Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 83 of 182
Found at i:25055495 original size:6 final size:6
Alignment explanation
Indices: 25055484--25055518 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
25055474 TCGGGAGGAA
*
25055484 TAATAT TAATAT TAATAT CAATAT TAATAAT TAAT
1 TAATAT TAATAT TAATAT TAATAT TAAT-AT TAAT
25055519 TACTTTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TAATAT
Found at i:25057735 original size:25 final size:25
Alignment explanation
Indices: 25057701--25057759 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
25057691 ATGTTTCAAG
25057701 AATGAGAGTTACAAAGCTAATAATT
1 AATGAGAGTTACAAAGCTAATAATT
*
25057726 AATGAGAGTTACAAAGCTAATAGTT
1 AATGAGAGTTACAAAGCTAATAATT
25057751 AATGAGAGT
1 AATGAGAGT
25057760 AATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (25 bp):
AATGAGAGTTACAAAGCTAATAATT
Found at i:25065308 original size:12 final size:11
Alignment explanation
Indices: 25065287--25065332 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
25065277 TATTGTATCC
25065287 TTATTATTATA
1 TTATTATTATA
25065298 TTATCTATTATA
1 TTAT-TATTATA
*
25065310 TTTATTATCATCA
1 -TTATTATTAT-A
25065323 TTATTATTAT
1 TTATTATTAT
25065333 TTCTATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 4 0.13
12 21 0.70
13 5 0.17
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTATTATA
Found at i:25067535 original size:130 final size:130
Alignment explanation
Indices: 25067302--25067544 Score: 450
Period size: 130 Copynumber: 1.9 Consensus size: 130
25067292 CCACTTAAGC
*
25067302 TCATGGTAATGCTATTACGGGTGTAATACATTATTGATCTAATCGGTGAAATCCACCGATTTCTA
1 TCATGCTAATGCTATTACGGGTGTAATACATTATTGATCTAATCGGTGAAATCCACCGATTTCTA
* * *
25067367 ATCCGTCTCTTTTGCTCAGTTTAGGTGCTGCTTCACTTTACCCTCCCTTTATTCCGTTGTTTGGT
66 ATCCGTCCCTTTTACTCAGTTTAGGCGCTGCTTCACTTTACCCTCCCTTTATTCCGTTGTTTGGT
25067432 TCATGCTAATGCTATTACGGGTGTAATACATTATTGATCTAATCGGTGAAATCCACCGATTTCTA
1 TCATGCTAATGCTATTACGGGTGTAATACATTATTGATCTAATCGGTGAAATCCACCGATTTCTA
25067497 ATCCGTCCCTTTTACTCAGTTTAGGCGCTGCTTCACTTTACCCTCCCT
66 ATCCGTCCCTTTTACTCAGTTTAGGCGCTGCTTCACTTTACCCTCCCT
25067545 GTTTTACCCT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (130 bp):
TCATGCTAATGCTATTACGGGTGTAATACATTATTGATCTAATCGGTGAAATCCACCGATTTCTA
ATCCGTCCCTTTTACTCAGTTTAGGCGCTGCTTCACTTTACCCTCCCTTTATTCCGTTGTTTGGT
Found at i:25067678 original size:19 final size:19
Alignment explanation
Indices: 25067654--25067690 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25067644 CTGTTTCTCA
25067654 CAGTTTCTGCCGATTTGCT
1 CAGTTTCTGCCGATTTGCT
25067673 CAGTTTCTGCCGATTTGC
1 CAGTTTCTGCCGATTTGC
25067691 GTCTTCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.41
Consensus pattern (19 bp):
CAGTTTCTGCCGATTTGCT
Found at i:25070798 original size:16 final size:16
Alignment explanation
Indices: 25070777--25070818 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
25070767 TTATTAAATT
*
25070777 ATATATTTTAATTATA
1 ATATATTTTAATAATA
25070793 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
25070808 AT-TATGTTTAA
1 ATATAT-TTTAA
25070819 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:25070803 original size:15 final size:15
Alignment explanation
Indices: 25070768--25070809 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25070758 TTAAGAATTT
*
25070768 TATTAAATTAT-ATA
1 TATTTAATTATAATA
25070782 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
25070796 TATTTAATAATAAT
1 TATTTAATTATAAT
25070810 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:25071056 original size:16 final size:16
Alignment explanation
Indices: 25071031--25071068 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
25071021 TTGATTTGCT
25071031 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
25071047 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
25071063 AATACA
1 ATTACA
25071069 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:25071636 original size:18 final size:17
Alignment explanation
Indices: 25071614--25071648 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25071604 TAATTATTAA
*
25071614 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25071632 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25071649 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25076592 original size:15 final size:15
Alignment explanation
Indices: 25076564--25076598 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25076554 ATACTCTGAT
*
25076564 AATATAAATTATATA
1 AATATAAATAATATA
*
25076579 AATATCAATAATATA
1 AATATAAATAATATA
25076594 AATAT
1 AATAT
25076599 TTAACCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAAATAATATA
Found at i:25080502 original size:156 final size:156
Alignment explanation
Indices: 25080213--25080507 Score: 387
Period size: 156 Copynumber: 1.9 Consensus size: 156
25080203 GTAGGATTGG
* * * * *
25080213 TTTCAAATGGTTGCAATTAGGGGGTTAGTTGTACAGGCTCTTGCTTAATGGGCACTACTTACTCT
1 TTTCAAATGGTTGCAATAAAGGGGTTACTTCTACAGGCTCTTGCTTAATGGGCACTACCTACTCT
* * * * * *
25080278 AAATATTCATATAGAGGTTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCATG
66 AAATATTCACATAGAGGCTCCAATTCAAAGTTTTAAAGTATATTCGATTCAGTCTAATTTTCACG
25080343 ATTTAGTCTAGTTTTAAAATTAAAAT
131 ATTTAGTCTAGTTTTAAAATTAAAAT
* * *
25080369 TTTCAAATGGTTG-AAGTAAAGGGGTTACTTCTATAGGCTCTTGGTTAGTGGGCATCT-CCTACT
1 TTTCAAATGGTTGCAA-TAAAGGGGTTACTTCTACAGGCTCTTGCTTAATGGGCA-CTACCTACT
* * * * *
25080432 CTAAATATTCACCTAGAGGCTCCAATTCTAAGTTTTGAAGTATATTCGATTTAGTCTAATTTTTA
64 CTAAATATTCACATAGAGGCTCCAATTCAAAGTTTTAAAGTATATTCGATTCAGTCTAATTTTCA
25080497 CGATTTAGTCT
129 CGATTTAGTCT
25080508 CTATACCAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
155 2 0.02
156 114 0.97
157 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (156 bp):
TTTCAAATGGTTGCAATAAAGGGGTTACTTCTACAGGCTCTTGCTTAATGGGCACTACCTACTCT
AAATATTCACATAGAGGCTCCAATTCAAAGTTTTAAAGTATATTCGATTCAGTCTAATTTTCACG
ATTTAGTCTAGTTTTAAAATTAAAAT
Found at i:25086181 original size:30 final size:30
Alignment explanation
Indices: 25086147--25086205 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
25086137 ATGGACTGGC
* *
25086147 ACATGGGCATGTGTCTAGCCTGTGTGGCTT
1 ACATGGGCATGTGTCCAGCCCGTGTGGCTT
*
25086177 ACATGGGCGTGTGTCCAGCCCGTGTGGCT
1 ACATGGGCATGTGTCCAGCCCGTGTGGCT
25086206 CCTGAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.36, T:0.29
Consensus pattern (30 bp):
ACATGGGCATGTGTCCAGCCCGTGTGGCTT
Found at i:25096127 original size:5 final size:6
Alignment explanation
Indices: 25096111--25096136 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25096101 ATTGCAATAT
25096111 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
25096137 TGTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:25098232 original size:89 final size:88
Alignment explanation
Indices: 25098110--25098625 Score: 387
Period size: 89 Copynumber: 5.8 Consensus size: 88
25098100 TCAGAGAGAT
* * * * *
25098110 AAGATCTGTGTCTTCGATCTATTTCACCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCT
1 AAGATCTGTATCTTCGATCTACTTCA-TACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * **
25098175 ACTTCACTGCTAGTACGAGAAGGT
65 ACTTCACTACCAGTACGAGAAGAC
* * * * * *
25098199 AAGATCTGTTATCCTT-GATCTACTTCATGCCAATACATGAAGACAAGATTTACTTTCTTCGATC
1 AAGATCTG-TAT-CTTCGATCTACTTCATACCAATATAGGAAGACAAGATCTGCTATCTTCGATC
* * * * *
25098263 TACTTCGCCACCAGTATGGGAAGAT
64 TACTTCACTACCAGTACGAGAAGAC
* * * * * * *
25098288 AAGATCTGCATCTTCGATCCACTTCGCTACTAATGTAGGAAGACAGGATTTGCTATCTTCGATCT
1 AAGATCTGTATCTTCGATCTACTTC-ATACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* *
25098353 ACTTCA-TGCCAATAC-ATGAAGAC
65 ACTTCACTACCAGTACGA-GAAGAC
* * * * * * * *
25098376 AAGATCTACTTTCTTTGATCTACTTCACCACTAGTATGGGAAGACAAGATCTTCATAT-TT-GAT
1 AAGATCT-GTATCTTCGATCTACTTCA-TACCAATATAGGAAGACAAGATCTGC-TATCTTCGAT
* * * *
25098439 CCACTTCGCTACCAATA-TAGGAAGAC
63 CTACTTCACTACCAGTACGA-GAAGAC
* ** * * * * *
25098465 AGGATCTGCTATCTTCGATCTACTTCATGTCAAAACATGAAGACAAGATCTACTTTCTTCGATCT
1 AAGATCTG-TATCTTCGATCTACTTCATACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * *
25098530 ACTTCGCCACCAGTATGGGAAGAC
65 ACTTCACTACCAGTACGAGAAGAC
* * *
25098554 AAGATCTGTATCTTCGATCCACTTCACTACCAATATAGGAAGACATGATCTGTTATCTTCGATCT
1 AAGATCTGTATCTTCGATCTACTTCA-TACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
25098619 ACTTCAC
65 ACTTCAC
25098626 GCCGATGCAT
Statistics
Matches: 327, Mismatches: 85, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
87 5 0.02
88 72 0.22
89 232 0.71
90 15 0.05
91 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (88 bp):
AAGATCTGTATCTTCGATCTACTTCATACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
CTTCACTACCAGTACGAGAAGAC
Found at i:25098368 original size:133 final size:133
Alignment explanation
Indices: 25098120--25098648 Score: 711
Period size: 133 Copynumber: 4.0 Consensus size: 133
25098110 AAGATCTGTG
* * * * *
25098120 TCTTCGATCTATTTCACCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCACTAC
* * * ** * *
25098185 TAGTA-CGAGAAGGTAAGATCTGTTATCCTT-GATCTACTTCATGCCAATACATGAAGACAAGAT
65 CAATATAG-GAAGACAGGATCTGCTAT-CTTCGATCTACTTCATGCCAATACATGAAGACAAGAT
*
25098248 TTACTT
128 CTACTT
* * * *
25098254 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCGCTACT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCACTACC
* *
25098319 AATGTAGGAAGACAGGATTTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTA
66 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTA
25098384 CTT
131 CTT
* * * * * *
25098387 TCTTTGATCTACTTCACCACTAGTATGGGAAGACAAGATCTTCATATTTGATCCACTTCGCTACC
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCACTACC
* *
25098452 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGTCAAAACATGAAGACAAGATCTA
66 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTA
25098517 CTT
131 CTT
* *
25098520 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTCGATCCACTTCACTACC
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCACTACC
* * * * *
25098585 AATATAGGAAGACATGATCTGTTATCTTCGATCTACTTCACGCCGATGCATGAAGACAAGATCT
66 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCT
25098649 GCTATTTTTT
Statistics
Matches: 349, Mismatches: 44, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
132 3 0.01
133 306 0.88
134 40 0.11
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (133 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCACTACC
AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTA
CTT
Found at i:25098640 original size:44 final size:44
Alignment explanation
Indices: 25098110--25098649 Score: 324
Period size: 44 Copynumber: 12.2 Consensus size: 44
25098100 TCAGAGAGAT
* * **
25098110 AAGATCTG-TGTCTTCGATCTATTTCACCACCAATATGGGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCA-CACCAATACAGGAAGAC
* * * * * **
25098154 AAGATCTGCTATCTTTGATCTACTTCACTGCTAGTAC-GAGAAGGT
1 AAGATCTGTTATCTTCGATCTACTTCAC-ACCAATACAG-GAAGAC
** *
25098199 AAGATCTGTTATCCTT-GATCTACTTCATGCCAATACATGAAGAC
1 AAGATCTGTTAT-CTTCGATCTACTTCACACCAATACAGGAAGAC
* * * * ** *
25098243 AAGATTTACTT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGAT
1 AAGATCT-GTTATCTTCGATCTACTTC-ACACCAATACAGGAAGAC
* * * * **
25098288 AAGATCTG-CATCTTCGATCCACTTCGCTACTAATGTAGGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCAC-ACCAATACAGGAAGAC
* * * ** *
25098332 AGGATTTGCTATCTTCGATCTACTTCATGCCAATACATGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCACACCAATACAGGAAGAC
* * * * **
25098376 AAGATCTACTT-TCTTTGATCTACTTCACCACTAGTATGGGAAGAC
1 AAGATCT-GTTATCTTCGATCTACTTCA-CACCAATACAGGAAGAC
* * * * * *
25098421 AAGATCT-TCATATTTGATCCACTTCGCTACCAATATAGGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCAC-ACCAATACAGGAAGAC
* * *** * *
25098465 AGGATCTGCTATCTTCGATCTACTTCATGTCAAAACATGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCACACCAATACAGGAAGAC
* * * **
25098509 AAGATCTACTT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCT-GTTATCTTCGATCTACTTC-ACACCAATACAGGAAGAC
* *
25098554 AAGATCTG-TATCTTCGATCCACTTCACTACCAATATAGGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCAC-ACCAATACAGGAAGAC
* * * * *
25098598 ATGATCTGTTATCTTCGATCTACTTCACGCCGATGCATGAAGAC
1 AAGATCTGTTATCTTCGATCTACTTCACACCAATACAGGAAGAC
25098642 AAGATCTG
1 AAGATCTG
25098650 CTATTTTTTA
Statistics
Matches: 371, Mismatches: 104, Indels: 42
0.72 0.20 0.08
Matches are distributed among these distances:
43 8 0.02
44 216 0.58
45 144 0.39
46 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
AAGATCTGTTATCTTCGATCTACTTCACACCAATACAGGAAGAC
Found at i:25113915 original size:15 final size:15
Alignment explanation
Indices: 25113886--25113933 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
25113876 AGTACACAAG
*
25113886 AAAAAATAAAGAAAAC
1 AAAAACTAAA-AAAAC
*
25113902 AAAATCTAAAAAAAC
1 AAAAACTAAAAAAAC
25113917 AAAAAC-AAAAACAAC
1 AAAAACTAAAAA-AAC
25113932 AA
1 AA
25113934 TTCGAGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.18
15 15 0.54
16 8 0.29
ACGTcount: A:0.79, C:0.12, G:0.02, T:0.06
Consensus pattern (15 bp):
AAAAACTAAAAAAAC
Found at i:25119111 original size:12 final size:12
Alignment explanation
Indices: 25119094--25119118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25119084 TTGTGAGTAA
25119094 ATTAAACTTGTG
1 ATTAAACTTGTG
25119106 ATTAAACTTGTG
1 ATTAAACTTGTG
25119118 A
1 A
25119119 AAGTGAGGTC
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTAAACTTGTG
Found at i:25120942 original size:23 final size:23
Alignment explanation
Indices: 25120914--25120958 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
25120904 ATTCAAAATT
*
25120914 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
25120937 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
25120959 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:25121167 original size:67 final size:66
Alignment explanation
Indices: 25121055--25121298 Score: 169
Period size: 70 Copynumber: 3.6 Consensus size: 66
25121045 AATACATATA
* * * *
25121055 AAATTTAAAAATTTTGATGAT-AATTCT-AGAATAATCATACGTGATAAATACAAAATAATAGTA
1 AAATTTAAAAATATTAATGATAAATT-TGA-AATAATAATACATGATAAAT-CAAAATAATAGTA
25121118 TAAT
63 TAAT
* *
25121122 AAATTTAAAAATATTAATGATAAATTTGAAATAGAT-ATACATGATAAATTTAAAAT-ATTGTTA
1 AAATTTAAAAATATTAATGATAAATTTGAAATA-ATAATACATGATAAA-TCAAAATAATAG-T-
*
25121185 ACAAT
62 ATAAT
* * * * *
25121190 GAATTTAAAATAATAATATTGATAAA-TTGAAAATAATAAAACATGATAAATCTAAAATAATAAT
1 AAATTT-AAA-AATATTAATGATAAATTTG-AAATAATAATACATGATAAATC-AAAATAATAGT
25121254 ATACAAT
62 AT--AAT
* * * *
25121261 ACACTTAGATAATATTAATGATTAATTT--AATAATAATA
1 AAATTTA-AAAATATTAATGATAAATTTGAAATAATAATA
25121299 AGTATAAACA
Statistics
Matches: 139, Mismatches: 22, Indels: 31
0.72 0.11 0.16
Matches are distributed among these distances:
66 3 0.02
67 41 0.29
68 26 0.19
69 10 0.07
70 48 0.35
71 11 0.08
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.35
Consensus pattern (66 bp):
AAATTTAAAAATATTAATGATAAATTTGAAATAATAATACATGATAAATCAAAATAATAGTATAA
T
Found at i:25121177 original size:24 final size:23
Alignment explanation
Indices: 25121017--25121251 Score: 111
Period size: 24 Copynumber: 10.3 Consensus size: 23
25121007 AATTTACAAT
* *
25121017 AAATAATAT--ATAATAAATTTG
1 AAATAATATACATGATAAATTTA
25121038 AAATAATAATACAT-ATAAAATTT-
1 AAATAAT-ATACATGAT-AAATTTA
* **
25121061 AAA-AATTTTGATGAT-AATTCTA
1 AAATAATATACATGATAAATT-TA
* * **
25121083 GAATAATCATACGTGATAAATACA
1 AAATAAT-ATACATGATAAATTTA
*
25121107 AAATAATAGT--ATAATAAATTT-
1 AAATAATA-TACATGATAAATTTA
*
25121128 AAA-AATATTA-ATGATAAATTTG
1 AAATAATA-TACATGATAAATTTA
25121150 AAATAGATATACATGATAAATTTA
1 AAATA-ATATACATGATAAATTTA
* * *
25121174 AAATATTGTTAACA--ATGAATTTA
1 AAATAAT-AT-ACATGATAAATTTA
* *
25121197 AAATAATAATA-TTGATAAATTGA
1 AAATAAT-ATACATGATAAATTTA
* *
25121220 AAATAATAAAACATGATAAATCTA
1 AAATAAT-ATACATGATAAATTTA
25121244 AAATAATA
1 AAATAATA
25121252 ATATACAATA
Statistics
Matches: 162, Mismatches: 31, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
20 9 0.06
21 24 0.15
22 20 0.12
23 46 0.28
24 57 0.35
25 6 0.04
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (23 bp):
AAATAATATACATGATAAATTTA
Found at i:25121664 original size:27 final size:26
Alignment explanation
Indices: 25121613--25121664 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
25121603 ACATAATATT
* *
25121613 AAAAAAATAAAGTATATAATTAATGG
1 AAAAAAATAAAGAATATAATGAATGG
25121639 AAAAAAATAAAAGAATGATAA-GAATG
1 AAAAAAAT-AAAGAAT-ATAATGAATG
25121665 ATTAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.36
27 10 0.45
28 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (26 bp):
AAAAAAATAAAGAATATAATGAATGG
Found at i:25122838 original size:22 final size:21
Alignment explanation
Indices: 25122814--25122873 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
25122804 TCCATTCATT
25122814 TTTTTTATTTTTTAAATTATA
1 TTTTTTATTTTTTAAATTATA
*
25122835 TTTTTTATTTTTATGAA-TATA
1 TTTTTTATTTTT-TAAATTATA
*
25122856 ATTTTTATTTTTTAAATT
1 TTTTTTATTTTTTAAATT
25122874 TAAAAATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.09
21 28 0.82
22 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTTTTAAATTATA
Found at i:25125614 original size:24 final size:25
Alignment explanation
Indices: 25125578--25125635 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
25125568 AATCTGTTGA
*
25125578 ATTTTTCAATTGAAAATGGTTTCTGT
1 ATTTTTC-ATTGAAAATGGATTCTGT
25125604 ATTTTTC-TTGAAAATGGATTCTGT
1 ATTTTTCATTGAAAATGGATTCTGT
*
25125628 AGTTTTCA
1 ATTTTTCA
25125636 ATTTGTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 22 0.76
26 7 0.24
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.50
Consensus pattern (25 bp):
ATTTTTCATTGAAAATGGATTCTGT
Found at i:25127131 original size:47 final size:48
Alignment explanation
Indices: 25127080--25127183 Score: 106
Period size: 47 Copynumber: 2.2 Consensus size: 48
25127070 TTTTAGTAAA
*
25127080 TTTATATAAGA-ATATTTAATATTAAGAATTTT-ATTAAATTATATATT
1 TTTATATAA-ATATATTTAATAATAAGAATTTTAATTAAATTATATATT
** * *
25127127 TTTAT-TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATT
1 TTTATATAAA-TATATTTAATAATAAGAATTTT-AATTAAATTATATATT
*
25127176 ATTATATA
1 TTTATATA
25127184 TTATGATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
45 1 0.02
46 3 0.07
47 23 0.50
49 17 0.37
50 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (48 bp):
TTTATATAAATATATTTAATAATAAGAATTTTAATTAAATTATATATT
Found at i:25127138 original size:120 final size:120
Alignment explanation
Indices: 25126978--25127233 Score: 485
Period size: 120 Copynumber: 2.1 Consensus size: 120
25126968 ATCTAGTTTT
25126978 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
1 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
*
25127043 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTA
66 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTA
25127098 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
1 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
* *
25127163 TATATTTTATATTATTATATATTATGATTTTAGTTAATTCATATAAGAATATTTA
66 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTA
25127218 ATATTAAGAATTTTAT
1 ATATTAAGAATTTTAT
25127234 ATTTTTATTA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 133 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (120 bp):
ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTA
Found at i:25127234 original size:61 final size:61
Alignment explanation
Indices: 25127046--25127241 Score: 215
Period size: 61 Copynumber: 3.2 Consensus size: 61
25127036 TTTAAATTAT
* *
25127046 ATTTTATAGTATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGA
1 ATTTTATATTATTATATATTATGATTTTAGTTAATTTATATAAGAATATTTAATATTAAGA
* * * * * * *
25127107 ATTTTAT-TAAATTATATATTTTTA-TTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-T
1 ATTTTATAT-TATTATATATTATGATTTTAGTTA-ATTTATATAAGAA-TA-TTTAATATTAAGA
*
25127166 ATTTTATATTATTATATATTATGATTTTAGTTAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATATTATTATATATTATGATTTTAGTTAATTTATATAAGAATATTTAATATTAAGA
*
25127227 ATTTTATATTTTTAT
1 ATTTTATATTATTAT
25127242 TAAATTATAA
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
58 5 0.05
59 28 0.26
60 26 0.24
61 43 0.40
62 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.54
Consensus pattern (61 bp):
ATTTTATATTATTATATATTATGATTTTAGTTAATTTATATAAGAATATTTAATATTAAGA
Found at i:25127777 original size:145 final size:145
Alignment explanation
Indices: 25127514--25127803 Score: 562
Period size: 145 Copynumber: 2.0 Consensus size: 145
25127504 AAATACATTT
25127514 GGCCCAATAGGGCCCAAGACATTGACCCAAGCCCAAATCTAACCCTGGCCCAACTGCAATGTGGC
1 GGCCCAATAGGGCCCAAGACATTGACCCAAGCCCAAATCTAACCCTGGCCCAACTGCAATGTGGC
25127579 CATCAACACCAAAAAAACAAACAGCAGTTACCCTAAGCAGTTCGCAGCAACCACGTCACAACAAC
66 CATCAACACCAAAAAAACAAACAGCAGTTACCCTAAGCAGTTCGCAGCAACCACGTCACAACAAC
*
25127644 CGCCGACGTTCGGCA
131 CGCCCACGTTCGGCA
25127659 GGCCCAATAGGGCCCAAGACATTGACCCAAGCCCAAATCTAACCCTGGCCCAACTGCAATGTGGC
1 GGCCCAATAGGGCCCAAGACATTGACCCAAGCCCAAATCTAACCCTGGCCCAACTGCAATGTGGC
*
25127724 CATCAACACCAAAAAAACAAACAGCAGTTACCCTAAGCAGTTCGCAGCAACCACGTCACAGCAAC
66 CATCAACACCAAAAAAACAAACAGCAGTTACCCTAAGCAGTTCGCAGCAACCACGTCACAACAAC
25127789 CGCCCACGTTCGGCA
131 CGCCCACGTTCGGCA
25127804 TCCTTTGCGT
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.34, C:0.36, G:0.18, T:0.12
Consensus pattern (145 bp):
GGCCCAATAGGGCCCAAGACATTGACCCAAGCCCAAATCTAACCCTGGCCCAACTGCAATGTGGC
CATCAACACCAAAAAAACAAACAGCAGTTACCCTAAGCAGTTCGCAGCAACCACGTCACAACAAC
CGCCCACGTTCGGCA
Found at i:25140707 original size:44 final size:44
Alignment explanation
Indices: 25140603--25141029 Score: 449
Period size: 44 Copynumber: 9.6 Consensus size: 44
25140593 TCTAGAGAAC
*** * * *
25140603 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
* *
25140648 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
*** * * *
25140692 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
* * *
25140737 AGGTCAAAGATAACAGATCTTGTCTTCATGTATTGGCGTAAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* * *** * * *
25140781 AGATCAAAGATAACAGATTTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
*
25140826 AGATCAAAGATAGCAAATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
*** * * * *
25140870 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAAT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
* * * *
25140915 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAAT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* *
25140959 AAATCAAAGATAGCCGATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* *
25141003 AAATCGAAGATAGCAGATCTTGTCTTC
1 AGATCAAAGATAGCAGATCTTGTCTTC
25141030 CCATACTGGT
Statistics
Matches: 311, Mismatches: 68, Indels: 7
0.81 0.18 0.02
Matches are distributed among these distances:
44 176 0.57
45 135 0.43
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
Found at i:25140754 original size:89 final size:89
Alignment explanation
Indices: 25140603--25141029 Score: 633
Period size: 89 Copynumber: 4.8 Consensus size: 89
25140593 TCTAGAGAAC
*
25140603 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
1 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCT
25140668 TGTCTTCATGTATTGGCGTGAAGT
66 TGTCTTCATGTATTGGCGTGAAGT
*
25140692 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGGTCAAAGATAA-CAGATC
1 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGA-AAGCAGATC
*
25140756 TTGTCTTCATGTATTGGCGTAAAGT
65 TTGTCTTCATGTATTGGCGTGAAGT
* * * *
25140781 AGATCAAAGATAACAGATTTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAAATCT
1 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCT
25140846 TGTCTTCATGTATTGGCGTGAAGT
66 TGTCTTCATGTATTGGCGTGAAGT
* *
25140870 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGCAGATCT
1 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCT
* *
25140935 TGTCTTCATGTATTGGCATGAAAT
66 TGTCTTCATGTATTGGCGTGAAGT
* * *** * * * * * *
25140959 AAATCAAAGATAGCCGATCTTGTCTTCATGTATTGG-CGTGAAGTAAATCGAAGATAGCAGATCT
1 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCT
25141023 TGTCTTC
66 TGTCTTC
25141030 CCATACTGGT
Statistics
Matches: 308, Mismatches: 28, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
88 31 0.10
89 275 0.89
90 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (89 bp):
AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCT
TGTCTTCATGTATTGGCGTGAAGT
Found at i:25141167 original size:42 final size:41
Alignment explanation
Indices: 25141106--25141185 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 41
25141096 TGAAGAAAAT
* *
25141106 GATCCTATCTCATTGAAGTTGCAGTGGAGCGGGTTAAAATCA
1 GATCCTATCTCATTAAAGTTGCAGT-GAGCGGATTAAAATCA
25141148 GATCCTATCTC-TCTAAAGTTGCAGTGAGCGGATTAAAA
1 GATCCTATCTCAT-TAAAGTTGCAGTGAGCGGATTAAAA
25141186 AACCACAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (41 bp):
GATCCTATCTCATTAAAGTTGCAGTGAGCGGATTAAAATCA
Found at i:25142445 original size:3 final size:3
Alignment explanation
Indices: 25142426--25142463 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
25142416 ATTTTTAATT
*
25142426 TTA TT- TTA TTAA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT
25142464 TCAATGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25143306 original size:114 final size:112
Alignment explanation
Indices: 25142930--25143343 Score: 344
Period size: 114 Copynumber: 3.7 Consensus size: 112
25142920 TAAAACTTGA
* * * *
25142930 AGAACTAGTGGCGTTTCTAA-AAAACGCCG-TAAAAGAACA-TAATTAGTGGCGTTTATTGTAAG
1 AGAATTAGTGGCGTTTTTAATAAAACGCCGCT-AAAGAACAGT-ATTAGCGGCGTTTATTGAAAG
**
25142992 CGCCGCAAAATACCTTAACCAAAACGCAGCG-TTGG-TTCAATTGTATATT
64 CGCCGCAAAAT-CCTTAACCAAAACGCAGCGTTTGGTTTTGA-TGTATATT
* * * * ***
25143041 AGAATTCGTGGCGTTTTTTATAAAAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAA
1 AGAATTAGTGGCG-TTTTTA-ATAAAACGCCGCTAAAGAACAGTATTAGCGGCGTTT-ATTGAAA
** * ** * * *
25143106 GCGCCGCAAATAT-CTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATT
63 GCGCCGCAAA-ATCCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATT
* * *
25143156 A-ATATTAGTGGCGTTTTTAAAAAAACGCCG-TAAAAGAACA-TAATTAGTGGCGTTTATTTGGA
1 AGA-ATTAGTGGCGTTTTTAATAAAACGCCGCT-AAAGAACAGT-ATTAGCGGCGTTTA-TTGAA
*
25143218 AGCGCCGCAAAATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATT
62 AGCGCCGCAAAAT-CCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATT
* ** * * *
25143270 AGAATTAGTGGCGTTTATGGTAAAACGCTGCTAAAGAATAGTATTAGCGGCGTTT-TCGGTAAAG
1 AGAATTAGTGGCGTTTTTAATAAAACGCCGCTAAAGAACAGTATTAGCGGCGTTTAT-TG-AAAG
25143334 CGCCGCAAAA
64 CGCCGCAAAA
25143344 CTACTTCAGC
Statistics
Matches: 237, Mismatches: 46, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
111 11 0.05
112 10 0.04
113 44 0.19
114 133 0.56
115 35 0.15
116 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (112 bp):
AGAATTAGTGGCGTTTTTAATAAAACGCCGCTAAAGAACAGTATTAGCGGCGTTTATTGAAAGCG
CCGCAAAATCCTTAACCAAAACGCAGCGTTTGGTTTTGATGTATATT
Found at i:25143723 original size:7 final size:7
Alignment explanation
Indices: 25143713--25143763 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
25143703 AGTTTACAGA
25143713 TTAGGGG
1 TTAGGGG
25143720 TTAGGGG
1 TTAGGGG
25143727 TTAGGGG
1 TTAGGGG
25143734 TTAGGGG
1 TTAGGGG
25143741 TTAGGGG
1 TTAGGGG
25143748 TTA--GG
1 TTAGGGG
25143753 TTAGGGG
1 TTAGGGG
25143760 TTAG
1 TTAG
25143764 ATGTTAAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.12
7 37 0.88
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:25143777 original size:33 final size:33
Alignment explanation
Indices: 25143718--25143785 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
25143708 ACAGATTAGG
* * *
25143718 GGTTAGGGGTTAGGGGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
* *
25143751 GGTTAGGGGTTAGATGTTAAGAGTTAGGGTTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
25143784 GG
1 GG
25143786 ATTTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (33 bp):
GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
Found at i:25143874 original size:7 final size:7
Alignment explanation
Indices: 25143862--25143951 Score: 92
Period size: 7 Copynumber: 12.9 Consensus size: 7
25143852 TAAATAAGTT
25143862 TTAGGGG
1 TTAGGGG
25143869 TTAGGGG
1 TTAGGGG
* *
25143876 TTAGAGA
1 TTAGGGG
* *
25143883 TCATGGG
1 TTAGGGG
*
25143890 TTAAGGGT
1 TT-AGGGG
25143898 TTA-GGG
1 TTAGGGG
*
25143904 TTAAGGG
1 TTAGGGG
*
25143911 TTAAGGG
1 TTAGGGG
*
25143918 TTAAGGG
1 TTAGGGG
25143925 TTAGGGG
1 TTAGGGG
25143932 TTAGGGG
1 TTAGGGG
25143939 TTAGGGG
1 TTAGGGG
25143946 TTAGGG
1 TTAGGG
25143952 ATTGGGTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.07
7 60 0.86
8 5 0.07
ACGTcount: A:0.21, C:0.01, G:0.48, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:25144109 original size:95 final size:96
Alignment explanation
Indices: 25143922--25144106 Score: 230
Period size: 95 Copynumber: 1.9 Consensus size: 96
25143912 TAAGGGTTAA
* * * * *
25143922 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGATTAATTAGTG
1 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
* * * *
25143987 TTTTTTATTTTATATATTAAATAAAGTTTAG
66 TTATTTAATTAACATATTAAATAAAGTTTAG
* * *
25144018 GGGTTAGGGGTTA-GGGTTATGGGTT-TGGAGTCGGGTTAGGGATTAAGATTTGGATTAATTAGT
1 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGA-TCGGGTTAGGGATTAAGATTTAGATTAATTAGT
25144081 ACTTATTTAATTAACATATTAAATAA
65 -CTTATTTAATTAACATATTAAATAA
25144107 GTTCTTTATA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
94 3 0.04
95 39 0.52
96 33 0.44
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.41
Consensus pattern (96 bp):
GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
TTATTTAATTAACATATTAAATAAAGTTTAG
Found at i:25144196 original size:14 final size:14
Alignment explanation
Indices: 25144177--25144203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25144167 GATATGCAAT
25144177 ATATAATAATTTGA
1 ATATAATAATTTGA
25144191 ATATAATAATTTG
1 ATATAATAATTTG
25144204 GAATTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATAATAATTTGA
Found at i:25144287 original size:18 final size:18
Alignment explanation
Indices: 25144240--25144280 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25144230 TCAAAATTAC
25144240 AAAAAATAAAATGAAAAT
1 AAAAAATAAAATGAAAAT
*
25144258 AAAAAATAAAAAG-AAAT
1 AAAAAATAAAATGAAAAT
25144275 AAAAAA
1 AAAAAA
25144281 ACTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAATGAAAAT
Found at i:25145116 original size:198 final size:198
Alignment explanation
Indices: 25144771--25145162 Score: 624
Period size: 198 Copynumber: 2.0 Consensus size: 198
25144761 CGCAATTTTA
*
25144771 AGAAATTGTTTACAAAAACGGCTCCGTTTTCTTATTTATCTTTAGTGGCGCTTTTAGTACACGCC
1 AGAAATTGTTTACAAAAACGGCTCCGTTTTCTTATTTATCTTTAGTGGCGCTTTTAGTAAACGCC
* * * * ** *
25144836 GCAAAATTATTTTAATTTTTATGGAGACGATGCCGTTTTGTCTAAAACGCCATGAGTTTTAGTTT
66 GCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTA
*
25144901 ACTAATCGGGGAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAG
131 ACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAG
25144966 TAC
196 TAC
** *
25144969 AGAAATTGTTTAGGAAAACGGCTTCGTTTTCTTATTTA-CTTTTAGTGGCGCTTTTAGTAAACGC
1 AGAAATTGTTTACAAAAACGGCTCCGTTTTCTTATTTATC-TTTAGTGGCGCTTTTAGTAAACGC
* *
25145033 CGCAAAAATGTTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAATGCAATGACTTAGAGTT
65 CGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTT
* *
25145098 AACTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTGGTATATAAACGCCGCAAA
130 AACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAA
25145163 TGGGTTAATT
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
197 1 0.01
198 176 0.99
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (198 bp):
AGAAATTGTTTACAAAAACGGCTCCGTTTTCTTATTTATCTTTAGTGGCGCTTTTAGTAAACGCC
GCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTA
ACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAG
TAC
Found at i:25145677 original size:10 final size:10
Alignment explanation
Indices: 25145662--25145686 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25145652 TCGAAAATTG
25145662 CAAAATTGTT
1 CAAAATTGTT
25145672 CAAAATTGTT
1 CAAAATTGTT
25145682 CAAAA
1 CAAAA
25145687 CCATGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (10 bp):
CAAAATTGTT
Found at i:25146242 original size:73 final size:73
Alignment explanation
Indices: 25146163--25146312 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
25146153 TAAAATAAAA
25146163 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
25146228 TTAATAAT
66 TTAATAAT
25146236 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
25146301 TTAATAAT
66 TTAATAAT
25146309 TATA
1 TATA
25146313 TTAGTAATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (73 bp):
TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
TTAATAAT
Found at i:25146279 original size:38 final size:38
Alignment explanation
Indices: 25146164--25146280 Score: 118
Period size: 38 Copynumber: 3.2 Consensus size: 38
25146154 AAAATAAAAT
25146164 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
*** * * * *
25146202 ATAAAATGTTAT-T---TTATTAAATATT-ATTAATAATT
1 ATAAAAAAATATGTGGAATATTAAA-ATTGACTATTAA-A
25146237 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
25146275 ATAAAA
1 ATAAAA
25146281 TGTTATTTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
34 13 0.22
35 12 0.21
36 1 0.02
37 1 0.02
38 18 0.31
39 13 0.22
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (38 bp):
ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
Found at i:25146432 original size:26 final size:26
Alignment explanation
Indices: 25146349--25146713 Score: 585
Period size: 26 Copynumber: 14.1 Consensus size: 26
25146339 ATTTTATTAA
25146349 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
25146375 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
25146402 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
25146428 ATAATACATTTATAACTTACAACTTAC
1 ATAATACA-TAATAACTTACAACTTAC
*
25146455 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
25146481 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
25146507 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
25146533 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
25146559 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
25146584 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
25146610 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
25146636 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
25146661 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
25146686 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
25146712 AT
1 AT
25146714 TTAACTTACA
Statistics
Matches: 315, Mismatches: 18, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
25 78 0.25
26 189 0.60
27 39 0.12
28 9 0.03
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:25146675 original size:18 final size:18
Alignment explanation
Indices: 25146654--25146741 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
25146644 TTTAACTTAC
25146654 AACTTACACAATACATTT
1 AACTTACACAATACATTT
*
25146672 AACTTACAACTTACATAATACATAAT
1 AACTT---AC--AC--AATACAT-TT
*
25146698 AACTTACA-ACTTACATTT
1 AACTTACACA-ATACATTT
*
25146716 AACTTACATAATACATTT
1 AACTTACACAATACATTT
25146734 AACTTACA
1 AACTTACA
25146742 TAACTTACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
18 30 0.54
19 6 0.11
21 3 0.05
23 4 0.07
25 7 0.12
26 6 0.11
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACACAATACATTT
Found at i:25146721 original size:11 final size:10
Alignment explanation
Indices: 25146705--25146758 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
25146695 AATAACTTAC
25146705 AACTTACATTT
1 AACTTACA-TT
25146716 AACTTACA-T
1 AACTTACATT
25146725 AA--TACATTT
1 AACTTACA-TT
25146734 AACTTACA-T
1 AACTTACATT
25146743 AACTTACA-T
1 AACTTACATT
25146752 AACTTAC
1 AACTTAC
25146759 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:25146742 original size:18 final size:18
Alignment explanation
Indices: 25146679--25146744 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
25146669 TTTAACTTAC
*
25146679 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
25146698 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
25146716 AACTTACATAATACATTT
1 AACTTACATAATACATTT
25146734 AACTTACATAA
1 AACTTACATAA
25146745 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:25148578 original size:39 final size:39
Alignment explanation
Indices: 25148525--25148602 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
25148515 GAAGTATTTT
25148525 TTTTGAGTTGCCTTATTGGGAGCATCACCTATTACGACA
1 TTTTGAGTTGCCTTATTGGGAGCATCACCTATTACGACA
25148564 TTTTGAGTTGCCTTATTGGGAGCATCACCTATTACGACA
1 TTTTGAGTTGCCTTATTGGGAGCATCACCTATTACGACA
25148603 CAATCTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (39 bp):
TTTTGAGTTGCCTTATTGGGAGCATCACCTATTACGACA
Found at i:25153803 original size:16 final size:16
Alignment explanation
Indices: 25153778--25153815 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
25153768 TTGAATTACT
*
25153778 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
25153794 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
25153810 ATTACA
1 ATTACA
25153816 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:25162622 original size:23 final size:22
Alignment explanation
Indices: 25162578--25162626 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
25162568 TGATGATTGG
25162578 TTGATGAAATTATGATATGAAA
1 TTGATGAAATTATGATATGAAA
*
25162600 TTGA-GAAATTGATTATAATGAAA
1 TTGATGAAATT-ATGAT-ATGAAA
25162623 TTGA
1 TTGA
25162627 AATAAGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (22 bp):
TTGATGAAATTATGATATGAAA
Found at i:25162628 original size:21 final size:19
Alignment explanation
Indices: 25162582--25162629 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
25162572 GATTGGTTGA
25162582 TGAAATTATGATATGAAAT
1 TGAAATTATGATATGAAAT
*
25162601 TGAGAAATTGATTATAATGAAAT
1 T--GAAATT-ATGAT-ATGAAAT
25162624 TGAAAT
1 TGAAAT
25162630 AAGGATGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
21 11 0.46
22 4 0.17
23 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (19 bp):
TGAAATTATGATATGAAAT
Found at i:25165328 original size:17 final size:18
Alignment explanation
Indices: 25165308--25165349 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
25165298 TACATAAATA
* *
25165308 TTTTTTATACATTGTT-G
1 TTTTTTATAAATTATTAG
25165325 TTTTTTA-AAATTATTAG
1 TTTTTTATAAATTATTAG
25165342 TTTTTTAT
1 TTTTTTAT
25165350 TTTTTTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTTTATAAATTATTAG
Found at i:25171395 original size:16 final size:16
Alignment explanation
Indices: 25171374--25171442 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
25171364 TTTGGTTCGC
25171374 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
25171390 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
25171406 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
25171423 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
25171439 TGTA
1 TGTA
25171443 ATAGCAAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:25171420 original size:33 final size:32
Alignment explanation
Indices: 25171374--25171442 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
25171364 TTTGGTTCGC
25171374 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
25171406 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
25171439 TGTA
1 TGTA
25171443 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:25171698 original size:16 final size:16
Alignment explanation
Indices: 25171658--25171712 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
25171648 TTAATCATAT
*
25171658 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
25171674 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
25171689 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
25171707 -TAAAAT
1 TTAAAAT
25171713 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:25171705 original size:18 final size:17
Alignment explanation
Indices: 25171678--25171712 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25171668 TTTTTATTAA
*
25171678 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25171696 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25171713 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25171873 original size:19 final size:18
Alignment explanation
Indices: 25171798--25171953 Score: 77
Period size: 18 Copynumber: 8.0 Consensus size: 18
25171788 TTATTATTAA
*
25171798 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAATT
25171816 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
* ***
25171834 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAATT
25171853 ATATGAATTTAATAAAATT
1 ATAT-AATTTAATAAAATT
* *
25171872 ATA-ATATATAATACTATAA-A
1 ATATA-ATTTAATA--A-AATT
25171892 ATATAATTTAAAATAATTATTATT
1 ATATAATTT--AATAA--A--ATT
25171916 AAATATAATTTAATAGAAA-T
1 --ATATAATTTAATA-AAATT
25171936 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
25171954 CTTAATATTT
Statistics
Matches: 106, Mismatches: 13, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
17 8 0.08
18 41 0.39
19 16 0.15
20 12 0.11
21 9 0.08
22 4 0.04
23 2 0.02
24 4 0.04
25 1 0.01
26 9 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAATT
Found at i:25171906 original size:22 final size:23
Alignment explanation
Indices: 25171864--25171906 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25171854 TATGAATTTA
*
25171864 ATAAAATTATAATATATAATACT
1 ATAAAATTATAATATAAAATACT
*
25171887 ATAAAA-TATAATTTAAAATA
1 ATAAAATTATAATATAAAATA
25171907 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAATTATAATATAAAATACT
Found at i:25172022 original size:121 final size:120
Alignment explanation
Indices: 25171656--25172195 Score: 752
Period size: 120 Copynumber: 4.5 Consensus size: 120
25171646 ATTTAATCAT
* * *
25171656 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAA-ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAT-
* * ** * * * * *
25171721 ATT-AATA----GAAATTTG-TTTTGGTAAATTATTATTAACA-ATAAATAATTTAAAAGATA
64 ATTAAATATTCTTAAA--TGAATTTACTAAA--ATCA-TAATATAT-AATACTATAAAATATA
*
25171777 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
* * *
25171842 TAAATATTCTTATATGAATTTAATAAAATTATAATATATAATACTATAAAATATA
66 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
25171897 ATTTAAAATAATTATTATTAAATATAATTTAATAGAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-
25171962 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
65 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
25172018 ATTTAAAATAATTATTATTAAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
25172083 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
66 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
25172138 ATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATCAAAT
1 ATTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAAT
25172196 CATTATATTC
Statistics
Matches: 386, Mismatches: 23, Indels: 19
0.90 0.05 0.04
Matches are distributed among these distances:
119 3 0.01
120 211 0.55
121 127 0.33
122 36 0.09
123 7 0.02
124 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:25172393 original size:25 final size:25
Alignment explanation
Indices: 25172319--25172397 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
25172309 ATTGCAAAAA
25172319 GAAATTACTGTAAGTTAGAGCATAT
1 GAAATTACTGTAAGTTAGAGCATAT
*
25172344 GAAATTACT-T---TTTGAAGCATAT
1 GAAATTACTGTAAGTTAG-AGCATAT
25172366 GAAATTACTGTAAGTTAGAGCATAT
1 GAAATTACTGTAAGTTAGAGCATAT
25172391 GAAATTA
1 GAAATTA
25172398 AGCAAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.06
22 16 0.34
23 1 0.02
24 1 0.02
25 23 0.49
26 3 0.06
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (25 bp):
GAAATTACTGTAAGTTAGAGCATAT
Found at i:25183977 original size:19 final size:19
Alignment explanation
Indices: 25183953--25183990 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25183943 TGAAAATGTT
25183953 AGTATGTTCTCATAGTAAA
1 AGTATGTTCTCATAGTAAA
25183972 AGTATGTTCTCATAGTAAA
1 AGTATGTTCTCATAGTAAA
25183991 TTGCGTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
AGTATGTTCTCATAGTAAA
Found at i:25188684 original size:41 final size:41
Alignment explanation
Indices: 25188555--25188685 Score: 97
Period size: 41 Copynumber: 3.2 Consensus size: 41
25188545 GATATTTTGG
* * * *
25188555 GCATTTTTCTCATAAACGCCGCTATTGC-TAACCTTTTGCT
1 GCATTTTTCTCATAAACACCGCTACTGCTTTACATTTTGCT
** * *** * *
25188595 GTGTTTATGAGAAAAACACCGCTACTGTTTTACATTTTGCT
1 GCATTTTTCTCATAAACACCGCTACTGCTTTACATTTTGCT
* *
25188636 GCGTTTTTCTCATAAACACCGCTATTGCTTTAC-TTATTGC-
1 GCATTTTTCTCATAAACACCGCTACTGCTTTACATT-TTGCT
25188676 GACATTTTTC
1 G-CATTTTTC
25188686 GATTAATGCC
Statistics
Matches: 67, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
40 21 0.31
41 46 0.69
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (41 bp):
GCATTTTTCTCATAAACACCGCTACTGCTTTACATTTTGCT
Found at i:25190719 original size:20 final size:20
Alignment explanation
Indices: 25190696--25190801 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
25190686 GTGCTTCTGA
*
25190696 TAGCACATTCATGCTCATGT
1 TAGCACATTCGTGCTCATGT
* *
25190716 TAGCAC-TACGGTGCTCATGA
1 TAGCACATTC-GTGCTCATGT
* * *
25190736 TAGAACATTCGTGCTCCTAT
1 TAGCACATTCGTGCTCATGT
* * * *
25190756 TTGCAC-TATGGTGTTCATGA
1 TAGCACAT-TCGTGCTCATGT
* *
25190776 TAGCACATTCATGCTCTTGT
1 TAGCACATTCGTGCTCATGT
25190796 TAGCAC
1 TAGCAC
25190802 TATGGTATTC
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
19 3 0.05
20 55 0.90
21 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (20 bp):
TAGCACATTCGTGCTCATGT
Found at i:25190730 original size:40 final size:41
Alignment explanation
Indices: 25190686--25190831 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 41
25190676 TCCTGAACAA
*
25190686 GTGCTTC-TGATAGCACATTCATGCTCATGTTAGCACTACG
1 GTGCTTCATGATAGCACATTCATGCTCATGTTAGCACTATG
* * * * *
25190726 GTGC-TCATGATAGAACATTCGTGCTCCTATTTGCACTATG
1 GTGCTTCATGATAGCACATTCATGCTCATGTTAGCACTATG
*
25190766 GTG-TTCATGATAGCACATTCATGCTCTTGTTAGCACTATG
1 GTGCTTCATGATAGCACATTCATGCTCATGTTAGCACTATG
* * *
25190806 GT-ATTCTTGATAGCATATTCATGCTC
1 GTGCTTCATGATAGCACATTCATGCTC
25190832 CTATTTGAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 88 0.98
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (41 bp):
GTGCTTCATGATAGCACATTCATGCTCATGTTAGCACTATG
Found at i:25195801 original size:22 final size:21
Alignment explanation
Indices: 25195752--25195802 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
25195742 GTGTAAAAAG
**
25195752 AGGCACACGGTCGTGTGGAAT
1 AGGCACACGCCCGTGTGGAAT
25195773 -GGCACACGCCCGTGTGGAAT
1 AGGCACACGCCCGTGTGGAAT
25195793 AAGGCACACG
1 -AGGCACACG
25195803 ACTGTGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.14
Consensus pattern (21 bp):
AGGCACACGCCCGTGTGGAAT
Found at i:25195809 original size:22 final size:20
Alignment explanation
Indices: 25195753--25195810 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
25195743 TGTAAAAAGA
**
25195753 GGCACACGGTCGTGTGGAAT
1 GGCACACGACCGTGTGGAAT
*
25195773 GGCACACGCCCGTGTGGAAT
1 GGCACACGACCGTGTGGAAT
*
25195793 AAGGCACACGACTGTGTG
1 --GGCACACGACCGTGTG
25195811 AACAGACCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 18 0.56
22 14 0.44
ACGTcount: A:0.22, C:0.24, G:0.36, T:0.17
Consensus pattern (20 bp):
GGCACACGACCGTGTGGAAT
Found at i:25199368 original size:15 final size:15
Alignment explanation
Indices: 25199348--25199381 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25199338 CCGATTTTTA
25199348 TAATTTTTAATATTT
1 TAATTTTTAATATTT
* *
25199363 TAATTTTTGATTTTT
1 TAATTTTTAATATTT
25199378 TAAT
1 TAAT
25199382 AATTTATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TAATTTTTAATATTT
Found at i:25204600 original size:21 final size:22
Alignment explanation
Indices: 25204575--25204618 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
25204565 ACGACTGAAC
25204575 AAAAAGATGTCATCCTTATCCAAA
1 AAAAAGATGTCATCCTTATCC--A
25204599 AAAAAGATGTCATCCTTATC
1 AAAAAGATGTCATCCTTATC
25204619 AAGAAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAAAGATGTCATCCTTATCCA
Found at i:25209476 original size:28 final size:29
Alignment explanation
Indices: 25209425--25209481 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
25209415 CCCACCTCTT
25209425 TATTTTAAAGAAAAAAAGGAAAATGGAAA
1 TATTTTAAAGAAAAAAAGGAAAATGGAAA
25209454 TATTTTAAAG-AAAAAAGGAAAATGGAAA
1 TATTTTAAAGAAAAAAAGGAAAATGGAAA
25209482 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (29 bp):
TATTTTAAAGAAAAAAAGGAAAATGGAAA
Found at i:25219257 original size:33 final size:33
Alignment explanation
Indices: 25219210--25219309 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
25219200 AGTTGAACAA
* *
25219210 AATGATGAAACTGCCCCAATAGATGTTCCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
25219243 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
* * * *
25219276 ATTGATGAAGTTGCCCTGATAGATGTTTCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
25219309 A
1 A
25219310 CTTATGTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (33 bp):
AATGATGAAGCTGCCCCGATAGATGTTCCAATC
Found at i:25223813 original size:14 final size:16
Alignment explanation
Indices: 25223785--25223817 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
25223775 GAATCACCAA
25223785 AAAATAAAATGAAAAG
1 AAAATAAAATGAAAAG
25223801 AAAA-AAAAT-AAAAG
1 AAAATAAAATGAAAAG
25223815 AAA
1 AAA
25223818 TCCTCCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAATAAAATGAAAAG
Found at i:25228895 original size:34 final size:34
Alignment explanation
Indices: 25228852--25228917 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
25228842 ATCAATTTAA
25228852 TTCATAAAGTTACAGAGTGAATAGATAAAAAAAG
1 TTCATAAAGTTACAGAGTGAATAGATAAAAAAAG
25228886 TTCATAAAGTTACAGAGTGAATAGATAAAAAA
1 TTCATAAAGTTACAGAGTGAATAGATAAAAAA
25228918 GTAATCCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (34 bp):
TTCATAAAGTTACAGAGTGAATAGATAAAAAAAG
Found at i:25230731 original size:35 final size:34
Alignment explanation
Indices: 25230692--25230771 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
25230682 AATTTAATTT
25230692 ATATTTTATTATTTGATTCA-AATATAATCTGTAAA-
1 ATATTTTATTATTTGATT-AGAATATAAT-T-TAAAG
*
25230727 ATATTTTGA-TATTTTATTATGAATATAATTTAAAG
1 ATATTTT-ATTATTTGATTA-GAATATAATTTAAAG
25230762 ATATTTTATT
1 ATATTTTATT
25230772 GTATATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
34 6 0.15
35 24 0.62
36 9 0.23
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (34 bp):
ATATTTTATTATTTGATTAGAATATAATTTAAAG
Found at i:25230938 original size:19 final size:18
Alignment explanation
Indices: 25230896--25230941 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
25230886 ATATAATTGT
*
25230896 AATAATTTTTAATTATTT
1 AATAATTTTTAATTATTA
* *
25230914 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTATTA
25230933 AATAATTTT
1 AATAATTTT
25230942 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTATTA
Found at i:25231082 original size:21 final size:21
Alignment explanation
Indices: 25231054--25231108 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
25231044 ACCGCTGTTT
25231054 CTAATCTCACCGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
25231076 C-AATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
25231096 CTAATCTCACCGC
1 CTAATCTCACCGC
25231109 CACCGCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:25235429 original size:4 final size:4
Alignment explanation
Indices: 25235420--25235449 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
25235410 TATCTTAGAT
25235420 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
25235450 TTAGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:25235620 original size:28 final size:28
Alignment explanation
Indices: 25235586--25235653 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
25235576 ATAAAAAAAA
*
25235586 TAACCAAAATATTATAACTTTTTTTTAT
1 TAACCAAAATATTATAAATTTTTTTTAT
*
25235614 TTACCAAAATATTATAAATTTTTTTTAT
1 TAACCAAAATATTATAAATTTTTTTTAT
25235642 TAACCAAAATAT
1 TAACCAAAATAT
25235654 ACCAAAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
TAACCAAAATATTATAAATTTTTTTTAT
Found at i:25235681 original size:16 final size:16
Alignment explanation
Indices: 25235662--25235693 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25235652 ATACCAAAAA
*
25235662 CAAAAACAAAAACCTG
1 CAAAAAAAAAAACCTG
25235678 CAAAAAAAAAAACCTG
1 CAAAAAAAAAAACCTG
25235694 TGGCGGCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (16 bp):
CAAAAAAAAAAACCTG
Found at i:25238460 original size:14 final size:14
Alignment explanation
Indices: 25238441--25238471 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25238431 TTTGATTGGT
*
25238441 GGAAAATATTTTCC
1 GGAAAATATTTTAC
25238455 GGAAAATATTTTAC
1 GGAAAATATTTTAC
25238469 GGA
1 GGA
25238472 TTTTCCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (14 bp):
GGAAAATATTTTAC
Found at i:25238968 original size:27 final size:27
Alignment explanation
Indices: 25238882--25238979 Score: 103
Period size: 27 Copynumber: 3.6 Consensus size: 27
25238872 AAAGGTATAT
25238882 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
* * * *
25238909 TTTCTGGGT---TAGTTCTTTATGTTATTGG
1 TTTCT-TGTCCATAG-T-TTTGTG-AATCGG
25238937 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
25238964 TTTCTTGTCCATAGTT
1 TTTCTTGTCCATAGTT
25238980 AAAAAGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 32 0.57
28 16 0.29
29 1 0.02
30 3 0.05
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.52
Consensus pattern (27 bp):
TTTCTTGTCCATAGTTTTGTGAATCGG
Found at i:25241075 original size:26 final size:26
Alignment explanation
Indices: 25241046--25241103 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
25241036 CATCCTCAAA
25241046 CTATAATCTAGATATTAAATTGGTCT
1 CTATAATCTAGATATTAAATTGGTCT
*
25241072 CTATAATCTAGATTTTAAATTGGTCT
1 CTATAATCTAGATATTAAATTGGTCT
25241098 CTATAA
1 CTATAA
25241104 ATTTTGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
CTATAATCTAGATATTAAATTGGTCT
Found at i:25241447 original size:14 final size:15
Alignment explanation
Indices: 25241425--25241501 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
25241415 CAATCAAACA
25241425 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
25241439 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
25241454 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
25241474 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
25241488 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
25241502 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:25241466 original size:20 final size:20
Alignment explanation
Indices: 25241441--25241480 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25241431 AATATTTTCC
*
25241441 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25241461 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
25241481 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25241486 original size:34 final size:35
Alignment explanation
Indices: 25241429--25241495 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
25241419 CAAACACCAG
*
25241429 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
25241464 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25241496 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25241502 original size:14 final size:14
Alignment explanation
Indices: 25241464--25241503 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25241454 ACAGAAAAGT
*
25241464 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
25241478 AAATCATTTTACGG
1 AAAACATTTTACAG
25241492 AAAACATTTTAC
1 AAAACATTTTAC
25241504 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:25248946 original size:23 final size:23
Alignment explanation
Indices: 25248883--25248949 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
25248873 ATTATTAACT
*
25248883 GGAAGCTCCGGATAGCCATATATCG
1 GGAAGCTCCGGAGAGCC--ATATCG
* ** *
25248908 GGAAGTTCAAGCGAGCCATATCG
1 GGAAGCTCCGGAGAGCCATATCG
*
25248931 GGAAGGTCCGGAGAGCCAT
1 GGAAGCTCCGGAGAGCCAT
25248950 TAATTAGGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 21 0.64
25 12 0.36
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.16
Consensus pattern (23 bp):
GGAAGCTCCGGAGAGCCATATCG
Found at i:25249135 original size:24 final size:25
Alignment explanation
Indices: 25249107--25249168 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
25249097 TAAGAACCAT
*
25249107 ATAACGAGAA-GCTCGA-GAGGGCTA
1 ATAACGAGAATGCTC-ATGAGAGCTA
25249131 ATAAC-AGAATGCTCATGAGAGCTA
1 ATAACGAGAATGCTCATGAGAGCTA
*
25249155 ATAACG-GGATGCTC
1 ATAACGAGAATGCTC
25249169 TTTCGAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 5 0.15
24 28 0.85
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (25 bp):
ATAACGAGAATGCTCATGAGAGCTA
Found at i:25250503 original size:16 final size:17
Alignment explanation
Indices: 25250482--25250525 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
25250472 ACATGTGGCA
25250482 AAAAATTATAAAA-AAT
1 AAAAATTATAAAAGAAT
25250498 AAAAATTCATAAAAGTAAT
1 AAAAATT-ATAAAAG-AAT
*
25250517 AAAAGTTAT
1 AAAAATTAT
25250526 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 2 0.08
19 9 0.38
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAAATTATAAAAGAAT
Found at i:25250569 original size:18 final size:19
Alignment explanation
Indices: 25250524--25250562 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
25250514 AATAAAAGTT
25250524 ATTAAATTTTAATTAAAAA
1 ATTAAATTTTAATTAAAAA
*
25250543 ATTACATTTT-ATTAAAAA
1 ATTAAATTTTAATTAAAAA
25250561 AT
1 AT
25250563 AGAATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAATTTTAATTAAAAA
Found at i:25250814 original size:18 final size:19
Alignment explanation
Indices: 25250776--25250814 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
25250766 GTACGATAAC
25250776 TTTTATAATTTTTTTACAA
1 TTTTATAATTTTTTTACAA
25250795 TTTT-TAATATTTTTTA-AA
1 TTTTATAAT-TTTTTTACAA
25250813 TT
1 TT
25250815 ATTTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTTACAA
Found at i:25256359 original size:9 final size:10
Alignment explanation
Indices: 25256339--25256363 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25256329 AAAATGAGAG
25256339 TTTTAGGTTT
1 TTTTAGGTTT
25256349 TTTTAGGTTT
1 TTTTAGGTTT
25256359 TTTTA
1 TTTTA
25256364 ACAGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (10 bp):
TTTTAGGTTT
Found at i:25256844 original size:3 final size:3
Alignment explanation
Indices: 25256826--25256881 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
25256816 CATTAAATTA
* * *
25256826 ATT ATT -TT AAT ATT ATT ATT ACT ATT A-T ATT A-C ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25256871 ATT ATT ATT AT
1 ATT ATT ATT AT
25256882 GATTTACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 5 0.11
3 39 0.89
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:25256952 original size:24 final size:25
Alignment explanation
Indices: 25256919--25256966 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
25256909 TCAAATTTTG
*
25256919 TTGTATATATGTACATACATACATT
1 TTGTATATATATACATACATACATT
* *
25256944 TTGT-TATATATATATACGTACAT
1 TTGTATATATATACATACATACAT
25256967 ATTTTTCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.46
Consensus pattern (25 bp):
TTGTATATATATACATACATACATT
Found at i:25256953 original size:28 final size:28
Alignment explanation
Indices: 25256913--25256967 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
25256903 TTAATTTCAA
* *
25256913 ATTTTGTTGTATATATGTACATACATAC
1 ATTTTGTTATATATATATACATACATAC
*
25256941 ATTTTGTTATATATATATACGTACATA
1 ATTTTGTTATATATATATACATACATA
25256968 TTTTTCTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (28 bp):
ATTTTGTTATATATATATACATACATAC
Found at i:25257378 original size:46 final size:47
Alignment explanation
Indices: 25257327--25257416 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 47
25257317 CACATCCCTG
* *
25257327 TATATATACATACTTACATATATTTTTATATTGC-ATAATTTTAAAA
1 TATATATACATACATACATATATTTTTACATTGCTATAATTTTAAAA
* * *
25257373 TATATATACATACATATATATCTTTTTACATTTCTATAATTTTA
1 TATATATACATACATACATATATTTTTACATTGCTATAATTTTA
25257417 TTCATCTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
46 29 0.76
47 9 0.24
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (47 bp):
TATATATACATACATACATATATTTTTACATTGCTATAATTTTAAAA
Found at i:25261533 original size:18 final size:16
Alignment explanation
Indices: 25261510--25261549 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
25261500 TACTTCACTT
25261510 GAAAAAAGGAAACAAAAA
1 GAAAAAA-GAAA-AAAAA
25261528 GAAAAAAGAAAAAAAA
1 GAAAAAAGAAAAAAAA
*
25261544 TAAAAA
1 GAAAAA
25261550 CAAAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
GAAAAAAGAAAAAAAA
Found at i:25261535 original size:7 final size:7
Alignment explanation
Indices: 25261523--25261567 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
25261513 AAAAGGAAAC
25261523 AAAAAGA
1 AAAAAGA
25261530 AAAAAGA
1 AAAAAGA
*
25261537 AAAAAAA
1 AAAAAGA
*
25261544 TAAAAACA
1 -AAAAAGA
25261552 AAAAAGA
1 AAAAAGA
*
25261559 AAAAGGA
1 AAAAAGA
25261566 AA
1 AA
25261568 GGCCAAGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:25262560 original size:44 final size:44
Alignment explanation
Indices: 25262512--25263290 Score: 306
Period size: 44 Copynumber: 17.8 Consensus size: 44
25262502 AAGATTATAG
* *
25262512 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * **
25262556 ATCTTATCT-TCT-CG-AGATAGTAGGAAGCAGATTTAAG-CCACTA
1 ATCTTATCTCCCTAAGCAG-TAGT-GG-AGCAGATTGAAGACGGCTA
* * * * * * * **
25262599 GTCCTATCTCACTGAGCAGCAGTGGAGTAGGTTGAAGATAG-TA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * **
25262642 GATCTTATCTCCCTAAACAGTAGTGGAGCAGGTTGAAGATAG-TA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * *
25262686 GATCTTATCTCCTTAAACAGTAGTTGAGCAGATCGAAGACGGCAA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * ** *
25262731 ATCTTATCTTCCCGATA-TAGTAG-GAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTA-AGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * * * * ***
25262774 TTCCTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TTATA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * *
25262817 GATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * ** *
25262862 ATCTTATCTTCCC-GAGATAGTAGT-AAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAG-CAGTAGTGGAGCAGATTGAAGACGGCTA
** * * * * ** * *
25262905 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTTG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * *
25262949 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * **
25262993 ATCTTATCT-TCTCAAGGTATTAG-GGAAGCAGATTTAAG-CCACTA
1 ATCTTATCTCCCT-AA-GCAGTAGTGG-AGCAGATTGAAGACGGCTA
** * * * * **
25263037 GCCTTATTTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTG-TA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * *
25263080 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * * * ** *
25263125 ATCTTATCTTCCTAAGGTATTAG-GGAAGCAGATTTAAG-CCACCA
1 ATCTTATCTCCCTAA-GCAGTAGTGG-AGCAGATTGAAGACGGCTA
** * * * * **
25263169 GCCTTATCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATTG-TA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
* * **
25263212 GATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGGGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
*
25263257 ATCTTATCTTCCC-AAGGTAGTAG-GGAAGCAGATT
1 ATCTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATT
25263291 TAAGCCACCA
Statistics
Matches: 528, Mismatches: 169, Indels: 75
0.68 0.22 0.10
Matches are distributed among these distances:
41 3 0.01
42 21 0.04
43 98 0.19
44 328 0.62
45 75 0.14
46 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCTA
Found at i:25262718 original size:131 final size:131
Alignment explanation
Indices: 25262472--25262708 Score: 309
Period size: 131 Copynumber: 1.8 Consensus size: 131
25262462 TATCAAGCCG
* * *
25262472 TATCTCCCTGAGCAGTAGCGGAGTAGGTCGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCACTGAGCAGCAGCGGAGTAGGTCGAAGATTATAGATCTTATCTCCCTAAACAGTAGTGG
* * * * *
25262537 AGCAGATCGAAGACGGCGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCACTAGTC
66 AGCAGATCGAAGAAGGAGAATCTTATCTCCTCGAAACAGTAGGAAGCAGATTTAAGCCACTAGTC
25262602 C
131 C
* *
25262603 TATCTCACTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGTAGATCTTATCTCCCTAAACAGTAGTG
1 TATCTCACTGAGCAGCAGCGGAGTAGGTCGAAGATTA-TAGATCTTATCTCCCTAAACAGTAGTG
* * * *
25262667 GAGCAGGTTGAAGATAGTAG-ATCTTATCTCCT-TAAACAGTAG
65 GAGCAGATCGAAGA-AGGAGAATCTTATCTCCTCGAAACAGTAG
25262709 TTGAGCAGAT
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
130 9 0.10
131 79 0.88
132 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
TATCTCACTGAGCAGCAGCGGAGTAGGTCGAAGATTATAGATCTTATCTCCCTAAACAGTAGTGG
AGCAGATCGAAGAAGGAGAATCTTATCTCCTCGAAACAGTAGGAAGCAGATTTAAGCCACTAGTC
C
Found at i:25262763 original size:175 final size:175
Alignment explanation
Indices: 25262472--25262855 Score: 585
Period size: 175 Copynumber: 2.2 Consensus size: 175
25262462 TATCAAGCCG
* * * *
25262472 TATCTCCCTGAGCAGTAGCGGAGTAGGTCGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTATAGATCTTATCTCCCTAAACAGTAGTGG
* * *
25262537 AGCAGATCGAAGACGGCGAATCTTATCTTCTCGAGATAGTAGGAAGCAGATTTAAGCCACTAGTC
66 AGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGTC
25262602 CTATC-TCACTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGTAGATCT
131 CTATCTTC-CTGAGCAGCAGTGGAGTAGGTTGAAGATTA-TAGATCT
* * * *
25262647 TATCTCCCTAAACAGTAGTGGAGCAGGTTGAAGA-TAGTAGATCTTATCTCCTTAAACAGTAGTT
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTA-TAGATCTTATCTCCCTAAACAGTAGTG
* *
25262711 GAGCAGATCGAAGACGGCAAATCTTATCTTCCCGATATAGTAGGAAGCAGATTTAAGCCACCATT
65 GAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGT
25262776 CCTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
130 CCTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
* *
25262822 TATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGA
25262856 CGGCAAATCT
Statistics
Matches: 189, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
174 2 0.01
175 183 0.97
176 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (175 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTATAGATCTTATCTCCCTAAACAGTAGTGG
AGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGTC
CTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
Found at i:25262782 original size:131 final size:132
Alignment explanation
Indices: 25262645--25263315 Score: 1006
Period size: 132 Copynumber: 5.1 Consensus size: 132
25262635 GATAGTAGAT
* * * * * * *
25262645 CTTATCTCCCTAAACAGTAGTGGAGCAGGTTGAAGATAGTAGATCTTATCTCCTTAAACAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * * **
25262710 TGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGATATAGTA-GGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
*
25262774 TTC
131 -GC
* *
25262777 C-TATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * * * *
25262841 AGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGATAGTA-GTAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
25262905 GC
131 GC
*
25262907 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTTGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * * *
25262972 GGAGTAGATCGAAGACGGCGAATCTTATCTTCTCAAGGTATTAGGGAAGCAGATTTAAGCCACTA
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
25263037 GC
131 GC
* *
25263039 CTTATTTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * *
25263104 GGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGGTATTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
25263169 GC
131 GC
* *
25263171 CTTATCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* *
25263236 GAAGCAGATCGAAGACGGGGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
25263301 GC
131 GC
25263303 CTTATCTCCCTGA
1 CTTATCTCCCTGA
25263316 AGTTGCAGTG
Statistics
Matches: 494, Mismatches: 43, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
130 2 0.00
131 211 0.43
132 281 0.57
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
GC
Found at i:25263331 original size:44 final size:44
Alignment explanation
Indices: 25263283--25263507 Score: 190
Period size: 44 Copynumber: 5.2 Consensus size: 44
25263273 GTAGTAGGGA
* * * *
25263283 AGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGACACTAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * *
25263327 AGCAGATT-AAAAC-CATAGATCTTATCTCTCTGAAGTAGCAGTAG
1 AGCAGATTGAAGACAC-TAG-TCTTATCTCCCTGAAGTTGCAGTGG
* * * *
25263371 AGCAGATTG--CACA-TAGTCTTATATCCTTGAAGTTGCATTGG
1 AGCAGATTGAAGACACTAGTCTTATCTCCCTGAAGTTGCAGTGG
** * * *
25263412 AGCAGACAGAAGAAACTAATTTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGACACTAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
25263456 AACAGATTGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAGACACTAGTCTTATCTCCCTGAAGTTGCAGTGG
*
25263500 AGCGGATT
1 AGCAGATT
25263508 AAAATGATGG
Statistics
Matches: 143, Mismatches: 31, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
41 26 0.18
42 4 0.03
43 9 0.06
44 104 0.73
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AGCAGATTGAAGACACTAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:25263526 original size:44 final size:41
Alignment explanation
Indices: 25263303--25263546 Score: 175
Period size: 44 Copynumber: 5.7 Consensus size: 41
25263293 AGCCACCAGC
25263303 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA--AT-GAT
* * * ** *
25263347 CTTATCTCTCTGAAGTAGCAGTAGAGCAGATTGCACAT-AGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATGA-T
* * * ** *
25263388 CTTATATCCTTGAAGTTGCATTGGAGCAGACAGAAGAAACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AAA-TGAT
* * **
25263432 TTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AAA-TGAT
* *
25263476 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA--AT-GAT
* * *
25263520 CTTATCTCTCTGAAGTTACAGTAGAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGC
25263547 GGATCGCATC
Statistics
Matches: 156, Mismatches: 35, Indels: 18
0.75 0.17 0.09
Matches are distributed among these distances:
40 1 0.01
41 25 0.16
42 4 0.03
43 4 0.03
44 121 0.78
45 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATGAT
Found at i:25265241 original size:26 final size:28
Alignment explanation
Indices: 25265192--25265245 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
25265182 TTAATTTCAA
*
25265192 ATTTTGTTGTATATATGTACATACATAC
1 ATTTTGTTGTATATATATACATACATAC
*
25265220 ATTTTG-T-TATATATATATATACATAC
1 ATTTTGTTGTATATATATACATACATAC
25265246 GTACATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.71
27 1 0.04
28 6 0.25
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTTTGTTGTATATATATACATACATAC
Found at i:25265666 original size:46 final size:47
Alignment explanation
Indices: 25265593--25265682 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
25265583 CACATCCCTG
* * *
25265593 TATATATACATACTTACATATATTTTTATATTGC-ATAATTTTAAAA
1 TATATATACATACATACATATACTTTTACATTGCTATAATTTTAAAA
* * *
25265639 TATATATACATACATATATATCCTTTTACATTTCTATAATTTTA
1 TATATATACATACATACATATACTTTTACATTGCTATAATTTTA
25265683 TTCATCTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 28 0.76
47 9 0.24
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (47 bp):
TATATATACATACATACATATACTTTTACATTGCTATAATTTTAAAA
Found at i:25268728 original size:4 final size:4
Alignment explanation
Indices: 25268719--25268750 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25268709 AATACATATT
25268719 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
25268751 ATATAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:25275652 original size:40 final size:40
Alignment explanation
Indices: 25275597--25275675 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
25275587 CTTCATCCTT
25275597 GATGAACATAGATATTTTTTTCTTCTATGGAACTTTTGAG
1 GATGAACATAGATATTTTTTTCTTCTATGGAACTTTTGAG
25275637 GATGAACATAGATATTTTTTTCTTCTATGGAACTTTTGA
1 GATGAACATAGATATTTTTTTCTTCTATGGAACTTTTGA
25275676 AATAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (40 bp):
GATGAACATAGATATTTTTTTCTTCTATGGAACTTTTGAG
Found at i:25279547 original size:23 final size:23
Alignment explanation
Indices: 25279504--25279548 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25279494 TTGTAAAAGA
* *
25279504 TTTAAATATATATATAAATATAT
1 TTTAAATATATAAAGAAATATAT
25279527 TTTAAA-ATATAAAGAACATATA
1 TTTAAATATATAAAGAA-ATATA
25279549 CAAGTATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTAAATATATAAAGAAATATAT
Found at i:25279640 original size:48 final size:48
Alignment explanation
Indices: 25279529--25279636 Score: 146
Period size: 49 Copynumber: 2.2 Consensus size: 48
25279519 AAATATATTT
* *
25279529 TAAAATATAAAGAACATATACAAGTATGTATATATATATTTTGAAATTA
1 TAAAATATAAAG-ACATATACAAGTATGCATATATATATTTTAAAATTA
* * *
25279578 TAAAATATGAAAGACATTTATATGTATGCATATATAT-TTTTAAAATTA
1 TAAAATAT-AAAGACATATACAAGTATGCATATATATATTTTAAAATTA
25279626 TAAAATATAAA
1 TAAAATATAAA
25279637 AGACGTATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
47 3 0.06
48 18 0.34
49 28 0.53
50 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (48 bp):
TAAAATATAAAGACATATACAAGTATGCATATATATATTTTAAAATTA
Found at i:25279659 original size:48 final size:47
Alignment explanation
Indices: 25279557--25279664 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
25279547 TACAAGTATG
* * * **
25279557 TATATATATATTTTGAAATTATAAAATATGAAAGACATTTATATGTA
1 TATATATATATTTTAAAATTATAAAATATAAAAGACATGTATATACA
25279604 TGCATATATAT-TTTTAAAATTATAAAATATAAAAGACGTATGTATATACA
1 T--ATATATATATTTTAAAATTATAAAATATAAAAGAC--ATGTATATACA
25279654 TATATATATAT
1 TATATATATAT
25279665 GAAAATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
47 1 0.02
48 32 0.63
49 9 0.18
50 9 0.18
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (47 bp):
TATATATATATTTTAAAATTATAAAATATAAAAGACATGTATATACA
Found at i:25279901 original size:58 final size:59
Alignment explanation
Indices: 25279818--25279928 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 59
25279808 AAAAGGATAT
* *
25279818 ATGTATGTATATATATATAGGAGTTAT-GAAATATAAAACACATATAT-TATAAGAATGC
1 ATGTATATATATATATATAGAAGTTATAG-AATATAAAACACATATATGTATAAGAATGC
* * * * *
25279876 ATGTATATATATATATTTTGAAGTTATAGAATATACAATACGTATATGTATAA
1 ATGTATATATATATATATAGAAGTTATAGAATATAAAACACATATATGTATAA
25279929 ATATAAAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
58 38 0.86
59 6 0.14
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.38
Consensus pattern (59 bp):
ATGTATATATATATATATAGAAGTTATAGAATATAAAACACATATATGTATAAGAATGC
Found at i:25280919 original size:15 final size:14
Alignment explanation
Indices: 25280891--25280917 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25280881 TAGCCGAAAG
25280891 AAAAAAAGAAAAAT
1 AAAAAAAGAAAAAT
25280905 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
25280918 ATCCCCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.07, T:0.04
Consensus pattern (14 bp):
AAAAAAAGAAAAAT
Found at i:25287127 original size:21 final size:21
Alignment explanation
Indices: 25287094--25287138 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25287084 TTAGTCAAAA
*
25287094 TTTTTATAATTTCTTTTTACAT
1 TTTTTATAATTTCATTTTA-AT
*
25287116 TTTTTAT-GTTTCATTTTAAT
1 TTTTTATAATTTCATTTTAAT
25287136 TTT
1 TTT
25287139 AAAATGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTATAATTTCATTTTAAT
Found at i:25288696 original size:15 final size:15
Alignment explanation
Indices: 25288633--25288708 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
25288623 CTCTATTTGT
*
25288633 TATTAGTTATTCATTA
1 TATTAATTATT-ATTA
*
25288649 T-TAAATTAATTATT-
1 TATTAATT-ATTATTA
* *
25288663 T-TTACATTCTTATTG
1 TATTA-ATTATTATTA
25288678 TATTAATTATTATTA
1 TATTAATTATTATTA
25288693 TATT-ATATATTATTA
1 TATTAAT-TATTATTA
25288708 T
1 T
25288709 TGTACCTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.20
15 32 0.65
16 7 0.14
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (15 bp):
TATTAATTATTATTA
Found at i:25288794 original size:11 final size:11
Alignment explanation
Indices: 25288778--25288802 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25288768 TTTAAATACA
25288778 TATACATATTT
1 TATACATATTT
25288789 TATACATATTT
1 TATACATATTT
25288800 TAT
1 TAT
25288803 TATTATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATACATATTT
Found at i:25291854 original size:23 final size:22
Alignment explanation
Indices: 25291828--25291877 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
25291818 TGTCTTTACA
*
25291828 TTCATTTTTCGAGTAAATATTCT
1 TTCATTTTT-GAATAAATATTCT
*
25291851 TTCA-TTTTGAATAATTATTCT
1 TTCATTTTTGAATAAATATTCT
25291872 TTCATT
1 TTCATT
25291878 CTTTTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.62
22 5 0.21
23 4 0.17
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (22 bp):
TTCATTTTTGAATAAATATTCT
Found at i:25291963 original size:12 final size:12
Alignment explanation
Indices: 25291948--25291973 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25291938 CGTAAATTTA
25291948 TATATTCTTTGG
1 TATATTCTTTGG
25291960 TATATTCTTTGG
1 TATATTCTTTGG
25291972 TA
1 TA
25291974 CCTACCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (12 bp):
TATATTCTTTGG
Found at i:25292666 original size:18 final size:17
Alignment explanation
Indices: 25292643--25292676 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
25292633 TTCAGATATT
25292643 AAAAAAAAGCAAAAGAAG
1 AAAAAAAAG-AAAAGAAG
25292661 AAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAAGAA
25292677 AAAGGAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAG
Found at i:25292756 original size:7 final size:7
Alignment explanation
Indices: 25292744--25292782 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
25292734 AGTGATGTGA
25292744 AAAAATG
1 AAAAATG
25292751 AAAAATG
1 AAAAATG
25292758 -AAAATG
1 AAAAATG
**
25292764 AAAAACA
1 AAAAATG
25292771 AAAAATG
1 AAAAATG
25292778 AAAAA
1 AAAAA
25292783 GTGGAGAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:25292761 original size:13 final size:14
Alignment explanation
Indices: 25292743--25292782 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
25292733 AAGTGATGTG
25292743 AAAAAATGAAAAA-
1 AAAAAATGAAAAAC
**
25292756 TGAAAATGAAAAAC
1 AAAAAATGAAAAAC
25292770 AAAAAATGAAAAA
1 AAAAAATGAAAAA
25292783 GTGGAGAGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAAATGAAAAAC
Done.