Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_pilon, whole genome shotgun sequence
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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 28
Found at i:3805934 original size:43 final size:43
Alignment explanation
Indices: 3805864--3805946 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
3805854 GTTTTCATAC
* * * * *
3805864 AAATGTCGCTATAGAGTTGGACAATAGTGGCATTTTGTTTTGT
1 AAATGTCGCAATAAAGTAGCACAATAGTGGCATTTGGTTTTGT
* *
3805907 AAATGTCGCAATAAAGTAGCACTATAGTGGCGTTTGGTTT
1 AAATGTCGCAATAAAGTAGCACAATAGTGGCATTTGGTTT
3805947 ACAAATGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (43 bp):
AAATGTCGCAATAAAGTAGCACAATAGTGGCATTTGGTTTTGT
Found at i:3806138 original size:21 final size:21
Alignment explanation
Indices: 3806112--3806156 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
3806102 CCAGCTTCGC
3806112 GCCATCAGTCACGACTGTCGT
1 GCCATCAGTCACGACTGTCGT
3806133 GCCATCAGTCACGACTGTCGT
1 GCCATCAGTCACGACTGTCGT
3806154 GCC
1 GCC
3806157 TTCATCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.22
Consensus pattern (21 bp):
GCCATCAGTCACGACTGTCGT
Found at i:3807820 original size:19 final size:18
Alignment explanation
Indices: 3807774--3807825 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
3807764 ATATGATCAA
* *
3807774 ATAAAAGAAAT-TAAATT
1 ATAAAATAAATATAAAGT
3807791 ATAAAACTAAATATAAAGT
1 ATAAAA-TAAATATAAAGT
*
3807810 ATTAAAATAAAGATAA
1 A-TAAAATAAATATAA
3807826 TATTCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 14 0.48
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
ATAAAATAAATATAAAGT
Found at i:3809064 original size:3 final size:3
Alignment explanation
Indices: 3809050--3809129 Score: 65
Period size: 3 Copynumber: 27.0 Consensus size: 3
3809040 GTTGTATCTG
* * * * *
3809050 TAA TAA -AA TAA TAA TAA TAA TAT TAA TAA CAA AAA AAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3809097 TAA TAA AAA TAA AAA TTA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
3809130 AACCAAATGT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.93
4 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:3809094 original size:24 final size:23
Alignment explanation
Indices: 3809050--3809131 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
3809040 GTTGTATCTG
* *
3809050 TAATAAAATAATAATAATAATAT
1 TAATAAAAAAAAAATAATAATAT
*
3809073 TAATAACAAAAAAAATAATAATAG
1 TAATAA-AAAAAAAATAATAATAT
*
3809097 TAATAAAAATAAAAATTATAA-AT
1 TAATAAAAA-AAAAATAATAATAT
*
3809120 ATAATAATAAAA
1 -TAATAAAAAAA
3809132 CCAAATGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.24
24 38 0.76
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (23 bp):
TAATAAAAAAAAAATAATAATAT
Found at i:3809621 original size:113 final size:113
Alignment explanation
Indices: 3809477--3810068 Score: 1085
Period size: 113 Copynumber: 5.2 Consensus size: 113
3809467 TGCAAAAGAG
*
3809477 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
** *
3809542 TCGACCTGGCAATATTGATCCATCGAATGATGAATTCAAGCGAAAAGT
66 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
*
3809590 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
3809655 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
66 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
3809703 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* * *
3809768 TCGTCCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGT
66 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
*
3809816 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
3809881 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
66 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
*
3809929 TGAACAAATTCTTCTCATTATGAGCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
3809994 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAATT
66 TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
3810042 TGAACAAATTCTTCTCATTATGAACTT
1 TGAACAAATTCTTCTCATTATGAACTT
3810069 TTCCACTAGG
Statistics
Matches: 464, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 464 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
TCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGT
Found at i:3810355 original size:302 final size:304
Alignment explanation
Indices: 3809814--3810370 Score: 865
Period size: 302 Copynumber: 1.8 Consensus size: 304
3809804 CAAGCGAAAA
*
3809814 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * ***
3809879 ACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTGAAAAGTTGAACAAATTCTTCT
66 ACTC-ACCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCT
*
3809944 CATTATGAGCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGC
130 CATTATGA-CATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGC
* ** * *
3810009 TGATCCATCGAATGATGAATTCAAGTGAAAATTTGAACAAATTCTTCTCATTATGAACTTTTCCA
194 TGATCCATCAAATGATGAATTCAAGACAAAAGTCGAACAAATTCTTCTCATTATGAACTTTTCCA
3810074 CTAGGGATGATAATTTGTCTCCTTTTGTAATGTAATTTGGAAAAGG
259 CTAGGGATGATAATTTGTCTCCTTTTGTAATGTAATTTGGAAAAGG
3810120 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
** * *
3810184 ACT-TTCTGGAAAAGTTGATCCATTGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
66 ACTCACCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
*
3810248 ATTATGA-AT-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
131 ATTATGACATCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCGACCTGGCAATG
3810310 CTGATCCATCAAATGATGAATTCAA-ACAAAAGGTCGAACAAATTCTTCTCATTATGAACTT
193 CTGATCCATCAAATGATGAATTCAAGACAAAA-GTCGAACAAATTCTTCTCATTATGAACTT
3810371 CTTCTTCCTT
Statistics
Matches: 230, Mismatches: 17, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
299 11 0.05
300 5 0.02
301 5 0.02
302 84 0.37
303 59 0.26
305 29 0.13
306 37 0.16
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (304 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTCACCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
ATTATGACATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTG
ATCCATCAAATGATGAATTCAAGACAAAAGTCGAACAAATTCTTCTCATTATGAACTTTTCCACT
AGGGATGATAATTTGTCTCCTTTTGTAATGTAATTTGGAAAAGG
Found at i:3810361 original size:112 final size:110
Alignment explanation
Indices: 3810114--3810521 Score: 513
Period size: 112 Copynumber: 3.7 Consensus size: 110
3810104 TGTAATTTGG
* *
3810114 AAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATA-AGTTCTTCTCA
1 AAAA-GGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTTCTTCTTCAGATAGAGTTCTTCTCA
* * **
3810178 TTATGAACTTTCTGGAAAAGTTGATCCATTGAATGATGAATTCAAAC
64 TTATGAACTTCCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
*
3810225 AAAAAGTTGAACAAATTCTTCTCATTATGAA-T-TTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
* *
3810288 TTATGAACTCTACCTGGCAATGCTGATCCATCAAATGATGAATTCAAAC
64 TTATGAACT-T-CCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
*
3810337 AAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATAGAGTTCTTCTCA
* * * ** *
3810401 TTATGAACTTTCTCTGGAAAAGCTGGTCCATCAAGTGATGGATTTGAAT
64 TTATGAAC-TTC-CTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
*
3810450 AAAAGGTTGAACAAATTTTTCTCATTATGAA-T-TTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
3810513 TTATGAACT
64 TTATGAACT
3810522 CTGCCTAGCA
Statistics
Matches: 262, Mismatches: 21, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
107 15 0.06
108 2 0.01
109 11 0.04
110 50 0.19
111 7 0.03
112 81 0.31
113 78 0.30
114 2 0.01
115 5 0.02
116 11 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (110 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATAGAGTTCTTCTCATT
ATGAACTTCCTGGAAAAGCTGATCCATCAAATGATGAATTCAAAC
Found at i:3810462 original size:415 final size:417
Alignment explanation
Indices: 3809701--3810480 Score: 1175
Period size: 415 Copynumber: 1.9 Consensus size: 417
3809691 CAAGTGAAAA
*
3809701 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * * * *
3809766 ACTCGTCCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCT
66 ACTC-TCCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCT
3809831 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGC
130 CATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGC
* ** * *
3809896 TGATCCATCGAATGATGAATTCAAGTGAAAAGTTGAACAAATTCTTCTCATTATGAGCTTCTTCT
194 TGATCCATCAAATGATGAATTCAAGACAAAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCT
* *
3809961 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATG
259 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCGAATGATG
*
3810026 AATTCAAGTGAAAATTTGAACAAATTCTTCTCATTATGAACTTTTCCACTAGGGATGATAATTTG
324 AATTCAAGTGAAAAGTTGAACAAATTCTTCTCATTATGAACTTTTCCACTAGGGATGATAATTTG
3810091 TCTCCTTTTGTAATGTAATTTGGAAAAGG
389 TCTCCTTTTGTAATGTAATTTGGAAAAGG
*
3810120 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * *
3810184 ACT-TTCTGGAAAAGTTGATCCATTGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
66 ACTCTCCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
*
3810248 ATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
131 ATTATGAACTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCGACCTGGCAATG
3810310 CTGATCCATCAAATGATGAATTCAA-ACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTT
193 CTGATCCATCAAATGATGAATTCAAGACAAAA-GTCGAACAAATTCTTCTCATTATGAACTTCTT
** *
3810374 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGGTCCATC-AAGT
257 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CTGGAAAAGCTGATCCATCGAA-T
* * *
3810437 GATGGATTTGAA-T-AAAAGGTTGAACAAATTTTTCTCATTATGAA
320 GAT-GAATTCAAGTGAAAA-GTTGAACAAATTCTTCTCATTATGAA
3810481 TTTCTTCTTC
Statistics
Matches: 328, Mismatches: 25, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
412 11 0.03
413 5 0.02
414 12 0.04
415 168 0.51
416 67 0.20
418 29 0.09
419 36 0.11
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (417 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTCTCCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
ATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTG
ATCCATCAAATGATGAATTCAAGACAAAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCGAATGATGAA
TTCAAGTGAAAAGTTGAACAAATTCTTCTCATTATGAACTTTTCCACTAGGGATGATAATTTGTC
TCCTTTTGTAATGTAATTTGGAAAAGG
Found at i:3810474 original size:225 final size:223
Alignment explanation
Indices: 3810114--3810552 Score: 666
Period size: 225 Copynumber: 2.0 Consensus size: 223
3810104 TGTAATTTGG
* *
3810114 AAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
* *
3810179 TATGAACTTTCTGGAAAAGTTGATCCATTGAATGATGAATTCAAACAAAAAGTTGAACAAATTCT
66 TATGAACTTTCTGGAAAAGCTGATCCATTCAATGATGAATTCAAACAAAAAGTTGAACAAATTCT
*
3810244 TCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAT
131 TCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGCAAT
*
3810309 GCTGATCCATCAAATGATGAATTCAAAC
196 ACTGATCCATCAAATGATGAATTCAAAC
*
3810337 AAAA-GGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCA
* * ** * *
3810401 TTATGAACTTTCTCTGGAAAAGCTGGTCCA-TCAAGTGATGGATTTGAATAAAAGGTTGAACAAA
65 TTATGAAC-TT-TCTGGAAAAGCTGATCCATTCAA-TGATGAATTCAAACAAAAAGTTGAACAAA
* *
3810465 TTTTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTGCCTAG
127 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAG
* **
3810530 CAATATTGATCCATTGAATGATG
192 CAATACTGATCCATCAAATGATG
3810553 GATTTAAATC
Statistics
Matches: 194, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
222 36 0.19
223 32 0.16
224 5 0.03
225 121 0.62
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (223 bp):
AAAAGGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTGGAAAAGCTGATCCATTCAATGATGAATTCAAACAAAAAGTTGAACAAATTCT
TCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGCAAT
ACTGATCCATCAAATGATGAATTCAAAC
Found at i:3810988 original size:22 final size:22
Alignment explanation
Indices: 3810960--3811014 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3810950 CATAAAGCTT
3810960 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3810982 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3811004 TCATCTTTGAA
1 TCATCTTTGAA
3811015 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3811463 original size:54 final size:54
Alignment explanation
Indices: 3811381--3811536 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
3811371 TGAATAGCAG
* *
3811381 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
3811435 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
* * * * *
3811489 GTTCGTAAAGCGTTTGACAACACATTCATCATTTTCTGTTGTTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGC
3811537 CAAGATTTCT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:3818067 original size:14 final size:13
Alignment explanation
Indices: 3818048--3818123 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 13
3818038 AAATGTAAGT
3818048 ATGCAAAGATGCAA
1 ATGCAAA-ATGCAA
*
3818062 ATGCAAACATGAAA
1 ATGCAAA-ATGCAA
* *
3818076 ATG-TAAATACAA
1 ATGCAAAATGCAA
* *
3818088 ACGTAAAAATGCAAA
1 ATG-CAAAATGC-AA
3818103 TATGCAAAATGCAA
1 -ATGCAAAATGCAA
3818117 ATGCAAA
1 ATGCAAA
3818124 TGTAAATATG
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
12 6 0.12
13 9 0.19
14 22 0.46
15 9 0.19
16 2 0.04
ACGTcount: A:0.55, C:0.13, G:0.14, T:0.17
Consensus pattern (13 bp):
ATGCAAAATGCAA
Found at i:3818088 original size:20 final size:20
Alignment explanation
Indices: 3818056--3818104 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3818046 GTATGCAAAG
* *
3818056 ATGCAAATGCAAACATGAAA
1 ATGCAAATACAAACATAAAA
* *
3818076 ATGTAAATACAAACGTAAAA
1 ATGCAAATACAAACATAAAA
3818096 ATGCAAATA
1 ATGCAAATA
3818105 TGCAAAATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (20 bp):
ATGCAAATACAAACATAAAA
Found at i:3818129 original size:35 final size:34
Alignment explanation
Indices: 3818060--3818129 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
3818050 GCAAAGATGC
*
3818060 AAATGCAAACATGAAAATGTAAATACAAACGTAA
1 AAATGCAAACATGAAAATGCAAATACAAACGTAA
* * *
3818094 AAATGCAAATATGCAAAATGCAAATGCAAATGTAA
1 AAATGCAAACATG-AAAATGCAAATACAAACGTAA
3818129 A
1 A
3818130 TATGTGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (34 bp):
AAATGCAAACATGAAAATGCAAATACAAACGTAA
Found at i:3818868 original size:167 final size:167
Alignment explanation
Indices: 3818592--3818912 Score: 642
Period size: 167 Copynumber: 1.9 Consensus size: 167
3818582 CAGCTTGGTG
3818592 ACCCCTATTATCCACTCTTCTGGGGTACTTCCTAGGCCAACATTTTGAAAGGTTTGACTGATCTT
1 ACCCCTATTATCCACTCTTCTGGGGTACTTCCTAGGCCAACATTTTGAAAGGTTTGACTGATCTT
3818657 CTGAAAATCTTCCTGCATGGTTTTCATTTCTGTGCTCAATTTCTTGTTTTGGTCGTTCAAGTCCT
66 CTGAAAATCTTCCTGCATGGTTTTCATTTCTGTGCTCAATTTCTTGTTTTGGTCGTTCAAGTCCT
3818722 TCAAATAACATGCTTGAGCTTCATAAAACCTCCTCTA
131 TCAAATAACATGCTTGAGCTTCATAAAACCTCCTCTA
3818759 ACCCCTATTATCCACTCTTCTGGGGTACTTCCTAGGCCAACATTTTGAAAGGTTTGACTGATCTT
1 ACCCCTATTATCCACTCTTCTGGGGTACTTCCTAGGCCAACATTTTGAAAGGTTTGACTGATCTT
3818824 CTGAAAATCTTCCTGCATGGTTTTCATTTCTGTGCTCAATTTCTTGTTTTGGTCGTTCAAGTCCT
66 CTGAAAATCTTCCTGCATGGTTTTCATTTCTGTGCTCAATTTCTTGTTTTGGTCGTTCAAGTCCT
3818889 TCAAATAACATGCTTGAGCTTCAT
131 TCAAATAACATGCTTGAGCTTCAT
3818913 GGTCGTTCAA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 154 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (167 bp):
ACCCCTATTATCCACTCTTCTGGGGTACTTCCTAGGCCAACATTTTGAAAGGTTTGACTGATCTT
CTGAAAATCTTCCTGCATGGTTTTCATTTCTGTGCTCAATTTCTTGTTTTGGTCGTTCAAGTCCT
TCAAATAACATGCTTGAGCTTCATAAAACCTCCTCTA
Found at i:3818927 original size:39 final size:39
Alignment explanation
Indices: 3818873--3818951 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3818863 TTTCTTGTTT
3818873 TGGTCGTTCAAGTCCTTCAAATAACATGCTTGAGCTTCA
1 TGGTCGTTCAAGTCCTTCAAATAACATGCTTGAGCTTCA
3818912 TGGTCGTTCAAGTCCTTCAAATAACATGCTTGAGCTTCA
1 TGGTCGTTCAAGTCCTTCAAATAACATGCTTGAGCTTCA
3818951 T
1 T
3818952 AAAAACCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (39 bp):
TGGTCGTTCAAGTCCTTCAAATAACATGCTTGAGCTTCA
Found at i:3819953 original size:13 final size:13
Alignment explanation
Indices: 3819917--3819955 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3819907 TTAATACCTG
*
3819917 AATAAAATAAAAA
1 AATAAAATAATAA
* *
3819930 AATATATTAATAA
1 AATAAAATAATAA
3819943 AATAAAATAATAA
1 AATAAAATAATAA
3819956 GTAATAAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAAATAATAA
Found at i:3819965 original size:21 final size:21
Alignment explanation
Indices: 3819917--3819964 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3819907 TTAATACCTG
*
3819917 AATAAAATAAAAAAATATATT
1 AATAAAATAAAAAAATATAGT
*
3819938 AATAAAATAAAATAATA-AGT
1 AATAAAATAAAAAAATATAGT
3819958 AATAAAA
1 AATAAAA
3819965 AATTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAAAATAAAAAAATATAGT
Found at i:3822236 original size:3 final size:3
Alignment explanation
Indices: 3822222--3822304 Score: 89
Period size: 3 Copynumber: 28.0 Consensus size: 3
3822212 GTTGTATCTG
* * *
3822222 TAA TAA -AA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAT TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3822269 AAA TAA TAA TAA TAG TAA TAA AAA TAA -ATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
3822305 ATATAATTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 3 0.05
3 62 0.94
4 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3822305 original size:15 final size:15
Alignment explanation
Indices: 3822270--3822316 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3822260 TAATAACAAA
*
3822270 AATAATAAT-AATAGT
1 AATAAAAATAAATA-T
3822285 AATAAAAATAAATAT
1 AATAAAAATAAATAT
* *
3822300 AATAAATATAATTAT
1 AATAAAAATAAATAT
3822315 AA
1 AA
3822317 AACCAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATAAAAATAAATAT
Found at i:3825225 original size:84 final size:84
Alignment explanation
Indices: 3825042--3825225 Score: 212
Period size: 84 Copynumber: 2.2 Consensus size: 84
3825032 CATACAACAT
**
3825042 CATTTTTATAGTAAAACACCACTATTGACAATTATATAGTGCATTTTTAGTCATAAATGCCACAA
1 CATTTTTATAGTAAAACACCACTATTGACAATTATATAGTGCATTTTTAGTCATAAACACCACAA
*
3825107 ATTATCTAAACTTTAGTGG
66 ATAATCTAAACTTTAGTGG
* * * * * * * * *
3825126 CGTTTTTATACTAAAACATCGCTATTGACAATTTTATAGTGGCTTTTTTTTGT-ATAAACATCGC
1 CATTTTTATAGTAAAACACCACTATTGACAATTATATAGT-GC-ATTTTTAGTCATAAACACCAC
3825190 AAATAATCTAAAACTTTAGTGG
64 AAATAATCT-AAACTTTAGTGG
3825212 CATTTTT-T-GTAAAA
1 CATTTTTATAGTAAAA
3825226 TGACGCTAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
84 40 0.48
85 18 0.22
86 25 0.30
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (84 bp):
CATTTTTATAGTAAAACACCACTATTGACAATTATATAGTGCATTTTTAGTCATAAACACCACAA
ATAATCTAAACTTTAGTGG
Found at i:3825352 original size:21 final size:21
Alignment explanation
Indices: 3825328--3825371 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3825318 CATGACATCT
* * *
3825328 ATAACAACAAACTTTAATTCC
1 ATAACAAAAAACTTCAAATCC
3825349 ATAACAAAAAACTTCAAATCC
1 ATAACAAAAAACTTCAAATCC
3825370 AT
1 AT
3825372 TATAGTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAACAAAAAACTTCAAATCC
Found at i:3831666 original size:41 final size:41
Alignment explanation
Indices: 3831609--3831965 Score: 212
Period size: 40 Copynumber: 8.9 Consensus size: 41
3831599 ATTATGAACT
* *
3831609 AGTATTTAGCGGCGTTTGTATAAAAATACCACTATAGTATG
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * **
3831650 AGTCTTTAGCGACGTTTATAT-AAAACGCCACTAAAGTACG
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * * * *
3831690 AGTTTTTACCGGGGGTTGTACAAAAACT-TCACTAAAGTAC-
1 AGTATTTAGCGGCGTTTGTATAAAAA-TACCACTAAAGTACG
* *
3831730 AATATTTAGCGGCGTTTATATAAAAATACCACTAAAGTACG
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * * *
3831771 AGTATTTACCAGCGTTTGT-TAAAAAAAGGCCACTATATTAC-
1 AGTATTTAGCGGCGTTTGTATAAAAATA--CCACTAAAGTACG
* * * * * *
3831812 AATATTTAACGGCGTTTTTATCAAAACACCACTAAAATACG
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * * ** * *
3831853 AGTCTTTAGAGGTGTTTGTACAAAACGA-AACAAAAGTAC-
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * * **
3831892 AATATTTAGTGTCGTTTATA-AAAAACGCCACTAAA-TACG
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
* * * * *
3831931 AGTGTTTACCGGCG-TTGTTTAAAAATGCCGCTAAA
1 AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAA
3831966 AACTCATGTT
Statistics
Matches: 233, Mismatches: 72, Indels: 24
0.71 0.22 0.07
Matches are distributed among these distances:
38 10 0.04
39 42 0.18
40 84 0.36
41 81 0.35
42 16 0.07
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (41 bp):
AGTATTTAGCGGCGTTTGTATAAAAATACCACTAAAGTACG
Found at i:3831826 original size:82 final size:80
Alignment explanation
Indices: 3831662--3831948 Score: 242
Period size: 82 Copynumber: 3.6 Consensus size: 80
3831652 TCTTTAGCGA
* * * * * **
3831662 CGTTTATATAAAACGCCACTAAAGTACGAGTTTTTACCGGGGGTTGTACAAAAACTTCACTAAAG
1 CGTTTATATAAAACACCACTAAAGTACGAGTATTTACCAGCGGTTGTAAAAAAACGCCACTAAAG
*
3831727 TACAATATTTAGCGG
66 TACAATATTTAACGG
* * * *
3831742 CGTTTATATAAAAATACCACTAAAGTACGAGTATTTACCAGCGTTTGTTAAAAAAAGGCCACTAT
1 CGTTTATAT-AAAACACCACTAAAGTACGAGTATTTACCAGCGGTTG-TAAAAAAACGCCACTAA
*
3831807 ATTACAATATTTAACGG
64 AGTACAATATTTAACGG
* * * * * ** *
3831824 CGTTTTTATCAAAACACCACTAAAATACGAGTCTTTA-GAG-GTGTTTGT-ACAAAACGAAACAA
1 CGTTTATAT-AAAACACCACTAAAGTACGAGTATTTACCAGCG-G-TTGTAAAAAAACGCCACTA
** *
3831886 AAGTACAATATTTAGTGT
63 AAGTACAATATTTAACGG
* * * *
3831904 CGTTTATAAAAAACGCCACTAAA-TACGAGTGTTTACCGGC-GTTGT
1 CGTTTATATAAAACACCACTAAAGTACGAGTATTTACCAGCGGTTGT
3831949 TTAAAAATGC
Statistics
Matches: 165, Mismatches: 36, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
77 4 0.02
78 12 0.07
79 14 0.08
80 39 0.24
81 34 0.21
82 62 0.38
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (80 bp):
CGTTTATATAAAACACCACTAAAGTACGAGTATTTACCAGCGGTTGTAAAAAAACGCCACTAAAG
TACAATATTTAACGG
Found at i:3835244 original size:22 final size:21
Alignment explanation
Indices: 3835209--3835264 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3835199 TAGCCGTTCG
* *
3835209 TGAAGGGGGTATCAATAGTCA
1 TGAAGGGAGTATCAATACTCA
3835230 TGAAGGAGAGTATCAATACTCA
1 TGAAGG-GAGTATCAATACTCA
**
3835252 CCAAGGGAGTATC
1 TGAAGGGAGTATC
3835265 GGTACTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (21 bp):
TGAAGGGAGTATCAATACTCA
Found at i:3848259 original size:31 final size:31
Alignment explanation
Indices: 3848224--3848284 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3848214 GTTTTCTTAA
* * *
3848224 TCAATTGACAATGTACGCATATCTTGCAAAT
1 TCAATTGACAACGTACACATATCTTACAAAT
*
3848255 TCAATTGATAACGTACACATATCTTACAAA
1 TCAATTGACAACGTACACATATCTTACAAA
3848285 GTGACTGCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (31 bp):
TCAATTGACAACGTACACATATCTTACAAAT
Found at i:3854347 original size:16 final size:15
Alignment explanation
Indices: 3854307--3854344 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3854297 TGTTCATTTA
3854307 ATAAATAA-ACGAAC
1 ATAAATAACACGAAC
*
3854321 ATAAACGAACACGAAC
1 ATAAA-TAACACGAAC
3854337 ATAAATAA
1 ATAAATAA
3854345 ACAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.63, C:0.16, G:0.08, T:0.13
Consensus pattern (15 bp):
ATAAATAACACGAAC
Found at i:3855692 original size:17 final size:18
Alignment explanation
Indices: 3855667--3855701 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3855657 TTATCTCCCA
*
3855667 TCATTTATTTA-CTAATT
1 TCATATATTTACCTAATT
3855684 TCATATATTTACCTAATT
1 TCATATATTTACCTAATT
3855702 CAGTTTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATATATTTACCTAATT
Found at i:3859987 original size:18 final size:18
Alignment explanation
Indices: 3859966--3860025 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
3859956 AATGTTCCGA
*
3859966 AGGACCGCTATGTCCCGG
1 AGGACCACTATGTCCCGG
*
3859984 AGGACCACTATGTCTCGG
1 AGGACCACTATGTCCCGG
*
3860002 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGG
3860020 AGGACC
1 AGGACC
3860026 GTGTAGACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (18 bp):
AGGACCACTATGTCCCGG
Found at i:3860465 original size:17 final size:18
Alignment explanation
Indices: 3860440--3860474 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3860430 TTATCTCCCA
*
3860440 TCATTTATTTA-CTAATT
1 TCATATATTTACCTAATT
3860457 TCATATATTTACCTAATT
1 TCATATATTTACCTAATT
3860475 CAGTTTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATATATTTACCTAATT
Found at i:3862074 original size:23 final size:23
Alignment explanation
Indices: 3862044--3862087 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3862034 GGGATGTTAC
*
3862044 ATAAACGAACACGAACGAACACA
1 ATAAACGAACACAAACGAACACA
*
3862067 ATAAACGAACATAAACGAACA
1 ATAAACGAACACAAACGAACA
3862088 ACACAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.07
Consensus pattern (23 bp):
ATAAACGAACACAAACGAACACA
Found at i:3862095 original size:23 final size:23
Alignment explanation
Indices: 3862046--3862095 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3862036 GATGTTACAT
* *
3862046 AAACGAACACGAACGAACACAAT
1 AAACGAACACAAACGAACACAAC
*
3862069 AAACGAACATAAACGAACA-ACAC
1 AAACGAACACAAACGAACACA-AC
3862092 AAAC
1 AAAC
3862096 ACAAAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.60, C:0.26, G:0.10, T:0.04
Consensus pattern (23 bp):
AAACGAACACAAACGAACACAAC
Found at i:3862363 original size:14 final size:14
Alignment explanation
Indices: 3862344--3862396 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
3862334 GCCCTCTGTT
3862344 CGAACATAAATGAA
1 CGAACATAAATGAA
3862358 CGAACATAAAT---
1 CGAACATAAATGAA
3862369 -GAACATAAATGAA
1 CGAACATAAATGAA
*
3862382 CGAACATAAACGAA
1 CGAACATAAATGAA
3862396 C
1 C
3862397 ATATAATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 10 0.29
14 24 0.71
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:3862374 original size:24 final size:24
Alignment explanation
Indices: 3862344--3862409 Score: 105
Period size: 24 Copynumber: 2.7 Consensus size: 24
3862334 GCCCTCTGTT
3862344 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
*
3862368 TGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
3862392 CGAACATATAATTGAACG
1 CGAACATA-AA-TGAACG
3862410 TTCACGAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 30 0.79
25 2 0.05
26 6 0.16
ACGTcount: A:0.55, C:0.15, G:0.14, T:0.17
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:3863519 original size:166 final size:165
Alignment explanation
Indices: 3863246--3863551 Score: 542
Period size: 166 Copynumber: 1.8 Consensus size: 165
3863236 TATGTTTTAT
3863246 TTTTTAATTTGGTCACTTAAATCTAAAAAGCTGCAAAAAAATAATAAATTATATTTTATTTTTTT
1 TTTTTAATTTGGTCACTTAAATCTAAAAAGCTGCAAAAAAATAATAAATTATATTTTATTTTTTT
*
3863311 GTGTCACCTATAATAAATTTTAGCGATGACATAACGTGACTGGTTTGATGATTAGTTAAAAATAA
66 GTGTCACCTATAATAAATTTTAGCGATGACATAACGTGACTGGTTTGATGATTAATTAAAAATAA
3863376 AATTAAAATTGCAAGTTGATTGTTTAATTATAAAC
131 AATTAAAATTGCAAGTTGATTGTTTAATTATAAAC
* * *
3863411 TTTTTAATTTTGTCACTTAAATCTAAAAAGCTGCAAAATGACTAATAAATTATATTTTATTTTTT
1 TTTTTAATTTGGTCACTTAAATCTAAAAAGCTGCAAAA-AAATAATAAATTATATTTTATTTTTT
3863476 TG-GTTCACCTATAATAAATTTTAGCGATGACATAACGTGACTGGTTTGATGATTAATTAAAAAT
65 TGTG-TCACCTATAATAAATTTTAGCGATGACATAACGTGACTGGTTTGATGATTAATTAAAAAT
*
3863540 AAATTTAAAATT
129 AAAATTAAAATT
3863552 TAAAAGTATA
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
165 38 0.28
166 96 0.72
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (165 bp):
TTTTTAATTTGGTCACTTAAATCTAAAAAGCTGCAAAAAAATAATAAATTATATTTTATTTTTTT
GTGTCACCTATAATAAATTTTAGCGATGACATAACGTGACTGGTTTGATGATTAATTAAAAATAA
AATTAAAATTGCAAGTTGATTGTTTAATTATAAAC
Found at i:3865578 original size:27 final size:27
Alignment explanation
Indices: 3865540--3865602 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
3865530 ACTTGCCTCG
3865540 ATCACAAATCAATCACGATCTGTACAA
1 ATCACAAATCAATCACGATCTGTACAA
*
3865567 ATCACAAATCAATCACGATTTGTACAA
1 ATCACAAATCAATCACGATCTGTACAA
3865594 ATCACAAAT
1 ATCACAAAT
3865603 TCATAACAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (27 bp):
ATCACAAATCAATCACGATCTGTACAA
Found at i:3866106 original size:29 final size:30
Alignment explanation
Indices: 3866032--3866099 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
3866022 ATTGTTGAAT
*
3866032 TGGTCCCCCAACTTTAAAAAAATTATAAAA
1 TGGTCCCCCAACTTTTAAAAAATTATAAAA
* *
3866062 TGGTCCCCCAACTTTTAAAAATTTATAGAA
1 TGGTCCCCCAACTTTTAAAAAATTATAAAA
3866092 TGGTCCCC
1 TGGTCCCC
3866100 AATTTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (30 bp):
TGGTCCCCCAACTTTTAAAAAATTATAAAA
Found at i:3871167 original size:2 final size:2
Alignment explanation
Indices: 3871160--3871188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3871150 CATCATCACA
3871160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3871189 CAACTATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3876565 original size:27 final size:27
Alignment explanation
Indices: 3876530--3876584 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3876520 GGCTTATTTA
* *
3876530 TAATCATATTTTAATTCAATGATATAT
1 TAATAATATTTTAATTCAATAATATAT
*
3876557 TAATAATATTTTAATTGAATAATATAT
1 TAATAATATTTTAATTCAATAATATAT
3876584 T
1 T
3876585 GACATAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATAATATTTTAATTCAATAATATAT
Found at i:3877858 original size:24 final size:24
Alignment explanation
Indices: 3877831--3877886 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3877821 CAGCTAAGTG
**
3877831 CCACGTAGAGTTTGTCCCGAAGGA
1 CCACGTAGAAATTGTCCCGAAGGA
*
3877855 CCACGTAGAAATTGTCCCTAAGGA
1 CCACGTAGAAATTGTCCCGAAGGA
3877879 CCACGTAG
1 CCACGTAG
3877887 GAATATTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.20
Consensus pattern (24 bp):
CCACGTAGAAATTGTCCCGAAGGA
Found at i:3886341 original size:13 final size:13
Alignment explanation
Indices: 3886323--3886390 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
3886313 TGCGTCATAA
3886323 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
3886336 ATTTATGACACAC
1 ATTTATGACGCGC
**
3886349 ATTTATGACATGC
1 ATTTATGACGCGC
3886362 ATTTATGACGCGC
1 ATTTATGACGCGC
*
3886375 ATTTATGACGCTC
1 ATTTATGACGCGC
3886388 ATT
1 ATT
3886391 GCGCGTCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:3886554 original size:2 final size:2
Alignment explanation
Indices: 3886547--3886571 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3886537 TGTCTTAAAT
3886547 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3886572 TGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3893067 original size:193 final size:196
Alignment explanation
Indices: 3892738--3893130 Score: 756
Period size: 193 Copynumber: 2.0 Consensus size: 196
3892728 TAGTTTAGTA
3892738 GCATATTTTCTTTTCAGACATTGTATGGACATTTTCATACTTTATTTTATTTCACTTTTCGTAAA
1 GCATATTTTCTTTTCAGACATTGTATGGACATTTTCATACTTTATTTTATTTCACTTTTCGTAAA
3892803 CTTTTTTTATATACTTATATGGGGACTTTGGAATATTATGTTTTTACTAGTTTTGAACTTTAAAA
66 CTTTTTTTATATACTTATATGGGGACTTTGGAATATTATGTTTTTACTAGTTTTGAACTTTAAAA
*
3892868 TCGTATTATGGTATTTATTATGAA-TA-T-TTTTTGTTTATGGATTTATACCAATTTTCTAACAA
131 TCGTATTATGGTATTTATTATGAACTATTATTTTTGGTTATGGATTTATACCAATTTTCTAACAA
3892930 T
196 T
3892931 GCATATTTTCTTTTCAGACATTGTATGGACATTTTCATACTTTATTTTATTTCACTTTTCGTAAA
1 GCATATTTTCTTTTCAGACATTGTATGGACATTTTCATACTTTATTTTATTTCACTTTTCGTAAA
3892996 CTTTTTTTATATACTTATATGGGGACTTTGGAATATTATGTTTTTACTAGTTTTGAACTTTAAAA
66 CTTTTTTTATATACTTATATGGGGACTTTGGAATATTATGTTTTTACTAGTTTTGAACTTTAAAA
3893061 TCGTATTATGGTATTTATTATGAACTATTATTTTTGGTTATGGATTTATACCAATTTTCTAACAA
131 TCGTATTATGGTATTTATTATGAACTATTATTTTTGGTTATGGATTTATACCAATTTTCTAACAA
3893126 T
196 T
3893127 GCAT
1 GCAT
3893131 GCTATAATAT
Statistics
Matches: 196, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
193 154 0.79
194 2 0.01
195 1 0.01
196 39 0.20
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.51
Consensus pattern (196 bp):
GCATATTTTCTTTTCAGACATTGTATGGACATTTTCATACTTTATTTTATTTCACTTTTCGTAAA
CTTTTTTTATATACTTATATGGGGACTTTGGAATATTATGTTTTTACTAGTTTTGAACTTTAAAA
TCGTATTATGGTATTTATTATGAACTATTATTTTTGGTTATGGATTTATACCAATTTTCTAACAA
T
Found at i:3895042 original size:9 final size:9
Alignment explanation
Indices: 3895028--3895053 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3895018 GGTTACTGTT
3895028 CACGCGCCG
1 CACGCGCCG
3895037 CACGCGCCG
1 CACGCGCCG
3895046 CACGCGCC
1 CACGCGCC
3895054 ACCCCCGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.58, G:0.31, T:0.00
Consensus pattern (9 bp):
CACGCGCCG
Found at i:3895224 original size:10 final size:10
Alignment explanation
Indices: 3895201--3895264 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
3895191 GTAAAATGGT
*
3895201 CGACTGTTGGC
1 CGAC-GTTGAC
3895212 CGACGTTGAC
1 CGACGTTGAC
3895222 CGACGTTGAC
1 CGACGTTGAC
3895232 C-ACAGTTGAC
1 CGAC-GTTGAC
*
3895242 CAGAACTTTGAC
1 C-G-ACGTTGAC
*
3895254 CGGCGTTGAC
1 CGACGTTGAC
3895264 C
1 C
3895265 ATGCATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
9 2 0.04
10 30 0.67
11 5 0.11
12 6 0.13
13 2 0.04
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (10 bp):
CGACGTTGAC
Found at i:3905188 original size:71 final size:71
Alignment explanation
Indices: 3905100--3905240 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 71
3905090 ATTTTGTTAG
* * ** * *
3905100 TTTGATTATGTGTCATGTTTGTACAAGAGATTAGTTTTTAATTTAACACTAAACTTAAGATTAAA
1 TTTGATTATATGACATGTCAGTACAAGAGATTACTTTTTAATTTAACACTAAACTTAAGATAAAA
3905165 TATTAT
66 TATTAT
* * *
3905171 TTTGATTATATGACATGTCAGTACAAGAGATTACTTTTTTATTTAATACTAAACTTTAGATAAAA
1 TTTGATTATATGACATGTCAGTACAAGAGATTACTTTTTAATTTAACACTAAACTTAAGATAAAA
3905236 TATTA
66 TATTA
3905241 ATTTAACGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (71 bp):
TTTGATTATATGACATGTCAGTACAAGAGATTACTTTTTAATTTAACACTAAACTTAAGATAAAA
TATTAT
Found at i:3905276 original size:30 final size:29
Alignment explanation
Indices: 3905242--3905303 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
3905232 AAAATATTAA
* *
3905242 TTTAACG-CTAAACTAATATTTTATCTAAAG
1 TTTAACGTCCAAA-TAAAATTTTATCT-AAG
*
3905272 TTTAAGGTCCAAATAAAATTTTATCTAAG
1 TTTAACGTCCAAATAAAATTTTATCTAAG
3905301 TTT
1 TTT
3905304 TATGGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 18 0.64
31 4 0.14
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTAACGTCCAAATAAAATTTTATCTAAG
Found at i:3914614 original size:17 final size:17
Alignment explanation
Indices: 3914592--3914627 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3914582 AATTAAGAGT
3914592 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
3914609 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
3914626 TA
1 TA
3914628 ACCTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:3918767 original size:120 final size:120
Alignment explanation
Indices: 3918554--3918778 Score: 301
Period size: 120 Copynumber: 1.9 Consensus size: 120
3918544 ATCAAATCCA
* * *
3918554 ATTGAATATAATCTCCTCTAGTGTGATAACATGATAATGATATAATCAATACCTTTTAAACATCG
1 ATTGAATATAATCTCCTCTAGTGTGATAACATGAGAATGATATAATCAATAACTTCTAAACATCG
*
3918619 ATTCATGAAATACATTATAAATCTTATCCATTTCTAAAGGTAGCGCTAGTTACCG
66 ATTCATAAAATACATTATAAATCTTATCCATTTCTAAAGGTAGCGCTAGTTACCG
* * * * **
3918674 ATTGAATATATTCTCCT-TCGGTGTGATAACATGAGAATGATCTGATTGATAACTTCTAAGA-AT
1 ATTGAATATAATCTCCTCT-AGTGTGATAACATGAGAATGATATAATCAATAACTTCTAA-ACAT
* * *
3918737 CTATTCATAAAATACATTATGAATCTTATCCATTTCTGAAGG
64 CGATTCATAAAATACATTATAAATCTTATCCATTTCTAAAGG
3918779 AAGAGTTAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
119 1 0.01
120 88 0.98
121 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (120 bp):
ATTGAATATAATCTCCTCTAGTGTGATAACATGAGAATGATATAATCAATAACTTCTAAACATCG
ATTCATAAAATACATTATAAATCTTATCCATTTCTAAAGGTAGCGCTAGTTACCG
Found at i:3920908 original size:160 final size:161
Alignment explanation
Indices: 3920639--3921034 Score: 650
Period size: 161 Copynumber: 2.5 Consensus size: 161
3920629 AGTTCTTCGG
* * *
3920639 GGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATAGAAGGAGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGAGTGCC
* * *
3920704 CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTG-CCCAGAAGGACATGAGTGA
66 CCCGGGAACACACTTTCACCACTTTGGGTACTGAAATGAATAGTGTCCCAGAAGGACATGAGTGA
*
3920768 CATAATAGGGTAATGATAACATAGCCCTCGA
131 CATAATAGGGTAATGATAACATAGCCCCCGA
* * *
3920799 GGGATATGAGTGATATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGAGTGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGAGTGCC
* * *
3920864 CCCGGAAACACACTTTCACCACTTTGGGTACTGAAATGAATAGTGTCCCCGAGGGACATGAGTGA
66 CCCGGGAACACACTTTCACCACTTTGGGTACTGAAATGAATAGTGTCCCAGAAGGACATGAGTGA
3920929 CATAATAGGGTAATGATAACATAGCCCCCGA
131 CATAATAGGGTAATGATAACATAGCCCCCGA
* *
3920960 GGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGTGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGAGTGCC
3921025 CCCGGGAACA
66 CCCGGGAACA
3921035 TGCCTTCACA
Statistics
Matches: 216, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
160 100 0.46
161 116 0.54
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (161 bp):
GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGAGTGCC
CCCGGGAACACACTTTCACCACTTTGGGTACTGAAATGAATAGTGTCCCAGAAGGACATGAGTGA
CATAATAGGGTAATGATAACATAGCCCCCGA
Found at i:3920961 original size:44 final size:44
Alignment explanation
Indices: 3920910--3920995 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
3920900 TGAATAGTGT
* *
3920910 CCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATAGC
1 CCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATAGC
3920954 CCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATA
1 CCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATA
3920996 TTCTCTGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (44 bp):
CCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATAGC
Found at i:3922422 original size:82 final size:82
Alignment explanation
Indices: 3922283--3922491 Score: 303
Period size: 82 Copynumber: 2.5 Consensus size: 82
3922273 GAATCATGTA
** ** * *
3922283 CATAGGGCTTACTTTAAGCACACGGCAAAAAGGACGCCAACCTAAGGATAGGCTTTGGGGCCTGT
1 CATAGGGCTTACCCTAAGCACACAAC-AAAGGGA-GCCAACCTAAGGATAGGCTTTGGGGCCTAT
*
3922348 ATC-CTTAAGTTCGTAAGTC
64 A-CACTTAAGTTCATAAGTC
*
3922367 CATAGGGCTTACCCTAAGCACACATCAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTATAC
1 CATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTATAC
3922432 ACTTAAGTTCATAAGTC
66 ACTTAAGTTCATAAGTC
*
3922449 CATAGGGCTTACCCTAAGCACAAAACAAAGGGAGCCAACCTAA
1 CATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAA
3922492 TGGAGCATAT
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
81 1 0.01
82 86 0.75
83 6 0.05
84 22 0.19
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (82 bp):
CATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTATAC
ACTTAAGTTCATAAGTC
Found at i:3927615 original size:82 final size:82
Alignment explanation
Indices: 3927471--3927682 Score: 325
Period size: 82 Copynumber: 2.6 Consensus size: 82
3927461 CTAGAACCGC
* * * * *
3927471 GTCCATAGGGCTTACCTTAAGCACACGAAAAAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCT
1 GTCCATAGGGCTTACCCTAAGCACAC--AACAAAGGGAGCCAACCTAAGGATAGGCTCTGGGGCC
* *
3927536 TGTATCCTTAAGTCCGTAA
64 TGTACCCTTAAGTCCATAA
*
3927555 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTCTGGGGCCTG
1 GTCCATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAAGGATAGGCTCTGGGGCCTG
*
3927620 TACCCTTAAGTTCATAA
66 TACCCTTAAGTCCATAA
3927637 GTCCATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAA
1 GTCCATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAA
3927683 TGGAGCATCT
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
82 93 0.79
84 25 0.21
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (82 bp):
GTCCATAGGGCTTACCCTAAGCACACAACAAAGGGAGCCAACCTAAGGATAGGCTCTGGGGCCTG
TACCCTTAAGTCCATAA
Found at i:3933420 original size:22 final size:24
Alignment explanation
Indices: 3933395--3933443 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
3933385 TTTATTATAT
*
3933395 TTATTTAATAT-AATAATTAA-TA
1 TTATTTAATATAAAAAATTAATTA
*
3933417 TTATTTACTATAAAAAATTAATTA
1 TTATTTAATATAAAAAATTAATTA
3933441 TTA
1 TTA
3933444 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTAATATAAAAAATTAATTA
Found at i:3938236 original size:3 final size:3
Alignment explanation
Indices: 3938228--3938303 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
3938218 ATTCTTGCTG
3938228 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3938276 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3938304 TCTGGATACT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3938775 original size:2 final size:2
Alignment explanation
Indices: 3938768--3938798 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3938758 GTTGGTCGAT
3938768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3938799 TTAATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3945286 original size:24 final size:24
Alignment explanation
Indices: 3945259--3945306 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3945249 TGCGAAAGAA
*
3945259 GAAGAGTAATCGAAGAAAATAGAG
1 GAAGAGTAATCAAAGAAAATAGAG
3945283 GAAGAGTAATCAAAGAAAATAGAG
1 GAAGAGTAATCAAAGAAAATAGAG
3945307 AAAATGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.27, T:0.12
Consensus pattern (24 bp):
GAAGAGTAATCAAAGAAAATAGAG
Found at i:3945720 original size:2 final size:2
Alignment explanation
Indices: 3945713--3945770 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3945703 AGTATTTTAA
3945713 AT AT AT AT AT AT 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
3945755 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3945771 TTTAAAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3947497 original size:20 final size:18
Alignment explanation
Indices: 3947469--3947507 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3947459 AGAAAATTAA
3947469 AAAAATTAAAAGTATGAGTG
1 AAAAATT-AAAGT-TGAGTG
*
3947489 AAAATTTAAAGTTGAGTG
1 AAAAATTAAAGTTGAGTG
3947507 A
1 A
3947508 GTAAGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (18 bp):
AAAAATTAAAGTTGAGTG
Found at i:3947506 original size:18 final size:19
Alignment explanation
Indices: 3947470--3947507 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3947460 GAAAATTAAA
3947470 AAAATTAAAAGTATGAGTG
1 AAAATTAAAAGTATGAGTG
*
3947489 AAAATTTAAAGT-TGAGTG
1 AAAATTAAAAGTATGAGTG
3947507 A
1 A
3947508 GTAAGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (19 bp):
AAAATTAAAAGTATGAGTG
Found at i:3947692 original size:24 final size:22
Alignment explanation
Indices: 3947638--3947680 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3947628 TCACTATCCA
3947638 AACACCTAAAATATTAACGTTG
1 AACACCTAAAATATTAACGTTG
3947660 AACACCTAAAATATTAACGTT
1 AACACCTAAAATATTAACGTT
3947681 TGTAACATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.28
Consensus pattern (22 bp):
AACACCTAAAATATTAACGTTG
Found at i:3948865 original size:2 final size:2
Alignment explanation
Indices: 3948858--3948885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3948848 TATTAATTTC
3948858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3948886 CACGAGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3949277 original size:21 final size:21
Alignment explanation
Indices: 3949252--3949292 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3949242 AAATATTAAA
*
3949252 AAATATTAATATTTTAGGTAT
1 AAATAATAATATTTTAGGTAT
3949273 AAATAATAATATTTTAGGTA
1 AAATAATAATATTTTAGGTA
3949293 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAT
Found at i:3949928 original size:27 final size:27
Alignment explanation
Indices: 3949892--3949959 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
3949882 TTATTATTTC
*
3949892 TACCGATTTTGTTATTATTAGACACTT
1 TACCGGTTTTGTTATTATTAGACACTT
*
3949919 TACCGGTTTTATTATTATTAGACACTT
1 TACCGGTTTTGTTATTATTAGACACTT
3949946 TACCGGTTTTGTTA
1 TACCGGTTTTGTTA
3949960 ACATATTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.49
Consensus pattern (27 bp):
TACCGGTTTTGTTATTATTAGACACTT
Found at i:3957773 original size:12 final size:12
Alignment explanation
Indices: 3957756--3957785 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3957746 CTAATGAGAG
3957756 TTGATTAGGGAT
1 TTGATTAGGGAT
*
3957768 TTGATTATGGAT
1 TTGATTAGGGAT
3957780 TTGATT
1 TTGATT
3957786 GTATAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (12 bp):
TTGATTAGGGAT
Found at i:3969834 original size:2 final size:2
Alignment explanation
Indices: 3969827--3969858 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3969817 CCAATAAATC
3969827 AT 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
3969859 TATGTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3976268 original size:24 final size:24
Alignment explanation
Indices: 3976232--3976284 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
3976222 TTATATTTTA
* *
3976232 AAATTAATCTAATTATTTTTATAT
1 AAATCAATATAATTATTTTTATAT
3976256 AAATCAATATAATTATTTTTATAT
1 AAATCAATATAATTATTTTTATAT
*
3976280 TAATC
1 AAATC
3976285 TTCTATGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATCAATATAATTATTTTTATAT
Found at i:3991027 original size:20 final size:20
Alignment explanation
Indices: 3991002--3991120 Score: 116
Period size: 20 Copynumber: 5.8 Consensus size: 20
3990992 TGTGCACTTG
3991002 GTATCGATACTACTCACATA
1 GTATCGATACTACTCACATA
* *
3991022 GTATCGATACTACTCCTTCATG
1 GTATCGATACTACT-C-ACATA
* *
3991044 GTATCGATACTACTCGCCTA
1 GTATCGATACTACTCACATA
*
3991064 GTATCGATACTATTCATC-TA
1 GTATCGATACTACTCA-CATA
* *
3991084 GTACCGATACTACTTA-ATA
1 GTATCGATACTACTCACATA
3991103 GGGTATCGATACTACTCA
1 --GTATCGATACTACTCA
3991121 AAATTTTCCT
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
19 2 0.02
20 45 0.56
21 17 0.21
22 17 0.21
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (20 bp):
GTATCGATACTACTCACATA
Found at i:3991163 original size:20 final size:20
Alignment explanation
Indices: 3991140--3991191 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3991130 TTGAAGTATC
3991140 GATACTCCTCGAGGAGTACA
1 GATACTCCTCGAGGAGTACA
3991160 GATACTCCTCGAGGAGTACA
1 GATACTCCTCGAGGAGTACA
* *
3991180 AATACTACTCGA
1 GATACTCCTCGA
3991192 CGATTTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
GATACTCCTCGAGGAGTACA
Found at i:3991620 original size:23 final size:23
Alignment explanation
Indices: 3991589--3991633 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3991579 ATTATATATG
* *
3991589 TATATTATTGTTTTTCACAAAAC
1 TATACTATTGTGTTTCACAAAAC
*
3991612 TATACTATTGTGTTTCATAAAA
1 TATACTATTGTGTTTCACAAAA
3991634 TTGTTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (23 bp):
TATACTATTGTGTTTCACAAAAC
Found at i:3992941 original size:22 final size:22
Alignment explanation
Indices: 3992913--3992956 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3992903 GATTCAATGT
3992913 AGTGGATGATAGGATCGACGCA
1 AGTGGATGATAGGATCGACGCA
3992935 AGTGGATGATAGGATCGACGCA
1 AGTGGATGATAGGATCGACGCA
3992957 CTTACTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.36, T:0.18
Consensus pattern (22 bp):
AGTGGATGATAGGATCGACGCA
Found at i:3998976 original size:26 final size:26
Alignment explanation
Indices: 3998936--3998997 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
3998926 ATTGCTTGGT
* *
3998936 TCGACTCGATAGCTCAACTCAATGAC
1 TCGACTCGACAGCTCAACTCAACGAC
* * *
3998962 TCGACTCGACGGCTCAAGTTAACGAC
1 TCGACTCGACAGCTCAACTCAACGAC
*
3998988 TCAACTCGAC
1 TCGACTCGAC
3998998 TTGACAACTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (26 bp):
TCGACTCGACAGCTCAACTCAACGAC
Found at i:4000824 original size:20 final size:21
Alignment explanation
Indices: 4000799--4000854 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
4000789 TTAGACAGGT
*
4000799 GGGAATCCGTACCCCCT-GGG
1 GGGAATCTGTACCCCCTGGGG
*
4000819 GGGAATCTGTTCCCCCTGGGG
1 GGGAATCTGTACCCCCTGGGG
4000840 GGGAATCTGTACCCC
1 GGGAATCTGTACCCC
4000855 TGGACAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.20
Consensus pattern (21 bp):
GGGAATCTGTACCCCCTGGGG
Found at i:4000855 original size:20 final size:20
Alignment explanation
Indices: 4000799--4000857 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
4000789 TTAGACAGGT
*
4000799 GGGAATCCGTACCCCCT-GGG
1 GGGAATCTGTA-CCCCTGGGG
*
4000819 GGGAATCTGTTCCCCCTGGGG
1 GGGAATCTG-TACCCCTGGGG
4000840 GGGAATCTGTACCCCTGG
1 GGGAATCTGTACCCCTGG
4000858 ACAATCTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.20
Consensus pattern (20 bp):
GGGAATCTGTACCCCTGGGG
Found at i:4001828 original size:13 final size:13
Alignment explanation
Indices: 4001810--4001857 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
4001800 GTCACAACCC
4001810 GACCCGACCCGTT
1 GACCCGACCCGTT
4001823 GACCCGACCTGACCGGTT
1 GACCCGA-C---CC-GTT
4001841 GACCCGACCCGTT
1 GACCCGACCCGTT
4001854 GACC
1 GACC
4001858 GTTGATTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 14 0.47
14 3 0.10
17 3 0.10
18 10 0.33
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:4001829 original size:18 final size:18
Alignment explanation
Indices: 4001806--4001851 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
4001796 ATCGGTCACA
4001806 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
4001824 ACCCGACCTGACCGGTTG
1 ACCCGACCCGACCCGTTG
4001842 ACCCGACCCG
1 ACCCGACCCG
4001852 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:4003134 original size:18 final size:18
Alignment explanation
Indices: 4003111--4003148 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4003101 TTATGAGTAA
4003111 ATACCTAAAGAACAATTT
1 ATACCTAAAGAACAATTT
4003129 ATACCTAAAGAACAATTT
1 ATACCTAAAGAACAATTT
4003147 AT
1 AT
4003149 TGGAGGGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (18 bp):
ATACCTAAAGAACAATTT
Found at i:4004077 original size:14 final size:14
Alignment explanation
Indices: 4004053--4004109 Score: 87
Period size: 14 Copynumber: 4.1 Consensus size: 14
4004043 GCATTGTTTC
*
4004053 TGGGAGCTATTCAT
1 TGGGAGATATTCAT
* *
4004067 TTGGAGTTATTCAT
1 TGGGAGATATTCAT
4004081 TGGGAGATATTCAT
1 TGGGAGATATTCAT
4004095 TGGGAGATATTCAT
1 TGGGAGATATTCAT
4004109 T
1 T
4004110 TCTTCCTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (14 bp):
TGGGAGATATTCAT
Found at i:4004362 original size:24 final size:24
Alignment explanation
Indices: 4004335--4004422 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
4004325 TTCTATTATA
* *
4004335 ATACATGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTTTGATCGG
* * *
4004359 ATACTTGACCTAGATTTTGATTGA
1 ATACTTGACCTGGATTTTGATCGG
*
4004383 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCGG
*
4004407 ATACTTGACCTCGATT
1 ATACTTGACCTGGATT
4004423 ATGTTATGAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATCGG
Found at i:4004485 original size:19 final size:19
Alignment explanation
Indices: 4004461--4004518 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
4004451 CGGACGGAAC
4004461 ATGTTTTACTTGGGGGGTA
1 ATGTTTTACTTGGGGGGTA
** **
4004480 ATGTTTTAC--GGACGAAA
1 ATGTTTTACTTGGGGGGTA
4004497 CATGTTTTACTTGGGGGGTA
1 -ATGTTTTACTTGGGGGGTA
4004517 AT
1 AT
4004519 ATTAAAGGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 11 0.39
20 4 0.14
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (19 bp):
ATGTTTTACTTGGGGGGTA
Found at i:4004488 original size:37 final size:37
Alignment explanation
Indices: 4004447--4004518 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
4004437 GATATATCTG
*
4004447 TTTACGGACGGAACATGTTTTACTTGGGGGGTAATGT
1 TTTACGGACGAAACATGTTTTACTTGGGGGGTAATGT
4004484 TTTACGGACGAAACATGTTTTACTTGGGGGGTAAT
1 TTTACGGACGAAACATGTTTTACTTGGGGGGTAAT
4004519 ATTAAAGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.35
Consensus pattern (37 bp):
TTTACGGACGAAACATGTTTTACTTGGGGGGTAATGT
Found at i:4005280 original size:168 final size:168
Alignment explanation
Indices: 4005002--4005338 Score: 674
Period size: 168 Copynumber: 2.0 Consensus size: 168
4004992 TCGACTTCAG
4005002 TAAGGGAATTCTTCCGGCGTTGTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTGTAT
1 TAAGGGAATTCTTCCGGCGTTGTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTGTAT
4005067 TTTGATTTATATACGAGTATGGAAATCTGTTTTATTTTTAAATAGTGACAACTGATTTTATAAGT
66 TTTGATTTATATACGAGTATGGAAATCTGTTTTATTTTTAAATAGTGACAACTGATTTTATAAGT
4005132 TACACATTTCAATAAAAGTTTTAAATTTTCCGCTATTT
131 TACACATTTCAATAAAAGTTTTAAATTTTCCGCTATTT
4005170 TAAGGGAATTCTTCCGGCGTTGTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTGTAT
1 TAAGGGAATTCTTCCGGCGTTGTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTGTAT
4005235 TTTGATTTATATACGAGTATGGAAATCTGTTTTATTTTTAAATAGTGACAACTGATTTTATAAGT
66 TTTGATTTATATACGAGTATGGAAATCTGTTTTATTTTTAAATAGTGACAACTGATTTTATAAGT
4005300 TACACATTTCAATAAAAGTTTTAAATTTTCCGCTATTT
131 TACACATTTCAATAAAAGTTTTAAATTTTCCGCTATTT
4005338 T
1 T
4005339 TACAGTGGGT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (168 bp):
TAAGGGAATTCTTCCGGCGTTGTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTGTAT
TTTGATTTATATACGAGTATGGAAATCTGTTTTATTTTTAAATAGTGACAACTGATTTTATAAGT
TACACATTTCAATAAAAGTTTTAAATTTTCCGCTATTT
Found at i:4006760 original size:18 final size:18
Alignment explanation
Indices: 4006737--4006782 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
4006727 ACCGGTCACA
4006737 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
4006755 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCGTTG
4006773 ACCCGACCCG
1 ACCCGACCCG
4006783 GTTGACAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:4006775 original size:13 final size:14
Alignment explanation
Indices: 4006741--4006788 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 14
4006731 GTCACAACCC
4006741 GACCCGACCC-GTT
1 GACCCGACCCGGTT
4006754 GACCCGACCCGATCCGTT
1 GACCCGACCCG----GTT
4006772 GACCCGACCCGGTT
1 GACCCGACCCGGTT
4006786 GAC
1 GAC
4006789 AGTTGACCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.33
14 6 0.20
18 14 0.47
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.15
Consensus pattern (14 bp):
GACCCGACCCGGTT
Found at i:4007944 original size:18 final size:18
Alignment explanation
Indices: 4007921--4007958 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4007911 TTATGAGTAA
*
4007921 ATACCTAAAGAATAATTT
1 ATACCTAAAGAACAATTT
4007939 ATACCTAAAGAACAATTT
1 ATACCTAAAGAACAATTT
4007957 AT
1 AT
4007959 TGGAGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (18 bp):
ATACCTAAAGAACAATTT
Found at i:4008781 original size:14 final size:14
Alignment explanation
Indices: 4008758--4008798 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
4008748 TTGTTTCTGA
4008758 GAGCTATTCATTTG
1 GAGCTATTCATTTG
* *
4008772 GAGTTATTCATTGG
1 GAGCTATTCATTTG
4008786 GAGCTATTCATTT
1 GAGCTATTCATTT
4008799 CTTCCTTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (14 bp):
GAGCTATTCATTTG
Found at i:4009050 original size:24 final size:24
Alignment explanation
Indices: 4009023--4009110 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
4009013 TTCTATTATA
*
4009023 ATACATGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* * *
4009047 ATACTTGACCTAGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
* *
4009071 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
4009095 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
4009111 ATGTTATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:4009120 original size:24 final size:24
Alignment explanation
Indices: 4009023--4009120 Score: 108
Period size: 24 Copynumber: 4.1 Consensus size: 24
4009013 TTCTATTATA
* **
4009023 ATACATGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATATG
*
4009047 ATACTTGACCTAGATTCTGAT-TG
1 ATACTTGACCTGGATTCTGATATG
* *
4009070 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTCTGATATG
* *
4009095 ATACTTGACCTGGATTATGTTATG
1 ATACTTGACCTGGATTCTGATATG
4009119 AT
1 AT
4009121 TTTTGATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.95
25 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATATG
Found at i:4009176 original size:37 final size:37
Alignment explanation
Indices: 4009135--4009206 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
4009125 GATATATCTG
* *
4009135 TTTACGGACGGAACATGTTTTACTTGGGGGGTAATGT
1 TTTACAGACGAAACATGTTTTACTTGGGGGGTAATGT
4009172 TTTACAGACGAAACATGTTTTACTTGGGGGGTAAT
1 TTTACAGACGAAACATGTTTTACTTGGGGGGTAAT
4009207 ATTAAAGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (37 bp):
TTTACAGACGAAACATGTTTTACTTGGGGGGTAATGT
Found at i:4011284 original size:23 final size:23
Alignment explanation
Indices: 4011258--4011308 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
4011248 ACCGGTCACA
*
4011258 ACCCGACCCGACCCGTTCACCCG
1 ACCCGACCCAACCCGTTCACCCG
*
4011281 ACCCGACCCAACCCGTTGACCCG
1 ACCCGACCCAACCCGTTCACCCG
4011304 ACCCG
1 ACCCG
4011309 TTGATAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.55, G:0.18, T:0.08
Consensus pattern (23 bp):
ACCCGACCCAACCCGTTCACCCG
Found at i:4011311 original size:13 final size:13
Alignment explanation
Indices: 4011262--4011312 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
4011252 GTCACAACCC
4011262 GACCCGACCCGTT
1 GACCCGACCCGTT
*
4011275 CACCCGACCC---
1 GACCCGACCCGTT
*
4011285 GACCCAACCCGTT
1 GACCCGACCCGTT
4011298 GACCCGACCCGTT
1 GACCCGACCCGTT
4011311 GA
1 GA
4011313 TAGTTGACCG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 8 0.26
13 23 0.74
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:4013498 original size:14 final size:14
Alignment explanation
Indices: 4013476--4013517 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
4013466 ATTGTTTCTG
4013476 GGAGCTATTCATTT
1 GGAGCTATTCATTT
* *
4013490 GGAGTTATTCATTG
1 GGAGCTATTCATTT
4013504 GGAGCTATTCATTT
1 GGAGCTATTCATTT
4013518 CTTCCTTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (14 bp):
GGAGCTATTCATTT
Found at i:4013773 original size:24 final size:24
Alignment explanation
Indices: 4013742--4013829 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
4013732 TTCTATTATA
4013742 ATACTTGACTTGGATTCTGATCGG
1 ATACTTGACTTGGATTCTGATCGG
* * *
4013766 ATAATTGACTTGGATTCTGATTGA
1 ATACTTGACTTGGATTCTGATCGG
* * *
4013790 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACTTGGATTCTGATCGG
4013814 ATACTTGA-TCTGGATT
1 ATACTTGACT-TGGATT
4013830 ATATTATGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (24 bp):
ATACTTGACTTGGATTCTGATCGG
Found at i:4013839 original size:24 final size:24
Alignment explanation
Indices: 4013742--4013839 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 24
4013732 TTCTATTATA
* * **
4013742 ATACTTGACTTGGATTCTGATCGG
1 ATACTTGACCTGGATTATGATATG
* * *
4013766 ATAATTGACTTGGATTCTGAT-TG
1 ATACTTGACCTGGATTATGATATG
* *
4013789 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTATGATATG
*
4013814 ATACTTGATCTGGATTAT-ATTATG
1 ATACTTGACCTGGATTATGA-TATG
4013838 AT
1 AT
4013840 TTTTGATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (24 bp):
ATACTTGACCTGGATTATGATATG
Found at i:4014045 original size:2 final size:2
Alignment explanation
Indices: 4014038--4014105 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
4014028 CAGATGGGGG
4014038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4014079 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4014106 TTTTTTAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4015714 original size:34 final size:34
Alignment explanation
Indices: 4015671--4015888 Score: 157
Period size: 34 Copynumber: 5.8 Consensus size: 34
4015661 CTTTGGAATC
*
4015671 CTTTCATGCCAATAATACACCCATATGCATTATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATT
* * *
4015705 CTTTCATGCCGATAATGTACCCATATACATATCAGCTAAGGCAT
1 CTTTCATGCCAATAATGCACCCATATGCAT-T-A--T------T
*
4015749 CCTTTCATGCCAATAATGCACCCATATGTATTATT
1 -CTTTCATGCCAATAATGCACCCATATGCATTATT
* * *
4015784 CTTTCATGCCGATAATGTACCCATATACATATCAGCTAAGGCAT
1 CTTTCATGCCAATAATGCACCCATATGCAT-T-A--T------T
4015828 CCTTTCATGCCAATAATGCACCCATATGCATTATT
1 -CTTTCATGCCAATAATGCACCCATATGCATTATT
*
4015863 CTTTCATGCCGATAATGCACCCATAT
1 CTTTCATGCCAATAATGCACCCATAT
4015889 ACATATCAGC
Statistics
Matches: 146, Mismatches: 16, Indels: 44
0.71 0.08 0.21
Matches are distributed among these distances:
34 77 0.53
35 4 0.03
36 2 0.01
38 2 0.01
41 2 0.01
43 2 0.01
44 4 0.03
45 53 0.36
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.33
Consensus pattern (34 bp):
CTTTCATGCCAATAATGCACCCATATGCATTATT
Found at i:4015756 original size:45 final size:44
Alignment explanation
Indices: 4015705--4015912 Score: 177
Period size: 45 Copynumber: 5.1 Consensus size: 44
4015695 ATGCATTATT
*
4015705 CTTTCATGCCGATAATGTACCCATATACATATCAGCTAAGGCATC
1 CTTTCATGCCGATAATGCACCCATATACATATCAGCTAA-GCATC
* * *
4015750 CTTTCATGCCAATAATGCACCCATAT--GTAT----T----ATT
1 CTTTCATGCCGATAATGCACCCATATACATATCAGCTAAGCATC
*
4015784 CTTTCATGCCGATAATGTACCCATATACATATCAGCTAAGGCATC
1 CTTTCATGCCGATAATGCACCCATATACATATCAGCTAA-GCATC
* *
4015829 CTTTCATGCCAATAATGCACCCATATGCAT-T-A--T-----T-
1 CTTTCATGCCGATAATGCACCCATATACATATCAGCTAAGCATC
4015863 CTTTCATGCCGATAATGCACCCATATACATATCAGCTAAAGCATC
1 CTTTCATGCCGATAATGCACCCATATACATATCAGCT-AAGCATC
*
4015908 ATTTC
1 CTTTC
4015913 TAATGAACCT
Statistics
Matches: 127, Mismatches: 14, Indels: 44
0.69 0.08 0.24
Matches are distributed among these distances:
34 54 0.43
35 2 0.02
36 4 0.03
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
43 4 0.03
44 2 0.02
45 57 0.45
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (44 bp):
CTTTCATGCCGATAATGCACCCATATACATATCAGCTAAGCATC
Found at i:4015771 original size:79 final size:79
Alignment explanation
Indices: 4015668--4016020 Score: 531
Period size: 79 Copynumber: 4.6 Consensus size: 79
4015658 TAACTTTGGA
*
4015668 ATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
4015733 ATATCAGCTAAGGC
66 ATATCAGCTAAGGC
*
4015747 ATCCTTTCATGCCAATAATGCACCCATATGTATTATTCTTTCATGCCGATAATGTACCCATATAC
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
4015812 ATATCAGCTAAGGC
66 ATATCAGCTAAGGC
*
4015826 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATAC
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
*
4015891 ATATCAGCTAAAGC
66 ATATCAGCTAAGGC
* * * * *
4015905 AT-CATT--T--C--TAATGAACCTATATGCATTATTCTTTCATGTCGATAATGTACCCAAATAC
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
**
4015963 ATATCAAATAAGGC
66 ATATCAGCTAAGGC
* * *
4015977 ATCATTTCATGCCCATAATGTACCCATATGCATTATTCTTTCAT
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCAT
4016021 TCATTAGTTT
Statistics
Matches: 249, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
72 58 0.23
73 2 0.01
74 1 0.00
75 1 0.00
76 1 0.00
77 1 0.00
78 3 0.01
79 182 0.73
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (79 bp):
ATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATAC
ATATCAGCTAAGGC
Found at i:4015963 original size:72 final size:72
Alignment explanation
Indices: 4015841--4016020 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 72
4015831 TTCATGCCAA
* * **
4015841 TAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATACATATCAGCTAAAGCA
1 TAATGAACCCATATGCATTATTCTTTCATGCCGATAATGCACCCAAATACATATCAAATAAAGCA
4015906 TCATTTC
66 TCATTTC
* * * *
4015913 TAATGAACCTATATGCATTATTCTTTCATGTCGATAATGTACCCAAATACATATCAAATAAGGCA
1 TAATGAACCCATATGCATTATTCTTTCATGCCGATAATGCACCCAAATACATATCAAATAAAGCA
4015978 TCATTTCATGCCC
66 TCA-TT--T---C
*
4015991 ATAATGTACCCATATGCATTATTCTTTCAT
1 -TAATGAACCCATATGCATTATTCTTTCAT
4016021 TCATTAGTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
72 60 0.66
73 2 0.02
75 1 0.01
78 1 0.01
79 27 0.30
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (72 bp):
TAATGAACCCATATGCATTATTCTTTCATGCCGATAATGCACCCAAATACATATCAAATAAAGCA
TCATTTC
Found at i:4016002 original size:151 final size:155
Alignment explanation
Indices: 4015672--4016020 Score: 517
Period size: 151 Copynumber: 2.3 Consensus size: 155
4015662 TTTGGAATCC
* *
4015672 TTTCATGCCAATAATACACCCATATGCATTATTCTTTCATGCCGATAATGTACCCATATACATAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATACATAT
* * * *
4015737 CAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGTATTATTCTTTCATGCCGATAATGT
66 CAGCTAAAGCATCCATT-AT-CC-ATAATGAACCCATATGCATTATTCTTTCATGCCGATAATGT
* ** *
4015802 ACCCATATACATATCAGCTAAGGCATCC
128 ACCCAAATACATATCAAATAAGGCATCA
4015830 TTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATACATAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATACATAT
* *
4015895 CAGCTAAAGCAT-CATT-T-C-TAATGAACCTATATGCATTATTCTTTCATGTCGATAATGTACC
66 CAGCTAAAGCATCCATTATCCATAATGAACCCATATGCATTATTCTTTCATGCCGATAATGTACC
4015956 CAAATACATATCAAATAAGGCATCA
131 CAAATACATATCAAATAAGGCATCA
* *
4015981 TTTCATGCCCATAATGTACCCATATGCATTATTCTTTCAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTTTCAT
4016021 TCATTAGTTT
Statistics
Matches: 177, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
151 98 0.55
153 1 0.01
155 1 0.01
157 3 0.02
158 74 0.42
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (155 bp):
TTTCATGCCAATAATGCACCCATATGCATTATTCTTTCATGCCGATAATGCACCCATATACATAT
CAGCTAAAGCATCCATTATCCATAATGAACCCATATGCATTATTCTTTCATGCCGATAATGTACC
CAAATACATATCAAATAAGGCATCA
Found at i:4016433 original size:20 final size:20
Alignment explanation
Indices: 4016404--4016458 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
4016394 TTATCCTTCA
* * *
4016404 GTATCCATACCCTTATTATG
1 GTATCGATACCCCTACTATG
4016424 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
4016446 GTATCGATACCCC
1 GTATCGATACCCC
4016459 CTACCAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:4016448 original size:22 final size:23
Alignment explanation
Indices: 4016411--4016455 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
4016401 TCAGTATCCA
*
4016411 TACCCTTATTATGGTATCGATAC
1 TACCCTTACTATGGTATCGATAC
4016434 TACCC-TACTATGGTATCGATAC
1 TACCCTTACTATGGTATCGATAC
4016456 CCCCTACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (23 bp):
TACCCTTACTATGGTATCGATAC
Found at i:4021166 original size:21 final size:21
Alignment explanation
Indices: 4021142--4021183 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4021132 TTATTGTATT
4021142 TTTGTAAG-AGTACTTTGTGTA
1 TTTG-AAGTAGTACTTTGTGTA
*
4021163 TTTGGAGTAGTACTTTGTGTA
1 TTTGAAGTAGTACTTTGTGTA
4021184 CTACGGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (21 bp):
TTTGAAGTAGTACTTTGTGTA
Found at i:4023825 original size:18 final size:18
Alignment explanation
Indices: 4023804--4023844 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4023794 TAAATTGTTC
4023804 GAAATGACTGAATTAAAT
1 GAAATGACTGAATTAAAT
* *
4023822 GAAAGGACTGAATTGAAT
1 GAAATGACTGAATTAAAT
4023840 GAAAT
1 GAAAT
4023845 ACCCTTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (18 bp):
GAAATGACTGAATTAAAT
Found at i:4024602 original size:26 final size:27
Alignment explanation
Indices: 4024552--4024604 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4024542 TGTATTTGAG
* *
4024552 TATTTTCCTCTGATTTTAAATTATGAT
1 TATTTTCCTCTGATTTAAAAATATGAT
*
4024579 TATTTT-CTTTGATTTAAAAATATGAT
1 TATTTTCCTCTGATTTAAAAATATGAT
4024605 CTTTGATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.55
Consensus pattern (27 bp):
TATTTTCCTCTGATTTAAAAATATGAT
Found at i:4035736 original size:214 final size:214
Alignment explanation
Indices: 4035367--4035792 Score: 825
Period size: 214 Copynumber: 2.0 Consensus size: 214
4035357 AGAATTATGC
*
4035367 TGAGCCCATAATTATGCTAGTTTACCTTCTAGACTCTATTTCTATCCGTCCGCATGTAGATCCAT
1 TGAGCCCAAAATTATGCTAGTTTACCTTCTAGACTCTATTTCTATCCGTCCGCATGTAGATCCAT
*
4035432 AATTACGTATTTTTGGGGTTAACCCATTACCCTACATGCGACTAATAAAGAGATCCACGTATCTT
66 AATTACGTATTTTTGGGGTTAACCCATTACCCTACATGCGACTAATAAAGAGATCCACGTATCTC
4035497 ATATTAAAAATGGGTTATTTATTTCATATCATTTTTATTTTATTTTATTCAATTTGATCTCTTAT
131 ATATTAAAAATGGGTTATTTATTTCATATCATTTTTATTTTATTTTATTCAATTTGATCTCTTAT
4035562 TTTCTATACATGTAAATGA
196 TTTCTATACATGTAAATGA
4035581 TGAGCCCAAAATTATGCTAGTTTACCTTCTAGACTCTATTTCTATCCGTCCGCATGTAGATCCAT
1 TGAGCCCAAAATTATGCTAGTTTACCTTCTAGACTCTATTTCTATCCGTCCGCATGTAGATCCAT
4035646 AATTACGTATTTTTGGGGTTAACCCATTACCCTACATGCGACTAATAAAGAGATCCACGTATCTC
66 AATTACGTATTTTTGGGGTTAACCCATTACCCTACATGCGACTAATAAAGAGATCCACGTATCTC
*
4035711 ATATTGAAAATGGGTTATTTATTTCATATCATTTTTATTTTATTTTATTCAATTTGATCTCTTAT
131 ATATTAAAAATGGGTTATTTATTTCATATCATTTTTATTTTATTTTATTCAATTTGATCTCTTAT
4035776 TTTCTATACATGTAAAT
196 TTTCTATACATGTAAAT
4035793 TAATCTTGTC
Statistics
Matches: 209, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 209 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (214 bp):
TGAGCCCAAAATTATGCTAGTTTACCTTCTAGACTCTATTTCTATCCGTCCGCATGTAGATCCAT
AATTACGTATTTTTGGGGTTAACCCATTACCCTACATGCGACTAATAAAGAGATCCACGTATCTC
ATATTAAAAATGGGTTATTTATTTCATATCATTTTTATTTTATTTTATTCAATTTGATCTCTTAT
TTTCTATACATGTAAATGA
Found at i:4036513 original size:34 final size:30
Alignment explanation
Indices: 4036475--4036543 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
4036465 TTGATATAAC
4036475 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
4036509 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
4036538 AATTTA
1 AATTTA
4036544 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:4036554 original size:29 final size:30
Alignment explanation
Indices: 4036484--4036543 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
4036474 CAATTTAAGG
4036484 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
4036515 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
4036544 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:4036657 original size:13 final size:13
Alignment explanation
Indices: 4036641--4036670 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4036631 CATGCACCCC
4036641 TGCAGTGCATCCA
1 TGCAGTGCATCCA
*
4036654 TGCAGTGCATCTA
1 TGCAGTGCATCCA
4036667 TGCA
1 TGCA
4036671 CCTGCACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (13 bp):
TGCAGTGCATCCA
Found at i:4036799 original size:20 final size:20
Alignment explanation
Indices: 4036734--4036807 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
4036724 AATGCAATTA
*
4036734 GTGCATCGATGCATCCTT-CT
1 GTGCATCGATGCAT-CTTGAT
**
4036754 GTGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-TTGAT
*
4036775 GTGCATCGATGCATCTTGTT
1 GTGCATCGATGCATCTTGAT
*
4036795 GTGCATCCATGCA
1 GTGCATCGATGCA
4036808 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 28 0.62
21 16 0.36
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGAT
Found at i:4045644 original size:23 final size:22
Alignment explanation
Indices: 4045611--4045666 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
4045601 GTAACTTAGT
*
4045611 AAAATCAATTATA-AATTCTCAAA
1 AAAATAAATTATATAA-T-TCAAA
*
4045634 AATATAAATTA-ATAATTCAAA
1 AAAATAAATTATATAATTCAAA
4045655 AAAATAAATTAT
1 AAAATAAATTAT
4045667 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.54
22 2 0.07
23 11 0.39
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATAAATTATATAATTCAAA
Found at i:4058001 original size:2 final size:2
Alignment explanation
Indices: 4057994--4058031 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4057984 AATTAATACA
4057994 AT AT AT AT 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
4058032 GCAAAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4058140 original size:17 final size:19
Alignment explanation
Indices: 4058118--4058158 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
4058108 TTATTTATCA
*
4058118 ATATTAT-ATTTTTTA-TT
1 ATATTATCATATTTTAGTT
4058135 ATATTATCATATTTTAGTT
1 ATATTATCATATTTTAGTT
4058154 ATATT
1 ATATT
4058159 TAAGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATTATCATATTTTAGTT
Found at i:4058155 original size:22 final size:22
Alignment explanation
Indices: 4058100--4058155 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
4058090 GAATTTTTTC
*
4058100 TATTTTAATTATTTATCAATATTA
1 TATTTT-ATTA-TTATCAATATCA
*
4058124 TATTTT-TTATTAT-ATTATCA
1 TATTTTATTATTATCAATATCA
4058144 TATTTTAGTTAT
1 TATTTTA-TTAT
4058156 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 7 0.25
24 6 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTTATTATTATCAATATCA
Found at i:4058583 original size:18 final size:18
Alignment explanation
Indices: 4058552--4058590 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4058542 CGATTGAATC
* *
4058552 AAAAATATTTAAAAAATA
1 AAAAAAATTAAAAAAATA
4058570 AAAAAAATTAAAAAAATA
1 AAAAAAATTAAAAAAATA
4058588 AAA
1 AAA
4058591 GTATTTTAAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAAATTAAAAAAATA
Found at i:4065632 original size:15 final size:14
Alignment explanation
Indices: 4065596--4065634 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4065586 GTTTTGTTAT
*
4065596 TTTTAAATTTAATC
1 TTTTAATTTTAATC
*
4065610 TCTTAATTTTAATAC
1 TTTTAATTTTAAT-C
4065625 TTTTAATTTT
1 TTTTAATTTT
4065635 TTAATATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATTTTAATC
Found at i:4066341 original size:12 final size:12
Alignment explanation
Indices: 4066324--4066348 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4066314 TTTTCCCTTG
4066324 ATTATTTTAATA
1 ATTATTTTAATA
4066336 ATTATTTTAATA
1 ATTATTTTAATA
4066348 A
1 A
4066349 ATAGTTGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTTTAATA
Found at i:4066929 original size:47 final size:47
Alignment explanation
Indices: 4066860--4066953 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
4066850 ATAGTATTAC
* * *
4066860 TTTATTTTCCAAATAAATGTATGTGAACTAGAAATCATGCGGTTAGG
1 TTTATTTTCCAAACAAATGTATGTGAACTAGAAAGCATGAGGTTAGG
4066907 TTTATTTTTCCAAACAAA-GTATGTGAACTAGAAAGCATGAGGTTAGG
1 TTTA-TTTTCCAAACAAATGTATGTGAACTAGAAAGCATGAGGTTAGG
4066954 ATATATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 31 0.72
48 12 0.28
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGTATGTGAACTAGAAAGCATGAGGTTAGG
Found at i:4067237 original size:184 final size:188
Alignment explanation
Indices: 4066924--4067298 Score: 695
Period size: 184 Copynumber: 2.0 Consensus size: 188
4066914 TTCCAAACAA
4066924 AGTATGTGAACTAGAAAGCATGAGGTTAGGATATATATATATACCATGATGAATATGATCTTTTC
1 AGTATGTGAACTAGAAAGCATGAGGTTAGG--A-ATATATATACCATGATGAATATGATCTTTTC
4066989 TTTCTATTAATTGGTACTATCCATTTTATTTTTTCTTATCTTTATCTATTCTGTAGATACATTTT
63 TTTCTATTAATTGGTACTATCCATTTTATTTTTTCTTATCTTTATCTATTCTGTAGATACATTTT
4067054 A-TTTGCTCTTACTTGTTTATATTGATTTC-TTT-TTTACATTGAATGATCATGACATGAT
128 ATTTTGCTCTTACTTGTTTATATTGATTTCTTTTGTTTACATTGAATGATCATGACATGAT
4067112 AGTATGTGAACTAGAAAGCATGAGGTTAGG-ATATATATACCATGATGAATATGATCTTTTCTTT
1 AGTATGTGAACTAGAAAGCATGAGGTTAGGAATATATATACCATGATGAATATGATCTTTTCTTT
4067176 CTATTAATTGGTACTATCCATTTTATTTTTTCTTATCTTTATCTATTCTGTAGATACATTTTATT
66 CTATTAATTGGTACTATCCATTTTATTTTTTCTTATCTTTATCTATTCTGTAGATACATTTTATT
4067241 TTGCTCTTACTTGTTTATATTGATTTCTTTTGTTTACATTGAATGATCATGACATGAT
131 TTGCTCTTACTTGTTTATATTGATTTCTTTTGTTTACATTGAATGATCATGACATGAT
4067299 TAGAATGTAT
Statistics
Matches: 184, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
184 97 0.53
185 28 0.15
186 3 0.02
187 26 0.14
188 30 0.16
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (188 bp):
AGTATGTGAACTAGAAAGCATGAGGTTAGGAATATATATACCATGATGAATATGATCTTTTCTTT
CTATTAATTGGTACTATCCATTTTATTTTTTCTTATCTTTATCTATTCTGTAGATACATTTTATT
TTGCTCTTACTTGTTTATATTGATTTCTTTTGTTTACATTGAATGATCATGACATGAT
Done.