Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 163 of 295
Found at i:55661254 original size:43 final size:43
Alignment explanation
Indices: 55661194--55661426 Score: 160
Period size: 43 Copynumber: 5.5 Consensus size: 43
55661184 CCTGATTTCA
* *
55661194 TCACCGGCAATAAGCCTGCTAGACCTTTAAGTCCGATATCATT
1 TCACCAGCATTAAGCCTGCTAGACCTTTAAGTCCGATATCATT
* * * * *** * * *
55661237 TCATCGGCATTACGCCTGCTAG-GCTCGGAGCCCGATA-AAAT
1 TCACCAGCATTAAGCCTGCTAGACCTTTAAGTCCGATATCATT
* *
55661278 TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGTCCGTTATCATT
1 TCACCAGCATT-AAGCCTGCTAGACCTTTAAGTCCGATATCATT
* * * *
55661321 TCACCAGCATTATGTCTGCTAG-GC-TCAGAG-CTCGATA--ATAT
1 TCACCAGCATTAAGCCTGCTAGACCTTTA-AGTC-CGATATCAT-T
*
55661362 TCACCAGC-TTAAAGCTTGCTAGACCTTTAAGTCCGATATCATT
1 TCACCAGCATT-AAGCCTGCTAGACCTTTAAGTCCGATATCATT
* * *
55661405 TCATCACCATTACGCCTGCTAG
1 TCACCAGCATTAAGCCTGCTAG
55661427 GCTCAAAGCC
Statistics
Matches: 139, Mismatches: 37, Indels: 28
0.68 0.18 0.14
Matches are distributed among these distances:
40 6 0.04
41 37 0.27
42 34 0.24
43 56 0.40
44 6 0.04
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (43 bp):
TCACCAGCATTAAGCCTGCTAGACCTTTAAGTCCGATATCATT
Found at i:55661382 original size:41 final size:41
Alignment explanation
Indices: 55661253--55661383 Score: 101
Period size: 41 Copynumber: 3.1 Consensus size: 41
55661243 GCATTACGCC
* * *
55661253 TGCTAGGCTCGGAGCCCGATAAAATTCACCAGCTTAAAGCT
1 TGCTAGGCTCAGAGCTCGATAATATTCACCAGCTTAAAGCT
* * * *
55661294 TGCTAGACCTTTA-AG-TCCG-TTATCATTTCACCAGCATT-ATG-T
1 TGCTAG-GC-TCAGAGCT-CGATAAT-A-TTCACCAGC-TTAAAGCT
55661336 CTGCTAGGCTCAGAGCTCGATAATATTCACCAGCTTAAAGCT
1 -TGCTAGGCTCAGAGCTCGATAATATTCACCAGCTTAAAGCT
55661378 TGCTAG
1 TGCTAG
55661384 ACCTTTAAGT
Statistics
Matches: 67, Mismatches: 11, Indels: 24
0.66 0.11 0.24
Matches are distributed among these distances:
40 2 0.03
41 27 0.40
42 14 0.21
43 22 0.33
44 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCTAGGCTCAGAGCTCGATAATATTCACCAGCTTAAAGCT
Found at i:55661450 original size:84 final size:84
Alignment explanation
Indices: 55661205--55661439 Score: 371
Period size: 84 Copynumber: 2.8 Consensus size: 84
55661195 CACCGGCAAT
* * *
55661205 AAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCGGCATTACGCCTGCTAGGCTCGGAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCTAGGCTCAGAGCCC
*
55661270 GATAAAATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
* * * * *
55661289 AAGCTTGCTAGACCTTTAAGTCCGTTATCATTTCACCAGCATTATGTCTGCTAGGCTCAGAGCTC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCTAGGCTCAGAGCCC
55661354 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
* *
55661373 AAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCACCATTACGCCTGCTAGGCTCAAAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCTAGGCTCAGAGCCC
55661438 GA
66 GA
55661440 AATTCATCAC
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 135 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (84 bp):
AAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCTAGGCTCAGAGCCC
GATAATATTCACCAGCTTA
Found at i:55661466 original size:84 final size:82
Alignment explanation
Indices: 55661190--55661467 Score: 292
Period size: 84 Copynumber: 3.3 Consensus size: 82
55661180 ATAACCTGAT
* *
55661190 TTCATCACCGGCAATAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCGGCATTACGCCTG
1 TTCATCACCGG-TA-AAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTG
*
55661255 CTAGGCTCGGAGCCCGATAAAA
64 CTAGGCTCAGAGCCCG---AAA
* * * * * * * *
55661277 TTCACCAGC-TTAAAGCTTGCTAGACCTTTAAGTCCGTTATCATTTCACCAGCATTATGTCTGCT
1 TTCATCACCGGTAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCT
*
55661341 AGGCTCAGAGCTCGATAA
66 AGGCTCAGAGCCCGA-AA
* * *
55661359 -T-ATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGTCCGATATCATTTCATCACCATTACGCCT
1 TTCA-TCACC-G-GTAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCT
*
55661422 GCTAGGCTCAAAGCCCGAAA
63 GCTAGGCTCAGAGCCCGAAA
55661442 TTCATCACCGGTACAAGGCCTGCTAG
1 TTCATCACCGGTA-AA-GCCTGCTAG
55661468 GTTTGAAACC
Statistics
Matches: 159, Mismatches: 23, Indels: 21
0.78 0.11 0.10
Matches are distributed among these distances:
80 1 0.01
81 5 0.03
82 4 0.03
83 5 0.03
84 135 0.85
85 2 0.01
87 7 0.04
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (82 bp):
TTCATCACCGGTAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCATCAGCATTACGCCTGCT
AGGCTCAGAGCCCGAAA
Found at i:55663345 original size:14 final size:15
Alignment explanation
Indices: 55663316--55663345 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55663306 CAAAATTAAG
55663316 ACATGATACTTTCAC
1 ACATGATACTTTCAC
55663331 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
55663345 A
1 A
55663346 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:55670700 original size:22 final size:21
Alignment explanation
Indices: 55670659--55670701 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
55670649 TTAACATCAA
*
55670659 TTTAATCCATTTCATACCTAG
1 TTTAATCAATTTCATACCTAG
55670680 TTTAATTCAATTTACAT-CCTAG
1 TTTAA-TCAATTT-CATACCTAG
55670702 GAAAAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 11 0.58
23 3 0.16
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTAATCAATTTCATACCTAG
Found at i:55676052 original size:26 final size:24
Alignment explanation
Indices: 55675986--55676036 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
55675976 TATACCTAAC
55675986 TAATTATTTAGTATAGATTTTAAT
1 TAATTATTTAGTATAGATTTTAAT
55676010 TAATTATTTAGTATAGATTTTAAT
1 TAATTATTTAGTATAGATTTTAAT
55676034 TAA
1 TAA
55676037 CTTTATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
TAATTATTTAGTATAGATTTTAAT
Found at i:55680617 original size:49 final size:48
Alignment explanation
Indices: 55680535--55680692 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
55680525 CTTACTTTGA
*
55680535 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
55680582 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
55680631 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
55680680 GAATGTGATAAGT
1 GAATGTGA-AAGT
55680693 CCCGAAGGGC
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
47 13 0.12
49 89 0.84
50 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:55680866 original size:37 final size:37
Alignment explanation
Indices: 55680810--55680888 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
55680800 CCGAGCTCTA
* * *
55680810 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55680847 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55680884 AAGAC
1 AAGAC
55680889 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55682801 original size:43 final size:43
Alignment explanation
Indices: 55682753--55682855 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
55682743 TTGGTTTTCA
55682753 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
55682796 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
55682839 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
55682856 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:55682872 original size:29 final size:29
Alignment explanation
Indices: 55682837--55682910 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
55682827 GTTGTGAGAT
* *
55682837 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
55682866 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
55682895 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55682911 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:55683340 original size:40 final size:40
Alignment explanation
Indices: 55683296--55683652 Score: 507
Period size: 40 Copynumber: 8.9 Consensus size: 40
55683286 GAGTTACTAA
*
55683296 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
55683336 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
55683376 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
55683416 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTAATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
55683456 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
55683496 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
55683536 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * * *
55683576 ATCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
55683616 ATCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
55683653 CGTGTATTCG
Statistics
Matches: 291, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 291 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:55683354 original size:80 final size:80
Alignment explanation
Indices: 55683255--55683647 Score: 495
Period size: 80 Copynumber: 4.9 Consensus size: 80
55683245 TAAGTGACCA
* * * ** *
55683255 TATCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAG
1 TATCCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTTA-TGTATCCGGGCTAAGTTCCGAAGAG
55683318 CATTCATGCTAGCGATG
64 CATTCATGCTAGCGATG
* *
55683335 TATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTTATGTATCCGGGCTAAGTTCCGAAGAGCA
55683400 TTCATGCTAGCGATG
66 TTCATGCTAGCGATG
* *
55683415 TATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTAATGTATCCGGGCTAAGTTCCGAAGAGCA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTTATGTATCCGGGCTAAGTTCCGAAGAGCA
* *
55683480 TTCGTGCTAGTGATG
66 TTCATGCTAGCGATG
* *
55683495 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTTATGTATCCGGGCTAAGTTCCGAAGAGCA
* * *
55683560 TTCGTGCTAGTGATA
66 TTCATGCTAGCGATG
* ** * * * * * *
55683575 TATCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGT-TATATCCGGGCTAGGTCCCGAAGAGT
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT-TATGTATCCGGGCTAAGTTCCGAAGAGC
*
55683639 AATCATGCT
65 ATTCATGCT
55683648 GGTGACGTGT
Statistics
Matches: 282, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
79 1 0.00
80 269 0.95
81 12 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTTATGTATCCGGGCTAAGTTCCGAAGAGCA
TTCATGCTAGCGATG
Found at i:55683865 original size:24 final size:25
Alignment explanation
Indices: 55683816--55683865 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
55683806 GTGTATTAAC
55683816 GAATGAATAAGAGCACTATGTATGT
1 GAATGAATAAGAGCACTATGTATGT
* * *
55683841 GAATGATTAAG-GCACTGTGTGTGT
1 GAATGAATAAGAGCACTATGTATGT
55683865 G
1 G
55683866 CGAATTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (25 bp):
GAATGAATAAGAGCACTATGTATGT
Found at i:55687203 original size:49 final size:48
Alignment explanation
Indices: 55687121--55687278 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
55687111 CTTACTTTGA
*
55687121 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
55687168 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
55687217 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
55687266 GAATGTGATAAGT
1 GAATGTGA-AAGT
55687279 CCCGAAGGGC
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
47 13 0.12
49 89 0.84
50 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:55687452 original size:37 final size:37
Alignment explanation
Indices: 55687396--55687474 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
55687386 CCGAGCTCTA
* * *
55687396 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55687433 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55687470 AAGAC
1 AAGAC
55687475 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55694577 original size:29 final size:28
Alignment explanation
Indices: 55694479--55694593 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 28
55694469 TACCTGTATC
* *
55694479 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
* * * *
55694507 TGGCCCATTAGGATCAAACCACCTGT-ATA
1 TGGCCCATTAGG-CCCAATCACAT-TCATA
*
55694536 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* *
55694565 TGGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
55694593 T
1 T
55694594 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
28 25 0.36
29 44 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:55697978 original size:18 final size:17
Alignment explanation
Indices: 55697957--55697991 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55697947 TGAAAACCCT
55697957 TCTTAAAATAAAAAAACA
1 TCTTAAAA-AAAAAAACA
*
55697975 TCTTAAAAAAATAAACA
1 TCTTAAAAAAAAAAACA
55697992 CCTTTCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
TCTTAAAAAAAAAAACA
Found at i:55699080 original size:29 final size:29
Alignment explanation
Indices: 55699042--55699118 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
55699032 AATTATATTC
**
55699042 ATATGGCCCATTAGGGTCAAACCACATGT
1 ATATGGCCCATTAGGCCCAAACCACATGT
* *
55699071 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAACCACATGT
*
55699100 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
55699119 GTCACATTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAACCACATGT
Found at i:55699370 original size:8 final size:8
Alignment explanation
Indices: 55699354--55699387 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
55699344 CAGATTTTAA
55699354 GCATTTCG
1 GCATTTCG
*
55699362 GCTTTTCG
1 GCATTTCG
55699370 GCATTTCG
1 GCATTTCG
55699378 GCATTTCG
1 GCATTTCG
55699386 GC
1 GC
55699388 TTTTGCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.38
Consensus pattern (8 bp):
GCATTTCG
Found at i:55702092 original size:33 final size:33
Alignment explanation
Indices: 55702055--55702125 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
55702045 ATACTTAAGT
* *
55702055 TTGAAGGTAAATTGGAAAGGTATTTTCCTTTGG
1 TTGAAGGTAAATTCGAAAGGTATTTGCCTTTGG
** **
55702088 TTGAATTTACTTTCGAAAGGTATTTGCCTTTGG
1 TTGAAGGTAAATTCGAAAGGTATTTGCCTTTGG
55702121 TTGAA
1 TTGAA
55702126 TTTACTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.42
Consensus pattern (33 bp):
TTGAAGGTAAATTCGAAAGGTATTTGCCTTTGG
Found at i:55702126 original size:33 final size:33
Alignment explanation
Indices: 55702069--55702132 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
55702059 AGGTAAATTG
*
55702069 GAAAGGTATTTTCCTTTGGTTGAATTTACTTTC
1 GAAAGGTATTTGCCTTTGGTTGAATTTACTTTC
55702102 GAAAGGTATTTGCCTTTGGTTGAATTTACTT
1 GAAAGGTATTTGCCTTTGGTTGAATTTACTT
55702133 ATAATAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47
Consensus pattern (33 bp):
GAAAGGTATTTGCCTTTGGTTGAATTTACTTTC
Found at i:55718271 original size:49 final size:49
Alignment explanation
Indices: 55718194--55718438 Score: 294
Period size: 49 Copynumber: 4.9 Consensus size: 49
55718184 TAGCCGAAGC
* * * * *
55718194 TATCTGGTACGCATGGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
55718243 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * * * * *
55718293 CATCTGATACACGTACTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* * * *
55718344 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGGGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
55718393 TATCTC-GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATC-CGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
55718439 TCACAATAGC
Statistics
Matches: 166, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
49 82 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:55718374 original size:101 final size:98
Alignment explanation
Indices: 55718210--55718438 Score: 307
Period size: 100 Copynumber: 2.3 Consensus size: 98
55718200 GTACGCATGG
* * * *
55718210 TAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTAGTA
1 TAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTAGTA
* *
55718275 CTACACACGTGACCTAACCATCT-GATACACGTAC
66 CTACACACGGGACC-AACCATCTCG-TACACATAC
* *
55718309 TAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAG
1 TAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACTTAG
* ** *
55718374 TACTACACATGGGACCAATTATCTCGTACACATAG
64 TACTACACACGGGACCAACCATCTCGTACACATAC
55718409 TAGCCTGCACTTAGTACTACACACGTGACC
1 TAGCCTGCACTTAGTACTACACACGTGACC
55718439 TCACAATAGC
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
99 27 0.24
100 44 0.39
101 43 0.38
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (98 bp):
TAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTAGTA
CTACACACGGGACCAACCATCTCGTACACATAC
Found at i:55719119 original size:30 final size:30
Alignment explanation
Indices: 55719085--55719144 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55719075 CTCTAATATG
55719085 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
55719115 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
55719145 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:55746787 original size:12 final size:12
Alignment explanation
Indices: 55746770--55746794 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55746760 TCATGTTTAC
55746770 CTAATTGGGACT
1 CTAATTGGGACT
55746782 CTAATTGGGACT
1 CTAATTGGGACT
55746794 C
1 C
55746795 CTTGACTTGT
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (12 bp):
CTAATTGGGACT
Found at i:55747648 original size:48 final size:48
Alignment explanation
Indices: 55747596--55747881 Score: 302
Period size: 48 Copynumber: 5.8 Consensus size: 48
55747586 TACATGAATC
*
55747596 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACGCTGGCA
1 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGCA
* * * *
55747644 CACATATCATCGCCAATGCCATGTCCCAGACATGGTCTTACACAGGCA
1 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGCA
* *
55747692 CACATATCATCACCGATGCTATGTGCTATGTCCCAAACATGGTCTTACACAGACA
1 CACATATCATCACCGATGC------C-ATGTCCCAAACATGGTCTTACACTGGCA
** * *
55747747 CACATATCATCACTAATGCCATGTCCTAGACATGGTCTTACACTGGCA
1 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGCA
* * * * * *
55747795 CATATATCATCGCTGATGCCATATCCCAGACATGGTCTTACACTGGTA
1 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGCA
* * *** *
55747843 CATATACCATCGTTGATGCCATGTACCAAACATGGTCTT
1 CACATATCATCACCGATGCCATGTCCCAAACATGGTCTT
55747882 TGTAATATCC
Statistics
Matches: 205, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
48 160 0.78
49 1 0.00
54 1 0.00
55 43 0.21
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.26
Consensus pattern (48 bp):
CACATATCATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGCA
Found at i:55747813 original size:103 final size:103
Alignment explanation
Indices: 55747616--55747805 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 103
55747606 CACCGATGCC
* * * *
55747616 ATGTCCCAAACATGGTCTTACGCTGGCACACATATCATCGCCAATGCCATGTCCCAGACATGGTC
1 ATGTCCCAAACATGGTCTTACACAGACACACATATCATCACCAATGCCATGTCCCAGACATGGTC
55747681 TTACACAGGCACACATATCATCACCGATGCTATGTGCT
66 TTACACAGGCACACATATCATCACCGATGCTATGTGCT
* *
55747719 ATGTCCCAAACATGGTCTTACACAGACACACATATCATCACTAATGCCATGTCCTAGACATGGTC
1 ATGTCCCAAACATGGTCTTACACAGACACACATATCATCACCAATGCCATGTCCCAGACATGGTC
* *
55747784 TTACACTGGCACATATATCATC
66 TTACACAGGCACACATATCATC
55747806 GCTGATGCCA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (103 bp):
ATGTCCCAAACATGGTCTTACACAGACACACATATCATCACCAATGCCATGTCCCAGACATGGTC
TTACACAGGCACACATATCATCACCGATGCTATGTGCT
Found at i:55747861 original size:151 final size:150
Alignment explanation
Indices: 55747566--55747853 Score: 389
Period size: 151 Copynumber: 1.9 Consensus size: 150
55747556 AGTACCAATA
* * * *
55747566 CTATGTCTCTAACATGGTCTTACATGAATCCACATATCATCACCGATGCCATGTCCCAAACATGG
1 CTATGTCCCAAACATGGTCTTACAAGAA-CCACATATCATCACCAATGCCATGTCCCAAACATGG
* *
55747631 TCTTACGCTGGCACACATATCATCGCCAATGCCATGTCCCAGACATGGTCTTACACAGGCACACA
65 TCTTACACTGGCACACATATCATCGCCAATGCCATATCCCAGACATGGTCTTACACAGGCACACA
* *
55747696 TATCATCACCGATGCTATGTG
130 TACCATCACCGATGCCATGTG
* * *
55747717 CTATGTCCCAAACATGGTCTTACACAG-ACACACATATCATCACTAATGCCATGTCCTAGACATG
1 CTATGTCCCAAACATGGTCTTACA-AGAAC-CACATATCATCACCAATGCCATGTCCCAAACATG
* ** * * *
55747781 GTCTTACACTGGCACATATATCATCGCTGATGCCATATCCCAGACATGGTCTTACACTGGTACAT
64 GTCTTACACTGGCACACATATCATCGCCAATGCCATATCCCAGACATGGTCTTACACAGGCACAC
55747846 ATACCATC
129 ATACCATC
55747854 GTTGATGCCA
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
150 1 0.01
151 117 0.98
152 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (150 bp):
CTATGTCCCAAACATGGTCTTACAAGAACCACATATCATCACCAATGCCATGTCCCAAACATGGT
CTTACACTGGCACACATATCATCGCCAATGCCATATCCCAGACATGGTCTTACACAGGCACACAT
ACCATCACCGATGCCATGTG
Found at i:55749302 original size:93 final size:93
Alignment explanation
Indices: 55749143--55749313 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
55749133 GGATGGTTGA
* *
55749143 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
55749208 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * * *
55749236 GCATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCGAACGCCCTAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
55749301 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55749314 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55749316 original size:46 final size:46
Alignment explanation
Indices: 55749147--55749318 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
55749137 GGTTGAGCAT
* * * *
55749147 CCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
55749193 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
* *
55749238 ATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* *
55749286 CCTAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
55749319 GGGGCGAGTT
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.55
47 27 0.26
48 5 0.05
50 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:55753343 original size:49 final size:49
Alignment explanation
Indices: 55753290--55753514 Score: 281
Period size: 49 Copynumber: 4.5 Consensus size: 49
55753280 CTGGTACGCA
*
55753290 TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCCGGTACACG
* * ** * *
55753339 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGAGACC-AATTATCCGGTACACG
* * * * *
55753389 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCAGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGAGA-CCAA-TTATCCGGTACACG
* *
55753440 TAGTAGCCTGCACTTAGTACTACACATGCA-ACCAATAATCCGGTACACT
1 TAGTAGCCTGCACTTAGTACTACACATG-AGACCAATTATCCGGTACACG
55753489 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
55753515 CATGACCTCA
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
49 67 0.44
50 46 0.30
51 38 0.25
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCCGGTACACG
Found at i:55753462 original size:101 final size:98
Alignment explanation
Indices: 55753290--55753514 Score: 297
Period size: 100 Copynumber: 2.3 Consensus size: 98
55753280 CTGGTACGCA
* **
55753290 TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCCGGTACATGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
** * *
55753355 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCAACC-AACAATCCGATACACG
* * *
55753389 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGAGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACT
* * * *
55753454 TAGTACTACACATGCAACCAATAATCCGGTACACT
64 TAGTACTACACACGCAACCAACAATCCGATACACG
55753489 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
55753515 CATGACCTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
99 30 0.27
100 40 0.36
101 40 0.36
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACATGAGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCAACCAACAATCCGATACACG
Found at i:55760923 original size:45 final size:45
Alignment explanation
Indices: 55760859--55761033 Score: 232
Period size: 45 Copynumber: 4.0 Consensus size: 45
55760849 TATCGTAAAG
*
55760859 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCCGGTGAAA
* * *
55760904 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGATGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCCGGTGAAA
* * * *
55760949 TACTATTCGGGCCTTCGAGTCTAGCGGGCTATCATGCTGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCCGGTGAAA
*
55760994 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCTA-AATGCCGGTGA
1 T-ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCCGGTGA
55761034 TTTGATAAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
42 9 0.08
43 17 0.15
44 5 0.04
45 84 0.72
46 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCCGGTGAAA
Found at i:55780547 original size:46 final size:46
Alignment explanation
Indices: 55780497--55780672 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
55780487 TGGTTGAGCA
55780497 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
55780543 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
55780588 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
55780636 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55780673 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:55780653 original size:93 final size:93
Alignment explanation
Indices: 55780494--55780665 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55780484 GGATGGTTGA
* *
55780494 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55780559 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
55780587 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55780652 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
55780666 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55785982 original size:13 final size:13
Alignment explanation
Indices: 55785964--55785989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55785954 TTTTATAATG
55785964 TATTTTGAATTTA
1 TATTTTGAATTTA
55785977 TATTTTGAATTTA
1 TATTTTGAATTTA
55785990 ACTATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTGAATTTA
Found at i:55786412 original size:20 final size:20
Alignment explanation
Indices: 55786387--55786452 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
55786377 CATGATAGCA
55786387 TAGCACATTCATGCTCCTGT
1 TAGCACATTCATGCTCCTGT
* *
55786407 TAGCAC-TACAGTGCTCCTGA
1 TAGCACATTCA-TGCTCCTGT
** *
55786427 TAGCACATTTTTGCTCTTGT
1 TAGCACATTCATGCTCCTGT
55786447 TAGCAC
1 TAGCAC
55786453 TAGGTTCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.08
20 33 0.89
21 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (20 bp):
TAGCACATTCATGCTCCTGT
Found at i:55786481 original size:39 final size:40
Alignment explanation
Indices: 55786386--55786486 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
55786376 TCATGATAGC
*
55786386 ATAGCACATTCATGCTCCTGTTAGCACTACAGTGCTCCTG
1 ATAGCACATTTATGCTCCTGTTAGCACTACAGTGCTCCTG
* * * * *
55786426 ATAGCACATTTTTGCTCTTGTTAGCACTA-GGTTCTCTTG
1 ATAGCACATTTATGCTCCTGTTAGCACTACAGTGCTCCTG
*
55786465 ATAGCATATTTATGCTCCTGTT
1 ATAGCACATTTATGCTCCTGTT
55786487 TGCATTATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 26 0.50
40 26 0.50
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (40 bp):
ATAGCACATTTATGCTCCTGTTAGCACTACAGTGCTCCTG
Found at i:55787822 original size:18 final size:18
Alignment explanation
Indices: 55787786--55787824 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55787776 TTTGTATGTG
**
55787786 TTTTTAAAATTTTTTATT
1 TTTTTAAAATTTTAAATT
55787804 TTTTTAAAATTTTAAATT
1 TTTTTAAAATTTTAAATT
55787822 TTT
1 TTT
55787825 GTTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTAAAATTTTAAATT
Found at i:55793126 original size:34 final size:34
Alignment explanation
Indices: 55793033--55793106 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
55793023 AGTGCCACGA
* * *
55793033 TTCACAACTCAGTATGGAAACACCATACCTACGT
1 TTCACAGCTCGGTATGGAAATACCATACCTACGT
55793067 TTCACAGCTCGGTATGGAAATACCATACCTACGT
1 TTCACAGCTCGGTATGGAAATACCATACCTACGT
55793101 TTCACA
1 TTCACA
55793107 CTTTTTCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (34 bp):
TTCACAGCTCGGTATGGAAATACCATACCTACGT
Found at i:55793192 original size:27 final size:27
Alignment explanation
Indices: 55793161--55793222 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
55793151 GATCACTAAA
* * *
55793161 CACTTTGCTATGTTTGGCACACTATAT
1 CACTTTGCCATGATTGACACACTATAT
*
55793188 CACTTTGCCATGATTGACACACTTTAT
1 CACTTTGCCATGATTGACACACTATAT
55793215 CACTTTGC
1 CACTTTGC
55793223 ATAGTTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (27 bp):
CACTTTGCCATGATTGACACACTATAT
Found at i:55793357 original size:31 final size:31
Alignment explanation
Indices: 55793314--55793460 Score: 240
Period size: 31 Copynumber: 4.7 Consensus size: 31
55793304 TTTGTCACTT
*
55793314 GTAGCCGAAGCTACCACTATTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTAATCAG
* *
55793345 GTAGCTGGAGCTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTAATCAG
*
55793376 GTAGCCGAAGCTACTACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTAATCAG
* *
55793407 GTAGCCAAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTAATCAG
55793438 GTAGCCGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
55793461 TATTGTACAC
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTAATCAG
Found at i:55793504 original size:32 final size:32
Alignment explanation
Indices: 55793454--55793566 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 32
55793444 GAAGCTACCA
*
55793454 CTTTTCATA-TTGTACACACAAGCCGTACATTTT
1 CTTTTCA-AGTTGTACACACAAG-TGTACATTTT
*
55793487 CTTTTCAAG-TGTACACACAAAGTGTACGTTTT
1 CTTTTCAAGTTGTACACAC-AAGTGTACATTTT
*
55793519 CTATTT-AAGTTGTACACACACAGTGTACATTTC
1 CT-TTTCAAGTTGTACACACA-AGTGTACATTTT
*
55793552 CTTTTCCAGTTGTAC
1 CTTTTCAAGTTGTAC
55793567 CTTTTAGGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
32 27 0.39
33 42 0.61
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (32 bp):
CTTTTCAAGTTGTACACACAAGTGTACATTTT
Found at i:55795266 original size:11 final size:11
Alignment explanation
Indices: 55795250--55795302 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
55795240 TATACTAAAT
55795250 AAATAATAATA
1 AAATAATAATA
55795261 AAATAATAAT-
1 AAATAATAATA
* *
55795271 AAATATCTCATTA
1 AAATA-AT-AATA
*
55795284 AAATATTAATA
1 AAATAATAATA
55795295 AAATAATA
1 AAATAATA
55795303 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 3 0.09
13 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATA
Found at i:55795309 original size:31 final size:33
Alignment explanation
Indices: 55795250--55795315 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
55795240 TATACTAAAT
*
55795250 AAATAATAATAAAATAATAATAAATATCTCATTA
1 AAATAATAATAAAATAATAAT-AATATCTAATTA
* *
55795284 AAATATTAATAAAATAAT-AT-TTATCTAATTA
1 AAATAATAATAAAATAATAATAATATCTAATTA
55795315 A
1 A
55795316 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATAATAATAAAATAATAATAATATCTAATTA
Found at i:55801681 original size:7 final size:7
Alignment explanation
Indices: 55801669--55801697 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55801659 CCTAGTTGAA
55801669 TTGGGTT
1 TTGGGTT
55801676 TTGGGTT
1 TTGGGTT
55801683 TTGGGTT
1 TTGGGTT
55801690 TTGGGTT
1 TTGGGTT
55801697 T
1 T
55801698 CATAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (7 bp):
TTGGGTT
Found at i:55803252 original size:29 final size:29
Alignment explanation
Indices: 55803212--55803296 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
55803202 AATGTGACTG
*
55803212 GGCCTAACGGGCTATATAAATGTGATTTA
1 GGCCTAATGGGCTATATAAATGTGATTTA
* ** * *
55803241 GGCCTAATGGGCCATATTTAGGTGATTTG
1 GGCCTAATGGGCTATATAAATGTGATTTA
*
55803270 GGCCTAATGGG-TCATATAAATATGATT
1 GGCCTAATGGGCT-ATATAAATGTGATT
55803297 GGGCTTAGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (29 bp):
GGCCTAATGGGCTATATAAATGTGATTTA
Found at i:55815239 original size:18 final size:18
Alignment explanation
Indices: 55815216--55815258 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55815206 TCTTGTCACT
*
55815216 ATATATTTTGAAAT-TAAA
1 ATATATATT-AAATGTAAA
55815234 ATATATATTAAATGTAAA
1 ATATATATTAAATGTAAA
*
55815252 AAATATA
1 ATATATA
55815259 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATATATTAAATGTAAA
Found at i:55816696 original size:88 final size:88
Alignment explanation
Indices: 55816547--55816724 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
55816537 TAAAAAGGCT
* * *
55816547 CTAGTAGCTTAGTTAAATAGTTAGCATACGATTGGAATGTCAATAGGGAACTTCTGTTACTAGCA
1 CTAGTAGCTTAGTTAAAAAGTTAACATACGATTGGAATGCCAATAGGGAACTTCTGTTACTAGCA
55816612 CTATAGTACTTCTATTATTAGTA
66 CTATAGTACTTCTATTATTAGTA
* * *
55816635 CTAGTAGCTTAGTTAAAAAGTTAACATACGATTGGCATGCCAATAGGGGACTTCTGTTACTAGTA
1 CTAGTAGCTTAGTTAAAAAGTTAACATACGATTGGAATGCCAATAGGGAACTTCTGTTACTAGCA
55816700 CTATAGTACTTCTATTATTAGTA
66 CTATAGTACTTCTATTATTAGTA
55816723 CT
1 CT
55816725 TTGGTACATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (88 bp):
CTAGTAGCTTAGTTAAAAAGTTAACATACGATTGGAATGCCAATAGGGAACTTCTGTTACTAGCA
CTATAGTACTTCTATTATTAGTA
Found at i:55818848 original size:14 final size:14
Alignment explanation
Indices: 55818829--55818857 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55818819 AGGAGTCTGG
55818829 GGAGTATACTGTTC
1 GGAGTATACTGTTC
55818843 GGAGTATACTGTTC
1 GGAGTATACTGTTC
55818857 G
1 G
55818858 TAGTGGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (14 bp):
GGAGTATACTGTTC
Found at i:55823379 original size:44 final size:44
Alignment explanation
Indices: 55823331--55823471 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 44
55823321 CCTGTTTCCC
55823331 TACTGCTTAGGGGGATAAGGCTCACCATCTTCGATCCGCTCCAT
1 TACTGCTTAGGGGGATAAGGCTCACCATCTTCGATCCGCTCCAT
* * * ** * * *
55823375 TACTGCTTAGGGAGATGA-GATCTATAATCTTC-AGCCTGTTTCC-C
1 TACTGCTTAGGGGGATAAGGCTC-ACCATCTTCGATCC-G-CTCCAT
* * *
55823419 TACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCAT
1 TACTGCTTAGGGGGATAAGGCTCACCATCTTCGATCCGCTCCAT
55823463 TACTGCTTA
1 TACTGCTTA
55823472 AGGAGTTGAG
Statistics
Matches: 72, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 9 0.12
44 55 0.76
45 8 0.11
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (44 bp):
TACTGCTTAGGGGGATAAGGCTCACCATCTTCGATCCGCTCCAT
Found at i:55823410 original size:88 final size:87
Alignment explanation
Indices: 55823295--55824230 Score: 1189
Period size: 88 Copynumber: 10.7 Consensus size: 87
55823285 CTGCAACTTG
*
55823295 AGGGAGATAAGA-CTTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCAT
1 AGGGAGATAAGATC-TGTAAT-TTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCAT
* *
55823359 CTTCGATCCGCTCCATTACTGCTT
64 CTTCGATCTGCTCCACTACTGCTT
* * *
55823383 AGGGAGATGAGATCTATAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAAT-TTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
*
55823448 TTCGATCTGCTCCATTACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * * **
55823471 AAGGAGTTGAGATCTGTAATTTCTAGCCTGTTTCTTTACTGCTTAGGGGGTTAAGGCTCACCGA-
1 AGGGAGATAAGATCTGTAATTTC-AGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACC-AT
*
55823535 CTTCGATTTGCTCCACTACTGCTT
64 CTTCGATCTGCTCCACTACTGCTT
* * * *
55823559 AGGGATATAAGATCTGTAATTTCCAACCAGTTTCCCTA-TGCTTAGGAGGTTAAGGCTCACCATC
1 AGGGAGATAAGATCTGTAATTT-CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
*** *
55823623 TTCGATCAATTCCAC-ATTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * * * *
55823645 AGGGAGATAAGATCTGAAATTTTAGGCCTATTTCTCTACTGCTTAGGGGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATTTCA-GCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* *
55823710 TTTGATCTGCTCCAGTACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * * **
55823733 AGGGAGATAAGATTTGTAATTTCTAGCTTGTTTCCCTACTGCTTAGGGGGTTACGGCTCACTGTC
1 AGGGAGATAAGATCTGTAATTTC-AGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* *
55823798 CTCGATCCGCTCCACTACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * * **
55823821 AGGAAGATAAGATCTGTAATTTTCAGCTTGTTTTCCTACTGCTTAGGGGGTTAAGGCTCACTGTC
1 AGGGAGATAAGATCTGTAA-TTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* *
55823886 TTCAATCTGCTCCACCACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * *
55823909 AGGGAGATAAGATCTGTAATTTCCAACCTCTTTCCCTACTGCTTAGGGGATTAAGGCTCACCATC
1 AGGGAGATAAGATCTGTAATTT-CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* *
55823974 TTCGATCTGTTCCAC-ACTGTTT
65 TTCGATCTGCTCCACTACTGCTT
* * **
55823996 AGGGAGATAAGATCTGTAATTTCTAGCCTGTTTTCCTACCGCTTAGGGGGTTAAAACTCACCATC
1 AGGGAGATAAGATCTGTAATTTC-AGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
55824061 TTCGATCTGCTCCACTACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* * * * * *
55824084 AGGGAGATAATATATGTAATTTCCAGCCTATTTTCCTACTGCTTAAGGGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATTT-CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
55824149 TTCGATCTGCTCCACTACTGCTT
65 TTCGATCTGCTCCACTACTGCTT
* *
55824172 AGGGAGATAAAATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGAGGGTTAAGGCTC
1 AGGGAGATAAGATCTGTAA-TTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTC
55824231 GTGAATTCAC
Statistics
Matches: 737, Mismatches: 96, Indels: 30
0.85 0.11 0.03
Matches are distributed among these distances:
85 1 0.00
86 37 0.05
87 150 0.20
88 538 0.73
89 11 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (87 bp):
AGGGAGATAAGATCTGTAATTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATCT
TCGATCTGCTCCACTACTGCTT
Found at i:55824044 original size:263 final size:263
Alignment explanation
Indices: 55823295--55824230 Score: 1227
Period size: 263 Copynumber: 3.6 Consensus size: 263
55823285 CTGCAACTTG
*
55823295 AGGGAGATAAGA-CTTGTAATCTT-CAGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCA
1 AGGGAGATAAGATC-TGTAAT-TTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCA
* ** * *
55823358 TCTTCGATCCGCTCCATTACTGCTTAGGGAGATGAGATCTATAATCTTCAGCCTGTTTCCCTACT
64 TCTTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTGTTTCCCTACT
* * * *
55823423 GCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCATTACTGCTTAAGGAGTTGAGATCTGT
128 GCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCAGTACTGCTTAGGGAGATAAGATCTGT
* * *
55823488 AATTTCTAGCCTG-TTTCTTTACTGCTTAGGGGGTTAAGGCTCACCGACTTCGATTTGCTCCACT
193 AATTTCTAGCCTGTTTTC-CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACT
55823552 ACTGCTT
257 ACTGCTT
* * * *
55823559 AGGGATATAAGATCTGTAATTTCCAACCAGTTTCCCTA-TGCTTAGGAGGTTAAGGCTCACCATC
1 AGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
*** * * * * *
55823623 TTCGATCAATTCCA-CATTGCTTAGGGAGATAAGATCTGAAATTTTAGGCCTATTTCTCTACTGC
66 TTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAATTTCA-GCCTGTTTCCCTACTGC
* *
55823687 TTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCAGTACTGCTTAGGGAGATAAGATTTGTAA
130 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCAGTACTGCTTAGGGAGATAAGATCTGTAA
* * * * * *
55823752 TTTCTAGCTTGTTTCCCTACTGCTTAGGGGGTTACGGCTCACTGTCCTCGATCCGCTCCACTACT
195 TTTCTAGCCTGTTTTCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACT
55823817 GCTT
260 GCTT
* * * * **
55823821 AGGAAGATAAGATCTGTAATTTTCAGCTTGTTTTCCTACTGCTTAGGGGGTTAAGGCTCACTGTC
1 AGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* * *
55823886 TTCAATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTCTTTCCCTACTGC
66 TTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTGTTTCCCTACTGC
* * * * *
55823951 TTAGGGGATTAAGGCTCACCATCTTCGATCTGTTCCA-CACTGTTTAGGGAGATAAGATCTGTAA
130 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCAGTACTGCTTAGGGAGATAAGATCTGTAA
* ** *
55824015 TTTCTAGCCTGTTTTCCTACCGCTTAGGGGGTTAAAACTCACCATCTTCGATCTGCTCCACTACT
195 TTTCTAGCCTGTTTTCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACT
55824080 GCTT
260 GCTT
* * * * * *
55824084 AGGGAGATAATATATGTAATTTCCAGCCTATTTTCCTACTGCTTAAGGGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
* *
55824149 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATTTTCAGCCTGTTTCCCTACTGC
66 TTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTGTTTCCCTACTGC
*
55824214 TTAGAGGGTTAAGGCTC
130 TTAGGGGGTTAAGGCTC
55824231 GTGAATTCAC
Statistics
Matches: 581, Mismatches: 83, Indels: 17
0.85 0.12 0.02
Matches are distributed among these distances:
261 3 0.01
262 184 0.32
263 284 0.49
264 108 0.19
265 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (263 bp):
AGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCATC
TTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTGTAATTTCAGCCTGTTTCCCTACTGCT
TAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCAGTACTGCTTAGGGAGATAAGATCTGTAAT
TTCTAGCCTGTTTTCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTG
CTT
Found at i:55824399 original size:64 final size:64
Alignment explanation
Indices: 55824297--55824424 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
55824287 TCATGTATCT
* *
55824297 ATGCTTATACCAAATAATTAGGATACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATACCAAATAATTAGGATACTATGATCAAAATGAAACAAATGCTCCTAACTAGATGTG
** * * * *
55824361 ATGCTTATGTCAAATAGTTAGGATGCTATGATCAAAATGAAACCAGTGCTCCTAACTAGATGTG
1 ATGCTTATACCAAATAATTAGGATACTATGATCAAAATGAAACAAATGCTCCTAACTAGATGTG
55824425 TTATGAATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCTTATACCAAATAATTAGGATACTATGATCAAAATGAAACAAATGCTCCTAACTAGATGTG
Found at i:55826189 original size:13 final size:12
Alignment explanation
Indices: 55826173--55826244 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
55826163 ATAACTATTA
55826173 AATATTTGTAATT
1 AATATTT-TAATT
**
55826186 AATATTTTAAAA
1 AATATTTTAATT
55826198 AATATTTT--TT
1 AATATTTTAATT
*
55826208 TAT-TTTTAATT
1 AATATTTTAATT
55826219 AATAATTTTAA-T
1 AAT-ATTTTAATT
55826231 AA-ATTTGTAATT
1 AATATTT-TAATT
55826243 AA
1 AA
55826245 GTACCAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.09
10 6 0.13
11 7 0.15
12 17 0.36
13 13 0.28
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
AATATTTTAATT
Found at i:55844610 original size:9 final size:9
Alignment explanation
Indices: 55844593--55844629 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55844583 TGAGTTTTCG
55844593 AATTCGAAT
1 AATTCGAAT
*
55844602 AACTCGAAT
1 AATTCGAAT
55844611 AATTCGAAT
1 AATTCGAAT
55844620 AATTCGAAT
1 AATTCGAAT
55844629 A
1 A
55844630 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55853364 original size:13 final size:13
Alignment explanation
Indices: 55853346--55853380 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
55853336 GTGGTCAAAT
55853346 AAATAGGAGTGTA
1 AAATAGGAGTGTA
55853359 AAATAGGAGTGTA
1 AAATAGGAGTGTA
55853372 AAATAGGAG
1 AAATAGGAG
55853381 GATTTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (13 bp):
AAATAGGAGTGTA
Found at i:55853525 original size:26 final size:26
Alignment explanation
Indices: 55853489--55853598 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
55853479 TGATACAAAT
55853489 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
55853515 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
55853541 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
55853567 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
55853593 TGATAA
1 TGATAA
55853599 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:55855197 original size:26 final size:26
Alignment explanation
Indices: 55855162--55855213 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
55855152 AATGTGAAAG
*
55855162 GGGGTTGCTATGTGCTAATTCCCCGA
1 GGGGTTGCTAAGTGCTAATTCCCCGA
*
55855188 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTAATTCCCCGA
55855214 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTAATTCCCCGA
Found at i:55857659 original size:28 final size:26
Alignment explanation
Indices: 55857617--55857691 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
55857607 AAAATTAGCT
* *
55857617 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
55857645 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
55857671 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
55857692 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:55857836 original size:27 final size:27
Alignment explanation
Indices: 55857795--55857915 Score: 170
Period size: 27 Copynumber: 4.4 Consensus size: 27
55857785 GAGGAAGCGT
*
55857795 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
55857822 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
55857849 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
55857876 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
*
55857904 TCTGGTGACTCT
1 TCTGGTGGCTCT
55857916 ATCACATTAT
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 73 0.88
28 10 0.12
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:55857880 original size:54 final size:55
Alignment explanation
Indices: 55857795--55857934 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
55857785 GAGGAAGCGT
* * * *
55857795 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
* *
55857849 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
* **
55857904 TCTGGTGACTCTATCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
55857935 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
Found at i:55857924 original size:27 final size:28
Alignment explanation
Indices: 55857795--55857934 Score: 157
Period size: 27 Copynumber: 5.2 Consensus size: 28
55857785 GAGGAAGCGT
* *
55857795 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
*
55857822 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
55857849 TCTGGTGGCTCTGCCAC-ATATATCTGT-
1 TCTGGTGGCTCTGCCACAAT-TATCTGTA
* *
55857876 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAATTATCTGTA
* **
55857904 TCTGGTGACTCTATCAC-ATTATCTGT-
1 TCTGGTGGCTCTGCCACAATTATCTGTA
55857930 TCTGG
1 TCTGG
55857935 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
26 6 0.06
27 81 0.79
28 15 0.15
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAATTATCTGTA
Found at i:55861281 original size:3 final size:3
Alignment explanation
Indices: 55861273--55861335 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
55861263 AAGTGCACAA
* * * *
55861273 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC CTT ACT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55861321 ATT AAAT ATT ATT AT
1 ATT -ATT ATT ATT AT
55861336 CTTTTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 49 0.96
4 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:55861853 original size:154 final size:152
Alignment explanation
Indices: 55861684--55861983 Score: 469
Period size: 155 Copynumber: 2.0 Consensus size: 152
55861674 ATTTTTTTTT
* *
55861684 AAAAAGAGAAAGTTTATA-TTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGA-AAGT
1 AAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATG-TTTTTTAGTCATTTTAAAGGAGAAGT
* *
55861747 TTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCGAAATCAAAGTTTTGATCTTT
65 TTAAAATTTTAAAACAAAGTTTTGA--TCTTTTTCAACTATTTCAAAAT-AAAGTTTTGATCTTT
*
55861812 TAGAAAAGTAGTGATTTTTTAATTAA
127 AAGAAAAGTAGTGATTTTTTAATTAA
* * *
55861838 AAAAAAAGAAAGTTTAGATTTTTAAGAATAAAAATCTGTTTTTTAGTCGTTTTAAAGGAGAAGTT
1 AAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAGAAGTT
*
55861903 TAAAATTTTAAAACAAAGTTTTGATCTTTTTCAATTATTTCAAAATAAAGTTTTGATCTTTAAGA
66 TAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATCTTTAAGA
55861968 AAAGTAGTGATTTTTT
131 AAAGTAGTGATTTTTT
55861984 TAAAAATAAA
Statistics
Matches: 135, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
152 34 0.25
153 19 0.14
154 36 0.27
155 46 0.34
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.43
Consensus pattern (152 bp):
AAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAGAAGTT
TAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATCTTTAAGA
AAAGTAGTGATTTTTTAATTAA
Found at i:55865183 original size:16 final size:16
Alignment explanation
Indices: 55865164--55865215 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
55865154 AATTTAATAC
55865164 TTATTTAGATAGTATT
1 TTATTTAGATAGTATT
* ** * *
55865180 TTATTAATTTAATA-C
1 TTATTTAGATAGTATT
55865195 TTATTTAGATAGTATT
1 TTATTTAGATAGTATT
55865211 TTATT
1 TTATT
55865216 AATTTAATAT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (16 bp):
TTATTTAGATAGTATT
Found at i:55865190 original size:31 final size:31
Alignment explanation
Indices: 55865152--55865224 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
55865142 AATATTAGAT
55865152 TTAATTTAATACTTATTTAGATAGTATTTTA
1 TTAATTTAATACTTATTTAGATAGTATTTTA
55865183 TTAATTTAATACTTATTTAGATAGTATTTTA
1 TTAATTTAATACTTATTTAGATAGTATTTTA
55865214 TTAATTTAATA
1 TTAATTTAATA
55865225 TTAAATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
TTAATTTAATACTTATTTAGATAGTATTTTA
Found at i:55865226 original size:11 final size:11
Alignment explanation
Indices: 55865152--55865294 Score: 54
Period size: 11 Copynumber: 13.0 Consensus size: 11
55865142 AATATTAGAT
55865152 TTAATTTAATA
1 TTAATTTAATA
55865163 CTT-ATTTAGATA
1 -TTAATTTA-ATA
*
55865175 GT-ATTT--TA
1 TTAATTTAATA
55865183 TTAATTTAATA
1 TTAATTTAATA
55865194 CTT-ATTTAGATA
1 -TTAATTTA-ATA
*
55865206 GT-ATTT--TA
1 TTAATTTAATA
55865214 TTAATTTAATA
1 TTAATTTAATA
* *
55865225 TTAAATTTTTATC
1 TT-AA-TTTAATA
55865238 TTAATATTAA-A
1 TTAAT-TTAATA
55865249 TTTAATTTAATA
1 -TTAATTTAATA
* *
55865261 TTTATCTTATAGA
1 TTAAT-TTA-ATA
* *
55865274 TAAATTT-CTA
1 TTAATTTAATA
55865284 TTAATTTAATA
1 TTAATTTAATA
55865295 GGTTTAATAT
Statistics
Matches: 98, Mismatches: 16, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
8 6 0.06
9 8 0.08
10 7 0.07
11 37 0.38
12 28 0.29
13 12 0.12
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:55868092 original size:27 final size:27
Alignment explanation
Indices: 55868053--55868147 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
55868043 ACATGCTAGA
*
55868053 AAAATGGAA-CCTTTATAGCAATCTGTG
1 AAAAT-GAAGCCTTTATAGCAATCTATG
* * *
55868080 AAAAGGGAGCCTTGATAGCAATCTATG
1 AAAATGAAGCCTTTATAGCAATCTATG
*
55868107 AAAATGAAGCCTTTATGGCAATCTATG
1 AAAATGAAGCCTTTATAGCAATCTATG
55868134 AAAATGAAGCCTTT
1 AAAATGAAGCCTTT
55868148 GTGGTGCACT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 2 0.03
27 57 0.97
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (27 bp):
AAAATGAAGCCTTTATAGCAATCTATG
Found at i:55870744 original size:42 final size:42
Alignment explanation
Indices: 55870634--55870781 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
55870624 TACCATACCA
* * * *
55870634 ATGCCATATCCCAGATATGGTCTTATATG-GGATCTCGTATCA
1 ATGCCATATCCCAGATATGGTCTTACATGAAG-TCTCATATCG
* * * *
55870676 ATGCCAAAAGCCTA-ACCATGGTCTTACATGAAGTCTCATATCG
1 ATGCC-ATATCCCAGA-TATGGTCTTACATGAAGTCTCATATCG
* ** *
55870719 ATGCCATATCCTAGATATGGTCTTACACAAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACATGAAGTCTCATATCG
*
55870761 ATGTCATATCCCAGATATGGT
1 ATGCCATATCCCAGATATGGT
55870782 TTTATACATA
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 54 0.63
43 31 0.36
44 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAGTCTCATATCG
Found at i:55870795 original size:42 final size:42
Alignment explanation
Indices: 55870693--55870797 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
55870683 AAGCCTAACC
** * *
55870693 ATGGTCTTACATGAAGTCTCATATCGATGCCATATCCTAGAT
1 ATGGTCTTACACAAAGTCTCATATAGATGCCATATCCCAGAT
*
55870735 ATGGTCTTACACAAAGTCTCATATAGATGTCATATCCCAGAT
1 ATGGTCTTACACAAAGTCTCATATAGATGCCATATCCCAGAT
* * *
55870777 ATGGTTTTATACATAGTCTCA
1 ATGGTCTTACACAAAGTCTCA
55870798 GTAACCCTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (42 bp):
ATGGTCTTACACAAAGTCTCATATAGATGCCATATCCCAGAT
Found at i:55875535 original size:16 final size:16
Alignment explanation
Indices: 55875514--55875572 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 16
55875504 AAGTCCTACG
55875514 CAATATAAACCCAATC
1 CAATATAAACCCAATC
55875530 CAATATATATAAACCCAA-C
1 C---A-ATATAAACCCAATC
55875549 TCAATATAAACCCAATC
1 -CAATATAAACCCAATC
55875566 CAATATA
1 CAATATA
55875573 TATAAACCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 20 0.54
17 2 0.05
19 2 0.05
20 13 0.35
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
CAATATAAACCCAATC
Found at i:55875541 original size:20 final size:20
Alignment explanation
Indices: 55875516--55875583 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
55875506 GTCCTACGCA
55875516 ATATAAACCCAATCCAATAT
1 ATATAAACCCAATCCAATAT
55875536 ATATAAACCCAA--C--TCA-
1 ATATAAACCCAATCCAAT-AT
55875552 ATATAAACCCAATCCAATAT
1 ATATAAACCCAATCCAATAT
55875572 ATATAAACCCAA
1 ATATAAACCCAA
55875584 CTCGACCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
16 13 0.31
17 1 0.02
18 2 0.05
19 1 0.02
20 25 0.60
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.22
Consensus pattern (20 bp):
ATATAAACCCAATCCAATAT
Found at i:55875555 original size:36 final size:36
Alignment explanation
Indices: 55875514--55875586 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
55875504 AAGTCCTACG
55875514 CAATATAAACCCAATCCAATATATATAAACCCAACT
1 CAATATAAACCCAATCCAATATATATAAACCCAACT
55875550 CAATATAAACCCAATCCAATATATATAAACCCAACT
1 CAATATAAACCCAATCCAATATATATAAACCCAACT
55875586 C
1 C
55875587 GACCCAATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (36 bp):
CAATATAAACCCAATCCAATATATATAAACCCAACT
Found at i:55882110 original size:2 final size:2
Alignment explanation
Indices: 55882103--55882129 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55882093 TGGTTCTGAT
55882103 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
55882130 GCGCTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55888441 original size:22 final size:22
Alignment explanation
Indices: 55888416--55888460 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55888406 GATAGTTTTG
55888416 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
55888438 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
55888460 T
1 T
55888461 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:55892169 original size:22 final size:22
Alignment explanation
Indices: 55892141--55892185 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55892131 AGGGGGAGTG
55892141 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
55892163 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
55892185 T
1 T
55892186 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:55894469 original size:14 final size:14
Alignment explanation
Indices: 55894447--55894476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55894437 TTATAACTTG
*
55894447 GAAAGAGAAAAAAA
1 GAAAAAGAAAAAAA
55894461 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
55894475 GA
1 GA
55894477 GTTTAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:55895729 original size:4 final size:4
Alignment explanation
Indices: 55895704--55895745 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
55895694 AAAGGAAAAG
55895704 AACA AA-A AA-A AA-A AACA CAACA AACA AACA AACA AACA AACA
1 AACA AACA AACA AACA AACA -AACA AACA AACA AACA AACA AACA
55895746 CCCTAGTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 9 0.25
4 23 0.64
5 4 0.11
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:55900529 original size:27 final size:27
Alignment explanation
Indices: 55900499--55900583 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
55900489 TAGGAAAAGA
*
55900499 AAATGCTTATGTTATTAGTGTGGTGCC
1 AAATGCTTATGTTATTGGTGTGGTGCC
55900526 AAATGCTTATGTTATTGGTGTGGTGCC
1 AAATGCTTATGTTATTGGTGTGGTGCC
* *
55900553 AAATACTTATGTTATTGGTGTAGTGCC
1 AAATGCTTATGTTATTGGTGTGGTGCC
55900580 AAAT
1 AAAT
55900584 TTGGTGAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (27 bp):
AAATGCTTATGTTATTGGTGTGGTGCC
Found at i:55905163 original size:13 final size:14
Alignment explanation
Indices: 55905147--55905177 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55905137 GTTAAAAGTG
55905147 TAAATTAA-TAAAA
1 TAAATTAAGTAAAA
55905160 TAAATTAAGTAAAA
1 TAAATTAAGTAAAA
55905174 TAAA
1 TAAA
55905178 AATAACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAATTAAGTAAAA
Found at i:55907640 original size:24 final size:25
Alignment explanation
Indices: 55907595--55907646 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
55907585 TTATATTCCC
55907595 TATTACGCACATATCTTAATAC-TA
1 TATTACGCACATATCTTAATACATA
* *
55907619 TATTACGTACAT-TTTTACATACATA
1 TATTACGCACATATCTTA-ATACATA
55907644 TAT
1 TAT
55907647 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (25 bp):
TATTACGCACATATCTTAATACATA
Found at i:55908037 original size:40 final size:40
Alignment explanation
Indices: 55907988--55908070 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
55907978 TTATTATTAT
55907988 TTTCATTTTCGTTATCATCGTCATTTTTATTTTTGCCATG
1 TTTCATTTTCGTTATCATCGTCATTTTTATTTTTGCCATG
*
55908028 TTTCGTTTTCGTTATCATCGTCATTTTTATTTTTGCCATG
1 TTTCATTTTCGTTATCATCGTCATTTTTATTTTTGCCATG
55908068 TTT
1 TTT
55908071 AACATTTGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.13, C:0.17, G:0.11, T:0.59
Consensus pattern (40 bp):
TTTCATTTTCGTTATCATCGTCATTTTTATTTTTGCCATG
Found at i:55912337 original size:20 final size:20
Alignment explanation
Indices: 55912298--55912337 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55912288 AAATAGTGAG
*
55912298 ATTTTATTTTCTAAGTATAA
1 ATTTTATTTTCTAAGAATAA
* *
55912318 ATTTTATTTTTTGAGAATAA
1 ATTTTATTTTCTAAGAATAA
55912338 CAAATCTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTATTTTCTAAGAATAA
Found at i:55917781 original size:18 final size:17
Alignment explanation
Indices: 55917756--55917794 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
55917746 TTTATGTAAC
55917756 TATT-ACTTTTAATAATT
1 TATTAACTTTTAA-AATT
*
55917773 TATTAACTTTTAACATT
1 TATTAACTTTTAAAATT
55917790 TATTA
1 TATTA
55917795 TACATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAACTTTTAAAATT
Found at i:55923260 original size:39 final size:39
Alignment explanation
Indices: 55923202--55923321 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
55923192 GATATTGATG
* * *
55923202 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
55923241 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
* * *
55923280 TATGTCCGGGCTTAAGGTCCGCAGGCTACGTGCTGAAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
55923319 TAT
1 TAT
55923322 GTTCGGGCTA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
Found at i:55923322 original size:39 final size:39
Alignment explanation
Indices: 55923206--55923354 Score: 183
Period size: 39 Copynumber: 3.8 Consensus size: 39
55923196 TTGATGTATA
* * * *
55923206 TCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATA
1 TCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATG
55923245 TCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATG
1 TCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATG
* *
55923284 TCCGGGCTTAAGGTCCGCAGGCTACGTGCTGAAAATATG
1 TCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATG
* * * * *
55923323 TTCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGG
1 TCCGGACTTAAGGT-CCGCAGGCTACGTGCTGG
55923355 TATTATACCG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 5 0.05
39 93 0.95
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (39 bp):
TCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATG
Found at i:55924837 original size:16 final size:16
Alignment explanation
Indices: 55924783--55924837 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
55924773 CAACAAAATA
*
55924783 AAAAAAATTAA-AATT
1 AAAAAAATAAACAATT
* * *
55924798 ACAAACAGAAACAA-T
1 AAAAAAATAAACAATT
*
55924813 AATAAAATAAACAATT
1 AAAAAAATAAACAATT
55924829 AAAAAAATA
1 AAAAAAATA
55924838 TGAATAATCT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAACAATT
Found at i:55924906 original size:21 final size:20
Alignment explanation
Indices: 55924880--55924928 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
55924870 AAGGATGAAT
55924880 AAATAATAA-TAAATAAATAA
1 AAATAATAAGTAAATAAAT-A
55924900 CAAATAA-AAGTAAATAAATA
1 -AAATAATAAGTAAATAAATA
55924920 AAATAATAA
1 AAATAATAA
55924929 AAAAATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAATAAGTAAATAAATA
Found at i:55928336 original size:27 final size:24
Alignment explanation
Indices: 55928295--55928362 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
55928285 TAGTAAATGC
*
55928295 TAATATTTA-AAATAAATACTAATA
1 TAATATATATAAATAAATACT-ATA
*
55928319 TATATATATATAATATAAATAGTATA
1 TA-ATATATATAA-ATAAATACTATA
*
55928345 TAATTTA-ATAAATAAATA
1 TAATATATATAAATAAATA
55928363 ATTATTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.18
24 6 0.16
25 10 0.26
26 7 0.18
27 8 0.21
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
TAATATATATAAATAAATACTATA
Found at i:55928355 original size:24 final size:24
Alignment explanation
Indices: 55928328--55928376 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
55928318 ATATATATAT
55928328 ATAATATAAAT-AGTATATAATTTA
1 ATAA-ATAAATAAGTATATAATTTA
* *
55928352 ATAAATAAATAATTATTTAATTTA
1 ATAAATAAATAAGTATATAATTTA
55928376 A
1 A
55928377 ATTAAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAAATAAATAAGTATATAATTTA
Found at i:55929337 original size:309 final size:310
Alignment explanation
Indices: 55928774--55929352 Score: 729
Period size: 309 Copynumber: 1.9 Consensus size: 310
55928764 TGGAAATTAC
* * * *
55928774 GTATTTAAAATATAGATGTGTGCTTAAAAATAACATAAGATAAATAATGAAACGTATGATTTGAA
1 GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
* * * *
55928839 ACTAACTAATAATAACATATGAAATATATACGATATTAAAATAAGAAAAATTAGATTTAATTGTG
66 ACTAAATAATAATAACATATGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATTATA
** * * *
55928904 AGTAAAACGAAATTTAAACACAAAAATACATCACGCTAAGAATACTAAATGAATATAATTGTTTA
131 AGTAAAACGAAATCCAAACACAAAAATACATCACGCTAAGAATACTAAATAAATACAATTATTTA
* * * ** * * *
55928969 TGATGGTGTTATCATCAATCCTGAGTTCGTGTCGAGTTAATTTGTGATATCAACTCAATCAACAA
196 TCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATCAACAA
55929034 CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAAGTCAT
261 CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAAGTCAT
* * * * * *
55929084 GTATTTAAAATACAAATTTGTGTTTAAACATAGCGTAAAATAAATAATAAAATGTATGATTTGAA
1 GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
* * *
55929149 ACTAATTAATAATAATAACATTTGAAATATGTATGATATTAAAAT-A-AAAAA-T-GATTAAATT
66 ACT-A--AATAATAATAACATATGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATT
* * * *
55929210 ATAAGTAAAACGAAATCCAAACA-AATGAATACATCA-GATTAAGACTACTAAATAAATACGATT
128 ATAAGTAAAACGAAATCCAAACACAA-AAATACATCACG-CTAAGAATACTAAATAAATACAATT
* * * *
55929273 ATTTATCTTGGTGCTGTCATCAATCCTAAGTAAGTGTTGAGTTAACTTGTGACACCATCTCAATC
191 ATTTATCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATC
55929338 AACAACATTATTAAT
256 AACAACATTATTAAT
55929353 ATATACAATT
Statistics
Matches: 226, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
308 3 0.01
309 123 0.54
310 59 0.26
311 6 0.03
312 1 0.00
313 34 0.15
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (310 bp):
GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
ACTAAATAATAATAACATATGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATTATA
AGTAAAACGAAATCCAAACACAAAAATACATCACGCTAAGAATACTAAATAAATACAATTATTTA
TCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATCAACAA
CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAAGTCAT
Found at i:55930516 original size:17 final size:18
Alignment explanation
Indices: 55930494--55930528 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55930484 TAAAAAGTTG
55930494 TTATAAG-GTTAGATAAA
1 TTATAAGTGTTAGATAAA
*
55930511 TTATAAGTGTTGGATAAA
1 TTATAAGTGTTAGATAAA
55930529 AGTCTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (18 bp):
TTATAAGTGTTAGATAAA
Found at i:55931273 original size:30 final size:30
Alignment explanation
Indices: 55931237--55931298 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
55931227 TTCATCACTA
55931237 ATAATAACTTCTTAGCATTACAACTCTTTT
1 ATAATAACTTCTTAGCATTACAACTCTTTT
*
55931267 ATAATAACTTCTTAGCGTTACAACTCTTTT
1 ATAATAACTTCTTAGCATTACAACTCTTTT
55931297 AT
1 AT
55931299 TATTTTCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (30 bp):
ATAATAACTTCTTAGCATTACAACTCTTTT
Found at i:55932734 original size:2 final size:2
Alignment explanation
Indices: 55932727--55932767 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
55932717 AGTAAAAATA
55932727 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55932768 CAAATTTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55938382 original size:19 final size:19
Alignment explanation
Indices: 55938336--55938383 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
55938326 GTATATATTT
55938336 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
55938354 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
55938373 TAAGTTTTATT
1 TAAATTTTATT
55938384 CATATTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:55938487 original size:42 final size:42
Alignment explanation
Indices: 55938406--55938489 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
55938396 ATATTTTATT
* *
55938406 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
1 TTATATTTTAATAGTTTATTAGAATAAGGGAACTATTTTCCC
*
55938448 TTATATTTTAATAGTTTATTAGAATAAGGGAATTATTTTCCC
1 TTATATTTTAATAGTTTATTAGAATAAGGGAACTATTTTCCC
55938490 AATTAGGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (42 bp):
TTATATTTTAATAGTTTATTAGAATAAGGGAACTATTTTCCC
Found at i:55939131 original size:197 final size:197
Alignment explanation
Indices: 55938796--55939197 Score: 759
Period size: 197 Copynumber: 2.0 Consensus size: 197
55938786 TGGTCGCAGT
*
55938796 CCGTAAAATTAGCAATTGATGGGAGCGGCAAGCTAAGTCATTTAAATGGAGAAGTCAAGCAACCA
1 CCGTAAAATTAGCAATTGATGGGAGCGGCAAGCTAAGTCATTTAAATGAAGAAGTCAAGCAACCA
*
55938861 CAGGTGCGCGATCCAAAGATAGCCAGTGGAGGTTAGAAAATTCTATGATAATTGCGTGGCTTATT
66 CAGGTGCGCGATCCAAAGATAGCCAGTGGAGGTTAGAAAATTCTATGATAATTGCGTAGCTTATT
55938926 AATTCCATGGAAGCATCCATAGGTAAACCTTTTCTTTTTCTCCCAACTGCTAAACATGTTTGGGA
131 AATTCCATGGAAGCATCCATAGGTAAACCTTTTCTTTTTCTCCCAACTGCTAAACATGTTTGGGA
55938991 TG
196 TG
55938993 CCGTAAAATTAGCAATTGATGGGAGCGGCAAGCTAAGTCATTTAAATGAAGAAGTCAAGCAACCA
1 CCGTAAAATTAGCAATTGATGGGAGCGGCAAGCTAAGTCATTTAAATGAAGAAGTCAAGCAACCA
*
55939058 CAGGTGGGCGATCCAAAGATAGCCAGTGGAGGTTAGAAAATTCTATGATAATTGCGTAGCTTATT
66 CAGGTGCGCGATCCAAAGATAGCCAGTGGAGGTTAGAAAATTCTATGATAATTGCGTAGCTTATT
*
55939123 AATTCCATGGAAGCATCCATAGGTAAACTTTTTCTTTTTCTCCCAACTGCTAAACATGTTTGGGA
131 AATTCCATGGAAGCATCCATAGGTAAACCTTTTCTTTTTCTCCCAACTGCTAAACATGTTTGGGA
55939188 TG
196 TG
*
55939190 CTGTAAAA
1 CCGTAAAA
55939198 GACATCTATT
Statistics
Matches: 200, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 200 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (197 bp):
CCGTAAAATTAGCAATTGATGGGAGCGGCAAGCTAAGTCATTTAAATGAAGAAGTCAAGCAACCA
CAGGTGCGCGATCCAAAGATAGCCAGTGGAGGTTAGAAAATTCTATGATAATTGCGTAGCTTATT
AATTCCATGGAAGCATCCATAGGTAAACCTTTTCTTTTTCTCCCAACTGCTAAACATGTTTGGGA
TG
Found at i:55941532 original size:13 final size:13
Alignment explanation
Indices: 55941514--55941539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55941504 AAGTGAAAGG
55941514 AGGCTATTTTAGA
1 AGGCTATTTTAGA
55941527 AGGCTATTTTAGA
1 AGGCTATTTTAGA
55941540 GGAGATGTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AGGCTATTTTAGA
Found at i:55943190 original size:42 final size:42
Alignment explanation
Indices: 55943109--55943192 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
55943099 ATATTTTATT
55943109 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
* *
55943151 TTATGTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
55943193 AATTAGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (42 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
Found at i:55943719 original size:20 final size:20
Alignment explanation
Indices: 55943696--55943769 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
55943686 AAATTACAAA
*
55943696 AAAAAAATCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
55943716 AAAAAATTGAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
55943736 -TAAAATTCAAAAT-A-TTT
1 AAAAAATTCAAAATAATTTT
55943753 ATAAAAATTCTAAAATA
1 A-AAAAATTC-AAAATA
55943770 TGTATTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.07
18 1 0.02
19 18 0.40
20 23 0.51
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:55943810 original size:18 final size:18
Alignment explanation
Indices: 55943775--55943810 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55943765 AAATATGTAT
*
55943775 TTTTAAAAAAATTATAAA
1 TTTTAAAAAAAATATAAA
*
55943793 TTTTAAAAAAAATCTAAA
1 TTTTAAAAAAAATATAAA
55943811 AAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTTAAAAAAAATATAAA
Found at i:55944179 original size:21 final size:21
Alignment explanation
Indices: 55944153--55944192 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55944143 ACCTTATCTA
*
55944153 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
55944174 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
55944193 CATTGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:55955171 original size:14 final size:14
Alignment explanation
Indices: 55955152--55955179 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55955142 TCAATATCAC
55955152 ATGTTTTTCCTTAA
1 ATGTTTTTCCTTAA
55955166 ATGTTTTTCCTTAA
1 ATGTTTTTCCTTAA
55955180 CCTATAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
ATGTTTTTCCTTAA
Found at i:55956784 original size:19 final size:19
Alignment explanation
Indices: 55956760--55956798 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55956750 ATTAAATTAA
55956760 ATAATTGGACCCAATACAT
1 ATAATTGGACCCAATACAT
55956779 ATAATTGGACCCAATACAT
1 ATAATTGGACCCAATACAT
55956798 A
1 A
55956799 AAAGGCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
ATAATTGGACCCAATACAT
Found at i:55959103 original size:20 final size:20
Alignment explanation
Indices: 55959075--55959114 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55959065 CTGATGAGAT
55959075 ATCTCATTATTATATATTGG
1 ATCTCATTATTATATATTGG
*
55959095 ATCTTATTATTATATATTGG
1 ATCTCATTATTATATATTGG
55959115 CTATTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (20 bp):
ATCTCATTATTATATATTGG
Found at i:55959829 original size:16 final size:16
Alignment explanation
Indices: 55959798--55959842 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
55959788 AAATAACATA
55959798 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
55959812 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
55959828 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
55959843 CCCGATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:55959840 original size:17 final size:16
Alignment explanation
Indices: 55959796--55959842 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
55959786 ATAAATAACA
55959796 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
55959811 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
55959827 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
55959843 CCCGATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:55961947 original size:27 final size:27
Alignment explanation
Indices: 55961906--55961964 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
55961896 AGAACTGTTT
* *
55961906 CTTCAGAGTTTGCCATATGTACTATTC
1 CTTCAGAGTTCGCCATACGTACTATTC
55961933 CTTCAGAGTTCGCCATACGTACTATTC
1 CTTCAGAGTTCGCCATACGTACTATTC
55961960 CTTCA
1 CTTCA
55961965 ATGTTAGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (27 bp):
CTTCAGAGTTCGCCATACGTACTATTC
Found at i:55962025 original size:53 final size:53
Alignment explanation
Indices: 55961960--55962069 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 53
55961950 CGTACTATTC
*
55961960 CTTCAATGTTAGCAACACATATCATTCCTTCGA-GGTTTGTCACACTTACCATG
1 CTTCAATGTTAGCAACACATATCATT-CTTCGAGGGTTGGTCACACTTACCATG
* * * * *
55962013 CTTCAGAT-TTAGCTATACATATCATTCTTCTAGGGTTGGTCATACTTACCATT
1 CTTCA-ATGTTAGCAACACATATCATTCTTCGAGGGTTGGTCACACTTACCATG
55962066 CTTC
1 CTTC
55962070 TCCTTTAGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
52 5 0.10
53 42 0.86
54 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (53 bp):
CTTCAATGTTAGCAACACATATCATTCTTCGAGGGTTGGTCACACTTACCATG
Found at i:55962346 original size:27 final size:27
Alignment explanation
Indices: 55962154--55962345 Score: 199
Period size: 27 Copynumber: 7.1 Consensus size: 27
55962144 AGGCATTCTT
* * *
55962154 TTTCATAGATCGCCATAAAGGCTTTAA
1 TTTCATAGATTGCCACAAAGGCTTTCA
* *
55962181 TTTCATAGATTTCCACAAAGGCTTTAA
1 TTTCATAGATTGCCACAAAGGCTTTCA
* * * * *
55962208 TTTTATAAATCT-TCACAAATGCTTCCA
1 TTTCATAGAT-TGCCACAAAGGCTTTCA
* * *
55962235 TTTCAGAGATTGTCACAAAGGCTTCCA
1 TTTCATAGATTGCCACAAAGGCTTTCA
*
55962262 TTTCATAGATTGCCACAAAGGCTTCCA
1 TTTCATAGATTGCCACAAAGGCTTTCA
*
55962289 CTTCATAGATTGCCACAAAGGC-TTCTA
1 TTTCATAGATTGCCACAAAGGCTTTC-A
* *
55962316 TTTTATAGATTGCCACAAAGACTTTCA
1 TTTCATAGATTGCCACAAAGGCTTTCA
55962343 TTT
1 TTT
55962346 TCTAATGTGT
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.02
27 134 0.95
28 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (27 bp):
TTTCATAGATTGCCACAAAGGCTTTCA
Found at i:55966291 original size:38 final size:39
Alignment explanation
Indices: 55966248--55966333 Score: 149
Period size: 38 Copynumber: 2.2 Consensus size: 39
55966238 TTAAATTGTT
55966248 TTTTAATTTTGTTTAATATATGTTA-TTTAGATTAATTAA
1 TTTTAATTTTGTTTAATATATGTTATTTTAG-TTAATTAA
55966287 -TTTAATTTTGTTTAATATATGTTATTTTAGTTAATTAA
1 TTTTAATTTTGTTTAATATATGTTATTTTAGTTAATTAA
55966325 TTTTAATTT
1 TTTTAATTT
55966334 GGTTCTTCGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
38 32 0.71
39 13 0.29
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (39 bp):
TTTTAATTTTGTTTAATATATGTTATTTTAGTTAATTAA
Found at i:55966314 original size:19 final size:19
Alignment explanation
Indices: 55966253--55966314 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
55966243 TTGTTTTTTA
55966253 ATTTTGTTTAATATATGTT
1 ATTTTGTTTAATATATGTT
* *
55966272 ATTTAGATTAAT-TAAT-TT
1 ATTTTGTTTAATAT-ATGTT
55966290 AATTTTGTTTAATATATGTT
1 -ATTTTGTTTAATATATGTT
55966310 ATTTT
1 ATTTT
55966315 AGTTAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.09
19 29 0.83
20 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
ATTTTGTTTAATATATGTT
Found at i:55966320 original size:19 final size:20
Alignment explanation
Indices: 55966260--55966321 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
55966250 TTAATTTTGT
55966260 TTAATATATGTTA-TTTAGA
1 TTAATATATGTTATTTTAGA
*
55966279 TTAAT-TAAT-TTAATTTT-GT
1 TTAATAT-ATGTT-ATTTTAGA
55966298 TTAATATATGTTATTTTAG-
1 TTAATATATGTTATTTTAGA
55966317 TTAAT
1 TTAAT
55966322 TAATTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
18 3 0.08
19 26 0.72
20 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTAATATATGTTATTTTAGA
Found at i:55971120 original size:40 final size:40
Alignment explanation
Indices: 55971065--55971202 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
55971055 CAGATGATAA
55971065 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55971105 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
55971145 CCAGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
55971185 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55971203 TACTTGATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 16 0.17
40 76 0.83
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55973105 original size:4 final size:4
Alignment explanation
Indices: 55973010--55973088 Score: 140
Period size: 4 Copynumber: 19.8 Consensus size: 4
55973000 GAGAAGTTAC
*
55973010 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
55973058 TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
55973089 GAAGCATTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:55977290 original size:26 final size:27
Alignment explanation
Indices: 55977261--55977321 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
55977251 GCCAGAAGTT
*
55977261 TTCCTTTACA-A-ATAGCCACGAAGGTG
1 TTCCTTTACAGATATAGCCACGAAGG-C
*
55977287 TTCCTTTTCAGATATAGCCACGAAGGC
1 TTCCTTTACAGATATAGCCACGAAGGC
55977314 TTCCTTTA
1 TTCCTTTA
55977322 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 9 0.30
27 8 0.27
28 13 0.43
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (27 bp):
TTCCTTTACAGATATAGCCACGAAGGC
Found at i:55977578 original size:59 final size:57
Alignment explanation
Indices: 55977452--55977587 Score: 148
Period size: 59 Copynumber: 2.4 Consensus size: 57
55977442 TGCTATAAGG
* * *
55977452 GCTTACCTTTCTATAGTTTTGCCACGAAGGCTATCCTTTAACAGATTCAACACAAAG
1 GCTTACCTTTCTAAAGTTTTACCACGAAGGCTATCCTTTAACAGATTCAACACAAAA
* * * * * *
55977509 GCTTACCTTTCTAAAGTTTTACCA-GAAAGGTTGTCTTCTTTAATAGGTTCACCATAAAA
1 GCTTACCTTTCTAAAGTTTTACCACG-AAGGCTATC--CTTTAACAGATTCAACACAAAA
*
55977568 GCTTACCTTTCCAAAGTTTT
1 GCTTACCTTTCTAAAGTTTT
55977588 TCTATAAAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
56 1 0.02
57 29 0.44
59 36 0.55
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (57 bp):
GCTTACCTTTCTAAAGTTTTACCACGAAGGCTATCCTTTAACAGATTCAACACAAAA
Found at i:55977863 original size:53 final size:52
Alignment explanation
Indices: 55977752--55977904 Score: 175
Period size: 53 Copynumber: 2.9 Consensus size: 52
55977742 AATTTTTTCC
* ** *
55977752 CCATATGATGCTATAACCCACTAGTTATAGTCTTACACGATATGGTATTATTT
1 CCATATGATGCCATAACCCACTAGTTACGGTCTTACACGATATGGT-CTATTT
* *
55977805 TCATATGATGCCATAACCCACTAGTTACGGTCTTACACAATATGGTCTACTTT
1 CCATATGATGCCATAACCCACTAGTTACGGTCTTACACGATATGGTCTA-TTT
* * *
55977858 CCATATGAT-CCTACAACCCA-TCAGTTACGATCTTACATGATATGGTC
1 CCATATGATGCC-ATAACCCACT-AGTTACGGTCTTACACGATATGGTC
55977905 CTTTAGTGCG
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 5 0.06
53 81 0.94
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (52 bp):
CCATATGATGCCATAACCCACTAGTTACGGTCTTACACGATATGGTCTATTT
Done.