Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 111 of 444
Found at i:28028992 original size:14 final size:14
Alignment explanation
Indices: 28028973--28029006 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
28028963 TAGACATAGT
28028973 ATGTTATTATAAGC
1 ATGTTATTATAAGC
28028987 ATGTTATTATAAGC
1 ATGTTATTATAAGC
28029001 ATGTTA
1 ATGTTA
28029007 GATGTTGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (14 bp):
ATGTTATTATAAGC
Found at i:28039744 original size:32 final size:32
Alignment explanation
Indices: 28039708--28039833 Score: 162
Period size: 32 Copynumber: 3.9 Consensus size: 32
28039698 TTTCTGAGTG
* **
28039708 GTACACACAAAGTATACCTTTCCTTTTCAAGT
1 GTACACACAAAGTATACATAACCTTTTCAAGT
*
28039740 GTACACACAAAGTGTACATAACCTTTTCAAGT
1 GTACACACAAAGTATACATAACCTTTTCAAGT
* * *
28039772 GTACACACAAAGTGTACATAACATTTTCATGT
1 GTACACACAAAGTATACATAACCTTTTCAAGT
* *
28039804 GATATACACAAAGTATACCTAACCTTTTCA
1 G-TACACACAAAGTATACATAACCTTTTCA
28039834 CATTCGATAG
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
32 59 0.71
33 24 0.29
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (32 bp):
GTACACACAAAGTATACATAACCTTTTCAAGT
Found at i:28039868 original size:30 final size:30
Alignment explanation
Indices: 28039828--28039895 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
28039818 ATACCTAACC
28039828 TTTTCACATTCGATAGCCGAAGCTATCCCT
1 TTTTCACATTCGATAGCCGAAGCTATCCCT
* *
28039858 TTTTTACATTCGATAGTCGAAGCTATCCC-
1 TTTTCACATTCGATAGCCGAAGCTATCCCT
*
28039887 ATTTCACAT
1 TTTTCACAT
28039896 GGTACACACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (30 bp):
TTTTCACATTCGATAGCCGAAGCTATCCCT
Found at i:28047587 original size:66 final size:66
Alignment explanation
Indices: 28047508--28047632 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
28047498 GGGATTCGAG
*
28047508 TGATGTTTTTGTTTGTTTATTTTGAAAATATACTCATTAAGGATTCCAATCATATAAATATTAGA
1 TGATGTTTCTGTTTGTTTATTTTGAAAATATACTCATTAAGGATTCCAATCATATAAATATTAGA
28047573 A
66 A
*
28047574 TGATGTTTCTGTTTGTTTATTTTGAAAATATACTCATTAAGGATTCCAATTATATAAAT
1 TGATGTTTCTGTTTGTTTATTTTGAAAATATACTCATTAAGGATTCCAATCATATAAAT
28047633 TTTATCCCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (66 bp):
TGATGTTTCTGTTTGTTTATTTTGAAAATATACTCATTAAGGATTCCAATCATATAAATATTAGA
A
Found at i:28048476 original size:49 final size:49
Alignment explanation
Indices: 28048365--28048493 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
28048355 ATCAAAGTGG
* *
28048365 ATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGCCCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAGCCCA
* * * * **
28048414 ATGTCGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGTCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAG-CCCA
* *
28048463 ATGCCATGCCCCAGACAGGTTTTACACTGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGAC
28048494 ACACAACAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
48 1 0.02
49 65 0.98
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGAGCCCA
Found at i:28051317 original size:19 final size:20
Alignment explanation
Indices: 28051271--28051319 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
28051261 GTGCATGACA
*
28051271 AGGCCGTGTGATGGCCGAAG
1 AGGCTGTGTGATGGCCGAAG
*
28051291 AGGCTGTGTGATGGCTGAAG
1 AGGCTGTGTGATGGCCGAAG
28051311 A-GCTGTGTG
1 AGGCTGTGTG
28051320 CTAGACACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.22
Consensus pattern (20 bp):
AGGCTGTGTGATGGCCGAAG
Found at i:28057333 original size:31 final size:31
Alignment explanation
Indices: 28057292--28057355 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28057282 CCTTTTCACA
*
28057292 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
28057323 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
28057354 TT
1 TT
28057356 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:28057595 original size:23 final size:24
Alignment explanation
Indices: 28057548--28057758 Score: 335
Period size: 23 Copynumber: 9.0 Consensus size: 24
28057538 GCTTTATCAT
*
28057548 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
28057573 ACAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057596 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057619 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057642 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057666 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28057689 ATAACTGGGGTATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057713 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28057736 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28057759 TGCACTTCCT
Statistics
Matches: 176, Mismatches: 5, Indels: 11
0.92 0.03 0.06
Matches are distributed among these distances:
23 108 0.61
24 61 0.35
25 7 0.04
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28057659 original size:47 final size:47
Alignment explanation
Indices: 28057548--28057758 Score: 347
Period size: 47 Copynumber: 4.5 Consensus size: 47
28057538 GCTTTATCAT
* *
28057548 ATAACTGGAGGCCT-AGCCTCTTTTAACAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCC-TTTA
28057596 ATAACTGGGGCA-AAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
28057642 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
*
28057689 ATAACTGGGGTATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
28057736 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28057759 TGCACTTCCT
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
46 33 0.21
47 115 0.74
48 8 0.05
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTA
Found at i:28057669 original size:70 final size:72
Alignment explanation
Indices: 28057548--28057758 Score: 335
Period size: 70 Copynumber: 3.0 Consensus size: 72
28057538 GCTTTATCAT
* *
28057548 ATAACTGGAGGCCT-AGCCTCTTTTAACAACTGGGGCA-AAGCCCTTTTAATAACTGGGGCA-AA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAA
28057610 GCCCTTTTA
64 GCCCTTTTA
28057619 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
28057683 CC-TTTA
66 CCTTTTA
*
28057689 ATAACTGGGGTATAAGCCCTTTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
28057753 CCTTTT
66 CCTTTT
28057759 TGCACTTCCT
Statistics
Matches: 132, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
69 15 0.11
70 73 0.55
71 44 0.33
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
CCTTTTA
Found at i:28057831 original size:9 final size:9
Alignment explanation
Indices: 28057817--28057873 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28057807 ATCTCATGTG
28057817 CATATCATA
1 CATATCATA
*
28057826 CATATCATGTG
1 CATATCA--TA
28057837 CATATCATA
1 CATATCATA
* *
28057846 CATGTCATGTG
1 CATATCA--TA
28057857 CATATCATA
1 CATATCATA
28057866 CATATCAT
1 CATATCAT
28057874 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:28057833 original size:20 final size:20
Alignment explanation
Indices: 28057805--28057875 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
28057795 GCATTTATGA
*
28057805 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
28057825 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
28057845 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
28057865 ACATATCATGT
1 ACATATCATGT
28057876 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:28057840 original size:11 final size:11
Alignment explanation
Indices: 28057810--28057864 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28057800 TATGAACATC
28057810 TCATGTGCATA
1 TCATGTGCATA
*
28057821 TCA--TACATA
1 TCATGTGCATA
28057830 TCATGTGCATA
1 TCATGTGCATA
* *
28057841 TCA--TACATG
1 TCATGTGCATA
28057850 TCATGTGCATA
1 TCATGTGCATA
28057861 TCAT
1 TCAT
28057865 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:28057954 original size:25 final size:24
Alignment explanation
Indices: 28057912--28057959 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
28057902 ATATATAAAC
* * *
28057912 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
28057937 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28057960 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:28059153 original size:27 final size:26
Alignment explanation
Indices: 28059118--28059195 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
28059108 GGGCATATTC
28059118 GTCATTTTACCATATAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
*
28059145 GTCACTTTACCCTATAGGGGCT-TTACG
1 GTCATTTTA-CCTATAGGGG-TATTACG
*
28059172 GTCTTTTTACCTAATAGGGGTATT
1 GTCATTTTACCT-ATAGGGGTATT
28059196 TTAGACATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.09
27 37 0.84
28 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:28059266 original size:27 final size:27
Alignment explanation
Indices: 28059214--28059451 Score: 212
Period size: 27 Copynumber: 8.7 Consensus size: 27
28059204 TTCATCCTAC
* * *
28059214 AAGGGTGTTTTGGTAAATCTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
** ** *
28059241 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* * * *
28059268 AATGGTATTTCT-ATAATTTTTAGAAAGT
1 AAGGGTATTT-TGGTAA-TTTTACAAACT
* *
28059296 CAAGGGTATTTTTGTAACTTTGTA-AATC-
1 -AAGGGTATTTTGGTAA-TTT-TACAAACT
* *
28059324 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAACT
* * *
28059351 GAGGGTATTTCGGTAATTTCACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
28059378 AAGGGTATTTTGGTAATTTTACAAAAT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
28059405 AGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
28059432 AAGGGTATTTTAGTAATTTT
1 AAGGGTATTTTGGTAATTTT
28059452 GTAAATCGAG
Statistics
Matches: 167, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.01
26 5 0.03
27 133 0.80
28 8 0.05
29 17 0.10
30 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACT
Found at i:28059463 original size:27 final size:27
Alignment explanation
Indices: 28059241--28059519 Score: 161
Period size: 27 Copynumber: 10.3 Consensus size: 27
28059231 TCTACAAACT
* * *
28059241 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTATAAATC
* *
28059268 AATGGTATTTCTA-TAATTTTTAGAAAGTC
1 AAGGGTATTT-TAGTAA-TTTTATAAA-TC
* * *
28059297 AAGGGTATTTTTGTAACTTTGTAAATC
1 AAGGGTATTTTAGTAATTTTATAAATC
* * * *
28059324 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTATAAATC
* ** * *
28059351 GAGGGTATTTCGGTAATTTCACAAA-C
1 AAGGGTATTTTAGTAATTTTATAAATC
* *
28059377 TAAGGGTATTTTGGTAATTTTACAAAAT-
1 -AAGGGTATTTTAGTAATTTTA-TAAATC
* * *
28059405 AGGGGTATTTTGGTAATTTTACAAA-C
1 AAGGGTATTTTAGTAATTTTATAAATC
*
28059431 TAAGGGTATTTTAGTAATTTTGTAAATC
1 -AAGGGTATTTTAGTAATTTTATAAATC
* **** * *
28059459 GAGGGTAAAACAGTAATTCTGTAAATC
1 AAGGGTATTTTAGTAATTTTATAAATC
*** *
28059486 AAGGGTAAAATAGTAATTCTATAAATC
1 AAGGGTATTTTAGTAATTTTATAAATC
*
28059513 GAGGGTA
1 AAGGGTA
28059520 AAACAGTAAT
Statistics
Matches: 201, Mismatches: 41, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
26 3 0.01
27 166 0.83
28 19 0.09
29 13 0.06
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTATAAATC
Found at i:28059520 original size:27 final size:27
Alignment explanation
Indices: 28059443--28059733 Score: 300
Period size: 27 Copynumber: 10.8 Consensus size: 27
28059433 AGGGTATTTT
*
28059443 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
28059470 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
28059497 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
28059524 AGTAATTCTGTAAATTGAAGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
28059551 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
28059578 -GATAATTATGTAAATC-AGAGGTAACAC
1 AG-TAATTCTGTAAATCGAG-GGTAAAAC
* * *
28059605 GGTAATTCTGTAAATCGGGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
28059632 AGTAATTCTGTAAA-CTAAGGGTAAAAT
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* * *
28059659 GGTGATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * * *
28059686 GGTAATTTTATAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
28059713 GGTAATTTTACAAATCGAGGG
1 AGTAATTCTGTAAATCGAGGG
28059734 CATTTCAGTA
Statistics
Matches: 225, Mismatches: 33, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
26 4 0.02
27 218 0.97
28 3 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:28063011 original size:16 final size:16
Alignment explanation
Indices: 28062990--28063021 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28062980 TGAAATCCGT
28062990 GTATTCGAATTATATC
1 GTATTCGAATTATATC
28063006 GTATTCGAATTATATC
1 GTATTCGAATTATATC
28063022 CGATTGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
GTATTCGAATTATATC
Found at i:28071928 original size:20 final size:20
Alignment explanation
Indices: 28071899--28071954 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
28071889 TGAAGGTCTC
*
28071899 ACACGTCCGTGTGCCATCAG
1 ACACGGCCGTGTGCCATCAG
28071919 ACACGGCCGTGTGCCATCAG
1 ACACGGCCGTGTGCCATCAG
28071939 ACACGGCCGTGTGCCA
1 ACACGGCCGTGTGCCA
28071955 GGCATACGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.16
Consensus pattern (20 bp):
ACACGGCCGTGTGCCATCAG
Found at i:28078103 original size:31 final size:31
Alignment explanation
Indices: 28078067--28078135 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
28078057 GGGCCGTGTG
* *
28078067 GGCCACACGAG-CATAGGGGCCCATATGGGTA
1 GGCCACA-GAGACATAGGGGCCCACACGGGTA
* **
28078098 GGCCACATAGACATTTGGGCCCACACGGGTA
1 GGCCACAGAGACATAGGGGCCCACACGGGTA
28078129 GGCCACA
1 GGCCACA
28078136 TGGGCATGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (31 bp):
GGCCACAGAGACATAGGGGCCCACACGGGTA
Found at i:28078151 original size:31 final size:31
Alignment explanation
Indices: 28078093--28078151 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28078083 GGGCCCATAT
* *
28078093 GGGTAGGCCACATAGACATTTGGGCCCACAC
1 GGGTAGGCCACATAGACATGTGAGCCCACAC
* *
28078124 GGGTAGGCCACATGGGCATGTGAGCCCA
1 GGGTAGGCCACATAGACATGTGAGCCCA
28078152 TTTTTCTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (31 bp):
GGGTAGGCCACATAGACATGTGAGCCCACAC
Found at i:28079603 original size:23 final size:22
Alignment explanation
Indices: 28079561--28079607 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
28079551 TAATGTAAAT
28079561 TTATTTCAACAATTACAAATCA
1 TTATTTCAACAATTACAAATCA
* *
28079583 TTATTTCCAATAATTATAAATCA
1 TTATTT-CAACAATTACAAATCA
28079606 TT
1 TT
28079608 TTTTAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTTCAACAATTACAAATCA
Found at i:28083596 original size:12 final size:12
Alignment explanation
Indices: 28083579--28083603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28083569 TTTCCAACAC
28083579 ACCTAATTAGAT
1 ACCTAATTAGAT
28083591 ACCTAATTAGAT
1 ACCTAATTAGAT
28083603 A
1 A
28083604 TCAATAATTG
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ACCTAATTAGAT
Found at i:28088707 original size:49 final size:50
Alignment explanation
Indices: 28088649--28088782 Score: 155
Period size: 50 Copynumber: 2.7 Consensus size: 50
28088639 TCAAGTCGAT
28088649 GCCATGTCCCAGACATGGTCTTACACTGACTATCA-AAAT-CGAGGCCAAC
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCCG-GGCCAAC
* * * ** * * *
28088698 GCCATGTCCCAAACATGGTCTTACACTAACTCTCACTTATCCGTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCCGGGCCAAC
*
28088748 GCCATGTCCTAGACATGGTCTTACACTGACATATC
1 GCCATGTCCCAGACATGGTCTTACACTGAC-TATC
28088783 TGTACTGATG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 32 0.46
50 33 0.47
51 5 0.07
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCCGGGCCAAC
Found at i:28088808 original size:44 final size:46
Alignment explanation
Indices: 28088646--28088857 Score: 195
Period size: 44 Copynumber: 4.5 Consensus size: 46
28088636 CCATCAAGTC
** *
28088646 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCG-AGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGAC-A-C-ATCTCGTA-GCT
* * * * *
28088695 AACGCCATGTCCCAAACATGGTCTTACACTAACTCTCACTTATC-CGT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA----CAC--ATCTCGTAGCT
* *
28088745 GATGCCATGTCCTAGACATGGTCTTACACTGACATATCT-GTA-CT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCT
28088789 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCT
28088835 GATG-CATGTCCCAGACAT-GTCTT
1 GATGCCATGTCCCAGACATGGTCTT
28088858 CAACTGGCTT
Statistics
Matches: 137, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
44 48 0.35
45 17 0.12
46 8 0.06
49 28 0.20
50 30 0.22
51 3 0.02
52 2 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCT
Found at i:28088873 original size:46 final size:46
Alignment explanation
Indices: 28088742--28088954 Score: 199
Period size: 46 Copynumber: 4.7 Consensus size: 46
28088732 ACTTATCCGT
* * *
28088742 GCCGATGCCATGTCCTAGACATGGTCTTACACTGAC--ATATCT-GTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGTA
* *
28088787 -CTGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCGTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGTA
* *
28088832 GCTGATGCATGTCCCAGACATGTCTT-CAACTGGCTTACATCTC-AA
1 GCCGATGCATGTCCCAGACATGTCTTAC-ACTGGCTTACATCTCGTA
* * * *
28088877 GGCCGATTCATGTCCTAGACATGTCTTACACTGGCTTAAATCTCGTG
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTA
* *
28088924 GCCGAAGCATATCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
28088955 AGCACACAAA
Statistics
Matches: 145, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.01
44 48 0.33
45 18 0.12
46 77 0.53
47 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTA
Found at i:28091118 original size:20 final size:19
Alignment explanation
Indices: 28091077--28091120 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
28091067 ATTAGAATGT
* *
28091077 AAAATTTAAATTAAAGACA
1 AAAATTTAAAATAAAAACA
*
28091096 AAAATATTAAAATAAAAATA
1 AAAAT-TTAAAATAAAAACA
28091116 AAAAT
1 AAAAT
28091121 GGCTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATTTAAAATAAAAACA
Found at i:28101576 original size:18 final size:19
Alignment explanation
Indices: 28101548--28101586 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
28101538 TGATTTTCAT
28101548 AACTAGATTTCCCAAACCC
1 AACTAGATTTCCCAAACCC
28101567 AACT-GATTTCCCAAACCC
1 AACTAGATTTCCCAAACCC
28101585 AA
1 AA
28101587 ACCCTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.38, C:0.36, G:0.05, T:0.21
Consensus pattern (19 bp):
AACTAGATTTCCCAAACCC
Found at i:28107883 original size:25 final size:25
Alignment explanation
Indices: 28107841--28107889 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
28107831 CTTTATTATT
* *
28107841 ATCATTATGAAGAATTATGTGATTA
1 ATCATTATCAAGAATTATATGATTA
* *
28107866 ATCATTATCATGAGTTATATGATT
1 ATCATTATCAAGAATTATATGATT
28107890 GGTCCTCCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATCATTATCAAGAATTATATGATTA
Found at i:28109612 original size:42 final size:42
Alignment explanation
Indices: 28109565--28109671 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
28109555 TATTGGTCTC
*
28109565 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
28109607 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
* *
28109649 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
28109672 ATTGTACAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
Found at i:28122398 original size:40 final size:40
Alignment explanation
Indices: 28122350--28122555 Score: 342
Period size: 40 Copynumber: 5.2 Consensus size: 40
28122340 GGACTAAGAT
* *
28122350 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
*
28122390 TCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* *
28122430 CTGAAGGCATTTGTACGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
28122470 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* *
28122510 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
28122549 CCGAAGG
1 CCGAAGG
28122556 TACTTGGGTT
Statistics
Matches: 156, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 15 0.10
40 141 0.90
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:28124152 original size:21 final size:21
Alignment explanation
Indices: 28124126--28124168 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28124116 GCAGCGCCTG
28124126 CTCCCGCGCAAGGGACAGCGC
1 CTCCCGCGCAAGGGACAGCGC
28124147 CTCCCGCGCAAGGGACAGCGC
1 CTCCCGCGCAAGGGACAGCGC
28124168 C
1 C
28124169 GGTGGACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.44, G:0.33, T:0.05
Consensus pattern (21 bp):
CTCCCGCGCAAGGGACAGCGC
Found at i:28128025 original size:427 final size:427
Alignment explanation
Indices: 28127220--28128069 Score: 1292
Period size: 427 Copynumber: 2.0 Consensus size: 427
28127210 GCTGTTTGCT
* * * *
28127220 TTACGATCGATGAATGTACACTTGTCTATTCTACCCGACAATGTGTTAGTAGCCGAATTAAAGGC
1 TTACGAGCGATGAATGTACACTTGTCGATTCTACCCGACAATGTGTTAGTAGCAGAAATAAAGGC
*
28127285 CAAACCATCATTGATTCATCAAATTCGTGAAGCTCAGAAAGTCGACGATAAGTTGGTTGCAAGAC
66 CAAACCATCATTGATTCATCAAATTCGTGAAGCTCAGAAAGTCGACGATAAGTTGGTTGCAAAAC
* ** * *
28127350 GGGCTGAATGTGTTCCGAATGTGGAATCAGAGTTTCAAGTTGATGATGACGATTGTTTGAGGTTC
131 GGGCTGAATGTGTTCCAAATAAGGAATCAGAGTTTCAAATTGATGATGACGATTGTTTAAGGTTC
* *
28127415 AGAAATCGTTTGTGTATTCCAAGAAATTCAGTACTTATTTCGATAATTCTGAACAAAGCCCATTG
196 AGAAATCGTTTGTGTATTCCAAGAAATTCAGAACTTATTTCGACAATTCTGAACAAAGCCCATTG
* * *
28127480 TAGCCGAATGGCAATCCACCCGGGGAGTACAAAGATGTACAATGATTTGAAACGTCGGTTTTGGT
261 TAGCCGAATGGCAATCCACCCGGGGAGTACAAAGATGTACAACGATCTGAAACGTCAGTTTTGGT
*
28127545 GGCATGGCATGAAACGAGACATCTTCGACTTTGTTTCGAGATGTTTGATATGTCAACAAGTGAAA
326 GGCATGGCATGAAACGAGACATCTTCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAA
* **
28127610 GCGGAACATCAAGTGCCTTCAGGATTACTTCAGTCGA
391 GCGAAACATCAAGTGCCGACAGGATTACTTCAGTCGA
* * * *
28127647 TTACGAGCGATGAATGTACATTTGTCGGTTCTATCCGATAATGTGTTAGTAGCAGAAATAAAGGC
1 TTACGAGCGATGAATGTACACTTGTCGATTCTACCCGACAATGTGTTAGTAGCAGAAATAAAGGC
** *
28127712 CAAACCATTGTTGATTCATCAAATTCGTGAAGCTCAGAAAGTCGATGATGAA-TTGGTTGCAAAA
66 CAAACCATCATTGATTCATCAAATTCGTGAAGCTCAGAAAGTCGACGAT-AAGTTGGTTGCAAAA
*
28127776 CGGGCTGAATGTGTTTCAAATAAGGAATCAGAGTTTCAAATTGATGATGACGATTGTTTAAGGTT
130 CGGGCTGAATGTGTTCCAAATAAGGAATCAGAGTTTCAAATTGATGATGACGATTGTTTAAGGTT
* * * *
28127841 CAGAAGTCGTTTGTGTGTTCCAAGAAATTCAGAACTTATTTCGACAATTCTGAACGAAGCTCATT
195 CAGAAATCGTTTGTGTATTCCAAGAAATTCAGAACTTATTTCGACAATTCTGAACAAAGCCCATT
* * * *
28127906 GTAGTCGAATGTCAATTCACCCGGGGAGTACGAAA-ATGTACAACGATCTGAGACGTCAGTTTTG
260 GTAGCCGAATGGCAATCCACCCGGGGAGTAC-AAAGATGTACAACGATCTGAAACGTCAGTTTTG
* * * *
28127970 GTGGCATGGTATGAAACGAGACATTTTCGATTTTGTTTCGA-AGTTTTTAATATGTCAACAAGTG
324 GTGGCATGGCATGAAACGAGACATCTTCGACTTTGTTTCGAGA-TGTTTAATATGTCAACAAGTG
*
28128034 AAAGCGAAACATCAAGTGCCGACAGGTTTACTTCAG
388 AAAGCGAAACATCAAGTGCCGACAGGATTACTTCAG
28128070 CCAATCATGA
Statistics
Matches: 380, Mismatches: 40, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
426 1 0.00
427 374 0.98
428 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (427 bp):
TTACGAGCGATGAATGTACACTTGTCGATTCTACCCGACAATGTGTTAGTAGCAGAAATAAAGGC
CAAACCATCATTGATTCATCAAATTCGTGAAGCTCAGAAAGTCGACGATAAGTTGGTTGCAAAAC
GGGCTGAATGTGTTCCAAATAAGGAATCAGAGTTTCAAATTGATGATGACGATTGTTTAAGGTTC
AGAAATCGTTTGTGTATTCCAAGAAATTCAGAACTTATTTCGACAATTCTGAACAAAGCCCATTG
TAGCCGAATGGCAATCCACCCGGGGAGTACAAAGATGTACAACGATCTGAAACGTCAGTTTTGGT
GGCATGGCATGAAACGAGACATCTTCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAA
GCGAAACATCAAGTGCCGACAGGATTACTTCAGTCGA
Found at i:28130983 original size:39 final size:40
Alignment explanation
Indices: 28130913--28131074 Score: 265
Period size: 40 Copynumber: 4.1 Consensus size: 40
28130903 CTAAGATCCA
* * *
28130913 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCTCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
28130953 AAGGCATTT-TGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
28130992 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* *
28131032 AAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
28131071 AAGG
1 AAGG
28131075 TACTTGGGTT
Statistics
Matches: 116, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 51 0.44
40 65 0.56
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
Found at i:28131034 original size:79 final size:79
Alignment explanation
Indices: 28130913--28131074 Score: 263
Period size: 79 Copynumber: 2.1 Consensus size: 79
28130903 CTAAGATCCA
* *
28130913 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCTCGAAGGCATTT-TGCGAGTTACTATAT
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28130977 CCGGGCTAAGTCCCG
66 CC-GGCTAAATCCCG
* *
28130992 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAT
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28131057 CCGGCTAAATCCCG
66 CCGGCTAAATCCCG
28131071 AAGG
1 AAGG
28131075 TACTTGGGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
79 61 0.79
80 16 0.21
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
CCGGCTAAATCCCG
Found at i:28133667 original size:23 final size:23
Alignment explanation
Indices: 28133641--28133687 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28133631 GGTCAAGTGG
28133641 TTTTAGAAAATGAGGTATCAGGA
1 TTTTAGAAAATGAGGTATCAGGA
28133664 TTTTAGAAAATGAGGTATCAGGA
1 TTTTAGAAAATGAGGTATCAGGA
28133687 T
1 T
28133688 CTCATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (23 bp):
TTTTAGAAAATGAGGTATCAGGA
Found at i:28134010 original size:20 final size:20
Alignment explanation
Indices: 28133973--28134010 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28133963 TGTTATTTTA
*
28133973 TTAATAAAATAAATAAAAGG
1 TTAATAAAATAAAGAAAAGG
*
28133993 TTAATAAAATTAAGAAAA
1 TTAATAAAATAAAGAAAA
28134011 CATGATAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
TTAATAAAATAAAGAAAAGG
Found at i:28134919 original size:25 final size:25
Alignment explanation
Indices: 28134862--28134945 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
28134852 TCATCTCGAG
* * *
28134862 AGAGCTTATTGATATTTAGCTCGCA
1 AGAGCTTATCGATATTCAGCTCGTA
* * *
28134887 CGAACTTACCGATATTCAGCTCGTA
1 AGAGCTTATCGATATTCAGCTCGTA
*
28134912 TGAGCTTATC-AT-TTACAGCTCGTA
1 AGAGCTTATCGATATT-CAGCTCGTA
*
28134936 AGAGCATATC
1 AGAGCTTATC
28134946 AATTTAGAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
23 2 0.04
24 19 0.40
25 26 0.55
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (25 bp):
AGAGCTTATCGATATTCAGCTCGTA
Found at i:28134956 original size:25 final size:24
Alignment explanation
Indices: 28134903--28134977 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 24
28134893 TACCGATATT
*
28134903 CAGCTCGTATGAGCTTATCATTTA
1 CAGCTCGTATGAGCATATCATTTA
*
28134927 CAGCTCGTAAGAGCATATCAATTTA
1 CAGCTCGTATGAGCATATC-ATTTA
* * *
28134952 GAGCTTGTATGAGCATA-CATGTA
1 CAGCTCGTATGAGCATATCATTTA
28134975 CAG
1 CAG
28134978 GAATTAATGG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.14
24 18 0.42
25 19 0.44
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (24 bp):
CAGCTCGTATGAGCATATCATTTA
Found at i:28135265 original size:71 final size:71
Alignment explanation
Indices: 28135184--28135330 Score: 249
Period size: 71 Copynumber: 2.1 Consensus size: 71
28135174 AGAAGAAACA
* * *
28135184 GTAAGAGAATGATATGTATCATGACATGTACATATATGAATATTTTTTATATGTTAATACATGAA
1 GTAAGAGAATGATATGTATCATGACATGTACATATACGAATATCTTTGATATGTTAATACATGAA
28135249 AATTAT
66 AATTAT
* *
28135255 GTAAGAGAATGGTATGTATCATGACATGTACATATACGAATATCTTTGATATGTTGATACATGAA
1 GTAAGAGAATGATATGTATCATGACATGTACATATACGAATATCTTTGATATGTTAATACATGAA
28135320 AATTAT
66 AATTAT
28135326 GTAAG
1 GTAAG
28135331 TTGAGACGAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (71 bp):
GTAAGAGAATGATATGTATCATGACATGTACATATACGAATATCTTTGATATGTTAATACATGAA
AATTAT
Found at i:28137428 original size:28 final size:28
Alignment explanation
Indices: 28137372--28137432 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
28137362 TTGCTGAATT
* *
28137372 TTTTTTGAATAAATTAGGGTTAGTCAAA
1 TTTTTTGAATAAATTAGGGTAACTCAAA
28137400 TTTTTTGAATGAAA-TAGGGCTAACT-AAA
1 TTTTTTGAAT-AAATTAGGG-TAACTCAAA
28137428 TTTTT
1 TTTTT
28137433 AAAAGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTTTGAATAAATTAGGGTAACTCAAA
Found at i:28138653 original size:16 final size:16
Alignment explanation
Indices: 28138622--28138658 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28138612 ATGTGAATAA
28138622 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
28138638 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
28138654 TATTA
1 TATTA
28138659 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:28138697 original size:16 final size:18
Alignment explanation
Indices: 28138672--28138730 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
28138662 TAAAATTAAA
28138672 ATATTAAATAATTTATTA-
1 ATATT-AATAATTTATTAT
28138690 ATA-TAATAAATTATATTTATT
1 ATATTAAT-AATT-TA-TTA-T
28138711 ATATTAATAATTTATTAT
1 ATATTAATAATTTATTAT
28138729 AT
1 AT
28138731 GACTAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 8 0.23
19 6 0.17
20 2 0.06
21 7 0.20
22 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAATAATTTATTAT
Found at i:28138710 original size:22 final size:22
Alignment explanation
Indices: 28138666--28138725 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
28138656 TTAAAATAAA
* *
28138666 ATTAAAATATTAAA-TA-ATTT
1 ATTAATATAATAAATTATATTT
28138686 ATTAATATAATAAATTATATTT
1 ATTAATATAATAAATTATATTT
*
28138708 ATT-ATATTAATAATTTAT
1 ATTAATA-TAATAAATTAT
28138726 TATATGACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.35
21 5 0.15
22 17 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAATATAATAAATTATATTT
Found at i:28138711 original size:34 final size:34
Alignment explanation
Indices: 28138629--28138711 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 34
28138619 TAATATTATT
*
28138629 TAAAATTATTATTT-TT-AAAATTTATTATTAAAA
1 TAAAATTA-TATTTATTAAAAATTTATTAATAAAA
** *
28138662 TAAAATTA-AAATATTAAATAATTTATTAATATAA
1 TAAAATTATATTTATTAAA-AATTTATTAATAAAA
28138696 T-AAATTATATTTATTA
1 TAAAATTATATTTATTA
28138712 TATTAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 16 0.40
34 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TAAAATTATATTTATTAAAAATTTATTAATAAAA
Found at i:28140851 original size:74 final size:74
Alignment explanation
Indices: 28140739--28140894 Score: 294
Period size: 74 Copynumber: 2.1 Consensus size: 74
28140729 TGTATTAAAT
28140739 AATTTATTATTATTATTGATAATATTTTAACTTAGCTTGTGAAAGGTTTTACTCCATTATTATTA
1 AATTTATTATTATTATTGATAATATTTTAACTTAGCTTGTGAAAGGTTTTACTCCATTATTATTA
28140804 TACTTGGAA
66 TACTTGGAA
* *
28140813 AATTTTTTATTATTATTGATAATATTTTAACTTCGCTTGTGAAAGGTTTTACTCCATTATTATTA
1 AATTTATTATTATTATTGATAATATTTTAACTTAGCTTGTGAAAGGTTTTACTCCATTATTATTA
28140878 TACTTGGAA
66 TACTTGGAA
28140887 AATTTATT
1 AATTTATT
28140895 CGATTCATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (74 bp):
AATTTATTATTATTATTGATAATATTTTAACTTAGCTTGTGAAAGGTTTTACTCCATTATTATTA
TACTTGGAA
Found at i:28145248 original size:96 final size:95
Alignment explanation
Indices: 28145075--28145486 Score: 384
Period size: 96 Copynumber: 4.3 Consensus size: 95
28145065 GATATGCGTT
* * *
28145075 CCAGTGTAAGACCATG-CTTGGGACATGGCATTGGCATTGATGTGTGTGCTAGTGTAAGACCATG
1 CCAGTGTAAGACCATGTC-TGGGACATGGCATCGGCATTGA-GTGAGAGCTAGTGTAAGACCATG
* * *
28145139 TCTAGGAAATGGCATCGGCCACAACATGAGAG
64 TCTGGGACATGGCATCGGCCACGACATGAGAG
* * *
28145171 CCAATGTAAGACCATGTCTGGGACATGGCATCGGCATTGATGTGTGTGCTAGTGTAAGACCATGT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GTGAGAGCTAGTGTAAGACCATGT
* * ** * *
28145236 CTGGGACCTGGCATCGG-CATTGATGTGTGTG
65 CTGGGACATGGCATCGGCCA-CGACATGAGAG
* * * *
28145267 CTAGTGTAAGACCATGACTGGGACATGGCATTGGCCACCTT-A-TGAGAGCCAGTGTAAGACCAT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CA--TTGAGTGAGAGCTAGTGTAAGACCAT
* * * ***
28145330 GTATGGGACATGGCATTGACCACCTTATGAGAG
63 GTCTGGGACATGGCATCGGCCACGACATGAGAG
* * * * *
28145363 CTAGTATAAGACTATGTCTGGGACATGGCATCGGCAATGAGACGAGAGCTAGTGTAAGACCATGT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG-TGAGAGCTAGTGTAAGACCATGT
* * *
28145428 CCGGGACATGACATCGGCCTCGACATGTA-AG
65 CTGGGACATGGCATCGGCCACGACATG-AGAG
* * *
28145459 CCAGTGTAAGACTATGTTTGGAACATGG
1 CCAGTGTAAGACCATGTCTGGGACATGG
28145487 AATCAGCAAT
Statistics
Matches: 258, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
93 1 0.00
94 1 0.00
95 4 0.02
96 243 0.94
97 6 0.02
98 1 0.00
99 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGTGAGAGCTAGTGTAAGACCATGTC
TGGGACATGGCATCGGCCACGACATGAGAG
Found at i:28145337 original size:144 final size:143
Alignment explanation
Indices: 28145077--28145486 Score: 470
Period size: 144 Copynumber: 2.9 Consensus size: 143
28145067 TATGCGTTCC
*
28145077 AGTGTAAGACCATG-CTTGGGACATGGCATTGGCATTGATGTGTGTGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTC-TGGGACATGGCATCGGCATTGATGTGTGTGCTAGTGTAAGACCATGTC
* * * * *
28145141 TAGGAAATGGCATCGGCCACAACATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCG-G
65 TGGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGAC
* *
28145205 CA-TTGATGTGTGTGCT
130 CACTT-A--TGAGAGCT
* *
28145221 AGTGTAAGACCATGTCTGGGACCTGGCATCGGCATTGATGTGTGTGCTAGTGTAAGACCATGACT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATGTGTGTGCTAGTGTAAGACCATGTCT
* *** *
28145286 GGGACATGGCATTGGCCACCTTATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATTGACC
66 GGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGACC
28145351 ACCTTATGAGAGCT
131 A-CTTATGAGAGCT
* * * * * *
28145365 AGTATAAGACTATGTCTGGGACATGGCATCGGCAATGA-GACGAGAGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATG-TGTGTGCTAGTGTAAGACCATGTC
* * * * * * *
28145429 CGGGACATGACATCGGCCTCGACATGTA-AGCCAGTGTAAGACTATGTTTGGAACATGG
65 TGGGACATGGCATCGGCCACAACATG-AGAGCCAGTGTAAGACCATGTATGGGACATGG
28145487 AATCAGCAAT
Statistics
Matches: 227, Mismatches: 33, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
143 1 0.00
144 219 0.96
145 4 0.02
146 1 0.00
147 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (143 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATGTGTGTGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGGCCACAACATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGACC
ACTTATGAGAGCT
Found at i:28145465 original size:48 final size:48
Alignment explanation
Indices: 28145077--28145486 Score: 340
Period size: 48 Copynumber: 8.5 Consensus size: 48
28145067 TATGCGTTCC
* * * * * *
28145077 AGTGTAAGACCATG-CTTGGGACATGGCATTGGCATTGATGTGTGTGCT
1 AGTGTAAGACCATGTC-TGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * * * *
28145125 AGTGTAAGACCATGTCTAGGAAATGGCATCGGCCACAACATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * * * *
28145173 AATGTAAGACCATGTCTGGGACATGGCATCGGCATTGATGTGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * * * *
28145221 AGTGTAAGACCATGTCTGGGACCTGGCATCGGCATTGATGTGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * ** *
28145269 AGTGTAAGACCATGACTGGGACATGGCATTGGCCACCTTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * * **
28145317 AGTGTAAGACCATGTATGGGACATGGCATTGACCACCTTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
* * * * *
28145365 AGTATAAGACTATGTCTGGGACATGGCATCGGCAAT-GAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATATGAGAGCT
* * * *
28145413 AGTGTAAGACCATGTCCGGGACATGACATCGGCCTCGACATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATG-AGAGCT
* * *
28145461 AGTGTAAGACTATGTTTGGAACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
28145487 AATCAGCAAT
Statistics
Matches: 292, Mismatches: 66, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
47 1 0.00
48 289 0.99
49 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATGAGAGCT
Found at i:28160835 original size:40 final size:40
Alignment explanation
Indices: 28160743--28160892 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
28160733 AATTGAATGA
* * * *
28160743 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAAT-T
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACATAC
* * *
28160782 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
28160823 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
28160862 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
28160893 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
38 3 0.03
39 31 0.34
40 54 0.59
41 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:28160906 original size:40 final size:40
Alignment explanation
Indices: 28160782--28160908 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
28160772 GCTGGAAATT
* * * * *
28160782 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
* * ** *
28160822 CATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CATTC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
28160862 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
28160902 TATCCGG
1 TATCCGG
28160909 TTATGTTCCG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 67 0.97
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
Found at i:28175782 original size:28 final size:28
Alignment explanation
Indices: 28175742--28175820 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
28175732 GCAATCAAAT
* * *
28175742 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
28175770 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
28175798 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
28175821 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:28177817 original size:28 final size:28
Alignment explanation
Indices: 28177786--28177997 Score: 199
Period size: 28 Copynumber: 7.5 Consensus size: 28
28177776 GTGAACATAG
* *
28177786 GCACTGTGTGTGTGAGTTCCGTAACCGA
1 GCACTGTGTGTGCGAGTTCCGTAACTGA
* * ***
28177814 GCACTGTGTGTGCGAGATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTCCGTAACTGA
* *
28177842 GGCACTGTGTGTGCGAGTTCTGTGACTGA
1 -GCACTGTGTGTGCGAGTTCCGTAACTGA
* * * ***
28177871 GCACTGTGTGTGCAAGATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTCCGTAACTGA
*
28177899 GGCACTGTGTGTGCGAGTTCCGTAACCGA
1 -GCACTGTGTGTGCGAGTTCCGTAACTGA
* * * *
28177928 GCACTGTGTGTGCGAGATCAGTTATTGA
1 GCACTGTGTGTGCGAGTTCCGTAACTGA
**
28177956 GGCACTGTGTGTGCGAGTTCCGTAACCAA
1 -GCACTGTGTGTGCGAGTTCCGTAACTGA
28177985 GCACTGTGTGTGC
1 GCACTGTGTGTGC
28177998 AAATCGGTTG
Statistics
Matches: 145, Mismatches: 36, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
28 79 0.54
29 66 0.46
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGTTCCGTAACTGA
Found at i:28177853 original size:29 final size:29
Alignment explanation
Indices: 28177814--28177972 Score: 180
Period size: 29 Copynumber: 5.6 Consensus size: 29
28177804 CCGTAACCGA
28177814 GCACTGTGTGTGCGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* * *
28177843 GCACTGTGTGTGCGAGTTCTG-TGACTGA-
1 GCACTGTGTGTGCGAGATCGGTTG-TTGAG
*
28177871 GCACTGTGTGTGCAAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* * ****
28177900 GCACTGTGTGTGCGAGTTCCGTAACCGA-
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* *
28177928 GCACTGTGTGTGCGAGATCAGTTATTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
28177957 GCACTGTGTGTGCGAG
1 GCACTGTGTGTGCGAG
28177973 TTCCGTAACC
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
28 46 0.43
29 61 0.57
ACGTcount: A:0.16, C:0.17, G:0.37, T:0.30
Consensus pattern (29 bp):
GCACTGTGTGTGCGAGATCGGTTGTTGAG
Found at i:28177853 original size:57 final size:57
Alignment explanation
Indices: 28177784--28178026 Score: 371
Period size: 57 Copynumber: 4.2 Consensus size: 57
28177774 AAGTGAACAT
*
28177784 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* * * *
28177841 AGGCACTGTGTGTGCGAGTTCTGTGACTGAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
28177898 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCAGTTATTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
28177955 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGC-AAATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
*
28178011 GGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
28178027 AAATAGATCA
Statistics
Matches: 168, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
56 16 0.10
57 145 0.86
58 7 0.04
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
Found at i:28182982 original size:28 final size:28
Alignment explanation
Indices: 28182950--28183019 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
28182940 TATGGTACTC
*
28182950 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
28182978 AGTGTGCGAGATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
28183006 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
28183020 CGAATGATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:28191933 original size:22 final size:21
Alignment explanation
Indices: 28191881--28191934 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
28191871 AAGCAATAAA
* *
28191881 TATTAATTATTTATAAACTTT
1 TATTAAATATATATAAACTTT
28191902 TATTAGAATATATATAAACTATAT
1 TATTA-AATATATATAAACT-T-T
28191926 T-TTAAATAT
1 TATTAAATAT
28191935 TTAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 4 0.14
24 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTAAATATATATAAACTTT
Found at i:28193544 original size:13 final size:13
Alignment explanation
Indices: 28193526--28193550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28193516 CAATATATTT
28193526 ATTAATTAAAAAC
1 ATTAATTAAAAAC
28193539 ATTAATTAAAAA
1 ATTAATTAAAAA
28193551 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:28194923 original size:107 final size:107
Alignment explanation
Indices: 28194810--28195132 Score: 610
Period size: 107 Copynumber: 3.0 Consensus size: 107
28194800 TAAATAAAAA
*
28194810 ATTAGTTTAACAAAATAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
*
28194875 ACTTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
28194917 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
28194982 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
*
28195024 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
28195089 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
28195132 A
1 A
28195133 CGTGTTTTTT
Statistics
Matches: 212, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
107 199 0.94
108 13 0.06
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (107 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
Found at i:28196120 original size:30 final size:31
Alignment explanation
Indices: 28196086--28196170 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
28196076 CTTAATTAAA
* * *
28196086 AAAGTTATAATTTGA-TCATTAAGTTATTCG
1 AAAGTTATAATTTAAGTCACTAAATTATTCG
* *
28196116 AAAGTTTTCATTTAAGTCACTAAATTATTCG
1 AAAGTTATAATTTAAGTCACTAAATTATTCG
* * *
28196147 AAAGTTTTTATTAAAAGTCACTAA
1 AAAGTTATAATT-TAAGTCACTAA
28196171 GCTATTAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 12 0.26
31 24 0.52
32 10 0.22
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (31 bp):
AAAGTTATAATTTAAGTCACTAAATTATTCG
Found at i:28196145 original size:31 final size:32
Alignment explanation
Indices: 28196109--28196170 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
28196099 GATCATTAAG
*
28196109 TTATTCGAAAGTTTTCATT-TAAGTCACTAAA
1 TTATTCGAAAGTTTTCATTAAAAGTCACTAAA
*
28196140 TTATTCGAAAGTTTTTATTAAAAGTCACTAA
1 TTATTCGAAAGTTTTCATTAAAAGTCACTAA
28196171 GCTATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (32 bp):
TTATTCGAAAGTTTTCATTAAAAGTCACTAAA
Found at i:28197471 original size:9 final size:9
Alignment explanation
Indices: 28197453--28197492 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
28197443 GAGTGTGTAA
*
28197453 TTTAAGTAT
1 TTTAAATAT
28197462 TTTAAATA-
1 TTTAAATAT
28197470 TTTAAATAT
1 TTTAAATAT
28197479 TTTAAATAT
1 TTTAAATAT
28197488 TTTAA
1 TTTAA
28197493 TTTATAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
TTTAAATAT
Found at i:28197474 original size:17 final size:17
Alignment explanation
Indices: 28197452--28197489 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28197442 CGAGTGTGTA
*
28197452 ATTTAAGTATTTTAAAT
1 ATTTAAATATTTTAAAT
28197469 ATTTAAATATTTTAAAT
1 ATTTAAATATTTTAAAT
28197486 ATTT
1 ATTT
28197490 TAATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTAAATATTTTAAAT
Found at i:28197545 original size:20 final size:21
Alignment explanation
Indices: 28197522--28197560 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28197512 ATTCAAATAA
28197522 TATATTATA-ATTTAAAATTT
1 TATATTATATATTTAAAATTT
*
28197542 TATATTATATTTTTAAAAT
1 TATATTATATATTTAAAAT
28197561 AATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTATATATTTAAAATTT
Found at i:28208057 original size:30 final size:30
Alignment explanation
Indices: 28208023--28208080 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28208013 TTTTCGAGCA
* *
28208023 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
*
28208053 TAGGGGCAAAATGGTTATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
28208081 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:28209538 original size:55 final size:56
Alignment explanation
Indices: 28209454--28209576 Score: 180
Period size: 55 Copynumber: 2.2 Consensus size: 56
28209444 ACTTAAAATC
**
28209454 TAAAGTCAGT-TTAGTACACGGACAGGCCACACGAGCGTGTGTTGTGGCCGTGTTT
1 TAAAGTCAGTGTTAGTACACGGACAGGCCACACGAGCGTGTGTCATGGCCGTGTTT
*
28209509 TAAAGTCAGTGTT-GTACAC-GAGCAGGCCACACGGGCGTGTGTCATGGCCGTGTTT
1 TAAAGTCAGTGTTAGTACACGGA-CAGGCCACACGAGCGTGTGTCATGGCCGTGTTT
*
28209564 CAAAGTCAGTGTT
1 TAAAGTCAGTGTT
28209577 TCACACGGGC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
54 2 0.03
55 58 0.94
56 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (56 bp):
TAAAGTCAGTGTTAGTACACGGACAGGCCACACGAGCGTGTGTCATGGCCGTGTTT
Found at i:28213771 original size:18 final size:19
Alignment explanation
Indices: 28213739--28213774 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28213729 GTATCAAAAA
28213739 AATGAGATATAATGTTTAT
1 AATGAGATATAATGTTTAT
28213758 AATGAGAT-TAATGTTTA
1 AATGAGATATAATGTTTA
28213775 AAAAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
AATGAGATATAATGTTTAT
Found at i:28222128 original size:87 final size:86
Alignment explanation
Indices: 28222004--28222165 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 86
28221994 CATGCATAAA
* **
28222004 GTTGAGTTTTTACTCTTAATAAATTCACATCCTAGAGTTTGGGTGGTCCTATTGAGATGAACTTG
1 GTTGAGTTTTTACTCTCAATAAATTCACATCCTAGAGTTTGGGTGGTCCTATTGAGACAAACTTG
28222069 ATGAATTCACCGATTTGAGAG
66 ATGAATTCACCGATTTGAGAG
* * *
28222090 GTTGAGTTTATTACTCTCAATGAGTTCATATCCTAGAGTTTGGGTGGTCCTATTGAGACAAACTT
1 GTTGAGTTT-TTACTCTCAATAAATTCACATCCTAGAGTTTGGGTGGTCCTATTGAGACAAACTT
28222155 GATGAATTCAC
65 GATGAATTCAC
28222166 TTAATCTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 9 0.13
87 60 0.87
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (86 bp):
GTTGAGTTTTTACTCTCAATAAATTCACATCCTAGAGTTTGGGTGGTCCTATTGAGACAAACTTG
ATGAATTCACCGATTTGAGAG
Found at i:28222665 original size:24 final size:24
Alignment explanation
Indices: 28222638--28222709 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
28222628 ATTGGTTAAG
28222638 TATAGGCTATTAAGAGGGTTTATA
1 TATAGGCTATTAAGAGGGTTTATA
* *
28222662 TATAGCCACATT-----GG-TTA-A
1 TATAGGC-TATTAAGAGGGTTTATA
28222680 GTATAGGCTATTAAGAGGGTTTATA
1 -TATAGGCTATTAAGAGGGTTTATA
28222705 TATAG
1 TATAG
28222710 CCTTACTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 18
0.61 0.07 0.32
Matches are distributed among these distances:
18 4 0.11
19 9 0.26
20 2 0.06
23 2 0.06
24 14 0.40
25 4 0.11
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (24 bp):
TATAGGCTATTAAGAGGGTTTATA
Found at i:28222676 original size:43 final size:43
Alignment explanation
Indices: 28222624--28222711 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
28222614 TGGGTATATC
28222624 CCACATTGGTTAAGTATAGGCTATTAAGAGGGTTTATATATAG
1 CCACATTGGTTAAGTATAGGCTATTAAGAGGGTTTATATATAG
28222667 CCACATTGGTTAAGTATAGGCTATTAAGAGGGTTTATATATAG
1 CCACATTGGTTAAGTATAGGCTATTAAGAGGGTTTATATATAG
28222710 CC
1 CC
28222712 TTACTTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (43 bp):
CCACATTGGTTAAGTATAGGCTATTAAGAGGGTTTATATATAG
Found at i:28225110 original size:61 final size:58
Alignment explanation
Indices: 28224999--28225114 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 58
28224989 ATCACTTTAA
28224999 TATTAAAATAATATAATACTTATCAAGATAAATATTAGAATAAATTTAATATTAAATC
1 TATTAAAATAATATAATACTTATCAAGATAAATATTAGAATAAATTTAATATTAAATC
* * *
28225057 TATTAAATTAATATAATATTTATCTATAAGATAAATATTA-AATTTAATTTAATATTAA
1 TATTAAAATAATATAATACTTATC---AAGATAAATATTAGAA-TAAATTTAATATTAA
28225115 GATAATCACT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 22 0.43
60 2 0.04
61 27 0.53
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (58 bp):
TATTAAAATAATATAATACTTATCAAGATAAATATTAGAATAAATTTAATATTAAATC
Found at i:28225129 original size:61 final size:61
Alignment explanation
Indices: 28225007--28225183 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 61
28224997 AATATTAAAA
* * *
28225007 TAATATAATACTTATC---AAGATAAATATTAGAA-TAAATTTAATATTAAATCTATTAAAT
1 TAATATAATATTTATCTATAAGATAAATATTA-AATTAAATTTAATATTAAATCAATCAAAT
* **
28225065 TAATATAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAAGAT-AATCACTT
1 TAATATAATATTTATCTATAAGATAAATATTAAATTAAATTTAATATTAA-ATCAATCAAAT
*
28225126 TAATATTAA-ATTAATAGAATACTATCAAGATAAGTATTAAATTAAATTTAATATTAAA
1 TAATA-TAATATT--T---AT-CTAT-AAGATAAATATTAAATTAAATTTAATATTAAA
28225184 AATATCCAAA
Statistics
Matches: 98, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
58 15 0.15
60 2 0.02
61 39 0.40
62 5 0.05
63 1 0.01
66 2 0.02
67 5 0.05
68 29 0.30
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (61 bp):
TAATATAATATTTATCTATAAGATAAATATTAAATTAAATTTAATATTAAATCAATCAAAT
Found at i:28227571 original size:32 final size:32
Alignment explanation
Indices: 28227530--28227593 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28227520 ATTTATAAAG
28227530 TAGAAGTAGAAAACTAGCTTGATAGGAGAATA
1 TAGAAGTAGAAAACTAGCTTGATAGGAGAATA
28227562 TAGAAGTAGAAAACTAGCTTGATAGGAGAATA
1 TAGAAGTAGAAAACTAGCTTGATAGGAGAATA
28227594 AAACGTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (32 bp):
TAGAAGTAGAAAACTAGCTTGATAGGAGAATA
Found at i:28232823 original size:22 final size:22
Alignment explanation
Indices: 28232793--28232835 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28232783 TAAGATGTAG
28232793 AACAAATCAG-ATACAAATGCAA
1 AACAAATCAGAAT-CAAATGCAA
*
28232815 AACAGATCAGAATCAAATGCA
1 AACAAATCAGAATCAAATGCA
28232836 GTTTCATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (22 bp):
AACAAATCAGAATCAAATGCAA
Found at i:28233799 original size:26 final size:25
Alignment explanation
Indices: 28233770--28233823 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
28233760 TTCTCTTTTT
28233770 AAAATATAAAAATATATATATGGATA
1 AAAATATAAAAATATATATATGGA-A
* * * *
28233796 AAAATTTTAACATATCTATATGGAA
1 AAAATATAAAAATATATATATGGAA
28233821 AAA
1 AAA
28233824 TATTCTAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAATATAAAAATATATATATGGAA
Found at i:28234732 original size:8 final size:8
Alignment explanation
Indices: 28234698--28234747 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
28234688 AAGGTTGCAT
28234698 TTTTTATA
1 TTTTTATA
*
28234706 TTATTCATA
1 TT-TTTATA
*
28234715 TATTTA-A
1 TTTTTATA
28234722 TTTTTATA
1 TTTTTATA
28234730 TTTTTAT-
1 TTTTTATA
*
28234737 TTTTTAAA
1 TTTTTATA
28234745 TTT
1 TTT
28234748 AAAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 12 0.35
8 16 0.47
9 6 0.18
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:28235651 original size:29 final size:30
Alignment explanation
Indices: 28235587--28235662 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
28235577 TTAAAATTAT
* * *
28235587 ACATGAACTTTGATTTTATGTACAATTGTAT
1 ACATGAACTTT-AATTTATGTACAATTATAC
*
28235618 ACATGAACTTTAATTTA-GTGCAATTATAC
1 ACATGAACTTTAATTTATGTACAATTATAC
*
28235647 ACATGAAACTCTAATT
1 ACATG-AACTTTAATT
28235663 GTGGTTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.36
30 14 0.36
31 11 0.28
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (30 bp):
ACATGAACTTTAATTTATGTACAATTATAC
Found at i:28238162 original size:6 final size:6
Alignment explanation
Indices: 28238151--28238180 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28238141 GGGACTGTTA
*
28238151 ATTTTT ATTTTT ATCTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
28238181 TGGTTGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:28238528 original size:12 final size:12
Alignment explanation
Indices: 28238511--28238535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28238501 GAGACATAGA
28238511 ATTTGCCGCTTT
1 ATTTGCCGCTTT
28238523 ATTTGCCGCTTT
1 ATTTGCCGCTTT
28238535 A
1 A
28238536 ATATGCTCCA
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:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTTGCCGCTTT
Found at i:28238725 original size:44 final size:44
Alignment explanation
Indices: 28238530--28238837 Score: 230
Period size: 44 Copynumber: 7.0 Consensus size: 44
28238520 TTTATTTGCC
* * * * *
28238530 GCTTTAATATGCTCCACTGTAACTTCA-AGGAGATGAGATTTCTA
1 GCTTTAATCTGCTCTACTGCAACTTCAGA-GAGATAAGATTTGTA
* * * * **
28238574 ACTTCAATCTACTCCACTTTAACTTCA-AGGAGATAAGATTTGTA
1 GCTTTAATCTGCTCTACTGCAACTTCAGA-GAGATAAGATTTGTA
* * * * * * *
28238618 ACTTAAATATGCT-TCACTGTAACTTTAGGGAGATAAGGTTTGTA
1 GCTTTAATCTGCTCT-ACTGCAACTTCAGAGAGATAAGATTTGTA
*
28238662 CCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTA
1 GCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTA
* ** * *
28238706 GCTTTAATCTACTCTACTGCGGCTTTAGAAAGATAAGATTTGTTA
1 GCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG-TA
* * * * *
28238751 -TTTTCAATCTGCT-TCATTGCAACTTCAGAGAGATAATATTTTTG
1 GCTTT-AATCTGCTCT-ACTGCAACTTCAGAGAGATAAGATTTGTA
* * * *
28238795 GCTTTAATCTGCTATATTGCAACTTTAGGGAGATAAGATTTGT
1 GCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGT
28238838 GGCTGATTTT
Statistics
Matches: 213, Mismatches: 43, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
44 179 0.84
45 34 0.16
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (44 bp):
GCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTA
Found at i:28243061 original size:32 final size:30
Alignment explanation
Indices: 28243011--28243077 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
28243001 TTAAAATTTA
*
28243011 AAAAAAAATCATTTCCCCTTTTGTTTTTTTT
1 AAAAAAAATCATTTCCCCTTTT-TTTTCTTT
* *
28243042 AAAAAAACTCCTTTACCCCTTTTTTTTCTTT
1 AAAAAAAATCATTT-CCCCTTTTTTTTCTTT
*
28243073 GAAAA
1 AAAAA
28243078 TTTTTGGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.46
Consensus pattern (30 bp):
AAAAAAAATCATTTCCCCTTTTTTTTCTTT
Found at i:28244472 original size:14 final size:15
Alignment explanation
Indices: 28244455--28244483 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28244445 ATTTTTAAAC
28244455 ATTTAAT-TTTCAGT
1 ATTTAATATTTCAGT
28244469 ATTTAATATTTCAGT
1 ATTTAATATTTCAGT
28244484 TTATCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTTAATATTTCAGT
Found at i:28245863 original size:3 final size:3
Alignment explanation
Indices: 28245855--28245908 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
28245845 AAGAGCAAGC
*
28245855 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28245903 TAT TAT
1 TAT TAT
28245909 AGTTTTCTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28251218 original size:6 final size:6
Alignment explanation
Indices: 28251207--28251233 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28251197 AAGCAGGAAT
28251207 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
28251234 AATCTAGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:28251603 original size:29 final size:29
Alignment explanation
Indices: 28251534--28251603 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
28251524 TAAATTGTAT
*
28251534 TTTATATAAAATAATAAATTAATCTAATA
1 TTTATATAAAATAATAAATTAATCTAAAA
* ** *
28251563 TATATACCAAATAATAAAATTACT-TAAAA
1 TTTATATAAAATAAT-AAATTAATCTAAAA
*
28251592 TTTATATTAAAT
1 TTTATATAAAAT
28251604 CATTAAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTATATAAAATAATAAATTAATCTAAAA
Found at i:28252115 original size:21 final size:22
Alignment explanation
Indices: 28252068--28252115 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
28252058 AAAATAGTAG
* * *
28252068 TAAAATAGTGAAAAAATAATAA
1 TAAAATAGTCAAAAAAGAACAA
*
28252090 GAAAATAG-CAAAAAAGAACAA
1 TAAAATAGTCAAAAAAGAACAA
28252111 TAAAA
1 TAAAA
28252116 AATAGCAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.15
Consensus pattern (22 bp):
TAAAATAGTCAAAAAAGAACAA
Found at i:28253658 original size:13 final size:13
Alignment explanation
Indices: 28253640--28253664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28253630 AGGAAAGACA
28253640 CATTTTAATTTCG
1 CATTTTAATTTCG
28253653 CATTTTAATTTC
1 CATTTTAATTTC
28253665 AATTTGGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
CATTTTAATTTCG
Found at i:28260539 original size:13 final size:13
Alignment explanation
Indices: 28260521--28260545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28260511 CTGGCCCAAA
28260521 GAAAAGAAAAAGG
1 GAAAAGAAAAAGG
28260534 GAAAAGAAAAAG
1 GAAAAGAAAAAG
28260546 AAAAAAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAGG
Found at i:28269188 original size:24 final size:24
Alignment explanation
Indices: 28269160--28269229 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
28269150 AAAAGCTGTC
* *
28269160 AGGAGAAGATTTGGGAGCTGATAA
1 AGGAGAGGATTTAGGAGCTGATAA
28269184 AGGAGAGGATTTAGGAGCTGATAA
1 AGGAGAGGATTTAGGAGCTGATAA
*
28269208 GGGAGAGGATTTAGGAGCTGAT
1 AGGAGAGGATTTAGGAGCTGAT
28269230 TGGGAGAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.21
Consensus pattern (24 bp):
AGGAGAGGATTTAGGAGCTGATAA
Found at i:28270705 original size:27 final size:26
Alignment explanation
Indices: 28270664--28270774 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
28270654 AGGAAGCGTC
**
28270664 CTGGTGGCTA-TGCCACAATTATCTAAT
1 CTGGTGGC-ACTGCCAC-ATTATCTGTT
*
28270691 CTAGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAT-TATCTGTT
**
28270718 CTGGTGGCTTTGCCACAATTATCTGTT
1 CTGGTGGCACTGCCAC-ATTATCTGTT
* *
28270745 CTGGTGACACTGTCACATTATCTGTT
1 CTGGTGGCACTGCCACATTATCTGTT
28270771 CTGG
1 CTGG
28270775 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 17 0.24
27 52 0.73
28 2 0.03
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
CTGGTGGCACTGCCACATTATCTGTT
Found at i:28270756 original size:54 final size:53
Alignment explanation
Indices: 28270664--28270774 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
28270654 AGGAAGCGTC
*
28270664 CTGGTGGCTATGCCACAATTATCTAATCTAGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACAT-TATCTGTT
* ** * *
28270718 CTGGTGGCTTTGCCACAATTATCTGTTCTGGTGACACTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACATTATCTGTT
28270771 CTGG
1 CTGG
28270775 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 12 0.24
54 39 0.76
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTAATCTAGTGACACTGCCACATTATCTGTT
Found at i:28273510 original size:40 final size:40
Alignment explanation
Indices: 28273479--28273672 Score: 289
Period size: 40 Copynumber: 4.8 Consensus size: 40
28273469 ATAGCAAATC
* * *
28273479 GCACAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
28273519 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* * *
28273559 GCAGAAAATGCCTTCGGGTCTTAGCCCGGATATCGTCACTA
1 GCA-CAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* *
28273600 GCGCAAATGCCTTCGGGACTTAACCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
*
28273640 GCACAAAGTGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAA-TGCCTTCGGGACTTAGCCCGGATAT
28273673 CATCCGAATA
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 79 0.57
41 59 0.43
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
Found at i:28273607 original size:81 final size:81
Alignment explanation
Indices: 28273479--28273673 Score: 302
Period size: 81 Copynumber: 2.4 Consensus size: 81
28273469 ATAGCAAATC
* * * * *
28273479 GCAC-AAATGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 GCACAAAATGCCTTCGGGTCTTAGCCCGGATATCGTAACTAGCACAAATGCCTTCGGGACTTAAC
28273543 CCGGATATAGTCACTA
66 CCGGATATAGTCACTA
* * *
28273559 GCAGAAAATGCCTTCGGGTCTTAGCCCGGATATCGTCACTAGCGCAAATGCCTTCGGGACTTAAC
1 GCACAAAATGCCTTCGGGTCTTAGCCCGGATATCGTAACTAGCACAAATGCCTTCGGGACTTAAC
28273624 CCGGATATAGTCACTA
66 CCGGATATAGTCACTA
*
28273640 GCACAAAGTGCCTTCGGGTCTTAGCCCGGATATC
1 GCACAAAATGCCTTCGGGTCTTAGCCCGGATATC
28273674 ATCCGAATAA
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 3 0.03
81 101 0.97
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (81 bp):
GCACAAAATGCCTTCGGGTCTTAGCCCGGATATCGTAACTAGCACAAATGCCTTCGGGACTTAAC
CCGGATATAGTCACTA
Found at i:28285325 original size:6 final size:6
Alignment explanation
Indices: 28285302--28285347 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
28285292 AATGTTGAAT
*
28285302 AAAT-A AAAT-A ATATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
28285348 TTATAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:28285353 original size:18 final size:17
Alignment explanation
Indices: 28285302--28285355 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
28285292 AATGTTGAAT
28285302 AAAT-AAAATAATATAA
1 AAATAAAAATAATATAA
*
28285318 AAATAAAAATAAAAATAA
1 AAATAAAAAT-AATATAA
28285336 AAATAAAAATAATTATAA
1 AAATAAAAATAA-TATAA
28285354 AA
1 AA
28285356 TTTTTCATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 22 0.67
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAAAATAATATAA
Found at i:28287739 original size:26 final size:26
Alignment explanation
Indices: 28287709--28287820 Score: 118
Period size: 28 Copynumber: 4.2 Consensus size: 26
28287699 AGCATGGCTG
* *
28287709 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
28287735 CCAGATACAGATAATCGTGGTAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28287763 CCAGAAC-GATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28287789 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
28287817 CCAG
1 CCAG
28287821 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 26 0.36
27 17 0.24
28 29 0.40
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28287818 original size:54 final size:54
Alignment explanation
Indices: 28287709--28287820 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
28287699 AGCATGGCTG
* *
28287709 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAACCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
* * * *
28287763 CCAGAAC-GATATATGTGGCAGAGCCACCAGAT-CAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAA-TCGTGGCAGAACCA
28287817 CCAG
1 CCAG
28287821 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
53 11 0.22
54 39 0.78
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
Found at i:28289256 original size:24 final size:24
Alignment explanation
Indices: 28289229--28289299 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
28289219 CTAGATTTCC
**
28289229 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28289253 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28289277 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
28289300 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:28294189 original size:40 final size:40
Alignment explanation
Indices: 28294134--28294335 Score: 275
Period size: 40 Copynumber: 5.1 Consensus size: 40
28294124 TGAATGATAC
* * * *
28294134 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
28294174 CCGGGTTAAGACCCGAAGGCA-TTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
28294213 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
28294253 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATA-
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* ** *
28294292 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
28294332 CCGG
1 CCGG
28294336 CTAAATTCCG
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 66 0.46
40 79 0.54
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.27
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:28294265 original size:79 final size:79
Alignment explanation
Indices: 28294134--28294339 Score: 301
Period size: 79 Copynumber: 2.6 Consensus size: 79
28294124 TGAATGATAC
* * * *
28294134 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGTTAAGACCCGAAGGCA-TT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
28294197 GTGCGAGTTGCTATA
65 GTGCGAGTTGCTATA
*
28294212 TCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
1 -CCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
28294277 GTGCGAGTTGCTATA
65 GTGCGAGTTGCTATA
* * *
28294292 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAA
28294340 ATTCCGAAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
78 6 0.05
79 91 0.78
80 19 0.16
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (79 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGCTATA
Found at i:28302296 original size:40 final size:40
Alignment explanation
Indices: 28302241--28302484 Score: 310
Period size: 40 Copynumber: 6.1 Consensus size: 40
28302231 TGAATGATAC
* * * * *
28302241 CCGGGCTAAGCCCCGAAGACATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
28302281 CCGGGTTAAGACCCGAAGGCAATTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
28302321 CCGGGTTAAGACCCGAAGTCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
28302361 CCTGGTTAAGACCCGAAGGCATTTATGCAAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
28302401 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* ** *
28302441 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
28302481 CCGG
1 CCGG
28302485 CTAAATTCGA
Statistics
Matches: 176, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 174 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:28302467 original size:120 final size:120
Alignment explanation
Indices: 28302247--28302482 Score: 357
Period size: 120 Copynumber: 2.0 Consensus size: 120
28302237 ATACCCGGGC
* * *
28302247 TAAGCCCCGAAGACATTTATGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAG
1 TAAGACCCGAAGACATTTATGCAAGTGATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAG
* * * *
28302312 TTGCTATATCCGGGTTAAGACCCGAAGTCATTTGTGCGAGTTGTTATATCCTGGT
66 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCCTGGT
* *
28302367 TAAGACCCGAAGGCATTTATGCAAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA
1 TAAGACCCGAAGACATTTATGCAAG-TGATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA
**
28302431 GTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC
65 GTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCC
28302483 GGCTAAATTC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
120 102 0.98
121 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (120 bp):
TAAGACCCGAAGACATTTATGCAAGTGATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAG
TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCCTGGT
Found at i:28307613 original size:30 final size:30
Alignment explanation
Indices: 28307577--28307677 Score: 127
Period size: 28 Copynumber: 3.5 Consensus size: 30
28307567 GACAAGATTG
* * *
28307577 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
28307607 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
28307635 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
28307664 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28307678 GATTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
29 20 0.32
30 19 0.31
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:28307671 original size:29 final size:29
Alignment explanation
Indices: 28307577--28307677 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
28307567 GACAAGATTG
* * * *
28307577 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTGAAAA-TATATA
*
28307607 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-TTGAAAATATATA
*
28307635 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTTGAAAATATATA
28307664 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28307678 GATTCACTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 22 0.36
30 15 0.25
31 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTGAAAATATATA
Found at i:28317430 original size:2 final size:2
Alignment explanation
Indices: 28317373--28317411 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
28317363 TGGTATTTAA
*
28317373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28317412 ATAGTATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28318001 original size:15 final size:14
Alignment explanation
Indices: 28317983--28318016 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
28317973 TTCTTCTTTT
28317983 TTTTTTTGGGTTAGG
1 TTTTTTTGGG-TAGG
28317998 TTTTTTTGGGTAGG
1 TTTTTTTGGGTAGG
28318012 TTTTT
1 TTTTT
28318017 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.06, C:0.00, G:0.29, T:0.65
Consensus pattern (14 bp):
TTTTTTTGGGTAGG
Found at i:28318032 original size:17 final size:17
Alignment explanation
Indices: 28318012--28318047 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
28318002 TTTGGGTAGG
28318012 TTTTTCTTT-TTCTTTTT
1 TTTTTCTTTGTT-TTTTT
28318029 TTTTTCTTTGTTTTTTT
1 TTTTTCTTTGTTTTTTT
28318046 TT
1 TT
28318048 GGGTTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTTTCTTTGTTTTTTT
Found at i:28318042 original size:12 final size:11
Alignment explanation
Indices: 28318012--28318045 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
28318002 TTTGGGTAGG
28318012 TTTTTCTTTTTC
1 TTTTT-TTTTTC
28318024 TTTTTTTTTTC
1 TTTTTTTTTTC
28318035 TTTGTTTTTTT
1 TTT-TTTTTTT
28318046 TTGGGTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:28318800 original size:88 final size:83
Alignment explanation
Indices: 28318693--28319270 Score: 299
Period size: 88 Copynumber: 7.0 Consensus size: 83
28318683 AACAGACATT
** * *
28318693 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
28318758 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AAC-TG
* * * ** *
28318781 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
28318845 GTTGA-TTTTTGAAAAACAG
64 GTTGATTTTTTGAAAAACTG
* * * * ** *** *
28318864 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
28318925 ATGAGTTGAATTTTTTTG-AAAA---
60 ATGAGTTG-A-TTTTTTGAAAAACTG
** * *
28318947 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
28319012 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-CTG
* * * * * *
28319035 AAAAACAGATTTTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
28319100 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAACTG
* *** *** * *
28319118 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
28319178 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAACTG
* * * * * * *
28319195 ATAGA-A-A--TTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
28319256 TTGATTTTTTGAAAA
65 TTGATTTTTTGAAAA
28319271 CAGAAATTGA
Statistics
Matches: 384, Mismatches: 69, Indels: 84
0.72 0.13 0.16
Matches are distributed among these distances:
76 9 0.02
77 47 0.12
78 2 0.01
79 64 0.17
80 3 0.01
81 11 0.03
82 38 0.10
83 14 0.04
84 41 0.11
85 9 0.02
86 6 0.02
87 19 0.05
88 115 0.30
90 6 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAACTG
Found at i:28318897 original size:30 final size:30
Alignment explanation
Indices: 28318861--28318922 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
28318851 TTTTGAAAAA
28318861 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
28318891 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
28318921 CA
1 CA
28318923 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:28319041 original size:14 final size:14
Alignment explanation
Indices: 28319018--28319052 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28319008 TGAGTTGATT
28319018 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
28319031 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
28319045 TTTGAAAA
1 TTTGAAAA
28319053 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:28319353 original size:72 final size:73
Alignment explanation
Indices: 28319070--28319602 Score: 397
Period size: 72 Copynumber: 6.8 Consensus size: 73
28319060 ACATGTAACC
* * * *
28319070 CGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG--AAAATAC
* *
28319135 CTCAGTGTGTGAT
62 CTCAGCGTGT-CT
* * *
28319148 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGC
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
28319213 TCAGCGCATGAGC-
63 TCAGCG--TG-TCT
* * *
28319226 CAAGGGTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
28319291 ACGTGTCT
66 GCGTGTCT
* ** * * *
28319299 TGAGGCTCAACTCATTTCTCACAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
28319363 GCGTGTCC
66 GCGTGTCT
*
28319371 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTTTTGAAATGCAGAAATTGAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--------TTTTTTGAAA-ACAGAAATTG--
** ** *
28319436 AAATGGAAATTGAAAATACCTCGACGTGTGAT
55 --A---AAA-T--ACCT-CAGC---GTGT-CT
* * *
28319468 CTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTTTGACAACAGAAATTGAAATTACCT
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
28319533 CAGCGTGTC-
64 CAGCGTGTCT
* *
28319542 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAAAAATTGAAAA
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAA
28319603 ACGGAAATTG
Statistics
Matches: 366, Mismatches: 56, Indels: 69
0.75 0.11 0.14
Matches are distributed among these distances:
72 65 0.18
73 29 0.08
74 43 0.12
75 32 0.09
76 14 0.04
77 41 0.11
78 5 0.01
79 51 0.14
80 2 0.01
81 8 0.02
82 10 0.03
83 2 0.01
86 2 0.01
89 2 0.01
90 10 0.03
91 9 0.02
92 2 0.01
93 2 0.01
96 4 0.01
97 1 0.00
98 32 0.09
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (73 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
GCGTGTCT
Found at i:28319555 original size:172 final size:168
Alignment explanation
Indices: 28319267--28319745 Score: 711
Period size: 165 Copynumber: 2.9 Consensus size: 168
28319257 TGATTTTTTG
* * * ** * *
28319267 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
28319330 TGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
* *
28319394 ATATGAGTTGATTTTTTTTTTTTTTGAAATGCAGAAATTGA
131 ATATGAGTTGA---TTTTTTTTTTTGAAAGGCAAAAATTGA
*
28319435 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
28319500 TGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
28319565 AATATGAGTTGA----TTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
* * * *
28319600 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
28319665 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
28319730 AATATGAGTTGATTTT
130 AATATGAGTTGATTTT
28319746 GAAAAAGTAG
Statistics
Matches: 284, Mismatches: 19, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
165 157 0.55
168 27 0.10
169 1 0.00
170 30 0.11
172 69 0.24
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (168 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
Found at i:28319564 original size:74 final size:75
Alignment explanation
Indices: 28319441--28319602 Score: 222
Period size: 74 Copynumber: 2.1 Consensus size: 75
28319431 TTGAAAAATG
*
28319441 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
28319506 TTTTGACAACA
65 TTTTGACAACA
* * *
28319517 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
28319580 TTTTGA-AAGGCA
65 TTTTGACAA--CA
*
28319592 AAAATTGAAAA
1 GAAATTGAAAA
28319603 ACGGAAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
73 2 0.03
74 42 0.55
75 12 0.16
76 21 0.27
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACA
Found at i:28319731 original size:74 final size:75
Alignment explanation
Indices: 28319606--28319745 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 75
28319596 TTGAAAAACG
* *
28319606 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
28319671 TTTTGACAACA
65 TTTTGACAACA
* * *
28319682 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
28319746 GAAAAAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 37 0.63
76 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:28319944 original size:72 final size:71
Alignment explanation
Indices: 28319810--28319975 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
28319800 TGAACAACGT
* * * *
28319810 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
28319875 GAGTTG
66 GAGTTG
*
28319881 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
28319946 TGAGTTG
65 TGAGTTG
**
28319953 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
28319976 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:28320118 original size:71 final size:71
Alignment explanation
Indices: 28319975--28320238 Score: 356
Period size: 70 Copynumber: 3.7 Consensus size: 71
28319965 AAAAATTAAA
* * * * *
28319975 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
28320038 GCCCCG
66 GCCCCG
* *
28320044 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
* **
28320109 GTCTTG
66 GCCCCG
* * *
28320115 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
28320178 TGCCCCG
65 TGCCCCG
*
28320185 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
28320239 GGCTTAACTC
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
69 31 0.19
70 61 0.37
71 58 0.35
72 14 0.08
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GCCCCG
Found at i:28320196 original size:70 final size:69
Alignment explanation
Indices: 28319975--28320238 Score: 339
Period size: 71 Copynumber: 3.7 Consensus size: 69
28319965 AAAAATTAAA
* ** * * *
28319975 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGC
28320040 CCCG
66 CCCG
* * *
28320044 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTAAAAACAAAAATTAAAAATACCTCAGCGT
* **
28320109 GTCTTG
64 GCCCCG
* *
28320115 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAA-ACAAAAATTAAAAATACCTCAGCGTG
28320180 CCCCG
65 CCCCG
*
28320185 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT-AAAAACAAAAATTAAAA
28320239 GGCTTAACTC
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
69 33 0.20
70 56 0.34
71 60 0.36
72 14 0.08
73 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGC
CCCG
Found at i:28320221 original size:263 final size:257
Alignment explanation
Indices: 28319813--28320405 Score: 1042
Period size: 257 Copynumber: 2.3 Consensus size: 257
28319803 ACAACGTAAA
* * * * * *
28319813 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
28319878 TTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
66 TTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
28319943 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
129 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
28320008 TTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
194 TT-----A-AAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
28320073 TGATT
253 TGATT
28320078 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
28320143 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
28320208 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
28320273 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
196 AAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
*
28320335 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
28320400 TTGATT
66 TTGATT
28320406 TTCCTTGAAA
Statistics
Matches: 320, Mismatches: 8, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
257 130 0.41
258 1 0.00
263 127 0.40
265 62 0.19
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (257 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
AAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Done.