Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 155 of 203
Found at i:49257713 original size:46 final size:44
Alignment explanation
Indices: 49257672--49257763 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 44
49257662 TTTGGTTCGT
*
49257672 TGAAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGAAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAA
* * *
49257718 TGGAATGGAATATAGGCGTAATGGTATTCTTGTGTTTGATTGAA
1 TGAAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAA
49257762 TG
1 TG
49257764 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 19 0.45
45 3 0.07
46 20 0.48
ACGTcount: A:0.28, C:0.04, G:0.29, T:0.38
Consensus pattern (44 bp):
TGAAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAA
Found at i:49257762 original size:44 final size:46
Alignment explanation
Indices: 49257675--49257767 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
49257665 GGTTCGTTGA
* *
49257675 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGG
*
49257721 AATGGAATATAGGCGTAAT-GGT-ATTCTTGTGTTTGATTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGG
49257765 AAT
1 AAT
49257768 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 3 0.07
46 18 0.41
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGATTGAATGG
Found at i:49257763 original size:39 final size:43
Alignment explanation
Indices: 49257675--49257779 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 43
49257665 GGTTCGTTGA
49257675 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAAT-GGTAATTC-TTTG-TTGGTTGAATGG
* * *
49257721 AATGGAATATAGGCGTAATGGT-ATTC-TTG-TGTTTG-ATTG
1 AATGGAATAGAGGCGTAATGGTAATTCTTTGTTGGTTGAATGG
*
49257760 AATGGAATAGAGGTGTAATG
1 AATGGAATAGAGGCGTAATG
49257780 TATGGCATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
39 21 0.39
40 5 0.09
42 3 0.06
44 4 0.07
45 3 0.06
46 18 0.33
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (43 bp):
AATGGAATAGAGGCGTAATGGTAATTCTTTGTTGGTTGAATGG
Found at i:49257961 original size:18 final size:18
Alignment explanation
Indices: 49257938--49258069 Score: 84
Period size: 18 Copynumber: 7.8 Consensus size: 18
49257928 TTATTATTAA
49257938 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
49257956 ATATAATTTAATAA-AAT
1 ATATAATTTAATAATAAT
*
49257973 ATATAAATTTACTAA-AAT
1 ATAT-AATTTAATAATAAT
* * * *
49257991 -CATAATAT-ATAGTACT
1 ATATAATTTAATAATAAT
* * *
49258007 ATAAAATATAAT-TTAA-
1 ATATAATTTAATAATAAT
* *
49258023 A-ATAA-TTATTATTAA-
1 ATATAATTTAATAATAAT
* *
49258038 ATATAATTTAACAAAAAT
1 ATATAATTTAATAATAAT
49258056 ATATAATTTAATAA
1 ATATAATTTAATAA
49258070 AATTTTTAGT
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
14 3 0.03
15 10 0.11
16 11 0.12
17 23 0.26
18 41 0.47
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAATAAT
Found at i:49258131 original size:61 final size:61
Alignment explanation
Indices: 49257972--49258182 Score: 161
Period size: 63 Copynumber: 3.4 Consensus size: 61
49257962 TTTAATAAAA
* *
49257972 TATATAAATTTACTAAAATCATAATATATAGTACTATAAAATATAATTTAAAATAATTATTAT
1 TATATAAA-TTACTAAAATCATAATATATAATACTATAAAATAT-ATTTAAAATAAATATTAT
* * * *
49258035 TAAATATAATT--TAACAA--A-AATATATAAT-TTAATAAAAT-T-TTTAGTATTAAATATTAT
1 TATATA-AATTACTAA-AATCATAATATATAATACT-ATAAAATATATTTA-AAATAAATATTAT
** *
49258092 TATATGAAATTACTAAAATCATAATATATAATACTATAAAATATAATTTTTAATAATTATTAT
1 TATAT-AAATTACTAAAATCATAATATATAATACTATAAAATAT-ATTTAAAATAAATATTAT
* *
49258155 T-TAATATAATTAATAAAATTCTTAATAT
1 TAT-ATA-AATTACTAAAA-TCATAATAT
49258183 TAAATATTCT
Statistics
Matches: 118, Mismatches: 13, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
56 4 0.03
57 18 0.15
58 5 0.04
59 19 0.16
60 2 0.02
61 20 0.17
62 6 0.05
63 31 0.26
64 13 0.11
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (61 bp):
TATATAAATTACTAAAATCATAATATATAATACTATAAAATATATTTAAAATAAATATTAT
Found at i:49258186 original size:101 final size:101
Alignment explanation
Indices: 49258056--49258271 Score: 351
Period size: 101 Copynumber: 2.1 Consensus size: 101
49258046 TAACAAAAAT
* *
49258056 ATATAATTTAATAAAATTTTTAGTATTAAATATTATTATATGAAATTACTAAAATCATAATATAT
1 ATATAA-TTAATAAAATTCTTAATATTAAATATTATTATATGAAATTACTAAAATCATAATATAT
** *
49258121 AATACTATAAAATATAATTTTTAATAATTATTATTTA
65 AATACTATAAAATATAATTTAAAATAATTATTATTAA
* *
49258158 ATATAATTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATA
1 ATATAATTAATAAAATTCTTAATATTAAATATTATTATATGAAATTACTAAAATCATAATATATA
49258223 ATACTATAAAATATAATTTAAAATAATTATTATTAA
66 ATACTATAAAATATAATTTAAAATAATTATTATTAA
*
49258259 ATATAATTTATAA
1 ATATAATTAATAA
49258272 TCTACTTTAT
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 100 0.94
102 6 0.06
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (101 bp):
ATATAATTAATAAAATTCTTAATATTAAATATTATTATATGAAATTACTAAAATCATAATATATA
ATACTATAAAATATAATTTAAAATAATTATTATTAA
Found at i:49270046 original size:26 final size:30
Alignment explanation
Indices: 49270015--49270072 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
49270005 TATGTGTACA
49270015 TATCTA-TTT-TTATATT-TTA-TATT-TTT
1 TATCTAGTTTCTT-TATTGTTATTATTGTTT
49270041 TATCTAGTTTCTTTATTGTTATTATTGTTT
1 TATCTAGTTTCTTTATTGTTATTATTGTTT
49270071 TA
1 TA
49270073 CTTGATGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.22
27 7 0.26
28 5 0.19
29 4 0.15
30 5 0.19
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (30 bp):
TATCTAGTTTCTTTATTGTTATTATTGTTT
Found at i:49270127 original size:16 final size:16
Alignment explanation
Indices: 49270092--49270125 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49270082 CATTTATTTA
*
49270092 TTTATTTATTTATATG
1 TTTATTTTTTTATATG
49270108 TTTATTTTTTTA-ATG
1 TTTATTTTTTTATATG
49270123 TTT
1 TTT
49270126 TAGTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTTATATG
Found at i:49270206 original size:15 final size:15
Alignment explanation
Indices: 49270188--49270218 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49270178 TTCTTATTCG
49270188 TTTTTGCTCATATTA
1 TTTTTGCTCATATTA
*
49270203 TTTTTGTTCATATTA
1 TTTTTGCTCATATTA
49270218 T
1 T
49270219 CATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTGCTCATATTA
Found at i:49270730 original size:108 final size:107
Alignment explanation
Indices: 49270273--49270806 Score: 734
Period size: 107 Copynumber: 5.0 Consensus size: 107
49270263 AAGGAAAATT
* * *
49270273 TTTCTAAA-TAAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTT
1 TTTC-AAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
* * ** *
49270337 CCGATTTTTTTGTTCAACCAAATAGCTAAATATCCTTTTAAAA
65 TCGATTTTTTCGTTTGACCAAATAGCTAAATATTCTTTTAAAA
* * * * *
49270380 TTTCAAAGTAAGGGAATATTTTGCATTTGGAAATTCGAGAAACCGTGCCCTAATGTGCTAGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
49270445 CGATTTTTTCATTTGACTAAATAGCTAAATATTCTTTTAAAA
66 CGATTTTTTCGTTTGACCAAATAGCTAAATATTCTTTTAAAA
*
49270487 TTTCAAAGTAAGGCAATATTTTGCGTTT-GAAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAG-AAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
* *
49270551 TCGATTTTTTCATTTGATCAAATAGCTAAATATTCTTTTAAAA
65 TCGATTTTTTCGTTTGACCAAATAGCTAAATATTCTTTTAAAA
49270594 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * * *
49270659 TGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
66 CGATTTTT-TCGTTTGACCAAATAGCTAAATATTCTTTTAAAA
* * ** *
49270702 TTTCAAAGTAAGGCAATATTTTGTGTTTAGAAATTCGAGGAAGTGTGCGCTAATGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
** *
49270767 CGA-TTTCCCGTTTGACCAAATAGGC-AAATATTCTCTTAAA
66 CGATTTTTTCGTTTGACCAAATA-GCTAAATATTCTTTTAAA
49270807 TCTCAATCCA
Statistics
Matches: 385, Mismatches: 37, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
106 30 0.08
107 263 0.68
108 92 0.24
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (107 bp):
TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTTCGTTTGACCAAATAGCTAAATATTCTTTTAAAA
Found at i:49272929 original size:15 final size:15
Alignment explanation
Indices: 49272909--49272939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49272899 TTTTCAGTAA
*
49272909 TTTTATTATTTTTAT
1 TTTTATTATTTATAT
49272924 TTTTATTATTTATAT
1 TTTTATTATTTATAT
49272939 T
1 T
49272940 ATTGTTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTATAT
Found at i:49273138 original size:13 final size:14
Alignment explanation
Indices: 49273120--49273157 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
49273110 CTTTTTATTC
49273120 TTTTCGTTTTTT-A
1 TTTTCGTTTTTTCA
49273133 TTTTCGTTTTTTCA
1 TTTTCGTTTTTTCA
*
49273147 TCTTC-TTTTTT
1 TTTTCGTTTTTT
49273158 TGTACATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTCGTTTTTTCA
Found at i:49274115 original size:36 final size:36
Alignment explanation
Indices: 49274074--49274145 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
49274064 ATTTCTTGAC
49274074 TCATAT-TTTTACATACATGTACAAAC-ATATATATAT
1 TCATATATTTTA-ATACATGTAC-AACTATATATATAT
* *
49274110 TCATATATTTTAATTCATGTACATCTATATATATAT
1 TCATATATTTTAATACATGTACAACTATATATATAT
49274146 ACCCATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.06
36 25 0.78
37 5 0.16
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (36 bp):
TCATATATTTTAATACATGTACAACTATATATATAT
Found at i:49274335 original size:3 final size:3
Alignment explanation
Indices: 49274327--49274386 Score: 102
Period size: 3 Copynumber: 19.7 Consensus size: 3
49274317 ATTTACGTTG
49274327 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
49274375 TTCA TGA TTA TT
1 TT-A TTA TTA TT
49274387 GCTTCTTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.96
4 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:49276225 original size:21 final size:19
Alignment explanation
Indices: 49276179--49276253 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
49276169 AATCTTCAAG
*
49276179 GATATGCGATCTTAGATAT
1 GATATGCAATCTTAGATAT
49276198 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
49276217 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
49276238 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
49276254 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:49286586 original size:42 final size:42
Alignment explanation
Indices: 49286482--49286641 Score: 154
Period size: 42 Copynumber: 3.8 Consensus size: 42
49286472 TAACTCGCAA
* * *
49286482 ATGCC-ATATCCTAGATATGGTCTTACA--AACTATCATATATCG
1 ATGCCAATGTCCTAGACATGGTCTTACACGAA-TCTCA-A-ATCG
49286524 ATGCCAATAG-CC-AG-CTATGGTCTTACACGAATCTCAAATCG
1 ATGCCAAT-GTCCTAGAC-ATGGTCTTACACGAATCTCAAATCG
* * *
49286565 ATGCCAATGTCCTAGACATGGTCTTACACGAATCTTATATCA
1 ATGCCAATGTCCTAGACATGGTCTTACACGAATCTCAAATCG
49286607 ATGCCAATGT-CTCAGACATGGTCTTACACGTAATC
1 ATGCCAATGTCCT-AGACATGGTCTTACACG-AATC
49286642 CCATCTCAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
40 1 0.01
41 16 0.16
42 70 0.69
43 13 0.13
44 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACATGGTCTTACACGAATCTCAAATCG
Found at i:49286628 original size:84 final size:83
Alignment explanation
Indices: 49286482--49286641 Score: 193
Period size: 84 Copynumber: 1.9 Consensus size: 83
49286472 TAACTCGCAA
* * *
49286482 ATGCCATATCCTAGATATGGTCTTACAAACTATCATATATCGATGCCAATAGCCAGCTATGGTCT
1 ATGCCATATCCTAGACATGGTCTTAC-AACAATCATATATCAATGCCAATAGCCAGCTATGGTCT
49286547 TACACG-AATCTCAAATCG
65 TACACGTAATCTCAAATCG
* *
49286565 ATGCCAATGTCCTAGACATGGTCTTAC-ACGAATCTTATATCAATGCCAAT-GTCTCAGAC-ATG
1 ATGCC-ATATCCTAGACATGGTCTTACAAC-AATCATATATCAATGCCAATAG-C-CAG-CTATG
49286627 GTCTTACACGTAATC
61 GTCTTACACGTAATC
49286642 CCATCTCAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
82 3 0.05
83 23 0.35
84 35 0.53
85 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (83 bp):
ATGCCATATCCTAGACATGGTCTTACAACAATCATATATCAATGCCAATAGCCAGCTATGGTCTT
ACACGTAATCTCAAATCG
Found at i:49288895 original size:16 final size:17
Alignment explanation
Indices: 49288865--49288898 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
49288855 TTCAGAAAAT
49288865 AAATAAAACAAACTAAG
1 AAATAAAACAAACTAAG
49288882 AAATAAAA-AAACTAAG
1 AAATAAAACAAACTAAG
49288898 A
1 A
49288899 TGAAATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.12
Consensus pattern (17 bp):
AAATAAAACAAACTAAG
Found at i:49290858 original size:17 final size:17
Alignment explanation
Indices: 49290836--49290868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49290826 ATGAAGTTGA
49290836 GATTTAGTAGGTTAGTG
1 GATTTAGTAGGTTAGTG
*
49290853 GATTTAGTGGGTTAGT
1 GATTTAGTAGGTTAGT
49290869 AGGAAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (17 bp):
GATTTAGTAGGTTAGTG
Found at i:49291835 original size:13 final size:14
Alignment explanation
Indices: 49291801--49291838 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
49291791 GACATGTTAA
49291801 ATCTGTTATTTCTGT
1 ATCTG-TATTTCTGT
*
49291816 ATTTGTATTT-TGT
1 ATCTGTATTTCTGT
49291829 ATCTGTATTT
1 ATCTGTATTT
49291839 GGGGTGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 5 0.24
15 4 0.19
ACGTcount: A:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (14 bp):
ATCTGTATTTCTGT
Found at i:49292715 original size:312 final size:312
Alignment explanation
Indices: 49292150--49292773 Score: 1230
Period size: 312 Copynumber: 2.0 Consensus size: 312
49292140 TTTCTGTTGG
*
49292150 GTTACACACTGAGTTTATGAAAACTAACATCTGTTGGTCTGCTCTATTTAGGTAATCCACAGACT
1 GTTACACACTGAGTTTATGAAAACTAACATCTGTTGGTCTGCTCTATTCAGGTAATCCACAGACT
49292215 TAGGCGGATCAGTGCAATGAAGTCTCATGGTGACCACGAGATGTAAACTGATTTAATAATGGTTT
66 TAGGCGGATCAGTGCAATGAAGTCTCATGGTGACCACGAGATGTAAACTGATTTAATAATGGTTT
49292280 TAATTATTTTAAGTGGTATTTCTCTGAGAGTGATGTAATTTTTGGACTCTCTGGACTGTTGGATT
131 TAATTATTTTAAGTGGTATTTCTCTGAGAGTGATGTAATTTTTGGACTCTCTGGACTGTTGGATT
49292345 TTATGTCTGGTTTCGAAGGTGTTTTTAACCTTTATTACAACATTTGACTAAAATCGCAGTTTTAC
196 TTATGTCTGGTTTCGAAGGTGTTTTTAACCTTTATTACAACATTTGACTAAAATCGCAGTTTTAC
49292410 GAAAACTAAAGTTTTTCCAAAAATACGAACTGGATTTTCGAAATATAACGAA
261 GAAAACTAAAGTTTTTCCAAAAATACGAACTGGATTTTCGAAATATAACGAA
49292462 GTTACACACTGAGTTTATGAAAACTAACATCTGTTGGTCTGCTCTATTCAGGTAATCCACAGACT
1 GTTACACACTGAGTTTATGAAAACTAACATCTGTTGGTCTGCTCTATTCAGGTAATCCACAGACT
*
49292527 TAGGCGGATCAGTGCAATGAAGTCTCATGGTGATCACGAGATGTAAACTGATTTAATAATGGTTT
66 TAGGCGGATCAGTGCAATGAAGTCTCATGGTGACCACGAGATGTAAACTGATTTAATAATGGTTT
49292592 TAATTATTTTAAGTGGTATTTCTCTGAGAGTGATGTAATTTTTGGACTCTCTGGACTGTTGGATT
131 TAATTATTTTAAGTGGTATTTCTCTGAGAGTGATGTAATTTTTGGACTCTCTGGACTGTTGGATT
49292657 TTATGTCTGGTTTCGAAGGTGTTTTTAACCTTTATTACAACATTTGACTAAAATCGCAGTTTTAC
196 TTATGTCTGGTTTCGAAGGTGTTTTTAACCTTTATTACAACATTTGACTAAAATCGCAGTTTTAC
49292722 GAAAACTAAAGTTTTTCCAAAAATACGAACTGGATTTTCGAAATATAACGAA
261 GAAAACTAAAGTTTTTCCAAAAATACGAACTGGATTTTCGAAATATAACGAA
49292774 TTTATTAGAC
Statistics
Matches: 310, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
312 310 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (312 bp):
GTTACACACTGAGTTTATGAAAACTAACATCTGTTGGTCTGCTCTATTCAGGTAATCCACAGACT
TAGGCGGATCAGTGCAATGAAGTCTCATGGTGACCACGAGATGTAAACTGATTTAATAATGGTTT
TAATTATTTTAAGTGGTATTTCTCTGAGAGTGATGTAATTTTTGGACTCTCTGGACTGTTGGATT
TTATGTCTGGTTTCGAAGGTGTTTTTAACCTTTATTACAACATTTGACTAAAATCGCAGTTTTAC
GAAAACTAAAGTTTTTCCAAAAATACGAACTGGATTTTCGAAATATAACGAA
Found at i:49296427 original size:21 final size:22
Alignment explanation
Indices: 49296403--49296445 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49296393 TTACATGTAA
* *
49296403 TTATTTAG-TAAATTATATTGT
1 TTATGTAGTTAAATAATATTGT
49296424 TTATGTAGTTAAATAATATTGT
1 TTATGTAGTTAAATAATATTGT
49296446 ACTTCGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTGT
Found at i:49301252 original size:27 final size:25
Alignment explanation
Indices: 49301211--49301283 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
49301201 ATATTTTGAT
* *
49301211 GATATTTTATAATTATTTAATTAGATAA
1 GATATTATATTATTATTT--TTA-ATAA
*
49301239 -ATATTATTTTATTAATATTTTAATAA
1 GATATTATATTATT-AT-TTTTAATAA
49301265 GATATTATATTATTATTTT
1 GATATTATATTATTATTTT
49301284 ATTTAGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
25 3 0.08
26 6 0.16
27 25 0.66
28 2 0.05
29 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
GATATTATATTATTATTTTTAATAA
Found at i:49303735 original size:3 final size:3
Alignment explanation
Indices: 49303727--49303754 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49303717 TTAACAACTA
49303727 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
49303755 CAAGTCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49313671 original size:31 final size:31
Alignment explanation
Indices: 49313653--49313722 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
49313643 TTGAACCACG
49313653 ATCAAAATT-ATATATATATAATTACACCAA
1 ATCAAAATTCATATATATATAATTACACCAA
*
49313683 ATCAAAATTCATATATA-A-AATTACACGTTAA
1 ATCAAAATTCATATATATATAATTACAC--CAA
49313714 ATCAAAATT
1 ATCAAAATT
49313723 GATTTATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.22
30 10 0.28
31 18 0.50
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (31 bp):
ATCAAAATTCATATATATATAATTACACCAA
Found at i:49313696 original size:29 final size:31
Alignment explanation
Indices: 49313653--49313722 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
49313643 TTGAACCACG
* *
49313653 ATCAAAATTATATATATATAATTACAC-CAA
1 ATCAAAATTACATATATAAAATTACACGCAA
*
49313683 ATCAAAATT-CATATATAAAATTACACGTTAA
1 ATCAAAATTACATATATAAAATTACACG-CAA
49313714 ATCAAAATT
1 ATCAAAATT
49313723 GATTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 15 0.43
30 9 0.26
31 11 0.31
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (31 bp):
ATCAAAATTACATATATAAAATTACACGCAA
Found at i:49313987 original size:19 final size:20
Alignment explanation
Indices: 49313965--49314018 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
49313955 ATAAAAAATC
49313965 ATAAAAATTTA-GAAAATAT
1 ATAAAAATTTATGAAAATAT
* *
49313984 AT-AAATTTTATGAAAATTT
1 ATAAAAATTTATGAAAATAT
*
49314003 CTAAAAA-TTATGAAAA
1 ATAAAAATTTATGAAAA
49314019 ATTCAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 19 0.66
20 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (20 bp):
ATAAAAATTTATGAAAATAT
Found at i:49314666 original size:11 final size:12
Alignment explanation
Indices: 49314635--49314664 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49314625 AAATTTATTT
49314635 ATAAAAATTAAA
1 ATAAAAATTAAA
*
49314647 ATAAAAATTAAT
1 ATAAAAATTAAA
49314659 ATAAAA
1 ATAAAA
49314665 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAATTAAA
Found at i:49317027 original size:20 final size:20
Alignment explanation
Indices: 49316990--49317028 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49316980 TAGTTTAGCC
*
49316990 ATTTTTATTTTCATTTTAAT
1 ATTTTTATTTTCAATTTAAT
* *
49317010 ATTTTTGTTTTTAATTTAA
1 ATTTTTATTTTCAATTTAA
49317029 CTTTTTACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTTATTTTCAATTTAAT
Found at i:49318234 original size:10 final size:10
Alignment explanation
Indices: 49318219--49318243 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49318209 TGGGATGGTC
49318219 AAGGTAATCA
1 AAGGTAATCA
49318229 AAGGTAATCA
1 AAGGTAATCA
49318239 AAGGT
1 AAGGT
49318244 CACAACTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (10 bp):
AAGGTAATCA
Found at i:49329083 original size:3 final size:3
Alignment explanation
Indices: 49329075--49329102 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49329065 GATAGAATGT
49329075 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
49329103 CAAAGCTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49329555 original size:17 final size:17
Alignment explanation
Indices: 49329519--49329556 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
49329509 GGGATTACTA
**
49329519 TAGTGATAATGACTCCT
1 TAGTGATAATGACTAAT
49329536 TAGTGATAATGACTAAT
1 TAGTGATAATGACTAAT
49329553 TAGT
1 TAGT
49329557 TAACTGGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (17 bp):
TAGTGATAATGACTAAT
Found at i:49338329 original size:41 final size:41
Alignment explanation
Indices: 49338272--49338355 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
49338262 AATGCATGTG
49338272 TTACAAGTGGCATCCACACATATGATTGAATATGATGTCAT
1 TTACAAGTGGCATCCACACATATGATTGAATATGATGTCAT
49338313 TTACAAGTGGCATCCACACATATGATTGAATATGATGTCAT
1 TTACAAGTGGCATCCACACATATGATTGAATATGATGTCAT
49338354 TT
1 TT
49338356 CTCTATTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (41 bp):
TTACAAGTGGCATCCACACATATGATTGAATATGATGTCAT
Found at i:49344961 original size:16 final size:17
Alignment explanation
Indices: 49344928--49344965 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
49344918 TACTTTTGTA
* *
49344928 ATATATTTATTTATTTT
1 ATATATTTATATAATTT
49344945 ATATA-TTATATAATTT
1 ATATATTTATATAATTT
49344961 ATATA
1 ATATA
49344966 CATAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATATTTATATAATTT
Found at i:49345330 original size:6 final size:6
Alignment explanation
Indices: 49345319--49345354 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
49345309 ACCAAACCCT
49345319 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA
49345355 CATCTCTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:49365959 original size:7 final size:8
Alignment explanation
Indices: 49365932--49365956 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
49365922 ATTTTTTTTT
49365932 AATTTTAA
1 AATTTTAA
49365940 AATTTTAA
1 AATTTTAA
49365948 AATTTTAA
1 AATTTTAA
49365956 A
1 A
49365957 TTTCAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:49367207 original size:24 final size:24
Alignment explanation
Indices: 49367175--49367235 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
49367165 TGGTCTCTAT
49367175 ATTTTTTTCGTTTTGA-G-TCATTTA
1 ATTTTTTTC-TTTT-ATGTTCATTTA
*
49367199 ATTTTTTTCTTTTATGTTCTTTTA
1 ATTTTTTTCTTTTATGTTCATTTA
49367223 ATTTTTTTTCTTT
1 A-TTTTTTTCTTT
49367236 ATTTTCTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 1 0.03
23 5 0.15
24 16 0.48
25 11 0.33
ACGTcount: A:0.13, C:0.08, G:0.07, T:0.72
Consensus pattern (24 bp):
ATTTTTTTCTTTTATGTTCATTTA
Found at i:49368570 original size:29 final size:28
Alignment explanation
Indices: 49368537--49368591 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
49368527 AGAATTGGAT
* *
49368537 CAAATCAAAATTTTATGTATAAAATTGCA
1 CAAAT-AAAAGTTCATGTATAAAATTGCA
*
49368566 CAAATTAAAGTTCATGTATAAAATTG
1 CAAATAAAAGTTCATGTATAAAATTG
49368592 TACATTAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (28 bp):
CAAATAAAAGTTCATGTATAAAATTGCA
Found at i:49368614 original size:31 final size:28
Alignment explanation
Indices: 49368548--49368617 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
49368538 AAATCAAAAT
*
49368548 TTTATGTATAAAATTGCACAAATTAAAG
1 TTTATGTATAAAATTGCACAAACTAAAG
* *
49368576 TTCATGTATAAAATTGTACATTAGACTAAAG
1 TTTATGTATAAAATTGCACA--A-ACTAAAG
49368607 TTTATGTATAA
1 TTTATGTATAA
49368618 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.51
30 1 0.03
31 16 0.46
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (28 bp):
TTTATGTATAAAATTGCACAAACTAAAG
Found at i:49385103 original size:22 final size:25
Alignment explanation
Indices: 49385077--49385124 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
49385067 TAAAAATTAA
49385077 TTATTTAT-AA-A-TTTTATAATTT
1 TTATTTATAAATATTTTTATAATTT
*
49385099 TTATTTCTAAATATTTTTATAATTT
1 TTATTTATAAATATTTTTATAATTT
49385124 T
1 T
49385125 GAAATAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 1 0.05
25 12 0.55
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTATAAATATTTTTATAATTT
Found at i:49404176 original size:16 final size:16
Alignment explanation
Indices: 49404157--49404190 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49404147 TATTTATATG
*
49404157 TTATTTTATTATACTA
1 TTATTTTATTAAACTA
*
49404173 TTATTTTTTTAAACTA
1 TTATTTTATTAAACTA
49404189 TT
1 TT
49404191 TCATAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTATTAAACTA
Found at i:49409262 original size:6 final size:6
Alignment explanation
Indices: 49409253--49409313 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
49409243 GGTTAAGATT
*
49409253 AAAAA- AAAAAC AAAAAC AAAAAC AAAAAAATC AAAAATC AAAATC AAAAATC
1 AAAAAC AAAAAC AAAAAC AAAAAC --AAAAA-C AAAAA-C AAAAAC AAAAA-C
*
49409305 AAAATC AAA
1 AAAAAC AAA
49409314 GTCAAAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.10
6 21 0.44
7 16 0.33
8 5 0.10
9 1 0.02
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (6 bp):
AAAAAC
Found at i:49409279 original size:21 final size:22
Alignment explanation
Indices: 49409255--49409302 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
49409245 TTAAGATTAA
49409255 AAAAAAAACAAAAA-CAAAAAC
1 AAAAAAAACAAAAATCAAAAAC
* *
49409276 AAAAAAATCAAAAATCAAAATC
1 AAAAAAAACAAAAATCAAAAAC
49409298 AAAAA
1 AAAAA
49409303 TCAAAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.06
Consensus pattern (22 bp):
AAAAAAAACAAAAATCAAAAAC
Found at i:49409280 original size:13 final size:13
Alignment explanation
Indices: 49409253--49409313 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
49409243 GGTTAAGATT
49409253 AAAA-AAAAAACA
1 AAAACAAAAAACA
*
49409265 AAAACAAAAACAAA
1 AAAACAAAAA-ACA
*
49409279 AAAATCAAAAATCA
1 AAAA-CAAAAAACA
* *
49409293 AAATCAAAAATCA
1 AAAACAAAAAACA
*
49409306 AAATCAAA
1 AAAACAAA
49409314 GTCAAAATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
12 4 0.10
13 22 0.52
14 10 0.24
15 6 0.14
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACAAAAAACA
Found at i:49409318 original size:6 final size:6
Alignment explanation
Indices: 49409279--49409332 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
49409269 CAAAAACAAA
* * *
49409279 AAAATC AAAAATC AAAATC AAAAATC AAAATC AAAGTC AAAATG AAAATG
1 AAAATC -AAAATC AAAATC -AAAATC AAAATC AAAATC AAAATC AAAATC
49409329 AAAA
1 AAAA
49409333 AAAGAGAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
6 31 0.72
7 12 0.28
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:49409347 original size:27 final size:27
Alignment explanation
Indices: 49409317--49409368 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
49409307 AATCAAAGTC
* *
49409317 AAAATGAAAATGAAAAAAAGAGAAGAA
1 AAAAAGAAAAAGAAAAAAAGAGAAGAA
* *
49409344 AAAAAGAAAAAGGAAAAAGGAGAAG
1 AAAAAGAAAAAGAAAAAAAGAGAAG
49409369 TCAAGGCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAAAGAAAAAAAGAGAAGAA
Found at i:49411072 original size:87 final size:87
Alignment explanation
Indices: 49410957--49411201 Score: 400
Period size: 87 Copynumber: 2.8 Consensus size: 87
49410947 AGATCAGTGA
* *
49410957 AGATCGAAAACAAAGCCTTGCTTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
49411022 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
** * * *
49411044 AGATCGAAAATGAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATTTTTC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
49411109 CTTCCTGCATTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* *
49411131 AGATCGAAAACAAAGCCTTGCCTCAATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
49411196 CTTCCT
66 CTTCCT
49411202 AAGCACTAGT
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 143 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTAACAGCGAAGC
Found at i:49411540 original size:44 final size:45
Alignment explanation
Indices: 49411448--49411606 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 45
49411438 CCGCATCGGG
* * * *
49411448 TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTG-AGAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAACAAA
* ** *
49411492 TCTTATCCCCCTGAAGTCACAGTGGAGCAGATTGAAG-AAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAACAAA
* * * *** *
49411536 TCTTAACTCCTTGAGGTTGCAGTGGAGCAGATTGAATTCAA-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAACAAA
* * *
49411580 TCCTATCTCCCTAAAGTTGTAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
49411607 TGGACCGAAC
Statistics
Matches: 89, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
44 86 0.97
45 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAACAAA
Found at i:49414942 original size:17 final size:17
Alignment explanation
Indices: 49414894--49414942 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
49414884 CGTGTAAGGT
* *
49414894 GACCGTGTGGGACACAC
1 GACCGTGCGGGAGACAC
49414911 GACCGTGCGGGAGACAC
1 GACCGTGCGGGAGACAC
*
49414928 GACCGTGCGGTAGAC
1 GACCGTGCGGGAGAC
49414943 CATGTTGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.39, T:0.10
Consensus pattern (17 bp):
GACCGTGCGGGAGACAC
Found at i:49420721 original size:24 final size:24
Alignment explanation
Indices: 49420671--49420725 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
49420661 AATATTTGCT
49420671 TTCTTTGAAAATAAAGTTCTTTCC
1 TTCTTTGAAAATAAAGTTCTTTCC
*
49420695 TTCCTTTGAAAAT-CAGTT-TTTCTC
1 TT-CTTTGAAAATAAAGTTCTTTC-C
49420719 TTCTTTG
1 TTCTTTG
49420726 TAAACTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 9 0.32
24 9 0.32
25 10 0.36
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (24 bp):
TTCTTTGAAAATAAAGTTCTTTCC
Found at i:49420738 original size:24 final size:23
Alignment explanation
Indices: 49420673--49420738 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
49420663 TATTTGCTTT
*
49420673 CTTTGAAAATAAAGTTCTTTCCTTC
1 CTTTGAAAATCAA-TT-TTTCCTTC
*
49420698 CTTTGAAAATCAGTTTTTCTCTT-
1 CTTTGAAAATCAATTTTTC-CTTC
*
49420721 CTTTGTAAACTCAATTTT
1 CTTTG-AAAATCAATTTT
49420739 ACCTGACATG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.26
24 15 0.43
25 11 0.31
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (23 bp):
CTTTGAAAATCAATTTTTCCTTC
Found at i:49424514 original size:19 final size:19
Alignment explanation
Indices: 49424492--49424561 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
49424482 ATAAAAAGCA
49424492 TAAAATTATAAAAAATAAT
1 TAAAATTATAAAAAATAAT
*
49424511 TAAAATTATAAAATAT-AT
1 TAAAATTATAAAAAATAAT
* * *
49424529 AAAAATTACTAGAAATTAAT
1 TAAAATTA-TAAAAAATAAT
*
49424549 TAAAATCATAAAA
1 TAAAATTATAAAA
49424562 TTTATAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 9 0.22
19 24 0.59
20 8 0.20
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (19 bp):
TAAAATTATAAAAAATAAT
Found at i:49424560 original size:38 final size:37
Alignment explanation
Indices: 49424493--49424572 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 37
49424483 TAAAAAGCAT
*
49424493 AAAATTATAAAAAATAATTAAAATTATAAAATATATA
1 AAAATTATAAAAAATAATTAAAATCATAAAATATATA
* * *
49424530 AAAATTACTAGAAATTAATTAAAATCATAAAATTTATA
1 AAAATTA-TAAAAAATAATTAAAATCATAAAATATATA
49424568 AAAAT
1 AAAAT
49424573 AATTTATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 7 0.18
38 31 0.82
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.33
Consensus pattern (37 bp):
AAAATTATAAAAAATAATTAAAATCATAAAATATATA
Found at i:49424571 original size:10 final size:9
Alignment explanation
Indices: 49424477--49424572 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 9
49424467 TTACATTTTG
49424477 AAATTATAA
1 AAATTATAA
**
49424486 AAAGCAT-A
1 AAATTATAA
49424494 AAATTATAAA
1 AAATTAT-AA
* *
49424504 AAATAATTA
1 AAATTATAA
49424513 AAATTAT-A
1 AAATTATAA
49424521 AAATATATAA
1 AAAT-TATAA
*
49424531 AAATTACTAG
1 AAATTA-TAA
*
49424541 AAATTAATTA
1 AAATT-ATAA
*
49424551 AAATCATAA
1 AAATTATAA
*
49424560 AATTTATAA
1 AAATTATAA
49424569 AAAT
1 AAAT
49424573 AATTTATTAA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
8 11 0.17
9 30 0.45
10 24 0.36
11 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:49427691 original size:46 final size:46
Alignment explanation
Indices: 49427622--49427882 Score: 429
Period size: 46 Copynumber: 5.7 Consensus size: 46
49427612 AGATTTGAGT
*
49427622 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
49427668 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
* *
49427714 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAACCTTAGCTAC
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
*
49427760 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTAC
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
* *
49427806 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGTTAC
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
* *
49427851 ACTTATCTGATC-AG-GGACAAGTGATAAGTGGT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGT
49427883 CATACGTAAG
Statistics
Matches: 203, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
43 15 0.07
44 2 0.01
45 18 0.09
46 168 0.83
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTAC
Found at i:49435667 original size:49 final size:49
Alignment explanation
Indices: 49435612--49435806 Score: 300
Period size: 49 Copynumber: 4.0 Consensus size: 49
49435602 TTCGTTTTCT
* *
49435612 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
49435661 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* * *
49435710 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
49435759 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-AATCACAT
49435807 GTTCACATGT
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 131 0.96
50 6 0.04
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
Found at i:49437160 original size:46 final size:46
Alignment explanation
Indices: 49437059--49437260 Score: 347
Period size: 46 Copynumber: 4.5 Consensus size: 46
49437049 TACGTATGAT
*
49437059 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
49437102 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
49437148 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
49437194 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
49437240 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
49437261 TCACTGATCA
Statistics
Matches: 150, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 10 0.07
44 5 0.03
45 20 0.13
46 115 0.77
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:49449579 original size:31 final size:31
Alignment explanation
Indices: 49449541--49449620 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
49449531 ATTATGCAAA
*
49449541 GAGTGACTAAATTGTAAATTTACTAATAGTT
1 GAGTGACTAAATTGTAAATTTACTAATAATT
*
49449572 GAGTGACTAAATTATAAATTTACTAATAATT
1 GAGTGACTAAATTGTAAATTTACTAATAATT
*
49449603 GAGTGACCAAATTGTAAA
1 GAGTGACTAAATTGTAAA
49449621 CTTGCTCGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (31 bp):
GAGTGACTAAATTGTAAATTTACTAATAATT
Found at i:49453134 original size:200 final size:200
Alignment explanation
Indices: 49452791--49453155 Score: 678
Period size: 200 Copynumber: 1.8 Consensus size: 200
49452781 TTAGCCTCGT
* *
49452791 GCGTGCCAAGTGGAGATTGCTGTTTGGTTCTGTCAAGGGAAGTAGTAACCGGATTTAAAAGTCCC
1 GCGTGCCAAGTAGAGATTGATGTTTGGTTCTGTCAAGGGAAGTAGTAACCGGATTTAAAAGTCCC
*
49452856 ACGCGGTTGAGGGCATTGGTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGAAGTTCTAAAT
66 ACACGGTTGAGGGCATTGGTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGAAGTTCTAAAT
49452921 CACGAACGTTTCGTGGTTATTCGATCGGTAAGAATGGAACGTTTCTAATCGGTTTTCTGTGAACA
131 CACGAACGTTTCGTGGTTATTCGATCGGTAAGAATGGAACGTTTCTAATCGGTTTTCTGTGAACA
49452986 CATTG
196 CATTG
*
49452991 GCGTGCCAAGTAGAGATTGATGTTTGGTT-TCGTCAAGGGAAGTAGTAACCGGATTTAAATGTCC
1 GCGTGCCAAGTAGAGATTGATGTTTGGTTCT-GTCAAGGGAAGTAGTAACCGGATTTAAAAGTCC
49453055 CACACGGTTGAGGGCATTGGTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGAAGTTCTAAA
65 CACACGGTTGAGGGCATTGGTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGAAGTTCTAAA
49453120 TCACGAACGTTTCGTGGTTATTCGATCGGTAAGAAT
130 TCACGAACGTTTCGTGGTTATTCGATCGGTAAGAAT
49453156 TAGTTATTGG
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
199 1 0.01
200 159 0.99
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (200 bp):
GCGTGCCAAGTAGAGATTGATGTTTGGTTCTGTCAAGGGAAGTAGTAACCGGATTTAAAAGTCCC
ACACGGTTGAGGGCATTGGTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGAAGTTCTAAAT
CACGAACGTTTCGTGGTTATTCGATCGGTAAGAATGGAACGTTTCTAATCGGTTTTCTGTGAACA
CATTG
Found at i:49455462 original size:16 final size:16
Alignment explanation
Indices: 49455437--49455469 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49455427 ATTAGATAAG
49455437 AATGGAGAAGAAGAAA
1 AATGGAGAAGAAGAAA
*
49455453 AATGGGGAAGAAGAAA
1 AATGGAGAAGAAGAAA
49455469 A
1 A
49455470 GGGGGGTTCG
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:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (16 bp):
AATGGAGAAGAAGAAA
Found at i:49457650 original size:20 final size:20
Alignment explanation
Indices: 49457627--49457733 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 20
49457617 TACATGCATG
49457627 CCCCTGATTGTACTTCGGTA
1 CCCCTGATTGTACTTCGGTA
* * * * *
49457647 CCCCTGAATGCACATAC-ATG
1 CCCCTGATTGTAC-TTCGGTA
* * *
49457667 CCTCTGATTGTATTTTGGTA
1 CCCCTGATTGTACTTCGGTA
* * * *
49457687 CCCCTGAATGCACATAC-GTG
1 CCCCTGATTGTAC-TTCGGTA
* *
49457707 CCACTGATTGTACTTCGATA
1 CCCCTGATTGTACTTCGGTA
49457727 CCCCTGA
1 CCCCTGA
49457734 ACACACATAC
Statistics
Matches: 56, Mismatches: 27, Indels: 8
0.62 0.30 0.09
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (20 bp):
CCCCTGATTGTACTTCGGTA
Found at i:49457667 original size:40 final size:40
Alignment explanation
Indices: 49457609--49457896 Score: 306
Period size: 40 Copynumber: 7.2 Consensus size: 40
49457599 ATGGTATGAA
** *
49457609 CCTGAATATACATGCATGCCCCTGATTGTACTTCGGTACC
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
* * *
49457649 CCTGAATGCACATACATGCCTCTGATTGTATTTTGGTACC
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
* * *
49457689 CCTGAATGCACATACGTGCCACTGATTGTACTTCGATACC
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
** *
49457729 CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACC
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
* * * * *
49457769 CATGAATGCACATACATGCCCTTAATTGTACTTCAGTACT
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
* * * *
49457809 CCTGAACGCACATACGTGCCCTTGATTGTACTTCGGTACT
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
* ** * * * * *
49457849 CTTGAACACGCATACGTGCCCTTGTTTGTACTACGGTACC
1 CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
*
49457889 CCTAAATG
1 CCTGAATG
49457897 TGTTTTAATG
Statistics
Matches: 208, Mismatches: 40, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 208 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (40 bp):
CCTGAATGCACATACATGCCCCTGATTGTACTTCGGTACC
Found at i:49457822 original size:120 final size:120
Alignment explanation
Indices: 49457609--49457889 Score: 368
Period size: 120 Copynumber: 2.3 Consensus size: 120
49457599 ATGGTATGAA
* * * * * *
49457609 CCTGAATATACATGCATGCCCCTGATTGTACTTCGGTACCCCTGAATGCACATACATGCCTCTGA
1 CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACCCATGAATGCACATACATGCCTCTAA
* ** *
49457674 TTGTATTTTGGTACCCCTGAATGCACATACGTGCCAC-TGATTGTACTTCGATACC
66 TTGTACTTCAGTACCCCTGAACGCACATACGTGCC-CTTGATTGTACTTCGATACC
49457729 CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACCCATGAATGCACATACATGCC-CTTA
1 CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACCCATGAATGCACATACATGCCTC-TA
* * *
49457793 ATTGTACTTCAGTACTCCTGAACGCACATACGTGCCCTTGATTGTACTTCGGTACT
65 ATTGTACTTCAGTACCCCTGAACGCACATACGTGCCCTTGATTGTACTTCGATACC
* * * * *
49457849 CTTGAACACGCATACGTGCCCTTGTTTGTACTACGGTACCC
1 CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACCC
49457890 CTAAATGTGT
Statistics
Matches: 141, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
119 2 0.01
120 139 0.99
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (120 bp):
CCTGAACACACATACATGCCCCTGTTTGTACTTCGGTACCCATGAATGCACATACATGCCTCTAA
TTGTACTTCAGTACCCCTGAACGCACATACGTGCCCTTGATTGTACTTCGATACC
Found at i:49461527 original size:11 final size:11
Alignment explanation
Indices: 49461507--49461536 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
49461497 TAAAAAAATA
49461507 AAAAAGTATTTT
1 AAAAA-TATTTT
49461519 AAAAATATTTT
1 AAAAATATTTT
49461530 AAAAATA
1 AAAAATA
49461537 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:49461529 original size:38 final size:37
Alignment explanation
Indices: 49461480--49461553 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
49461470 ATAAACACCA
*
49461480 AAAAATTATTTTTAAAATAAAAAAATAAAAAAGTATTTT
1 AAAAATTATTTTAAAAAT-AAAAAATAAAAAA-TATTTT
49461519 AAAAA-TATTTTAAAAATAAAAAATAAAAAATATTT
1 AAAAATTATTTTAAAAATAAAAAATAAAAAATATTT
49461554 ATTTATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 5 0.15
37 13 0.38
38 11 0.32
39 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (37 bp):
AAAAATTATTTTAAAAATAAAAAATAAAAAATATTTT
Found at i:49466876 original size:18 final size:17
Alignment explanation
Indices: 49466852--49466895 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
49466842 ATTTAGAAAT
49466852 TATTTTTATCAG-ATTAA
1 TATTTTTAT-AGAATTAA
49466869 TAATTTTTATAGTAATTAA
1 T-ATTTTTATAG-AATTAA
49466888 TATTTTTA
1 TATTTTTA
49466896 AAAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
TATTTTTATAGAATTAA
Found at i:49470815 original size:22 final size:22
Alignment explanation
Indices: 49470784--49470826 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49470774 TAAATGTCAA
* *
49470784 AAAAAGTAATTTAAAAAAGAAT
1 AAAAACTAATATAAAAAAGAAT
*
49470806 AAAAACTAATATAAAAGAGAA
1 AAAAACTAATATAAAAAAGAA
49470827 AAAGGAAAAG
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:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (22 bp):
AAAAACTAATATAAAAAAGAAT
Found at i:49471238 original size:17 final size:17
Alignment explanation
Indices: 49471211--49471256 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
49471201 CCAATGTAAT
* * *
49471211 AAATATATTTATTTTTA
1 AAATATTTTTAATTGTA
*
49471228 AAATTTTTTTAATTGTA
1 AAATATTTTTAATTGTA
49471245 AAATATTTTTAA
1 AAATATTTTTAA
49471257 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATATTTTTAATTGTA
Found at i:49471257 original size:11 final size:11
Alignment explanation
Indices: 49471243--49471318 Score: 63
Period size: 11 Copynumber: 7.3 Consensus size: 11
49471233 TTTTTAATTG
49471243 TAAAATATTTT
1 TAAAATATTTT
49471254 TAAAATACTTTT
1 TAAAATA-TTTT
****
49471266 TTTTTTATTTT
1 TAAAATATTTT
*
49471277 T-TAA--TTTT
1 TAAAATATTTT
49471285 -AAAATATTTT
1 TAAAATATTTT
49471295 TAAAATA-TTT
1 TAAAATATTTT
49471305 TAAAATATTTT
1 TAAAATATTTT
49471316 TAA
1 TAA
49471319 TTTTTAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
8 6 0.12
10 15 0.29
11 24 0.46
12 7 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:49471293 original size:10 final size:10
Alignment explanation
Indices: 49471280--49471329 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
49471270 TTATTTTTTA
49471280 ATTTTAAAAT
1 ATTTTAAAAT
49471290 ATTTTTAAAAT
1 A-TTTTAAAAT
49471301 ATTTTAAAAT
1 ATTTTAAAAT
*
49471311 ATTTT-TAAT
1 ATTTTAAAAT
49471320 -TTTTAAAAT
1 ATTTTAAAAT
49471329 A
1 A
49471330 AATTTTTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 4 0.11
9 6 0.17
10 15 0.43
11 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:49471336 original size:21 final size:19
Alignment explanation
Indices: 49471271--49471329 Score: 77
Period size: 18 Copynumber: 3.1 Consensus size: 19
49471261 CTTTTTTTTT
49471271 TATTTTTTAA-TTTTAAAA
1 TATTTTTTAATTTTTAAAA
*
49471289 TATTTTTAAAATATTTTAAAA
1 TATTTTT-TAAT-TTTTAAAA
49471310 TA-TTTTTAATTTTTAAAA
1 TATTTTTTAATTTTTAAAA
49471328 TA
1 TA
49471330 AATTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 17 0.47
19 5 0.14
20 4 0.11
21 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTTTAATTTTTAAAA
Found at i:49485484 original size:15 final size:16
Alignment explanation
Indices: 49485450--49485485 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
49485440 TCAATAAAAG
49485450 AAAAAATTGGAACAATAA
1 AAAAAATTGGAAC-A-AA
49485468 AAAAAATTGGAACAAA
1 AAAAAATTGGAACAAA
49485484 AA
1 AA
49485486 TTAATAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 1 0.06
18 13 0.72
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (16 bp):
AAAAAATTGGAACAAA
Found at i:49497996 original size:5 final size:5
Alignment explanation
Indices: 49497986--49498017 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
49497976 TGTTTATATA
*
49497986 TTATT TTATT TTATT TTATC TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
49498018 CCATATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:49501351 original size:33 final size:32
Alignment explanation
Indices: 49501309--49501373 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
49501299 TCGCCTTGGG
*
49501309 AAAGAGTCTACTAGTTTGCCAAGATGAGAAGA
1 AAAGAGTCTACTAGTTTGCCAAGATAAGAAGA
*
49501341 NAAAGAGTCTACTAGTTTGCCAATATAAGAAGA
1 -AAAGAGTCTACTAGTTTGCCAAGATAAGAAGA
49501374 CGGAGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (32 bp):
AAAGAGTCTACTAGTTTGCCAAGATAAGAAGA
Found at i:49510617 original size:44 final size:43
Alignment explanation
Indices: 49510388--49510711 Score: 196
Period size: 44 Copynumber: 7.5 Consensus size: 43
49510378 AGAATTGCAG
* * * * *
49510388 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTA
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACA-AA
* * * * **
49510432 ATCCTATCTCCCCGAGATTACAGTGGAGCGGATT--A-A-AGG
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAAA
* * * * * * *
49510471 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCG--CACCAG
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAAA
* * * * * *
49510512 CTCTTATTTCCCTGAGATTACAGTGGAACAGACTAAAGA-ATTTCAA
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACA----AA
* *
49510558 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAGGCCAGAA
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACA-AA
* * **
49510602 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACT
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAAA
* * * * *
49510645 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAATAAA
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAAA
*
49510687 GGATCTTATCTCCCTGAAGTTACAG
1 --ATCTTATCTCCCTGAGGTTACAG
49510712 CAGAGTAGAT
Statistics
Matches: 214, Mismatches: 54, Indels: 24
0.73 0.18 0.08
Matches are distributed among these distances:
39 26 0.12
40 2 0.01
41 27 0.13
42 5 0.02
43 30 0.14
44 91 0.43
46 32 0.15
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAAA
Found at i:49510827 original size:218 final size:214
Alignment explanation
Indices: 49510388--49510809 Score: 485
Period size: 218 Copynumber: 2.0 Consensus size: 214
49510378 AGAATTGCAG
* * *
49510388 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCCGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCCGAGATTAC
* * *
49510453 AGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGCTCTTA
66 AGTGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCACAAGCTCTTA
*** * * * * * *
49510518 TTTCCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAAATCTTATCTCCCTGAGGTTACAGTG
131 TTTCCCTGAGATTACAGTGGAACAGACTAAAGAACAACAAATCATACCCCCCTAAAGTTACAGCG
** *
49510583 GAGCAGATTGAGGCCAGAA
196 GAGCAGACAGAGGACAGAA
*
49510602 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACT-ATCCTATCTCCCTGA-AGTTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCCGAGA-TTA
*
49510665 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAA
65 CAGTGGAGCGGA-T----TAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCA-CAA
* * * * *
49510730 G-TCTTATTTCCCTGAAGA-TGCAGTGGAATAGACTGAA-AACAACAAGTCATGCCCCCCTAAAG
124 GCTCTTATTTCCCTG-AGATTACAGTGGAACAGACTAAAGAACAACAAATCATACCCCCCTAAAG
** *
49510792 TTGTAGCGGAGCGGACAG
188 TTACAGCGGAGCAGACAG
49510810 TAGATAGCAA
Statistics
Matches: 173, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
212 1 0.01
213 29 0.17
214 41 0.24
217 27 0.16
218 69 0.40
219 6 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (214 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCCGAGATTAC
AGTGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCACAAGCTCTTA
TTTCCCTGAGATTACAGTGGAACAGACTAAAGAACAACAAATCATACCCCCCTAAAGTTACAGCG
GAGCAGACAGAGGACAGAA
Found at i:49512595 original size:3 final size:3
Alignment explanation
Indices: 49512587--49512622 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
49512577 GTTTGTTTAG
*
49512587 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49512623 CCTTACTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49519864 original size:12 final size:12
Alignment explanation
Indices: 49519830--49519855 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49519820 TTGGAGCAAC
49519830 TGCTGCTGCTGT
1 TGCTGCTGCTGT
49519842 TGCTGCTGCTGT
1 TGCTGCTGCTGT
49519854 TG
1 TG
49519856 TTGTTGCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (12 bp):
TGCTGCTGCTGT
Found at i:49521902 original size:4 final size:4
Alignment explanation
Indices: 49521890--49521922 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
49521880 TGATGGATGG
49521890 CATC ACATC CATC CATC CATC CATC CATC CATC
1 CATC -CATC CATC CATC CATC CATC CATC CATC
49521923 ATGAATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.27, C:0.48, G:0.00, T:0.24
Consensus pattern (4 bp):
CATC
Found at i:49527458 original size:13 final size:12
Alignment explanation
Indices: 49527433--49527475 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
49527423 GAAACGAAAC
49527433 AGAAAGAAAAAA
1 AGAAAGAAAAAA
49527445 AGAAAGACAAAAA
1 AGAAAGA-AAAAA
*
49527458 AGAAA-AAAGGAA
1 AGAAAGAAA-AAA
49527470 AGAAAG
1 AGAAAG
49527476 GAAGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 15 0.56
13 10 0.37
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:49528474 original size:40 final size:40
Alignment explanation
Indices: 49528387--49528480 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
49528377 TAATTTGATC
*
49528387 AGACACTGGGTGCC-AA-T-TTACTTCGATTTAACCAAAG
1 AGACACTGGGTGCCAAATTATTACTTCGAATTAACCAAAG
* * * *
49528424 AGACATTGGGTGTCAAATTATTACTTCGAATTATCCAATG
1 AGACACTGGGTGCCAAATTATTACTTCGAATTAACCAAAG
*
49528464 AGGCACTGGGTGCCAAA
1 AGACACTGGGTGCCAAA
49528481 CTGGTGTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 12 0.26
38 2 0.04
39 1 0.02
40 31 0.67
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (40 bp):
AGACACTGGGTGCCAAATTATTACTTCGAATTAACCAAAG
Found at i:49532281 original size:20 final size:20
Alignment explanation
Indices: 49532250--49532308 Score: 79
Period size: 18 Copynumber: 3.1 Consensus size: 20
49532240 TTGTAAATTT
49532250 AATATA-TATATTATAATAA
1 AATATATTATATTATAATAA
*
49532269 AATATGTTATATTATAAT--
1 AATATATTATATTATAATAA
*
49532287 ATTATATTATATTATAATAA
1 AATATATTATATTATAATAA
49532307 AA
1 AA
49532309 CAAAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 16 0.48
19 5 0.15
20 12 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AATATATTATATTATAATAA
Found at i:49532497 original size:24 final size:24
Alignment explanation
Indices: 49532470--49532518 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
49532460 ACCCTCATAG
*
49532470 TCATCTTCATCTCCAC-TCTCGACT
1 TCATCTTCATCCCCACAT-TCGACT
49532494 TCATCTTCATCCCCACATTCGACT
1 TCATCTTCATCCCCACATTCGACT
49532518 T
1 T
49532519 TGTTTTCGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.18, C:0.41, G:0.04, T:0.37
Consensus pattern (24 bp):
TCATCTTCATCCCCACATTCGACT
Found at i:49539444 original size:45 final size:45
Alignment explanation
Indices: 49539367--49539497 Score: 106
Period size: 45 Copynumber: 2.9 Consensus size: 45
49539357 TATAGACGTA
* * * *
49539367 AAAATAAGTAAGATCATAGTTGAAAGATGCTATAACATCATGACG
1 AAAATAAGTAAGACCATAGCTGAAAAACGCTATAACATCATGACG
* * **
49539412 AAAATGAGTAAGACCATGGCTGAAAAACGCTATGGCATCATG--G
1 AAAATAAGTAAGACCATAGCTGAAAAACGCTATAACATCATGACG
** * *
49539455 TAAAA-AAGACTAAGACCATAATTGAAAAATGCTATAGCATCAT
1 -AAAATAAG--TAAGACCATAGCTGAAAAACGCTATAACATCAT
49539498 TGATAGTTCA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
43 3 0.04
44 4 0.06
45 62 0.90
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (45 bp):
AAAATAAGTAAGACCATAGCTGAAAAACGCTATAACATCATGACG
Found at i:49546546 original size:42 final size:42
Alignment explanation
Indices: 49546442--49546554 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
49546432 TCAAAATCTG
* * * *
49546442 AACAGAAGCTTATTAGAGCTAAACAAAAACCCATAAGGGTTG
1 AACAGAAGCTCAATAGAGCTGAACAAAAACCCATAAGGGTTA
* * *
49546484 AACAGAAGCTCGCA-AGAGCTGAACAGAAACTCATAAGGGTTA
1 AACAGAAGCTC-AATAGAGCTGAACAAAAACCCATAAGGGTTA
*
49546526 AACAGAAGCTCAATAAAGCTGAACAAAAA
1 AACAGAAGCTCAATAGAGCTGAACAAAAA
49546555 GTAAACACGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAATAGAGCTGAACAAAAACCCATAAGGGTTA
Found at i:49546550 original size:21 final size:20
Alignment explanation
Indices: 49546423--49546550 Score: 69
Period size: 21 Copynumber: 6.2 Consensus size: 20
49546413 ATACATCGTT
*
49546423 AACAGAAGCTCA-AAATCTG
1 AACAGAAGCTCATAAAGCTG
* * *
49546442 AACAGAAGCTTATTAGAGCTA
1 AACAGAAGCTCA-TAAAGCTG
* * * * *
49546463 AACAAAAACCCATAAGGGTTG
1 AACAGAAGCTCATAA-AGCTG
**
49546484 AACAGAAGCTCGCAAGAGCTG
1 AACAGAAGCTCATAA-AGCTG
* * * *
49546505 AACAGAAACTCATAAGGGTTA
1 AACAGAAGCTCATAA-AGCTG
49546526 AACAGAAGCTCAATAAAGCTG
1 AACAGAAGCTC-ATAAAGCTG
49546547 AACA
1 AACA
49546551 AAAAGTAAAC
Statistics
Matches: 76, Mismatches: 29, Indels: 6
0.68 0.26 0.05
Matches are distributed among these distances:
19 11 0.14
20 2 0.03
21 59 0.78
22 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (20 bp):
AACAGAAGCTCATAAAGCTG
Found at i:49549171 original size:26 final size:26
Alignment explanation
Indices: 49549112--49549172 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
49549102 GGAAAAGTGT
* *
49549112 TATTTTCCCATTAAAAGTAAAGAAAA
1 TATTTTCTCACTAAAAGTAAAGAAAA
49549138 TATTTTCTCACTAAAAGTAAAGAAAA
1 TATTTTCTCACTAAAAGTAAAGAAAA
49549164 TATTTTCTC
1 TATTTTCTC
49549173 TTCTTGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (26 bp):
TATTTTCTCACTAAAAGTAAAGAAAA
Found at i:49555215 original size:7 final size:7
Alignment explanation
Indices: 49555205--49555229 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49555195 TCATCTTTCA
49555205 TATTAAT
1 TATTAAT
49555212 TATTAAT
1 TATTAAT
49555219 TATTAAT
1 TATTAAT
49555226 TATT
1 TATT
49555230 CGTTGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTAAT
Found at i:49557724 original size:19 final size:19
Alignment explanation
Indices: 49557700--49557742 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
49557690 AATATTGGTA
49557700 AAATCTCAT-AAATTTTCGT
1 AAATCT-ATAAAATTTTCGT
*
49557719 AAATCTATAGAAATTTTGGT
1 AAATCTATA-AAATTTTCGT
49557739 AAAT
1 AAAT
49557743 TGTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 6 0.29
20 13 0.62
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATCTATAAAATTTTCGT
Found at i:49557795 original size:80 final size:80
Alignment explanation
Indices: 49557689--49557855 Score: 187
Period size: 80 Copynumber: 2.1 Consensus size: 80
49557679 GAAATTTTGG
* * * ** *
49557689 AAATATTGGTAAAATCTCATAAATTTTCGTAAAT-CTATAGAAATTTTGGTAAATTGTTAAATAT
1 AAATATTAGTAAAATCTCATAAATTTTCGTAAATCCT-TAAAAATTTTAGTAAATCATTAAACAT
*
49557753 GTTGGTAATTCCTTAA
65 GTTGGTAAATCCTTAA
* *
49557769 AAATATTAGT-AAATCATCA-AATATTTTGGTAAATCCTTAAAAATTTTAGTAAATCATTAGACA
1 AAATATTAGTAAAATC-TCATAA-ATTTTCGTAAATCCTTAAAAATTTTAGTAAATCATTAAACA
* *
49557832 TTTTGGTAAATCCTTAG
64 TGTTGGTAAATCCTTAA
49557849 AAATATT
1 AAATATT
49557856 GGGAAAACGT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 7 0.10
80 64 0.88
81 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (80 bp):
AAATATTAGTAAAATCTCATAAATTTTCGTAAATCCTTAAAAATTTTAGTAAATCATTAAACATG
TTGGTAAATCCTTAA
Found at i:49557981 original size:21 final size:19
Alignment explanation
Indices: 49557947--49557989 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
49557937 TAAGGTTTAG
49557947 AAAATTTAAAAATATCGGT
1 AAAATTTAAAAATATCGGT
*
49557966 AAAATTTTAGAAAATATTGGT
1 AAAA-TTTA-AAAATATCGGT
49557987 AAA
1 AAA
49557990 GTCTCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAATATCGGT
Found at i:49558310 original size:40 final size:40
Alignment explanation
Indices: 49557999--49558348 Score: 271
Period size: 40 Copynumber: 8.8 Consensus size: 40
49557989 AGTCTCATAA
* ** * *
49557999 ATATTGGTAATTCAATAAAAATTTTGGTAAATCGTTAGAT
1 ATATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
* * * *
49558039 ATTTTGATAAAACATT-GAAATTTTTGGTAAATTGTTAGAT
1 ATATTGGTAAATCCTTAGAAA-TTTTGGTAAATTGTTAGAT
* * * * *
49558079 GTTTTGGTAACA-CTTTA-AATTTTTTGGTAATTTGTTAGAT
1 ATATTGGTAA-ATCCTTAGAA-ATTTTGGTAAATTGTTAGAT
* * * * * * *
49558119 ATATCGATAATTTCTTAGAAATTTTGGTAAACTATTGGAT
1 ATATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
* *** * *
49558159 ATATTGGTAAATCCTTAGAAATATTGGTAAAACCTCACA-
1 ATATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
** * *
49558198 AGTATTGGTAAATCGATAGAAATTTTGGAAAACTGTTAGAT
1 A-TATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
*
49558239 ATTTTGGTAAATCCTTA-AAATTATTGGTAAATTGTTAGAT
1 ATATTGGTAAATCCTTAGAAATT-TTGGTAAATTGTTAGAT
* *
49558279 ATATTGGTAAATCCTTAGAAATTTTGGTAAATTATTAGAC
1 ATATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
* * *
49558319 ATTTTGGTAAAGT-CATAGAAATTTTAGTAA
1 ATATTGGTAAA-TCCTTAGAAATTTTGGTAA
49558349 TTATTATGAC
Statistics
Matches: 244, Mismatches: 55, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
39 9 0.04
40 225 0.92
41 10 0.04
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (40 bp):
ATATTGGTAAATCCTTAGAAATTTTGGTAAATTGTTAGAT
Found at i:49558337 original size:20 final size:20
Alignment explanation
Indices: 49557709--49558348 Score: 182
Period size: 20 Copynumber: 31.6 Consensus size: 20
49557699 AAAATCTCAT
*
49557709 AAATTTTCGTAAATC-TATAG
1 AAATTTTGGTAAATCAT-TAG
**
49557729 AAATTTTGGTAAATTGTTA-
1 AAATTTTGGTAAATCATTAG
* * * *
49557748 AATATGTTGGTAATTCCTTAA
1 AA-ATTTTGGTAAATCATTAG
* * *
49557769 AAATATTAGTAAATCATCA-
1 AAATTTTGGTAAATCATTAG
* *
49557788 AATATTTTGGTAAATCCTTAA
1 AA-ATTTTGGTAAATCATTAG
*
49557809 AAATTTTAGTAAATCATTAG
1 AAATTTTGGTAAATCATTAG
* *
49557829 ACATTTTGGTAAATCCTTAG
1 AAATTTTGGTAAATCATTAG
* * * *
49557849 AAATATTGGGAAAACGTTAG
1 AAATTTTGGTAAATCATTAG
* ** * * *
49557869 ATATACTAGTATATCCTTAG
1 AAATTTTGGTAAATCATTAG
*
49557889 ATATTTTGGTAAAGTCA-TAG
1 AAATTTTGGTAAA-TCATTAG
* **
49557909 AAATTTCGGT-AATTGTTA-
1 AAATTTTGGTAAATCATTAG
* *
49557927 AAACTTGGTATAAGGTTTAGAA-AATTTAA
1 AAA-TT--T-T--GG--TA-AATCA-TTAG
* * *
49557956 AAATATCGGTAAAAT-TTTAG
1 AAATTTTGGT-AAATCATTAG
* * *
49557976 AAAATATTGGTAAAGTC-TCAT
1 -AAATTTTGGTAAA-TCATTAG
* * * *
49557997 AAATATTGGTAATTCAATAA
1 AAATTTTGGTAAATCATTAG
*
49558017 AAATTTTGGTAAATCGTTAG
1 AAATTTTGGTAAATCATTAG
* * *
49558037 ATATTTTGATAAAACATT-G
1 AAATTTTGGTAAATCATTAG
**
49558056 AAATTTTTGGTAAATTGTTAG
1 AAA-TTTTGGTAAATCATTAG
** *
49558077 ATGTTTTGGTAACA-CTTTA-
1 AAATTTTGGTAA-ATCATTAG
* * **
49558096 AATTTTTTGGTAATTTGTTAG
1 AA-ATTTTGGTAAATCATTAG
* * * * *
49558117 ATATATCGATAATTTC-TTAG
1 AAATTTTGGTAA-ATCATTAG
*
49558137 AAATTTTGGTAAA-CTATTGG
1 AAATTTTGGTAAATC-ATTAG
* * *
49558157 ATATATTGGTAAATCCTTAG
1 AAATTTTGGTAAATCATTAG
* * * * *
49558177 AAATATTGGTAAAACCTCAC
1 AAATTTTGGTAAATCATTAG
* *
49558197 AAGTATTGGTAAATCGA-TAG
1 AAATTTTGGTAAATC-ATTAG
* *
49558217 AAATTTTGG-AAAACTGTTAG
1 AAATTTTGGTAAATC-ATTAG
* *
49558237 ATATTTTGGTAAATCCTTA-
1 AAATTTTGGTAAATCATTAG
**
49558256 AAATTATTGGTAAATTGTTAG
1 AAATT-TTGGTAAATCATTAG
* * *
49558277 ATATATTGGTAAATCCTTAG
1 AAATTTTGGTAAATCATTAG
*
49558297 AAATTTTGGTAAATTATTAG
1 AAATTTTGGTAAATCATTAG
*
49558317 ACATTTTGGTAAAGTCA-TAG
1 AAATTTTGGTAAA-TCATTAG
*
49558337 AAATTTTAGTAA
1 AAATTTTGGTAA
49558349 TTATTATGAC
Statistics
Matches: 452, Mismatches: 127, Indels: 82
0.68 0.19 0.12
Matches are distributed among these distances:
18 5 0.01
19 24 0.05
20 368 0.81
21 39 0.09
22 1 0.00
23 2 0.00
24 2 0.00
26 2 0.00
28 6 0.01
29 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (20 bp):
AAATTTTGGTAAATCATTAG
Found at i:49558444 original size:20 final size:20
Alignment explanation
Indices: 49558421--49558495 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
49558411 GGTAAAAAGA
*
49558421 TAGAATTTTTGGTAAATGCT
1 TAGAAATTTTGGTAAATGCT
* *
49558441 TAGAAATATTGGTAAATCCT
1 TAGAAATTTTGGTAAATGCT
* * *
49558461 TAGATATTATGGTAAA-GTT
1 TAGAAATTTTGGTAAATGCT
49558480 ATAGAAATTTTGGTAA
1 -TAGAAATTTTGGTAA
49558496 TTGTTAATAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (20 bp):
TAGAAATTTTGGTAAATGCT
Found at i:49558476 original size:60 final size:60
Alignment explanation
Indices: 49558383--49558495 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
49558373 AGAAAAATTG
*
49558383 GAAATATTGGTAAAGTCTCATAAATATTGGTAAAAAGATAGAATTTTTGGTAAATGCTTA
1 GAAATATTGGTAAAGTCTCATAAATATTGGTAAAAAGATAGAAATTTTGGTAAATGCTTA
* * ***
49558443 GAAATATTGGTAAA-TC-CTTAGATATTATGGTAAAGTTATAGAAATTTTGGTAA
1 GAAATATTGGTAAAGTCTCATAAATA-T-TGGTAAAAAGATAGAAATTTTGGTAA
49558496 TTGTTAATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 6 0.13
59 3 0.07
60 36 0.80
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (60 bp):
GAAATATTGGTAAAGTCTCATAAATATTGGTAAAAAGATAGAAATTTTGGTAAATGCTTA
Found at i:49558580 original size:147 final size:146
Alignment explanation
Indices: 49558260--49558623 Score: 389
Period size: 147 Copynumber: 2.5 Consensus size: 146
49558250 TCCTTAAAAT
* * * * ** *
49558260 TATTGGTAAATTGTTAGATATATTGGTAAATCCTTAGAAATTTTGGTAAATTATTAGACATTTTG
1 TATTGGTAAA-AGATAGAAATATTGGTAAATGCTTAGAAATTTTGGTAAATCCTTAGAAATTTTG
*
49558325 GTAAAGTCATAGAAATTTTAGTAATTATTATGACTTGGTATAGTGTTTAGAAAAATTGGAAATAT
65 GTAAAGTCATAGAAATTTTAGTAATTATTATGACTTGGTATAGTGTTTAGAAAAATTGAAAATAT
* *
49558390 TGGTAAAGTCTCATAAA
130 TGATAAAATCTCATAAA
* * * * *
49558407 TATTGGTAAAAAGATAGAATTTTTGGTAAATGCTTAGAAATATTGGTAAATCCTTAGATATTATG
1 TATTGGT-AAAAGATAGAAATATTGGTAAATGCTTAGAAATTTTGGTAAATCCTTAGAAATTTTG
* * * *
49558472 GTAAAGTTATAGAAATTTTGGTAATTGTTAAT-ACTTGGTATAAG-GTTTAGAAAATTTGAAAAT
65 GTAAAGTCATAGAAATTTTAGTAATTATT-ATGACTTGGTAT-AGTGTTTAGAAAAATTGAAAAT
*
49558535 ATTGATAAAATCT-TTAAA
128 ATTGATAAAATCTCATAAA
* * * *
49558553 TTTTCGGT-AAAGTCTCATAAATATTGGTAAAATGAC--AGAAATTTTGGTAAATCCTTAAAAAT
1 TATT-GGTAAAAG-AT-AGAAATATTGGT-AAATG-CTTAGAAATTTTGGTAAATCCTTAGAAAT
49558615 TTTGGTAAA
61 TTTGGTAAA
49558624 TCGTTAGATA
Statistics
Matches: 181, Mismatches: 28, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
145 4 0.02
146 8 0.04
147 156 0.86
148 12 0.07
149 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (146 bp):
TATTGGTAAAAGATAGAAATATTGGTAAATGCTTAGAAATTTTGGTAAATCCTTAGAAATTTTGG
TAAAGTCATAGAAATTTTAGTAATTATTATGACTTGGTATAGTGTTTAGAAAAATTGAAAATATT
GATAAAATCTCATAAA
Found at i:49558581 original size:20 final size:19
Alignment explanation
Indices: 49558531--49558585 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
49558521 GAAAATTTGA
* *
49558531 AAATATTGATAAAATCTTT
1 AAATATTGGTAAAATCTAT
* *
49558550 AAATTTTCGGTAAAGTCTCAT
1 AAATATT-GGTAAAATCT-AT
49558571 AAATATTGGTAAAAT
1 AAATATTGGTAAAAT
49558586 GACAGAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 6 0.21
20 15 0.54
21 7 0.25
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (19 bp):
AAATATTGGTAAAATCTAT
Found at i:49558620 original size:40 final size:40
Alignment explanation
Indices: 49558571--49558662 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
49558561 AAAGTCTCAT
49558571 AAATATTGGTAAAAT-GACAGAAATTTTGGTAAATCCTTAA
1 AAATATTGGTAAAATCGACAGAAATTTTGG-AAATCCTTAA
* ** * * *
49558611 AAATTTTGGT-AAATCGTTAGATATTTTGGGAATCCTTAG
1 AAATATTGGTAAAATCGACAGAAATTTTGGAAATCCTTAA
49558650 AAATATTGGTAAA
1 AAATATTGGTAAA
49558663 TCTTTAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 21 0.49
40 22 0.51
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (40 bp):
AAATATTGGTAAAATCGACAGAAATTTTGGAAATCCTTAA
Found at i:49558649 original size:19 final size:20
Alignment explanation
Indices: 49558589--49558664 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
49558579 GTAAAATGAC
49558589 AGAAATTTTGGTAAATCCTT
1 AGAAATTTTGGTAAATCCTT
* *
49558609 AAAAATTTTGGTAAATCGTT
1 AGAAATTTTGGTAAATCCTT
* *
49558629 AGATATTTTGG-GAATCCTT
1 AGAAATTTTGGTAAATCCTT
*
49558648 AGAAATATTGGTAAATC
1 AGAAATTTTGGTAAATC
49558665 TTTAAAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
19 15 0.33
20 31 0.67
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (20 bp):
AGAAATTTTGGTAAATCCTT
Found at i:49558659 original size:39 final size:40
Alignment explanation
Indices: 49558571--49558664 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
49558561 AAAGTCTCAT
49558571 AAATATTGGTAAAAT-GACAGAAATTTTGGTAAATCCTTAA
1 AAATATTGGT-AAATCGACAGAAATTTTGGTAAATCCTTAA
* ** * * *
49558611 AAATTTTGGTAAATCGTTAGATATTTTGG-GAATCCTTAG
1 AAATATTGGTAAATCGACAGAAATTTTGGTAAATCCTTAA
49558650 AAATATTGGTAAATC
1 AAATATTGGTAAATC
49558665 TTTAAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 26 0.57
40 20 0.43
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (40 bp):
AAATATTGGTAAATCGACAGAAATTTTGGTAAATCCTTAA
Found at i:49558802 original size:40 final size:40
Alignment explanation
Indices: 49558758--49558839 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
49558748 AGCCTCATAA
* ** *
49558758 ATATTGATATAATGATAGAAATATT-GATAAGTTGTTAGAT
1 ATATTGATAAAACAATAGAAAT-TTCGATAAATTGTTAGAT
* *
49558798 ATATTGGTAAAACAATATAAATTTCGATAAATTGTTAGAT
1 ATATTGATAAAACAATAGAAATTTCGATAAATTGTTAGAT
49558838 AT
1 AT
49558840 TTTGGTAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (40 bp):
ATATTGATAAAACAATAGAAATTTCGATAAATTGTTAGAT
Found at i:49559180 original size:20 final size:20
Alignment explanation
Indices: 49559129--49559181 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
49559119 GAAAATTTGG
*
49559129 AAATATTGATAAAATCTTAT
1 AAATATTGGTAAAATCTTAT
* * *
49559149 AAATTTTAGTAAAGTCTTAT
1 AAATATTGGTAAAATCTTAT
49559169 AAATATTGGTAAA
1 AAATATTGGTAAA
49559182 TCAATATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATATTGGTAAAATCTTAT
Found at i:49559572 original size:15 final size:15
Alignment explanation
Indices: 49559552--49559591 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
49559542 TTGAACCCAA
49559552 CATCTTCATCCTCGT
1 CATCTTCATCCTCGT
49559567 CATCTTCATCCTCGT
1 CATCTTCATCCTCGT
*
49559582 CTTCTTCATC
1 CATCTTCATC
49559592 AAGTGGTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.40, G:0.05, T:0.42
Consensus pattern (15 bp):
CATCTTCATCCTCGT
Found at i:49560979 original size:46 final size:46
Alignment explanation
Indices: 49560914--49561085 Score: 157
Period size: 46 Copynumber: 3.7 Consensus size: 46
49560904 TTTCGAACTA
* * * *
49560914 CTGCATATGTTGTGGACTCGAGAATGCAAGAATAGGTTCCAAGCTC
1 CTGCATACGTTGCGAACTCGAGAATACAAGAATAGGTTCCAAGCTC
* * * * ***
49560960 CTGCATACGTTGCGTACTCGAGAATATAGGATTAGGTTTTGAGCTC
1 CTGCATACGTTGCGAACTCGAGAATACAAGAATAGGTTCCAAGCTC
* * * * *
49561006 CTACATACATTGCGAACTTGAGAATACAAAAATAGGTTCCAAGTTC
1 CTGCATACGTTGCGAACTCGAGAATACAAGAATAGGTTCCAAGCTC
* * *
49561052 CTGCAT-CTATTGCGAACTTGAGAATACAAAAATA
1 CTGCATAC-GTTGCGAACTCGAGAATACAAGAATA
49561086 TTAAGCCCTG
Statistics
Matches: 102, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
45 1 0.01
46 101 0.99
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (46 bp):
CTGCATACGTTGCGAACTCGAGAATACAAGAATAGGTTCCAAGCTC
Found at i:49562795 original size:20 final size:21
Alignment explanation
Indices: 49562759--49562801 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
49562749 TATTTGTAAT
* *
49562759 ATTTATTTTTAATAGTTTTAA
1 ATTTATTATTAATAGTTTAAA
49562780 ATTTATTATT-ATAGTTTAAA
1 ATTTATTATTAATAGTTTAAA
49562800 AT
1 AT
49562802 GTAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
ATTTATTATTAATAGTTTAAA
Found at i:49563081 original size:22 final size:20
Alignment explanation
Indices: 49563056--49563110 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
49563046 AAATAATAAT
49563056 ATATTTTTTAAAATTATTATCA
1 ATATTTTTTAAAA-T-TTATCA
*
49563078 ATATGTTTT-AAATTTATCA
1 ATATTTTTTAAAATTTATCA
49563097 ATATTATTTTAAAA
1 ATATT-TTTTAAAA
49563111 AATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 10 0.34
20 5 0.17
21 6 0.21
22 8 0.28
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATTTTTTAAAATTTATCA
Found at i:49571461 original size:30 final size:31
Alignment explanation
Indices: 49571401--49571462 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
49571391 TAATAATGAT
* * * *
49571401 ATTTAATTATGAGAATGTTTTTGTTTTAATC
1 ATTTAATTATAAAAATGTTTTCGATTTAATC
49571432 ATTTAATTATAAAAAT-TTTTCGATTTAATC
1 ATTTAATTATAAAAATGTTTTCGATTTAATC
49571462 A
1 A
49571463 CTAAATTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (31 bp):
ATTTAATTATAAAAATGTTTTCGATTTAATC
Found at i:49573454 original size:251 final size:251
Alignment explanation
Indices: 49573003--49573514 Score: 920
Period size: 251 Copynumber: 2.0 Consensus size: 251
49572993 CACGACATGT
*
49573003 AAAT-CATTTACTAAAACTTACCATTTGGTACCAATCATACTACTTATTCAATAGCATCAAATAC
1 AAATACATATACTAAAACTTACCATTTGGTACCAATCATACTACTTATTCAATAGCATCAAATAC
49573067 ATATACACTTACTATAGCATAGTAACAAATCACACCAAGTTAGAAAAAGTACCTCATATGCATTT
66 ATATACACTTACTATAGCATAGTAACAAATCACACCAAGTTAGAAAAAGTACCTCATATGCATTT
*
49573132 TCAACTACTATTTTACCTTTCATCATTAAACTACAAATCATTCCACACATCAACATTTTAAAGCA
131 TCAACTACTATTTTACCTTTCATCATTAAACCACAAATCATTCCACACATCAACATTTTAAAGCA
49573197 AATTATGCACATA-TCAAAATACCAAAACATAAGCCAAATGAGTGGCTAAACTCAAC
196 AATTATGCACATACT-AAAATACCAAAACATAAGCCAAATGAGTGGCTAAACTCAAC
**
49573253 AAATACATATACTAAAACTTACCATTTGGTACCAATTGTACTACTTATTCAATAGCATCAAATAC
1 AAATACATATACTAAAACTTACCATTTGGTACCAATCATACTACTTATTCAATAGCATCAAATAC
* * *
49573318 ATATACACTTACTATAGCATAGTACCAAATCAGACCAAGTTAGAAAACGTACCTCATATGCATTT
66 ATATACACTTACTATAGCATAGTAACAAATCACACCAAGTTAGAAAAAGTACCTCATATGCATTT
* *
49573383 TCAACTACTATTTTACCTTTCATCATTCAACCACAAATCATTCCACACATCAACATTTTAAAGTA
131 TCAACTACTATTTTACCTTTCATCATTAAACCACAAATCATTCCACACATCAACATTTTAAAGCA
49573448 AATTATGCACATACTAAAATACCAAAACATAAGCCAAATGAGTGGCTAAACTCAAC
196 AATTATGCACATACTAAAATACCAAAACATAAGCCAAATGAGTGGCTAAACTCAAC
49573504 AAATACATATA
1 AAATACATATA
49573515 AGCCAACATT
Statistics
Matches: 251, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
250 4 0.02
251 246 0.98
252 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (251 bp):
AAATACATATACTAAAACTTACCATTTGGTACCAATCATACTACTTATTCAATAGCATCAAATAC
ATATACACTTACTATAGCATAGTAACAAATCACACCAAGTTAGAAAAAGTACCTCATATGCATTT
TCAACTACTATTTTACCTTTCATCATTAAACCACAAATCATTCCACACATCAACATTTTAAAGCA
AATTATGCACATACTAAAATACCAAAACATAAGCCAAATGAGTGGCTAAACTCAAC
Found at i:49574612 original size:21 final size:21
Alignment explanation
Indices: 49574586--49574646 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
49574576 ACACGTCAAT
*
49574586 AGAAGCTCGTGAAAGCTGAAC
1 AGAAGCTCGTGAGAGCTGAAC
*
49574607 AGAAGCTCGTTAGAGCTGAAC
1 AGAAGCTCGTGAGAGCTGAAC
49574628 AGAAGCTCGTGAGAGCTGA
1 AGAAGCTCGTGAGAGCTGA
49574647 TCCACCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.16
Consensus pattern (21 bp):
AGAAGCTCGTGAGAGCTGAAC
Found at i:49576877 original size:5 final size:5
Alignment explanation
Indices: 49576867--49576895 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
49576857 CTATAATGTT
49576867 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
49576896 TATTATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:49584922 original size:46 final size:45
Alignment explanation
Indices: 49584856--49585017 Score: 263
Period size: 46 Copynumber: 3.6 Consensus size: 45
49584846 TTTGAGTACT
*
49584856 TCTGATCAGTGGCAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
49584901 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
49584947 TCTGGTCAAGTGACAAAGTGATAAGTGGTAGCCTTAACTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
49584993 TCTGATCAGGGAC-AAGTGATAAGTG
1 TCTGATCAGTGACAAAGTGATAAGTG
49585018 ATCATACGTA
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
44 12 0.11
45 12 0.11
46 87 0.78
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (45 bp):
TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:49586829 original size:169 final size:169
Alignment explanation
Indices: 49586550--49586888 Score: 615
Period size: 169 Copynumber: 2.0 Consensus size: 169
49586540 ACTTCGCGTA
* *
49586550 TTTCACATAAATACCTGTACTAGTTCGAATCGAACTCATGTAACCTTAAATCATCACTGTACCCG
1 TTTCACATAAACACCTGTACTAGTTCGAATCGAACTCATGTAACCTCAAATCATCACTGTACCCG
49586615 TTGAACCATTTGGAATACTATCGGATACTCGGGTATCTCGCACACTAAGTGCCAATACGTGGTCG
66 TTGAACCATTTGGAATACTATCGGATACTCGGGTATCTCGCACACTAAGTGCCAATACGTGGTCG
*
49586680 AAACCACCTCTATCTCATATCTCATATAGATACTCACTC
131 AAACCACCTCTATCTCATATCTCATATAAATACTCACTC
* * *
49586719 TTTCACATAAACACCTGTACTAGTTTGAATCGAACTCATGTAACCTCAAATCATCACTGTGCTCG
1 TTTCACATAAACACCTGTACTAGTTCGAATCGAACTCATGTAACCTCAAATCATCACTGTACCCG
*
49586784 TTGAACCATTTGGAATACTATCGGATACTCGGGTATCTCGCACACTAAGTGCCAATACGTGGTTG
66 TTGAACCATTTGGAATACTATCGGATACTCGGGTATCTCGCACACTAAGTGCCAATACGTGGTCG
49586849 AAACCACCTCTATCTCATATCTCATATAAATACTCACTC
131 AAACCACCTCTATCTCATATCTCATATAAATACTCACTC
49586888 T
1 T
49586889 CGAGCCATCA
Statistics
Matches: 163, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 163 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (169 bp):
TTTCACATAAACACCTGTACTAGTTCGAATCGAACTCATGTAACCTCAAATCATCACTGTACCCG
TTGAACCATTTGGAATACTATCGGATACTCGGGTATCTCGCACACTAAGTGCCAATACGTGGTCG
AAACCACCTCTATCTCATATCTCATATAAATACTCACTC
Found at i:49590117 original size:41 final size:41
Alignment explanation
Indices: 49590067--49590184 Score: 136
Period size: 40 Copynumber: 2.9 Consensus size: 41
49590057 GTATCAGTGA
49590067 AATTCAGGCTTTGTGCTTAGCAGGCTTATTGCCGGTGAATT
1 AATTCAGGCTTTGTGCTTAGCAGGCTTATTGCCGGTGAATT
*
49590108 AATTCAGGCTTTGTGAC-TAGCAAGC-TATTGCCGGTGAATT
1 AATTCAGGCTTTGTG-CTTAGCAGGCTTATTGCCGGTGAATT
* ** *
49590148 ATTTCAAACTTTATG-TCTAGCAGGCTTCATT-CCGGTG
1 AATTCAGGCTTTGTGCT-TAGCAGGCTT-ATTGCCGGTG
49590185 TACCAAATCA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
40 33 0.50
41 29 0.44
42 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
AATTCAGGCTTTGTGCTTAGCAGGCTTATTGCCGGTGAATT
Found at i:49590148 original size:40 final size:41
Alignment explanation
Indices: 49590067--49590153 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
49590057 GTATCAGTGA
*
49590067 AATTCAGGCTTTGTGCTTAGCAGGCTTATTGCCGGTGAATT
1 AATTCAGGCTTTGTGCTTAGCAAGCTTATTGCCGGTGAATT
49590108 AATTCAGGCTTTGTGAC-TAGCAAGC-TATTGCCGGTGAATT
1 AATTCAGGCTTTGTG-CTTAGCAAGCTTATTGCCGGTGAATT
*
49590148 ATTTCA
1 AATTCA
49590154 AACTTTATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 20 0.47
41 22 0.51
42 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
AATTCAGGCTTTGTGCTTAGCAAGCTTATTGCCGGTGAATT
Found at i:49596519 original size:9 final size:9
Alignment explanation
Indices: 49596505--49596529 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
49596495 TATAGTTTAA
49596505 TATTCGAGT
1 TATTCGAGT
49596514 TATTCGAGT
1 TATTCGAGT
49596523 TATTCGA
1 TATTCGA
49596530 ATTCGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (9 bp):
TATTCGAGT
Found at i:49600220 original size:30 final size:30
Alignment explanation
Indices: 49600184--49600243 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
49600174 AAACCACATG
49600184 CCGTGTGTCATACACAGGC-AAAACACACGC
1 CCGTGTGTCATACACA-GCTAAAACACACGC
49600214 CCGTGTGTCATACACAGCTAAAACACACGC
1 CCGTGTGTCATACACAGCTAAAACACACGC
49600244 TCCTGTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (30 bp):
CCGTGTGTCATACACAGCTAAAACACACGC
Found at i:49613785 original size:40 final size:41
Alignment explanation
Indices: 49613721--49613800 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
49613711 TAAAAATAAT
*
49613721 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
49613762 TTATATTAAAAAA-ACATA-AATAAATATAATATATATTTT
1 TTATATTAAAAAACAC-TACAATAAATATAATAAATATTTT
49613801 TGTATTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 21 0.58
41 15 0.42
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:49615803 original size:88 final size:88
Alignment explanation
Indices: 49615687--49615862 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
49615677 TCCTTCTTCT
49615687 TCTTCTTCTTCTTTTTTGTGTTTGATTGGTGAGAAAGTAGAATGGAGAATCCTTCATCTTCTTCT
1 TCTTCTTCTTCTTTTTTGTGTTTGATTGGTGAGAAAGTAGAATGGAGAATCCTTCATCTTCTTCT
*
49615752 TCATCATCATCACCACCTGCTGA
66 TCATCATCATCACCACCAGCTGA
49615775 TCTTCTTCTTCTTTTTTGTGTTTGATTGGTGAGAAAGTAGAATGGAGAATCCTTCATCTTCTTCT
1 TCTTCTTCTTCTTTTTTGTGTTTGATTGGTGAGAAAGTAGAATGGAGAATCCTTCATCTTCTTCT
49615840 TCATCATCATCACCACCAGCTGA
66 TCATCATCATCACCACCAGCTGA
49615863 ACATGGTGAG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (88 bp):
TCTTCTTCTTCTTTTTTGTGTTTGATTGGTGAGAAAGTAGAATGGAGAATCCTTCATCTTCTTCT
TCATCATCATCACCACCAGCTGA
Found at i:49616960 original size:49 final size:49
Alignment explanation
Indices: 49616888--49616985 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
49616878 CTAGACTAAA
49616888 TCTATATAAGCTCAAAATATGATGAGACATAAACAAGAATAAATATGGT
1 TCTATATAAGCTCAAAATATGATGAGACATAAACAAGAATAAATATGGT
*
49616937 TCTATATAAGCTCAAAATATGATGAGAGATAAACAAGAATAAATATGGT
1 TCTATATAAGCTCAAAATATGATGAGACATAAACAAGAATAAATATGGT
49616986 CTAAGAACCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (49 bp):
TCTATATAAGCTCAAAATATGATGAGACATAAACAAGAATAAATATGGT
Found at i:49622193 original size:20 final size:20
Alignment explanation
Indices: 49622170--49622219 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
49622160 AAAACACCGT
*
49622170 AGTGAAAACAAAGGCACCAA
1 AGTGCAAACAAAGGCACCAA
* *
49622190 AGTGCAAACAGAGGCATCAA
1 AGTGCAAACAAAGGCACCAA
49622210 AGTGCAAACA
1 AGTGCAAACA
49622220 TGTACAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.20, G:0.22, T:0.08
Consensus pattern (20 bp):
AGTGCAAACAAAGGCACCAA
Done.