Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000779.1 Hibiscus syriacus cultivar Beakdansim tig00001514_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: 115038
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1172 original size:2 final size:2
Alignment explanation
Indices: 1165--1197 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1155 TTGTTGTTCC
1165 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 T
1198 TTATTGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1886 original size:36 final size:36
Alignment explanation
Indices: 1841--1951 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 36
1831 CACCCTAAAC
*
1841 CCGACCCGACCTGAATATCACACTTAAAAAACCCGA
1 CCGACCCGACCCGAATATCACACTTAAAAAACCCGA
1877 CCGACCCGACCCGAATAT-ACACTTAAAAAAACCCGA
1 CCGACCCGACCCGAATATCACACTT-AAAAAACCCGA
*
1913 CCCGACTCGACCCGAATATCACACTTAAAAAACCCGA
1 -CCGACCCGACCCGAATATCACACTTAAAAAACCCGA
1950 CC
1 CC
1952 CGACAAAAGT
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
35 6 0.09
36 30 0.43
37 28 0.40
38 6 0.09
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.13
Consensus pattern (36 bp):
CCGACCCGACCCGAATATCACACTTAAAAAACCCGA
Found at i:1918 original size:37 final size:37
Alignment explanation
Indices: 1839--1955 Score: 193
Period size: 37 Copynumber: 3.2 Consensus size: 37
1829 TTCACCCTAA
*
1839 ACCCGACCCGACCTGAATATCACACTTAAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAACCCG
1876 A-CCGACCCGACCCGAATAT-ACACTTAAAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTT-AAAAAACCCG
*
1912 ACCCGACTCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAACCCG
1949 ACCCGAC
1 ACCCGAC
1956 AAAAGTTTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
35 6 0.08
36 28 0.37
37 35 0.47
38 6 0.08
ACGTcount: A:0.38, C:0.38, G:0.11, T:0.12
Consensus pattern (37 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAACCCG
Found at i:2597 original size:2 final size:2
Alignment explanation
Indices: 2590--2620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2580 TTATTGTCTT
2590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2621 TCCATGTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5473 original size:23 final size:23
Alignment explanation
Indices: 5447--5496 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
5437 TGTTCTCTGT
5447 CTTTATGACACGTTTATCTCTAC
1 CTTTATGACACGTTTATCTCTAC
* * * * *
5470 CTTTGTGTCATGTTTTTCTCTGC
1 CTTTATGACACGTTTATCTCTAC
5493 CTTT
1 CTTT
5497 TGGTAGTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (23 bp):
CTTTATGACACGTTTATCTCTAC
Found at i:8973 original size:19 final size:18
Alignment explanation
Indices: 8949--8984 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
8939 CGAGATTATA
8949 ATATTATTATTTTCATATT
1 ATATTATTATTTT-ATATT
8968 ATATTATTATTTTATAT
1 ATATTATTATTTTATAT
8985 AAATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTATTATTTTATATT
Found at i:10137 original size:16 final size:16
Alignment explanation
Indices: 10116--10162 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
10106 TCCGGAAGCA
10116 ATGAACACCATTAATG
1 ATGAACACCATTAATG
10132 ATGAACACCATTAATG
1 ATGAACACCATTAATG
10148 ATGAACACCATTAAT
1 ATGAACACCATTAAT
10163 TTAATTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (16 bp):
ATGAACACCATTAATG
Found at i:10719 original size:30 final size:30
Alignment explanation
Indices: 10685--10741 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
10675 TTGACTACAT
*
10685 ATATTATATATATCTTAATTGAAATTCTTA
1 ATATTATATATATCTTAACTGAAATTCTTA
*
10715 ATATTTTATATATCTTAACTGAAATTC
1 ATATTATATATATCTTAACTGAAATTC
10742 ACATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (30 bp):
ATATTATATATATCTTAACTGAAATTCTTA
Found at i:10782 original size:24 final size:26
Alignment explanation
Indices: 10755--10810 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
10745 TATTAAATTA
10755 ATTTTACATCTT-A-TCATTAAAAAT
1 ATTTTACATCTTAATTCATTAAAAAT
** * *
10779 ATTTTTTATCTTAATTTATTAAATAT
1 ATTTTACATCTTAATTCATTAAAAAT
10805 ATTTTA
1 ATTTTA
10811 TTCTTTTCGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 10 0.40
25 1 0.04
26 14 0.56
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTACATCTTAATTCATTAAAAAT
Found at i:10863 original size:30 final size:30
Alignment explanation
Indices: 10827--10937 Score: 105
Period size: 30 Copynumber: 3.7 Consensus size: 30
10817 TCGTAACCTC
* * *
10827 AAAATATATTTTATTCTTATTTTAATTTTA
1 AAAATATATTTTATTCTAATTTTAAATTAA
* * * *
10857 AAAATATATTCTAATCTCATCTTAAATTAA
1 AAAATATATTTTATTCTAATTTTAAATTAA
* *
10887 AAAATATAATTTATTCTAATTTTAACTTAA
1 AAAATATATTTTATTCTAATTTTAAATTAA
** *
10917 ATATTTATATTTTATTATAAT
1 A-AAATATATTTTATTCTAAT
10938 AATATTTTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
30 49 0.77
31 15 0.23
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.51
Consensus pattern (30 bp):
AAAATATATTTTATTCTAATTTTAAATTAA
Found at i:11038 original size:30 final size:29
Alignment explanation
Indices: 11004--11278 Score: 178
Period size: 30 Copynumber: 9.2 Consensus size: 29
10994 TTTTTTAGCT
*
11004 AAAATAAAATTATATTTTAAATTTAAGATA
1 AAAATAAAA-TATATTTTAAAGTTAAGATA
* *
11034 AAAATAAAATATATGTTTTAAGTTAAAAT-
1 AAAATAAAATATAT-TTTAAAGTTAAGATA
* * * *
11063 ATAATTAATTATA-TTTAATATTTTAAGATA
1 AAAATAAAATATATTTTAA-A-GTTAAGATA
* * * *
11093 AGAATATAAA-ATATTTAATAATTTAAGTTA
1 AAAATA-AAATATATTTTA-AAGTTAAGATA
* * * * *
11123 AGAATATAATTTATGTAATAAGTTAAGATA
1 AAAATAAAATATATTTTA-AAGTTAAGATA
* *
11153 AGAATAAAATATATTTTTTAAGTTAAGATA
1 AAAATAAAATATA-TTTTAAAGTTAAGATA
* * * *
11183 AAGACTAAAATATATTTTTAGGTTAAGACA
1 AA-AATAAAATATATTTTAAAGTTAAGATA
* * *
11213 AGAATAAAATATATTTAATAAGTTAATATA
1 AAAATAAAATATATTTTA-AAGTTAAGATA
* *
11243 AAAATAAAATATATTTTTAATGTTATGATA
1 AAAATAAAATATA-TTTTAAAGTTAAGATA
11273 TAAAAT
1 -AAAAT
11279 TAATTTAATA
Statistics
Matches: 192, Mismatches: 40, Indels: 25
0.75 0.16 0.10
Matches are distributed among these distances:
27 4 0.02
28 1 0.01
29 36 0.19
30 123 0.64
31 27 0.14
32 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.40
Consensus pattern (29 bp):
AAAATAAAATATATTTTAAAGTTAAGATA
Found at i:11130 original size:65 final size:58
Alignment explanation
Indices: 11011--11178 Score: 150
Period size: 58 Copynumber: 2.8 Consensus size: 58
11001 GCTAAAATAA
**
11011 AATTATATTTTAAATTTAAGATAAAAATAAAATATATGTTTTAAGTTAAAATATAATT
1 AATTATATTTTAAATTTAAGATAAAAATAAAATATATAATTTAAGTTAAAATATAATT
11069 AATTATA-TTTAATATTTTAAGATAAGAATATAAAATATTTAATAATTTAAGTTAAGAATATAAT
1 AATTATATTTTAA-A-TTTAAGATAA-AA-ATAAAATA--T-ATAATTTAAGTTAA-AATATAAT
11133 T
58 T
* * * **
11134 TATGTA-A---T-AAGTTAAGATAAGAATAAAATATATTTTTTAAGTTAA
1 AAT-TATATTTTAAATTTAAGATAAAAATAAAATATATAATTTAAGTTAA
11179 GATAAAGACT
Statistics
Matches: 94, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
55 12 0.13
56 1 0.01
57 5 0.05
58 16 0.17
59 11 0.12
60 11 0.12
61 9 0.10
62 1 0.01
63 2 0.02
64 12 0.13
65 12 0.13
66 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (58 bp):
AATTATATTTTAAATTTAAGATAAAAATAAAATATATAATTTAAGTTAAAATATAATT
Found at i:11154 original size:60 final size:60
Alignment explanation
Indices: 11026--11257 Score: 206
Period size: 60 Copynumber: 3.9 Consensus size: 60
11016 TATTTTAAAT
* * * * * * **
11026 TTAAGATAAAAATAAAATATATGTT-TTAAGTTAA-A-ATATAATTAATTATATTTAATATT
1 TTAAGATAAGAATAAAATATAT-TTAATAAGTTAAGATAAAGAATAAAATATA-TTAATAAG
* * * *
11085 TTAAGATAAGAATATAAA-ATATTTAATAATTTAAG-TTAAGAATATAATTTATGTAATAAG
1 TTAAGATAAGAATA-AAATATATTTAATAAGTTAAGATAAAGAATAAAATATAT-TAATAAG
** * ** *
11145 TTAAGATAAGAATAAAATATATTTTTTAAGTTAAGATAAAGACTAAAATATATTTTTAGG
1 TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAGAATAAAATATATTAATAAG
* *
11205 TTAAGACAAGAATAAAATATATTTAATAAGTTAATATAAA-AATAAAATATATT
1 TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAGAATAAAATATATT
11258 TTTAATGTTA
Statistics
Matches: 139, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
58 2 0.01
59 40 0.29
60 84 0.60
61 13 0.09
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (60 bp):
TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAGAATAAAATATATTAATAAG
Found at i:16581 original size:18 final size:18
Alignment explanation
Indices: 16555--16591 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16545 TTCATCAAAA
16555 AATTCTAAAATTTAAGGT
1 AATTCTAAAATTTAAGGT
* *
16573 AATTTTAAAATTTCAGGT
1 AATTCTAAAATTTAAGGT
16591 A
1 A
16592 GGCGACTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (18 bp):
AATTCTAAAATTTAAGGT
Found at i:19011 original size:17 final size:17
Alignment explanation
Indices: 18989--19023 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18979 CACGACATCT
18989 ACTGATGTATTAGGTAA
1 ACTGATGTATTAGGTAA
19006 ACTGATGTATTAGGTAA
1 ACTGATGTATTAGGTAA
19023 A
1 A
19024 GCACCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (17 bp):
ACTGATGTATTAGGTAA
Found at i:20419 original size:34 final size:36
Alignment explanation
Indices: 20375--20476 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
20365 TTTCGTCCTA
*
20375 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
20410 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
20445 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
20477 GTTATACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:20889 original size:16 final size:18
Alignment explanation
Indices: 20866--20904 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
20856 ATTATATGGA
20866 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
20882 T-TTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
20899 TATTAT
1 TATTAT
20905 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 5 0.25
18 4 0.20
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:24129 original size:7 final size:8
Alignment explanation
Indices: 24117--24185 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
24107 CAAAAAGGGC
24117 AAAAAG-A
1 AAAAAGAA
24124 AAAAAGAA
1 AAAAAGAA
*
24132 AAAAAGCA
1 AAAAAGAA
*
24140 AAAAAGGA
1 AAAAAGAA
*
24148 AAAAACAA
1 AAAAAGAA
24156 GAACAAA-AA
1 -AA-AAAGAA
*
24165 AGAAAGAA
1 AAAAAGAA
*
24173 CAAAAATAA
1 -AAAAAGAA
24182 AAAA
1 AAAA
24186 GGGAACAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
7 9 0.18
8 28 0.56
9 10 0.20
10 3 0.06
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:24162 original size:21 final size:21
Alignment explanation
Indices: 24117--24187 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
24107 CAAAAAGGGC
* *
24117 AAAAAGAAAAAAGAAAAAAAGCA
1 AAAAAGGAAAAA-ACAAAAA-CA
*
24140 AAAAAGGAAAAAACAAGAACA
1 AAAAAGGAAAAAACAAAAACA
* *
24161 AAAAA-GAAAGAACAAAAATA
1 AAAAAGGAAAAAACAAAAACA
24181 AAAAAGG
1 AAAAAGG
24188 GAACAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.41
21 8 0.20
22 5 0.12
23 11 0.27
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (21 bp):
AAAAAGGAAAAAACAAAAACA
Found at i:24829 original size:22 final size:22
Alignment explanation
Indices: 24801--24851 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
24791 CCCCATCAAT
*
24801 CCTTTGAGTATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
24823 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
24845 CCTTTGA
1 CCTTTGA
24852 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:25756 original size:36 final size:35
Alignment explanation
Indices: 25720--26048 Score: 226
Period size: 36 Copynumber: 9.3 Consensus size: 35
25710 TGATTATTTT
* * *
25720 TCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTT
1 TCTTAAAACAA-ATTTGTCTCTCTTGAGACAGTTTC
* * **
25756 TAC-TATAAGAGTTTTGTCTCTCTTGAGACAGTTTC
1 T-CTTAAAACAAATTTGTCTCTCTTGAGACAGTTTC
* *
25791 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1 TCTTAAAACAAA-TTTGTCTCTCTTGAGACAGTTTC
* *
25827 TCTTTAAACAAATTTCGTCTATCTTGAGACAGTTTC
1 TCTTAAAACAAATTT-GTCTCTCTTGAGACAGTTTC
* * *
25863 CCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTC
1 TCTTAAAACAAA-TTTGTCTCTCTTGAGACAGTTTC
* * * * *
25899 CCTTGAAACAAA-----ATAT-TTGA-ATATGTTT-
1 TCTTAAAACAAATTTGTCTCTCTTGAGACA-GTTTC
* *
25927 TCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
1 TC-TTAAAACAAATTT-GTCTCTCTTGAGACAGTTTC
* ** *
25964 TTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTC
1 TCTTAAAAC-AA-ATTTGTCTCTCTTGAGACAGTTTC
* * *
26001 TCTTGAAACAATTTTCGTCTATCTTGAGACAGTTTC
1 TCTTAAAACAAATTT-GTCTCTCTTGAGACAGTTTC
* *
26037 CCTTGAAACAAA
1 TCTTAAAACAAA
26049 ACCTTTGAAT
Statistics
Matches: 236, Mismatches: 38, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.01
29 18 0.08
30 2 0.01
34 1 0.00
35 32 0.14
36 142 0.60
37 35 0.15
38 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (35 bp):
TCTTAAAACAAATTTGTCTCTCTTGAGACAGTTTC
Found at i:25869 original size:72 final size:71
Alignment explanation
Indices: 25768--26048 Score: 308
Period size: 72 Copynumber: 4.0 Consensus size: 71
25758 CTATAAGAGT
* * *
25768 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTTA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
25833 AACAAA
66 AACAAA
*
25839 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
25904 AAACAAA
65 AAACAAA
* * * * * * **
25911 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
25969 GAACTAAGT
65 AAAC-AA-A
* * *
25978 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
26042 AAACAAA
65 AAACAAA
26049 ACCTTTGAAT
Statistics
Matches: 170, Mismatches: 28, Indels: 24
0.77 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 46 0.27
66 5 0.03
71 3 0.02
72 73 0.43
73 39 0.23
74 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:26040 original size:138 final size:137
Alignment explanation
Indices: 25787--26111 Score: 420
Period size: 138 Copynumber: 2.4 Consensus size: 137
25777 CTTGAGACAG
*
25787 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTTAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACAAATTTCGTCTATCTT
* *
25852 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
25917 GAATATG
131 GAATATA
* * * * * * *
25924 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTTGGAACTAAGTTTTGTCTCTC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTT-AAAC-AAATTTCGTCTATC
* * *
25988 TTGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACC
64 TTGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACA
*
26052 TTTGAATTTA
128 TTTGAATATA
* * * * * *
26062 TTTCCCCTAAAACAAATTTTTTCTCCCTTTAGACAGTTGCTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACA
26112 CAAAATCTTC
Statistics
Matches: 159, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
136 3 0.02
137 47 0.30
138 107 0.67
139 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:26995 original size:105 final size:105
Alignment explanation
Indices: 26816--27749 Score: 1443
Period size: 105 Copynumber: 9.0 Consensus size: 105
26806 GCACTCGAGG
* * * ** *
26816 CAACACAAGTTCAACTTCACAACGAATGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
26881 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
26922 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
26987 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
27027 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* ** *
27089 ACCAATTTCAACTTCACAATAAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
27129 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
27194 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
27234 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
27299 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
27339 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
27404 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
27444 AAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
27509 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
27549 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
27609 TTCAATTTTAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * * ** *
27649 TAACACAAGTTCAACGTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
27714 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
27750 TGGAACAATG
Statistics
Matches: 775, Mismatches: 44, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
100 81 0.10
101 3 0.00
102 102 0.13
103 4 0.01
104 3 0.00
105 509 0.66
106 73 0.09
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:27491 original size:312 final size:312
Alignment explanation
Indices: 26821--27749 Score: 1399
Period size: 312 Copynumber: 3.0 Consensus size: 312
26811 CGAGGCAACA
* * ** *
26821 CAAGTTCAACTTCACAACGAATGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--AC-AACAACTTCTCAATTTCAGAGCCA
26886 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
63 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
26951 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATAT
128 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
27016 TGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTC
193 TGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC
* * ** * *
27078 TCAATTTCAGAACCAATTTCAACTTCACAATAAAGGATATTGGACTTCAGACAACG
258 CCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACG
27134 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--ACAACAACTTCTCAATTTCAGAGCCAA
27199 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
64 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
27264 CCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
129 CCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
27329 GGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCC
194 GGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCC
*
27394 CAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAATG
259 CAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACG
* * *
27449 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGTCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--ACAACAACTTCTCAATTTCAGAGCCAA
27514 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
64 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
** *
27579 CCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTTAACTTCACAACGAAGGATATT
129 CCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * * * * * *
27639 GGAC-TCGAGATAACACAAGTTCAACGTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
194 GGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTT
** * *
27703 CCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
257 CCCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
27750 TGGAACAATG
Statistics
Matches: 577, Mismatches: 32, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
309 2 0.00
310 80 0.14
311 49 0.08
312 205 0.36
313 37 0.06
314 3 0.01
315 201 0.35
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (312 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACG
Found at i:28329 original size:34 final size:36
Alignment explanation
Indices: 28285--28386 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
28275 TTTCGTCCTA
*
28285 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
28320 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
28355 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
28387 GTTATACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:28800 original size:17 final size:18
Alignment explanation
Indices: 28778--28813 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28768 ATATGGATAT
*
28778 TTATTCAT-TTATTTTTA
1 TTATTCATGTTATTATTA
28795 TTATTCATGTTATTATTA
1 TTATTCATGTTATTATTA
28813 T
1 T
28814 ATGTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTCATGTTATTATTA
Found at i:28901 original size:47 final size:49
Alignment explanation
Indices: 28823--28947 Score: 123
Period size: 49 Copynumber: 2.6 Consensus size: 49
28813 TATGTATATA
* * * * * * *
28823 TATATATATAAATTATTTCATTTATTTTTTTAC-TAT-ATTTTATTATTAT
1 TATATATATATA-TATTTC-TTTAATATTTTACTTATAAATCTAATATTAC
28872 TATATATATATATATTTCTTTAATATTTTACTTATAAATCTAATATTAC
1 TATATATATATATATTTCTTTAATATTTTACTTATAAATCTAATATTAC
* *
28921 TATATATA-AT-TATTACTTTACTATTTT
1 TATATATATATATATTTCTTTAATATTTT
28948 TTTTTCTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 26 0.40
48 11 0.17
49 28 0.43
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (49 bp):
TATATATATATATATTTCTTTAATATTTTACTTATAAATCTAATATTAC
Found at i:30506 original size:37 final size:36
Alignment explanation
Indices: 30447--30566 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
30437 ATCCCATTAT
* *
30447 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
30483 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
30519 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
30554 CATTTTCTCAAAG
1 CATTTT-TCAAAG
30567 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 16 0.21
37 26 0.34
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:30522 original size:21 final size:21
Alignment explanation
Indices: 30498--30558 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
30488 TTCAAAGAAA
30498 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
30519 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
30533 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
30554 CATTT
1 CATTT
30559 TCTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:30575 original size:35 final size:33
Alignment explanation
Indices: 30501--30628 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 33
30491 AAAGAAACAT
****
30501 TTACCAAACTTTGAAAACCA-TTTTCAAAGAAACAT
1 TTACCAAAC-TTGAAAACCATTTTTCAAAG--TTGG
30536 TTACCAAACTTTGAAAACCATTTTCTCAAAGTTGG
1 TTACCAAAC-TTGAAAACCATTTT-TCAAAGTTGG
30571 TTACCAAACTTGAAAACCATTTTTTTCAAAGTTGG
1 TTACCAAACTTGAAAACCA--TTTTTCAAAGTTGG
30606 TTACCAAACTTGAAAACCATTTT
1 TTACCAAACTTGAAAACCATTTT
30629 AATACTTTTA
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
33 4 0.05
34 10 0.12
35 58 0.68
36 7 0.08
37 6 0.07
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (33 bp):
TTACCAAACTTGAAAACCATTTTTCAAAGTTGG
Found at i:30589 original size:34 final size:34
Alignment explanation
Indices: 30536--30628 Score: 159
Period size: 35 Copynumber: 2.7 Consensus size: 34
30526 AAAGAAACAT
30536 TTACCAAACTTTGAAAACCATTTTCTCAAAGTTGG
1 TTACCAAAC-TTGAAAACCATTTTCTCAAAGTTGG
*
30571 TTACCAAACTTGAAAACCATTTTTTTCAAAGTTGG
1 TTACCAAACTTGAAAACCA-TTTTCTCAAAGTTGG
30606 TTACCAAACTTGAAAACCATTTT
1 TTACCAAACTTGAAAACCATTTT
30629 AATACTTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 14 0.25
35 42 0.75
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (34 bp):
TTACCAAACTTGAAAACCATTTTCTCAAAGTTGG
Found at i:30601 original size:72 final size:72
Alignment explanation
Indices: 30447--30594 Score: 180
Period size: 72 Copynumber: 2.1 Consensus size: 72
30437 ATCCCATTAT
* * *
30447 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACT
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG-AACAGTTACCAAACT
30511 TTGAAAAC
65 TTGAAAAC
* ***
30519 CA-TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTCTCAAAG-TTGGTTACCAAAC-
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTT-TCAAAGAACAGTTACCAAACT
30580 TTGAAAAC
65 TTGAAAAC
30588 CATTTTT
1 CATTTTT
30595 TTCAAAGTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
69 10 0.15
70 13 0.20
71 15 0.23
72 28 0.42
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (72 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTTTCAAAGAACAGTTACCAAACTT
TGAAAAC
Found at i:35165 original size:37 final size:36
Alignment explanation
Indices: 35106--35259 Score: 183
Period size: 35 Copynumber: 4.3 Consensus size: 36
35096 ATCCCATTAT
* *
35106 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
35142 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
35178 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
****
35213 CATTTTTTCAAAG--TTGGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
35247 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
35260 TTGGTTACCA
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
34 21 0.20
35 44 0.41
36 13 0.12
37 29 0.27
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:35181 original size:21 final size:21
Alignment explanation
Indices: 35157--35217 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
35147 TTCAAAGAAA
35157 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
35178 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
35192 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
35213 CATTT
1 CATTT
35218 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:35248 original size:34 final size:34
Alignment explanation
Indices: 35195--35286 Score: 166
Period size: 34 Copynumber: 2.7 Consensus size: 34
35185 AAAGAAACAT
35195 TTACCAAACTTTGAAAACCATTTTTTCAAAGTTGG
1 TTACCAAAC-TTGAAAACCATTTTTTCAAAGTTGG
35230 TTACCAAACTTGAAAACCATTTTTTCAAAGTTGG
1 TTACCAAACTTGAAAACCATTTTTTCAAAGTTGG
*
35264 TTACCAAACTTAAAAACCATTTT
1 TTACCAAACTTGAAAACCATTTT
35287 AATACTTTCA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
34 47 0.84
35 9 0.16
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (34 bp):
TTACCAAACTTGAAAACCATTTTTTCAAAGTTGG
Found at i:40914 original size:13 final size:13
Alignment explanation
Indices: 40898--40940 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
40888 AGCCCGTTGG
40898 CTTTGACTTTGAC
1 CTTTGACTTTGAC
40911 CTTTGACCAGTTTGAC
1 CTTTGA-C--TTTGAC
*
40927 CGTTGACTTTGAC
1 CTTTGACTTTGAC
40940 C
1 C
40941 AAAAAGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.50
14 1 0.04
15 1 0.04
16 11 0.42
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (13 bp):
CTTTGACTTTGAC
Found at i:41822 original size:27 final size:27
Alignment explanation
Indices: 41792--41864 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
41782 GAACGGAAGG
** * *
41792 AAATGACTGAAATACCCTTGAATTATA
1 AAATGACCAAAATACCCCTGAAGTATA
*
41819 AAATGACCAAAATACCCCTGAAGTGTA
1 AAATGACCAAAATACCCCTGAAGTATA
* *
41846 AAATAACCTAAAGTACCCC
1 AAATGACC-AAAATACCCC
41865 CAAGCCCTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 29 0.76
28 9 0.24
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (27 bp):
AAATGACCAAAATACCCCTGAAGTATA
Found at i:43049 original size:32 final size:32
Alignment explanation
Indices: 42947--43068 Score: 113
Period size: 32 Copynumber: 3.8 Consensus size: 32
42937 CCTAAGGTGA
* ** *
42947 CCTTGGGTAAGCTTTAAGGCCCCAAGACATTT
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGTACTT
* * *
42979 CCTTGTGTAGGCTCTAAGGCCCCAAGTTACTT
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGTACTT
* *
43011 CCTTGGGTAAGCTCTTAGGCCCTAAGGTAC-T
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGTACTT
* *
43042 CCATTGGG-AAGGCTATCAGGCCCCAAG
1 CC-TTGGGTAA-GCTCTAAGGCCCCAAG
43069 ATAATCTCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
31 5 0.07
32 69 0.93
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (32 bp):
CCTTGGGTAAGCTCTAAGGCCCCAAGGTACTT
Found at i:45385 original size:30 final size:28
Alignment explanation
Indices: 45349--45405 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
45339 AATACGGTCT
45349 ATTAAAATAAAAATATTATAAATTATATTA
1 ATTAAAATAAAAATATTAT--ATTATATTA
*
45379 ATTAAAATAATAATATTATATTATATT
1 ATTAAAATAAAAATATTATATTATATT
45406 TTAAAAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.31
30 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTAAAATAAAAATATTATATTATATTA
Found at i:45396 original size:14 final size:14
Alignment explanation
Indices: 45348--45396 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
45338 TAATACGGTC
*
45348 TATTAAAATAAAAA
1 TATTAAAATAATAA
* *
45362 TATTATAAATTATAT
1 TATTA-AAATAATAA
45377 TAATTAAAATAATAA
1 T-ATTAAAATAATAA
45392 TATTA
1 TATTA
45397 TATTATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 9 0.32
15 15 0.54
16 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:45489 original size:27 final size:25
Alignment explanation
Indices: 45459--45582 Score: 78
Period size: 27 Copynumber: 4.9 Consensus size: 25
45449 GTATTAAAAT
*
45459 TAAATACATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATCATT-ATTA
* *
45486 TAAATAATTTAATAATATCATTTTTA
1 TAAATAA-TAAATAATATCATTATTA
*
45512 TGAAATTAATAAATAATATAAATT-TTA
1 T-AAA-TAATAAATAATAT-CATTATTA
* ** *
45539 TTAATAATTTATTATAT-ATTATTA
1 TAAATAATAAATAATATCATTATTA
*
45563 -AAA-AATATATAATATC-TTAT
1 TAAATAATAAATAATATCATTAT
45583 ATTATTATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
22 14 0.18
23 5 0.06
24 3 0.04
25 10 0.13
26 7 0.09
27 34 0.43
28 6 0.08
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (25 bp):
TAAATAATAAATAATATCATTATTA
Found at i:45582 original size:22 final size:22
Alignment explanation
Indices: 45516--45582 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
45506 TTTTTATGAA
* *
45516 ATTAATAAATAATATAA-ATTTT
1 ATTAAAAAAT-ATATAATATATT
* * *
45538 ATT-AATAATTTATTATATATT
1 ATTAAAAAATATATAATATATT
*
45559 ATTAAAAAATATATAATATCTT
1 ATTAAAAAATATATAATATATT
45581 AT
1 AT
45583 ATTATTATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 19 0.56
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAAAATATATAATATATT
Found at i:46775 original size:16 final size:16
Alignment explanation
Indices: 46754--46784 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46744 AGAATATTTG
46754 ATCCAAAAATCCGAAT
1 ATCCAAAAATCCGAAT
*
46770 ATCCAAAAATTCGAA
1 ATCCAAAAATCCGAA
46785 CAACCAATTT
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:0.52, C:0.23, G:0.06, T:0.19
Consensus pattern (16 bp):
ATCCAAAAATCCGAAT
Found at i:47011 original size:14 final size:14
Alignment explanation
Indices: 46994--47042 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
46984 AATATGTTTG
46994 TTTATGTGTGTTCA
1 TTTATGTGTGTTCA
**
47008 TTTATGT-TCGTTTG
1 TTTATGTGT-GTTCA
47022 TTTATGTGTGTTCA
1 TTTATGTGTGTTCA
47036 TTTATGT
1 TTTATGT
47043 TTAGCCCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.61
Consensus pattern (14 bp):
TTTATGTGTGTTCA
Found at i:47021 original size:28 final size:28
Alignment explanation
Indices: 46989--47043 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
46979 TCAGTAATAT
46989 GTTTGTTTATGTGTGTTCATTTATGTTC
1 GTTTGTTTATGTGTGTTCATTTATGTTC
47017 GTTTGTTTATGTGTGTTCATTTATGTT
1 GTTTGTTTATGTGTGTTCATTTATGTT
47044 TAGCCCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.05, G:0.22, T:0.62
Consensus pattern (28 bp):
GTTTGTTTATGTGTGTTCATTTATGTTC
Found at i:47311 original size:20 final size:20
Alignment explanation
Indices: 47272--47312 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
47262 CGTTTACGTT
* *
47272 CGTTCGTTTGTGTTCATTTA
1 CGTTCGTTTATATTCATTTA
*
47292 CGTTCGTTTATATTCTTTTA
1 CGTTCGTTTATATTCATTTA
47312 C
1 C
47313 ATCCGTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (20 bp):
CGTTCGTTTATATTCATTTA
Found at i:47333 original size:14 final size:14
Alignment explanation
Indices: 47316--47350 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
47306 CTTTTACATC
*
47316 CGTTTGTTTATGTT
1 CGTTTATTTATGTT
*
47330 CGTTTATTTGTGTT
1 CGTTTATTTATGTT
47344 CGTTTAT
1 CGTTTAT
47351 CATTTAAATG
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:0.09, C:0.09, G:0.20, T:0.63
Consensus pattern (14 bp):
CGTTTATTTATGTT
Found at i:51072 original size:32 final size:32
Alignment explanation
Indices: 51034--51103 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
51024 TCAGAGCCTC
* *
51034 TGAATCATTCAACGTTTGAATCATTCAGCGTT
1 TGAATCATTCAACATTTGAATCATTCAGCGCT
* **
51066 TGAATCATTTAGTATTTGAATCATTCAGCGCT
1 TGAATCATTCAACATTTGAATCATTCAGCGCT
51098 T-AATCA
1 TGAATCA
51104 ATCTGAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (32 bp):
TGAATCATTCAACATTTGAATCATTCAGCGCT
Found at i:51083 original size:16 final size:16
Alignment explanation
Indices: 51034--51094 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
51024 TCAGAGCCTC
* *
51034 TGAATCATTCAACGTT
1 TGAATCATTCAGCATT
*
51050 TGAATCATTCAGCGTT
1 TGAATCATTCAGCATT
* *
51066 TGAATCATTTAGTATT
1 TGAATCATTCAGCATT
51082 TGAATCATTCAGC
1 TGAATCATTCAGC
51095 GCTTAATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:52735 original size:29 final size:29
Alignment explanation
Indices: 52701--52759 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52691 CCTAAATTAA
52701 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
52730 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
52759 T
1 T
52760 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:57429 original size:29 final size:29
Alignment explanation
Indices: 57395--57453 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
57385 CCTAAATTAA
57395 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
57424 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
57453 T
1 T
57454 AGCTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:62766 original size:16 final size:16
Alignment explanation
Indices: 62735--62780 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
62725 TAATAATTAA
*
62735 AATATAATTTA-ATAT
1 AATATAATTTATTTAT
*
62750 AGTA-ATATTTATTTAT
1 AATATA-ATTTATTTAT
62766 AATATAATTTATTTA
1 AATATAATTTATTTA
62781 ATACTAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.04
15 8 0.32
16 15 0.60
17 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATATAATTTATTTAT
Found at i:63348 original size:59 final size:59
Alignment explanation
Indices: 63249--63443 Score: 268
Period size: 59 Copynumber: 3.3 Consensus size: 59
63239 ATATGCACTG
* * * *
63249 TAGTGCTAA-CCCGAGTATGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTT
1 TAGTGC-AATCCCGAATATGACACATAAGATCGTGCCCACCATATGCACTAGTTATACTT
* * * *
63308 TAGTGCAGTCCCGAATATGACACATAAGATTGTGCTCACCATATACACTAGTTATAC-T
1 TAGTGCAATCCCGAATATGACACATAAGATCGTGCCCACCATATGCACTAGTTATACTT
* * *
63366 TAGTGAAATCCCAAATATGACACATAAGATCGTGCCCACCATATGCACTAGTTATATTT
1 TAGTGCAATCCCGAATATGACACATAAGATCGTGCCCACCATATGCACTAGTTATACTT
63425 TAGTGCAATCCCGAATATG
1 TAGTGCAATCCCGAATATG
63444 CAGCCTGCTA
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
58 52 0.44
59 65 0.56
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (59 bp):
TAGTGCAATCCCGAATATGACACATAAGATCGTGCCCACCATATGCACTAGTTATACTT
Found at i:63611 original size:24 final size:24
Alignment explanation
Indices: 63584--63630 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
63574 ATGAAATAAC
*
63584 ATTCGCAACAAACATCATATATAT
1 ATTCACAACAAACATCATATATAT
** *
63608 ATTCATGATAAACATCATATATA
1 ATTCACAACAAACATCATATATA
63631 ATATACAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (24 bp):
ATTCACAACAAACATCATATATAT
Found at i:63641 original size:26 final size:24
Alignment explanation
Indices: 63593--63642 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
63583 CATTCGCAAC
*
63593 AAACATCATATATATATTCATGAT
1 AAACATCATATATATATACATGAT
63617 AAACATCATATATAATATACAATGAT
1 AAACATCATATAT-ATATAC-ATGAT
63643 CAATGCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
25 5 0.22
26 5 0.22
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (24 bp):
AAACATCATATATATATACATGAT
Found at i:65334 original size:21 final size:21
Alignment explanation
Indices: 65286--65335 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
65276 TATTTTTTAA
*
65286 TAAAATTAATAATTTACCTTT
1 TAAAATTAATAATATACCTTT
*
65307 T-AAATTAATATATATA-TTTT
1 TAAAATTAATA-ATATACCTTT
65327 TAAAATTAA
1 TAAAATTAA
65336 ATACGACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAATTAATAATATACCTTT
Found at i:65746 original size:19 final size:20
Alignment explanation
Indices: 65722--65774 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
65712 AATGCATTTT
65722 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAATACC
65741 ATGCATCGATGCACAATACC
1 ATGCATCGATGCACAATACC
*
65761 CTGCATCGATGCAC
1 ATGCATCGATGCAC
65775 TCAGGCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGCACAATACC
Found at i:74044 original size:20 final size:20
Alignment explanation
Indices: 74015--74052 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
74005 TTTCAAAGTG
74015 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
74035 ATGCATCGATGCATCAAT
1 ATGCACCGATGCACCAAT
74053 TAATTTTTCA
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:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:74104 original size:19 final size:19
Alignment explanation
Indices: 74080--74177 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
74070 AATGCATTTT
74080 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
74099 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
**
74118 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCA--CA-T--A--CC
74144 ATGCATCGATGCACAATACC
1 ATGCATCGATGCAC-ATACC
74164 ATGCATCGATGCAC
1 ATGCATCGATGCAC
74178 TCAGGCTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
19 32 0.48
20 14 0.21
21 2 0.03
22 2 0.03
24 3 0.04
25 1 0.01
26 13 0.19
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:74213 original size:65 final size:64
Alignment explanation
Indices: 74015--74222 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
74005 TTTCAAAGTG
* **
74015 ATGCACCGATGCACCAAT-CCATGCATCGATGCA-TCAATTAATTTTTCAAACATCGAATGCATT
1 ATGCATCGATGCA-CAATACCATGCATCGATGCACTC-A-TGCTTTTTCAAACATCGAATGCATT
74078 TT
63 TT
* ** *
74080 ATGCATCGATGCAC-ATACCATGCATCGATGCACATACCATGC---ATCGATGCACTC-AGTGCA
1 ATGCATCGATGCACAATACCATGCATCGATGCAC-T--CATGCTTTTTC-AAACA-TCGAATGCA
*
74140 TTTG
61 TTTT
* *
74144 ATGCATCGATGCACAATACCATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCCTTTT
1 ATGCATCGATGCACAATACCATGCATCGATGCACTCATGCTTTTTC-AAACATCGAATGCATTTT
74209 ATGCATCGATGCAC
1 ATGCATCGATGCAC
74223 TCTTAGTGCA
Statistics
Matches: 115, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
62 4 0.03
63 4 0.03
64 44 0.38
65 59 0.51
66 2 0.02
67 1 0.01
68 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACAATACCATGCATCGATGCACTCATGCTTTTTCAAACATCGAATGCATTTT
Found at i:77752 original size:60 final size:60
Alignment explanation
Indices: 77631--77764 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
77621 AACATAACAA
* ** *
77631 ATAGTCGAGTGACCATATTGTAACTTTTAATAGTCTAGGAACTCAACAAGGCAACACTAT
1 ATAGTCGAGTGACCATATTGCAACTTTTAATAGTAAAGGAACTCAACAAAGCAACACTAT
* * * * * *
77691 ATAGTCAGAG-GACCATTTTGCAACTTTTAATAGTAAAGGGACTTAACAAAGTAATATTAT
1 ATAGTC-GAGTGACCATATTGCAACTTTTAATAGTAAAGGAACTCAACAAAGCAACACTAT
* *
77751 ATAGTTGAGGGACC
1 ATAGTCGAGTGACC
77765 GTTTGCGTTC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
59 3 0.05
60 55 0.90
61 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (60 bp):
ATAGTCGAGTGACCATATTGCAACTTTTAATAGTAAAGGAACTCAACAAAGCAACACTAT
Found at i:78763 original size:45 final size:46
Alignment explanation
Indices: 78710--78798 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
78700 TTTTTGTAGA
*
78710 ACGTTATTTAAAATATTA-TTTTTCTACCAAAAATATTAATATCGG
1 ACGTTATTTAAAATATTATTTTTTATACCAAAAATATTAATATCGG
* * *
78755 ACGTTATTTAAAATGTTATTTTTTATATCAGAAATATTAATATC
1 ACGTTATTTAAAATATTATTTTTTATACCAAAAATATTAATATC
78799 AAAAATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 17 0.44
46 22 0.56
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (46 bp):
ACGTTATTTAAAATATTATTTTTTATACCAAAAATATTAATATCGG
Found at i:78808 original size:45 final size:45
Alignment explanation
Indices: 78714--78809 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 45
78704 TGTAGAACGT
* * ***
78714 TATTTAAAATATTATTTTTCTACCAAAAATATTAATATCGGACGT
1 TATTTAAAATATTATTTTTATACCAAAAATATTAATATCGAAAAA
* * *
78759 TATTTAAAATGTTATTTTTTATATCAGAAATATTAATATC-AAAAA
1 TATTTAAAATATTA-TTTTTATACCAAAAATATTAATATCGAAAAA
78804 TATTTA
1 TATTTA
78810 TTTTATGTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (45 bp):
TATTTAAAATATTATTTTTATACCAAAAATATTAATATCGAAAAA
Found at i:79491 original size:16 final size:17
Alignment explanation
Indices: 79470--79503 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
79460 AACTTTGAGG
79470 ATAAAT-ATTTTAAAAT
1 ATAAATAATTTTAAAAT
*
79486 ATAAATAATTTTATAAT
1 ATAAATAATTTTAAAAT
79503 A
1 A
79504 GTTTTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATAATTTTAAAAT
Found at i:80222 original size:21 final size:21
Alignment explanation
Indices: 80198--80243 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
80188 AGAGGTGATA
80198 TTTTTTAGCTTTACATTCTAT
1 TTTTTTAGCTTTACATTCTAT
*
80219 TTTTTTAGGTTTACATTCTAT
1 TTTTTTAGCTTTACATTCTAT
80240 TTTT
1 TTTT
80244 ATTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTTAGCTTTACATTCTAT
Found at i:80263 original size:10 final size:10
Alignment explanation
Indices: 80233--80295 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
80223 TTAGGTTTAC
80233 ATTCTATTTTT
1 ATTC-ATTTTT
* *
80244 ATTGAATTTT
1 ATTCATTTTT
*
80254 ATTCACTTTTA
1 ATTCA-TTTTT
*
80265 ATTCTTTTTT
1 ATTCATTTTT
80275 ATTGCATTTTT
1 ATT-CATTTTT
*
80286 ATTGATTTTT
1 ATTCATTTTT
80296 TAAAAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (10 bp):
ATTCATTTTT
Found at i:80263 original size:21 final size:21
Alignment explanation
Indices: 80238--80295 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
80228 TTTACATTCT
*
80238 ATTTTTATTGAATTTTATT-C
1 ATTTTTATTGATTTTTATTGC
* **
80258 ACTTTTAATTCTTTTTTATTGC
1 A-TTTTTATTGATTTTTATTGC
80280 ATTTTTATTGATTTTT
1 ATTTTTATTGATTTTT
80296 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTATTGATTTTTATTGC
Found at i:86613 original size:39 final size:39
Alignment explanation
Indices: 86559--86637 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
86549 ATGAAGAGGG
*
86559 AACTATGCTTCTTTCAAGTGATGATGATTGCAATGATGT
1 AACTATGCTTCTTTCAAGTGATGATGATTGCAATAATGT
*
86598 AACTATGCTTGTTTCAAGTGATGATGATTGCAATAATGT
1 AACTATGCTTCTTTCAAGTGATGATGATTGCAATAATGT
86637 A
1 A
86638 TCTGTTGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (39 bp):
AACTATGCTTCTTTCAAGTGATGATGATTGCAATAATGT
Found at i:90557 original size:24 final size:24
Alignment explanation
Indices: 90526--90575 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
90516 TTCATTAATA
*
90526 TATTTGTTTATATTAGTTTATTTT
1 TATTTGTTTATATTAGTTTATATT
*
90550 TATTTGTTTATATTCGTTTATATT
1 TATTTGTTTATATTAGTTTATATT
90574 TA
1 TA
90576 GTTGGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (24 bp):
TATTTGTTTATATTAGTTTATATT
Found at i:112060 original size:28 final size:29
Alignment explanation
Indices: 112007--112061 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
111997 CTCAAAAATT
* *
112007 CATTTATTGAAAAAGTAACCCTCAAACAA
1 CATTAATTGAAAAAGTAACCCCCAAACAA
112036 CATTAATTG-AAAA-TATACCCCCAAAC
1 CATTAATTGAAAAAGTA-ACCCCCAAAC
112062 TATCCACGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 13 0.57
29 8 0.35
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (29 bp):
CATTAATTGAAAAAGTAACCCCCAAACAA
Found at i:112535 original size:9 final size:9
Alignment explanation
Indices: 112523--112556 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
112513 GAATTCGGTT
*
112523 AATTAACTG
1 AATTAACCG
112532 AATTAACCG
1 AATTAACCG
112541 AATTAACCG
1 AATTAACCG
112550 AAATTAA
1 -AATTAA
112557 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:112872 original size:181 final size:178
Alignment explanation
Indices: 112562--112930 Score: 580
Period size: 181 Copynumber: 2.1 Consensus size: 178
112552 ATTAAATTTT
* *
112562 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
112627 TTTAAGATCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATGTAAATTTTT
66 TTTAAGATCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAAATTATCTAAATTTTT
* *
112692 A-TTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
130 ATTTTATAA-T-TATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAA
* *
112743 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * *
112808 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATT-AAAATTTATCTGGAATTTT
66 TTTAAGAT-CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATCT-AAATTTT
112872 TATTTTATAATTATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
129 TATTTTATAATTATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
112922 AAATATTAA
1 AAATATTAA
112931 TTTTTATATA
Statistics
Matches: 175, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
179 21 0.12
180 34 0.19
181 78 0.45
182 42 0.24
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (178 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATCTAAATTTTTA
TTTTATAATTATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
Done.