Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 154 of 318
Found at i:48151572 original size:12 final size:13
Alignment explanation
Indices: 48151557--48151586 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
48151547 TATGAATTAT
48151557 TAAAATATT-AAA
1 TAAAATATTAAAA
48151569 TAAAATATTAAAA
1 TAAAATATTAAAA
48151582 TAAAA
1 TAAAA
48151587 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAATATTAAAA
Found at i:48152031 original size:212 final size:214
Alignment explanation
Indices: 48151650--48152107 Score: 816
Period size: 212 Copynumber: 2.1 Consensus size: 214
48151640 CTATATGCAC
* *
48151650 ATTTTAATTTAATTTTAATAATGCATACTTTATCTGGATAAAGTATGTATTAGCAAATTCACTAA
1 ATTTTAATTTAATTTTAATAATGCATATTTTATCCGGATAAAGTATGTATTAGCAAATTCACTAA
48151715 TATGATTATATATATATATAGATATTTAAGCATGTATCACATTACAAAAAAAAAATTAAATACTT
66 TATGATTATATATATATATAGATATTTAAGCATGTATCACATTACAAAAAAAAAATTAAATACTT
48151780 ATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACATATTGTTTTATA
131 ATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACATATTGTTTTATA
48151845 ATTTTATTTCTTATTTAAT
196 ATTTTATTTCTTATTTAAT
* * *
48151864 ATTTTAGTTTAATTTTAATAATGCATATTTTATCCGGATAAAGTATGTATTAGTAGATTCACTAA
1 ATTTTAATTTAATTTTAATAATGCATATTTTATCCGGATAAAGTATGTATTAGCAAATTCACTAA
*
48151929 TATGA-T-TATATATATATAGAT-TTT-CGCATGTATCACATTACAAAAACAAAAATTTAAATAC
66 TATGATTATATATATATATAGATATTTAAGCATGTATCACATTACAAAAA-AAAAA-TTAAATAC
48151990 TTATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACATATTGTTTTA
129 TTATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACATATTGTTTTA
48152055 TAATTTTATTTCTTATTTAAT
194 TAATTTTATTTCTTATTTAAT
48152076 ATTTTAATTTAATTTTAATAATGCATATTTTA
1 ATTTTAATTTAATTTTAATAATGCATATTTTA
48152108 ATTTTATTTT
Statistics
Matches: 235, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
210 21 0.09
211 8 0.03
212 140 0.60
213 1 0.00
214 65 0.28
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (214 bp):
ATTTTAATTTAATTTTAATAATGCATATTTTATCCGGATAAAGTATGTATTAGCAAATTCACTAA
TATGATTATATATATATATAGATATTTAAGCATGTATCACATTACAAAAAAAAAATTAAATACTT
ATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACATATTGTTTTATA
ATTTTATTTCTTATTTAAT
Found at i:48152211 original size:17 final size:19
Alignment explanation
Indices: 48152189--48152232 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
48152179 ACATGACCCA
48152189 TTTTTTTTCGTTTTC-A-G
1 TTTTTTTTCGTTTTCAATG
*
48152206 TTTTTTTTCTTTTTCAATG
1 TTTTTTTTCGTTTTCAATG
48152225 TTTTTTTT
1 TTTTTTTT
48152233 ACTGCTACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
18 1 0.04
19 9 0.38
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTTTTCGTTTTCAATG
Found at i:48152701 original size:17 final size:17
Alignment explanation
Indices: 48152661--48152709 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
48152651 TGTATAAATA
*
48152661 AATATTAATTTATTAATT
1 AATATTAAATT-TTAATT
48152679 -AT-TTAAATTTTAATT
1 AATATTAAATTTTAATT
*
48152694 AATATTAAATTGTAAT
1 AATATTAAATTTTAAT
48152710 GCAATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTAAATTTTAATT
Found at i:48157462 original size:83 final size:84
Alignment explanation
Indices: 48157225--48157479 Score: 388
Period size: 85 Copynumber: 3.0 Consensus size: 84
48157215 AAAATGTAAG
*
48157225 TGGTATATATCTACATCTGTAGAGAAGAATAATGAAGACTTTCAAGTGAAGGTGCTAAAAAACAA
1 TGGTATATATCTACATCTGTGGAGAAGAATAATGAAGACTTTCAAGTGAAGGTGCTAAAAAACAA
* *
48157290 ACATAAATGCAACCCTTTA
66 ACATAAGTGCAACCCTTGA
* * * *
48157309 TGGTATATATCTACATCTGTGGAGAAGAATAAAAGAAGACTTTCGAGTGAAGGTTCTAAAAAAGA
1 TGGTATATATCTACATCTGTGGAGAAGAAT-AATGAAGACTTTCAAGTGAAGGTGCTAAAAAACA
48157374 AACATAAGTGCAACCCTTGA
65 AACATAAGTGCAACCCTTGA
* * *
48157394 TGGTATATATCTACATATATGGAGAAGAATAATGAA-ACTTTCAAGTGAAGATGCTTAAAAAA-A
1 TGGTATATATCTACATCTGTGGAGAAGAATAATGAAGACTTTCAAGTGAAGGTGC-TAAAAAACA
48157457 AACATAAGTGCAACCCTTGA
65 AACATAAGTGCAACCCTTGA
48157477 TGG
1 TGG
48157480 AAGGTGCAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
83 39 0.25
84 41 0.26
85 76 0.49
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (84 bp):
TGGTATATATCTACATCTGTGGAGAAGAATAATGAAGACTTTCAAGTGAAGGTGCTAAAAAACAA
ACATAAGTGCAACCCTTGA
Found at i:48159246 original size:17 final size:18
Alignment explanation
Indices: 48159219--48159254 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
48159209 CAAAATCTCA
*
48159219 AAAAGGAGGTTGAGCCCC
1 AAAAGGAGGTTAAGCCCC
48159237 AAAA-GAGGTTAAGCCCC
1 AAAAGGAGGTTAAGCCCC
48159254 A
1 A
48159255 CTTTAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (18 bp):
AAAAGGAGGTTAAGCCCC
Found at i:48162257 original size:20 final size:20
Alignment explanation
Indices: 48162231--48162279 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
48162221 CCTGTTCTTA
48162231 AGAAAAATTTTAAGATTTTG
1 AGAAAAATTTTAAGATTTTG
* *
48162251 GGAAAAATTTTAAGATTTTT
1 AGAAAAATTTTAAGATTTTG
48162271 AGAAAAATT
1 AGAAAAATT
48162280 CCCTAAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (20 bp):
AGAAAAATTTTAAGATTTTG
Found at i:48178083 original size:21 final size:21
Alignment explanation
Indices: 48178029--48178090 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
48178019 TTTTAGTTAG
*
48178029 CCCTAATGGGTTTCAGTTAAA
1 CCCTAATGGGTTTCAGTTTAA
* * * *
48178050 CTCTTACGAGTTTCAGTTTAA
1 CCCTAATGGGTTTCAGTTTAA
* *
48178071 CCCTCATGGGTTTCCGTTTA
1 CCCTAATGGGTTTCAGTTTA
48178091 GCTCCTATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
CCCTAATGGGTTTCAGTTTAA
Found at i:48180784 original size:19 final size:19
Alignment explanation
Indices: 48180762--48180800 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
48180752 GTAAGTGTTT
48180762 TTAACCCCACATGGTGTGA
1 TTAACCCCACATGGTGTGA
48180781 TTAACCCCACATGGTGTGA
1 TTAACCCCACATGGTGTGA
48180800 T
1 T
48180801 GGGATGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (19 bp):
TTAACCCCACATGGTGTGA
Found at i:48186776 original size:21 final size:20
Alignment explanation
Indices: 48186735--48186776 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
48186725 AAATGATTAA
*
48186735 AGTATATTATAAGTAATAAT
1 AGTATATTATAAATAATAAT
48186755 AGTATATTTATAACATAA-AAT
1 AGTATA-TTATAA-ATAATAAT
48186776 A
1 A
48186777 AAAACAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 10 0.53
22 3 0.16
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
AGTATATTATAAATAATAAT
Found at i:48195120 original size:3 final size:3
Alignment explanation
Indices: 48195106--48195155 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
48195096 GTTACTTATG
*
48195106 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48195154 TT
1 TT
48195156 CCCTATATTA
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:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48200728 original size:53 final size:53
Alignment explanation
Indices: 48200648--48200751 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
48200638 ACTCCCAATC
*
48200648 AATTTCCTTCTTATTATATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
* * *
48200701 AATTTCCTTCTTATTGCATTTTCTATCTTTGATTAATTTATTCATTTCGAG
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAG
48200752 CTATGCTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.55
Consensus pattern (53 bp):
AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:48201250 original size:46 final size:46
Alignment explanation
Indices: 48201154--48201252 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
48201144 TCAATTGATT
*
48201154 GAAGAAGATACAAATCCTATACCTCTGAGTTGCAGTAAGATGGATT
1 GAAGAAGATACAAATCCTATACCTCTGAGTTGCAGTAAGATGGATA
* * ** *
48201200 GAAGATGATACAAATCCTATACC-CTTGAGTTGTAGTGGGTTGGATA
1 GAAGAAGATACAAATCCTATACCTC-TGAGTTGCAGTAAGATGGATA
48201246 GAAGAAG
1 GAAGAAG
48201253 GCAAAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.26
Consensus pattern (46 bp):
GAAGAAGATACAAATCCTATACCTCTGAGTTGCAGTAAGATGGATA
Found at i:48208142 original size:161 final size:162
Alignment explanation
Indices: 48207876--48208199 Score: 641
Period size: 161 Copynumber: 2.0 Consensus size: 162
48207866 ATGATTTCAC
48207876 AAGTCGATTTGGATCTATGTTGTCTTAAGTTTTATATGTTTTTTTTATTTGTTTTTCCATTGTTT
1 AAGTCGATTTGGATCTATGTTGTCTTAAGTTTTATATGTTTTTTTTATTTGTTTTTCCATTGTTT
48207941 ATTAAGTCTTCAGTTTTAAAAGTTTTTGTCTACTCTTGTAACACAATTTTTAGTCTTGCTTATGT
66 ATTAAGTCTTCAGTTTTAAAAGTTTTTGTCTACTCTTGTAACACAATTTTTAGTCTTGCTTATGT
48208006 ATGTAATCTTAATTTTAAAAGTGATTTTAGGG
131 ATGTAATCTTAATTTTAAAAGTGATTTTAGGG
48208038 AAGTCGATTTGGATCTATGTTGTCTTAAGTTTTATATG-TTTTTTTATTTGTTTTTCCATTGTTT
1 AAGTCGATTTGGATCTATGTTGTCTTAAGTTTTATATGTTTTTTTTATTTGTTTTTCCATTGTTT
48208102 ATTAAGTCTTCAGTTTTAAAAGTTTTTGTCTACTCTTGTAACACAATTTTTAGTCTTGCTTATGT
66 ATTAAGTCTTCAGTTTTAAAAGTTTTTGTCTACTCTTGTAACACAATTTTTAGTCTTGCTTATGT
48208167 ATGTAATCTTAATTTTAAAAGTGATTTTAGGG
131 ATGTAATCTTAATTTTAAAAGTGATTTTAGGG
48208199 A
1 A
48208200 TGGTTTTGTT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 124 0.77
162 38 0.23
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (162 bp):
AAGTCGATTTGGATCTATGTTGTCTTAAGTTTTATATGTTTTTTTTATTTGTTTTTCCATTGTTT
ATTAAGTCTTCAGTTTTAAAAGTTTTTGTCTACTCTTGTAACACAATTTTTAGTCTTGCTTATGT
ATGTAATCTTAATTTTAAAAGTGATTTTAGGG
Found at i:48223708 original size:15 final size:17
Alignment explanation
Indices: 48223671--48223714 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
48223661 AAAATAAAAT
48223671 AAAAAGAATAAAGAAGATC
1 AAAAAGAA-AAAGAAGA-C
48223690 AAAAAGAAAAAGAA-A-
1 AAAAAGAAAAAGAAGAC
48223705 AAAAAGAAAA
1 AAAAAGAAAA
48223715 CACCTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
17 1 0.04
18 6 0.24
19 8 0.32
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAGAAGAC
Found at i:48224984 original size:46 final size:46
Alignment explanation
Indices: 48224928--48225028 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
48224918 ATTTTTGCCT
*
48224928 TCTTCTATCCAACCCACTACAACTCA-AGGGTATAGGATTTGTATCA
1 TCTTCAATCCAACCCACTACAACTCAGA-GGTATAGGATTTGTATCA
* ** * *
48224974 TCTTCAATCCATCTTACTGCAACTCAGAGGTATAGGATTTGTATCT
1 TCTTCAATCCAACCCACTACAACTCAGAGGTATAGGATTTGTATCA
48225020 TCTTCAATC
1 TCTTCAATC
48225029 AATTGATCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 47 0.98
47 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (46 bp):
TCTTCAATCCAACCCACTACAACTCAGAGGTATAGGATTTGTATCA
Found at i:48225483 original size:53 final size:53
Alignment explanation
Indices: 48225426--48225529 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
48225416 AAGAGCATAG
*
48225426 CTCGAAATGAATAAATTAATCAAAGATAGAAAATGCAATAAGAAGGAAATTAA
1 CTCGAAATGAATAAATTAATCAAAGATAGAAAATACAATAAGAAGGAAATTAA
* * *
48225479 CTCGAAATGAATAAGTTAATCAAAGATAGCAAATATAATAAGAAGGAAATT
1 CTCGAAATGAATAAATTAATCAAAGATAGAAAATACAATAAGAAGGAAATT
48225530 GATTGGGAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.22
Consensus pattern (53 bp):
CTCGAAATGAATAAATTAATCAAAGATAGAAAATACAATAAGAAGGAAATTAA
Found at i:48231048 original size:3 final size:3
Alignment explanation
Indices: 48231040--48231095 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
48231030 TAATATAGGG
48231040 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
48231088 AAC AAT AA
1 AAT AAT AA
48231096 CATAAGTAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:48231540 original size:3 final size:3
Alignment explanation
Indices: 48231532--48231557 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48231522 ACAATTTAAA
48231532 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
48231558 GAGGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48245470 original size:17 final size:19
Alignment explanation
Indices: 48245448--48245484 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
48245438 CTGATCATCC
48245448 ATCACA-CATGT-GGGTTA
1 ATCACACCATGTGGGGTTA
48245465 ATCACACCATGTGGGGTTA
1 ATCACACCATGTGGGGTTA
48245484 A
1 A
48245485 AAAAACTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (19 bp):
ATCACACCATGTGGGGTTA
Found at i:48247994 original size:21 final size:21
Alignment explanation
Indices: 48247964--48248025 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
48247954 TTATAGGAGC
* *
48247964 TAAACGGAAACCCATGAGGGT
1 TAAACTGAAACCCATAAGGGT
* * *
48247985 TAAACTGAAACTCGTAAGAGT
1 TAAACTGAAACCCATAAGGGT
* *
48248006 TTAACTGAAACCCATTAGGG
1 TAAACTGAAACCCATAAGGG
48248026 CTAACTAAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (21 bp):
TAAACTGAAACCCATAAGGGT
Found at i:48248047 original size:41 final size:41
Alignment explanation
Indices: 48247970--48248070 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
48247960 GAGCTAAACG
* * *
48247970 GAAACCCATGAGGGTTAAACTGAAACTCGTAAGAGTTTAACT
1 GAAACCCATGAGGGCTAAACTAAAACTCATAAGAG-TTAACT
* *
48248012 GAAACCCATTAGGGCT-AACTAAAACTCATATGAGTTAACT
1 GAAACCCATGAGGGCTAAACTAAAACTCATAAGAGTTAACT
* * *
48248052 GAAGCTCATGAGAGCTAAA
1 GAAACCCATGAGGGCTAAA
48248071 TGGAAAGCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 18 0.37
41 17 0.35
42 14 0.29
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (41 bp):
GAAACCCATGAGGGCTAAACTAAAACTCATAAGAGTTAACT
Found at i:48269442 original size:28 final size:28
Alignment explanation
Indices: 48269379--48269476 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
48269369 ATATTAAGTC
*
48269379 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
48269406 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
48269434 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
48269463 CGCACACTTAGTGC
1 CGCACACTTAGTGC
48269477 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:48277728 original size:28 final size:28
Alignment explanation
Indices: 48277666--48277762 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
48277656 TATTAAGTCT
*
48277666 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
48277693 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * *
48277721 GCACACTTAGTGCTGA-ACAATTTAAACCC
1 GCACACTTAGTGCT-ATATAA-TCAAACTC
48277750 GCACACTTAGTGC
1 GCACACTTAGTGC
48277763 CAATCTCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 21 0.33
28 22 0.35
29 20 0.32
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:48284326 original size:18 final size:17
Alignment explanation
Indices: 48284303--48284348 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
48284293 TTCGTTTCAC
48284303 TTTCTTTTTCATTCTCCT
1 TTTCTTTTTCATTCT-CT
*
48284321 TTTCTTTTTCATTCTTT
1 TTTCTTTTTCATTCTCT
*
48284338 TTTCTTCTTCA
1 TTTCTTTTTCA
48284349 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCTTTTTCATTCTCT
Found at i:48284340 original size:17 final size:17
Alignment explanation
Indices: 48284303--48284357 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
48284293 TTCGTTTCAC
*
48284303 TTTCTTTTTCATTCTCCT
1 TTTCTTTTTCATTCT-TT
48284321 TTTCTTTTTCATTCTTT
1 TTTCTTTTTCATTCTTT
* *
48284338 TTTCTTCTTCACTCTTT
1 TTTCTTTTTCATTCTTT
48284355 TTT
1 TTT
48284358 TCTCTCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTTTTCATTCTTT
Found at i:48287209 original size:14 final size:14
Alignment explanation
Indices: 48287190--48287220 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48287180 CATGGGCATG
48287190 CTTTTACTTTCATT
1 CTTTTACTTTCATT
*
48287204 CTTTTACTTTCTTT
1 CTTTTACTTTCATT
48287218 CTT
1 CTT
48287221 CCATCAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (14 bp):
CTTTTACTTTCATT
Found at i:48287366 original size:105 final size:109
Alignment explanation
Indices: 48287226--48287428 Score: 315
Period size: 105 Copynumber: 1.9 Consensus size: 109
48287216 TTCTTCCATC
*
48287226 AAACCCCCTCAAAATTTCTCTCATTTGCTTACCATCCAATCACCATCAAAA-T-TTC-TTCTTTA
1 AAACCCCCTCAAAATTTCTCTCATTTGCTTACCATCCAATCACCACCAAAATTCTTCTTTCTTTA
48287288 TTCTATCAAATTATACACTAAATCTTTCTTCTTTCTTTCGTTAA
66 TTCTATCAAATTATACACTAAATCTTTCTTCTTTCTTTCGTTAA
* * *
48287332 AAACCCCCT-AAATTTTCTCTCATTTTCTTGCCATCCAATCACCACCAAAATTTCTTCTTTCTTT
1 AAACCCCCTCAAAATTTCTCTCATTTGCTTACCATCCAATCACCACCAAAA-TTCTTCTTTCTTT
* *
48287396 CTTCTGTCAAATTATACACTAAATCTTTCTTCT
65 ATTCTATCAAATTATACACTAAATCTTTCTTCT
48287429 GTCCAAAACC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
105 37 0.43
106 9 0.10
107 1 0.01
108 3 0.03
109 37 0.43
ACGTcount: A:0.28, C:0.29, G:0.02, T:0.42
Consensus pattern (109 bp):
AAACCCCCTCAAAATTTCTCTCATTTGCTTACCATCCAATCACCACCAAAATTCTTCTTTCTTTA
TTCTATCAAATTATACACTAAATCTTTCTTCTTTCTTTCGTTAA
Found at i:48287461 original size:102 final size:103
Alignment explanation
Indices: 48287236--48287507 Score: 281
Period size: 102 Copynumber: 2.6 Consensus size: 103
48287226 AAACCCCCTC
* *
48287236 AAAA-TTTCTCTCA-TTTGCTTACCATCCAATCACCATCAAAA--TTTC-TTCTTTATTCTATCA
1 AAAATTTTCTCTCACTTT-CTCACCATCCAATCACCATCAAAATTTTTCTTTCTTTATTCTGTCA
* *
48287296 AATTATACACTAAATCTTTCTTCTTTCTTTCGTTAAAAACCCCC
65 AATTATACACTAAATCTTTCTTCTGTC--TC--T-AAAACCCCA
* * ** * *
48287340 TAAATTTTCTCTCATTTTCTTGCCATCCAATCACCACCAAAATTTCTTCTTTCTTTCTTCTGTCA
1 AAAATTTTCTCTCACTTTCTCACCATCCAATCACCATCAAAATTT-TTCTTTCTTTATTCTGTCA
48287405 AATTATACACTAAATCTTTCTTCTGTC-C-AAAACCCCA
65 AATTATACACTAAATCTTTCTTCTGTCTCTAAAACCCCA
* * * *
48287442 AAAATTTTC-CTTCACTTTCTCACTATCCAATCACCATGAAAATTTATTCTTTCTTTTTTTTGTC
1 AAAATTTTCTC-TCACTTTCTCACCATCCAATCACCATCAAAATTT-TTCTTTCTTTATTCTGTC
48287506 AA
64 AA
48287508 CCCCCCAAAA
Statistics
Matches: 144, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
101 1 0.01
102 62 0.43
104 3 0.02
105 31 0.22
106 4 0.03
107 1 0.01
108 3 0.02
109 39 0.27
ACGTcount: A:0.28, C:0.27, G:0.03, T:0.43
Consensus pattern (103 bp):
AAAATTTTCTCTCACTTTCTCACCATCCAATCACCATCAAAATTTTTCTTTCTTTATTCTGTCAA
ATTATACACTAAATCTTTCTTCTGTCTCTAAAACCCCA
Found at i:48305666 original size:22 final size:21
Alignment explanation
Indices: 48305623--48305693 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
48305613 AATCTTCAAA
*
48305623 GATTTGTAATCTT--AGATTT
1 GATTTGTAATATTAGAGATTT
* *
48305642 GATATGTAATATTAGAAGATAT
1 GATTTGTAATATTAG-AGATTT
*
48305664 GATTTTGTAATCTTAGAGATTT
1 GA-TTTGTAATATTAGAGATTT
48305686 GATTTGTA
1 GATTTGTA
48305694 GATACCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.26
21 6 0.14
22 14 0.33
23 11 0.26
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.46
Consensus pattern (21 bp):
GATTTGTAATATTAGAGATTT
Found at i:48309261 original size:21 final size:22
Alignment explanation
Indices: 48309221--48309261 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48309211 GCGATTTTAG
**
48309221 CTCAAGGGACAATTTCTATACA
1 CTCAAGGGACAACGTCTATACA
48309243 CTCAAGGG-CAACGTCTATA
1 CTCAAGGGACAACGTCTATA
48309262 TGTGCCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (22 bp):
CTCAAGGGACAACGTCTATACA
Found at i:48313998 original size:27 final size:27
Alignment explanation
Indices: 48313960--48314026 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
48313950 ACACACTTAA
48313960 GCTCTT-ATGAGCTTCTCGATTATATG
1 GCTCTTCATGAGCTTCTCGATTATATG
48313986 GCTCTTCATGAGCTTCTCGATTATATG
1 GCTCTTCATGAGCTTCTCGATTATATG
48314013 GCTCTTCATGAGCT
1 GCTCTTCATGAGCT
48314027 CCCTGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (27 bp):
GCTCTTCATGAGCTTCTCGATTATATG
Found at i:48337626 original size:16 final size:16
Alignment explanation
Indices: 48337601--48337633 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48337591 ATTCTGGAAC
*
48337601 ATGTCGTACGTCACTA
1 ATGTCATACGTCACTA
48337617 ATGTCATACGTCACTA
1 ATGTCATACGTCACTA
48337633 A
1 A
48337634 GTGTTTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (16 bp):
ATGTCATACGTCACTA
Found at i:48361031 original size:123 final size:123
Alignment explanation
Indices: 48360803--48361034 Score: 392
Period size: 123 Copynumber: 1.9 Consensus size: 123
48360793 CTGGAGCATG
* *
48360803 AAATTGCACGAGCTTCAATAAAAAATTAGAAGGAAAATGGTGAGTTCAAGCTGGAGAAGAATTTT
1 AAATTGCACGAGCTTCAATAAAAAATTAGAAGGAAAATGGTGAGTTCAAGCTAGAGAAGAAGTTT
* * * *
48360868 GAGTTTGAAATATAGATATCTAACGTCATTGAACCTTGTTAGATTTAATCGGAACATA
66 GAGTTTGAAATATAGATATCTAACATCACTAAACCCTGTTAGATTTAATCGGAACATA
* *
48360926 AAATTGCACGAGCTTCAGTAAAAAATTAGAAGGAAAGTGGTGAGTTCAAGCTAGAGAAGAAGTTT
1 AAATTGCACGAGCTTCAATAAAAAATTAGAAGGAAAATGGTGAGTTCAAGCTAGAGAAGAAGTTT
48360991 GAGTTTGAAATATAGATATCTAACATCACTAAACCCTGTTAGAT
66 GAGTTTGAAATATAGATATCTAACATCACTAAACCCTGTTAGAT
48361035 ATGATATATT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 101 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (123 bp):
AAATTGCACGAGCTTCAATAAAAAATTAGAAGGAAAATGGTGAGTTCAAGCTAGAGAAGAAGTTT
GAGTTTGAAATATAGATATCTAACATCACTAAACCCTGTTAGATTTAATCGGAACATA
Found at i:48362256 original size:85 final size:85
Alignment explanation
Indices: 48362089--48362256 Score: 187
Period size: 85 Copynumber: 2.0 Consensus size: 85
48362079 ACTCCACATA
* * *
48362089 CTTGTGTTGTTGCAAGTATGTTAGAAGATAATCCGAAATTGGATTCTGATCGGATCTCTAATATG
1 CTTGTGTTGTTGCAAGCATGTCAGAAGATAATCCGAAATTGGATTCTGATCGGATCTCTAACATG
* * **
48362154 ATTTTACTTATTTTGAAATC
66 ATCTTACCTATGGTGAAATC
* * * * *
48362174 CTTGTGTTGTTGCAGGCATGTCATAGGATCATACC-AAATTGGATTCTGA-CATGATCTCTAACA
1 CTTGTGTTGTTGCAAGCATGTCAGAAGATAAT-CCGAAATTGGATTCTGATC-GGATCTCTAACA
*
48362237 TTATCTTACCTATGGTGAAA
64 TGATCTTACCTATGGTGAAA
48362257 GCGAGTCTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
84 1 0.01
85 65 0.96
86 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (85 bp):
CTTGTGTTGTTGCAAGCATGTCAGAAGATAATCCGAAATTGGATTCTGATCGGATCTCTAACATG
ATCTTACCTATGGTGAAATC
Found at i:48367734 original size:56 final size:56
Alignment explanation
Indices: 48367668--48367785 Score: 236
Period size: 56 Copynumber: 2.1 Consensus size: 56
48367658 GAAAGAAGTA
48367668 AGCTTATAGAGCTTAGTAAGTTCACATGTAAAATAATAAGCATTAGCAATCAATTT
1 AGCTTATAGAGCTTAGTAAGTTCACATGTAAAATAATAAGCATTAGCAATCAATTT
48367724 AGCTTATAGAGCTTAGTAAGTTCACATGTAAAATAATAAGCATTAGCAATCAATTT
1 AGCTTATAGAGCTTAGTAAGTTCACATGTAAAATAATAAGCATTAGCAATCAATTT
48367780 AGCTTA
1 AGCTTA
48367786 CTACTATTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (56 bp):
AGCTTATAGAGCTTAGTAAGTTCACATGTAAAATAATAAGCATTAGCAATCAATTT
Found at i:48368031 original size:16 final size:15
Alignment explanation
Indices: 48368010--48368048 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
48368000 TCATCACTTA
*
48368010 CTCAATACTTGATAAT
1 CTCAATACTT-ACAAT
48368026 CTCAATTACTTACAAT
1 CTCAA-TACTTACAAT
48368042 CTCAATA
1 CTCAATA
48368049 TTAAATAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 14 0.67
17 5 0.24
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (15 bp):
CTCAATACTTACAAT
Found at i:48368283 original size:55 final size:53
Alignment explanation
Indices: 48368161--48368348 Score: 209
Period size: 55 Copynumber: 3.5 Consensus size: 53
48368151 AACTTACCAT
* * * *
48368161 TGCCATGTCTTGACATGATCTTACGT-GGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATAGG-A-CCTTGCCTTATAGAACTCATCAA
*
48368214 TGCCATGCCTTGACATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCGTCAA
1 TGCCATGCCTTGACATGGTCTTACATAGGACC-TTGCCTTATAG-AACTCATCAA
* * *** *
48368269 TGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACAT-AGGACCTTGCCTTATAGAACTCATCAA
*
48368323 TGCCATGCCTTGGCATGGTCTTACAT
1 TGCCATGCCTTGACATGGTCTTACAT
48368349 GATATCCTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.02
53 33 0.29
54 34 0.30
55 43 0.37
56 3 0.03
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATAGGACCTTGCCTTATAGAACTCATCAA
Found at i:48368391 original size:47 final size:47
Alignment explanation
Indices: 48368336--48368457 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
48368326 CATGCCTTGG
* *
48368336 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
48368383 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
48368430 CATGGTCTTACGTGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
48368458 GTGCCAATGC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:48370245 original size:5 final size:5
Alignment explanation
Indices: 48370235--48370261 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
48370225 GCATTTTTCG
48370235 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
48370262 ATTACATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:48371411 original size:48 final size:48
Alignment explanation
Indices: 48371310--48371412 Score: 131
Period size: 48 Copynumber: 2.1 Consensus size: 48
48371300 GTTCACACAC
*
48371310 CCGTGTCTATTTAACACATTACAACACGGCCTAAGCCACACCACATGG
1 CCGTGTCTATTTAACACATTACAACACGGCCTAAGCCACACCACACGG
*
48371358 CCGTGTCTATTTAGAGAC-TCTA-AACACGGCCTAAGCCAC-CTCACACGG
1 CCGTGTCTATTTA-ACACAT-TACAACACGGCCTAAGCCACAC-CACACGG
*
48371406 GCGTGTC
1 CCGTGTC
48371413 ACATGGGCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
47 1 0.02
48 43 0.88
49 5 0.10
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.21
Consensus pattern (48 bp):
CCGTGTCTATTTAACACATTACAACACGGCCTAAGCCACACCACACGG
Found at i:48372065 original size:41 final size:41
Alignment explanation
Indices: 48372020--48372231 Score: 257
Period size: 41 Copynumber: 5.2 Consensus size: 41
48372010 TAGCGGCGTT
* * * *
48372020 CCGCTAAA-AACTGAGCAATAGCAGCGTTTTTTGTTAAAACG
1 CCGCTAAAGAACAGAGCATTAGCAGCG-CTTTTGGTAAAACG
*
48372061 CCGCTAAA-AATAGAGCATTAGCAGCGCTTTTGGTAAAACG
1 CCGCTAAAGAACAGAGCATTAGCAGCGCTTTTGGTAAAACG
* *
48372101 CCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACG
1 CCGCTAAAGAACAGAGCATTAGCAGCGCTTTTGGTAAAACG
* * *
48372142 CCGCGAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACG
1 CCGCTAAAGAACAGAGCATTAGCAGCGCTTTTGGTAAAACG
* * * * *
48372183 CCGCTAAAGACCAGAACATTTGCGGCGCTTTTAGTAAAACG
1 CCGCTAAAGAACAGAGCATTAGCAGCGCTTTTGGTAAAACG
*
48372224 CCACTAAA
1 CCGCTAAA
48372232 AGTCATATAA
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 20 0.13
41 136 0.87
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (41 bp):
CCGCTAAAGAACAGAGCATTAGCAGCGCTTTTGGTAAAACG
Found at i:48372977 original size:13 final size:13
Alignment explanation
Indices: 48372961--48372987 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48372951 TAATTTCACA
48372961 ACTGAATTAATAT
1 ACTGAATTAATAT
48372974 ACTGAATTAATAT
1 ACTGAATTAATAT
48372987 A
1 A
48372988 TTTGATGTAA
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:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ACTGAATTAATAT
Found at i:48378414 original size:43 final size:43
Alignment explanation
Indices: 48378297--48378437 Score: 185
Period size: 43 Copynumber: 3.3 Consensus size: 43
48378287 GTTTATGATT
48378297 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCAT-GTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTC
* * * * *
48378339 TTTAGTGGTGTTTGTGTGAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTC
* * * *
48378382 TTTAGCGGCGTTTGTAAAAAAAACGCCACTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTC
*
48378425 TTTAGCCGCGTTT
1 TTTAGCGGCGTTT
48378438 TTTTAAATAA
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 34 0.41
43 49 0.59
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTC
Found at i:48382362 original size:17 final size:17
Alignment explanation
Indices: 48382342--48382380 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
48382332 AAAAAAAGTT
*
48382342 AAAATTTTAAAAAATAA
1 AAAATTTGAAAAAATAA
* *
48382359 AAAAATTGAAAATATAA
1 AAAATTTGAAAAAATAA
48382376 AAAAT
1 AAAAT
48382381 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATTTGAAAAAATAA
Found at i:48382388 original size:24 final size:23
Alignment explanation
Indices: 48382316--48382388 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 23
48382306 CAAAAATATG
*
48382316 TTGAAAATTTAAAAATAAAAAAA
1 TTGAAAATTAAAAAATAAAAAAA
48382339 GTT-AAAATTTTAAAAAATAAAAAAA
1 -TTGAAAA--TTAAAAAATAAAAAAA
*
48382364 TTGAAAATATAAAAAATCAAAAAA
1 TTGAAAAT-TAAAAAATAAAAAAA
48382388 T
1 T
48382389 AATTTGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 5 0.12
24 19 0.44
25 19 0.44
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (23 bp):
TTGAAAATTAAAAAATAAAAAAA
Found at i:48382696 original size:27 final size:27
Alignment explanation
Indices: 48382657--48382708 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 27
48382647 TTTTTCTTGA
48382657 AATTATATATATTGTCTTGA-ATTTTTAT
1 AATTATATATATT-TCTT-ATATTTTTAT
48382685 AATT-TATATATTTCTTATATTTTT
1 AATTATATATATTTCTTATATTTTT
48382709 CTAAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.04
26 10 0.43
27 8 0.35
28 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (27 bp):
AATTATATATATTTCTTATATTTTTAT
Found at i:48383318 original size:30 final size:30
Alignment explanation
Indices: 48383277--48383335 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
48383267 CTCCTTCAAC
*
48383277 CTCTCACCATTGCTGTCACCACTATAGCTG
1 CTCTCAACATTGCTGTCACCACTATAGCTG
* * *
48383307 CTCTCAACATTGTTGTGACCAGTATAGCT
1 CTCTCAACATTGCTGTCACCACTATAGCT
48383336 ATTTAGTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (30 bp):
CTCTCAACATTGCTGTCACCACTATAGCTG
Found at i:48392773 original size:46 final size:45
Alignment explanation
Indices: 48392706--48392875 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 45
48392696 AACCCGCCCC
*
48392706 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCA
*
48392752 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCA
* * * * *
48392800 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCA
48392845 T-AGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
48392876 AATGCTCAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 17
0.80 0.08 0.13
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 27 0.25
46 32 0.30
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
Found at i:48392819 original size:93 final size:92
Alignment explanation
Indices: 48392711--48392880 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 92
48392701 GCCCCTAAGT
* * *
48392711 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
*
48392776 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGAATGCCTAGTTACATCTCAC
* *
48392804 GAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCATAGTGAACTCGGACTCAACTCAAC
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
48392869 GAGTTCGAATGC
66 GAGTTCGAATGC
48392881 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 34 0.48
93 37 0.52
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGAATGCCTAGTTACATCTCAC
Found at i:48404290 original size:3 final size:3
Alignment explanation
Indices: 48404282--48404311 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
48404272 TTCTACTTAA
48404282 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48404312 CTTTAATACA
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48404394 original size:12 final size:13
Alignment explanation
Indices: 48404377--48404407 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
48404367 CTAATGTGTC
48404377 TATATTATGTAT-
1 TATATTATGTATA
48404389 TATATTATGTATA
1 TATATTATGTATA
48404402 TATATT
1 TATATT
48404408 TTTTATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (13 bp):
TATATTATGTATA
Found at i:48404717 original size:24 final size:24
Alignment explanation
Indices: 48404689--48404748 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
48404679 TTTGTATTGT
48404689 TATCATATATTATG-TATATGTATA
1 TATCATATA-TATGTTATATGTATA
*
48404713 TATCATATATGTGTTATATGTAT-
1 TATCATATATATGTTATATGTATA
*
48404736 TATGTATATATAT
1 TAT-CATATATAT
48404749 TTTCAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (24 bp):
TATCATATATATGTTATATGTATA
Found at i:48410655 original size:20 final size:19
Alignment explanation
Indices: 48410609--48410656 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
48410599 ACACATTTTT
* *
48410609 TTTTATTAAAATTTTTTAA
1 TTTTATTAAAACTTTTAAA
48410628 TTTATATTAAAACTTTTAACA
1 TTT-TATTAAAACTTTTAA-A
48410649 TTTTATTA
1 TTTTATTA
48410657 TATCTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.72
21 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTAAAACTTTTAAA
Found at i:48413028 original size:30 final size:30
Alignment explanation
Indices: 48412992--48413054 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
48412982 ACTTAACAAG
*
48412992 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
48413022 CAAATGCCTTTAAAATTATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
48413052 CAA
1 CAA
48413055 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:48413109 original size:22 final size:22
Alignment explanation
Indices: 48413084--48413126 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
48413074 TATCTAAACA
48413084 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
48413106 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
48413127 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:48414348 original size:38 final size:39
Alignment explanation
Indices: 48414300--48414481 Score: 176
Period size: 38 Copynumber: 4.8 Consensus size: 39
48414290 ATACCGACAT
* *
48414300 AAAGCCTGCTAGGCACGGAGCCCTAATAAT-ATCTGCAC
1 AAAGCCTGCTAGGCACGGAGCCCAAATAATCATCGGCAC
* ** ** *
48414338 AAAGCATGCTAGATACAAAGCCCAAATAA-CATAGGCAC
1 AAAGCCTGCTAGGCACGGAGCCCAAATAATCATCGGCAC
* * *
48414376 AAAGCCTACTAGGCACGAAGCTCAAAT-ATCATCGGCAC
1 AAAGCCTGCTAGGCACGGAGCCCAAATAATCATCGGCAC
* * *
48414414 AAAGCCTGTTAGGCACTGAGCCCAAAT-ATCA-CTAGCAC
1 AAAGCCTGCTAGGCACGGAGCCCAAATAATCATC-GGCAC
* *
48414452 AAAGCCTGCTAGGCACGGAGCTCGAATAAT
1 AAAGCCTGCTAGGCACGGAGCCCAAATAAT
48414482 GTTATGTTTC
Statistics
Matches: 115, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
37 2 0.02
38 111 0.97
39 2 0.02
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (39 bp):
AAAGCCTGCTAGGCACGGAGCCCAAATAATCATCGGCAC
Found at i:48416848 original size:19 final size:19
Alignment explanation
Indices: 48416803--48416848 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
48416793 TTTTTATGTG
*
48416803 TTATAAATTATATAATATA
1 TTATAAATAATATAATATA
* *
48416822 TAAAAAATAATATAATATA
1 TTATAAATAATATAATATA
48416841 TTATAAAT
1 TTATAAAT
48416849 TTAGAAAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTATAAATAATATAATATA
Found at i:48418101 original size:6 final size:6
Alignment explanation
Indices: 48418092--48418129 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
48418082 GTGCGGCGGG
*
48418092 CGGCGG CGGCGA CGGCGA CGGCGA CGGCGA CGGCGA CG
1 CGGCGA CGGCGA CGGCGA CGGCGA CGGCGA CGGCGA CG
48418130 AGTAACCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.13, C:0.34, G:0.53, T:0.00
Consensus pattern (6 bp):
CGGCGA
Found at i:48425496 original size:27 final size:27
Alignment explanation
Indices: 48425455--48425509 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
48425445 TTAAGCTAGA
*
48425455 ACTTATTTTCTATCTAACCTCACCATC
1 ACTTATTTTCCATCTAACCTCACCATC
48425482 ACTTATTTTCCATCTAACCTCACCATC
1 ACTTATTTTCCATCTAACCTCACCATC
48425509 A
1 A
48425510 TCCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (27 bp):
ACTTATTTTCCATCTAACCTCACCATC
Found at i:48425949 original size:24 final size:24
Alignment explanation
Indices: 48425920--48425992 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
48425910 AACGACTCAT
*
48425920 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
48425944 CTGGAAGAAGCAGTCACGTAAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
48425968 CTGGAAGAAGCAGCCATGGCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
48425992 C
1 C
48425993 AATTACACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (24 bp):
CTGGAAGAAGCAGTCATGTCAGCA
Found at i:48429894 original size:23 final size:23
Alignment explanation
Indices: 48429864--48429909 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
48429854 TAGGATTGAT
* *
48429864 ATCGCGACATGAGGGAGTTCCTC
1 ATCGCGACACGAGGAAGTTCCTC
48429887 ATCGCGACACGAGGAAGTTCCTC
1 ATCGCGACACGAGGAAGTTCCTC
48429910 GTCGTGACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
ATCGCGACACGAGGAAGTTCCTC
Found at i:48442800 original size:39 final size:40
Alignment explanation
Indices: 48442700--48442884 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
48442690 TTGAATGATG
* * * *
48442700 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
48442739 ATCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
48442780 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
48442819 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
48442858 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
48442885 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 36 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:48442906 original size:79 final size:79
Alignment explanation
Indices: 48442753--48442917 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
48442743 GGACTAAGAT
* **
48442753 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
48442818 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
48442832 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
48442895 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
48442911 CCGAAGG
1 CCGAAGG
48442918 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:48450665 original size:79 final size:81
Alignment explanation
Indices: 48450525--48450709 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
48450515 TTGAATGATG
*
48450525 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGACTAAGATCCGAAGGCATT
48450589 TGTGAGAGATACTA-A
66 TGTGAGAGATACTATA
* * * * **
48450604 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGACTAAGAT-CCGAAGGCA
* *
48450666 TTTGTGCGAGTTACTATA
64 TTTGTGAGAGATACTATA
* *
48450684 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
48450710 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGACTAAGATCCGAAGGCATT
TGTGAGAGATACTATA
Found at i:48450716 original size:40 final size:40
Alignment explanation
Indices: 48450525--48450709 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
48450515 TTGAATGATG
* * * *
48450525 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
48450565 TCCAGACTAAGAT-CCGAAGGCATTTGTGAGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
48450605 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48450644 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
48450685 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
48450710 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 80 0.65
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:48450731 original size:79 final size:79
Alignment explanation
Indices: 48450578--48450742 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
48450568 AGACTAAGAT
* **
48450578 CCGAAGGCATTTGTGAGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGAGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
48450643 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
48450657 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGAGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
48450720 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
48450736 CCGAAGG
1 CCGAAGG
48450743 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGAGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:48459254 original size:27 final size:27
Alignment explanation
Indices: 48459231--48459284 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
48459221 TTTAAATTTG
**
48459231 ACATATTTAATTTTTTTAAAAAATTAA
1 ACATATTTAATTTTTAAAAAAAATTAA
48459258 ACATATTTAATTTTTAAAAAAAATTAA
1 ACATATTTAATTTTTAAAAAAAATTAA
48459285 CTCAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
ACATATTTAATTTTTAAAAAAAATTAA
Found at i:48459645 original size:17 final size:17
Alignment explanation
Indices: 48459619--48459652 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48459609 TGTTTTCTTA
48459619 TATTAATATTTAATTTT
1 TATTAATATTTAATTTT
* *
48459636 TATTATTATTTTATTTT
1 TATTAATATTTAATTTT
48459653 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTAATATTTAATTTT
Found at i:48459886 original size:16 final size:16
Alignment explanation
Indices: 48459857--48459908 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
48459847 TTAATATTTT
* *
48459857 TATAATATATAAATTA
1 TATAAAATAAAAATTA
48459873 TATAAAATAAAAATTA
1 TATAAAATAAAAATTA
*
48459889 TAAAAACATTAAAAA-TA
1 TATAAA-A-TAAAAATTA
48459906 TAT
1 TAT
48459909 TAATGATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 19 0.63
17 5 0.17
18 6 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAATAAAAATTA
Found at i:48460231 original size:26 final size:26
Alignment explanation
Indices: 48460202--48460255 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
48460192 GTCAATAACT
48460202 AATGATCACAACATCGTTGACATGGA
1 AATGATCACAACATCGTTGACATGGA
48460228 AATGATCACAACATCGTTGACATGGA
1 AATGATCACAACATCGTTGACATGGA
48460254 AA
1 AA
48460256 AAAAGAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (26 bp):
AATGATCACAACATCGTTGACATGGA
Found at i:48464037 original size:31 final size:31
Alignment explanation
Indices: 48463994--48464067 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
48463984 TGGATATGGG
48463994 ACACGCCCGTGTGGGCAGGCCGTGTGGTCAC
1 ACACGCCCGTGTGGGCAGGCCGTGTGGTCAC
*
48464025 ACACACCCGTGTGGGCAGGCCGTGTGGTCAC
1 ACACGCCCGTGTGGGCAGGCCGTGTGGTCAC
*
48464056 ATACGCCCGTGT
1 ACACGCCCGTGT
48464068 CCCGACCTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (31 bp):
ACACGCCCGTGTGGGCAGGCCGTGTGGTCAC
Found at i:48469895 original size:101 final size:101
Alignment explanation
Indices: 48469720--48469921 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
48469710 AACTAGTTAA
48469720 AAAGGACTAAATCGAAAAAGATGCAAAAGTTGGTTTCTATTAGTCAAATAGATCAAAAAGCTTTA
1 AAAGGACTAAATCGAAAAAGATGCAAAAGTTGGTTTCTATTAGTCAAATAGATCAAAAAGCTTTA
48469785 AAAAGATAAACTAATGGACTTCAATGGTAATTATAC
66 AAAAGATAAACTAATGGACTTCAATGGTAATTATAC
48469821 AAAGGACTAAATCGAAAAAGATGCAAAAGTTGGTTTCTATTAGTCAAATAGATCAAAAAGCTTTA
1 AAAGGACTAAATCGAAAAAGATGCAAAAGTTGGTTTCTATTAGTCAAATAGATCAAAAAGCTTTA
48469886 AAAAGATAAACTAATGGACTTCAATGGTAATTATAC
66 AAAAGATAAACTAATGGACTTCAATGGTAATTATAC
48469922 CATACTTAAA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (101 bp):
AAAGGACTAAATCGAAAAAGATGCAAAAGTTGGTTTCTATTAGTCAAATAGATCAAAAAGCTTTA
AAAAGATAAACTAATGGACTTCAATGGTAATTATAC
Found at i:48473294 original size:12 final size:12
Alignment explanation
Indices: 48473250--48473298 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
48473240 CATTAATTAA
48473250 TTAATTTTTATG
1 TTAATTTTTATG
*
48473262 TTAACTTTTTTTG
1 TTAA-TTTTTATG
*
48473275 TGACAATTTTTATG
1 T--TAATTTTTATG
48473289 TTAATTTTTA
1 TTAATTTTTA
48473299 ATAAACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 12 0.40
13 8 0.27
14 8 0.27
15 2 0.07
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.63
Consensus pattern (12 bp):
TTAATTTTTATG
Found at i:48494569 original size:21 final size:20
Alignment explanation
Indices: 48494531--48494577 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
48494521 CAGAATGCTA
48494531 ATTTG-GTATCAAATTTTTT
1 ATTTGAGTATCAAATTTTTT
*
48494550 ATTTGAGTATCGATATTTTTT
1 ATTTGAGTATC-AAATTTTTT
48494571 ATATTGA
1 AT-TTGA
48494578 TACCCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 10 0.42
22 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (20 bp):
ATTTGAGTATCAAATTTTTT
Found at i:48494653 original size:12 final size:12
Alignment explanation
Indices: 48494638--48494662 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48494628 TTTTGGTATC
48494638 GATTTTCAAAAA
1 GATTTTCAAAAA
48494650 GATTTTCAAAAA
1 GATTTTCAAAAA
48494662 G
1 G
48494663 GTATCGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (12 bp):
GATTTTCAAAAA
Found at i:48495739 original size:34 final size:33
Alignment explanation
Indices: 48495687--48495782 Score: 131
Period size: 34 Copynumber: 2.9 Consensus size: 33
48495677 TTAGAGTTTT
* *
48495687 TTTAAAA-AAATAATTAAATTAGGTTTTAAAGG
1 TTTAAAATAAATAAATAAATTAGGGTTTAAAGG
**
48495719 TTTAAAATAAATAAACTAAATTAGGGTTTATGGG
1 TTTAAAATAAATAAA-TAAATTAGGGTTTAAAGG
48495753 TTTAAAATAAATAAATAAAATTAGGGTTTA
1 TTTAAAATAAATAAAT-AAATTAGGGTTTA
48495783 GTTTTTTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.12
33 7 0.12
34 43 0.75
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (33 bp):
TTTAAAATAAATAAATAAATTAGGGTTTAAAGG
Found at i:48495791 original size:34 final size:32
Alignment explanation
Indices: 48495687--48495796 Score: 123
Period size: 34 Copynumber: 3.3 Consensus size: 32
48495677 TTAGAGTTTT
* * *
48495687 TTTAAAA-AAATAATTAAATTAGGTTTTAAAGG
1 TTTAAAATAAATAAATAAATTAGGGTTT-ATGG
48495719 TTTAAAATAAATAAACTAAATTAGGGTTTATGGG
1 TTTAAAATAAATAAA-TAAATTAGGGTTTAT-GG
**
48495753 TTTAAAATAAATAAATAAAATTAGGGTTTAGTTT
1 TTTAAAATAAATAAAT-AAATTAGGGTTTA-TGG
48495787 TTTAAAATAA
1 TTTAAAATAA
48495797 TTTTTGTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.10
33 8 0.12
34 52 0.76
35 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATAAATAAATTAGGGTTTATGG
Found at i:48499325 original size:12 final size:12
Alignment explanation
Indices: 48499310--48499336 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
48499300 GCTCCCCGAT
48499310 GATGTCTCGTGC
1 GATGTCTCGTGC
48499322 GATGTCTCGTGC
1 GATGTCTCGTGC
48499334 GAT
1 GAT
48499337 CCCTCCTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (12 bp):
GATGTCTCGTGC
Found at i:48510813 original size:27 final size:26
Alignment explanation
Indices: 48510783--48510866 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
48510773 AAAATATAAG
*
48510783 TACTTAATTAGGACAAAAAAACTTAAA
1 TACTTAAATAGGA-AAAAAAACTTAAA
* * *** *
48510810 TACTAAAATATTGAAGTTAAACTAAAA
1 TACTTAAATA-GGAAAAAAAACTTAAA
48510837 TACTTAAATAGGATAAAAAGAACTTAAA
1 TACTTAAATAGGA-AAAAA-AACTTAAA
48510865 TA
1 TA
48510867 TCAATTTTTT
Statistics
Matches: 41, Mismatches: 13, Indels: 5
0.69 0.22 0.08
Matches are distributed among these distances:
26 2 0.05
27 28 0.68
28 11 0.27
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (26 bp):
TACTTAAATAGGAAAAAAAACTTAAA
Found at i:48520858 original size:20 final size:19
Alignment explanation
Indices: 48520820--48520862 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
48520810 TAATTTTTTT
*
48520820 ATTTTTTATTTTTTAAATA
1 ATTTTTTAATTTTTAAATA
48520839 CATTTTTATAATTTTT-AATA
1 -ATTTTT-TAATTTTTAAATA
48520859 ATTT
1 ATTT
48520863 ATTCAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTAATTTTTAAATA
Found at i:48525840 original size:27 final size:26
Alignment explanation
Indices: 48525808--48525881 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
48525798 ATAATTTATT
*
48525808 AAAATAAAATATATAAAATCACTTAAA
1 AAAATAAAATATATAAAA-AACTTAAA
*
48525835 AAAAT--AATGATATAAAAAATTTAAA
1 AAAATAAAAT-ATATAAAAAACTTAAA
*
48525860 AAAATATAAAAATACTAAAAAA
1 AAAATA-AAATATA-TAAAAAA
48525882 AAGTCTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 14 0.36
26 8 0.21
27 8 0.21
28 9 0.23
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (26 bp):
AAAATAAAATATATAAAAAACTTAAA
Found at i:48528820 original size:23 final size:23
Alignment explanation
Indices: 48528790--48528833 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
48528780 GAGAGCCTAA
48528790 ATGGCAATTTTTCATTTAGGAGG
1 ATGGCAATTTTTCATTTAGGAGG
48528813 ATGGCAATTTTTCATTTAGGA
1 ATGGCAATTTTTCATTTAGGA
48528834 AGAGCCGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (23 bp):
ATGGCAATTTTTCATTTAGGAGG
Found at i:48538891 original size:3 final size:3
Alignment explanation
Indices: 48538883--48538912 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
48538873 AGAACTTTAA
48538883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48538913 TAAGCCATTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48539545 original size:20 final size:21
Alignment explanation
Indices: 48539491--48539545 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
48539481 TGGTATAATA
48539491 ATTTTTATAATTTT-TTTATG
1 ATTTTTATAATTTTCTTTATG
* *
48539511 AATCTTAT-A-TTTCTTTAT-
1 ATTTTTATAATTTTCTTTATG
48539529 ATTTTTATAATTTTCTT
1 ATTTTTATAATTTTCTT
48539546 ACGACTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 12 0.43
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTATAATTTTCTTTATG
Found at i:48539621 original size:29 final size:28
Alignment explanation
Indices: 48539531--48539623 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
48539521 TTCTTTATAT
* * *
48539531 TTTTATAATTTTCTTACGACTTAATAAAA
1 TTTTATAATTTTTTTACGA-TTTATTAAA
* * *
48539560 TTTTATAATTTTTTT-CTATATCTCTACATA
1 TTTTATAATTTTTTTACGATTTAT-TA-A-A
*
48539590 TTTTATAATTTTTTTACGATTTTTGTAAA
1 TTTTATAATTTTTTTACGATTTAT-TAAA
48539619 TTTTA
1 TTTTA
48539624 AAAAAAAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 21 0.42
30 17 0.34
31 7 0.14
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATAATTTTTTTACGATTTATTAAA
Found at i:48539658 original size:18 final size:20
Alignment explanation
Indices: 48539637--48539713 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 20
48539627 AAAAATATAT
48539637 TTTTTTTTAC-AATTTTT-A
1 TTTTTTTTACTAATTTTTAA
48539655 TTTTTTTT-CTAATTTTTAA
1 TTTTTTTTACTAATTTTTAA
* * **
48539674 TATTTTTTAGTAAAATTTAA
1 TTTTTTTTACTAATTTTTAA
*
48539694 TAATTTTTTTA-TAACTTTTA
1 T--TTTTTTTACTAATTTTTA
48539714 TTAAATAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.02
18 15 0.32
19 8 0.17
20 9 0.19
21 7 0.15
22 7 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (20 bp):
TTTTTTTTACTAATTTTTAA
Found at i:48539671 original size:19 final size:20
Alignment explanation
Indices: 48539632--48539681 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
48539622 TAAAAAAAAA
48539632 TATATTTTTTTTTACAATTT
1 TATATTTTTTTTTACAATTT
*
48539652 T-TATTTTTTTTCTA-ATTTT
1 TATATTTTTTTT-TACAATTT
48539671 TAATATTTTTT
1 T-ATATTTTTT
48539682 AGTAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 15 0.58
20 3 0.12
21 8 0.31
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TATATTTTTTTTTACAATTT
Found at i:48539713 original size:21 final size:20
Alignment explanation
Indices: 48539633--48539713 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
48539623 AAAAAAAAAT
* *
48539633 ATATTTTTTTTTACAATTTTT
1 ATATTTTTTTATA-AATTTTA
* *
48539654 AT-TTTTTTTCTAATTTTTA
1 ATATTTTTTTATAAATTTTA
*
48539673 ATA-TTTTTTAGTAAAATTTA
1 ATATTTTTTTA-TAAATTTTA
*
48539693 ATAATTTTTTTATAACTTTTA
1 AT-ATTTTTTTATAAATTTTA
48539714 TTAAATAACA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.27
20 18 0.38
21 10 0.21
22 7 0.15
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
ATATTTTTTTATAAATTTTA
Found at i:48541837 original size:12 final size:12
Alignment explanation
Indices: 48541822--48541846 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48541812 TTTTTTTATC
48541822 ACCTTTTACTTA
1 ACCTTTTACTTA
48541834 ACCTTTTACTTA
1 ACCTTTTACTTA
48541846 A
1 A
48541847 AATAGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
ACCTTTTACTTA
Found at i:48543282 original size:50 final size:50
Alignment explanation
Indices: 48543158--48543406 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
48543148 GATAATAACA
* * ** * *
48543158 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
48543209 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
48543259 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
48543309 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
48543364 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
48543407 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:48543336 original size:100 final size:104
Alignment explanation
Indices: 48543157--48543406 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
48543147 TGATAATAAC
**
48543157 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
48543222 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
48543259 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
48543322 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
48543364 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
48543407 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:48543522 original size:13 final size:13
Alignment explanation
Indices: 48543501--48543532 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
48543491 GCTTGGATCA
*
48543501 TCATCAAATAAAT
1 TCATAAAATAAAT
48543514 TCATAAAATAAAT
1 TCATAAAATAAAT
48543527 TCATAA
1 TCATAA
48543533 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:48543780 original size:30 final size:29
Alignment explanation
Indices: 48543744--48543800 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
48543734 CCTCGACTCT
*
48543744 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTGCCCCTA
*
48543774 AACTTTTACATAATTACATTTTGCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
48543801 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Found at i:48544565 original size:40 final size:40
Alignment explanation
Indices: 48544503--48544597 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 40
48544493 CTTTTCTTTT
* * *
48544503 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTA
*
48544544 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTA
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTA
48544584 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
48544598 TTCTTTGTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.67
41 16 0.33
ACGTcount: A:0.01, C:0.28, G:0.07, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTA
Found at i:48544623 original size:5 final size:5
Alignment explanation
Indices: 48544607--48544672 Score: 100
Period size: 5 Copynumber: 13.2 Consensus size: 5
48544597 TTTCTTTGTC
48544607 ATATA TATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- AT-TA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
48544656 ATAATA ATATA ATATA A
1 AT-ATA ATATA ATATA A
48544673 AAACATAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 43 0.75
6 9 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:48546647 original size:6 final size:7
Alignment explanation
Indices: 48546635--48546688 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 7
48546625 ATTCTTATGA
48546635 AATTTTT
1 AATTTTT
48546642 -ATTTTT
1 AATTTTT
48546648 AATTTTTT
1 AA-TTTTT
*
48546656 AATTTTG
1 AATTTTT
48546663 AA--TTT
1 AATTTTT
48546668 AA-TTTT
1 AATTTTT
48546674 AATTTTTT
1 AA-TTTTT
48546682 AATTTTT
1 AATTTTT
48546689 TTATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 4 0.10
6 11 0.28
7 12 0.30
8 13 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:48546698 original size:27 final size:26
Alignment explanation
Indices: 48546644--48546704 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
48546634 AAATTTTTAT
**
48546644 TTTTAATTTTTTAATTTTGAATTTAA
1 TTTTAATTTTTTAATTTTGAATAAAA
**
48546670 TTTTAATTTTTTAATTTTTTTATAAAA
1 TTTTAATTTTTTAA-TTTTGAATAAAA
48546697 TTTTAATT
1 TTTTAATT
48546705 ATTTGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTAATTTTTTAATTTTGAATAAAA
Found at i:48548627 original size:16 final size:17
Alignment explanation
Indices: 48548602--48548635 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
48548592 AAATTTATAA
*
48548602 ATAAAGTATT-AAAAAT
1 ATAAAATATTCAAAAAT
48548618 ATAAAATATTCAAAAAT
1 ATAAAATATTCAAAAAT
48548635 A
1 A
48548636 ATCAATCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAAATATTCAAAAAT
Found at i:48549449 original size:30 final size:31
Alignment explanation
Indices: 48549408--48549480 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 31
48549398 TTTATGTAAC
48549408 TATATATATATTTTATATTTTTATAA-AATTT
1 TATA-ATATATTTTATATTTTTATAATAATTT
*
48549439 TATAATATATTTTATCTTTTTATAATAATTT
1 TATAATATATTTTATATTTTTATAATAATTT
48549470 T-T-ATATATTTT
1 TATAATATATTTT
48549481 GAAGTTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 9 0.22
30 21 0.52
31 10 0.25
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (31 bp):
TATAATATATTTTATATTTTTATAATAATTT
Found at i:48549470 original size:12 final size:11
Alignment explanation
Indices: 48549422--48549480 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 11
48549412 TATATATTTT
48549422 ATATTTTTATA
1 ATATTTTTATA
*
48549433 A-AATTTTATA
1 ATATTTTTATA
*
48549443 ATATATTT-T-
1 ATATTTTTATA
*
48549452 ATCTTTTTATA
1 ATATTTTTATA
48549463 ATAATTTTTAT-
1 AT-ATTTTTATA
48549474 ATATTTT
1 ATATTTT
48549481 GAAGTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
9 6 0.16
10 16 0.42
11 9 0.24
12 7 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTTTATA
Found at i:48549489 original size:30 final size:28
Alignment explanation
Indices: 48549410--48549495 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
48549400 TATGTAACTA
48549410 TATATATATTTTATATTTTTATAAAATTT
1 TATATATATTTTA-ATTTTTATAAAATTT
*
48549439 TATAATATATTTTATCTTTTTATAATAATTT
1 TAT-ATATATTTTA-ATTTTTATAA-AATTT
*
48549470 T-TATATATTTTGAAGTTTT-TAAAATT
1 TATATATATTTT-AATTTTTATAAAATT
48549496 ATAATTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 16 0.31
30 22 0.43
31 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (28 bp):
TATATATATTTTAATTTTTATAAAATTT
Found at i:48557410 original size:104 final size:104
Alignment explanation
Indices: 48557230--48557438 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
48557220 ATCACAGAGA
48557230 AGCAGAAAATGTACAGGCCCTTTGTAACCTATATATGGACATTTTGTCTTCCTTATTTACCTTTT
1 AGCAGAAAATGTACAGGCCCTTTGTAACCTATATATGGACATTTTGTCTTCCTTATTTACCTTTT
48557295 CTAGTTTATAACTAATTAACCGATCATTAATAATAAGCC
66 CTAGTTTATAACTAATTAACCGATCATTAATAATAAGCC
48557334 AGCAGAAAATGTACAGGCCCTTTGTAACCTATATATGGACATTTTGTCTTCCTTATTTACCTTTT
1 AGCAGAAAATGTACAGGCCCTTTGTAACCTATATATGGACATTTTGTCTTCCTTATTTACCTTTT
48557399 CTAGTTTATAACTAATTAACCGATCATTAATAATAAGCC
66 CTAGTTTATAACTAATTAACCGATCATTAATAATAAGCC
48557438 A
1 A
48557439 AAAGAAGTGG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (104 bp):
AGCAGAAAATGTACAGGCCCTTTGTAACCTATATATGGACATTTTGTCTTCCTTATTTACCTTTT
CTAGTTTATAACTAATTAACCGATCATTAATAATAAGCC
Found at i:48563187 original size:28 final size:28
Alignment explanation
Indices: 48563068--48563172 Score: 146
Period size: 28 Copynumber: 3.9 Consensus size: 28
48563058 GATATGACAT
* * *
48563068 TGTGCTAAGTGGAATAAGACCATGAC-A
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
48563095 --T-CTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
*
48563120 TGTGCTAAGTGAAATAAGTCTATGGCAA
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
48563148 TGTGCTAAGTGAAATAAGTCCATGG
1 TGTGCTAAGTGAAATAAGTCCATGG
48563173 TATTGCGCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.28
25 2 0.03
27 1 0.01
28 47 0.68
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (28 bp):
TGTGCTAAGTGAAATAAGTCCATGGCAA
Found at i:48563295 original size:51 final size:51
Alignment explanation
Indices: 48563211--48563308 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
48563201 TGAACCTTAG
*
48563211 GAATAAAATAGCTTTGGAAACAAGTGTGATACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGAAACAAGGGTGATACTATGTGAAGGCCACTTTGT
** *
48563262 GAATAAAATAGCTTTGGCTACAAGGGTGGTACTATGTGAAGGCCACT
1 GAATAAAATAGCTTTGGAAACAAGGGTGATACTATGTGAAGGCCACT
48563309 GTGTATCCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGAAACAAGGGTGATACTATGTGAAGGCCACTTTGT
Found at i:48565154 original size:41 final size:40
Alignment explanation
Indices: 48565008--48565154 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 40
48564998 CACTGACTCA
* * *
48565008 AAAAACCCTTCGAGACCAAGCTCGAATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCG-GTTATGACATTGGCTC
* * * * * * * * *
48565049 GAAGGCCCTTCGAAACTAGGTTCAGTTATGACACTGGCTT
1 AAAAGCCCTTCGAGACCAAGCTCGGTTATGACATTGGCTC
48565089 AAAAGCCCTTCGAGACCAAGCTCGGCTTATGACATTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGG-TTATGACATTGGCTC
48565130 AAAAGCCCTTCGAGACCAAGCTCGG
1 AAAAGCCCTTCGAGACCAAGCTCGG
48565155 ATTTAAACCC
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
40 30 0.36
41 54 0.64
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAAGCCCTTCGAGACCAAGCTCGGTTATGACATTGGCTC
Found at i:48572683 original size:40 final size:40
Alignment explanation
Indices: 48572653--48572862 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
48572643 GGACTAAGAT
* * * *
48572653 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
48572693 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
48572733 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
48572773 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
48572813 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
48572852 CCGAAGGCATT
1 CCGAAGGCATT
48572863 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:48572737 original size:80 final size:80
Alignment explanation
Indices: 48572600--48572862 Score: 316
Period size: 80 Copynumber: 3.3 Consensus size: 80
48572590 TTGAATGCTG
* * * * * **
48572600 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCCT
*
48572663 TTGTGCGAGATACTAAA
64 TTGTGCGAGTTACTAAA
* * *
48572680 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
48572745 GTGCGAGTTATTAAA
66 GTGCGAGTTACTAAA
* * * *
48572760 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
48572824 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
48572839 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
48572863 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 36 0.23
80 117 0.74
81 6 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:48572814 original size:120 final size:120
Alignment explanation
Indices: 48572600--48572862 Score: 325
Period size: 120 Copynumber: 2.2 Consensus size: 120
48572590 TTGAATGCTG
* * *
48572600 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
48572664 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * * **
48572720 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * *
48572783 TCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
48572839 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
48572863 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
119 35 0.29
120 81 0.66
121 6 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:48572882 original size:79 final size:80
Alignment explanation
Indices: 48572653--48572897 Score: 253
Period size: 80 Copynumber: 3.1 Consensus size: 80
48572643 GGACTAAGAT
* * * * * ** * *
48572653 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAG-GAGCT
48572717 AAATCCGGGTTAAGTC
65 AAATCCGGGTTAAGTC
* * * ** ** *
48572733 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
48572798 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
48572813 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
48572877 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
48572891 CCGAAGG
1 CCGAAGG
48572898 TACGTGATTT
Statistics
Matches: 144, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
78 14 0.10
79 47 0.33
80 83 0.58
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:48576385 original size:40 final size:41
Alignment explanation
Indices: 48576296--48576440 Score: 202
Period size: 41 Copynumber: 3.6 Consensus size: 41
48576286 CGCTGACTCA
*
48576296 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
* * * * * * * *
48576337 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTT
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
48576377 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
48576418 AAAAGCCCTTCGAGACCAAGCTC
1 AAAAGCCCTTCGAGACCAAGCTC
48576441 AAATTTAAAC
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 31 0.36
41 55 0.64
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
Found at i:48591833 original size:6 final size:6
Alignment explanation
Indices: 48591824--48591849 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48591814 ATTATTATTA
48591824 TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
48591850 CTTTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:48597939 original size:10 final size:10
Alignment explanation
Indices: 48597916--48597960 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
48597906 ATTCTAAAAA
48597916 ATAAATACAA-
1 ATAAATA-AAG
48597926 ATAAATAAAG
1 ATAAATAAAG
*
48597936 ATAATTAAAG
1 ATAAATAAAG
*
48597946 ATAAATAAAT
1 ATAAATAAAG
48597956 ATAAA
1 ATAAA
48597961 AGCTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 2 0.06
10 29 0.94
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:48599233 original size:9 final size:9
Alignment explanation
Indices: 48599219--48599325 Score: 78
Period size: 8 Copynumber: 11.4 Consensus size: 9
48599209 ATTATTTTAG
48599219 AAAATTTTT
1 AAAATTTTT
48599228 AAAA-TTTT
1 AAAATTTTT
*
48599236 AACATTTTTT
1 AA-AATTTTT
*
48599246 ATATATTTTTT
1 A-A-AATTTTT
*
48599257 AAATTTTTTTT
1 AAA--ATTTTT
48599268 AAAA-TTTT
1 AAAATTTTT
48599276 AAAATTTTTT
1 AAAA-TTTTT
48599286 AAAA-TTTT
1 AAAATTTTT
*
48599294 AAATTTTTT
1 AAAATTTTT
48599303 AATAA-TTTT
1 AA-AATTTTT
48599312 AAAATTTTTT
1 AAAA-TTTTT
48599322 AAAA
1 AAAA
48599326 ATATAAATTT
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
8 23 0.28
9 18 0.22
10 23 0.28
11 18 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (9 bp):
AAAATTTTT
Found at i:48599246 original size:18 final size:17
Alignment explanation
Indices: 48599223--48599336 Score: 120
Period size: 18 Copynumber: 6.2 Consensus size: 17
48599213 TTTTAGAAAA
48599223 TTTTTAAAATTTTAACAT
1 TTTTTAAAATTTTAA-AT
*
48599241 TTTTTATATATTTTTTAAATTT
1 TTTTTA-A-A-ATTTTAAA--T
48599263 TTTTTAAAATTTTAAAAT
1 TTTTTAAAATTTT-AAAT
48599281 TTTTTAAAATTTTAAAT
1 TTTTTAAAATTTTAAAT
48599298 TTTTTAATAATTTTAAAAT
1 TTTTTAA-AATTTT-AAAT
* *
48599317 TTTTTAAAAATATAAAT
1 TTTTTAAAATTTTAAAT
48599334 TTT
1 TTT
48599337 GAATTTTTCA
Statistics
Matches: 84, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
17 18 0.21
18 30 0.36
19 16 0.19
20 6 0.07
21 7 0.08
22 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAAAATTTTAAAT
Found at i:48599255 original size:11 final size:11
Alignment explanation
Indices: 48599239--48599324 Score: 61
Period size: 11 Copynumber: 8.9 Consensus size: 11
48599229 AAATTTTAAC
*
48599239 ATTTTTTATAT
1 ATTTTTTAAAT
48599250 ATTTTTTAAAT
1 ATTTTTTAAAT
*
48599261 TTTTTTTAAA-
1 ATTTTTTAAAT
48599271 A--TTTTAAA-
1 ATTTTTTAAAT
48599279 ATTTTTTAAA-
1 ATTTTTTAAAT
48599289 A--TTTT-AA-
1 ATTTTTTAAAT
48599296 ATTTTTT-AAT
1 ATTTTTTAAAT
*
48599306 A-ATTTTAAA-
1 ATTTTTTAAAT
48599315 ATTTTTTAAA
1 ATTTTTTAAA
48599325 AATATAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.05
8 12 0.19
9 11 0.17
10 18 0.29
11 19 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:48603099 original size:19 final size:18
Alignment explanation
Indices: 48603077--48603120 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 18
48603067 TTTGAGTTTT
48603077 TTTTTAAAATTATTTTGAA
1 TTTTTAAAATTATTTT-AA
48603096 TTTTTGAAAATTATTTTAA
1 TTTTT-AAAATTATTTTAA
48603115 TTTTTA
1 TTTTTA
48603121 TTATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.04
19 12 0.50
20 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTTAAAATTATTTTAA
Found at i:48603105 original size:20 final size:19
Alignment explanation
Indices: 48603076--48603119 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
48603066 ATTTGAGTTT
*
48603076 TTTTTTAAAATTATTTTGAA
1 TTTTTGAAAATTATTTT-AA
48603096 TTTTTGAAAATTATTTTAA
1 TTTTTGAAAATTATTTTAA
48603115 TTTTT
1 TTTTT
48603120 ATTATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTGAAAATTATTTTAA
Found at i:48611527 original size:21 final size:21
Alignment explanation
Indices: 48611478--48611544 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
48611468 CCTCTTTGAA
* * *
48611478 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
48611501 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
48611522 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
48611543 CC
1 CC
48611545 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:48611898 original size:13 final size:13
Alignment explanation
Indices: 48611843--48611885 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
48611833 ATAGGTGCGT
* *
48611843 AAAAAAAAGTTCA
1 AAAAAAAAATTGA
48611856 AAAAAAAAATTGA
1 AAAAAAAAATTGA
48611869 AAAAAAAAATTGA
1 AAAAAAAAATTGA
48611882 AAAA
1 AAAA
48611886 TTGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTGA
Done.