Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007533.1 Hibiscus syriacus cultivar Beakdansim tig00021044_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: 114393
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1381 original size:20 final size:20
Alignment explanation
Indices: 1346--1383 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1336 TTATAAATAG
**
1346 TCGAATTTATTCAATTTAAA
1 TCGAATTTATAAAATTTAAA
1366 TCGAATTTATAAAATTTA
1 TCGAATTTATAAAATTTA
1384 TGTATGAGCA
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:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TCGAATTTATAAAATTTAAA
Found at i:1571 original size:65 final size:64
Alignment explanation
Indices: 1490--1689 Score: 162
Period size: 65 Copynumber: 3.2 Consensus size: 64
1480 GATTAATAAG
* * * *
1490 TTACTAATAATGATTTA-ATAATTA-TTATTAATCTAATGATTTGATATTTAATGATTTAGTAAT
1 TTACTAATAATGATTTATATAAATATTTAATAAT-TAA-GATTTGATA-CTAATAATTTAGTAAT
1553 GA
63 GA
* * * *
1555 TTACTAGTAATTATTTATTATAAATATTTAATGATTTAGATTTGATACTAATAATTTAGTAATGA
1 TTACTAATAATGATTTA-TATAAATATTTAATAATTAAGATTTGATACTAATAATTTAGTAATGA
* ** * * * * *
1620 TTACTAATAATAAAAT-TAT-AAGATTTGATAA-T--GATTTGATAATAATATTTTAATAATGA
1 TTACTAATAATGATTTATATAAATATTTAATAATTAAGATTTGATACTAATAATTTAGTAATGA
*
1679 TTACTACTAAT
1 TTACTAATAAT
1690 TTGATAATAT
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
59 34 0.30
61 1 0.01
62 9 0.08
63 3 0.03
65 43 0.38
66 9 0.08
67 8 0.07
68 6 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (64 bp):
TTACTAATAATGATTTATATAAATATTTAATAATTAAGATTTGATACTAATAATTTAGTAATGA
Found at i:1953 original size:15 final size:15
Alignment explanation
Indices: 1933--1961 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1923 TTTATTATTA
1933 ATATTTAATGATTTG
1 ATATTTAATGATTTG
1948 ATATTTAATGATTT
1 ATATTTAATGATTT
1962 AGTAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:2017 original size:24 final size:23
Alignment explanation
Indices: 1990--2067 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 23
1980 TAATGTTTAC
1990 TAATAATGTTTTATTATTAATATT
1 TAATAATGTTTTA-TATTAATATT
* * *
2014 TAATGA--TTTGATACTAATGATT
1 TAATAATGTTTTATATTAAT-ATT
*
2036 TAATAATG-ATTACTATTAATTATT
1 TAATAATGTTTTA-TATTAA-TATT
2060 TAATAATG
1 TAATAATG
2068 ATTAAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
21 6 0.14
22 12 0.29
23 2 0.05
24 21 0.50
25 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.50
Consensus pattern (23 bp):
TAATAATGTTTTATATTAATATT
Found at i:2044 original size:11 final size:11
Alignment explanation
Indices: 2014--2075 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
2004 TATTAATATT
2014 TAATGATTTGATA
1 TAATGATTT-A-A
2027 CTAATGATTTAA
1 -TAATGATTTAA
*
2039 TAATGATTACTAT
1 TAATGATT--TAA
*
2052 TAATTATTTAA
1 TAATGATTTAA
*
2063 TAATGATTAAA
1 TAATGATTTAA
2074 TA
1 TA
2076 TTTAAATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 21 0.51
12 1 0.02
13 10 0.24
14 9 0.22
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:2150 original size:22 final size:22
Alignment explanation
Indices: 2122--2165 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2112 AAATAGTTGA
*
2122 ATTTATAAATAGTCGAATTTAT
1 ATTTATAAATAGCCGAATTTAT
2144 ATTTATAAATAGCCGAATTTAT
1 ATTTATAAATAGCCGAATTTAT
2166 TCTTTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (22 bp):
ATTTATAAATAGCCGAATTTAT
Found at i:2163 original size:16 final size:16
Alignment explanation
Indices: 2102--2144 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
2092 TCAATTTAAA
2102 TCGAATTTATAAATAG
1 TCGAATTTATAAATAG
*
2118 TTGAATTTATAAATAG
1 TCGAATTTATAAATAG
2134 TCGAATTTATA
1 TCGAATTTATA
2145 TTTATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (16 bp):
TCGAATTTATAAATAG
Found at i:2228 original size:17 final size:17
Alignment explanation
Indices: 2194--2250 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
2184 GGAGGAATGC
*
2194 ATATTTAA-TATT-ATA
1 ATATTTAAGTTTTAATA
2209 ATATTTAAGTTTTAATA
1 ATATTTAAGTTTTAATA
2226 ATATTTAAGTTTTAATA
1 ATATTTAAGTTTTAATA
2243 ATATTTAA
1 ATATTTAA
2251 CATATTTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 8 0.21
16 3 0.08
17 28 0.72
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
ATATTTAAGTTTTAATA
Found at i:4957 original size:111 final size:111
Alignment explanation
Indices: 4776--5060 Score: 399
Period size: 111 Copynumber: 2.6 Consensus size: 111
4766 ATGGATGCAT
* * * *
4776 ACTTGTTCCATTGTCACTCATGGAATATCAAATCTTGAAAGAGAGAGATTTGTTCCTCTTCTTCT
1 ACTTGTTCCGTTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCT
* * *
4841 AAGGGAATATCATATATGGGAAAGTTGATCCACTGAATTAGGGTAG
66 AAGGGAATATCAGATATGGGAAAGTTGATCCACTAAATCAGGGTAG
* * * *
4887 ACTTGTTGCGTTGTCACTCAAGGAATATCAAATCATGGAAGAGAGGGATTTGTTCCGCTTTTTCT
1 ACTTGTTCCGTTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCT
* * * *
4952 AAGGGAATATCAGATCTTGGAAAGTTTATCCATTAAATCAGGGTAG
66 AAGGGAATATCAGATATGGGAAAGTTGATCCACTAAATCAGGGTAG
* * * *
4998 ACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGCTCCACTTCTT
1 ACTTGTTCCGTTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTT
5061 TGAAAAGGAA
Statistics
Matches: 151, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
111 151 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (111 bp):
ACTTGTTCCGTTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCT
AAGGGAATATCAGATATGGGAAAGTTGATCCACTAAATCAGGGTAG
Found at i:5090 original size:48 final size:48
Alignment explanation
Indices: 5019--5128 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
5009 TGTCACTCAG
** *
5019 GGAATATCAAATCTTGAAAGAGAGGGATTTGCTCCACTTCTTTGAAAA
1 GGAATATCAAATCTTGAAAGAGAGGGAAATGCTCCACTTCTTGGAAAA
* * * * *
5067 GGAATATTAAATCTTGGAAGAGAGTGAAATGTTCCACTTCTTGGAAAG
1 GGAATATCAAATCTTGAAAGAGAGGGAAATGCTCCACTTCTTGGAAAA
*
5115 GGAATATCATATCT
1 GGAATATCAAATCT
5129 GGGGGAATTG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (48 bp):
GGAATATCAAATCTTGAAAGAGAGGGAAATGCTCCACTTCTTGGAAAA
Found at i:5173 original size:160 final size:159
Alignment explanation
Indices: 4906--5235 Score: 365
Period size: 160 Copynumber: 2.1 Consensus size: 159
4896 GTTGTCACTC
** * * * *
4906 AAGGAATATCAAATCATGGAAGAGAGGGATTTGTTCCGCTTTTTCTAAGGGAATATCAGATCTTG
1 AAGGAATATCAAATCATGGAAGAGAGGGAAATGTTCCACTTTTGCAAAGGGAATATCAGATCTGG
* ** *
4971 GAAAGTTTATCCATTAAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGA
66 GAAAGTTGATCCATTAAATCAGGACAGACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTTGA
5036 AAGAGAGGGATTTGCTCCACTTCTTTGAA
131 AAGAGAGGGATTTGCTCCACTTCTTTGAA
* * * * *
5065 AAGGAATATTAAATCTTGGAAGAGAGTGAAATGTTCCACTTCTTGGAAAGGGAATATCATATCTG
1 AAGGAATATCAAATCATGGAAGAGAGGGAAATGTTCCACTT-TTGCAAAGGGAATATCAGATCT-
* * ** * *
5130 GGGGAA-TTGATCCATTGAATCAGGACAGACTTGTTTTGCTGTCATTCAAGGTATATCAAATCTT
64 GGGAAAGTTGATCCATTAAATCAGGACAGACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTT
* * ** * * * *
5194 GGAAGAAAAAGATATGTTCCGCGTCTTTGAA
129 GAAAGAGAGGGATTTGCTCCACTTCTTTGAA
*
5225 AGGGAATATCA
1 AAGGAATATCA
5236 GATCTGCAGG
Statistics
Matches: 138, Mismatches: 31, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
159 35 0.25
160 99 0.72
161 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (159 bp):
AAGGAATATCAAATCATGGAAGAGAGGGAAATGTTCCACTTTTGCAAAGGGAATATCAGATCTGG
GAAAGTTGATCCATTAAATCAGGACAGACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTTGA
AAGAGAGGGATTTGCTCCACTTCTTTGAA
Found at i:19132 original size:18 final size:17
Alignment explanation
Indices: 19105--19219 Score: 71
Period size: 17 Copynumber: 6.8 Consensus size: 17
19095 AAGAAGAAAT
19105 AAAAGAGAAAAAATGAA
1 AAAAGAGAAAAAATGAA
19122 AAAATGAGAAAAAA-GAA
1 AAAA-GAGAAAAAATGAA
* *
19139 AAATGATGGAAAAAACGAA
1 AAAAGA--GAAAAAATGAA
**
19158 AAGAA-A-AAAAAA-GGG
1 AA-AAGAGAAAAAATGAA
*
19173 AAAAGGGAAAAAAATGAA
1 AAAAGAG-AAAAAATGAA
* *
19191 AAATGA-AAAAAAAGAGA
1 AAAAGAGAAAAAATGA-A
19208 AAAA-AGAAAAAA
1 AAAAGAGAAAAAA
19220 GAGAAATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.03
15 3 0.04
16 17 0.22
17 26 0.34
18 21 0.28
19 6 0.08
20 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (17 bp):
AAAAGAGAAAAAATGAA
Found at i:20789 original size:111 final size:110
Alignment explanation
Indices: 20591--20830 Score: 313
Period size: 111 Copynumber: 2.2 Consensus size: 110
20581 GTTGAAGATT
* * *
20591 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACAAATTCGTTGAAGATTGTTCGAGTTCTATA
* * *
20656 CTCTCTGAAGGAATAGAGAGCGGGCCTGTTTCATGAAGATTGTTC
66 CTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
** * *
20701 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAAACACGTT-TTATGAAGATTGTTTGAGTTCTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCG-AACAAATTCGT-TGAAGATTGTTCGAGTTCTA
* **
20765 TACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTGTGAAGATTGTTC
64 TACTCCCTGAA-GGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
*
20812 GAGTTCTATACTCCCTGAA
1 GAGTTCTATACTCTCTGAA
20831 CGGATAGGGA
Statistics
Matches: 113, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
110 31 0.27
111 80 0.71
112 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (110 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACAAATTCGTTGAAGATTGTTCGAGTTCTATA
CTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
Found at i:20870 original size:166 final size:164
Alignment explanation
Indices: 20589--20972 Score: 413
Period size: 166 Copynumber: 2.3 Consensus size: 164
20579 TTGTTGAAGA
* * *** *
20589 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAATTCGTTGAAGATTGTTCGAGTTCT
1 TTGAGTTCTATACTCCCTGAAGG-ATAGGGAGCGGACCCGTTTTG-TGAAGATTGTTCGAGTTCT
* * * *
20653 ATACTCTCTGAAGGAATAGAGAGCGGGCCTGTTTCATGAAGATTGTTCGAGT-TCTATACTCTCT
64 ATACTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTCT-TATACTCTCT
* **
20717 GAAGGAATAGAGAGCGAAACACGTTTTATGAA-GATTGT
128 GAACGAATAGAGAGC-AAACACG-TTTACCAAGGATTGT
20755 TTGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTGTGAAGATTGTTCGAGTTCTA
1 TTGAGTTCTATACTCCCTGAA-GGATAGGGAGCGGACCCGTTTTGTGAAGATTGTTCGAGTTCTA
* * *
20820 TACTCCCTGAACGG-ATAGGGAGTGGACCCGTTT-GTCGAAGATTATTCGAGTCTTATACTCTCT
65 TACTCCCTGAA-GGAATAGAGAGCGGACCCGTTTCAT-GAAGATTATTCGAGTCTTATACTCTCT
* * *
20883 GAACGAATAGGGAGCAGACACGTTTGCCAAGGATTGT
128 GAACGAATAGAGAGCAAACACGTTTACCAAGGATTGT
* * * *
20920 TTGAG-TCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTTATT-TGAAGATT
1 TTGAGTTC-TATACTCCCTG-AAGGATAGGGAGCGGACCCGTT-TTGTGAAGATT
20973 TTTCAAGTAT
Statistics
Matches: 186, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
164 7 0.04
165 53 0.28
166 117 0.63
167 9 0.05
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (164 bp):
TTGAGTTCTATACTCCCTGAAGGATAGGGAGCGGACCCGTTTTGTGAAGATTGTTCGAGTTCTAT
ACTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTCTTATACTCTCTGAA
CGAATAGAGAGCAAACACGTTTACCAAGGATTGT
Found at i:20907 original size:55 final size:54
Alignment explanation
Indices: 20591--20972 Score: 349
Period size: 55 Copynumber: 6.9 Consensus size: 54
20581 GTTGAAGATT
* * ** *
20591 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACACGTTTG-TGAAGATTGTTC
* * * *
20646 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGGC-CTGTTTCATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACAC-GTTT-GTGAAGATTGTTC
* * * * *
20701 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAAACACGTTTTATGAAGATTGTTT
1 GAGTTCTATACTCTCTGAACGAATAGGGAGCG-GACACG-TTTGTGAAGATTGTTC
* * *
20757 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTGTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACACG-TTTGTGAAGATTGTTC
* * * * *
20812 GAGTTCTATACTCCCTGAACGGATAGGGAGTGGACCCGTTTGTCGAAGATTATTC
1 GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACACGTTTGT-GAAGATTGTTC
* ** *
20867 GAG-TCTTATACTCTCTGAACGAATAGGGAGCAGACACGTTTGCCAAGGATTGTTT
1 GAGTTC-TATACTCTCTGAACGAATAGGGAGCGGACACGTTTGTGAA-GATTGTTC
* * * * *
20922 GAG-TCTTATACTC-CTTGAAAGAAAAGGGAGCAGACCCGTTATTTGAAGATT
1 GAGTTC-TATACTCTC-TGAACGAATAGGGAGCGGACACGTT-TGTGAAGATT
20973 TTTCAAGTAT
Statistics
Matches: 282, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
54 10 0.04
55 223 0.79
56 45 0.16
57 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (54 bp):
GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACACGTTTGTGAAGATTGTTC
Found at i:20918 original size:110 final size:111
Alignment explanation
Indices: 20635--20940 Score: 279
Period size: 111 Copynumber: 2.8 Consensus size: 111
20625 CAAATTCGTT
* * * * * *
20635 GAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGGC-CTGTTTCATG--AAGATT
1 GAAGATTATTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACAC-GTTT--TGCCAAGATT
* *
20697 GTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAAACACGTTTTAT
63 GTTCGAGTTCTATACTCCCTGAAGGAATAGAGAGCGAAACACGTTTTAC
* * * * * **
20746 GAAGATTGTTTGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTGTGAAGATTGTT
1 GAAGATTATTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACACGTTTTGCCAAGATTGTT
* * * *
20811 CGAGTTCTATACTCCCTGAACGG-ATAGGGAGTG-GACCCGTTTGT-C
66 CGAGTTCTATACTCCCTGAA-GGAATAGAGAGCGAAACACGTTT-TAC
*
20856 GAAGATTATTCGAG-TCTTATACTCTCTGAACGAATAGGGAGCAGACACG-TTTGCCAAGGATTG
1 GAAGATTATTCGAGTTC-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTTGCCAA-GATTG
* *
20919 TTTGAG-TCTTATACTCCTTGAA
64 TTCGAGTTC-TATACTCCCTGAA
20941 AGAAAAGGGA
Statistics
Matches: 165, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
109 12 0.07
110 69 0.42
111 81 0.49
112 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (111 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACACGTTTTGCCAAGATTGTT
CGAGTTCTATACTCCCTGAAGGAATAGAGAGCGAAACACGTTTTAC
Found at i:25715 original size:14 final size:14
Alignment explanation
Indices: 25696--25728 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
25686 TTTCTTCTCG
25696 CTAGAGGCTTTCGA
1 CTAGAGGCTTTCGA
25710 CTAGAGGCTTTCGA
1 CTAGAGGCTTTCGA
25724 CTAGA
1 CTAGA
25729 TTCTCCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (14 bp):
CTAGAGGCTTTCGA
Found at i:28083 original size:22 final size:22
Alignment explanation
Indices: 28055--28101 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28045 CCTTATAGAT
*
28055 CCCTAAATATCAGGTAATAAAA
1 CCCTAAATACCAGGTAATAAAA
* *
28077 CCCTAAATACCGGGTAATAGAA
1 CCCTAAATACCAGGTAATAAAA
28099 CCC
1 CCC
28102 AATCTCTGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.19
Consensus pattern (22 bp):
CCCTAAATACCAGGTAATAAAA
Found at i:32760 original size:4 final size:4
Alignment explanation
Indices: 32751--32786 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
32741 AAACTATGCC
32751 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA
32787 TAATTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CTAA
Found at i:32846 original size:4 final size:4
Alignment explanation
Indices: 32837--32888 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
32827 GCCCTTCTTC
* **
32837 TTCT TTCT TTCCT TTCT TTC- TTCT CTCT TTCT TTC- TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
32884 TTCT T
1 TTCT T
32889 CTTACAACCG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 6 0.15
4 29 0.74
5 4 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTCT
Found at i:32868 original size:15 final size:14
Alignment explanation
Indices: 32837--32890 Score: 83
Period size: 15 Copynumber: 3.8 Consensus size: 14
32827 GCCCTTCTTC
32837 TTCTTTCTT-TCCT
1 TTCTTTCTTCTCCT
32850 TTCTTTCTTCTCTCT
1 TTCTTTCTTCTC-CT
32865 TTCTTTCTTCTCCCT
1 TTCTTTCTTCT-CCT
32880 TTCTTTCTTCT
1 TTCTTTCTTCT
32891 TACAACCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 26 0.68
16 1 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTTTCTTCTCCT
Found at i:32870 original size:19 final size:19
Alignment explanation
Indices: 32831--32888 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
32821 TTACGGGCCC
32831 TTCTTCT-TCTTTCTTTCCT
1 TTCTTCTCTCTTTCTTT-CT
*
32850 TTCTT-TCTTCTCTCTTTCT
1 TTCTTCTC-TCTTTCTTTCT
*
32869 TTCTTCTCCCTTTCTTTCT
1 TTCTTCTCTCTTTCTTTCT
32888 T
1 T
32889 CTTACAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.03
19 22 0.67
20 10 0.30
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCTTCTCTCTTTCTTTCT
Found at i:32883 original size:30 final size:26
Alignment explanation
Indices: 32830--32891 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 26
32820 CTTACGGGCC
32830 CTTCTTCTTCTTTCTTTCCTTTCTTT
1 CTTCTTCTTCTTTCTTTCCTTTCTTT
32856 CTTCTCTCTTTCTTTCTTCTCCCTTTCTTT
1 CTTCT-TC-TTCTTTCTT-T-CCTTTCTTT
32886 CTTCTT
1 CTTCTT
32892 ACAACCGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.16
27 2 0.06
28 9 0.28
29 2 0.06
30 14 0.44
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (26 bp):
CTTCTTCTTCTTTCTTTCCTTTCTTT
Found at i:39303 original size:21 final size:21
Alignment explanation
Indices: 39277--39324 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39267 ATTTTCAGAT
*
39277 TCGCAACCCGAACTTCGACTA
1 TCGCAACCCAAACTTCGACTA
** *
39298 TCGCAATGCAAACTTGGACTA
1 TCGCAACCCAAACTTCGACTA
39319 TCGCAA
1 TCGCAA
39325 TGCGAATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (21 bp):
TCGCAACCCAAACTTCGACTA
Found at i:39325 original size:21 final size:21
Alignment explanation
Indices: 39287--39327 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39277 TCGCAACCCG
39287 AACTTCGACTATCGCAATGCA
1 AACTTCGACTATCGCAATGCA
*
39308 AACTTGGACTATCGCAATGC
1 AACTTCGACTATCGCAATGC
39328 GAATATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (21 bp):
AACTTCGACTATCGCAATGCA
Found at i:39364 original size:16 final size:16
Alignment explanation
Indices: 39343--39386 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
39333 TGTAAATCGC
39343 ATTGCGATAGTCGAAT
1 ATTGCGATAGTCGAAT
39359 ATTGCGATAGTCGAAT
1 ATTGCGATAGTCGAAT
39375 ATTGCGATAGTC
1 ATTGCGATAGTC
39387 CAAGTTCGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (16 bp):
ATTGCGATAGTCGAAT
Found at i:39445 original size:21 final size:21
Alignment explanation
Indices: 39419--39488 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
39409 AAGTTCGCGT
39419 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
* *
39440 TTGCGA--TATTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
39461 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
39482 TTGCGAT
1 TTGCGAT
39489 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCG
Found at i:39476 original size:42 final size:43
Alignment explanation
Indices: 39400--39492 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 43
39390 GTTCGCATTA
39400 CGATAGTCAAAGTTCGCGTTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCAAAGTTCGCGTTTGCGATTTATTCCAAATTCGTTG
* *
39443 CGATATTCGAAGTTCGCG-TTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCAAAGTTCGCGTTTGCGATTTATTCCAAATTCGTTG
39485 CGATAGTC
1 CGATAGTC
39493 CAAAATCGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 31 0.66
43 16 0.34
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
CGATAGTCAAAGTTCGCGTTTGCGATTTATTCCAAATTCGTTG
Found at i:40887 original size:15 final size:15
Alignment explanation
Indices: 40868--40922 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
40858 ATTCTCTAAA
40868 TTTTAAAAATTTATC
1 TTTTAAAAATTTATC
* *
40883 CTTTAAAACTTATAAAT-
1 TTTTAAAAATT-T--ATC
40900 TTTTAAAAATTTATC
1 TTTTAAAAATTTATC
40915 TTTTAAAA
1 TTTTAAAA
40923 CTTATAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.06
15 17 0.53
16 2 0.06
17 9 0.28
18 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAAAAATTTATC
Found at i:40899 original size:31 final size:32
Alignment explanation
Indices: 40864--40930 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
40854 TTTCATTCTC
40864 TAAA-TTTTAAAAATTTATCCTTTAAAACTTA
1 TAAATTTTTAAAAATTTATCCTTTAAAACTTA
*
40895 TAAATTTTTAAAAATTTATCTTTTAAAACTTA
1 TAAATTTTTAAAAATTTATCCTTTAAAACTTA
40927 TAAA
1 TAAA
40931 AGTTAGCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAATTTTTAAAAATTTATCCTTTAAAACTTA
Found at i:59126 original size:136 final size:140
Alignment explanation
Indices: 58874--59166 Score: 366
Period size: 136 Copynumber: 2.1 Consensus size: 140
58864 TTATTTACTA
58874 CTAACTACTAACTTTTATTTTATTGCACTTTAATCATTGTTATTTATTTATTTATGTATGTATGT
1 CTAACTACTAACTTTTATTTTATTGCACTTTAATCATTGTTATTTATTTATTTATGTATGTATGT
* * * ** *
58939 ATTGTTTCTAATATTCGATTTGGCCTTTTGGTGATCCGATCTTAGGTATGAT-CTACATTATTAT
66 A-T-TTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGAGGTATGATCCGA-ATTATTAT
*
59003 GGTTTGAACTCTG
128 GGTTCGAACTCTG
* *
59016 CTAACTACTGACTTTTATTTTATTGCA-TTCTAATCATTGTTTATTTATTTGTTTAT-T-T-TAT
1 CTAACTACTAACTTTTATTTTATTGCACTT-TAATCATTG-TTATTTATTTATTTATGTATGTAT
*
59077 -TA-TTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCGAATTATTATG
64 GTATTTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGAGGTATGATCCGAATTATTATG
* *
59140 GTTCGGACTTTG
129 GTTCGAACTCTG
**
59152 CTAACCGCTAACTTT
1 CTAACTACTAACTTT
59167 CCCAACAACT
Statistics
Matches: 133, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
136 72 0.54
137 2 0.02
139 2 0.02
140 3 0.02
141 3 0.02
142 36 0.27
143 15 0.11
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (140 bp):
CTAACTACTAACTTTTATTTTATTGCACTTTAATCATTGTTATTTATTTATTTATGTATGTATGT
ATTTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGAGGTATGATCCGAATTATTATGGT
TCGAACTCTG
Found at i:61905 original size:210 final size:210
Alignment explanation
Indices: 61536--61921 Score: 499
Period size: 210 Copynumber: 1.8 Consensus size: 210
61526 AATGAGGTCT
* * * * * *
61536 GCTCGAAGATCGTGCAACATTCGAGACTGAAATGATGATCCACTGATTTGATGAGTAATCCAACA
1 GCTCCAAGATCGTGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
* * * *
61601 GTGGAATCTTATCTACAATCATATCATCGCTAGTCATCAAGGAGCGACGCAATGGCTTCAGCACA
66 GTAGAATCTTATCTACAAGCATATCATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCACA
* * * * *
61666 GCTGAGGGATTAACGGAGTTAGTTTACAAAGCATTGAGGGGCATCAGTTCCAAATACAAAGATCC
131 GCTGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCAGTTCCAAATACAAAGATCC
61731 GAGACGAAGTAGTGA
196 GAGACGAAGTAGTGA
* * **
61746 GCTCCAAGATCGTGCAACATTTGAGAATGATATGATAATCCACTAATTCGAGGAGTAATCCAGTA
1 GCTCCAAGATCGTGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
* * * * * *
61811 GTAGATTCTTATCTACGAGCAT-TCCATCGCTAATCATTAAGGAGTGACGTATTGACTTCAGCAC
66 GTAGAATCTTATCTACAAGCATAT-CATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCA-
61875 CA-CATG-GGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCA
129 CAGC-TGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCA
61922 TTTTCGCGAA
Statistics
Matches: 148, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
209 1 0.01
210 143 0.97
211 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (210 bp):
GCTCCAAGATCGTGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
GTAGAATCTTATCTACAAGCATATCATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCACA
GCTGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCAGTTCCAAATACAAAGATCC
GAGACGAAGTAGTGA
Found at i:63468 original size:12 final size:12
Alignment explanation
Indices: 63453--63501 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
63443 AAAAAAAGTG
63453 CAAAGAAAAAAA
1 CAAAGAAAAAAA
63465 CAAAGAGAAAAGAAA
1 C-AA-AGAAAA-AAA
*
63480 CAAAGAAAAAAT
1 CAAAGAAAAAAA
63492 CAAAGTAAAA
1 CAAAG-AAAA
63502 GAAAAAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 8 0.25
13 12 0.38
14 8 0.25
15 4 0.12
ACGTcount: A:0.76, C:0.08, G:0.12, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAA
Found at i:63480 original size:15 final size:14
Alignment explanation
Indices: 63456--63521 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 14
63446 AAAAGTGCAA
63456 AGAAAAAAACAAAG
1 AGAAAAAAACAAAG
63470 AGAAAAGAAAC-AA-
1 AGAAAA-AAACAAAG
*
63483 AGAAAAAATCAAAG
1 AGAAAAAAACAAAG
*
63497 TAAAAGAAAAAACAAAG
1 --AGA-AAAAAACAAAG
63514 AGCAAAAA
1 AG-AAAAA
63522 GAAAACAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
12 3 0.07
13 8 0.20
14 8 0.20
15 9 0.22
16 3 0.07
17 10 0.24
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (14 bp):
AGAAAAAAACAAAG
Found at i:63483 original size:27 final size:26
Alignment explanation
Indices: 63453--63505 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
63443 AAAAAAAGTG
63453 CAAAGAAAAAAACAAAGAGAAAAGAAA
1 CAAAGAAAAAAACAAAG-GAAAAGAAA
* *
63480 CAAAGAAAAAATCAAAGTAAAAGAAA
1 CAAAGAAAAAAACAAAGGAAAAGAAA
63506 AAACAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.04
Consensus pattern (26 bp):
CAAAGAAAAAAACAAAGGAAAAGAAA
Found at i:63488 original size:26 final size:27
Alignment explanation
Indices: 63453--63505 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
63443 AAAAAAAGTG
63453 CAAAGAAAAAAA-CAAAGAGAAAAGAAA
1 CAAAGAAAAAAATCAAAG-GAAAAGAAA
*
63480 CAAAG-AAAAAATCAAAGTAAAAGAAA
1 CAAAGAAAAAAATCAAAGGAAAAGAAA
63506 AAACAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.04
Consensus pattern (27 bp):
CAAAGAAAAAAATCAAAGGAAAAGAAA
Found at i:64563 original size:28 final size:28
Alignment explanation
Indices: 64523--64584 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
64513 ATATCTATCT
*
64523 GAAGCTCAAGATCGAAGTTGGGGCAAGA
1 GAAGCTCAAGATCGAAGCTGGGGCAAGA
64551 GAAGCTCAAGATCGAAGCTGGGGCAAGA
1 GAAGCTCAAGATCGAAGCTGGGGCAAGA
64579 GAAGCT
1 GAAGCT
64585 AAATTTTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.13
Consensus pattern (28 bp):
GAAGCTCAAGATCGAAGCTGGGGCAAGA
Found at i:65262 original size:105 final size:105
Alignment explanation
Indices: 65130--65436 Score: 451
Period size: 105 Copynumber: 2.9 Consensus size: 105
65120 CTTAAGACAA
* *
65130 TTTCTCTT-AAAAC-AATCTTCGGCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAAT
1 TTTCT-TTCAAAACAAAT-TTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAAT
65193 TTGCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
64 TTGCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
65235 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
1 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
* * *
65300 GCTTCACATAAAACAAAATTAATCTCACTTGAGATTGTTG
66 GCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
* * * * * *
65340 TTTATTTCAAAACAAATTTCATCTCGCTTGAGACATTTTTTCTCTGAGATACAAA-TTTAAATTA
1 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
*
65404 G-TTGTATTTGAAACAAAATTAATCTCACTTGAG
66 GCTT-TACTTGAAACAAAATTAATCTCACTTGAG
65437 TTTTTCAAAA
Statistics
Matches: 184, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
103 2 0.01
104 35 0.19
105 144 0.78
106 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (105 bp):
TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
GCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
Found at i:65647 original size:28 final size:29
Alignment explanation
Indices: 65583--65647 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
65573 AGTTTCTCTT
*
65583 GAAACAAATCTTTGAGTATGTTCCTTTTGA
1 GAAA-AAATCTTTGAGTATGTTCCTTGTGA
*
65613 -ATAAAAATCTTTGAGT-TGTTTCTTGTGA
1 GA-AAAAATCTTTGAGTATGTTCCTTGTGA
65641 GAAAAAA
1 GAAAAAA
65648 ATTAGAGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 15 0.48
29 14 0.45
30 2 0.06
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (29 bp):
GAAAAAATCTTTGAGTATGTTCCTTGTGA
Found at i:65647 original size:29 final size:30
Alignment explanation
Indices: 65583--65649 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
65573 AGTTTCTCTT
* *
65583 GAAACAAATCTTTGAGTATGTTCCTTTTGA
1 GAAAAAAATCTTTGAGTATGTTCCTTGTGA
* *
65613 -ATAAAAATCTTTGAGT-TGTTTCTTGTGA
1 GAAAAAAATCTTTGAGTATGTTCCTTGTGA
65641 GAAAAAAAT
1 GAAAAAAAT
65650 TAGAGTCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (30 bp):
GAAAAAAATCTTTGAGTATGTTCCTTGTGA
Found at i:65876 original size:66 final size:67
Alignment explanation
Indices: 65806--65990 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 67
65796 ACAAAATCAT
* *
65806 CTTTGAGTTTATTT-CTTTAAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAA-AACC
1 CTTTGAGATTATTTCCTTT-AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCAATGAAACAACC
65869 A-A
65 ATA
* * * * *
65871 CCTTTGAGATTGTTTCCCTTAAAACGAATTTTTTCTCAT-TTGAGACAGTTTCCCATGAAACAAC
1 -CTTTGAGATTATTTCCTTTAAAACAAATTTTGTCTC-TCTTGAGACAGTTTCCAATGAAACAAC
*
65935 GATA
64 CATA
** *
65939 -TTTGAGAACATTTCCCTTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCC
1 CTTTGAGATTATTT-CCTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
65991 TTTAAACATC
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
66 56 0.57
67 41 0.42
68 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (67 bp):
CTTTGAGATTATTTCCTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCAATGAAACAACCA
TA
Found at i:65876 original size:96 final size:96
Alignment explanation
Indices: 65708--65886 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 96
65698 TCATGAAAAA
* * **
65708 ATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAA
1 ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
*
65773 AAACTTTGAGTTTGTTTCTACTAACAAAATC
66 AAACTTTGAGATTGTTTCTACTAACAAAATC
* *
65804 ATCTTTGAGTTTATTTCTTTAAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTAATGA-AAAA
1 ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
*
65867 CCAACCTTTGAGATTGTTTC
66 --AAACTTTGAGATTGTTTC
65887 CCTTAAAACG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 4 0.05
95 30 0.41
96 39 0.53
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (96 bp):
ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
AAACTTTGAGATTGTTTCTACTAACAAAATC
Found at i:66158 original size:38 final size:37
Alignment explanation
Indices: 66066--66203 Score: 158
Period size: 37 Copynumber: 3.7 Consensus size: 37
66056 TTGAAACATT
*
66066 TATCTTTGAGTCTGTTTCACTTGAAAAAAAACAAAGAA
1 TATCTTTGAGTCTGTTTCACTTGAAACAAAACAAA-AA
*
66104 -ATCTTTGAGTCTGTTTCACTTGCAACAAAACAAAAA
1 TATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
* *
66140 TCATATTTGAGTTTGTTTC-CTTTGAAACAAAAC--AAA
1 T-ATCTTTGAGTCTGTTTCAC-TTGAAACAAAACAAAAA
* *
66176 TATCTTTGAGATTTGTTTCCCTTGAAAC
1 TATCTTTGAG-TCTGTTTCACTTGAAAC
66204 CAATTTTGTC
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.09
36 21 0.24
37 34 0.38
38 26 0.29
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (37 bp):
TATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAAA
Found at i:66227 original size:20 final size:21
Alignment explanation
Indices: 66187--66229 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
66177 ATCTTTGAGA
*
66187 TTTGTTTCCCTTGAAACCAAT
1 TTTGTCTCCCTTGAAACCAAT
*
66208 TTTGTCTCCCTTGAGA-CAAT
1 TTTGTCTCCCTTGAAACCAAT
66228 TT
1 TT
66230 CTATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTGTCTCCCTTGAAACCAAT
Found at i:66676 original size:134 final size:133
Alignment explanation
Indices: 66348--66665 Score: 417
Period size: 134 Copynumber: 2.4 Consensus size: 133
66338 CGTAGGAACC
*
66348 GTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCTTAGATAACC-GGTCG
1 GTGTCATCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTC-ACCTTAGATAACCAGCTCG
* * * **
66412 TCCTCATCACGTAGGAATCGAGTTATCACCATTCTTAAAAATGGCCAGAACTCTTCACCGCGTAT
64 TCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTAT
66477 GATCA
129 GATCA
* * * * *
66482 GTGTCATCCCTCGACCAAACCACCTCATCACGTAGGAGCCGTGTCACCCATAGATAACCAGCT-G
1 GTGTCATCCC-CGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCTTAGATAACCAGCTCG
* * * *
66546 TCCTCATCACGTAGGAACCGAGTTATCATCATTCCTAAAGATGACCAGATCTCTTCATCAAGTAT
64 TCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTAT
*
66611 GAGT-T
129 GA-TCA
66616 GTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTT
1 GTGTCATCC-CCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTT
66666 TAGACGACCA
Statistics
Matches: 158, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
133 4 0.03
134 149 0.94
135 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (133 bp):
GTGTCATCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTTAGATAACCAGCTCGTC
CTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTATGA
TCA
Found at i:67939 original size:138 final size:139
Alignment explanation
Indices: 67785--68066 Score: 442
Period size: 139 Copynumber: 2.0 Consensus size: 139
67775 TTATTTACTA
*
67785 CTAACTACTAACTTTTATTTTATTACACTT-TAATCATTG-TTATTTATTTATTTATGTATTTAT
1 CTAACTACTAACTTTTATTTTATTACA-TTCTAACCATTGTTTATTTATTTATTTATGTATTTAT
* *
67848 TGTTTCTAATATTCGATTCGGCCTTGTGGTGATCCGATCCGGGGTATGATCCACATTATTATGGT
65 TATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTATTATGGT
*
67913 TTGGACTCTG
130 TCGGACTCTG
* * * * *
67923 CTAACTACTGACTTTTATTTTATTGCATTCTAACCATTGTTTATTTATTTGTTTGTTTATTTATT
1 CTAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTTATGTATTTATT
* *
67988 ATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATTCGGGGTATGATCCGCATTATTATGGTT
66 ATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTT
68053 CGGACTCTG
131 CGGACTCTG
68062 CTAAC
1 CTAAC
68067 CGCTAATTAT
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
137 2 0.02
138 33 0.25
139 96 0.73
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (139 bp):
CTAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTTATGTATTTATT
ATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTT
CGGACTCTG
Found at i:69438 original size:5 final size:5
Alignment explanation
Indices: 69430--69459 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
69420 TTTTGCTTTG
*
69430 TTAAA TTAAA TTAAA TTAAA TTAAA ATAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
69460 GTTATTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TTAAA
Found at i:75178 original size:19 final size:19
Alignment explanation
Indices: 75154--75208 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
75144 ATTTTTTTGT
75154 TTGAATTTCGAATTCGAGC
1 TTGAATTTCGAATTCGAGC
75173 TTGAATTTCGAATTCGAGC
1 TTGAATTTCGAATTCGAGC
*
75192 TTGAATTTCGAGTTCGA
1 TTGAATTTCGAATTCGA
75209 ATAATTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (19 bp):
TTGAATTTCGAATTCGAGC
Found at i:76434 original size:40 final size:40
Alignment explanation
Indices: 76379--76465 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
76369 TGAATTTATC
*
76379 GAATCAAATTAGATTTTATTCGACTACTCGTTAAGATCTT
1 GAATCAAATTAGATTTTATTCGACTACTCATTAAGATCTT
*
76419 GAATCAAATTGGATTTTATTCGACTACTCATTAAGATCTT
1 GAATCAAATTAGATTTTATTCGACTACTCATTAAGATCTT
76459 GAATCAA
1 GAATCAA
76466 GTTCAATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (40 bp):
GAATCAAATTAGATTTTATTCGACTACTCATTAAGATCTT
Found at i:79043 original size:5 final size:5
Alignment explanation
Indices: 79033--79076 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
79023 TTAAAAGGGA
* *
79033 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAC CAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
79077 AAATTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:80382 original size:4 final size:4
Alignment explanation
Indices: 80358--80416 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
80348 TAAAAAATAA
*
80358 AAAT AAAAT GAAAT AAAAT AAAT AAAT AAAT AATAT AAAT AACT AAAT
1 AAAT -AAAT -AAAT -AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT
80406 ATAAT -AAT AAA
1 A-AAT AAAT AAA
80417 AACTATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
3 3 0.06
4 25 0.53
5 19 0.40
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:80384 original size:13 final size:13
Alignment explanation
Indices: 80348--80412 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 13
80338 GATTTGGACC
80348 TAAA-AAATAAAAA
1 TAAATAAAT-AAAA
80361 TAAAATGAAATAAAA
1 T-AAAT-AAATAAAA
80376 TAAATAAAT-AAA
1 TAAATAAATAAAA
*
80388 TAATATAAAT-AAC
1 TAA-ATAAATAAAA
80401 TAAATATAATAA
1 TAAATA-AATAA
80413 TAAAAACTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
12 9 0.20
13 19 0.42
14 8 0.18
15 5 0.11
16 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:80390 original size:17 final size:17
Alignment explanation
Indices: 80358--80416 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
80348 TAAAAAATAA
80358 AAATAAAATGAAATAAAAT
1 AAAT-AAAT-AAATAAAAT
*
80377 AAATAAATAAATAATAT
1 AAATAAATAAATAAAAT
* *
80394 AAATAACTAAATATAAT
1 AAATAAATAAATAAAAT
80411 -AATAAA
1 AAATAAA
80417 AACTATATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 5 0.14
17 22 0.63
18 4 0.11
19 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAAATAAATAAAAT
Found at i:80431 original size:29 final size:29
Alignment explanation
Indices: 80348--80416 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
80338 GATTTGGACC
*
80348 TAAA-AAATAAA-AATA-AAATGAAATAAAA
1 TAAATAAATAAATAATATAAAT-AACT-AAA
80376 TAAATAAATAAATAATATAAATAACTAAA
1 TAAATAAATAAATAATATAAATAACTAAA
80405 TATAAT-AATAAA
1 TA-AATAAATAAA
80417 AACTATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 4 0.11
29 18 0.50
30 10 0.28
31 4 0.11
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (29 bp):
TAAATAAATAAATAATATAAATAACTAAA
Found at i:80572 original size:37 final size:35
Alignment explanation
Indices: 80485--80786 Score: 358
Period size: 35 Copynumber: 8.5 Consensus size: 35
80475 AAAAATTCGT
* * *
80485 TTTTAAAAAAATATATATTATACGTTTTCAAAAGTA
1 TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
** **
80521 TTTTAAAAACTATATACCATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
*
80556 TTTTAAAAACTATATATTATATG-TTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
** *
80590 TTTTAAAAAC--TATATTATACATTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* * *
80623 TTTAAAAAAAACTATATACTATATGTTTTCAAAACTG
1 TTT--TAAAAACTATATATTATATGTTTTCAAAACTA
* *
80660 TTTTAAAACCTATATATTATACGTTTTTCAAAACTA
1 TTTTAAAAACTATATATTATATG-TTTTCAAAACTA
*
80696 TTTTTAAAAAACTATATATTATATGTTTTCAAAATTA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
**
80733 TTTTAAAAACTATATATTATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
80768 TTTTAAAAACTATATATTA
1 TTTTAAAAACTATATATTA
80787 AAAAATAAGT
Statistics
Matches: 227, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
32 9 0.04
33 14 0.06
34 18 0.08
35 114 0.50
36 19 0.08
37 36 0.16
38 17 0.07
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAACTA
Found at i:80836 original size:26 final size:29
Alignment explanation
Indices: 80767--80837 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 29
80757 TTTCAAAACC
80767 GTTTT-AAAAACTATATATTAAAAAATAA
1 GTTTTCAAAAACTATATATTAAAAAATAA
* * *
80795 GTTTCCAAAAACTATATATT-ATATAT-A
1 GTTTTCAAAAACTATATATTAAAAAATAA
80822 -TTTTCAAAAACTATAT
1 GTTTTCAAAAACTATAT
80838 TTGAAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.39
27 1 0.03
28 8 0.21
29 14 0.37
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
GTTTTCAAAAACTATATATTAAAAAATAA
Found at i:92647 original size:11 final size:11
Alignment explanation
Indices: 92631--92660 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
92621 GTTAAAAGAG
92631 AAAATAATAAT
1 AAAATAATAAT
92642 AAAATAATAAT
1 AAAATAATAAT
92653 AATAATAA
1 AA-AATAA
92661 AATGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:92688 original size:14 final size:14
Alignment explanation
Indices: 92631--92688 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
92621 GTTAAAAGAG
92631 AAAATAATAATAAA
1 AAAATAATAATAAA
* *
92645 ATAATAATAATAAT
1 AAAATAATAATAAA
* ** *
92659 AAAATGATTTTTAA
1 AAAATAATAATAAA
92673 AAAATAATAATAAA
1 AAAATAATAATAAA
92687 AA
1 AA
92689 CACTTGATAA
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAATAATAATAAA
Found at i:93895 original size:18 final size:18
Alignment explanation
Indices: 93868--93910 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
93858 TTGGACCTAA
*
93868 AAAATGAAATAAATAAAT
1 AAAATAAAATAAATAAAT
* *
93886 AAAATAAAATGACTAAAT
1 AAAATAAAATAAATAAAT
*
93904 ATAATAA
1 AAAATAA
93911 TAAAAACTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAATAAAATAAATAAAT
Found at i:94070 original size:37 final size:35
Alignment explanation
Indices: 93984--94412 Score: 443
Period size: 35 Copynumber: 12.0 Consensus size: 35
93974 AAAAAAACAT
* * *
93984 TTTTAAAAAATATATATTATAAGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
** *
94019 TTTTAAAAACTATATACCATATGTTTTCAAAACCA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
94054 TTTTAAAAACTATATATTATACG-TTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
94088 -TTTAAAAA--ATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* **
94120 GTTTTAAAAAACTATATACTATATGTTTTCAAAACCG
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* * **
94157 TTTTAAAAACTATATACTATATTTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
94192 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
*
94227 TTTTTAAAAAACTATATATTATACGTTTTCAAAACTA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* *
94264 TTTTTAAAAAACTATATATTATATGCTTTCAAAATTA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* * **
94301 TTTTTAAAAATTATATATTATATGTTTTTAAAACCG
1 -TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
94337 TTTTAAAAACTATATATTATATGTTTTTAAAAAATAA
1 TTTTAAAAACTATATATTATATG-TTTTCAAAACT-A
* * *
94374 GTTTACAAAAACTATATATTATATATTTTTTAAAACTA
1 -TTT-TAAAAACTATATATTATAT-GTTTTCAAAACTA
94412 T
1 T
94413 ATTTGAAATT
Statistics
Matches: 339, Mismatches: 42, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.04
32 11 0.03
33 8 0.02
34 12 0.04
35 135 0.40
36 41 0.12
37 89 0.26
38 4 0.01
39 27 0.08
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAACTA
Found at i:96204 original size:3 final size:3
Alignment explanation
Indices: 96198--96232 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
96188 ATAAATATAT
96198 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
96233 TGACATGTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:99988 original size:18 final size:20
Alignment explanation
Indices: 99965--100058 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 20
99955 CATTGGGGGT
99965 ATCGATTCCC-TT-GAGGGA
1 ATCGATTCCCATTAGAGGGA
99983 ATCGATTCCCATTCAAAGAGGGA
1 ATCGATTCCCATT---AGAGGGA
*
100006 ATCGATTCCCATTCAAAGGGGGA
1 ATCGATTCCCATT---AGAGGGA
* * *
100029 ATCGGTTCCCCTTCA-AGGGT
1 ATCGATTCCCATT-AGAGGGA
100049 ATCGATTCCC
1 ATCGATTCCC
100059 TCTGCCCTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
18 10 0.16
19 2 0.03
20 12 0.19
21 1 0.02
23 39 0.61
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGATTCCCATTAGAGGGA
Found at i:100003 original size:23 final size:23
Alignment explanation
Indices: 99977--100044 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
99967 CGATTCCCTT
99977 GAGGGAATCGATTCCCATTCAAA
1 GAGGGAATCGATTCCCATTCAAA
100000 GAGGGAATCGATTCCCATTCAAA
1 GAGGGAATCGATTCCCATTCAAA
* * *
100023 GGGGGAATCGGTTCCCCTTCAA
1 GAGGGAATCGATTCCCATTCAA
100045 GGGTATCGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
GAGGGAATCGATTCCCATTCAAA
Found at i:105778 original size:22 final size:22
Alignment explanation
Indices: 105733--105795 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
105723 ATGTGAAATT
*
105733 TGTCCCGAAGTACCTCA--TATA
1 TGTCCCGAAGGACCT-ATGTATA
* *
105754 TGTCCTGAATGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
105776 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
105796 ACCCTCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 22 0.63
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:105932 original size:16 final size:16
Alignment explanation
Indices: 105911--106000 Score: 86
Period size: 16 Copynumber: 5.9 Consensus size: 16
105901 ATAAGCTTAT
105911 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
105927 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
105941 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
105957 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
105971 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
105987 GTCAC-TTATCATAT
1 GTCACATTCTCATAT
106001 CATGTATCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
13 6 0.10
14 14 0.23
15 16 0.26
16 19 0.31
17 6 0.10
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (16 bp):
GTCACATTCTCATATG
Found at i:105943 original size:30 final size:30
Alignment explanation
Indices: 105904--105991 Score: 167
Period size: 30 Copynumber: 2.9 Consensus size: 30
105894 TAGTCATATA
*
105904 AGCTTATGTCACATTCTCATATGGTCACAT
1 AGCTCATGTCACATTCTCATATGGTCACAT
105934 AGCTCATGTCACATTCTCATATGGTCACAT
1 AGCTCATGTCACATTCTCATATGGTCACAT
105964 AGCTCATGTCACATTCTCATATGGTCAC
1 AGCTCATGTCACATTCTCATATGGTCAC
105992 TTATCATATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (30 bp):
AGCTCATGTCACATTCTCATATGGTCACAT
Found at i:105946 original size:14 final size:14
Alignment explanation
Indices: 105927--105977 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
105917 TTCTCATATG
105927 GTCACATAGCTCAT
1 GTCACATAGCTCAT
*
105941 GTCACAT-TCTCATAT
1 GTCACATAGCTC--AT
105956 GGTCACATAGCTCAT
1 -GTCACATAGCTCAT
105971 GTCACAT
1 GTCACAT
105978 TCTCATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 14 0.45
15 4 0.13
16 7 0.23
17 3 0.10
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (14 bp):
GTCACATAGCTCAT
Found at i:109950 original size:22 final size:22
Alignment explanation
Indices: 109905--109965 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
109895 GTGAAATTTA
*
109905 TCCCGAATGACCTCATG--TATG
1 TCCCGAAAGACCT-ATGTATATG
109926 TCCCGAAAGACCTATGTATATG
1 TCCCGAAAGACCTATGTATATG
*
109948 TCCCGAAGGACCTATGTA
1 TCCCGAAAGACCTATGTA
109966 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 3 0.08
21 12 0.33
22 21 0.58
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (22 bp):
TCCCGAAAGACCTATGTATATG
Found at i:110118 original size:30 final size:30
Alignment explanation
Indices: 110077--110159 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
110067 ATATAAGCTT
* *
110077 ATGTCATATTCTCATATGGTCACATAGATC
1 ATGTCACATTCTCATATGGTCACACAGATC
* *
110107 ACT-TCACATTCTCATATGGTCACACAGCTT
1 A-TGTCACATTCTCATATGGTCACACAGATC
110137 ATGTCACATTCTCATATGGTCAC
1 ATGTCACATTCTCATATGGTCAC
110160 TTATCATATC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (30 bp):
ATGTCACATTCTCATATGGTCACACAGATC
Found at i:110154 original size:15 final size:16
Alignment explanation
Indices: 110110--110168 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
110100 ATAGATCACT
110110 TCACATTCTCATATGG
1 TCACATTCTCATATGG
* *
110126 TCACA--CAGCTTAT-G
1 TCACATTC-TCATATGG
110140 TCACATTCTCATATGG
1 TCACATTCTCATATGG
*
110156 TCAC-TTATCATAT
1 TCACATTCTCATAT
110169 CATCTATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.21
15 16 0.47
16 11 0.32
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (16 bp):
TCACATTCTCATATGG
Found at i:110727 original size:65 final size:64
Alignment explanation
Indices: 110599--110734 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 64
110589 ACACCATAAT
* * *
110599 TCGAATGCATTTTGTGTACCGATGCACAGCCATGCATCGATGAACTCCTAATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATGAACTCCTAATCTTATTAAAACA
* * * * **
110663 TCGAATGCGTTTTATGTATCGATGCACAGACTATGCATCGATGCACTCCTGGCTCTT-TTAAAAC
1 TCGAATGCATTTTATGTACCGATGCACAG-CCATGCATCGATGAACTCCT-AATCTTATTAAAAC
110727 A
64 A
110728 TCGAATG
1 TCGAATG
110735 TAATCAGTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 26 0.43
65 32 0.52
66 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATGAACTCCTAATCTTATTAAAACA
Done.