Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:1037638 original size:108 final size:108
Alignment explanation
Indices: 1037442--1037638 Score: 243
Period size: 108 Copynumber: 1.8 Consensus size: 108
1037432 GGGACCAAAT
* * * * *
1037442 CTATTATTTTTCCTTTTTCTTGCGTGTTATATAATTTTTGGTATATTCATTATTTAGTCCCTCTG
1 CTATTATTTTCCCTTTTTCTTGCATGGTATATAATTTTTGGTATATTCATTATTTAGTCCCTATA
* ** *
1037507 ACTTTAGCGTGTTTTTTATTTTGGTCATCTATGAGGACTGAAA
66 ACTTTAGCGTGCTTTACACTTTGGTCATCTATGAGGACTGAAA
* * * *
1037550 CTATTATTTTCCC-TTTTCTTTGCATGGTATATAATTTTTGGTCTATTTATTGTTTGGTCCCTAT
1 CTATTATTTTCCCTTTTTC-TTGCATGGTATATAATTTTTGGTATATTCATTATTTAGTCCCTAT
* *
1037614 AAGTTTAGTGTGCTTTACACTTTGG
65 AACTTTAGCGTGCTTTACACTTTGG
1037639 CCATATGTAG
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
107 5 0.07
108 68 0.93
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (108 bp):
CTATTATTTTCCCTTTTTCTTGCATGGTATATAATTTTTGGTATATTCATTATTTAGTCCCTATA
ACTTTAGCGTGCTTTACACTTTGGTCATCTATGAGGACTGAAA
Found at i:1040547 original size:43 final size:44
Alignment explanation
Indices: 1040450--1040547 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 44
1040440 AAAATTTTAT
* * * **
1040450 GAAATTGTAAAAAATTAGAGGCCTTAATTATAAAGGTAGAAATT
1 GAAATTGAAAAAAAATAGAGGCCTCAATTATAAAGGTAGAAAAA
1040494 GAAATT-AAAAAAAATAGAGGCCTCAATTATAAAGGTA-AAAAA
1 GAAATTGAAAAAAAATAGAGGCCTCAATTATAAAGGTAGAAAAA
**
1040536 GGGATTGAAAAA
1 GAAATTGAAAAA
1040548 TTAGAGAACT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 7 0.15
43 33 0.72
44 6 0.13
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.23
Consensus pattern (44 bp):
GAAATTGAAAAAAAATAGAGGCCTCAATTATAAAGGTAGAAAAA
Found at i:1047134 original size:23 final size:23
Alignment explanation
Indices: 1047080--1047135 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
1047070 GATATTGTGT
*
1047080 TCTTCTATCGGCATCAGTCTTGC
1 TCTTCTATTGGCATCAGTCTTGC
1047103 TCTTCTATTGGCATCAGTCTTTGC
1 TCTTCTATTGGCATCAGTC-TTGC
1047127 TCTT-TATTG
1 TCTTCTATTG
1047136 TTCATGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.46
Consensus pattern (23 bp):
TCTTCTATTGGCATCAGTCTTGC
Found at i:1050283 original size:31 final size:31
Alignment explanation
Indices: 1050226--1050304 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
1050216 AGTTCATAGA
*
1050226 TCCCGAAGAAC-TAGG-AAATAGTCCATATG
1 TCCCGAAGAACATAGGTAAACAGTCCATATG
1050255 TCCCGAAGAACATAGGTAAACAGTCCATATG
1 TCCCGAAGAACATAGGTAAACAGTCCATATG
1050286 TCCCGAAGAACATAGGTAA
1 TCCCGAAGAACATAGGTAA
1050305 GTCCTAGACC
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 11 0.23
30 4 0.09
31 32 0.68
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
TCCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:1054614 original size:30 final size:30
Alignment explanation
Indices: 1054531--1054620 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
1054521 CTCGAAGGAC
*
1054531 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGT-AA
* *
1054562 CA-TCCATATGT-CCGATAAAACATAAGTAA
1 CAGTCCATATGTCCCGA-AGAACATAGGTAA
1054591 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1054621 ACCCTCGACC
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
29 8 0.16
30 35 0.70
31 7 0.14
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (30 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:1055949 original size:3 final size:3
Alignment explanation
Indices: 1055941--1056046 Score: 130
Period size: 3 Copynumber: 35.0 Consensus size: 3
1055931 TCTCGTACAT
*
1055941 GAA GAA GAA GAA G-A GAAA GAA GGAA GAA GAAA GAA GAA GAA -AA G-C
1 GAA GAA GAA GAA GAA G-AA GAA -GAA GAA G-AA GAA GAA GAA GAA GAA
1055986 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA
1056031 GAA GAAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA
1056047 TATCTTTCAT
Statistics
Matches: 92, Mismatches: 2, Indels: 18
0.82 0.02 0.16
Matches are distributed among these distances:
2 7 0.08
3 71 0.77
4 14 0.15
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1066929 original size:13 final size:13
Alignment explanation
Indices: 1066911--1066958 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1066901 TAAAAAACAA
*
1066911 ATAATATATATAT
1 ATAATATATAAAT
1066924 ATAATATATAAAT
1 ATAATATATAAAT
* *
1066937 ATAAATATGTAAAA
1 AT-AATATATAAAT
1066951 ATAATATA
1 ATAATATA
1066959 ATAATGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:1066969 original size:18 final size:19
Alignment explanation
Indices: 1066909--1066959 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1066899 TTTAAAAAAC
* *
1066909 AAATAATATATATATATAA
1 AAATAATATAAATATGTAA
*
1066928 TATATAAATATAAATATGTAA
1 -AAAT-AATATAAATATGTAA
1066949 AAATAATATAA
1 AAATAATATAA
1066960 TAATGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 6 0.23
21 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATAATATAAATATGTAA
Found at i:1067110 original size:2 final size:2
Alignment explanation
Indices: 1067105--1067129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1067095 TAAAGAATGA
1067105 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 A
1067130 ATAAAAGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1069130 original size:36 final size:33
Alignment explanation
Indices: 1069064--1069139 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 33
1069054 AAAGGTTTTT
1069064 AAGAG-AATGATTTTAAAGGTTCTTTGTGTTTC
1 AAGAGAAATGATTTTAAAGGTTCTTTGTGTTTC
*
1069096 AAGAGAAATGATTTTCAAAGGTTTTTTTTGTGTTTC
1 AAGAGAAATGATTTT-AAAGG--TTCTTTGTGTTTC
1069132 AAGAGAAA
1 AAGAGAAA
1069140 CTGTCTCCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 5 0.13
33 9 0.23
34 5 0.13
36 20 0.51
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (33 bp):
AAGAGAAATGATTTTAAAGGTTCTTTGTGTTTC
Found at i:1069390 original size:65 final size:66
Alignment explanation
Indices: 1069298--1069436 Score: 235
Period size: 65 Copynumber: 2.1 Consensus size: 66
1069288 TGTTCTAAAA
* * *
1069298 GAAACTGTCTCAAGGGAGACGAAATTTGTTTAATGTAAAATATATTC-AAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAAGATTTTGTTTCAAG
*
1069362 T
66 G
1069363 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAAGATTTTGTTTCAAG
1069428 G
66 G
1069429 GAAACTGT
1 GAAACTGT
1069437 TTTCAAAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
65 44 0.64
66 25 0.36
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (66 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAAGATTTTGTTTCAAG
G
Found at i:1069601 original size:37 final size:37
Alignment explanation
Indices: 1069550--1069621 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1069540 TCAATGTTTA
* * *
1069550 TGTTTCAAGAGAAACTGTCTCGAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1069587 TGTTTCAGGGGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
1069622 CCATTTCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1069703 original size:37 final size:36
Alignment explanation
Indices: 1069652--1069824 Score: 127
Period size: 37 Copynumber: 5.0 Consensus size: 36
1069642 TCAATGTTTA
* *
1069652 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAA-GGAGACAAAATTT
*
1069689 TGTTTCAAGGGAAACTATCTTAA-GAGAC-AAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGAGACAAAATTT
** * * *
1069722 CATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGAGACAAAATTT
*
1069750 ATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAG-GAGACAAAATTT
*
1069788 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGACAAAATTT
1069825 AAGAAAAACA
Statistics
Matches: 106, Mismatches: 17, Indels: 26
0.71 0.11 0.17
Matches are distributed among these distances:
28 2 0.02
29 16 0.15
30 1 0.01
32 3 0.03
33 18 0.17
34 3 0.03
35 5 0.05
37 55 0.52
38 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGGAGACAAAATTT
Found at i:1069783 original size:201 final size:204
Alignment explanation
Indices: 1069421--1069822 Score: 677
Period size: 201 Copynumber: 2.0 Consensus size: 204
1069411 AAAGATTTTG
1069421 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1069486 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGAGAAATGTTTTCAATGTTTAT
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTAT
* * * *
1069551 GTTTCAAGAGAAACTGTCTCGAGGGAGACAAAATTTTGTTTCAGGGGAAACTATCTCAAGAGAGA
131 GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1069616 CAAAATCCA
196 CAAAATCCA
*
1069625 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
* *
1069689 TGTTTCAAGGGAAACTATCT-TA-AGAGAC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTA
*
1069751 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
130 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1069816 ATAAAAT
195 ACAAAAT
1069823 TTAAGAAAAA
Statistics
Matches: 187, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
201 98 0.52
202 6 0.03
203 49 0.26
204 34 0.18
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (204 bp):
TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTAT
GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAATCCA
Found at i:1069794 original size:99 final size:102
Alignment explanation
Indices: 1069251--1069823 Score: 674
Period size: 102 Copynumber: 5.7 Consensus size: 102
1069241 CAAAAGATTT
* * * * ** * *
1069251 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTTG-TTCTAAAAGAAACTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTC-AAGGGAAACTATCTCAAGAGA
* ** ** * * *
1069315 GACGAAATTTGTTT-AATGTAAAATATATTCAAAGATTT-
65 GACAAAATTCATTTCAA-GGGAAATGTTTTCAATG-TTTA
* * **
1069353 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT-AATGTAAAACATAT-TCAA-A-
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA-GGGAAAC-TATCTCAAGAG
* ** *
1069413 AG----ATTTTGTTTCAAGGGAAACTGTTTTCAAAGTTTA
64 AGACAAAATTCATTTCAAGGGAAA-TGTTTTCAATGTTTA
1069449 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
1069513 ACAAAATTTATTTCAAGAGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1069550 TGTTTCAAGAGAAACTGTCTCGAGGGAGACAAAATTTTGTTTCAGGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1069615 ACAAAATCCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1069652 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCT-TA-AGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1069715 AC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
1069751 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1069816 ATAAAATT
66 ACAAAATT
1069824 TAAGAAAAAC
Statistics
Matches: 419, Mismatches: 34, Indels: 36
0.86 0.07 0.07
Matches are distributed among these distances:
95 18 0.04
96 59 0.14
97 3 0.01
98 2 0.00
99 90 0.21
100 9 0.02
101 64 0.15
102 174 0.42
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1069905 original size:36 final size:36
Alignment explanation
Indices: 1069865--1070186 Score: 177
Period size: 36 Copynumber: 8.9 Consensus size: 36
1069855 TCTTTCGAGT
1069865 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
* ** * * * * ** *
1069901 AAAACAATCTTGAGGGAAATAAA-TCCTATTCCAAGT
1 AAAACAGTCTCAAGTGAGACAAAGT-CTGTTTTAAGA
* *
1069937 AAAACAGTCTCAAGTGAGACAAGGTTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
** * * * * * * * *
1069973 ATGACAATCTTAAGGGAAATAAA-TCCTCTTTCAAGT
1 AAAACAGTCTCAAGTGAGACAAAGT-CTGTTTTAAGA
*
1070009 AAAACAGTCTCAAGTGAGACAAGGTCTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
* ** * * * * ** *
1070045 AAAACAATCTTGAGGGAAATAAA-TCCTCTTCCAAGT
1 AAAACAGTCTCAAGTGAGACAAAGT-CTGTTTTAAGA
*
1070081 AAAACAGTCTCAAGTGAGACAAGGTCTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
** * * * * *
1070117 ATGACAATCTCAAGGGAAATAAA-TCT-TCTTTGAAGT
1 AAAACAGTCTCAAGTGAGACAAAGTCTGT-TTT-AAGA
* *
1070153 AAAACAGTCTCAAGTGAGACAAGGTCTGTATTAA
1 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAA
1070187 ATGAGACTGT
Statistics
Matches: 193, Mismatches: 83, Indels: 20
0.65 0.28 0.07
Matches are distributed among these distances:
34 1 0.01
35 9 0.05
36 174 0.90
37 8 0.04
38 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGA
Found at i:1069939 original size:72 final size:72
Alignment explanation
Indices: 1069822--1070186 Score: 577
Period size: 72 Copynumber: 5.1 Consensus size: 72
1069812 CGAGATAAAA
* *
1069822 TTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCGAGTAAAACAGTCTCAAGTGAGACAA
1 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
*
1069887 AGTCTGT
66 GGTCTGT
* *
1069894 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTATTCCAAGTAAAACAGTCTCAAGTGAGACAA
1 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
*
1069959 GGTTTGT
66 GGTCTGT
** *
1069966 TTTAAGAATGACAATCTTAAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1070031 GGTCTGT
66 GGTCTGT
*
1070038 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTCCAAGTAAAACAGTCTCAAGTGAGACAA
1 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1070103 GGTCTGT
66 GGTCTGT
** ** * *
1070110 TTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTGAAGTAAAACAGTCTCAAGTGAGACAA
1 TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1070175 GGTCTGT
66 GGTCTGT
*
1070182 ATTAA
1 TTTAA
1070187 ATGAGACTGT
Statistics
Matches: 269, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 269 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (72 bp):
TTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
GGTCTGT
Found at i:1071475 original size:83 final size:89
Alignment explanation
Indices: 1071366--1071592 Score: 261
Period size: 95 Copynumber: 2.6 Consensus size: 89
1071356 GGCTAGCTGA
* * * *
1071366 ATCCATAAAGCCGGGGCATTTTACCAATTGCTCTAGAGGGACATCTTAA-TA-T-T-TA-AAT-A
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGTATAGAATCA
* * *
1071425 CCTTTATCAGGTTAGTTGAATCTT
66 CCTTTATCAGGCTAGCTGAATATT
1071449 ATCCATAAAGCCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTCAA---TTATTGTATA--
1071513 GTAATCACCTTTATCAGGCTAGCTGAATATT
60 G-AATCACCTTTATCAGGCTAGCTGAATATT
* *
1071544 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1071593 GCTTTATTGT
Statistics
Matches: 121, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
82 1 0.01
83 43 0.36
87 2 0.02
88 1 0.01
89 1 0.01
90 2 0.02
94 3 0.02
95 67 0.55
96 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (89 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGTATAGAATCA
CCTTTATCAGGCTAGCTGAATATT
Found at i:1071590 original size:95 final size:95
Alignment explanation
Indices: 1071424--1071605 Score: 303
Period size: 95 Copynumber: 1.9 Consensus size: 95
1071414 ATATTTAAAT
* * *
1071424 ACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1071489 ACAACTCAAGCTTTATTGTATAGTGTAATC
66 ACAACTCAAGCTTTATTGTATAGTGTAATC
*
1071519 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGTGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGG
*
1071583 GATAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
1071606 TATATAATAT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 2 0.02
95 79 0.98
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTGTAATC
Found at i:1075956 original size:2 final size:2
Alignment explanation
Indices: 1075951--1075975 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1075941 TAAAGAATGA
1075951 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 A
1075976 ATAAAAGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1076104 original size:7 final size:8
Alignment explanation
Indices: 1076093--1076168 Score: 55
Period size: 8 Copynumber: 9.1 Consensus size: 8
1076083 ATTAAGAGGA
1076093 AAAAATA-
1 AAAAATAT
1076100 AAAAATAT
1 AAAAATAT
1076108 AATAAATAT
1 AA-AAATAT
1076117 AAAAATAT
1 AAAAATAT
* * *
1076125 ATATACAT
1 AAAAATAT
*
1076133 AAAATATAA
1 AAAA-ATAT
1076142 AAGAAATAAT
1 AA-AAAT-AT
* *
1076152 GAAAATAA
1 AAAAATAT
1076160 AAAAATAT
1 AAAAATAT
1076168 A
1 A
1076169 TACATATACA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
7 7 0.13
8 23 0.44
9 18 0.35
10 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:1078907 original size:3 final size:3
Alignment explanation
Indices: 1078899--1078933 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1078889 ATGGTGTTTG
1078899 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1078934 TACAACTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1082522 original size:20 final size:20
Alignment explanation
Indices: 1082497--1082560 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1082487 AAAAATCATG
1082497 ATTTTATAAATTATGATGAA
1 ATTTTATAAATTATGATGAA
* * *
1082517 ATTTTATAAATAAACT-CTAAA
1 ATTTTATAAAT-TA-TGATGAA
1082538 ATTTTAT-AATTATGATGAA
1 ATTTTATAAATTATGATGAA
1082557 ATTT
1 ATTT
1082561 ATTTTATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.03
19 8 0.23
20 14 0.40
21 11 0.31
22 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTTATAAATTATGATGAA
Found at i:1084091 original size:17 final size:17
Alignment explanation
Indices: 1084069--1084107 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1084059 ATGCTATATT
*
1084069 ATATACAAATATAAAT-A
1 ATATACAAACA-AAATAA
1084086 ATATACAAACAAAATAA
1 ATATACAAACAAAATAA
1084103 ATATA
1 ATATA
1084108 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATACAAACAAAATAA
Found at i:1086001 original size:105 final size:105
Alignment explanation
Indices: 1085862--1086134 Score: 413
Period size: 105 Copynumber: 2.6 Consensus size: 105
1085852 CCTTTTTTCG
* * * *
1085862 GATGAGTTCTTCTCATTATGAACTATTCTAGAAATATTGATTCACCTCCTTCTGGGGTGAATTTG
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTG
*
1085927 AAAGGAACA-AGCTCTTCTCATTACGACCCTTCTCCTTTAA
66 AAAGGAACAGA-CTCTTCTCATTACGAACCTTCTCCTTTAA
* * * *
1085967 GATGAGTTCTTCTCATTATAAACTCTTATGGAAATGTTGGTTCACCTCCTTCTGTGGTGGATTTG
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTG
*
1086032 AAAGGAACAGACTCTTCTCATTACGAACCTTCTCCTTTAG
66 AAAGGAACAGACTCTTCTCATTACGAACCTTCTCCTTTAA
** *
1086072 GACAAGTTCTTCTTATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATT
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATT
1086135 ATAGTTGTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 149 0.99
106 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (105 bp):
GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGAATTTG
AAAGGAACAGACTCTTCTCATTACGAACCTTCTCCTTTAA
Found at i:1087078 original size:15 final size:14
Alignment explanation
Indices: 1087028--1087078 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 14
1087018 CGAACCCTCC
*
1087028 TTTTTCTT-TTTCT
1 TTTTTCTTCATTCT
1087041 TTTTT-TTCATT-T
1 TTTTTCTTCATTCT
1087053 TTTTTCATTCATTCAT
1 TTTTTC-TTCATTC-T
1087069 TTTTTCTTCA
1 TTTTTCTTCA
1087079 AGCATAATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 8 0.25
13 7 0.22
14 6 0.19
15 4 0.12
16 7 0.22
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCTTCATTCT
Found at i:1096473 original size:19 final size:19
Alignment explanation
Indices: 1096449--1096486 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1096439 ATTTTGGGCA
*
1096449 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
1096468 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
1096487 TTGAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:1106365 original size:14 final size:14
Alignment explanation
Indices: 1106346--1106380 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1106336 ACATACATTT
*
1106346 ATAAAAATAAATAA
1 ATAAAAATAAAAAA
1106360 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
*
1106374 ACAAAAA
1 ATAAAAA
1106381 CAAAGGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:1112889 original size:29 final size:29
Alignment explanation
Indices: 1112826--1112883 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
1112816 TTTCTTAATA
1112826 TTAAAAAATAAATAAATATTAATAAAACG
1 TTAAAAAATAAATAAATATTAATAAAACG
* *
1112855 TTAAAAAATAATATATATAATTTATAAAA
1 TTAAAAAATAA-ATAAAT-ATTAATAAAA
1112884 GTAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 5 0.20
31 9 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
TTAAAAAATAAATAAATATTAATAAAACG
Found at i:1112891 original size:24 final size:24
Alignment explanation
Indices: 1112864--1112974 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 24
1112854 GTTAAAAAAT
1112864 AATATATATAATTTATAAAAGTAA
1 AATATATATAATTTATAAAAGTAA
1112888 AATAT-T-T-ATTTA-AAAA-T--
1 AATATATATAATTTATAAAAGTAA
1112905 AATATATATAATTTATAAAAGTAA
1 AATATATATAATTTATAAAAGTAA
1112929 AATAT-T-T-ATTTA-AAAA-T--
1 AATATATATAATTTATAAAAGTAA
1112946 AATATATATAATTTATAAAAGTAA
1 AATATATATAATTTATAAAAGTAA
1112970 AATAT
1 AATAT
1112975 TTATTTATTA
Statistics
Matches: 73, Mismatches: 0, Indels: 28
0.72 0.00 0.28
Matches are distributed among these distances:
17 10 0.14
18 2 0.03
19 4 0.05
20 18 0.25
21 18 0.25
22 4 0.05
23 2 0.03
24 15 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
AATATATATAATTTATAAAAGTAA
Found at i:1112892 original size:22 final size:21
Alignment explanation
Indices: 1112858--1112987 Score: 133
Period size: 22 Copynumber: 6.2 Consensus size: 21
1112848 TAAAACGTTA
* *
1112858 AAAAATAATATATATAATTTAT
1 AAAAGTAAAATAT-TAATTTAT
*
1112880 AAAAGTAAAATATTTATTTA-
1 AAAAGTAAAATATTAATTTAT
*
1112900 AAAA-TAATATATATAATTTAT
1 AAAAGTAAAATAT-TAATTTAT
*
1112921 AAAAGTAAAATATTTATTTA-
1 AAAAGTAAAATATTAATTTAT
*
1112941 AAAA-TAATATATATAATTTAT
1 AAAAGTAAAATAT-TAATTTAT
*
1112962 AAAAGTAAAATATTTATTTATT
1 AAAAGTAAAATATTAATTTA-T
1112984 AAAA
1 AAAA
1112988 ATATCAGAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
19 14 0.16
20 20 0.22
21 26 0.29
22 30 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAGTAAAATATTAATTTAT
Found at i:1112896 original size:17 final size:17
Alignment explanation
Indices: 1112874--1112978 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 17
1112864 AATATATATA
1112874 ATTTATAAAAGTAAAAT
1 ATTTATAAAAGTAAAAT
*
1112891 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAGT-A-A-A-AT
1112914 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAGTAAAAT
*
1112932 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAGT-A-A-A-AT
1112955 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAGTAAAAT
1112973 ATTTAT
1 ATTTAT
1112979 TTATTAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 28
0.69 0.04 0.27
Matches are distributed among these distances:
17 16 0.23
18 4 0.06
19 14 0.20
20 4 0.06
21 4 0.06
22 14 0.20
23 4 0.06
24 10 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTATAAAAGTAAAAT
Found at i:1112991 original size:41 final size:41
Alignment explanation
Indices: 1112858--1112981 Score: 248
Period size: 41 Copynumber: 3.0 Consensus size: 41
1112848 TAAAACGTTA
1112858 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1112899 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1112940 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1112981 A
1 A
1112982 TTAAAAATAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (41 bp):
AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:1113981 original size:20 final size:20
Alignment explanation
Indices: 1113956--1114008 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1113946 CGGCGTTTCG
*
1113956 GTTCTCTGGCGACGTTTGGA
1 GTTCTCCGGCGACGTTTGGA
1113976 GTTCTCCGGCGACGTTTGGA
1 GTTCTCCGGCGACGTTTGGA
* *
1113996 GCTCTCCGACGAC
1 GTTCTCCGGCGAC
1114009 AGAGTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.11, C:0.28, G:0.32, T:0.28
Consensus pattern (20 bp):
GTTCTCCGGCGACGTTTGGA
Found at i:1114498 original size:3 final size:3
Alignment explanation
Indices: 1114492--1114537 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
1114482 AATATTTTAT
1114492 TAA TAA TAA TAA TAA TAA TAA TATA TAA T-A TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA
1114537 T
1 T
1114538 CAAATGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1115040 original size:113 final size:113
Alignment explanation
Indices: 1114839--1115399 Score: 619
Period size: 113 Copynumber: 4.9 Consensus size: 113
1114829 ATATAGAATG
* *
1114839 AAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCC-TCTTCAGATAAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * *
1114902 TCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAATTC
66 TCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTC
* * *
1114950 AAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTTTTCTTCATTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *** * *
1115015 TCATTATGAACTTTCTCTGGAAAAGTTGATGCTAATCTATCTCCTTCTATGATAGAGTC
66 TCATTATGAACTTTCTCTGG--AA----ATGCTGATCCATC-GAGT-GATG--A-ATTC
** * *
1115074 ATGCAAAAGGTTGAACAAGCTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1115139 TCATTATGAACTTTATCTGGCAATGCTAATCCATCGAGTGATGAATT-
66 TCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTC
* *
1115186 AAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTT
1 AAA-CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* * * * *
1115251 CTCATTATGAACTCTAC-CTGGCAATGCTGATCCATCAAGTGACGGATTC
65 CTCATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAGTGATGAATTC
* * * * *
1115300 GAGCGAAAGGTTGAACAAATTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1115365 TTATTATGAACTCTAC-CTGGAAATGCTGATCCATC
66 TCATTATGAACT-TTCTCTGGAAATGCTGATCCATC
1115400 AAGCGATGGA
Statistics
Matches: 384, Mismatches: 50, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
111 4 0.01
112 40 0.10
113 225 0.59
114 3 0.01
115 2 0.01
116 3 0.01
117 1 0.00
118 12 0.03
119 8 0.02
120 1 0.00
121 3 0.01
122 1 0.00
123 1 0.00
124 80 0.21
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (113 bp):
AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTC
Found at i:1115206 original size:237 final size:235
Alignment explanation
Indices: 1114753--1115263 Score: 724
Period size: 237 Copynumber: 2.2 Consensus size: 235
1114743 GTTGAACAAA
* * * *
1114753 TTCTTC-TCCTTCTTCAGATGAATTCTTCTCATTATGAAC-TCCTTCTGGAAATGCTGATACTGA
1 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGCTGATACTAA
* * * *
1114816 TCTATCTCCTTCTATATAGAATGAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
66 TCTATCTCCTTCTATATAGAATCAAACAAAGGTTGAACAAGCTCTTCCCATTATGAACTTCTTCT
* * * *
1114881 TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGA
131 TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTATCTGGAAAAGCTAATCCATCGAGTAATGA
1114946 ATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
196 ATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* * * *
1114986 TTTTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGATGCTAA
1 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGCTGATACTAA
* **
1115050 TCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCCCATTATGAACTTCTT
66 TCTATCTCCTTCTAT-ATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCCCATTATGAACTTCTT
* * * * *
1115115 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGCAATGCTAATCCATCGAGTGA
129 CTTCC-TCTTCAGATAAGTTCTTCTCATTACGAACTTTATCTGGAAAAGCTAATCCATCGAGTAA
1115180 TGAATT-AAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
193 TGAATTCAAA-CAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* *
1115223 TTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACT
1 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
1115264 CTACCTGGCA
Statistics
Matches: 245, Mismatches: 27, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
233 5 0.02
234 62 0.25
235 10 0.04
236 41 0.17
237 127 0.52
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (235 bp):
TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGCTGATACTAA
TCTATCTCCTTCTATATAGAATCAAACAAAGGTTGAACAAGCTCTTCCCATTATGAACTTCTTCT
TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTATCTGGAAAAGCTAATCCATCGAGTAATGA
ATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
Found at i:1122919 original size:7 final size:7
Alignment explanation
Indices: 1122885--1122926 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1122875 ACAAAAGTAT
1122885 AAATGCA
1 AAATGCA
1122892 AAATG-A
1 AAATGCA
1122898 AGAATGCA
1 A-AATGCA
1122906 AAGATGCA
1 AA-ATGCA
1122914 AAATGC-
1 AAATGCA
1122920 AAATGCA
1 AAATGCA
1122927 TGTATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.26
7 14 0.45
8 9 0.29
ACGTcount: A:0.55, C:0.12, G:0.19, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1125717 original size:41 final size:41
Alignment explanation
Indices: 1125670--1125792 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
1125660 AAAACGTTAA
1125670 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125711 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125752 -AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125792 A
1 A
1125793 TTAAAAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
40 40 0.49
41 41 0.51
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (41 bp):
AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:1125767 original size:40 final size:40
Alignment explanation
Indices: 1125671--1125792 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1125661 AAACGTTAAA
1125671 AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125711 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 -AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125752 AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1125792 A
1 A
1125793 TTAAAAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
40 41 0.51
41 40 0.49
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (40 bp):
AAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:1125905 original size:13 final size:14
Alignment explanation
Indices: 1125887--1125917 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1125877 TTATTTTTCG
1125887 TAAAATT-AATTTA
1 TAAAATTAAATTTA
1125900 TAAAATTAAATTTA
1 TAAAATTAAATTTA
1125914 TAAA
1 TAAA
1125918 CAGGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAATTAAATTTA
Found at i:1127255 original size:3 final size:3
Alignment explanation
Indices: 1127249--1127294 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
1127239 AATATTTTAT
1127249 TAA TAA TAA TAA TAA TAA TAA TATA TAA T-A TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA
1127294 T
1 T
1127295 CAAATGACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1129439 original size:20 final size:21
Alignment explanation
Indices: 1129402--1129441 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1129392 TGTTCATGCT
1129402 TAAAAAATCTACAACACTACA
1 TAAAAAATCTACAACACTACA
* *
1129423 TAAAAATTCT-CATCACTAC
1 TAAAAAATCTACAACACTAC
1129442 TTTTTTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAATCTACAACACTACA
Found at i:1132689 original size:23 final size:23
Alignment explanation
Indices: 1132646--1132690 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1132636 CCAAAAACAT
* *
1132646 TTTTTAATTTTAAATAAAAATTA
1 TTTTTAATTTAAAACAAAAATTA
1132669 TTTTTAA-TTAAAACAACAAATT
1 TTTTTAATTTAAAACAA-AAATT
1132691 GAGGTTTGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTAATTTAAAACAAAAATTA
Found at i:1135035 original size:55 final size:55
Alignment explanation
Indices: 1135005--1135366 Score: 414
Period size: 55 Copynumber: 6.6 Consensus size: 55
1134995 AAACGGGACC
* *
1135005 GCTCCCTATTCTTTCAGGGAGTATAGGACTTGAGCAATCTTC-GAAAAACGAGTCT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTG-AAAACGAGTCT
* * * *
1135060 GCTCTCTATTCTTTCAGGGAGTATAGGACTTGAGCAATCTTC-GAAAAATGAGTCT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTG-AAAACGAGTCT
* * * * * *
1135115 GTTCCTTATTCTTTCAAGGAGTATAGAACTTGAACAATCTTCTGAACATGGGTCT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCT
**
1135170 GCTCCCTATTCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAAC-ATGT-T
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGA-GTCT
* * *
1135224 CGCTCCATATTCTTTTA-GGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCT
1 -GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCT
* * **
1135279 ACTTCCTATTCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAAC-ATGT-T
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGA-GTCT
* *
1135333 CGCTCCATATTCTTTCAGGGAGTATAGGACTTGA
1 -GCTCCCTATTCTTTCAGGGAGTATAGAACTTGA
1135367 TCTTCATAAA
Statistics
Matches: 267, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
54 48 0.18
55 218 0.82
56 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (55 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCT
Found at i:1135290 original size:109 final size:110
Alignment explanation
Indices: 1135004--1135366 Score: 484
Period size: 110 Copynumber: 3.3 Consensus size: 110
1134994 AAAACGGGAC
* * *
1135004 CGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAGCAATCTTC-GAAAAACGAGTCTGC-TCTCT
1 CGCTCCATATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTG-AAAACGAGTCTGCTTC-CT
* ** * *
1135067 ATTCTTTCAGGGAGTATAGGACTTGAGCAATCTTC-GAAAA-ATGAGT
64 ATTCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATG-TT
* * * * * * *
1135113 CTGTTCCTTATTCTTTCAAGGAGTATAGAACTTGAACAATCTTCTGAACATGGGTCTGCTCCCTA
1 C-GCTCCATATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCTGCTTCCTA
1135178 TTCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATGTT
65 TTCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATGTT
* * *
1135224 CGCTCCATATTCTTTTA-GGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCTACTTCCTAT
1 CGCTCCATATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCTGCTTCCTAT
1135288 TCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATGTT
66 TCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATGTT
*
1135333 CGCTCCATATTCTTTCAGGGAGTATAGGACTTGA
1 CGCTCCATATTCTTTCAGGGAGTATAGAACTTGA
1135367 TCTTCATAAA
Statistics
Matches: 222, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
109 103 0.46
110 107 0.48
111 9 0.04
112 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (110 bp):
CGCTCCATATTCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGAAAACGAGTCTGCTTCCTAT
TCTTTCAGGGAGTATAGAACTCAAACAATCTTCTGAAAACATGTT
Found at i:1135498 original size:37 final size:37
Alignment explanation
Indices: 1135387--1135500 Score: 142
Period size: 37 Copynumber: 3.1 Consensus size: 37
1135377 ATGAGTCTGC
* * * *
1135387 TTCACTACTCTTCCGTGATGGC-TAATATATGATTTGCT
1 TTCACTACTCTTTCGTGAAGGCTTAAGAT-TGAATTG-T
1135425 TT-ACTACTCTTTCGTGAAGGCTTAAGATTGAATTGT
1 TTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTGT
* *
1135461 TTCACTACTCTTTCATGAAGGCTTAAGATTGACTTGT
1 TTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTGT
1135498 TTC
1 TTC
1135501 TAAGGTCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.04
37 58 0.85
38 7 0.10
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (37 bp):
TTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTGT
Found at i:1136783 original size:6 final size:6
Alignment explanation
Indices: 1136774--1136849 Score: 93
Period size: 6 Copynumber: 12.2 Consensus size: 6
1136764 CCCCTTTTTA
1136774 TTTTCT TTTTCT TTTT-T TTTTCT TTGTTCT TTTTCT TTGTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT TTTTCT TT-TTCT TTTTCT
1136823 TTGTTC- TTTTCT TTTTCAT TTCTTCT T
1 TT-TTCT TTTTCT TTTTC-T TT-TTCT T
1136850 CCATTTTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 13
0.83 0.00 0.17
Matches are distributed among these distances:
5 8 0.13
6 32 0.51
7 20 0.32
8 3 0.05
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:1136806 original size:13 final size:13
Alignment explanation
Indices: 1136776--1136849 Score: 102
Period size: 13 Copynumber: 5.8 Consensus size: 13
1136766 CCTTTTTATT
1136776 TTCTTTTTCTTT-
1 TTCTTTTTCTTTG
1136788 TT-TTTTTCTTTG
1 TTCTTTTTCTTTG
1136800 TTCTTTTTCTTTG
1 TTCTTTTTCTTTG
1136813 TTCTTTTTCTTTG
1 TTCTTTTTCTTTG
1136826 TTC-TTTTCTTT-
1 TTCTTTTTCTTTG
1136837 TTCATTTCTTCTT
1 TTC-TTT-TTCTT
1136850 CCATTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
11 12 0.21
12 12 0.21
13 28 0.49
14 5 0.09
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (13 bp):
TTCTTTTTCTTTG
Found at i:1136865 original size:9 final size:9
Alignment explanation
Indices: 1136834--1136896 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 9
1136824 TGTTCTTTTC
1136834 TTTTTCATT
1 TTTTTCATT
1136843 TCTTCTTCCATT
1 T-TT-TT-CATT
1136855 TTTTTCATTTTT
1 TTTTTCA---TT
1136867 TTTTTCATT
1 TTTTTCATT
1136876 TTTTTCAATT
1 TTTTTC-ATT
*
1136886 TTTCTCATT
1 TTTTTCATT
1136895 TT
1 TT
1136897 CATTTTTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
9 16 0.35
10 12 0.26
11 4 0.09
12 14 0.30
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1136869 original size:31 final size:30
Alignment explanation
Indices: 1136829--1136911 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 30
1136819 TTCTTTGTTC
* *
1136829 TTTTCTTTTTCATTTCTTCTTCCATTTTTTTCA
1 TTTT-TTTTTCATTT-TT-TTCAATTTTTCTCA
1136862 TTTTTTTTTTCATTTTTTTCAATTTTTCTCA
1 -TTTTTTTTTCATTTTTTTCAATTTTTCTCA
*
1136893 TTTTCATTTTTTATTTTTT
1 TTTT--TTTTTCATTTTTT
1136912 CTTCTTCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.09
31 12 0.27
32 14 0.32
33 10 0.23
34 4 0.09
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTTTTTTCATTTTTTTCAATTTTTCTCA
Found at i:1136912 original size:31 final size:31
Alignment explanation
Indices: 1136829--1136911 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 31
1136819 TTCTTTGTTC
* * *
1136829 TTTTCTTTTTCATTTCTTCTTCCATTTTTTTCA
1 TTTTTTTTTTCATTT-TT-TTCAATTTTTCTCA
1136862 TTTTTTTTTTCATTTTTTTCAATTTTTCTCA
1 TTTTTTTTTTCATTTTTTTCAATTTTTCTCA
1136893 TTTTCATTTTTT-ATTTTTT
1 TTTT--TTTTTTCATTTTTT
1136912 CTTCTTCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.36
32 9 0.20
33 20 0.44
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTTTTTTTCATTTTTTTCAATTTTTCTCA
Found at i:1136919 original size:21 final size:22
Alignment explanation
Indices: 1136834--1136919 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 22
1136824 TGTTCTTTTC
* *
1136834 TTTTTCATTTCTTC-TTCCATT
1 TTTTTCATTTTTTCTTTTCATT
1136855 TTTTTCATTTTTT-TTTTCATT
1 TTTTTCATTTTTTCTTTTCATT
1136876 TTTTTCAATTTTTCTCATTTTCA-T
1 TTTTTC-ATTTTT-TC-TTTTCATT
1136900 TTTTT-ATTTTTTCTTCTTCA
1 TTTTTCATTTTTTCTT-TTCA
1136920 AGAAAAATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.04
21 30 0.53
22 12 0.21
23 1 0.02
24 6 0.11
25 6 0.11
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTCATTTTTTCTTTTCATT
Found at i:1139443 original size:93 final size:93
Alignment explanation
Indices: 1139284--1139464 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 93
1139274 CCTAACACAC
**
1139284 CCTTTTATAGCCAAGTGACCCTAATCATATTAGGTTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTGACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
1139349 ATTTAATTAATTGGAATTTAATAATAAT
66 ATTTAATTAATTGAAATTAAATAATAAT
* * * *
1139377 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAATTTAT
1 CCTTTTATAGCCAAGTGACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1139442 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
1139465 TTCGAGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (93 bp):
CCTTTTATAGCCAAGTGACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAATAAT
Found at i:1162093 original size:17 final size:17
Alignment explanation
Indices: 1162071--1162104 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1162061 ATTTGCATTA
1162071 TCTTCAACCTCTTTCTG
1 TCTTCAACCTCTTTCTG
1162088 TCTTCAACCTCTTTCTG
1 TCTTCAACCTCTTTCTG
1162105 AACCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTTCAACCTCTTTCTG
Found at i:1163370 original size:16 final size:16
Alignment explanation
Indices: 1163351--1163384 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1163341 AAAATTAATT
*
1163351 TTAATTAAAAAACAAA
1 TTAATTAAAAAAAAAA
1163367 TTAATTAAAAAAAAAA
1 TTAATTAAAAAAAAAA
1163383 TT
1 TT
1163385 GAGGTTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAATTAAAAAAAAAA
Found at i:1166147 original size:5 final size:5
Alignment explanation
Indices: 1166133--1166203 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
1166123 ATCAAAGATG
* * * *
1166133 AAAAT AAAAAT AAAAT AAAAAT AGAAT GATAT AAAAT AAAAT AAAAT AATAAG
1 AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
* *
1166186 ATAA- AAAAT AAAAC AAAA
1 AAAAT AAAAT AAAAT AAAA
1166204 AAGAAGACTA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
4 3 0.06
5 36 0.69
6 13 0.25
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1166170 original size:26 final size:26
Alignment explanation
Indices: 1166138--1166208 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
1166128 AGATGAAAAT
*
1166138 AAAAATAAAATAAAAATAGAATGATA
1 AAAAATAAAATAAAAATAGAAAGATA
*
1166164 TAAAATAAAAT-AAAATA-ATAAGATA
1 AAAAATAAAATAAAAATAGA-AAGATA
*
1166189 AAAAATAAAACAAAAA-AGAA
1 AAAAATAAAATAAAAATAGAA
1166209 GACTATCGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 1 0.03
25 22 0.58
26 15 0.39
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (26 bp):
AAAAATAAAATAAAAATAGAAAGATA
Found at i:1166189 original size:13 final size:12
Alignment explanation
Indices: 1166133--1166205 Score: 69
Period size: 12 Copynumber: 5.9 Consensus size: 12
1166123 ATCAAAGATG
1166133 AAAAT-AAAAAT
1 AAAATAAAAAAT
1166144 AAAAT-AAAAAT
1 AAAATAAAAAAT
*
1166155 AGAATGATATAAAAT
1 A-AA--ATAAAAAAT
1166170 AAAATAAAATAAT
1 AAAATAAAA-AAT
*
1166183 AAGATAAAAAAT
1 AAAATAAAAAAT
*
1166195 AAAACAAAAAA
1 AAAATAAAAAA
1166206 GAAGACTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
11 12 0.23
12 19 0.37
13 11 0.21
14 4 0.08
15 6 0.12
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1168448 original size:123 final size:122
Alignment explanation
Indices: 1168072--1168500 Score: 448
Period size: 122 Copynumber: 3.5 Consensus size: 122
1168062 AGATTTAAAA
* * ** * * * ** *
1168072 ATGACATTGTTCCTTAAT-GTTGAGGACTTCGGGTCAATTTGGATATAATTTGGTGTTGAAGATG
1 ATGACGTTGTTCCTT-CTCGTTGAGGAAATCAGGTCAATCTGGAGATAATACGGTGTTGAAGAAG
** * ** * * * * **
1168136 ACAATACTCGTCCACGTTGAAGAGATCTGGCTGCTTTCAGATAAATTGTTTGTTGAAG
65 ACTCTACTCATCCGTGTTGAAGAGTTCTAGCCGCTTTCAGGTAAATTGTTTACTGAAG
* * * * * * *
1168194 ATGACGTTGTTACTTCTCATTGAGAAAAT-AGGGTCAATTTGGAGATAAAACGATGTTGAAGACG
1 ATGACGTTGTTCCTTCTCGTTGAGGAAATCA-GGTCAATCTGGAGATAATACGGTGTTGAAGAAG
*
1168258 ACTCTACTCATCCGTGTTGAAGAGTTCTAGCCGCTTTCAGGTAAATTATTTACTGAAG
65 ACTCTACTCATCCGTGTTGAAGAGTTCTAGCCGCTTTCAGGTAAATTGTTTACTGAAG
* *
1168316 ATGACGTTGTTCCTTCTCGTTGAGGAAATCAGGTTAATCTGGAGATAATACGGTGTTGAATAAGA
1 ATGACGTTGTTCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATACGGTGTTGAAGAAGA
* * *
1168381 CTCTGCTCATCCCGTGTTGAAGAGTTCTAGCCACTTTCAGGTAAATTGTTAACTGAAG
66 CTCTACTCAT-CCGTGTTGAAGAGTTCTAGCCGCTTTCAGGTAAATTGTTTACTGAAG
* * * * * **
1168439 ATGACGTTGTTCTTTCTTGTTAAGGAAGTCAGGTCAATCTAGAGATAATTTGGTGTTGAAGA
1 ATGACGTTGTTCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATACGGTGTTGAAGA
1168501 TGTTCTAGAA
Statistics
Matches: 255, Mismatches: 48, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
121 1 0.00
122 156 0.61
123 98 0.38
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (122 bp):
ATGACGTTGTTCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATACGGTGTTGAAGAAGA
CTCTACTCATCCGTGTTGAAGAGTTCTAGCCGCTTTCAGGTAAATTGTTTACTGAAG
Found at i:1168677 original size:83 final size:83
Alignment explanation
Indices: 1168538--1168726 Score: 227
Period size: 83 Copynumber: 2.3 Consensus size: 83
1168528 AGACAATATG
* * * * * *
1168538 GTTCCTTTGTGTTGAGGAAATATGATTGTCTAAGGATGACACTGCTCCTTCGCGTTG-AGAAGAT
1 GTTCCTTCGTATTGAGGAAGTCTGATTGTCTAAGGATGACACTGCTCCTTCACGTTGAAG-AGAC
*
1168602 ATGGTCGGTGGGCGACATT
65 ATGGTCGGTGGACGACATT
* * * *
1168621 GTTCCTTCTTATTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCACGTTGAAGAGACC
1 GTTCCTTCGTATTGAGGAAGTCTGATTGTCTAAGGATGACACTGCTCCTTCACGTTGAAGAGACA
* *
1168686 TGGTCGGTGGATGAGATT
66 TGGTCGGTGGACGACATT
* *
1168704 TTTCCTTCGTGTTGAGGAAGTCT
1 GTTCCTTCGTATTGAGGAAGTCT
1168727 AGCCGTTCTA
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 87 0.98
84 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (83 bp):
GTTCCTTCGTATTGAGGAAGTCTGATTGTCTAAGGATGACACTGCTCCTTCACGTTGAAGAGACA
TGGTCGGTGGACGACATT
Found at i:1173766 original size:13 final size:13
Alignment explanation
Indices: 1173714--1173766 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
1173704 GCTTCTTGTC
*
1173714 TTCTTTTTTTCTTT
1 TTCTTTTTTTC-AT
*
1173728 TTCTTTTTTGTTTAT
1 TTC-TTTTT-TTCAT
1173743 TTCTTTTTTTCAT
1 TTCTTTTTTTCAT
1173756 TTCTTTTTTTC
1 TTCTTTTTTTC
1173767 TCTTTGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 15 0.44
14 8 0.24
15 9 0.26
16 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTTCAT
Found at i:1178310 original size:5 final size:5
Alignment explanation
Indices: 1178293--1178361 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
1178283 ATCAAAGATG
* * *
1178293 AAAAT ACAAAT AAAAT AAATAT AGAAT GAGAT AAAAT AAAAT AAAAT --AAT
1 AAAAT A-AAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
1178343 AAGAT AAAAAT AAAA- AAAA
1 AAAAT -AAAAT AAAAT AAAA
1178362 ACAATAAGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 31 0.61
6 13 0.25
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1178329 original size:26 final size:24
Alignment explanation
Indices: 1178300--1178370 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
1178290 ATGAAAATAC
*
1178300 AAATAAAATAAATATAGAATGAGAT-A
1 AAATAAAATAAA-AT--AATAAGATAA
1178326 AAATAAAATAAAATAATAAGATAA
1 AAATAAAATAAAATAATAAGATAA
* *
1178350 AAATAAAAAAAAACAATAAGA
1 AAATAAAATAAAATAATAAGA
1178371 CTATCGAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 7 0.17
24 20 0.49
25 2 0.05
26 12 0.29
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.18
Consensus pattern (24 bp):
AAATAAAATAAAATAATAAGATAA
Found at i:1179232 original size:73 final size:73
Alignment explanation
Indices: 1179085--1179256 Score: 269
Period size: 73 Copynumber: 2.4 Consensus size: 73
1179075 TAGTTTATAC
* *
1179085 AATAAAA-TAA-AATGTTAGTAAGTTAGTAAGAACAATAAAATAAAAAGGTCAGTATGTTGGTAT
1 AATAAAAGTAAGAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAAAGGTCAGAATGTTAGTAT
*
1179148 GAATAATA
66 GAACAATA
* *
1179156 AATAAAAGTTAGAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAAA-GTTAGAATGTTAGTAT
1 AATAAAAGTAAGAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAAAGGTCAGAATGTTAGTAT
1179220 GAACAATAA
66 GAACAAT-A
1179229 AATAAAAGTAAGAATGTTAGTAAGTTAG
1 AATAAAAGTAAGAATGTTAGTAAGTTAG
1179257 AAAAGTTAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 7 0.08
72 21 0.23
73 64 0.70
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.28
Consensus pattern (73 bp):
AATAAAAGTAAGAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAAAGGTCAGAATGTTAGTAT
GAACAATA
Found at i:1179243 original size:32 final size:33
Alignment explanation
Indices: 1179083--1179252 Score: 139
Period size: 33 Copynumber: 5.0 Consensus size: 33
1179073 ATTAGTTTAT
* *
1179083 ACAATAAAATAAAATGTTAGTAA-GTTAGTAAGA
1 ACAATAAAATAAAAAGTAAG-AATGTTAGTAAGA
* * * *
1179116 ACAATAAAATAAAAAGGTCAGTATGTTGGTATGA
1 ACAATAAAATAAAAA-GTAAGAATGTTAGTAAGA
* * *
1179150 ATAATAAATAAAAGTTAGAATGTTAGTAA-GTTAGTAAGA
1 ACAATAAA-ATAA---A-AA-GTAAG-AATGTTAGTAAGA
* *
1179189 ACAATAAAATAAAAAGTTAGAATGTTAGTATGA
1 ACAATAAAATAAAAAGTAAGAATGTTAGTAAGA
1179222 ACAATAAAAT-AAAAGTAAGAATGTTAGTAAG
1 ACAATAAAATAAAAAGTAAGAATGTTAGTAAG
1179253 TTAGAAAAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 19
0.76 0.12 0.13
Matches are distributed among these distances:
32 21 0.19
33 39 0.35
34 21 0.19
35 4 0.04
38 4 0.04
39 21 0.19
40 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (33 bp):
ACAATAAAATAAAAAGTAAGAATGTTAGTAAGA
Found at i:1180443 original size:13 final size:13
Alignment explanation
Indices: 1180425--1180450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1180415 GGGGGGGGGG
1180425 CTGTTTTTGCTTT
1 CTGTTTTTGCTTT
1180438 CTGTTTTTGCTTT
1 CTGTTTTTGCTTT
1180451 TACAGCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (13 bp):
CTGTTTTTGCTTT
Found at i:1181607 original size:14 final size:14
Alignment explanation
Indices: 1181590--1181621 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1181580 ATTATACAGA
1181590 GATTTATTAGCAGG
1 GATTTATTAGCAGG
*
1181604 GATTTATTAGCAGT
1 GATTTATTAGCAGG
1181618 GATT
1 GATT
1181622 ACTTCCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (14 bp):
GATTTATTAGCAGG
Found at i:1181684 original size:4 final size:4
Alignment explanation
Indices: 1181675--1181699 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1181665 TGTTCAAATG
1181675 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1181700 ACATACATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1185087 original size:16 final size:16
Alignment explanation
Indices: 1185062--1185092 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1185052 CAACACATAA
*
1185062 GTGTTTATATTATTAT
1 GTGTTAATATTATTAT
1185078 GTGTTAATATTATTA
1 GTGTTAATATTATTA
1185093 ATAATTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (16 bp):
GTGTTAATATTATTAT
Found at i:1185231 original size:18 final size:17
Alignment explanation
Indices: 1185203--1185237 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1185193 CGTTAATAAT
1185203 TCGAGTCGAGTTCGAGC
1 TCGAGTCGAGTTCGAGC
*
1185220 TCGAGCTCGAGTTGGAGC
1 TCGAG-TCGAGTTCGAGC
1185238 CCGTTCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (17 bp):
TCGAGTCGAGTTCGAGC
Found at i:1185775 original size:23 final size:23
Alignment explanation
Indices: 1185749--1185793 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1185739 GAAAACAACT
1185749 CTCAAGAAAACTCTCTAAATTCA
1 CTCAAGAAAACTCTCTAAATTCA
1185772 CTCAAGAAAACTCTCTAAATTC
1 CTCAAGAAAACTCTCTAAATTC
1185794 TCTAGTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (23 bp):
CTCAAGAAAACTCTCTAAATTCA
Found at i:1188019 original size:13 final size:13
Alignment explanation
Indices: 1188001--1188045 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1187991 TGCGTCATAA
*
1188001 ATTTATGACGTGC
1 ATTTATGACGCGC
*
1188014 ATTTATGACACGC
1 ATTTATGACGCGC
1188027 ATTTATGACGCGC
1 ATTTATGACGCGC
1188040 ATTTAT
1 ATTTAT
1188046 AACTTACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1188116 original size:85 final size:85
Alignment explanation
Indices: 1188027--1188192 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 85
1188017 TATGACACGC
*
1188027 ATTTATGACGCGCATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAAT-AAAGATG
1 ATTTATGACACGCATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAA-ATG
*
1188091 ACACACATTTGTGTGTCATAA
65 AAACACATTTGTGTGTCATAA
* * *
1188112 ATTTATGACACGTATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1188177 AACACATTTGTGTGTC
66 AACACATTTGTGTGTC
1188193 GTGATTGTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 72 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
AACACATTTGTGTGTCATAA
Found at i:1188219 original size:2 final size:2
Alignment explanation
Indices: 1188212--1188248 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1188202 TTTCGTGAAT
1188212 TA TA TA 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 TA TA TA T
1188249 TGTAGATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1194935 original size:13 final size:13
Alignment explanation
Indices: 1194917--1194958 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1194907 TGCTAACTTA
*
1194917 TTGCACTGAAAGT
1 TTGCACCGAAAGT
1194930 TTGCACCGAAAGT
1 TTGCACCGAAAGT
1194943 TTGCACCGAAAGT
1 TTGCACCGAAAGT
1194956 TTG
1 TTG
1194959 GCCATGTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (13 bp):
TTGCACCGAAAGT
Found at i:1195992 original size:5 final size:5
Alignment explanation
Indices: 1195982--1196250 Score: 483
Period size: 5 Copynumber: 54.0 Consensus size: 5
1195972 TAGTGGTGTT
1195982 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1196032 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATATA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA
1196083 TATTA TATTA TATTA TATTA TATTA TATTA TA-T- TATTA TATTTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA
1196132 TATTA TATTA TATTA TATTA TATTA TA-TA TATTA TATTA TATT- TATATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA
1196181 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1196231 TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA
1196251 CTTGAATCAA
Statistics
Matches: 257, Mismatches: 0, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.01
4 9 0.04
5 233 0.91
6 13 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:1207540 original size:19 final size:19
Alignment explanation
Indices: 1207516--1207567 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 19
1207506 TAAAGATGTT
1207516 TGTGTTCGTTGTTCGCGTA
1 TGTGTTCGTTGTTCGCGTA
*
1207535 TGTGTTCGTTTAATGTTTGCGTA
1 TGTGTTCG--T--TGTTCGCGTA
1207558 TGTGTTCGTT
1 TGTGTTCGTT
1207568 TAATGTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 9 0.32
21 2 0.07
23 17 0.61
ACGTcount: A:0.08, C:0.12, G:0.29, T:0.52
Consensus pattern (19 bp):
TGTGTTCGTTGTTCGCGTA
Found at i:1207551 original size:23 final size:23
Alignment explanation
Indices: 1207525--1207576 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1207515 TTGTGTTCGT
1207525 TGTTCGCGTATGTGTTCGTTTAA
1 TGTTCGCGTATGTGTTCGTTTAA
*
1207548 TGTTTGCGTATGTGTTCGTTTAA
1 TGTTCGCGTATGTGTTCGTTTAA
1207571 TGTTCG
1 TGTTCG
1207577 TGAACGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (23 bp):
TGTTCGCGTATGTGTTCGTTTAA
Found at i:1207585 original size:23 final size:23
Alignment explanation
Indices: 1207536--1207640 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 23
1207526 GTTCGCGTAT
* * * *
1207536 GTGTTCGTTTAATGTTTGCGTAT
1 GTGTTCGTTTAATGTTCGTGAAC
1207559 GTGTTCGTTTAATGTTCGTGAAC
1 GTGTTCGTTTAATGTTCGTGAAC
*** * *
1207582 GTGTTTAATTATATGTTCTTGGAC
1 GTGTTCGTTTA-ATGTTCGTGAAC
* * *
1207606 GTGTTCATTTAACGTTCACT-AAC
1 GTGTTCGTTTAATGTTC-GTGAAC
*
1207629 ATGTTCGTTTAA
1 GTGTTCGTTTAA
1207641 CTTACGTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
23 44 0.69
24 20 0.31
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (23 bp):
GTGTTCGTTTAATGTTCGTGAAC
Found at i:1208785 original size:39 final size:38
Alignment explanation
Indices: 1208733--1208939 Score: 178
Period size: 39 Copynumber: 5.4 Consensus size: 38
1208723 ATATATATTA
*
1208733 ATATAGTATAGTTTTTTAAAACATTTTGAAAACATATAT
1 ATATA-TATAGTTTTTAAAAACATTTTGAAAACATATAT
* *
1208772 ATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT
1 AT-ATATATAGTTTTTAAAAACATTTTGAAAACATATAT
*
1208811 AT-TATATAGTTTTGAAAAACAATTTTTGAAAACATATAT
1 ATATATATAGTTTTTAAAAAC-A-TTTTGAAAACATATAT
** **
1208850 AT-TATATAGTTTCGAAAATA-ATTTTTGAACGCATATAT
1 ATATATATAGTTTTTAAAA-ACA-TTTTGAAAACATATAT
* *
1208888 -CATATATAG-TTTTAAAAATGATTTTTTGAAAACATAT-T
1 ATATATATAGTTTTTAAAAA-CA--TTTTGAAAACATATAT
*
1208926 A-AT-TTTAGTTTTTA
1 ATATATATAGTTTTTA
1208940 TAATATATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
36 1 0.01
37 26 0.18
38 33 0.23
39 80 0.56
40 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (38 bp):
ATATATATAGTTTTTAAAAACATTTTGAAAACATATAT
Found at i:1208805 original size:28 final size:28
Alignment explanation
Indices: 1208756--1208809 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1208746 TTTTAAAACA
*
1208756 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATATAGT
*
1208784 TTTTGAAAACAT-TTTGAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
1208810 TATTATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATAGT
Found at i:1210242 original size:41 final size:39
Alignment explanation
Indices: 1210179--1210266 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 39
1210169 TACTTTTTCT
*
1210179 TTTTATTCTGTTATTTTTTTCTTACTTTCAAAATTTAACA
1 TTTT-TTCTGTTATTTTTTTCTTACTTTCAAAAATTAACA
* * *
1210219 TTTCTTTCTTTTATTTTTTTTCTTATTTTTAAAAATTAACA
1 TTT-TTTCTGTTA-TTTTTTTCTTACTTTCAAAAATTAACA
1210260 TTTTTTC
1 TTTTTTC
1210267 ACTCTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 14 0.33
41 28 0.67
ACGTcount: A:0.23, C:0.11, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTTTTCTGTTATTTTTTTCTTACTTTCAAAAATTAACA
Found at i:1213008 original size:13 final size:14
Alignment explanation
Indices: 1212977--1213008 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1212967 TTTAGTAATT
1212977 TAATTTTTATTTAG
1 TAATTTTTATTTAG
1212991 T-ATTTTTATTTA-
1 TAATTTTTATTTAG
1213003 TAATTT
1 TAATTT
1213009 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.06
13 15 0.88
14 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TAATTTTTATTTAG
Found at i:1217615 original size:59 final size:57
Alignment explanation
Indices: 1217452--1217627 Score: 200
Period size: 57 Copynumber: 3.1 Consensus size: 57
1217442 CAGCAGGCTG
* *
1217452 CATATTCAGGATCT-CACTAAAGTAT-TAGTGCATATGGTGGCCAAC-ACCTTATGTGT
1 CATATTCAGGAT-TGAACTAAAGTATATAGTGCATATGGTGGGC-ACGACCTTATGTGT
* * *
1217508 CATACTCATGATTGCAA-TAAAAGTATA-AGTGCATATGGTGGGAACGACCTTATGTGT
1 CATATTCAGGATTG-AACT-AAAGTATATAGTGCATATGGTGGGCACGACCTTATGTGT
* *
1217565 CATATTCAGGATTGAACTAAAGTATAAATAGTGCAGATGGTGGGCACGACCTTATGCGT
1 CATATTCAGGATTGAACTAAAGTAT--ATAGTGCATATGGTGGGCACGACCTTATGTGT
1217624 CATA
1 CATA
1217628 CTCGGGTTAG
Statistics
Matches: 101, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
55 1 0.01
56 22 0.22
57 46 0.46
58 1 0.01
59 31 0.31
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (57 bp):
CATATTCAGGATTGAACTAAAGTATATAGTGCATATGGTGGGCACGACCTTATGTGT
Found at i:1219433 original size:46 final size:46
Alignment explanation
Indices: 1219366--1219790 Score: 719
Period size: 46 Copynumber: 9.3 Consensus size: 46
1219356 CGTTAAATTT
* *
1219366 CATTTTATTTATGGCATCCTTTCACGCCTTAATGCATCATTTAATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
1219412 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCA-CCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
1219457 AATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
1219503 CACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
1219549 CATTTTATTTATGTCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
1219595 CATTTTATTTATGGCATCCTTTCATCCCTTAATGCATCATTTAATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
1219641 CATTTTATTTATGGCATCTTTTCATGCCTTAATGCA-CCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
1219686 CATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1219732 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1219778 CATTTTATTTATG
1 CATTTTATTTATG
1219791 TATTCGGTTT
Statistics
Matches: 355, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
45 83 0.23
46 272 0.77
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (46 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
Found at i:1219535 original size:137 final size:138
Alignment explanation
Indices: 1219366--1219790 Score: 737
Period size: 137 Copynumber: 3.1 Consensus size: 138
1219356 CGTTAAATTT
* * *
1219366 CATTTTATTTATGGCATCCTTTCACGCCTTAATGCATCATTTAATGCATTTTATTTATGGCATCC
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCC
*
1219431 TTTCATGCCTTAATGCA-CCTTTCATGAATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
66 TTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
1219495 ATTTCATG
131 ATTTCATG
* *
1219503 CACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGTCATCC
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCC
*
1219568 TTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATCCCTTAATGCATC
66 TTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
*
1219633 ATTTAATG
131 ATTTCATG
*
1219641 CATTTTATTTATGGCATCTTTTCATGCCTTAATGCA-CCTTTCATGCATTTTATTTATGGCATCC
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCC
* *
1219705 TTTTATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
66 TTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
1219770 ATTTCATG
131 ATTTCATG
1219778 CATTTTATTTATG
1 CATTTTATTTATG
1219791 TATTCGGTTT
Statistics
Matches: 272, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
137 186 0.68
138 86 0.32
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (138 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCC
TTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
ATTTCATG
Found at i:1219767 original size:229 final size:229
Alignment explanation
Indices: 1219366--1219791 Score: 791
Period size: 229 Copynumber: 1.9 Consensus size: 229
1219356 CGTTAAATTT
1219366 CATTTTATTTATGGCATCCTTTCACGCCTTAATGCATCATTTAATGCATTTTATTTATGGCATCC
1 CATTTTATTTATGGCATCCTTTCACGCCTTAATGCATCATTTAATGCATTTTATTTATGGCATCC
1219431 TTTCATGCCTTAATGCACCTTTCATGAATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCA
66 TTTCATGCCTTAATGCACCTTTCATGAATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCA
*
1219496 TTTCATGCACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTAT
131 TTTCATGCACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTAT
1219561 GTCATCCTTTCATGCCTTAATGCATCCTTTCATG
196 GTCATCCTTTCATGCCTTAATGCATCCTTTCATG
1219595 CATTTTATTTATGGCATCCTTTCATC-CCTTAATGCATCATTTAATGCATTTTATTTATGGCATC
1 CATTTTATTTATGGCATCCTTTCA-CGCCTTAATGCATCATTTAATGCATTTTATTTATGGCATC
* * *
1219659 TTTTCATGCCTTAATGCACCTTTCATGCATTTTATTTATGGCATCCTTTTATGCCTTAATGCATC
65 CTTTCATGCCTTAATGCACCTTTCATGAATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC
*
1219724 ATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTA
130 ATTTCATGCACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTA
1219789 TGT
195 TGT
1219792 ATTCGGTTTA
Statistics
Matches: 191, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
229 190 0.99
230 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (229 bp):
CATTTTATTTATGGCATCCTTTCACGCCTTAATGCATCATTTAATGCATTTTATTTATGGCATCC
TTTCATGCCTTAATGCACCTTTCATGAATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCA
TTTCATGCACTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTAT
GTCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:1226350 original size:6 final size:5
Alignment explanation
Indices: 1226319--1226349 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1226309 TCCAAGATGA
1226319 AAAAT AAAAT AAAAT AAAAT AAAATT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT
1226350 TGTATTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:1237659 original size:21 final size:22
Alignment explanation
Indices: 1237635--1237689 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1237625 TCCCTTGCTA
*
1237635 TGTATCGATACA-GCTTGAATG
1 TGTATCGATACATCCTTGAATG
1237656 TGTAAT-GATACATTCCTTGAATG
1 TGT-ATCGATACA-TCCTTGAATG
1237679 TGTATCGATAC
1 TGTATCGATAC
1237690 CCCTCGAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 16 0.55
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATCCTTGAATG
Found at i:1238136 original size:20 final size:20
Alignment explanation
Indices: 1238113--1238155 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1238103 TAAAAAATTA
*
1238113 TTTTTGTTTTAAAT-TGTTG
1 TTTTTGATTTAAATATGTTG
*
1238132 TTTTTGATTTAATTATGTTG
1 TTTTTGATTTAAATATGTTG
1238152 TTTT
1 TTTT
1238156 AATGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (20 bp):
TTTTTGATTTAAATATGTTG
Found at i:1240034 original size:11 final size:12
Alignment explanation
Indices: 1240003--1240035 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1239993 TAGAGTAATT
1240003 TTTCAAAAATGA
1 TTTCAAAAATGA
1240015 TTTCAAAAATGA
1 TTTCAAAAATGA
*
1240027 TTTTAAAAA
1 TTTCAAAAA
1240036 AGAAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (12 bp):
TTTCAAAAATGA
Found at i:1247750 original size:23 final size:23
Alignment explanation
Indices: 1247692--1247760 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
1247682 ATTTTAGTGC
* *
1247692 AGGAGGAATCGATACCCCCTTTGA
1 AGGA-GAACCGATTCCCCCTTTGA
* * *
1247716 AGGGGAATCGATTCCCCCTTTGG
1 AGGAGAACCGATTCCCCCTTTGA
* *
1247739 ATGAGAACCGATTTCCACCTTT
1 AGGAGAACCGA-TTCCCCCTTT
1247761 AGGGAATCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 25 0.68
24 12 0.32
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (23 bp):
AGGAGAACCGATTCCCCCTTTGA
Found at i:1257038 original size:20 final size:20
Alignment explanation
Indices: 1256998--1257040 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1256988 ACTAAAGTTT
* *
1256998 CGAATTTGAAAATCGCGTTG
1 CGAATTTGAAAATCACATTG
1257018 CGAATTTGAAAATCACATTG
1 CGAATTTGAAAATCACATTG
1257038 CGA
1 CGA
1257041 TAGTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
CGAATTTGAAAATCACATTG
Found at i:1257057 original size:77 final size:77
Alignment explanation
Indices: 1256964--1257251 Score: 450
Period size: 77 Copynumber: 3.7 Consensus size: 77
1256954 ACGCGAATTT
* * ** *
1256964 TAGTACTGTTTACCTATATCGATAACTAAAGTTTCGAATTTGAAAATCGCGTTGCGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
*
1257029 ATCACATTGCGA
66 ATCGCATTGCGA
* *
1257041 TAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTACGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
1257106 ATCGCATTGCGA
66 ATCGCATTGCGA
* * * *
1257118 TAGTACTGTTTACCTATATCTGTAATTAGCGTTACGAATTTGAATATCGTGTTGCGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
1257183 ATCGCATTGCGA
66 ATCGCATTGCGA
* *
1257195 TAGTACTGTTTACCTATATCGGTAATTATCGTTGCAAATTTGAAAATCGCGTTGCGA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGA
1257252 TTTACCTATT
Statistics
Matches: 191, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 191 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (77 bp):
TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
ATCGCATTGCGA
Found at i:1257098 original size:20 final size:20
Alignment explanation
Indices: 1257069--1257110 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1257059 TCGGTAATTA
*
1257069 GCGTTGCGAATTTGAAAATC
1 GCGTTACGAATTTGAAAATC
1257089 GCGTTACGAATTTGAAAATC
1 GCGTTACGAATTTGAAAATC
1257109 GC
1 GC
1257111 ATTGCGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (20 bp):
GCGTTACGAATTTGAAAATC
Found at i:1257192 original size:20 final size:20
Alignment explanation
Indices: 1257152--1257194 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1257142 ATTAGCGTTA
* **
1257152 CGAATTTGAATATCGTGTTG
1 CGAATTTGAAAATCGCATTG
1257172 CGAATTTGAAAATCGCATTG
1 CGAATTTGAAAATCGCATTG
1257192 CGA
1 CGA
1257195 TAGTACTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (20 bp):
CGAATTTGAAAATCGCATTG
Found at i:1257267 original size:20 final size:20
Alignment explanation
Indices: 1257243--1257294 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1257233 TTTGAAAATC
*
1257243 GCGTTGCGATTTACCTATTA
1 GCGTTGCGATTTACATATTA
* * *
1257263 TCGTTGCAATTTACATATTC
1 GCGTTGCGATTTACATATTA
1257283 GCGTTGCGATTT
1 GCGTTGCGATTT
1257295 TGGAACCTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:1257285 original size:40 final size:40
Alignment explanation
Indices: 1257219--1257294 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1257209 TATATCGGTA
1257219 ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
1 ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
*
1257259 ATTATCGTTGC-AATTT-ACATATTCGCGTTGCGATTT
1 ATTATCGTTGCAAATTTGA-A-AATCGCGTTGCGATTT
1257295 TGGAACCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 1 0.03
39 6 0.18
40 26 0.79
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
Found at i:1260000 original size:18 final size:18
Alignment explanation
Indices: 1259977--1260011 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1259967 TATTAACGAC
*
1259977 ACAATTATAATATGGAAA
1 ACAATTATAACATGGAAA
*
1259995 ACAATTGTAACATGGAA
1 ACAATTATAACATGGAA
1260012 TTATATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
ACAATTATAACATGGAAA
Found at i:1260764 original size:43 final size:43
Alignment explanation
Indices: 1260716--1260797 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
1260706 AAGCACAATG
*
1260716 TTGTCATTGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
1 TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
* * * *
1260759 TTGTCAATGATCCAACTCTTTCTGTGAATGATTGAGTGA
1 TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGA
1260798 CATGAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (43 bp):
TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
Found at i:1263844 original size:77 final size:77
Alignment explanation
Indices: 1263712--1264164 Score: 433
Period size: 77 Copynumber: 5.9 Consensus size: 77
1263702 AATGCCCTAC
* * * *
1263712 TTGCGATAGTACTGTTTATCTATATCGGTAATTAGCGTTGTGAATTTGAATATCGCGTTGCGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
*
1263777 ATGAAAATCACA
66 ATGAAAATCGCA
* * *
1263789 TTGCGATAGTACTGTTTGCCTATGTCAGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGTGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
*
1263854 ATAAAAATCGCA
66 ATGAAAATCGCA
* * * *
1263866 TTGCGATAGTACTGTTTACCTATAT-TGATAATTCGCGTTGTGAATTTGAAAATCGCATTGCGAA
1 TTGCGATAGTACTGTTTACCTATATCAG-TAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
* *
1263930 TTTGGAAAATCGCG
65 TAT-GAAAATCGCA
* * * * * * *
1263944 TTGCGAT-TTACCT-ATTATCGT-TA-CGATTTACCTATTATCGTTGCG-ATTT-ACATATTCAC
1 TTGCGATAGTA-CTGTTTA-CCTATATC-A-GTA---ATTAGCGTTGCGAATTTGA-A-AATCGC
* * *
1264003 GTTGCAAATTTGGAAAATCGCG
57 GTTGCGAATAT-GAAAATCGCA
* * *
1264025 TTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAGTTTGAAAAT--CGTTACGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
*
1264088 TTGAAAATCGCA
66 ATGAAAATCGCA
* *
1264100 TTGCGATAGTACTGTTTACCTATAT-ATGTAATTCGCGTTGCGAATTTGAAAATCGCATTGC-AA
1 TTGCGATAGTACTGTTTACCTATATCA-GTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
1264163 TA
65 TA
1264165 GTACTGTTTA
Statistics
Matches: 307, Mismatches: 48, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
75 58 0.19
76 14 0.05
77 136 0.44
78 34 0.11
79 5 0.02
80 6 0.02
81 46 0.15
82 7 0.02
83 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (77 bp):
TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
ATGAAAATCGCA
Found at i:1263848 original size:20 final size:20
Alignment explanation
Indices: 1263823--1263871 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1263813 TCAGTAATTA
* *
1263823 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATATAAAAATC
*
1263843 GCGTTGTGAATATAAAAATC
1 GCGTTGCGAATATAAAAATC
*
1263863 GCATTGCGA
1 GCGTTGCGA
1263872 TAGTACTGTT
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:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATATAAAAATC
Found at i:1263952 original size:20 final size:20
Alignment explanation
Indices: 1263898--1263949 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
1263888 TATTGATAAT
*
1263898 TCGCGTTGTGAATTTGAAAA
1 TCGCGTTGCGAATTTGAAAA
*
1263918 TCGCATTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTT-GAAAA
1263939 TCGCGTTGCGA
1 TCGCGTTGCGA
1263950 TTTACCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGAAAA
Found at i:1264007 original size:20 final size:20
Alignment explanation
Indices: 1263942--1263999 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1263932 TGGAAAATCG
1263942 CGTTGCGATTTACCTATTAT
1 CGTTGCGATTTACCTATTAT
*
1263962 CGTTACGATTTACCTATTAT
1 CGTTGCGATTTACCTATTAT
*
1263982 CGTTGCGATTTACATATT
1 CGTTGCGATTTACCTATT
1264000 CACGTTGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTACCTATTAT
Found at i:1264142 original size:37 final size:37
Alignment explanation
Indices: 1264020--1264142 Score: 90
Period size: 37 Copynumber: 3.3 Consensus size: 37
1264010 ATTTGGAAAA
**
1264020 TCGCGTTGCGATAGTACTGTTTACCTATATCGGTAAT
1 TCGCGTTGCGATAGTACTGTTTACCTATATATGTAAT
* * * * * * * *
1264057 TAGCGTTGCGAGTTTGAAAATCG-TTA-CGA-ATTTGAAAA
1 TCGCGTTGCGA--TAG-TACT-GTTTACCTATATATGTAAT
*
1264095 TCGCATTGCGATAGTACTGTTTACCTATATATGTAAT
1 TCGCGTTGCGATAGTACTGTTTACCTATATATGTAAT
1264132 TCGCGTTGCGA
1 TCGCGTTGCGA
1264143 ATTTGAAAAT
Statistics
Matches: 60, Mismatches: 19, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
34 1 0.02
35 5 0.08
36 4 0.07
37 26 0.43
38 14 0.23
39 4 0.07
40 5 0.08
41 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (37 bp):
TCGCGTTGCGATAGTACTGTTTACCTATATATGTAAT
Found at i:1264171 original size:57 final size:57
Alignment explanation
Indices: 1264078--1264211 Score: 205
Period size: 57 Copynumber: 2.4 Consensus size: 57
1264068 GTTTGAAAAT
* * * *
1264078 CGTTACGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATATGTAATTCG
1 CGTTGCGAATTTGAAAATCGCATTGCAATAGTACTGTTTACCTATATAGGTAATTAG
*
1264135 CGTTGCGAATTTGAAAATCGCATTGCAATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGAATTTGAAAATCGCATTGCAATAGTACTGTTTACCTATATAGGTAATTAG
* *
1264192 CATTGCAAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
1264212 AGTTGTGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 70 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (57 bp):
CGTTGCGAATTTGAAAATCGCATTGCAATAGTACTGTTTACCTATATAGGTAATTAG
Found at i:1264255 original size:20 final size:20
Alignment explanation
Indices: 1264213--1264262 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1264203 TGAAAATCGA
*
1264213 GTTGTGATTTACCTATTATC
1 GTTGTGATTTACCTATTAGC
*
1264233 GTTGTGATTTACCTATTCGC
1 GTTGTGATTTACCTATTAGC
*
1264253 GTTGCGATTT
1 GTTGTGATTT
1264263 TGGAACCTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
GTTGTGATTTACCTATTAGC
Found at i:1264276 original size:20 final size:20
Alignment explanation
Indices: 1264253--1264317 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1264243 ACCTATTCGC
1264253 GTTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
* ** **
1264273 GTTGCAAAATTGG-AGTTCGT
1 GTTGCGATTTTGGAACCT-GT
*
1264293 ATTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
1264313 GTTGC
1 GTTGC
1264318 AAAATTGAAG
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTTGGAACCTGT
Found at i:1264338 original size:40 final size:40
Alignment explanation
Indices: 1264248--1264344 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 40
1264238 GATTTACCTA
*
1264248 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGGAG
1 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
**
1264288 TTCGTATTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
1 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
*
1264328 TTCGCGTTGCGAATTTG
1 TTCGCGTTGCGATTTTG
1264345 TTGGTCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (40 bp):
TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
Found at i:1267066 original size:18 final size:18
Alignment explanation
Indices: 1267043--1267077 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1267033 TATTAATGAC
*
1267043 ACAATTATAATATGGAAA
1 ACAATTATAACATGGAAA
*
1267061 ACAATTGTAACATGGAA
1 ACAATTATAACATGGAA
1267078 TTATATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
ACAATTATAACATGGAAA
Found at i:1268594 original size:9 final size:9
Alignment explanation
Indices: 1268580--1268651 Score: 68
Period size: 8 Copynumber: 8.6 Consensus size: 9
1268570 TGACTTTGGT
1268580 TTTTTCTTC
1 TTTTTCTTC
1268589 TTTTTCTTC
1 TTTTTCTTC
1268598 TTTTTC-TC
1 TTTTTCTTC
1268606 -TTTTC-TC
1 TTTTTCTTC
1268613 -TTTTCTT-
1 TTTTTCTTC
1268620 TTTTTCTT-
1 TTTTTCTTC
*
1268628 TTTTAATTTTC
1 TTTT--TCTTC
1268639 TTTTTC-TC
1 TTTTTCTTC
1268647 TTTTT
1 TTTTT
1268652 TTTTTGCAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
7 12 0.21
8 21 0.38
9 16 0.29
10 3 0.05
11 4 0.07
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:1268622 original size:13 final size:13
Alignment explanation
Indices: 1268595--1268655 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
1268585 CTTCTTTTTC
1268595 TTCTTTTTCTCTT
1 TTCTTTTTCTCTT
*
1268608 TTCTCTTTTCTTTTT
1 TTCT-TTTTC-TCTT
*
1268623 TTCTTTTT-TAATT
1 TTCTTTTTCT-CTT
1268636 TTCTTTTTCTCTT
1 TTCTTTTTCTCTT
1268649 TT-TTTTT
1 TTCTTTTT
1268656 TGCAACGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 6 0.15
13 18 0.44
14 10 0.24
15 7 0.17
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTCTT
Found at i:1268626 original size:28 final size:27
Alignment explanation
Indices: 1268586--1268656 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
1268576 TGGTTTTTTC
*
1268586 TTCTTTTTCTTCTTTTTCT-CTTTTCTCTT
1 TTCTTTTT-TTCTTTTT-TAATTTTCT-TT
1268615 TTCTTTTTTTCTTTTTTAATTTTCTTT
1 TTCTTTTTTTCTTTTTTAATTTTCTTT
*
1268642 TTCTCTTTTT-TTTTT
1 TTCTTTTTTTCTTTTT
1268657 GCAACGGTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.13
27 12 0.31
28 14 0.36
29 8 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTCTTTTTTTCTTTTTTAATTTTCTTT
Found at i:1268648 original size:8 final size:8
Alignment explanation
Indices: 1268580--1268651 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 8
1268570 TGACTTTGGT
1268580 TTTTTCTTC
1 TTTTTC-TC
1268589 TTTTTCTTC
1 TTTTTC-TC
1268598 TTTTTCTC
1 TTTTTCTC
1268606 -TTTTCTC
1 TTTTTCTC
1268613 -TTTTCT-
1 TTTTTCTC
1268619 TTTTT-TC
1 TTTTTCTC
1268626 TTTTT-T-
1 TTTTTCTC
**
1268632 AATTT-TC
1 TTTTTCTC
1268639 TTTTTCTC
1 TTTTTCTC
1268647 TTTTT
1 TTTTT
1268652 TTTTTGCAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 5 0.09
7 26 0.47
8 9 0.16
9 15 0.27
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCTC
Found at i:1270897 original size:20 final size:20
Alignment explanation
Indices: 1270872--1270921 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1270862 TCGGTAATTA
*
1270872 GCGTTGCGAATTTGAATATC
1 GCGTTGCGAATTTGAAAATC
*
1270892 GCGTTGCGAATTTGAAAATT
1 GCGTTGCGAATTTGAAAATC
*
1270912 GCATTGCGAA
1 GCGTTGCGAA
1270922 AGTACTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1270964 original size:77 final size:77
Alignment explanation
Indices: 1270837--1271367 Score: 622
Period size: 77 Copynumber: 6.8 Consensus size: 77
1270827 TAATGCCCCA
*
1270837 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAATATCGCGTTGCGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
*
1270902 TTTGAAAATTGC
66 TTTGAAAATCGC
* * * * * *
1270914 ATTGCGAAAGTACTGTTTACCTATGTCGTTAATTAGCTTTGCAAATTTGAAAATCACGTTGCGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
* *
1270979 TATGAAAATCAC
66 TTTGAAAATCGC
* * *
1270991 ATTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATCGCATTGTGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
*
1271056 TTTGGAAAATTGC
66 TTT-GAAAATCGC
* * * * * * * *
1271069 ATTGCGAT-TTACCTATTATCATTGCGAT-TTGCCT-ATTATCGTTGCG-ATTT-ACATATTCGC
1 ATTGCGATAGTA-CTGTT-T-A--CCTATATCG-GTAATTAGCGTTGCGAATTTGA-A-AATCGC
*
1271129 GTTGAGAATTTGGAAAATCGC
58 GTTGCGAATTT-GAAAATCGC
* * *
1271150 GTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGTGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
1271215 TTTGAAAATCGC
66 TTTGAAAATCGC
* * * *
1271227 ATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGAATTTGAATATCGCGTTGCGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
1271292 TTTGAAAATCGC
66 TTTGAAAATCGC
* * * * *
1271304 ATTGCGATATTACGGTTTACCTATTTCGGTAATTAGCGTTGCGAATATGAAAATCGCATTGCGA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGA
1271368 TAGTACTGTT
Statistics
Matches: 379, Mismatches: 61, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
77 265 0.70
78 46 0.12
79 8 0.02
80 8 0.02
81 46 0.12
82 6 0.02
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (77 bp):
ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
TTTGAAAATCGC
Found at i:1271056 original size:20 final size:21
Alignment explanation
Indices: 1271024--1271072 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1271014 TATCGGTAAT
* *
1271024 TCGCGTTGCGAATTT-GAAAA
1 TCGCATTGTGAATTTGGAAAA
1271044 TCGCATTGTGAATTTGGAAAA
1 TCGCATTGTGAATTTGGAAAA
*
1271065 TTGCATTG
1 TCGCATTG
1271073 CGATTTACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGTGAATTTGGAAAA
Found at i:1271078 original size:20 final size:20
Alignment explanation
Indices: 1271024--1271075 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1271014 TATCGGTAAT
*
1271024 TCGCGTTGCGAATTTGAAAA
1 TCGCATTGCGAATTTGAAAA
*
1271044 TCGCATTGTGAATTTGGAAAA
1 TCGCATTGCGAATTT-GAAAA
*
1271065 TTGCATTGCGA
1 TCGCATTGCGA
1271076 TTTACCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGAATTTGAAAA
Found at i:1271091 original size:20 final size:20
Alignment explanation
Indices: 1271068--1271125 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1271058 TGGAAAATTG
1271068 CATTGCGATTTACCTATTAT
1 CATTGCGATTTACCTATTAT
*
1271088 CATTGCGATTTGCCTATTAT
1 CATTGCGATTTACCTATTAT
* *
1271108 CGTTGCGATTTACATATT
1 CATTGCGATTTACCTATT
1271126 CGCGTTGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (20 bp):
CATTGCGATTTACCTATTAT
Done.