Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 12 of 12
Found at i:2511863 original size:21 final size:21
Alignment explanation
Indices: 2511796--2511906 Score: 68
Period size: 21 Copynumber: 5.2 Consensus size: 21
2511786 GTTTAGTATC
2511796 GATACTAATAGTCTTATGTAA
1 GATACTAATAGTCTTATGTAA
* ** *
2511817 GATAAATTCGTAGT-TTA-GTATC
1 GAT--ACTAATAGTCTTATGTA-A
2511839 GATACTAATAGTCTTATGTAA
1 GATACTAATAGTCTTATGTAA
* ** *
2511860 GATAAATTCGTAGT-TTA-GTATC
1 GAT--ACTAATAGTCTTATGTA-A
2511882 GATACTAATAGTCTTATGTAA
1 GATACTAATAGTCTTATGTAA
2511903 GATA
1 GATA
2511907 AATTATTTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 20
0.64 0.16 0.20
Matches are distributed among these distances:
20 12 0.19
21 22 0.34
22 18 0.28
23 12 0.19
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
GATACTAATAGTCTTATGTAA
Found at i:2521584 original size:19 final size:19
Alignment explanation
Indices: 2521562--2521598 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2521552 AATAAAATTC
2521562 GAGATCGAAAAGGAATTTT
1 GAGATCGAAAAGGAATTTT
2521581 GAGATCGAAAAGGAATTT
1 GAGATCGAAAAGGAATTT
2521599 GGGGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.24
Consensus pattern (19 bp):
GAGATCGAAAAGGAATTTT
Found at i:2524376 original size:195 final size:196
Alignment explanation
Indices: 2524044--2524427 Score: 725
Period size: 195 Copynumber: 2.0 Consensus size: 196
2524034 CTCAGGAAGA
* *
2524044 AAACCAAGAAGGAGAGCAAGTACGAAGCAGCGGAGGCCATGGTGGCAAGAGGTCGCTCGAAAAGT
1 AAACCAAGAAAGAGAGCAAGTACGAAGCAGCGGAGGCCATGATGGCAAGAGGTCGCTCGAAAAGT
2524109 CAAAAGCCAAAGTGGAGAGGGAGATCAAAGTCGAAGTCCAGACTGGGAAAAGATGAATGTGCCTT
66 CAAAAGCCAAAGTGGAGAGGGAGATCAAAGTCGAAGTCCAGACTGGGAAAAGATGAATGTGCCTT
2524174 TTGTCATGAGAAAGACCATTGGAA-AAAGATTGTCCGAAGCTGAAGAAGAAAGGAAAAGCTGCTC
131 TTGTCATGAGAAAGACCATTGGAAGAAAGATTGTCCGAAGCTGAAGAAGAAAGGAAAAGCTGCTC
2524238 C
196 C
*
2524239 AAACCAAGAAAGAGAGCAAGTACGAAGCAGCGGAGGCCATGATGGCAAGATGTCGCTCGAAAAGT
1 AAACCAAGAAAGAGAGCAAGTACGAAGCAGCGGAGGCCATGATGGCAAGAGGTCGCTCGAAAAGT
2524304 CAAAAGCCAAAGTGGAGAGGGAGATCAAAGTCGAAGTCCAGACTGGGAAAAGATGAATGTGCCTT
66 CAAAAGCCAAAGTGGAGAGGGAGATCAAAGTCGAAGTCCAGACTGGGAAAAGATGAATGTGCCTT
*
2524369 TTGTCATGAGAAAGGCCATTGGAAGAAAGATTGTCCGAAGCTGAAGAAGAAAGGAAAAG
131 TTGTCATGAGAAAGACCATTGGAAGAAAGATTGTCCGAAGCTGAAGAAGAAAGGAAAAG
2524428 TTGATCCATA
Statistics
Matches: 184, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
195 150 0.82
196 34 0.18
ACGTcount: A:0.39, C:0.16, G:0.31, T:0.14
Consensus pattern (196 bp):
AAACCAAGAAAGAGAGCAAGTACGAAGCAGCGGAGGCCATGATGGCAAGAGGTCGCTCGAAAAGT
CAAAAGCCAAAGTGGAGAGGGAGATCAAAGTCGAAGTCCAGACTGGGAAAAGATGAATGTGCCTT
TTGTCATGAGAAAGACCATTGGAAGAAAGATTGTCCGAAGCTGAAGAAGAAAGGAAAAGCTGCTC
C
Found at i:2524673 original size:18 final size:19
Alignment explanation
Indices: 2524637--2524675 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2524627 TAAAAAAAAT
*
2524637 TCAAGAGCTTAATTAAAGC
1 TCAAGAGCTCAATTAAAGC
*
2524656 TCAAGA-CTCAATTCAAGC
1 TCAAGAGCTCAATTAAAGC
2524674 TC
1 TC
2524676 GAATTTGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAGAGCTCAATTAAAGC
Found at i:2526216 original size:7 final size:7
Alignment explanation
Indices: 2526201--2526355 Score: 105
Period size: 7 Copynumber: 22.3 Consensus size: 7
2526191 GTGCATAACT
*
2526201 TAAAACC
1 TAAACCC
2526208 TAAACCC
1 TAAACCC
2526215 TAAACCC
1 TAAACCC
*
2526222 TAAACCT
1 TAAACCC
*
2526229 TAAACCT
1 TAAACCC
*
2526236 TAAACTC
1 TAAACCC
*
2526243 TAAACCA
1 TAAACCC
*
2526250 TAAACCT
1 TAAACCC
* *
2526257 TAAATCA
1 TAAACCC
*
2526264 TAAACCA
1 TAAACCC
*
2526271 TAAACAC
1 TAAACCC
**
2526278 TAAACTA
1 TAAACCC
*
2526285 TAAACAC
1 TAAACCC
*
2526292 TAAACCA
1 TAAACCC
2526299 TAAACCC
1 TAAACCC
**
2526306 T-AACTA
1 TAAACCC
*
2526312 TAAACTC
1 TAAACCC
*
2526319 TAAACCA
1 TAAACCC
2526326 TAAACCC
1 TAAACCC
**
2526333 TAAATAC
1 TAAACCC
**
2526340 TAAACTA
1 TAAACCC
2526347 TAAACCC
1 TAAACCC
2526354 TA
1 TA
2526356 TCACATAATT
Statistics
Matches: 115, Mismatches: 32, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
6 4 0.03
7 111 0.97
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:2526223 original size:14 final size:14
Alignment explanation
Indices: 2526201--2526336 Score: 132
Period size: 14 Copynumber: 9.8 Consensus size: 14
2526191 GTGCATAACT
* *
2526201 TAAAACCTAAACCC
1 TAAACCCTAAACCA
*
2526215 TAAACCCTAAACCT
1 TAAACCCTAAACCA
*
2526229 TAAACCTTAAACTC-
1 TAAACCCTAAAC-CA
* *
2526243 TAAACCATAAACCT
1 TAAACCCTAAACCA
* *
2526257 TAAATCATAAACCA
1 TAAACCCTAAACCA
* *
2526271 TAAACACTAAACTA
1 TAAACCCTAAACCA
*
2526285 TAAACACTAAACCA
1 TAAACCCTAAACCA
*
2526299 TAAACCCT-AACTA
1 TAAACCCTAAACCA
*
2526312 TAAACTCTAAACCA
1 TAAACCCTAAACCA
2526326 TAAACCCTAAA
1 TAAACCCTAAA
2526337 TACTAAACTA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
13 12 0.12
14 90 0.87
15 1 0.01
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:2526452 original size:14 final size:14
Alignment explanation
Indices: 2526433--2526462 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2526423 TATAATTATC
*
2526433 AATAATGTATTTTT
1 AATAATGTAATTTT
2526447 AATAATGTAATTTT
1 AATAATGTAATTTT
2526461 AA
1 AA
2526463 AAAATATAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:2531061 original size:194 final size:196
Alignment explanation
Indices: 2530726--2531118 Score: 569
Period size: 194 Copynumber: 2.0 Consensus size: 196
2530716 CATTCCAGAC
*
2530726 AAGACACAGGGTCAGCCCTGCATAAAGTTAACATTCATCATGTTTGTCGTCTGGGATCCTAGGTG
1 AAGACACAGGGTCAGCCCTGCATAAAGTTAACATTCATCATGTTTCTCGTCTGGGATCCTAGGTG
2530791 TTTCTCAGACTCGTATGCAAGTGTTGCAACACAAGTTTCGAACACGATAATTCAACAAAAACGAA
66 TTTCTCAGACTCGTATGCAAGTGTTGCAACACAAGTTTCGAACACGATAATTCAACAAAAACGAA
* * * *
2530856 GAATCGAAACAACATAGATTCGGATTTAAGTTATACACTTT-GATAAGTAGCTTGCATACCTAAG
131 GAATCGAAACAACATAGATTCGAATCTAAGTTATACACTTTCGACAAGTAGCTTGCACACCTAAG
2530920 A
196 A
* * * *
2530921 AAGACACAGGGTCCA-TCCTGCAT-AATTTAACATTCATCATTTTTCTCGTCTTGGATCCTAGG-
1 AAGACACAGGGT-CAGCCCTGCATAAAGTTAACATTCATCATGTTTCTCGTCTGGGATCCTAGGT
* * * * *
2530983 GTTTACTCGGACTCGTATGCAAGTGTTGCAACATAAGTTTCGAATACGCTAATTCAACAAAAATG
65 GTTT-CTCAGACTCGTATGCAAGTGTTGCAACACAAGTTTCGAACACGATAATTCAACAAAAACG
* * * * *
2531048 AAGAATGGAAACAACGTAGCTTCGAATCTAAGTTATGCATTTTCGACAAGTAGCTTGCACACCTA
129 AAGAATCGAAACAACATAGATTCGAATCTAAGTTATACACTTTCGACAAGTAGCTTGCACACCTA
2531113 AGA
194 AGA
2531116 AAG
1 AAG
2531119 TGGAGAAAGC
Statistics
Matches: 176, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
193 4 0.02
194 126 0.72
195 44 0.25
196 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (196 bp):
AAGACACAGGGTCAGCCCTGCATAAAGTTAACATTCATCATGTTTCTCGTCTGGGATCCTAGGTG
TTTCTCAGACTCGTATGCAAGTGTTGCAACACAAGTTTCGAACACGATAATTCAACAAAAACGAA
GAATCGAAACAACATAGATTCGAATCTAAGTTATACACTTTCGACAAGTAGCTTGCACACCTAAG
A
Found at i:2541276 original size:66 final size:64
Alignment explanation
Indices: 2541129--2541320 Score: 275
Period size: 63 Copynumber: 3.0 Consensus size: 64
2541119 CCCAGTTTTT
* *
2541129 TGAAGCAAAACAAGGTTATGATTGAGGAACAAGATAATGAAGAAAA--TGATGTTGTTGATGAAA
1 TGAAGCAAAACAAGGTTTTGATTGAGGAACAAGATAA-GAAGAAAATGTGAAGTTGTTGATGAAA
* *
2541192 CGAAGCAAAACAAGGTTTTGATTGAGGAACAAGATAAAGAAGAAAATGGTGAAGATGTTGATGAA
1 TGAAGCAAAACAAGGTTTTGATTGAGGAACAAGAT-AAGAAGAAAAT-GTGAAGTTGTTGATGAA
2541257 A
64 A
*
2541258 TGAAGCAAAACAAGGTTTTGATTGAGGAACAAGAT--GAAGAAAATGATGAATTTGTTGATGAAA
1 TGAAGCAAAACAAGGTTTTGATTGAGGAACAAGATAAGAAGAAAATG-TGAAGTTGTTGATGAAA
2541321 CCGAGGATCT
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
62 1 0.01
63 65 0.56
64 2 0.02
66 49 0.42
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (64 bp):
TGAAGCAAAACAAGGTTTTGATTGAGGAACAAGATAAGAAGAAAATGTGAAGTTGTTGATGAAA
Found at i:2541745 original size:45 final size:45
Alignment explanation
Indices: 2541675--2541791 Score: 189
Period size: 45 Copynumber: 2.6 Consensus size: 45
2541665 GCTCCATCAA
* * * *
2541675 AGCCAAATATAGAGGTAATAACAGCAGCACCATCAGCGCCAACGG
1 AGCCAAATATAGAGGTAACAGCAGCACCACCATCAGCGCCAACAG
2541720 AGCCAAATATAGAGGTAACAGCAGCACCACCATCAGCGCCAACAG
1 AGCCAAATATAGAGGTAACAGCAGCACCACCATCAGCGCCAACAG
*
2541765 AGCCAGATATAGAGGTAACAGCAGCAC
1 AGCCAAATATAGAGGTAACAGCAGCAC
2541792 TCCCTCCACC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.40, C:0.27, G:0.22, T:0.10
Consensus pattern (45 bp):
AGCCAAATATAGAGGTAACAGCAGCACCACCATCAGCGCCAACAG
Found at i:2541925 original size:48 final size:48
Alignment explanation
Indices: 2541849--2541952 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
2541839 AGATGTATAT
*
2541849 CAGCACCAACAATGCCAAATATAGAGGTAACAGCAGCACAACCACTAC
1 CAGCGCCAACAATGCCAAATATAGAGGTAACAGCAGCACAACCACTAC
*
2541897 CAGCGCCAACAATGCCAAATATAGAGGTAACAGCAGCACAACCATTAC
1 CAGCGCCAACAATGCCAAATATAGAGGTAACAGCAGCACAACCACTAC
2541945 CAGCGCCA
1 CAGCGCCA
2541953 GTTATAGAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (48 bp):
CAGCGCCAACAATGCCAAATATAGAGGTAACAGCAGCACAACCACTAC
Found at i:2544037 original size:15 final size:15
Alignment explanation
Indices: 2544017--2544110 Score: 58
Period size: 15 Copynumber: 6.7 Consensus size: 15
2544007 AAAATATAAA
2544017 ATTATTATATAATAT
1 ATTATTATATAATAT
2544032 ATTATT-T-TAATA-
1 ATTATTATATAATAT
**
2544044 ATTTAAAATATAATA-
1 A-TTATTATATAATAT
* * *
2544059 AATA-AATATAAAAT
1 ATTATTATATAATAT
*
2544073 ATTATTATAAAATAT
1 ATTATTATATAATAT
*
2544088 ATTATT-T-TAAAAT
1 ATTATTATATAATAT
*
2544101 ATTAATATAT
1 ATTATTATAT
2544111 TTGGGTCGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
12 1 0.02
13 25 0.41
14 9 0.15
15 26 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTATATAATAT
Found at i:2544053 original size:41 final size:41
Alignment explanation
Indices: 2543987--2544078 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
2543977 TATATATTAA
* * *
2543987 AATATATTA-TTTAATTATTAAAAATATAA-AATTATTATAT
1 AATATATTATTTTAATAATTAAAAATATAATAAATA-AATAT
*
2544027 AATATATTATTTTAATAATTTAAAATATAATAAATAAATAT
1 AATATATTATTTTAATAATTAAAAATATAATAAATAAATAT
*
2544068 AAAATATTATT
1 AATATATTATT
2544079 ATAAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 9 0.20
41 32 0.71
42 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (41 bp):
AATATATTATTTTAATAATTAAAAATATAATAAATAAATAT
Found at i:2544055 original size:28 final size:28
Alignment explanation
Indices: 2544017--2544110 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 28
2544007 AAAATATAAA
*
2544017 ATTATTATATAATATATTATTTTAATAAT
1 ATTAATATATAATATATTATTTTAA-AAT
* * * * *
2544046 -TTAAAATATAATAAATAAATATAAAAT
1 ATTAATATATAATATATTATTTTAAAAT
* *
2544073 ATTATTATAAAATATATTATTTTAAAAT
1 ATTAATATATAATATATTATTTTAAAAT
2544101 ATTAATATAT
1 ATTAATATAT
2544111 TTGGGTCGGG
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
27 3 0.06
28 46 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATATATAATATATTATTTTAAAAT
Found at i:2544082 original size:23 final size:22
Alignment explanation
Indices: 2544023--2544083 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
2544013 TAAAATTATT
* *
2544023 ATATAATATATTATT-TTAATA
1 ATATAAAATATTATTATAAATA
*
2544044 ATTTAAAATA-TA--ATAAATAA
1 ATATAAAATATTATTATAAAT-A
2544064 ATATAAAATATTATTATAAA
1 ATATAAAATATTATTATAAA
2544084 ATATATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 10 0.32
23 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAAAATATTATTATAAATA
Found at i:2546608 original size:44 final size:46
Alignment explanation
Indices: 2546551--2546641 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 46
2546541 TTATTTGATG
2546551 TTTTATTGATAATGGAATGATC-TTTTG-AGAAATCAAAAACGTTA
1 TTTTATTGATAATGGAATGATCTTTTTGTAGAAATCAAAAACGTTA
2546595 TTTTATATG-TAATGGAATGATCTTTTTGTTAGAAATCAAAAACGTTA
1 TTTTAT-TGATAATGGAATGATCTTTTTG-TAGAAATCAAAAACGTTA
2546642 GTGACCGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
44 19 0.44
45 7 0.16
47 17 0.40
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (46 bp):
TTTTATTGATAATGGAATGATCTTTTTGTAGAAATCAAAAACGTTA
Found at i:2548940 original size:6 final size:6
Alignment explanation
Indices: 2548929--2548994 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
2548919 CATCCTCTAA
* * * *
2548929 TTCCTC TTCCTC AAT-CTC CTCCTC TTCCTC CTCCTC CTCCTC TTCCTC
1 TTCCTC TTCCTC -TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC
*
2548977 TTCCTC CTCCTC TTCCTC
1 TTCCTC TTCCTC TTCCTC
2548995 CAAATCACCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
5 1 0.02
6 49 0.96
7 1 0.02
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (6 bp):
TTCCTC
Found at i:2548953 original size:18 final size:18
Alignment explanation
Indices: 2548930--2548994 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
2548920 ATCCTCTAAT
2548930 TCCTCTTCCTCAAT-CTCC
1 TCCTCTTCCTC-ATCCTCC
*
2548948 TCCTCTTCCTCCTCCTCC
1 TCCTCTTCCTCATCCTCC
*
2548966 TCCTCTTCCTCTTCCTCC
1 TCCTCTTCCTCATCCTCC
2548984 TCCTCTTCCTC
1 TCCTCTTCCTC
2548995 CAAATCACCC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 1 0.02
18 43 0.98
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCTCTTCCTCATCCTCC
Found at i:2548959 original size:12 final size:12
Alignment explanation
Indices: 2548944--2548995 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
2548934 CTTCCTCAAT
2548944 CTCCTCCTCTTC
1 CTCCTCCTCTTC
*
2548956 CTCCTCCTCCTC
1 CTCCTCCTCTTC
*
2548968 CTCTTCCTCTTC
1 CTCCTCCTCTTC
2548980 CTCCTCCTCTTC
1 CTCCTCCTCTTC
2548992 CTCC
1 CTCC
2548996 AAATCACCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTCCTCTTC
Found at i:2554264 original size:13 final size:14
Alignment explanation
Indices: 2554246--2554282 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2554236 AATTTACGTA
*
2554246 AATAAATTATT-TT
1 AATAAATAATTATT
2554259 AATAAATAATTATT
1 AATAAATAATTATT
2554273 AA-AAATAATT
1 AATAAATAATT
2554283 CATTCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAATAATTATT
Found at i:2555580 original size:21 final size:22
Alignment explanation
Indices: 2555556--2555608 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2555546 CGATTCAACC
2555556 TAAATTTTTTTGAT-TTTTTAT
1 TAAATTTTTTTGATATTTTTAT
*
2555577 TAAATGTTTTTGATATTTTTAT
1 TAAATTTTTTTGATATTTTTAT
*
2555599 TTAATTTTTT
1 TAAATTTTTT
2555609 AAATAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (22 bp):
TAAATTTTTTTGATATTTTTAT
Found at i:2555595 original size:22 final size:20
Alignment explanation
Indices: 2555556--2555608 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2555546 CGATTCAACC
2555556 TAAATTTTTTTGATTTTTTAT
1 TAAA-TTTTTTGATTTTTTAT
2555577 TAAATGTTTTTGATATTTTTAT
1 TAAAT-TTTTTGAT-TTTTTAT
*
2555599 TTAATTTTTT
1 TAAATTTTTT
2555609 AAATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.59
22 11 0.38
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (20 bp):
TAAATTTTTTGATTTTTTAT
Found at i:2557159 original size:46 final size:47
Alignment explanation
Indices: 2557085--2557201 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 47
2557075 ATGATCACCG
* *
2557085 GTGACATCGGATCCAAACTAGTCAGTGGTTAAT-TACAAGATAATCA
1 GTGATATCGGATCCGAACTAGTCAGTGGTTAATGTACAAGATAATCA
* * * * *
2557131 GTGATATCGGATCTGAACTGGTCGGTGGTTAATGTACATGATAATTA
1 GTGATATCGGATCCGAACTAGTCAGTGGTTAATGTACAAGATAATCA
*
2557178 GTGATATCTGATCCGAACTA-TCAG
1 GTGATATCGGATCCGAACTAGTCAG
2557202 GTCCTCCAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 31 0.53
47 28 0.47
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (47 bp):
GTGATATCGGATCCGAACTAGTCAGTGGTTAATGTACAAGATAATCA
Found at i:2567109 original size:19 final size:20
Alignment explanation
Indices: 2567071--2567117 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
2567061 AATAGTAAAC
*
2567071 TAAAATTCCTAATAAAAATAA
1 TAAAA-TCCAAATAAAAATAA
2567092 TAAAATCCAAAT-AAAATAA
1 TAAAATCCAAATAAAAATAA
2567111 TAAAATC
1 TAAAATC
2567118 TAAAGTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 14 0.56
20 6 0.24
21 5 0.20
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATCCAAATAAAAATAA
Found at i:2567798 original size:18 final size:18
Alignment explanation
Indices: 2567775--2567820 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2567765 ACTAAAATTG
2567775 GTATCGATACTCAAACAA
1 GTATCGATACTCAAACAA
*
2567793 GTATCGATACTCAAGCAA
1 GTATCGATACTCAAACAA
2567811 GTATCGATAC
1 GTATCGATAC
2567821 CACAGACCAA
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:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (18 bp):
GTATCGATACTCAAACAA
Found at i:2568099 original size:15 final size:17
Alignment explanation
Indices: 2568078--2568120 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
2568068 GTAATTAACT
2568078 CATAACAACTAGGAT-A
1 CATAACAACTAGGATGA
*
2568094 -ATAACAATTAGGATGA
1 CATAACAACTAGGATGA
2568110 CATAA-AACTAG
1 CATAACAACTAG
2568121 CCTTGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 13 0.57
16 6 0.26
17 4 0.17
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (17 bp):
CATAACAACTAGGATGA
Found at i:2570986 original size:43 final size:43
Alignment explanation
Indices: 2570880--2571027 Score: 181
Period size: 43 Copynumber: 3.4 Consensus size: 43
2570870 GTTTTTTAAC
* *
2570880 AAAAAATGCCGCAATAGGTATTGATATTTAGCGGCGTTTGT-A
1 AAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
* * * *
2570922 CACAAACGCTGCAATAGGTGTTGATATTTAGCGGCGTTTTTCA
1 AAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
* * *
2570965 GAAAAACGCCGCAATAGGTGTTGATAATTAACGGCGTTTGTCA
1 AAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
* *
2571008 TAAAAAACGACGTAATAGGT
1 -AAAAAACGCCGCAATAGGT
2571028 TATGATGTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 35 0.39
43 38 0.43
44 16 0.18
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (43 bp):
AAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
Found at i:2571098 original size:43 final size:43
Alignment explanation
Indices: 2571036--2571299 Score: 309
Period size: 43 Copynumber: 6.2 Consensus size: 43
2571026 GTTATGATGT
* * * *
2571036 AAACGTCGCAGTAGATGTTGATGTTTTGCGGTGTTTTTCTCAC
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
* * * *
2571079 AAACGCCGTAGTAGGTGTTGCTGTTTTGCGGCG-TTTTCACAC
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
* * *
2571121 AAACGCTGCAGTAGGTTTTGATGTTTTGCGGAGTTTTTCTCAC
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
* * *
2571164 AAACGACGTAGTAGGTATTGATGTTTTGCGGCG-TTTTCCCAC
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
* * * *
2571206 AAACACCGCAGTAGGTTTTGATGTTTTGTGGCATTTTTCTCAC
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
* * *
2571249 AAACGCCGTAGTAGGTATTGATGTTTTGCGGCATTTTTGCT-AA
1 AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTT-CTCAC
2571292 AAACGCCG
1 AAACGCCG
2571300 GTAAAGGTCT
Statistics
Matches: 188, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 71 0.38
43 115 0.61
44 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (43 bp):
AAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTCTCAC
Found at i:2571179 original size:85 final size:85
Alignment explanation
Indices: 2571042--2571285 Score: 373
Period size: 85 Copynumber: 2.9 Consensus size: 85
2571032 ATGTAAACGT
* * * * *
2571042 CGCAGTAGATGTTGATGTTTTGCGGTGTTTTTCTCACAAACGCCGTAGTAGGTGTTGCTGTTTTG
1 CGCAGTAGGTTTTGATGTTTTGCGGAGTTTTTCTCACAAACGCCGTAGTAGGTATTGATGTTTTG
*
2571107 CGGCGTTTTCACACAAACGC
66 CGGCGTTTTCACACAAACAC
* *
2571127 TGCAGTAGGTTTTGATGTTTTGCGGAGTTTTTCTCACAAACGACGTAGTAGGTATTGATGTTTTG
1 CGCAGTAGGTTTTGATGTTTTGCGGAGTTTTTCTCACAAACGCCGTAGTAGGTATTGATGTTTTG
*
2571192 CGGCGTTTTCCCACAAACAC
66 CGGCGTTTTCACACAAACAC
*
2571212 CGCAGTAGGTTTTGATGTTTTGTGGCA-TTTTTCTCACAAACGCCGTAGTAGGTATTGATGTTTT
1 CGCAGTAGGTTTTGATGTTTTGCGG-AGTTTTTCTCACAAACGCCGTAGTAGGTATTGATGTTTT
*
2571276 GCGGCATTTT
65 GCGGCGTTTT
2571286 TGCTAAAAAC
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
85 144 0.99
86 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (85 bp):
CGCAGTAGGTTTTGATGTTTTGCGGAGTTTTTCTCACAAACGCCGTAGTAGGTATTGATGTTTTG
CGGCGTTTTCACACAAACAC
Found at i:2571749 original size:24 final size:22
Alignment explanation
Indices: 2571698--2571751 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
2571688 CTGTTGATAT
*
2571698 GCTGCTTC-TCTCTGTGCTGTC
1 GCTGCTTCTTCTCTGTGCTCTC
*
2571719 GCTGCTTCTTTCTCTGCTGCTCTG
1 GCTGCTTC-TTCTCTG-TGCTCTC
2571743 GCTGCTTCT
1 GCTGCTTCT
2571752 GCTGATGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.29
23 7 0.25
24 13 0.46
ACGTcount: A:0.00, C:0.33, G:0.22, T:0.44
Consensus pattern (22 bp):
GCTGCTTCTTCTCTGTGCTCTC
Found at i:2580684 original size:41 final size:41
Alignment explanation
Indices: 2580618--2580778 Score: 204
Period size: 41 Copynumber: 4.0 Consensus size: 41
2580608 GTTTATACAA
*
2580618 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACACCACTATTGATTATCACTATTGC-GGCGTTTGTT
*
2580658 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
2580698 CTAAAAACACCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGT-T
2580741 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
2580779 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (41 bp):
AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:2580736 original size:82 final size:81
Alignment explanation
Indices: 2580619--2580777 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 81
2580609 TTTATACAAA
* * *
2580619 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACACCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
2580683 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
2580700 AAAAACACCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACACCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
2580765 TATTGCGGCGTTT
65 TATTGCGGCGTTT
2580778 GAGGAATAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 17 0.24
82 54 0.75
83 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACACCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:2580924 original size:41 final size:42
Alignment explanation
Indices: 2580807--2581005 Score: 181
Period size: 42 Copynumber: 4.8 Consensus size: 42
2580797 GTGTGTAATA
*
2580807 TATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACCACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
* * * *
2580849 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTGG-TATAAACGCCGC-TAATTTACCACTC
* *
2580890 TATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
* * * * * *
2580932 TATTGCGGCATTTTTTGTAAAAACGCCGCTATATGT-CAACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTA-ATTTACCACTC
* * ** *
2580974 TATTGCAGCGTTTTTACTACAAACGCCGCTAA
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAA
2581006 AGTATCAATT
Statistics
Matches: 127, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
41 34 0.27
42 90 0.71
43 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (42 bp):
TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
Found at i:2583508 original size:17 final size:17
Alignment explanation
Indices: 2583488--2583521 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2583478 GTAAAATCAC
2583488 TATAAATCCAAAATATT
1 TATAAATCCAAAATATT
* *
2583505 TATAGATGCAAAATATT
1 TATAAATCCAAAATATT
2583522 CATCTTCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (17 bp):
TATAAATCCAAAATATT
Found at i:2586378 original size:39 final size:39
Alignment explanation
Indices: 2586324--2586402 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2586314 ATTTGATTAG
2586324 ATAAACTAATAAATATAAGTAAATTTAAAGCACCTTGTA
1 ATAAACTAATAAATATAAGTAAATTTAAAGCACCTTGTA
2586363 ATAAACTAATAAATATAAGTAAATTTAAAGCACCTTGTA
1 ATAAACTAATAAATATAAGTAAATTTAAAGCACCTTGTA
2586402 A
1 A
2586403 ACGGTTCCAA
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:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (39 bp):
ATAAACTAATAAATATAAGTAAATTTAAAGCACCTTGTA
Found at i:2587301 original size:16 final size:16
Alignment explanation
Indices: 2587264--2587308 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
2587254 TAAACTTTTT
2587264 TATTATATAATTTTCA
1 TATTATATAATTTTCA
*
2587280 TAATTATATATTTTTCA
1 T-ATTATATAATTTTCA
2587297 TATTATCATAAT
1 TATTAT-ATAAT
2587309 ACGGCTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATATAATTTTCA
Found at i:2588272 original size:27 final size:27
Alignment explanation
Indices: 2588237--2588289 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2588227 GATACAGATA
*
2588237 ATGAGTTTTGAT-TCGGATTTAGATTTG
1 ATGAATTTTGATATCGGATTT-GATTTG
*
2588264 ATGAATTTTGATATCGTATTTGATTT
1 ATGAATTTTGATATCGGATTTGATTT
2588290 ATAAGGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.51
Consensus pattern (27 bp):
ATGAATTTTGATATCGGATTTGATTTG
Found at i:2589330 original size:18 final size:19
Alignment explanation
Indices: 2589307--2589343 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2589297 TCAGTAATCC
2589307 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATCTTT
2589325 TATTCTCACTGGTAATCTT
1 TATTCT-ACTGGTAATCTT
2589344 ACATTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTT
Found at i:2591097 original size:30 final size:30
Alignment explanation
Indices: 2591061--2591140 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
2591051 TATTTTTTTA
* **
2591061 AAAAAATGACCAAAAAAATTATTAGGTGCT
1 AAAAAATGACCAAAAATATTATTAGACGCT
* *
2591091 AAAAAAT-ACCAGAAATATTATTATACGCT
1 AAAAAATGACCAAAAATATTATTAGACGCT
*
2591120 AAAAAATGACCGAAAATATTA
1 AAAAAATGACCAAAAATATTA
2591141 AAAAAATGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAAAATGACCAAAAATATTATTAGACGCT
Found at i:2596045 original size:21 final size:21
Alignment explanation
Indices: 2596021--2596068 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2596011 ATTATCCAAT
*
2596021 AAACTTGACATCCATAACATC
1 AAACTTGAAATCCATAACATC
*
2596042 AAACTTGAAATCCATAACATT
1 AAACTTGAAATCCATAACATC
2596063 AAACTT
1 AAACTT
2596069 TTAGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (21 bp):
AAACTTGAAATCCATAACATC
Found at i:2598154 original size:19 final size:20
Alignment explanation
Indices: 2598117--2598154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2598107 CTTTTTTTTA
*
2598117 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2598137 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2598155 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2600155 original size:41 final size:41
Alignment explanation
Indices: 2600105--2600323 Score: 237
Period size: 41 Copynumber: 5.4 Consensus size: 41
2600095 GATATATATA
* * * *
2600105 TATATAAACGCCACTAAAGTAAGAGTCTTTAGTGGCATTTG
1 TATAAAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTG
* *
2600146 TATAAAAACGCCACTAAAGT-ATAGTATTTAGCGGCGTTTA
1 TATAAAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTG
*
2600186 TATAAAAACGCCACTAAAGTACA-AGTATTTAGCGGCGCTTG
1 TATAAAAACGCCACTAAAGTA-AGAGTATTTAGCGGCGTTTG
* * * * *
2600227 TGCTTAAAACGCCACTAAAGT-ACAGTATTTGGCTGCGTTTG
1 T-ATAAAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTG
* * * * *
2600268 TATAAAAACACCACTAAAGTACGAGTTTTTAGCGGCATTTA
1 TATAAAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTG
*
2600309 TATAAAAACGGCACT
1 TATAAAAACGCCACT
2600324 TTATATAAAA
Statistics
Matches: 148, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
40 52 0.35
41 78 0.53
42 18 0.12
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (41 bp):
TATAAAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTG
Found at i:2600265 original size:82 final size:81
Alignment explanation
Indices: 2600103--2600323 Score: 264
Period size: 82 Copynumber: 2.7 Consensus size: 81
2600093 GTGATATATA
* * * *
2600103 TATATATAAACGCCACTAAAGTA-AGAGTCTTTAGTGGCATTTGTATAAAAACGCCACTAAAGTA
1 TATATAAAAACGCCACTAAAGTACA-AGTATTTAGCGGCACTTGTATAAAAACGCCACTAAAGTA
*
2600167 TAGTATTTAGCGGCGTT
65 CAGTATTTAGCGGCGTT
* * *
2600184 TATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCGCTTGTGCTTAAAACGCCACTAAAGTA
1 TATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCACTTGT-ATAAAAACGCCACTAAAGTA
* *
2600249 CAGTATTTGGCTGCGTT
65 CAGTATTTAGCGGCGTT
* * * * * * *
2600266 TGTATAAAAACACCACTAAAGTACGAGTTTTTAGCGGCATTTATATAAAAACGGCACT
1 TATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCACTTGTATAAAAACGCCACT
2600324 TTATATAAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
81 48 0.41
82 70 0.59
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (81 bp):
TATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCACTTGTATAAAAACGCCACTAAAGTAC
AGTATTTAGCGGCGTT
Found at i:2600333 original size:17 final size:18
Alignment explanation
Indices: 2600300--2600341 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2600290 GAGTTTTTAG
2600300 CGGCA-TTTATATAAAAA
1 CGGCACTTTATATAAAAA
2600317 CGGCACTTTATATAAAAA
1 CGGCACTTTATATAAAAA
2600335 CGGCACT
1 CGGCACT
2600342 AAAGTACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (18 bp):
CGGCACTTTATATAAAAA
Found at i:2606715 original size:23 final size:23
Alignment explanation
Indices: 2606671--2606716 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2606661 CGGGAATGAG
**
2606671 GTATTCGTTCCCTAAATGTTTTA
1 GTATTCGTTCCCTAAAAATTTTA
**
2606694 GTATTCGTTTTCTAAAAATTTTA
1 GTATTCGTTCCCTAAAAATTTTA
2606717 AATTATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (23 bp):
GTATTCGTTCCCTAAAAATTTTA
Found at i:2608233 original size:45 final size:45
Alignment explanation
Indices: 2608164--2608264 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
2608154 CGACCCTTTA
* * *
2608164 ATATCGATACTAGATGATTGAGATAGGTTGTTTGACCAAATGGGC
1 ATATCGATACTAGATGATTAAGATAGATTGTTTGACCAAATAGGC
* *
2608209 ATATCGATACTAGATGATTAAGATAGATTTTTTGACCAAATAGGT
1 ATATCGATACTAGATGATTAAGATAGATTGTTTGACCAAATAGGC
2608254 ATATCGATACT
1 ATATCGATACT
2608265 TTCCAGGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (45 bp):
ATATCGATACTAGATGATTAAGATAGATTGTTTGACCAAATAGGC
Found at i:2608379 original size:18 final size:19
Alignment explanation
Indices: 2608336--2608381 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2608326 CTCTTATTAA
*
2608336 GAGTATTGATACTCTACCTT
1 GAGTATCGATACTCTA-CTT
*
2608356 GGGTATCGATACTCT-CTT
1 GAGTATCGATACTCTACTT
2608374 GAGTATCG
1 GAGTATCG
2608382 GTACCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (19 bp):
GAGTATCGATACTCTACTT
Found at i:2608471 original size:20 final size:20
Alignment explanation
Indices: 2608421--2608472 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2608411 TTGTGGTTCC
2608421 CAGTATCGATACCACCCTGT
1 CAGTATCGATACCACCCTGT
**
2608441 GGGTA-CTGATACCTACCCTG-
1 CAGTATC-GATACC-ACCCTGT
2608461 CAGTATCGATAC
1 CAGTATCGATAC
2608473 TCATTGGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (20 bp):
CAGTATCGATACCACCCTGT
Found at i:2616003 original size:28 final size:28
Alignment explanation
Indices: 2615952--2616190 Score: 184
Period size: 29 Copynumber: 8.3 Consensus size: 28
2615942 CATTTTATAG
* *
2615952 AAATAGCACCATTTTTAAAATAATTACAA
1 AAATAGCA-CATTTTTAAATTAATTACTA
*
2615981 AAATAGCACATTTTTGAATTAATTACTA
1 AAATAGCACATTTTTAAATTAATTACTA
*
2616009 AAATAGCACACATTTTAAATTAATTACTA
1 AAATAGCACA-TTTTTAAATTAATTACTA
* *
2616038 AAATAACACCA-TTTTGAATTAATTACTA
1 AAATAGCA-CATTTTTAAATTAATTACTA
*
2616066 AAATAGCACCCA-TTTCAAATTAATTACTGA
1 AAATAGCA--CATTTTTAAATTAATTACT-A
**
2616096 AAA-AGCACCCA-TTTCGAATTAATTACTA
1 AAATAGCA--CATTTTTAAATTAATTACTA
* * * *
2616124 AAATAACACCCA-TTTCAAATTAATTATTG
1 AAATAGCA--CATTTTTAAATTAATTACTA
* **
2616153 AAATATCAC-TCATTTCGAATTAATTACTA
1 AAATAGCACAT--TTTTAAATTAATTACTA
2616182 AAATAGCAC
1 AAATAGCAC
2616191 CAGGTCCACG
Statistics
Matches: 182, Mismatches: 20, Indels: 16
0.83 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 54 0.30
29 121 0.66
30 6 0.03
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATAGCACATTTTTAAATTAATTACTA
Found at i:2616016 original size:57 final size:56
Alignment explanation
Indices: 2615952--2616192 Score: 297
Period size: 57 Copynumber: 4.2 Consensus size: 56
2615942 CATTTTATAG
* * * *
2615952 AAATAGCACCATTTTTAAAATAATTACAAAAATAGCA-CATTTTTGAATTAATTACTA
1 AAATAGCACCA-TTTCAAATTAATTACTAAAATAGCACCA-TTTCGAATTAATTACTA
* * *
2616009 AAATAGCACACATTTTAAATTAATTACTAAAATAACACCATTTTGAATTAATTACTA
1 AAATAGCAC-CATTTCAAATTAATTACTAAAATAGCACCATTTCGAATTAATTACTA
2616066 AAATAGCACCCATTTCAAATTAATTACTGAAAA-AGCACCCATTTCGAATTAATTACTA
1 AAATAGCA-CCATTTCAAATTAATTACT-AAAATAGCA-CCATTTCGAATTAATTACTA
* * * *
2616124 AAATAACACCCATTTCAAATTAATTATTGAAATATCACTCATTTCGAATTAATTACTA
1 AAATAGCA-CCATTTCAAATTAATTACTAAAATAGCAC-CATTTCGAATTAATTACTA
2616182 AAATAGCACCA
1 AAATAGCACCA
2616193 GGTCCACGAT
Statistics
Matches: 166, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
57 83 0.50
58 83 0.50
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.33
Consensus pattern (56 bp):
AAATAGCACCATTTCAAATTAATTACTAAAATAGCACCATTTCGAATTAATTACTA
Found at i:2616134 original size:58 final size:58
Alignment explanation
Indices: 2615996--2616191 Score: 288
Period size: 58 Copynumber: 3.4 Consensus size: 58
2615986 GCACATTTTT
* * *
2615996 GAATTAATTACTAAAATAGCACACATTTTAAATTAATTACT-AAAATAACA-CCATTTT
1 GAATTAATTACTAAAATAGCACCCATTTCAAATTAATTACTGAAAA-AACACCCATTTC
*
2616053 GAATTAATTACTAAAATAGCACCCATTTCAAATTAATTACTGAAAAAGCACCCATTTC
1 GAATTAATTACTAAAATAGCACCCATTTCAAATTAATTACTGAAAAAACACCCATTTC
* * * * *
2616111 GAATTAATTACTAAAATAACACCCATTTCAAATTAATTATTGAAATATCACTCATTTC
1 GAATTAATTACTAAAATAGCACCCATTTCAAATTAATTACTGAAAAAACACCCATTTC
2616169 GAATTAATTACTAAAATAGCACC
1 GAATTAATTACTAAAATAGCACC
2616192 AGGTCCACGA
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
57 42 0.33
58 85 0.67
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (58 bp):
GAATTAATTACTAAAATAGCACCCATTTCAAATTAATTACTGAAAAAACACCCATTTC
Found at i:2616235 original size:17 final size:18
Alignment explanation
Indices: 2616202--2616243 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
2616192 AGGTCCACGA
2616202 TCGGGTCGGGTCAACGGG
1 TCGGGTCGGGTCAACGGG
*
2616220 TCGGGTTGGG-CAACGGG
1 TCGGGTCGGGTCAACGGG
2616237 TCGGGTC
1 TCGGGTC
2616244 AAAATCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (18 bp):
TCGGGTCGGGTCAACGGG
Done.