final size:27
Alignment explanation
Indices: 861567--861627 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
861557 TATAAATTAT
861567 AAAAA-AAAATTTGATCTAAAATAA-A
1 AAAAATAAAATTTGATCTAAAATAATA
*
861592 AAAAATAAAGATTTGAT-TGAATATAATA
1 AAAAATAAA-ATTTGATCT-AAAATAATA
861620 AAATAATA
1 AAA-AATA
861628 TGGGTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 5 0.17
26 4 0.13
27 13 0.43
28 4 0.13
29 4 0.13
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (27 bp):
AAAAATAAAATTTGATCTAAAATAATA
Found at i:862419 original size:74 final size:74
Alignment explanation
Indices: 862298--862445 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
862288 ATGGACAGAA
* * *
862298 ACACTTATAGTTTTACCCCAAGTCCATACATAGTATTCTGCTGTAAAAGGAATACTTGTTTGTCT
1 ACACTTATAGTTTTACCCCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCT
862363 AAAAGGTTT
66 AAAAGGTTT
862372 ACACTTATAGTTTTACCCCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCT
1 ACACTTATAGTTTTACCCCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCT
862437 AAAAGGTTT
66 AAAAGGTTT
862446 CTTTATAGCC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (74 bp):
ACACTTATAGTTTTACCCCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCT
AAAAGGTTT
Found at i:862472 original size:74 final size:74
Alignment explanation
Indices: 862315--862461 Score: 190
Period size: 74 Copynumber: 2.0 Consensus size: 74
862305 TAGTTTTACC
* * *
862315 CCAAGTCCATACATAGTATTCTGCTGTAAAAGGAATACTTGTTTGTCTAAAAGGTTTACACTTAT
1 CCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCTAAAAGGTTTACACTTAT
**** *
862380 AGTTTTACC
66 AGCCAAACA
*
862389 CCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCTAAAAGGTTT-C-TTTAT
1 CCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCTAAAAGGTTTACACTTAT
862452 AGCCCAAACA
66 AG-CCAAACA
862462 ATCAATTCCA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 6 0.10
73 3 0.05
74 54 0.86
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (74 bp):
CCAACTCCATACACAGTATTCTGCTGTAAAAGGAATAATTGTTTGTCTAAAAGGTTTACACTTAT
AGCCAAACA
Found at i:862879 original size:31 final size:33
Alignment explanation
Indices: 862833--862893 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
862823 ATATAATACT
862833 TAAAATTTTTAATTAT-ATAAA-AAAATTTAAA
1 TAAAATTTTTAATTATGATAAATAAAATTTAAA
* *
862864 TAAATTTTTTTATTATGATAAATAAAATTT
1 TAAAATTTTTAATTATGATAAATAAAATTT
862894 TTATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 14 0.54
32 5 0.19
33 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (33 bp):
TAAAATTTTTAATTATGATAAATAAAATTTAAA
Found at i:862917 original size:31 final size:31
Alignment explanation
Indices: 862870--862956 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
862860 TAAATAAATT
*
862870 TTTTTATTATG-ATAAATAAAAT-TTTTATA
1 TTTTTATTTTGAATAAATAAAATCTTTTATA
**
862899 TTTTTATTTTGAACTAAAT-ATGTCTTTTATA
1 TTTTTATTTTGAA-TAAATAAAATCTTTTATA
* * *
862930 TTTTTATATTGAGTTAAATAAATTCTT
1 TTTTTATTTTGA-ATAAATAAAATCTT
862957 ATGACTAACA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 10 0.22
30 3 0.07
31 28 0.61
32 5 0.11
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTTTATTTTGAATAAATAAAATCTTTTATA
Found at i:866967 original size:6 final size:6
Alignment explanation
Indices: 866956--866980 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
866946 TGTTCCAAGG
866956 ATGATC ATGATC ATGATC ATGATC A
1 ATGATC ATGATC ATGATC ATGATC A
866981 AGAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ATGATC
Found at i:867233 original size:12 final size:12
Alignment explanation
Indices: 867200--867233 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
867190 CTGGGATTTC
*
867200 TCTTTCTTTCTT
1 TCTTTCTTTTTT
867212 TCTTTCTTTTTT
1 TCTTTCTTTTTT
*
867224 TTTTTCTTTT
1 TCTTTCTTTT
867234 ATCTTGCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTCTTTTTT
Found at i:874426 original size:31 final size:30
Alignment explanation
Indices: 874380--874455 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
874370 CCTTTATTCT
* *
874380 TAAAATTTTACATTAG-ACATAACATTTTAAA
1 TAAAATTTTAAATTAGTACA-AA-AATTTAAA
874411 -AAAACTTTTAAATTAGTTACAAAAATTTAAA
1 TAAAA-TTTTAAATTAG-TACAAAAATTTAAA
874442 TAAAATTTTAAATT
1 TAAAATTTTAAATT
874456 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 26 0.67
32 6 0.15
33 3 0.08
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAAATTTTAAATTAGTACAAAAATTTAAA
Found at i:874628 original size:13 final size:13
Alignment explanation
Indices: 874593--874641 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
874583 ATGTTAAAAT
874593 ATTATAATAA-ATA
1 ATTAT-ATAATATA
874606 ATTATATAATATA
1 ATTATATAATATA
*
874619 TTTATATAATATA
1 ATTATATAATATA
*
874632 ATAATATAAT
1 ATTATATAAT
874642 TTTATGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 4 0.12
13 28 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATATAATATA
Found at i:874639 original size:15 final size:15
Alignment explanation
Indices: 874590--874639 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
874580 ATTATGTTAA
874590 AATATTATAATA-AAT
1 AATA-TATAATATAAT
874605 AATTATATAATAT-AT
1 AA-TATATAATATAAT
*
874620 -TTATATAATATAAT
1 AATATATAATATAAT
874634 AATATA
1 AATATA
874640 ATTTTATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.34
14 2 0.07
15 15 0.52
16 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATAATATAAT
Found at i:874991 original size:27 final size:28
Alignment explanation
Indices: 874959--875036 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
874949 ATTATTAAAA
874959 AAATTTAAATAAATTTTTATTTTTA-TT
1 AAATTTAAATAAATTTTTATTTTTATTT
*
874986 AAATTTAATTAATATTTTATATTTTTATTTT
1 AAATTTAAATAA-ATTTT-TATTTTTA-TTT
* *
875017 GAA-TCAAATAAATTTTTATT
1 AAATTTAAATAAATTTTTATT
875037 ACTAATAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 11 0.26
28 9 0.21
29 13 0.30
30 6 0.14
31 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
AAATTTAAATAAATTTTTATTTTTATTT
Found at i:876882 original size:30 final size:30
Alignment explanation
Indices: 876816--876873 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
876806 TAATCAAGCT
876816 CTTATATCTTTATTTTAAGTCAAATAAACC
1 CTTATATCTTTATTTTAAGTCAAATAAACC
* *
876846 CTTATATTTTTATTTTGAGTCAAATAAA
1 CTTATATCTTTATTTTAAGTCAAATAAA
876874 TTTTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (30 bp):
CTTATATCTTTATTTTAAGTCAAATAAACC
Found at i:876929 original size:30 final size:29
Alignment explanation
Indices: 876893--876956 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
876883 AATCATCAAT
*
876893 TATAAGAATCTGGTTGACTCAAAATAAAAA
1 TATAAGAATCTAGTTGACTCAAAAT-AAAA
* * *
876923 TATAAGAGTTTATTTGACTCAAAATAAAA
1 TATAAGAATCTAGTTGACTCAAAATAAAA
876952 TATAA
1 TATAA
876957 AAGTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (29 bp):
TATAAGAATCTAGTTGACTCAAAATAAAA
Found at i:876961 original size:29 final size:30
Alignment explanation
Indices: 876906--876966 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
876896 AAGAATCTGG
*
876906 TTGACTCAAAATAAAAATATAAGAGTTTAT
1 TTGACTCAAAATAAAAATATAAAAGTTTAT
876936 TTGACTCAAAAT-AAAATATAAAAGTTTAT
1 TTGACTCAAAATAAAAATATAAAAGTTTAT
876965 TT
1 TT
876967 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (30 bp):
TTGACTCAAAATAAAAATATAAAAGTTTAT
Found at i:877177 original size:3 final size:3
Alignment explanation
Indices: 877169--877206 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
877159 ACATTATCAC
877169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
877207 CACAGGAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:889744 original size:117 final size:117
Alignment explanation
Indices: 889538--889773 Score: 454
Period size: 117 Copynumber: 2.0 Consensus size: 117
889528 AAGTATTACA
889538 ATGACAATGGCCTAGATCGAAGGGTATGCTTCATATATTGAAATAGATCATTCATCTCCTATTGA
1 ATGACAATGGCCTAGATCGAAGGGTATGCTTCATATATTGAAATAGATCATTCATCTCCTATTGA
889603 TTATGCATAAAACCCATCAAATGAAATGCATTGCGTAAATTGAAAATAATGT
66 TTATGCATAAAACCCATCAAATGAAATGCATTGCGTAAATTGAAAATAATGT
* *
889655 ATGACAATGGCCTAGATCGAGGGGTATGCTTCATATATTGAAATAGATCATTCATGTCCTATTGA
1 ATGACAATGGCCTAGATCGAAGGGTATGCTTCATATATTGAAATAGATCATTCATCTCCTATTGA
889720 TTATGCATAAAACCCATCAAATGAAATGCATTGCGTAAATTGAAAATAATGT
66 TTATGCATAAAACCCATCAAATGAAATGCATTGCGTAAATTGAAAATAATGT
889772 AT
1 AT
889774 CAAAGCACAT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (117 bp):
ATGACAATGGCCTAGATCGAAGGGTATGCTTCATATATTGAAATAGATCATTCATCTCCTATTGA
TTATGCATAAAACCCATCAAATGAAATGCATTGCGTAAATTGAAAATAATGT
Found at i:894938 original size:2 final size:2
Alignment explanation
Indices: 894931--894962 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
894921 TCTCTACAAT
894931 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
894963 ATTTCTATCA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:906636 original size:2 final size:2
Alignment explanation
Indices: 906629--906653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
906619 TATAAAACAA
906629 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
906654 ATCTCCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:911593 original size:24 final size:25
Alignment explanation
Indices: 911551--911600 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
911541 CGAAAGAAAA
*
911551 AAAAAAGTAAGATGAGAAGAAGGAG
1 AAAAAAGTAAGAAGAGAAGAAGGAG
*
911576 AAAAAGGTAAGAAG-GAAGAAGGAG
1 AAAAAAGTAAGAAGAGAAGAAGGAG
911600 A
1 A
911601 TGAAGACAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (25 bp):
AAAAAAGTAAGAAGAGAAGAAGGAG
Found at i:911611 original size:24 final size:23
Alignment explanation
Indices: 911565--911618 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
911555 AAGTAAGATG
**
911565 AGAAGAAGGAGAAAAAGGTAAGA
1 AGAAGAAGGAGAAAAAGACAAGA
**
911588 AGGAAGAAGGAGATGAAGACAAGA
1 A-GAAGAAGGAGAAAAAGACAAGA
911612 AGAAGAA
1 AGAAGAA
911619 AGTGCAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.59, C:0.02, G:0.35, T:0.04
Consensus pattern (23 bp):
AGAAGAAGGAGAAAAAGACAAGA
Found at i:912101 original size:54 final size:52
Alignment explanation
Indices: 912019--912123 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 52
912009 TTATCCAAAT
*
912019 TGACACTTAATTTTTCATGCTTTTATTATTTTATTTTAATGCAAGATCATAC
1 TGACACTTAATTTTTCATACTTTTATTATTTTATTTTAATGCAAGATCATAC
* *
912071 TGACACTTAATATTTTTTATACTTTTATTATTTTATTTTAATGTAAGATCATA
1 TGACACTT-A-ATTTTTCATACTTTTATTATTTTATTTTAATGCAAGATCATA
912124 TTTAAGAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 8 0.17
53 1 0.02
54 39 0.81
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (52 bp):
TGACACTTAATTTTTCATACTTTTATTATTTTATTTTAATGCAAGATCATAC
Found at i:913743 original size:19 final size:19
Alignment explanation
Indices: 913716--913752 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
913706 TCTAAAAACG
913716 TAAAAATATGTTATAAAAA
1 TAAAAATATGTTATAAAAA
* *
913735 TAAAGATATGTTTTAAAA
1 TAAAAATATGTTATAAAA
913753 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
TAAAAATATGTTATAAAAA
Found at i:923753 original size:12 final size:12
Alignment explanation
Indices: 923693--923754 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
923683 TTATGTACCT
*
923693 TATAGTTATTT-
1 TATAATTATTTA
*
923704 TTTAATTATTTA
1 TATAATTATTTA
* *
923716 TTTAATTATTTC
1 TATAATTATTTA
* *
923728 TATATTTCTTTA
1 TATAATTATTTA
*
923740 TACAATTATTTA
1 TATAATTATTTA
923752 TAT
1 TAT
923755 TTATATACTT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
11 9 0.23
12 30 0.77
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (12 bp):
TATAATTATTTA
Found at i:924458 original size:24 final size:24
Alignment explanation
Indices: 924422--924471 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
924412 TTAAAAAGGG
* *
924422 CAAACTATTCAATATCTTCCTATC
1 CAAACTATCCAATATATTCCTATC
924446 CAAACTATCCAATATATTCCTATC
1 CAAACTATCCAATATATTCCTATC
924470 CA
1 CA
924472 CTAAGTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (24 bp):
CAAACTATCCAATATATTCCTATC
Found at i:927413 original size:27 final size:28
Alignment explanation
Indices: 927376--927429 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
927366 TATCAATAAA
927376 ATTTAAATAAA-TTTTTATTTTTATTAC
1 ATTTAAATAAATTTTTTATTTTTATTAC
*
927403 ATTTAATTAAATTTTTTTATTTTTATT
1 ATTTAAATAAA-TTTTTTATTTTTATT
927430 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
29 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTAAATAAATTTTTTATTTTTATTAC
Found at i:927439 original size:26 final size:26
Alignment explanation
Indices: 927380--927440 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
927370 AATAAAATTT
*
927380 AAATAAA-TTTTTATTTTTATTACATTT
1 AAATAAATTTTTTATTTTTATT--ATTA
*
927407 AATTAAATTTTTTTATTTTTATT-TTA
1 AAATAAA-TTTTTTATTTTTATTATTA
927433 AAATAAAT
1 AAATAAAT
927441 AAACCCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 1 0.03
26 8 0.28
27 6 0.21
29 14 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
AAATAAATTTTTTATTTTTATTATTA
Found at i:927792 original size:21 final size:21
Alignment explanation
Indices: 927739--927793 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 21
927729 TAATAAGAAA
* *
927739 TAAATATTTATTTATATTTTT
1 TAAAAATTTATTTAAATTTTT
*
927760 T--AAA-TAATTTAAATTTTT
1 TAAAAATTTATTTAAATTTTT
927778 TAAAAATTTATTTAAA
1 TAAAAATTTATTTAAA
927794 AGAATCCCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 3 0.11
21 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAAATTTATTTAAATTTTT
Found at i:929163 original size:24 final size:23
Alignment explanation
Indices: 929108--929174 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
929098 ATTTTTGATT
929108 AATTTTAATATTAAAATATATTAA
1 AATTTTAATA-TAAAATATATTAA
* *
929132 AATATTAATATAAAATATTTTTAA
1 AATTTTAATATAAAATA-TATTAA
*
929156 TATTTTAATA-ATAAATATA
1 AATTTTAATATA-AAATATA
929175 ATTTAAAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTTAATATAAAATATATTAA
Found at i:929849 original size:20 final size:20
Alignment explanation
Indices: 929824--929862 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
929814 TCAATCCTTG
*
929824 TTCAAGTATGAGGGGGAATT
1 TTCAAGTATGAAGGGGAATT
929844 TTCAAGTATGAAGGGGAAT
1 TTCAAGTATGAAGGGGAAT
929863 AGAATCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.28
Consensus pattern (20 bp):
TTCAAGTATGAAGGGGAATT
Found at i:930901 original size:25 final size:25
Alignment explanation
Indices: 930872--930936 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
930862 ATTTTAATTT
930872 TAAAATATATTTAAAAATATTAATA
1 TAAAATATATTTAAAAATATTAATA
* * *
930897 TAAAATAT-TTTTAATATTTTAATA
1 TAAAATATATTTAAAAATATTAATA
930921 -ATAAATATAATTTAAA
1 TA-AAATAT-ATTTAAA
930937 GAGATCAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 19 0.58
25 8 0.24
26 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAAATATATTTAAAAATATTAATA
Found at i:937147 original size:19 final size:19
Alignment explanation
Indices: 937110--937146 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
937100 CAATGTTTGA
937110 CAAACCATTAAAAAATTTT
1 CAAACCATTAAAAAATTTT
*
937129 CAAATCATT-AAAAATTTT
1 CAAACCATTAAAAAATTTT
937147 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (19 bp):
CAAACCATTAAAAAATTTT
Found at i:940872 original size:21 final size:21
Alignment explanation
Indices: 940848--940890 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
940838 TATTTATTTT
940848 ATTTATACTAAAAAT-ATAAAA
1 ATTTA-ACTAAAAATAATAAAA
* *
940869 ATTTAATTAAATATAATAAAA
1 ATTTAACTAAAAATAATAAAA
940890 A
1 A
940891 ATATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAACTAAAAATAATAAAA
Found at i:944991 original size:2 final size:2
Alignment explanation
Indices: 944986--945016 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
944976 CCTCTCTCTT
944986 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 T
945017 TCCCCAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:945402 original size:2 final size:2
Alignment explanation
Indices: 945395--945437 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
945385 TTGTCACCAC
945395 CT CT CT CT CT CT C- 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 CT CT CT CT CT
945436 CT
1 CT
945438 TTGAGACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:957043 original size:29 final size:28
Alignment explanation
Indices: 957011--957091 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
957001 AAGAAGAATA
957011 ATTAGTGTAAATAAATTTTTATTTTTTTT
1 ATTAGT-TAAATAAATTTTTATTTTTTTT
* * *
957040 ATTACATTCAATTAAATTATTATACTTTTTTT
1 ATTA-GTT-AAATAAATT-TT-TATTTTTTTT
*
957072 -TTAGTTAAATAGATTTTTAT
1 ATTAGTTAAATAAATTTTTAT
957092 ATTGTAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
27 2 0.05
28 2 0.05
29 12 0.29
30 11 0.27
31 5 0.12
32 9 0.22
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (28 bp):
ATTAGTTAAATAAATTTTTATTTTTTTT
Found at i:957635 original size:2 final size:2
Alignment explanation
Indices: 957622--957656 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
957612 TTGTTTTTGG
*
957622 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
957657 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:960939 original size:7 final size:7
Alignment explanation
Indices: 960927--960955 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
960917 GAAGGGCACA
960927 CTGGAGG
1 CTGGAGG
960934 CTGGAGG
1 CTGGAGG
960941 CTGGAGG
1 CTGGAGG
960948 CTGGAGG
1 CTGGAGG
960955 C
1 C
960956 ATGCCTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.55, T:0.14
Consensus pattern (7 bp):
CTGGAGG
Found at i:969993 original size:14 final size:14
Alignment explanation
Indices: 969974--970000 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
969964 AGAAAAAAAA
969974 TTTCAAGTTCCTAT
1 TTTCAAGTTCCTAT
969988 TTTCAAGTTCCTA
1 TTTCAAGTTCCTA
970001 ACTGACAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTCAAGTTCCTAT
Found at i:973372 original size:22 final size:21
Alignment explanation
Indices: 973344--973401 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
973334 AACATAACTA
*
973344 GGTTGTAAGCATTGCTTGATTG
1 GGTTGTAAG-ATTGCATGATTG
*
973366 GGTTGTAGAGATTACATGATTG
1 GGTTGTA-AGATTGCATGATTG
*
973388 GGTTATAAGGATTG
1 GGTTGTAA-GATTG
973402 TGAGACTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 2 0.07
ACGTcount: A:0.24, C:0.05, G:0.33, T:0.38
Consensus pattern (21 bp):
GGTTGTAAGATTGCATGATTG
Found at i:973909 original size:28 final size:29
Alignment explanation
Indices: 973878--973932 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
973868 TTATTTAAAA
* *
973878 ATTTAAATAAATTTTTAT-TTTTTATTAT
1 ATTTAAATAAATCTTTATATATTTATTAT
*
973906 ATTTAATTAAATCTTTATATATTTATT
1 ATTTAAATAAATCTTTATATATTTATT
973933 GAGTCAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAATCTTTATATATTTATTAT
Found at i:992785 original size:16 final size:16
Alignment explanation
Indices: 992764--992804 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
992754 CGCAGCAAAG
992764 GAGAAAG-GAAGAGAAA
1 GAGAAAGAGAA-AGAAA
992780 GAGAAAGAGAAAGAAA
1 GAGAAAGAGAAAGAAA
*
992796 -AGGAAGAGA
1 GAGAAAGAGA
992805 GGGTTTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 12 0.52
17 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
GAGAAAGAGAAAGAAA
Found at i:993471 original size:12 final size:13
Alignment explanation
Indices: 993456--993497 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
993446 ATCAAAATTT
993456 TACATATATAT-A
1 TACATATATATAA
*
993468 TACATATATTTAA
1 TACATATATATAA
993481 TA-ATATATAATAA
1 TACATATAT-ATAA
993494 TACA
1 TACA
993498 ATAAACATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 16 0.64
13 8 0.32
14 1 0.04
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
TACATATATATAA
Found at i:994437 original size:18 final size:18
Alignment explanation
Indices: 994414--994453 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
994404 TACTTCTTGT
994414 CATGGATATGCCACGTGG
1 CATGGATATGCCACGTGG
*
994432 CATGGATATGCCATGTGG
1 CATGGATATGCCACGTGG
994450 CATG
1 CATG
994454 TTAGGGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (18 bp):
CATGGATATGCCACGTGG
Found at i:995026 original size:17 final size:17
Alignment explanation
Indices: 994982--995035 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
994972 CCTTAAGGGA
* *
994982 AAAAATGAGAAGAGAGAG
1 AAAAA-GAGAAAAGAAAG
995000 AAAAA-A-AAAAGAAAG
1 AAAAAGAGAAAAGAAAG
995015 AAAAAGAGAAAAGAAAAG
1 AAAAAGAGAAAAG-AAAG
995033 AAA
1 AAA
995036 CAAAAGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 12 0.39
16 2 0.06
17 5 0.16
18 12 0.39
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAAAGAGAAAAGAAAG
Found at i:995026 original size:22 final size:23
Alignment explanation
Indices: 994996--995040 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
994986 ATGAGAAGAG
*
994996 AGAGAAAAAAAAAAGAAAGAAAA
1 AGAGAAAAAAAAAAGAAACAAAA
*
995019 AGAG-AAAAGAAAAGAAACAAAA
1 AGAGAAAAAAAAAAGAAACAAAA
995041 GTAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (23 bp):
AGAGAAAAAAAAAAGAAACAAAA
Found at i:995027 original size:13 final size:13
Alignment explanation
Indices: 994996--995031 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
994986 ATGAGAAGAG
994996 AGAGAAAA-AAAA
1 AGAGAAAAGAAAA
995008 A-AG-AAAGAAAA
1 AGAGAAAAGAAAA
995019 AGAGAAAAGAAAA
1 AGAGAAAAGAAAA
995032 GAAACAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.14
11 7 0.33
12 3 0.14
13 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAGAAAAGAAAA
Found at i:995670 original size:39 final size:41
Alignment explanation
Indices: 995558--995671 Score: 119
Period size: 39 Copynumber: 2.8 Consensus size: 41
995548 CTATGCTTTT
* * *
995558 ACATTAGATTATATATTGCTTTTATTTCTTTTAGTAAGAGGAG
1 ACATTTGATTATATATTGCATTTATTT-TTTT-TTAAGAGGAG
* *
995601 ACATTTGATTATATATT--ATTTTTTTCTTTTTTTTA-A-GAG
1 ACATTTGATTATATATTGCA-TTTATT-TTTTTTTAAGAGGAG
995640 ACATTTGATTATATATTGCATTTATTTTTTTT
1 ACATTTGATTATATATTGCATTTATTTTTTTT
995672 CTTTTTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
39 26 0.43
40 6 0.10
41 3 0.05
42 9 0.15
43 17 0.28
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (41 bp):
ACATTTGATTATATATTGCATTTATTTTTTTTTAAGAGGAG
Found at i:1003521 original size:18 final size:18
Alignment explanation
Indices: 1003498--1003534 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1003488 CTAATTTTTG
1003498 TCTACACTAAACTCCCTT
1 TCTACACTAAACTCCCTT
1003516 TCTACACTAAACTCCCTT
1 TCTACACTAAACTCCCTT
1003534 T
1 T
1003535 TCCAAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (18 bp):
TCTACACTAAACTCCCTT
Found at i:1006124 original size:18 final size:18
Alignment explanation
Indices: 1006103--1006144 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1006093 TTTATTTTTG
1006103 AGTTAAATAAACTTTTAT
1 AGTTAAATAAACTTTTAT
1006121 AGTTAAATAAACTTTTAT
1 AGTTAAATAAACTTTTAT
1006139 AGTTAA
1 AGTTAA
1006145 TAGTTGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (18 bp):
AGTTAAATAAACTTTTAT
Found at i:1008552 original size:4 final size:4
Alignment explanation
Indices: 1008543--1008603 Score: 59
Period size: 4 Copynumber: 15.2 Consensus size: 4
1008533 TTTGTCACTC
* * * * *
1008543 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
1008591 ATGT ATGT ATAT A
1 ATAT ATAT ATAT A
1008604 CTGTTGAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:1008566 original size:18 final size:18
Alignment explanation
Indices: 1008543--1008603 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
1008533 TTTGTCACTC
* *
1008543 ATATATATATATATATAT
1 ATATATATATGTATGTAT
*
1008561 ATATATGTATGTATGTAT
1 ATATATATATGTATGTAT
*
1008579 GTATATATATGTATGTAT
1 ATATATATATGTATGTAT
*
1008597 GTATATA
1 ATATATA
1008604 CTGTTGAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
ATATATATATGTATGTAT
Found at i:1008586 original size:22 final size:22
Alignment explanation
Indices: 1008558--1008600 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1008548 TATATATATA
1008558 TATATATATGTATGTATGTATG
1 TATATATATGTATGTATGTATG
1008580 TATATATATGTATGTATGTAT
1 TATATATATGTATGTATGTAT
1008601 ATACTGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATATATATGTATGTATGTATG
Found at i:1012765 original size:29 final size:30
Alignment explanation
Indices: 1012704--1012768 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1012694 TAATTGACTA
* *
1012704 AAAAAAATAAAAATTTATTTAACTTAAAAT
1 AAAAATATAAAAATTTATTTAACATAAAAT
* **
1012734 AAAAATATTAAAATTTATTTAA-ATAATTT
1 AAAAATATAAAAATTTATTTAACATAAAAT
1012763 AAAAAT
1 AAAAAT
1012769 CTTTTTAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAAATATAAAAATTTATTTAACATAAAAT
Found at i:1012866 original size:3 final size:3
Alignment explanation
Indices: 1012858--1012907 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1012848 ATGGGAAGGG
*
1012858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1012906 AT
1 AT
1012908 AATAGCCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1013336 original size:2 final size:2
Alignment explanation
Indices: 1013324--1013353 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1013314 TGCTACCAAA
1013324 AT AT A- 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
1013354 AATTTCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1013575 original size:29 final size:29
Alignment explanation
Indices: 1013512--1013567 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1013502 TTATAATGAA
1013512 TTTAAATAAATTTTTATTTTCTTATTACG
1 TTTAAATAAATTTTTATTTTCTTATTACG
*
1013541 TTTAAATAAATTTTTATTTTTTTATTA
1 TTTAAATAAATTTTTATTTTCTTATTA
1013568 TTTATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTAAATAAATTTTTATTTTCTTATTACG
Found at i:1013803 original size:30 final size:30
Alignment explanation
Indices: 1013768--1013845 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
1013758 AATCATTAGT
1013768 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTTAAAATAAAAA
* *
1013798 TATAAAAATTTAATTGAA--TATAATAAAAA
1 TATAAAAATTT-ATTTAATTTAAAATAAAAA
*
1013827 -ATAAAGATTTATTTAATTT
1 TATAAAAATTTATTTAATTT
1013846 TTTTAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 9 0.22
29 11 0.27
30 11 0.27
31 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTTAAAATAAAAA
Found at i:1021051 original size:16 final size:17
Alignment explanation
Indices: 1021020--1021054 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1021010 GATGTGATAA
1021020 TATTTTTTAAATAATTT
1 TATTTTTTAAATAATTT
*
1021037 TATTTTTTATA-AATTT
1 TATTTTTTAAATAATTT
1021053 TA
1 TA
1021055 AAAATTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTTAAATAATTT
Found at i:1030493 original size:27 final size:27
Alignment explanation
Indices: 1030451--1030504 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1030441 CCTTGTGGTG
*
1030451 GCTGGAAGATAGTGTTCTTTATGAATT
1 GCTGGAAGATACTGTTCTTTATGAATT
1030478 GCTGGAAGATACTGTTCTTTATGAATT
1 GCTGGAAGATACTGTTCTTTATGAATT
1030505 TAATTCATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (27 bp):
GCTGGAAGATACTGTTCTTTATGAATT
Found at i:1052239 original size:19 final size:19
Alignment explanation
Indices: 1052217--1052259 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1052207 AACTCTATTC
*
1052217 AATTTTATTCAAATTTTTA
1 AATTTTATTAAAATTTTTA
*
1052236 AATTTTTTTAAAATTTTTA
1 AATTTTATTAAAATTTTTA
1052255 AATTT
1 AATTT
1052260 ATCCACCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTATTAAAATTTTTA
Found at i:1053875 original size:17 final size:19
Alignment explanation
Indices: 1053853--1053888 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1053843 TACCTTTTCT
1053853 TTTTTATTA-A-TTTAAAA
1 TTTTTATTATACTTTAAAA
1053870 TTTTTATTATACTTTAAAA
1 TTTTTATTATACTTTAAAA
1053889 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTATTATACTTTAAAA
Found at i:1061349 original size:31 final size:29
Alignment explanation
Indices: 1061294--1061363 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
1061284 CACCATATTA
1061294 GTGCCACATGGCATTACAGGTCATCACGTTC
1 GTGCCACATGGCATTACA-GTCATCACG-TC
* *
1061325 GTGCCACATGGCATGTCACA-TCATCATGTG
1 GTGCCACATGGCAT-T-ACAGTCATCACGTC
1061355 GTGCCACAT
1 GTGCCACAT
1061364 CATCAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 10 0.29
31 21 0.60
32 1 0.03
33 3 0.09
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (29 bp):
GTGCCACATGGCATTACAGTCATCACGTC
Found at i:1063047 original size:90 final size:90
Alignment explanation
Indices: 1062876--1063053 Score: 234
Period size: 90 Copynumber: 2.0 Consensus size: 90
1062866 CTAATCTCTC
* *
1062876 AAGTTTTAGTATTATTTTGTTTTCCTCATCTTCAAGCTTCAAAAAGATTTCAATGATTAGTCTTT
1 AAGTTTTAGTATTATTTTGTTTTCATCATCTCCAAGCTTCAAAAAGATTTCAATGATTAGTCTTT
* *
1062941 GATTTTTAATTTTAGCAAATCAGAT
66 GATTTCTAATTATAGCAAATCAGAT
* * * *
1062966 AAGTGTTT-GTATTATTTTGTTTTCATCATCTCCAAGCTTTAAAAGGATTTCAATGCTTGGTCTT
1 AAGT-TTTAGTATTATTTTGTTTTCATCATCTCCAAGCTTCAAAAAGATTTCAATGATTAGTCTT
**
1063030 T-AGTTTCTGGTTATAGCAAATCAG
65 TGA-TTTCTAATTATAGCAAATCAG
1063054 GTAAAAAACT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
89 1 0.01
90 72 0.95
91 3 0.04
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.46
Consensus pattern (90 bp):
AAGTTTTAGTATTATTTTGTTTTCATCATCTCCAAGCTTCAAAAAGATTTCAATGATTAGTCTTT
GATTTCTAATTATAGCAAATCAGAT
Found at i:1063362 original size:27 final size:27
Alignment explanation
Indices: 1063285--1063363 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
1063275 AATTCTAAGA
* * *
1063285 ATAATTTTATCCACCAGAAGTAGATGT
1 ATAACTTTATCCACCAGAAGTGGATGG
** *
1063312 ATAACTTTATCCATTAGAAATGGATGG
1 ATAACTTTATCCACCAGAAGTGGATGG
* *
1063339 GTAACTTTACCCACCAGAAGTGGAT
1 ATAACTTTATCCACCAGAAGTGGAT
1063364 AAGTACTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (27 bp):
ATAACTTTATCCACCAGAAGTGGATGG
Found at i:1063845 original size:27 final size:26
Alignment explanation
Indices: 1063798--1063852 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1063788 AAGATATTTT
1063798 TATATGTTTTTATTATATTTAAATAA
1 TATATGTTTTTATTATATTTAAATAA
* *
1063824 TATATTTTTATTATGTAT-TTTAATTAA
1 TATATGTTT-TTAT-TATATTTAAATAA
1063851 TA
1 TA
1063853 AATTATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 14 0.56
28 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
TATATGTTTTTATTATATTTAAATAA
Found at i:1063855 original size:34 final size:33
Alignment explanation
Indices: 1063791--1063862 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 33
1063781 TATCATGAAG
1063791 ATATTTTTATATGTTTTTATTATATTTAAATAAT
1 ATATTTTTATATGTTTTTATTATA-TTAAATAAT
*
1063825 ATATTTTTATTATGTATTTTAATTA-A-TAAATTAT
1 ATATTTTTA-TATGT-TTTT-ATTATATTAAATAAT
1063859 ATAT
1 ATAT
1063863 GTAATGCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
34 20 0.59
35 5 0.15
36 5 0.15
37 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (33 bp):
ATATTTTTATATGTTTTTATTATATTAAATAAT
Found at i:1065297 original size:44 final size:42
Alignment explanation
Indices: 1065177--1065297 Score: 140
Period size: 42 Copynumber: 2.8 Consensus size: 42
1065167 TATTAAATTT
* *
1065177 ACAAGTTCAACTAATATATATTAATTTTACATTTATTACTTC
1 ACAAGTTCAACTAATATAAATTAATTTTACATTTATAACTTC
*
1065219 ACAAGTTCAACTAATATAAA--AATTTTACATATT-TAAATTTGC
1 ACAAGTTCAACTAATATAAATTAATTTTACAT-TTAT-AACTT-C
*
1065261 ATCATAGTTCGACTAATATAAATTAATTTTACATTTA
1 A-CA-AGTTCAACTAATATAAATTAATTTTACATTTA
1065298 GTAGTTTACG
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
40 11 0.16
41 5 0.07
42 21 0.31
43 2 0.03
44 16 0.24
45 2 0.03
46 10 0.15
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.42
Consensus pattern (42 bp):
ACAAGTTCAACTAATATAAATTAATTTTACATTTATAACTTC
Found at i:1071273 original size:1 final size:1
Alignment explanation
Indices: 1071269--1071310 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
1071259 TTTTTTGAAA
* *
1071269 GGGGGGGGGGGGGGGGGGGGGGGGTGGGGGAGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1071311 TTTGTTGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.95, T:0.02
Consensus pattern (1 bp):
G
Found at i:1074999 original size:16 final size:17
Alignment explanation
Indices: 1074969--1075001 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1074959 AGACTTTTAG
*
1074969 TTTAGTTTTATTTAATT
1 TTTAGTTTTAATTAATT
1074986 TTTAG-TTTAATTAATT
1 TTTAGTTTTAATTAATT
1075002 AATTGATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTAGTTTTAATTAATT
Found at i:1079018 original size:20 final size:21
Alignment explanation
Indices: 1078974--1079018 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1078964 GGGGGACGGG
**
1078974 CTTTTTTTTATTATTTTTTCC
1 CTTTTTTTTATTATTCCTTCC
*
1078995 CTTTTTTTT-TTATTCCTTCT
1 CTTTTTTTTATTATTCCTTCC
1079015 CTTT
1 CTTT
1079019 GCTTCAGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
CTTTTTTTTATTATTCCTTCC
Found at i:1079229 original size:18 final size:16
Alignment explanation
Indices: 1079186--1079224 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1079176 ATTTTTTATT
1079186 TTTTATTATATTTAATTA
1 TTTTATTATATTT--TTA
*
1079204 ATTTATTATATTTTTA
1 TTTTATTATATTTTTA
1079220 TTTTA
1 TTTTA
1079225 AATTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATTATATTTTTA
Found at i:1079236 original size:30 final size:28
Alignment explanation
Indices: 1079171--1079237 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 28
1079161 TAAAAATATA
* *
1079171 TAAAT-ATTTTTTATTTTTTATTATATT
1 TAAATAATTTATTATTTTTTATTATAAT
* *
1079198 TAATTAATTTATTATATTTTTATTTTAAAT
1 TAAATAATTTATTAT-TTTTTATTAT-AAT
1079228 TAAATAATTT
1 TAAATAATTT
1079238 TTTAATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.12
28 8 0.25
29 9 0.28
30 11 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TAAATAATTTATTATTTTTTATTATAAT
Found at i:1079237 original size:15 final size:14
Alignment explanation
Indices: 1079219--1079262 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
1079209 TTATATTTTT
1079219 ATTTTAAATTAAATA
1 ATTTT-AATTAAATA
1079234 ATTTTTTAATTAAATA
1 A--TTTTAATTAAATA
1079250 ATTATTAATTAAA
1 ATT-TTAATTAAA
1079263 ATATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 10 0.38
17 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTAATTAAATA
Found at i:1079239 original size:16 final size:15
Alignment explanation
Indices: 1079219--1079262 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
1079209 TTATATTTTT
*
1079219 ATTTTAAATTAAATA
1 ATTTTTAATTAAATA
1079234 ATTTTTTAATTAAATA
1 A-TTTTTAATTAAATA
*
1079250 ATTATTAATTAAA
1 ATTTTTAATTAAA
1079263 ATATTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAATTAAATA
Found at i:1079270 original size:15 final size:15
Alignment explanation
Indices: 1079225--1079262 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1079215 TTTTATTTTA
*
1079225 AATTAAATAATTTTTT
1 AATTAAATAA-TTATT
1079241 AATTAAATAATTATT
1 AATTAAATAATTATT
1079256 AATTAAA
1 AATTAAA
1079263 ATATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:1079438 original size:21 final size:21
Alignment explanation
Indices: 1079412--1079452 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1079402 AATTTATATA
1079412 AATTTAAAATAAA-ATAATAAT
1 AATTT-AAATAAATATAATAAT
*
1079433 AATTTAATTAAATATAATAA
1 AATTTAAATAAATATAATAA
1079453 AAATCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTAAATAAATATAATAAT
Found at i:1096540 original size:7 final size:7
Alignment explanation
Indices: 1096529--1096568 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1096519 TTTTTTTTTT
1096529 TGGGGGG
1 TGGGGGG
1096536 -GGGGGG
1 TGGGGGG
*
1096542 GGGGGGG
1 TGGGGGG
*
1096549 TGGTGGG
1 TGGGGGG
1096556 TGGGGGG
1 TGGGGGG
1096563 TGGGGG
1 TGGGGG
1096569 TCACAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.00, C:0.00, G:0.88, T:0.12
Consensus pattern (7 bp):
TGGGGGG
Found at i:1099081 original size:4 final size:4
Alignment explanation
Indices: 1099074--1099102 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1099064 TCTCTCTCTC
1099074 TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1099103 ATAGCACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:1110066 original size:19 final size:20
Alignment explanation
Indices: 1110030--1110067 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1110020 AAATTTGATT
* *
1110030 AAAATAATTTTTAGTTTTTG
1 AAAATAATTTATAATTTTTG
1110050 AAAAT-ATTTATAATTTTT
1 AAAATAATTTATAATTTTT
1110068 ACTCATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AAAATAATTTATAATTTTTG
Found at i:1122832 original size:31 final size:30
Alignment explanation
Indices: 1122794--1122910 Score: 82
Period size: 30 Copynumber: 3.9 Consensus size: 30
1122784 TTAAGACAAC
1122794 TCTTGTCTTTAATTAGGACAAAAATATTTTA
1 TCTTGTC-TTAATTAGGACAAAAATATTTTA
* * *
1122825 TCTTGTCTAAATT-GAGACAAATATGTTTTA
1 TCTTGTCTTAATTAG-GACAAAAATATTTTA
* *
1122855 --TTATC-TAGATTAAGACAAAAAATATTTT-
1 TCTTGTCTTA-ATTAGGAC-AAAAATATTTTA
* * *
1122883 TCTTGTTTTAAATTATGACAAACATATT
1 TCTTGTCTT-AATTAGGACAAAAATATT
1122911 CTCTTGTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
27 1 0.02
28 10 0.15
29 10 0.15
30 29 0.44
31 15 0.23
32 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
TCTTGTCTTAATTAGGACAAAAATATTTTA
Found at i:1122924 original size:28 final size:28
Alignment explanation
Indices: 1122863--1122964 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 28
1122853 TATTATCTAG
* *
1122863 ATTAAGACAAAAAATATTTTTCTTGTTTTAA
1 ATTAAGAC-AAACATA-TTCTCTTG-TTTAA
*
1122894 ATTATGACAAACATATTCTCTTGTTTAA
1 ATTAAGACAAACATATTCTCTTGTTTAA
* * *
1122922 ATTAAGACCAAACATGTTTTCTTGTCTAA
1 ATTAAGA-CAAACATATTCTCTTGTTTAA
1122951 ATTAAGACAAACAT
1 ATTAAGACAAACAT
1122965 GTTAAAGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 18 0.29
29 32 0.51
30 6 0.10
31 7 0.11
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (28 bp):
ATTAAGACAAACATATTCTCTTGTTTAA
Found at i:1122926 original size:59 final size:56
Alignment explanation
Indices: 1122793--1122964 Score: 157
Period size: 59 Copynumber: 2.9 Consensus size: 56
1122783 TTTAAGACAA
* * * *
1122793 CTCTTGTCTTTAATTAGGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTT
1 CTCTTGT-TTAAATTAAGACAAAAATATTTT-TCTTGTCTAAATT-AGACAAACATATT
* * * * * *
1122852 TTATTATCTAGATTAAGACAAAAAATATTTTTCTTGTTTTAAATTATGACAAACATATT
1 CTCTTGTTTAAATTAAGAC-AAAAATATTTTTCTTG-TCTAAATTA-GACAAACATATT
* *
1122911 CTCTTGTTTAAATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACAT
1 CTCTTGTTTAAATTAAGA-CAAAAATATTTTTCTTGTCTAAATT-AGACAAACAT
1122965 GTTAAAGTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
57 16 0.18
58 23 0.26
59 50 0.56
60 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (56 bp):
CTCTTGTTTAAATTAAGACAAAAATATTTTTCTTGTCTAAATTAGACAAACATATT
Found at i:1124857 original size:16 final size:17
Alignment explanation
Indices: 1124822--1124858 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1124812 TGCTAATTAC
1124822 TTTAGATGAAGTTTTCT
1 TTTAGATGAAGTTTTCT
1124839 TTTAGATGAAGTTTT-T
1 TTTAGATGAAGTTTTCT
1124855 TTTA
1 TTTA
1124859 TTTTTCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (17 bp):
TTTAGATGAAGTTTTCT
Found at i:1126628 original size:60 final size:60
Alignment explanation
Indices: 1126514--1126681 Score: 185
Period size: 60 Copynumber: 2.8 Consensus size: 60
1126504 TAAGGAGTTC
* * * * **
1126514 CCACGAGTCGATAAAAGGGGATTTGAAGCCTAGTCTCATATTTGGTGGTGTGGGGAATTT
1 CCACGAGTAGGTAAAAGGGGATTTAAAGCCTAGACTCATATTTGGTGGCATGGGGAATTT
*
1126574 CCACGAGTAGGTAAAAGGGGATTTAAAG-CTCAGACTCATATTTGGTGGCATGGGGAGTTT
1 CCACGAGTAGGTAAAAGGGGATTTAAAGCCT-AGACTCATATTTGGTGGCATGGGGAATTT
* * ** ** * *
1126634 TCACAAGTAGGTAAAAAAGGACCTGAAGCCTTGACTCATATTTGGTGG
1 CCACGAGTAGGTAAAAGGGGATTTAAAGCCTAGACTCATATTTGGTGG
1126682 GGTAAAGAGA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
59 2 0.02
60 87 0.96
61 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (60 bp):
CCACGAGTAGGTAAAAGGGGATTTAAAGCCTAGACTCATATTTGGTGGCATGGGGAATTT
Found at i:1126717 original size:60 final size:59
Alignment explanation
Indices: 1126465--1126717 Score: 172
Period size: 60 Copynumber: 4.2 Consensus size: 59
1126455 TATTTGATAA
* * * * *
1126465 TAAAGGGGGAACTGAAGCCTCA-ACTTATATTTGGTGAGGTAAGGAG-TTCCCACGAGTCGA
1 TAAA-GGGGACCTGAAGCCT-AGACTCATATTTGGTGGGGTAAGGAGATT-CCACGAGTAGG
** * * **
1126525 TAAAAGGGGATTTGAAGCCTAGTCTCATATTTGGTGGTGTGGGGA-ATTTCCACGAGTAGG
1 T-AAAGGGGACCTGAAGCCTAGACTCATATTTGGTGGGGTAAGGAGA-TTCCACGAGTAGG
** * ** ** * * *
1126585 TAAAAGGGGATTTAAAG-CTCAGACTCATATTTGGTGGCATGGGGAGTTTTCACAAGTAGG
1 T-AAAGGGGACCTGAAGCCT-AGACTCATATTTGGTGGGGTAAGGAGATTCCACGAGTAGG
** * *
1126645 TAAAAAAGGACCTGAAGCCTTGACTCATATTTGGTGGGGTAAAGAGATTCCACGAGTAGG
1 T-AAAGGGGACCTGAAGCCTAGACTCATATTTGGTGGGGTAAGGAGATTCCACGAGTAGG
1126705 TAAAGGGAGACCT
1 TAAAGGG-GACCT
1126718 AAAAACCCAA
Statistics
Matches: 152, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
59 7 0.05
60 138 0.91
61 7 0.05
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (59 bp):
TAAAGGGGACCTGAAGCCTAGACTCATATTTGGTGGGGTAAGGAGATTCCACGAGTAGG
Found at i:1129528 original size:53 final size:53
Alignment explanation
Indices: 1129469--1129587 Score: 238
Period size: 53 Copynumber: 2.2 Consensus size: 53
1129459 TACCCAACAC
1129469 AAACTTTGGAAAGGAAAGATCGACTAAGGAAAGAAAGGATTAACCCAAGATAT
1 AAACTTTGGAAAGGAAAGATCGACTAAGGAAAGAAAGGATTAACCCAAGATAT
1129522 AAACTTTGGAAAGGAAAGATCGACTAAGGAAAGAAAGGATTAACCCAAGATAT
1 AAACTTTGGAAAGGAAAGATCGACTAAGGAAAGAAAGGATTAACCCAAGATAT
1129575 AAACTTTGGAAAG
1 AAACTTTGGAAAG
1129588 ATAGGACGAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.18
Consensus pattern (53 bp):
AAACTTTGGAAAGGAAAGATCGACTAAGGAAAGAAAGGATTAACCCAAGATAT
Found at i:1150775 original size:30 final size:31
Alignment explanation
Indices: 1150741--1150799 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1150731 ACATATACAA
* *
1150741 ATATGATTAATAAATATA-TAATACGACATG
1 ATATGAATAACAAATATATTAATACGACATG
* *
1150771 ATATGAATAACACATATATTAATATGACA
1 ATATGAATAACAAATATATTAATACGACA
1150800 GGTTAAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (31 bp):
ATATGAATAACAAATATATTAATACGACATG
Found at i:1150897 original size:20 final size:20
Alignment explanation
Indices: 1150844--1150903 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
1150834 AATTAAAATT
*
1150844 TATATAA-TT-TATGATTTA
1 TATATAATTTATATGATTAA
* *
1150862 TTTATACGATTGATATGATTAA
1 TATATA--ATTTATATGATTAA
*
1150884 TATATAATTTATATAATTAA
1 TATATAATTTATATGATTAA
1150904 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 5 0.16
20 13 0.41
21 1 0.03
22 13 0.41
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (20 bp):
TATATAATTTATATGATTAA
Found at i:1150968 original size:29 final size:28
Alignment explanation
Indices: 1150935--1150993 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
1150925 ATATAATTTT
* * *
1150935 AATATTTAAATTTATAATAAAAAATTATA
1 AATATTAAAATATATAA-AAAAAATAATA
*
1150964 AATATTAAAATATATAAAAAATATAATA
1 AATATTAAAATATATAAAAAAAATAATA
1150992 AA
1 AA
1150994 CTTTAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATTAAAATATATAAAAAAAATAATA
Found at i:1150986 original size:11 final size:12
Alignment explanation
Indices: 1150947--1150993 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1150937 TATTTAAATT
1150947 TATAATAAAAAA
1 TATAATAAAAAA
*
1150959 TTATAAATATTAAAA
1 -TAT-AATA-AAAAA
1150974 TAT-ATAAAAAA
1 TATAATAAAAAA
1150985 TATAATAAA
1 TATAATAAA
1150994 CTTTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 7 0.24
12 8 0.28
13 3 0.10
14 7 0.24
15 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TATAATAAAAAA
Found at i:1164458 original size:26 final size:26
Alignment explanation
Indices: 1164392--1164501 Score: 106
Period size: 26 Copynumber: 4.3 Consensus size: 26
1164382 ATTGCAACAG
*
1164392 TTTTTT-AACATAACGTGTAATAATTTT
1 TTTTTTCAACATGACGTGTAATAA--TT
1164419 TTCTTTTCAACATGACGTGT-ATAACTT
1 TT-TTTTCAACATGACGTGTAATAA-TT
1164446 TTTTTTCAACATGA--TGTATATAA-T
1 TTTTTTCAACATGACGTGTA-ATAATT
* *
1164470 TTTTTT-AATATGATGTGTAATAATT
1 TTTTTTCAACATGACGTGTAATAATT
1164495 TTTTTTC
1 TTTTTTC
1164502 CATTATGACG
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
23 6 0.08
24 14 0.19
25 11 0.15
26 16 0.22
27 6 0.08
28 8 0.11
29 11 0.15
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTTTCAACATGACGTGTAATAATT
Found at i:1164463 original size:24 final size:26
Alignment explanation
Indices: 1164392--1164501 Score: 81
Period size: 24 Copynumber: 4.3 Consensus size: 26
1164382 ATTGCAACAG
*
1164392 TTTTTT-AACATAACGTGTA-ATAATTTT
1 TTTTTTCAACATGAC-TGTATATAA--TT
*
1164419 TTCTTTTCAACATGACGTGTATA-ACTT
1 TT-TTTTCAACATGAC-TGTATATAATT
1164446 TTTTTTCAACATGA-TGTATATAA-T
1 TTTTTTCAACATGACTGTATATAATT
* *
1164470 TTTTTT-AATATGA-TGTGTAATAATT
1 TTTTTTCAACATGACTGTAT-ATAATT
1164495 TTTTTTC
1 TTTTTTC
1164502 CATTATGACG
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
23 10 0.14
24 17 0.24
25 8 0.11
26 12 0.17
27 6 0.08
28 4 0.06
29 13 0.18
30 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTTTCAACATGACTGTATATAATT
Found at i:1164482 original size:23 final size:25
Alignment explanation
Indices: 1164422--1164499 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 25
1164412 TAATTTTTTC
1164422 TTTTCAACATGACGTGTATAACT--TTT
1 TTTTCAACATGA--TGTATAA-TAATTT
1164448 TTTTCAACATGATGTAT-ATAATTT
1 TTTTCAACATGATGTATAATAATTT
* *
1164472 TTTT-AATATGATGTGTAATAATTT
1 TTTTCAACATGATGTATAATAATTT
1164496 TTTT
1 TTTT
1164500 TCCATTATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.02
23 11 0.23
24 23 0.49
26 12 0.26
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (25 bp):
TTTTCAACATGATGTATAATAATTT
Found at i:1164629 original size:25 final size:25
Alignment explanation
Indices: 1164598--1164665 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
1164588 GACGTTTAAT
1164598 AACTTTTTTATAATATGGCATGTAAC
1 AACTTTTTT-TAATATGGCATGTAAC
* * *
1164624 AATTTTTTTTTAATATGGTATGTAAT
1 AA-CTTTTTTTAATATGGCATGTAAC
*
1164650 AACTTCTTTTAATATG
1 AACTTTTTTTAATATG
1164666 CTGCGTAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 12 0.33
26 18 0.50
27 6 0.17
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.50
Consensus pattern (25 bp):
AACTTTTTTTAATATGGCATGTAAC
Found at i:1164630 original size:26 final size:25
Alignment explanation
Indices: 1164601--1164681 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
1164591 GTTTAATAAC
*
1164601 TTTTTTATAATATGGCATGTAACAA
1 TTTTTTTTAATATGGCATGTAACAA
* *
1164626 TTTTTTTTTAATATGGTATGTAATAA
1 -TTTTTTTTAATATGGCATGTAACAA
* *
1164652 CTTCTTTTAATAT-GC-TGCGTAACAA
1 TTTTTTTTAATATGGCAT--GTAACAA
1164677 TTTTT
1 TTTTT
1164682 ATTTTCAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 20 0.45
26 22 0.50
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (25 bp):
TTTTTTTTAATATGGCATGTAACAA
Found at i:1165997 original size:55 final size:52
Alignment explanation
Indices: 1165928--1166036 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 52
1165918 CAAGCACAAT
* * * *
1165928 TTACAATACTTAATGTGAAAATTTAATGTTAATTTTTCAGTTTGCTTTATGTCTA
1 TTACAATACCTAATGTGAAAATCTAATATTAATTTTT---TTTACTTTATGTCTA
*
1165983 TTACAATGCCTAATGTGAAAATCTAATATTAATTTTTTTTACTTTATGTCTA
1 TTACAATACCTAATGTGAAAATCTAATATTAATTTTTTTTACTTTATGTCTA
1166035 TT
1 TT
1166037 TATATTGGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 16 0.33
55 33 0.67
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (52 bp):
TTACAATACCTAATGTGAAAATCTAATATTAATTTTTTTTACTTTATGTCTA
Found at i:1166094 original size:18 final size:19
Alignment explanation
Indices: 1166063--1166104 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1166053 AAAACTTATA
*
1166063 TTTAAATTATTAATGAAAT
1 TTTATATTATTAATGAAAT
**
1166082 TTTATATTA-TAATTTAAT
1 TTTATATTATTAATGAAAT
1166100 TTTAT
1 TTTAT
1166105 TTTAAAAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATATTATTAATGAAAT
Found at i:1171385 original size:277 final size:278
Alignment explanation
Indices: 1170943--1171502 Score: 937
Period size: 277 Copynumber: 2.0 Consensus size: 278
1170933 ATTTAGTTGT
* *
1170943 AACTTTAAATAAGCTAAAGCTACGGTGTACTAGCTTGTTTATTGAGCTTTTATTGATAAATAAAA
1 AACTTTAAAGAAGCTAAAGCTACGGTGTACTAGCTTGCTTATTGAGCTTTTATTGATAAATAAAA
1171008 GTTTCATATTTTTTTAAAAAAATATATTATTTATAAGATGTTACTATTTAAAATAAAAACATAAA
66 GTTTCATATTTTTTTAAAAAAATATATTATTTATAAGATGTTACTATTTAAAATAAAAACATAAA
* **
1171073 AATTTGATTAAACAAATAAAAAATAAAAATAATTTTAAAGTTCTTAAATAATTTAAGATTTTTTT
131 AATTTGATTAAACAAATAAAAAATAAAAATAATTTTAAAATTCTTAAATAATTTAAGATTTAATT
* * *
1171138 AAATGTATATCTATTTAATTTAAGTTCAAACTATTTAGAATTAGAA-TTTTTTTGGGTCATGTTA
196 AAATATATATCTATTTAATTGAAGTTCAAACTATTTAGAATTAGAATTTTTTTTGGGTCATGCTA
1171202 TGCACTTTCATTGAATCC
261 TGCACTTTCATTGAATCC
1171220 AACTTTAAAGAAGCTAAAGCTACGGTGTACTAGCTTGCTTATTGAGCTTTTATTGATAAATAAAA
1 AACTTTAAAGAAGCTAAAGCTACGGTGTACTAGCTTGCTTATTGAGCTTTTATTGATAAATAAAA
* * *
1171285 GTTTCATATTTTTTTTAAAAAA-ATATTATTTATAAGATGTTACT-TATTAAAATAAATATATAA
66 GTTTCATATTTTTTTAAAAAAATATATTATTTATAAGATGTTACTAT-TTAAAATAAAAACATAA
** *
1171348 AAATTTGATTAAATGAATAAAAAATAAAAATTAATTTTAAAATTTTTAAATAATTTAAGATTTAA
130 AAATTTGATTAAACAAATAAAAAATAAAAA-TAATTTTAAAATTCTTAAATAATTTAAGATTTAA
*
1171413 TTAAATATATATCTATTTAATTGAAGTTCAAACTATTTAGAATTAGAATTTTTTTTGGGTCGTGC
194 TTAAATATATATCTATTTAATTGAAGTTCAAACTATTTAGAATTAGAATTTTTTTTGGGTCATGC
*
1171478 TATGTACTTTCATTGAATCC
259 TATGCACTTTCATTGAATCC
1171498 AACTT
1 AACTT
1171503 GGTTTTTCTC
Statistics
Matches: 264, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
275 1 0.00
276 65 0.25
277 160 0.61
278 38 0.14
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (278 bp):
AACTTTAAAGAAGCTAAAGCTACGGTGTACTAGCTTGCTTATTGAGCTTTTATTGATAAATAAAA
GTTTCATATTTTTTTAAAAAAATATATTATTTATAAGATGTTACTATTTAAAATAAAAACATAAA
AATTTGATTAAACAAATAAAAAATAAAAATAATTTTAAAATTCTTAAATAATTTAAGATTTAATT
AAATATATATCTATTTAATTGAAGTTCAAACTATTTAGAATTAGAATTTTTTTTGGGTCATGCTA
TGCACTTTCATTGAATCC
Found at i:1175323 original size:24 final size:25
Alignment explanation
Indices: 1175296--1175355 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1175286 AATTTTATGC
*
1175296 TTAAATATA-AAAATAATTAAAAAA
1 TTAAATATATAAAATAATAAAAAAA
* *
1175320 TTAAAAATATAATATAATAAAAAAA
1 TTAAATATATAAAATAATAAAAAAA
*
1175345 TAAAAATATAT
1 T-TAAATATAT
1175356 TTAATCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
TTAAATATATAAAATAATAAAAAAA
Found at i:1175365 original size:24 final size:24
Alignment explanation
Indices: 1175298--1175371 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
1175288 TTTTATGCTT
* *
1175298 AAATATAAAAATAATTAAAAAATTAA
1 AAATAT-AATATAA-TAAAAAAATAA
1175324 AAATATAATATAATAAAAAAATAA
1 AAATATAATATAATAAAAAAATAA
*
1175348 AAATAT-ATTTAATCAAAAAAATAA
1 AAATATAATATAAT-AAAAAAATAA
1175372 TCAAAATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 6 0.14
24 26 0.59
25 6 0.14
26 6 0.14
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATATAATATAATAAAAAAATAA
Found at i:1183535 original size:18 final size:17
Alignment explanation
Indices: 1183514--1183555 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1183504 AAATTAATTT
1183514 TTTATTTTAAATAAAAAA
1 TTTATTTT-AATAAAAAA
*
1183532 TTTATAATTAATAAAAAA
1 TTTAT-TTTAATAAAAAA
1183550 -TTATTT
1 TTTATTT
1183556 ATTAAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 4 0.19
18 14 0.67
19 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTTAATAAAAAA
Found at i:1183679 original size:21 final size:21
Alignment explanation
Indices: 1183655--1183698 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1183645 AATAAATATA
*
1183655 TTAAATAATTTTAAT-TTAATT
1 TTAAA-AATATTAATATTAATT
*
1183676 TTAAAAATATTATTATTAATT
1 TTAAAAATATTAATATTAATT
1183697 TT
1 TT
1183699 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAAATATTAATATTAATT
Found at i:1189385 original size:3 final size:3
Alignment explanation
Indices: 1189377--1189416 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1189367 ATCACTTTTG
1189377 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1189417 GTGGGCATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1191058 original size:2 final size:2
Alignment explanation
Indices: 1191051--1191078 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1191041 GATGCAAATT
1191051 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
1191079 AAAGGTGAGT
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):
TA
Found at i:1196405 original size:113 final size:115
Alignment explanation
Indices: 1196258--1196486 Score: 381
Period size: 113 Copynumber: 2.0 Consensus size: 115
1196248 TTTGGGTAGA
*
1196258 GAAACCACTACCCAAATCGGTTTCGGGTAGGGTACGGGTATCACTTTTTGAATACCCGTTACCTG
1 GAAACCACTACCCAAATCGGTTTCGAGTAGGGTACGGGTATCACTTTTTGAATACCCGTTACCTG
*
1196323 AACCTGATTAAATACCCATCTAAATAATTTAAAAAAA-A-AACAGATTTT
66 AACCCGATTAAATACCCATCTAAATAATTTAAAAAAAGAGAACAGATTTT
* * *
1196371 GAAACCACTACCCGAATCGGTTTCGAGTAGGGTACGGGTATCACTTTTTGGATACCTGTTACCTG
1 GAAACCACTACCCAAATCGGTTTCGAGTAGGGTACGGGTATCACTTTTTGAATACCCGTTACCTG
* *
1196436 AACCCGGTTAAATACCCATCTAAATAATTTAAAAAAAGAGAGCAGATTTT
66 AACCCGATTAAATACCCATCTAAATAATTTAAAAAAAGAGAACAGATTTT
1196486 G
1 G
1196487 TGGTTAATGT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 96 0.90
114 1 0.01
115 10 0.09
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (115 bp):
GAAACCACTACCCAAATCGGTTTCGAGTAGGGTACGGGTATCACTTTTTGAATACCCGTTACCTG
AACCCGATTAAATACCCATCTAAATAATTTAAAAAAAGAGAACAGATTTT
Found at i:1209808 original size:14 final size:14
Alignment explanation
Indices: 1209789--1209820 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1209779 GCATGCATGC
*
1209789 CACATATACACACA
1 CACATAGACACACA
1209803 CACATAGACACACA
1 CACATAGACACACA
1209817 CACA
1 CACA
1209821 CACATGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.38, G:0.03, T:0.09
Consensus pattern (14 bp):
CACATAGACACACA
Found at i:1211370 original size:22 final size:23
Alignment explanation
Indices: 1211321--1211428 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 23
1211311 GCTTCACAGG
* *
1211321 ATATCAGGTATTGTGTGACTAG-
1 ATATTAGGTATTGTGTGACTGGT
*
1211343 ATATTAGGTATTGTATGACTGGT
1 ATATTAGGTATTGTGTGACTGGT
* *
1211366 A-ATTATGTATTGCGTGACTGGT
1 ATATTAGGTATTGTGTGACTGGT
* * * * *
1211388 -TTTTAGGAATTGCGTGA-TTGA
1 ATATTAGGTATTGTGTGACTGGT
* *
1211409 ATATTAGGCAATGTGTGACT
1 ATATTAGGTATTGTGTGACT
1211429 AGATAGAAGG
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
21 2 0.03
22 63 0.94
23 2 0.03
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.40
Consensus pattern (23 bp):
ATATTAGGTATTGTGTGACTGGT
Found at i:1211487 original size:22 final size:22
Alignment explanation
Indices: 1211435--1211488 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1211425 GACTAGATAG
*
1211435 AAGGCATTGCTTGACTAGGTTT
1 AAGGCATTGCTGGACTAGGTTT
* *
1211457 AAGGAATTGCTGGAGTA-GTTT
1 AAGGCATTGCTGGACTAGGTTT
*
1211478 GTAGGCATTGC
1 -AAGGCATTGC
1211489 GTGATTGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (22 bp):
AAGGCATTGCTGGACTAGGTTT
Found at i:1214198 original size:18 final size:18
Alignment explanation
Indices: 1214145--1214200 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1214135 GCTTATCAAG
1214145 GATAATATCAAATTTAAA-
1 GATAATATC-AATTTAAAT
* * *
1214163 AATAAT-TTAATTAAAAAT
1 GATAATATCAATT-TAAAT
1214181 GATAATATCAATTTAAAT
1 GATAATATCAATTTAAAT
1214199 GA
1 GA
1214201 AATTTTACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 16 0.55
19 5 0.17
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (18 bp):
GATAATATCAATTTAAAT
Found at i:1227201 original size:12 final size:12
Alignment explanation
Indices: 1227186--1227230 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1227176 ATGTAAATAT
1227186 ATATATATATGC
1 ATATATATATGC
*
1227198 ATATATACATATAC
1 ATATAT--ATATGC
*
1227212 ATATACATATGC
1 ATATATATATGC
1227224 ATATATA
1 ATATATA
1227231 CATATACACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 17 0.63
14 10 0.37
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (12 bp):
ATATATATATGC
Found at i:1227201 original size:14 final size:14
Alignment explanation
Indices: 1227184--1227235 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
1227174 ATATGTAAAT
*
1227184 ATATATATATATGC
1 ATATATACATATGC
1227198 ATATATACATAT--
1 ATATATACATATGC
*
1227210 ACATATACATATGC
1 ATATATACATATGC
1227224 ATATATACATAT
1 ATATATACATAT
1227236 ACACATACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 11 0.33
14 22 0.67
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (14 bp):
ATATATACATATGC
Found at i:1227215 original size:26 final size:26
Alignment explanation
Indices: 1227186--1227243 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1227176 ATGTAAATAT
*
1227186 ATATATATATGCATATATACATATAC
1 ATATACATATGCATATATACATATAC
1227212 ATATACATATGCATATATACATATAC
1 ATATACATATGCATATATACATATAC
*
1227238 ACATAC
1 ATATAC
1227244 GTGCACACGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (26 bp):
ATATACATATGCATATATACATATAC
Found at i:1227237 original size:6 final size:6
Alignment explanation
Indices: 1227200--1227243 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
1227190 ATATATGCAT
* *
1227200 ATATAC ATATAC ATATAC ATATGCAT ATATAC ATATAC ACATAC
1 ATATAC ATATAC ATATAC ATAT--AC ATATAC ATATAC ATATAC
1227244 GTGCACACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 28 0.85
8 5 0.15
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:1227371 original size:20 final size:20
Alignment explanation
Indices: 1227346--1227443 Score: 119
Period size: 20 Copynumber: 5.0 Consensus size: 20
1227336 TATAAAAATT
* ** *
1227346 TATACATATGCATATATACA
1 TATACATATACATATGCATA
1227366 TATACATATACATATGCATA
1 TATACATATACATATGCATA
*
1227386 TATACATATACATAT--ACA
1 TATACATATACATATGCATA
*
1227404 TATACATATACGTATGCATA
1 TATACATATACATATGCATA
*
1227424 TATACATATATATATGCATA
1 TATACATATACATATGCATA
1227444 CGTGCACGCG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.24
20 51 0.76
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (20 bp):
TATACATATACATATGCATA
Found at i:1227375 original size:26 final size:26
Alignment explanation
Indices: 1227346--1227413 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1227336 TATAAAAATT
1227346 TATACATATGCATATATACATATACA
1 TATACATATGCATATATACATATACA
1227372 TATACATATGCATATATACATATACA
1 TATACATATGCATATATACATATACA
*
1227398 TATACATATACATATA
1 TATACATATGCATATA
1227414 CGTATGCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (26 bp):
TATACATATGCATATATACATATACA
Found at i:1227410 original size:38 final size:38
Alignment explanation
Indices: 1227359--1227443 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
1227349 ACATATGCAT
1227359 ATATACATATACATATACATATGCATATATACATATAC
1 ATATACATATACATATACATATGCATATATACATATAC
* *
1227397 ATATACATATACATATACGTATGCATATATACATATAT
1 ATATACATATACATATACATATGCATATATACATATAC
*
1227435 ATATGCATA
1 ATATACATA
1227444 CGTGCACGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (38 bp):
ATATACATATACATATACATATGCATATATACATATAC
Found at i:1227433 original size:6 final size:6
Alignment explanation
Indices: 1227359--1227425 Score: 89
Period size: 6 Copynumber: 10.8 Consensus size: 6
1227349 ACATATGCAT
*
1227359 ATATAC ATATAC ATATAC ATATGCAT ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATAT--AC ATATAC ATATAC ATATAC ATATAC
* *
1227409 ATATAC GTATGC ATATA
1 ATATAC ATATAC ATATA
1227426 TACATATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 48 0.91
8 5 0.09
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:1230730 original size:45 final size:45
Alignment explanation
Indices: 1230659--1230749 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
1230649 TTGGCAAAGC
* *
1230659 TAAAGACAAGGTTTCAGATACCGCACAAGAAGCTAAAGAGAAGGT
1 TAAAGAAAAGGTTTCAGAAACCGCACAAGAAGCTAAAGAGAAGGT
* * *
1230704 TAAAGAAAAGGTTTCGGAAACGGCACATGAAGCTAAAGAGAAGGT
1 TAAAGAAAAGGTTTCAGAAACCGCACAAGAAGCTAAAGAGAAGGT
1230749 T
1 T
1230750 TCAGAGACCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.26, T:0.16
Consensus pattern (45 bp):
TAAAGAAAAGGTTTCAGAAACCGCACAAGAAGCTAAAGAGAAGGT
Found at i:1230790 original size:33 final size:33
Alignment explanation
Indices: 1230704--1230790 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
1230694 AAGAGAAGGT
* * * *
1230704 TAAAGAAAAGGTTTCGGAAACGGCACATGAAGC
1 TAAAGAGAAGGTTTCGGAGACCGCACATAAAGC
* *
1230737 TAAAGAGAAGGTTTCAGAGACCGCACGTAAAGC
1 TAAAGAGAAGGTTTCGGAGACCGCACATAAAGC
*
1230770 TGAAGAGAAGGTTTCGGAGAC
1 TAAAGAGAAGGTTTCGGAGAC
1230791 AGCATGTGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.16
Consensus pattern (33 bp):
TAAAGAGAAGGTTTCGGAGACCGCACATAAAGC
Found at i:1233363 original size:23 final size:23
Alignment explanation
Indices: 1233337--1233408 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
1233327 ACGTGATTTT
* *
1233337 ATAATAAATACTTACGCGATTCC
1 ATAATAACTACTAACGCGATTCC
* * *
1233360 ATAACAACTAATAACGCGACTCC
1 ATAATAACTACTAACGCGATTCC
* * * *
1233383 ATATTTACTACTCACGTGATTCC
1 ATAATAACTACTAACGCGATTCC
1233406 ATA
1 ATA
1233409 TTTACTAGTC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (23 bp):
ATAATAACTACTAACGCGATTCC
Done.