Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005352.1 Hibiscus syriacus cultivar Beakdansim tig00012156_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: 85210
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:827 original size:21 final size:20
Alignment explanation
Indices: 776--830 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
766 TTTCCCTTGA
776 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
796 AGTGTATCGATGC--TCTTAAC
1 AGTGCATCGATGCATTC-T-AC
816 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
831 CTCCTTATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 15 0.52
21 11 0.38
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2763 original size:19 final size:18
Alignment explanation
Indices: 2739--2791 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
2729 CTTTATTTCA
2739 TTTGTTTTATTATTATTAT
1 TTTGTTTTATTATTA-TAT
*
2758 TTTGTTTTAATATTATAT
1 TTTGTTTTATTATTATAT
* *
2776 TATATTATTATTATTA
1 TTTGTT-TTATTATTA
2792 ATTAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (18 bp):
TTTGTTTTATTATTATAT
Found at i:2787 original size:16 final size:16
Alignment explanation
Indices: 2746--2789 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2736 TCATTTGTTT
* *
2746 TATTATTATTATTTTG
1 TATTATTATTATATTA
* *
2762 TTTTAATATTATATTA
1 TATTATTATTATATTA
2778 TATTATTATTAT
1 TATTATTATTAT
2790 TAATTAATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATTATTATATTA
Found at i:4195 original size:15 final size:15
Alignment explanation
Indices: 4175--4205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4165 AATATGTTTA
4175 AATTAATAATTATTT
1 AATTAATAATTATTT
*
4190 AATTAATTATTATTT
1 AATTAATAATTATTT
4205 A
1 A
4206 TTTTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTAATAATTATTT
Found at i:6271 original size:30 final size:30
Alignment explanation
Indices: 6236--6300 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
6226 AAGAGAATGT
* *
6236 CATGGAAGAAGTTGTAGTCCAGATAAGCAA
1 CATGGAAGAAGCTGTAGTCCAGACAAGCAA
*
6266 TATGGAAGAAGCTGTAGTCCAGACAAGCAA
1 CATGGAAGAAGCTGTAGTCCAGACAAGCAA
6296 CATGG
1 CATGG
6301 CCCATAAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (30 bp):
CATGGAAGAAGCTGTAGTCCAGACAAGCAA
Found at i:6510 original size:7 final size:7
Alignment explanation
Indices: 6498--6535 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
6488 CATACATACA
6498 TTTGCAT
1 TTTGCAT
6505 TTTGCAT
1 TTTGCAT
6512 CTTTGCAT
1 -TTTGCAT
*
6520 TTTTCAT
1 TTTGCAT
6527 TTTGCAT
1 TTTGCAT
6534 TT
1 TT
6536 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (7 bp):
TTTGCAT
Found at i:6518 original size:15 final size:14
Alignment explanation
Indices: 6498--6535 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
6488 CATACATACA
6498 TTTGCATTTTGCAT
1 TTTGCATTTTGCAT
*
6512 CTTTGCATTTTTCAT
1 -TTTGCATTTTGCAT
6527 TTTGCATTT
1 TTTGCATTT
6536 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (14 bp):
TTTGCATTTTGCAT
Found at i:6666 original size:34 final size:35
Alignment explanation
Indices: 6606--6683 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
6596 GCATTTGCAT
* *
6606 TTTTCATTTTTGCATTCTTATGTTTGTAT-TTACA
1 TTTTCATTTTTGCATTCTCATCTTTGTATATTACA
*
6640 TTTTCATTTTTTCATT-TCCATCTTTGTATAATTACA
1 TTTTCATTTTTGCATTCT-CATCTTTGTAT-ATTACA
6676 TTTT-ATTT
1 TTTTCATTT
6684 CAAACTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 1 0.03
34 24 0.63
35 4 0.11
36 9 0.24
ACGTcount: A:0.19, C:0.13, G:0.05, T:0.63
Consensus pattern (35 bp):
TTTTCATTTTTGCATTCTCATCTTTGTATATTACA
Found at i:9246 original size:17 final size:17
Alignment explanation
Indices: 9212--9246 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9202 AAGAAAAAGG
9212 AAAAAGGAAAAAAATGA
1 AAAAAGGAAAAAAATGA
* *
9229 AAAAAGGGAAAAATTGA
1 AAAAAGGAAAAAAATGA
9246 A
1 A
9247 TCAAGACGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAAGGAAAAAAATGA
Found at i:9907 original size:32 final size:32
Alignment explanation
Indices: 9871--9931 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
9861 TGGAAATAAT
* *
9871 AAGTATCTCTACGAGATGAGTATAACAACAAG
1 AAGTATCTCTACAAGATGAGCATAACAACAAG
9903 AAGTATCTCTACAAGATGAGCATAACAAC
1 AAGTATCTCTACAAGATGAGCATAACAAC
9932 CATTTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (32 bp):
AAGTATCTCTACAAGATGAGCATAACAACAAG
Found at i:14613 original size:113 final size:113
Alignment explanation
Indices: 14413--14834 Score: 616
Period size: 113 Copynumber: 3.7 Consensus size: 113
14403 GTTTTCAAAC
* *
14413 ATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 ATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
** * * *
14478 AAGAACTTGTTCAACCTTTTGCTCGAATTAATCACTCGGTGGATCAGT
66 AAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGT
*
14526 AGTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
1 ATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
** *
14591 AAGAACTTGTTCAATTTTTTGCTTTAATTCATCACTCGATGGATTATT
66 AAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGT
*
14639 ATTGCCAGTTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
1 ATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
* * *
14704 AAAAATTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATTAGCT
66 AAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAG-T
* * * * *
14753 -TTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAACAA-AAAGAAGAAGTTCATAATGA
1 ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAA
*
14815 GAAGAGCTTGTTCAACCTTT
65 GAAGAACTTGTTCAACCTTT
14835 GTATGACTCT
Statistics
Matches: 279, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
112 35 0.13
113 243 0.87
114 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
AAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGT
Found at i:15332 original size:3 final size:3
Alignment explanation
Indices: 15324--15373 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
15314 TTTGTTTTAT
* *
15324 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA -TA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15368 TTA TTA
1 TTA TTA
15374 AATAATTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:15366 original size:16 final size:16
Alignment explanation
Indices: 15328--15371 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
15318 TTTTATTTAT
* * *
15328 TATTATTATTTTGTTT
1 TATTATTATTATATTA
*
15344 TAATATTATTATATTA
1 TATTATTATTATATTA
15360 TATTATTATTAT
1 TATTATTATTAT
15372 TAAATAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATTATTATATTA
Found at i:15369 original size:19 final size:18
Alignment explanation
Indices: 15320--15373 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
15310 TTCATTTGTT
*
15320 TTATTTATTATTATTATT
1 TTATTTATTATTATTATA
* *
15338 TTGTTTTAATATTATTATA
1 TT-ATTTATTATTATTATA
15357 TTATATTATTATTATTA
1 TTAT-TTATTATTATTA
15374 AATAATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTATTATTATTATA
Found at i:24205 original size:24 final size:24
Alignment explanation
Indices: 24177--24262 Score: 154
Period size: 24 Copynumber: 3.6 Consensus size: 24
24167 TGAGATACAC
*
24177 GGGTAAAAATGAAGAGATTTTAAA
1 GGGTAAAAATGAGGAGATTTTAAA
24201 GGGTAAAAATGAGGAGATTTTAAA
1 GGGTAAAAATGAGGAGATTTTAAA
24225 GGGTAAAAATGAGGAGATTTTAAA
1 GGGTAAAAATGAGGAGATTTTAAA
*
24249 GGGTAAAACTGAGG
1 GGGTAAAAATGAGG
24263 TGGATAATGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.45, C:0.01, G:0.30, T:0.23
Consensus pattern (24 bp):
GGGTAAAAATGAGGAGATTTTAAA
Found at i:25898 original size:20 final size:19
Alignment explanation
Indices: 25869--25913 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
25859 TCCTTTAAAA
*
25869 AATATAAAATATAAAATTTT
1 AATATTAAATA-AAAATTTT
25889 AATATTAAATAAAAATTTT
1 AATATTAAATAAAAATTTT
25908 AA-ATTA
1 AATATTA
25914 TCAGATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTAAATAAAAATTTT
Found at i:29949 original size:96 final size:96
Alignment explanation
Indices: 29776--29975 Score: 292
Period size: 96 Copynumber: 2.1 Consensus size: 96
29766 TTCAAGTAGT
* *
29776 AACCAGTAGATTCCATGATCAATAATTCAGGAACGATCATATTTTCCAGTAAAAACAGGTAACCA
1 AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
* *
29841 GATAACACATTTCAGGTAACCATAGTTCATA
66 GAGAACACATTTCAAGTAACCATAGTTCATA
* * * * *
29872 AACCGGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTACAGTGAAAACAGGTAACTA
1 AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
* *
29937 GAGAACATATTTCAAGTAACCATAGTTCGTA
66 GAGAACACATTTCAAGTAACCATAGTTCATA
*
29968 GACCAGTA
1 AACCAGTA
29976 AATCAGTGAT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
GAGAACACATTTCAAGTAACCATAGTTCATA
Found at i:35619 original size:16 final size:17
Alignment explanation
Indices: 35594--35625 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35584 CAAAAAAAAG
35594 ATAT-ATTTTTTGAAAT
1 ATATAATTTTTTGAAAT
35610 ATATAATTTTTTGAAA
1 ATATAATTTTTTGAAA
35626 CGTTTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATAATTTTTTGAAAT
Found at i:35671 original size:38 final size:36
Alignment explanation
Indices: 35629--35821 Score: 136
Period size: 38 Copynumber: 5.3 Consensus size: 36
35619 TTTGAAACGT
*
35629 TTTTGAAAACTTATGTACAATATATAAGTTTT-AAAACA
1 TTTTGAAAA--TATGTATAATATAT-AGTTTTGAAAACA
* *
35667 TTTTGAAAAT-TGTATAGTATATAGTTTTGAAATCA
1 TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
*
35702 TTTTGAAAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTG--AAAATATGTATAATATATAGTTTTGAAAACA
* * *
35740 TTTTTTTG-AAATCT-TAT-ATA-ATA-TTTTTAAATCA
1 ---TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
*
35774 TTTTTGAAAACTA--TATAATATATAGTTTTGTAAA-A
1 -TTTTGAAAA-TATGTATAATATATAGTTTTGAAAACA
*
35809 TTTTTAAGAATAT
1 TTTTGAA-AATAT
35822 AATATATAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 31
0.74 0.08 0.18
Matches are distributed among these distances:
32 6 0.05
33 6 0.05
34 27 0.21
35 29 0.23
36 10 0.08
37 8 0.06
38 36 0.28
41 5 0.04
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
Found at i:35779 original size:73 final size:74
Alignment explanation
Indices: 35609--35813 Score: 193
Period size: 73 Copynumber: 2.9 Consensus size: 74
35599 TTTTTTGAAA
* ** * *
35609 TATATAAT-TTTTTGAAA-CGTTTTTGAAAACTTATGTACAATATATAAGTTTT-AAAACA---T
1 TATATAATATTTTT-AAATCATTTTTGAAAAAATATATATAATATAT-AGTTTTGAAAACATTTT
35668 TTTGAAAATTG
64 TTTGAAAATTG
*
35679 TATAGTATATAGTTTTGAAATCA-TTTTGAAAAAATATATATAATATATAGTTTTGAAAACATTT
1 TATA-TA-ATA-TTTTTAAATCATTTTTGAAAAAATATATATAATATATAGTTTTGAAAACATTT
35743 TTTTG-AAATCT-
63 TTTTGAAAAT-TG
* *
35754 TATATAATATTTTTAAATCATTTTTG--AAAA-CTATATAATATATAGTTTTGTAAA-ATTTTT
1 TATATAATATTTTTAAATCATTTTTGAAAAAATATATATAATATATAGTTTTGAAAACATTTTT
35814 AAGAATATAA
Statistics
Matches: 115, Mismatches: 9, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
69 6 0.05
70 26 0.23
71 6 0.05
72 18 0.16
73 38 0.33
74 7 0.06
75 8 0.07
76 6 0.05
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (74 bp):
TATATAATATTTTTAAATCATTTTTGAAAAAATATATATAATATATAGTTTTGAAAACATTTTTT
TGAAAATTG
Found at i:35825 original size:32 final size:32
Alignment explanation
Indices: 35716--35838 Score: 97
Period size: 34 Copynumber: 3.7 Consensus size: 32
35706 GAAAAAATAT
* **
35716 ATATAATATATAGTTTTGAAAACATTTTTTTGAA
1 ATATAATATATAGTTTT-TAAACATTTTTAAG-A
* * *
35750 ATCTTATATAATA-TTTTTAAATCATTTTTGAAAA
1 ATATAATAT-ATAGTTTTTAAA-CATTTTT-AAGA
35784 CTATATAATATATAGTTTTGTAAA-ATTTTTAAGA
1 --ATATAATATATAGTTTT-TAAACATTTTTAAGA
*
35818 ATATAATATATAATTTTTAAA
1 ATATAATATATAGTTTTTAAA
35839 AAAAATTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
31 4 0.06
32 16 0.22
33 3 0.04
34 22 0.31
35 12 0.17
36 11 0.15
37 4 0.06
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
ATATAATATATAGTTTTTAAACATTTTTAAGA
Found at i:37225 original size:12 final size:13
Alignment explanation
Indices: 37208--37239 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
37198 TCAAATCGAA
37208 TAATTTTAA-TTT
1 TAATTTTAATTTT
37220 TAATTTTAATTTT
1 TAATTTTAATTTT
37233 TAATTTT
1 TAATTTT
37240 CGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:37235 original size:7 final size:6
Alignment explanation
Indices: 37208--37239 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
37198 TCAAATCGAA
37208 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
37240 CGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:41156 original size:106 final size:106
Alignment explanation
Indices: 40992--42052 Score: 1786
Period size: 106 Copynumber: 10.0 Consensus size: 106
40982 TCCAATTTCA
* * * * *
40992 TTCAGAGTCTATTTCAACTTCACAACGAAGAAAATTGGACTCCAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41057 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* * *
41098 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41163 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
41204 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41269 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
41310 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41375 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
41416 TTTAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41481 CGACGAAGGGACCACTGGTTGTCAATAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
41522 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
41587 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
41628 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
41693 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
*
41734 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
41799 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
*
41840 TTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA-A-AACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
41903 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* * * * *
41944 TTCAGAGTCAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAAGTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
42009 CGACGAAGGGACCGCTGGTTGTCAATAAATAACTT-TCAAC
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
42049 TTCA
1 TTCA
42053 CGACGGGGGA
Statistics
Matches: 900, Mismatches: 53, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
104 95 0.11
105 9 0.01
106 796 0.88
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
Found at i:42380 original size:36 final size:36
Alignment explanation
Indices: 42326--42701 Score: 545
Period size: 36 Copynumber: 10.4 Consensus size: 36
42316 CTTTGAGATT
* * *
42326 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGGCA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
** * *
42362 GTTTATCTTAAAATAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
42398 GTTTCCGTTGAAGCAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
42434 GTTTCCCTTGAAGCAAATTTCGCCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* * *
42470 TTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
42506 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
42542 GTTTCTCTTCAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
42578 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
42614 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* * *
42650 GTTTCCCTTGAAACAAATTTGTGTATCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTT-CGTCTCCCTTGAGACA
*
42687 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
42702 CCAATCTTTG
Statistics
Matches: 308, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
36 281 0.91
37 27 0.09
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:42607 original size:21 final size:21
Alignment explanation
Indices: 42581--42645 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
42571 TGAGACAGTT
42581 TCCCTTGAAACAAATTTCGTC
1 TCCCTTGAAACAAATTTCGTC
* *
42602 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTCGTC
42617 TCCCTTGAAACAAATTTCGTC
1 TCCCTTGAAACAAATTTCGTC
42638 TCCCTTGA
1 TCCCTTGA
42646 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.35
17 1 0.03
19 1 0.03
21 20 0.59
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTCGTC
Found at i:42764 original size:67 final size:65
Alignment explanation
Indices: 42650--42797 Score: 178
Period size: 67 Copynumber: 2.3 Consensus size: 65
42640 CCTTGAGACA
* * * *
42650 GTTTCCCTTGAAAC-AAATTTGTGTATCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTG-A
1 GTTTCTCTTGAAACAAAATTTGTGTATCCCTTGAGACAATTTCTCTTGAAA-A--AACCTTTGAA
42713 ATAT
63 AT-T
* *
42717 GTTTTTCTTGAAACAAAATTT-TGTCTCCCTTGAGACAATTTCTCTTGAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACAAAATTTGTGTATCCCTTGAGACAATTTCTCTTGAAAAAACCTTTGAAATT
42781 GTTTCTCTTGAAA-AAAA
1 GTTTCTCTTGAAACAAAA
42798 CCTTTGAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
63 4 0.06
64 20 0.28
65 3 0.04
66 1 0.01
67 38 0.53
68 6 0.08
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (65 bp):
GTTTCTCTTGAAACAAAATTTGTGTATCCCTTGAGACAATTTCTCTTGAAAAAACCTTTGAAATT
Found at i:42804 original size:28 final size:28
Alignment explanation
Indices: 42755--42821 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
42745 CTTGAGACAA
*
42755 TTTCTCTTG-AAAAAACCTTTGAAATTG
1 TTTCTCTTGAAAAAAACCTTTGAAAATG
42782 TTTCTCTTGAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAAAAAACCTTTGAAAATG
42810 TTTCTCTTGAAA
1 TTTCTCTTGAAA
42822 CCCAAAGACC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTCTCTTGAAAAAAACCTTTGAAAATG
Found at i:43028 original size:80 final size:81
Alignment explanation
Indices: 42824--43230 Score: 433
Period size: 80 Copynumber: 5.0 Consensus size: 81
42814 TCTTGAAACC
* * * * * * * *
42824 CAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTC
*
42889 TAGAAGGGTTATCTGCCA
65 GAGAAGGGTTATCTG-CA
* * * * *
42907 CAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
1 CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
*
42972 AGAAGGGCTATCTG-A
66 AGAAGGGTTATCTGCA
*
42987 CAAAGACCTTTGAGCTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
1 CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
*
43052 AGAAGGGCTATCTGC-
66 AGAAGGGTTATCTGCA
*** * * * * * *
43067 CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCACAACTTAAGTC
1 CAAAGACCTTTGAGTTCGATTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * *
43132 TAGAAGGGTTGTTTGCCAA
65 GAGAAGGGTTATCTG-C-A
* * *
43151 CAAAAGACCTTTGAGTTCGATTTCACTCAGCTCCAAGGCCCATCATTTGCAGCGTAGCTTAAAG-
1 C-AAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTT-AAGT
*
43215 CAAGAAGGGTTATCTG
64 CGAGAAGGGTTATCTG
43231 TCAATAAAAT
Statistics
Matches: 267, Mismatches: 50, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
80 99 0.37
81 40 0.15
82 37 0.14
83 28 0.10
84 36 0.13
85 27 0.10
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
AGAAGGGTTATCTGCA
Found at i:43197 original size:165 final size:161
Alignment explanation
Indices: 42824--43230 Score: 449
Period size: 165 Copynumber: 2.5 Consensus size: 161
42814 TCTTGAAACC
* * * * * * *
42824 CAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAA-GC
* ** * *
42889 TAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGACACATCATTT
64 AAGAAGGGTTATCTGCCACAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGACACATCATTT
* *
42954 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGA
129 GCAGCACAACTTAAGTCGAGAAGGGCTATCTGA
* *
42987 CAAAGACCTTTGAGCTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
1 CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG-CA
* * * * * * *
43052 AGAAGGGCTATCTG-C-CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTT
65 AGAAGGGTTATCTGCCACAAAGACCCCCGAGTTCGACTACACTCAGC-TCCAAGACACATCATTT
* * * *
43115 GCAGCACAACTTAAGTCTAGAAGGGTTGTTTGCCAA
129 GCAGCACAACTTAAGTCGAGAAGGGCTATCTG---A
* * *
43151 CAAAAGACCTTTGAGTTCGATTTCACTCAGCTCCAAGGCCCATCATTTGCAGCGTAGCTTAAAGC
1 C-AAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTT-AAGC
43216 AAGAAGGGTTATCTG
64 AAGAAGGGTTATCTG
43231 TCAATAAAAT
Statistics
Matches: 205, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
160 24 0.12
161 41 0.20
162 36 0.18
163 31 0.15
164 2 0.01
165 68 0.33
166 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (161 bp):
CAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGCAA
GAAGGGTTATCTGCCACAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGACACATCATTTGC
AGCACAACTTAAGTCGAGAAGGGCTATCTGA
Found at i:43972 original size:38 final size:36
Alignment explanation
Indices: 43930--44044 Score: 135
Period size: 38 Copynumber: 3.1 Consensus size: 36
43920 TTTGAAACGT
*
43930 TTTTGAAAACTTATGTACAATATATAAGTTTT-AAAACA
1 TTTTGAAAA--TATGTATAATATAT-AGTTTTGAAAACA
* *
43968 TTTTGAAAAT-TGTATAGTATATAGTTTTGAAATCA
1 TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
*
44003 TTTTGGAAAAATATATATAATATATAGTTTTGAAAACA
1 TTTT-G-AAAATATGTATAATATATAGTTTTGAAAACA
44041 TTTT
1 TTTT
44045 TTGAAATCTT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
34 6 0.09
35 19 0.28
36 2 0.03
37 5 0.07
38 35 0.52
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
Found at i:44025 original size:73 final size:69
Alignment explanation
Indices: 43948--44091 Score: 177
Period size: 70 Copynumber: 2.0 Consensus size: 69
43938 ACTTATGTAC
43948 AATATATAAGTTTT-AAAACA-TTTTGAAAAT-TGTATAGTATATAGTTTTGAAATCATTTTGGA
1 AATATAT-AGTTTTGAAAACATTTTTG-AAATCT-TATA-TATAT--TTTT-AAATCATTTTGGA
44010 AAAATATATAT
59 AAAATATATAT
* *
44021 AATATATAGTTTTGAAAACATTTTTTGAAATCTTATATATATTTTTAAATCATTTTTGAAAACTA
1 AATATATAGTTTTGAAAACA-TTTTTGAAATCTTATATATATTTTTAAATCATTTTGGAAAAATA
44086 TATAT
65 TATAT
44091 A
1 A
44092 TAGTTTGTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
70 23 0.35
71 4 0.06
72 6 0.09
73 18 0.28
74 8 0.12
75 6 0.09
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (69 bp):
AATATATAGTTTTGAAAACATTTTTGAAATCTTATATATATTTTTAAATCATTTTGGAAAAATAT
ATAT
Found at i:44058 original size:31 final size:32
Alignment explanation
Indices: 44022--44098 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
44012 AATATATATA
*
44022 ATATATAGTTTTGAAAACATTTTTTGAAATCT-T
1 ATATATA-TTTTGAAAACA-TTTTTGAAAACTAT
* *
44055 ATATATATTTTTAAATCATTTTTGAAAACTAT
1 ATATATATTTTGAAAACATTTTTGAAAACTAT
*
44087 ATATATAGTTTG
1 ATATATATTTTG
44099 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 11 0.29
32 20 0.53
33 7 0.18
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (32 bp):
ATATATATTTTGAAAACATTTTTGAAAACTAT
Found at i:44058 original size:38 final size:37
Alignment explanation
Indices: 43919--44059 Score: 128
Period size: 38 Copynumber: 3.8 Consensus size: 37
43909 ATATATAATT
* * *
43919 TTTTG-AAACGTTTTTGAAAACTTATGTACAATATATAAG
1 TTTTGAAAACATTTTTGAAAAATTA--TATAATATAT-AG
* *
43958 TTTT-AAAACA-TTTTG-AAAATTGTATAGTATATAG
1 TTTTGAAAACATTTTTGAAAAATTATATAATATATAG
* *
43992 TTTTGAAATCATTTTGGAAAAATATATATAATATATAG
1 TTTTGAAAACATTTTTGAAAAAT-TATATAATATATAG
**
44030 TTTTGAAAACATTTTTTGAAATCTTATATA
1 TTTTGAAAACA-TTTTTGAAAAATTATATA
44060 TATTTTTAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
34 6 0.07
35 13 0.16
36 4 0.05
37 10 0.12
38 33 0.40
39 17 0.20
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTTGAAAACATTTTTGAAAAATTATATAATATATAG
Found at i:44108 original size:31 final size:32
Alignment explanation
Indices: 44041--44132 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 32
44031 TTTGAAAACA
* *
44041 TTTTTTGAAATCT-TATATATATTTTTAAATC
1 TTTTTTGAAAACTATATATATATTTGTAAATC
*
44072 ATTTTTGAAAACTATATATATAGTTTGT-AAT-
1 TTTTTTGAAAACTATATATATA-TTTGTAAATC
44103 TTTTTT-AAGAA-TATAATATATAATTT-TAAA
1 TTTTTTGAA-AACTAT-ATATAT-ATTTGTAAA
44133 AAATATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
30 6 0.12
31 29 0.57
32 12 0.24
33 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTTTTGAAAACTATATATATATTTGTAAATC
Found at i:45534 original size:12 final size:13
Alignment explanation
Indices: 45517--45548 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
45507 TCAAATCGAA
45517 TAATTTTAA-TTT
1 TAATTTTAATTTT
45529 TAATTTTAATTTT
1 TAATTTTAATTTT
45542 TAATTTT
1 TAATTTT
45549 CGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:45544 original size:7 final size:6
Alignment explanation
Indices: 45517--45548 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
45507 TCAAATCGAA
45517 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
45549 CGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:47737 original size:50 final size:51
Alignment explanation
Indices: 47658--47790 Score: 123
Period size: 50 Copynumber: 2.6 Consensus size: 51
47648 ATAATATCAT
* **
47658 ATATTATTATAAT-ATATTTGATTACATATTAATATAATATTAA-AAATAA-A
1 ATATTATTAAAATGATATTAAATTA-ATATTAATAT-ATATTAATAAATAATA
* * * *
47708 ATATTATTAAAATTATATTATATGT-ATATTAA-ATATTTTAATAATTAATA
1 ATATTATTAAAATGATATTAAAT-TAATATTAATATATATTAATAAATAATA
* *
47758 TTTTTATTAAAATGATATTAAATTAATATTAAT
1 ATATTATTAAAATGATATTAAATTAATATTAAT
47791 TAAATAAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
48 6 0.09
49 8 0.12
50 46 0.68
51 7 0.10
52 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (51 bp):
ATATTATTAAAATGATATTAAATTAATATTAATATATATTAATAAATAATA
Found at i:47979 original size:42 final size:42
Alignment explanation
Indices: 47919--47998 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
47909 TTATATTGGG
* * *
47919 AAAATCAATTACAACTATCAAACACTGTAAAATATTTTATAT
1 AAAACCAATTACAACTATCAAACACTGGAAAACATTTTATAT
* *
47961 AAAACCAATTATATCTATCAAACACTGGAAAACATTTT
1 AAAACCAATTACAACTATCAAACACTGGAAAACATTTT
47999 TCGAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (42 bp):
AAAACCAATTACAACTATCAAACACTGGAAAACATTTTATAT
Found at i:52211 original size:22 final size:23
Alignment explanation
Indices: 52159--52210 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
52149 CATAAACACA
*
52159 AAAAAAATTAATTTTGTCATGAC
1 AAAAAAATTAATTTTGCCATGAC
52182 AAAAAAATTAATTTTGCCATGAC
1 AAAAAAATTAATTTTGCCATGAC
52205 AAAAAA
1 AAAAAA
52211 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAAAAATTAATTTTGCCATGAC
Found at i:54006 original size:16 final size:16
Alignment explanation
Indices: 53961--54039 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 16
53951 TTCACGGAAT
53961 ATAAGATTACCAGTGAGA
1 ATAAGATTACCAG-G-GA
53979 ATGTAAGATTACCAGGGA
1 A--TAAGATTACCAGGGA
* *
53997 ATAGGATTA-CTGGGA
1 ATAAGATTACCAGGGA
54012 ATGTAAGATTACCAGGGA
1 A--TAAGATTACCAGGGA
*
54030 ATATGATTAC
1 ATAAGATTAC
54040 TGGGAATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 6 0.12
16 15 0.29
17 7 0.14
18 10 0.20
19 1 0.02
20 12 0.24
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (16 bp):
ATAAGATTACCAGGGA
Found at i:54013 original size:15 final size:15
Alignment explanation
Indices: 53982--54046 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
53972 AGTGAGAATG
*
53982 TAAGATTACCAGGGAA
1 TAAGATTA-CTGGGAA
*
53998 TAGGATTACTGGGAA
1 TAAGATTACTGGGAA
*
54013 TGTAAGATTACCAGGGAA
1 --TAAGATTA-CTGGGAA
*
54031 TATGATTACTGGGAA
1 TAAGATTACTGGGAA
54046 T
1 T
54047 GTTGTATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 13 0.32
16 14 0.35
17 7 0.17
18 6 0.15
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (15 bp):
TAAGATTACTGGGAA
Found at i:54015 original size:33 final size:33
Alignment explanation
Indices: 53977--54048 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
53967 TTACCAGTGA
53977 GAATGTAAGATTACCAGGGAATAGGATTACTGG
1 GAATGTAAGATTACCAGGGAATAGGATTACTGG
*
54010 GAATGTAAGATTACCAGGGAATATGATTACTGG
1 GAATGTAAGATTACCAGGGAATAGGATTACTGG
54043 GAATGT
1 GAATGT
54049 TGTATATTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.26
Consensus pattern (33 bp):
GAATGTAAGATTACCAGGGAATAGGATTACTGG
Found at i:57878 original size:11 final size:11
Alignment explanation
Indices: 57862--57921 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
57852 CTGTTAAGAG
57862 TGTTATTAGTT
1 TGTTATTAGTT
*
57873 TGTTA-TGGTT
1 TGTTATTAGTT
* **
57883 TATTATTAACT
1 TGTTATTAGTT
57894 TGTTATTAGTT
1 TGTTATTAGTT
57905 TGTTATTAGTT
1 TGTTATTAGTT
57916 TGTTAT
1 TGTTAT
57922 GTTGGTTACT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 8 0.20
11 32 0.80
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.62
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:59825 original size:11 final size:11
Alignment explanation
Indices: 59793--59839 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
59783 ATTAAGAGTA
59793 TTATTAGTTTG
1 TTATTAGTTTG
*
59804 TTA-TGGTTTG
1 TTATTAGTTTG
*
59814 TTATTAGCTTG
1 TTATTAGTTTG
*
59825 TTATTAATTTG
1 TTATTAGTTTG
59836 TTAT
1 TTAT
59840 GTGGTTACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:66430 original size:15 final size:15
Alignment explanation
Indices: 66406--66439 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
66396 TTAGATAAGC
*
66406 TTCTCTTTGCTTAGA
1 TTCTCATTGCTTAGA
66421 TTCTCATTGCTTAGA
1 TTCTCATTGCTTAGA
66436 TTCT
1 TTCT
66440 TCAACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.53
Consensus pattern (15 bp):
TTCTCATTGCTTAGA
Found at i:72486 original size:36 final size:37
Alignment explanation
Indices: 72440--72509 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
72430 TTTCATTCAA
* *
72440 TAAATCTAGTTCACTAATTAAACTAGCTCATTTATTT
1 TAAATCTAGTTCACTAAGTAAACTAGATCATTTATTT
*
72477 TAAAT-TAGTTCATTAAGTAAACTAGATCATTTA
1 TAAATCTAGTTCACTAAGTAAACTAGATCATTTA
72510 AAGCTTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (37 bp):
TAAATCTAGTTCACTAAGTAAACTAGATCATTTATTT
Found at i:80969 original size:3 final size:3
Alignment explanation
Indices: 80957--81001 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
80947 AATATTCTAG
80957 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
81002 ACATGGACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:81595 original size:40 final size:40
Alignment explanation
Indices: 81550--81677 Score: 193
Period size: 40 Copynumber: 3.2 Consensus size: 40
81540 TTCAAACCAC
* * **
81550 AATATTAACTCTAGAACAATAAAATCCATAAGGAAACAAT
1 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACAAT
*
81590 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACCAT
1 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACAAT
*
81630 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACCAT
1 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACAAT
*
81670 AATTTTAA
1 AATATTAA
81678 AGTTTCAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (40 bp):
AATATTAAGTCTAAAACAATAAAATCCATAAACAAACAAT
Found at i:81606 original size:20 final size:20
Alignment explanation
Indices: 81583--81651 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
81573 ATCCATAAGG
81583 AAACAATAATATTAAGTCTA
1 AAACAATAATATTAAGTCTA
* ** **
81603 AAACAATAAAATCCA-TAAA
1 AAACAATAATATTAAGTCTA
*
81622 CAAACCATAATATTAAGTCTA
1 -AAACAATAATATTAAGTCTA
81643 AAACAATAA
1 AAACAATAA
81652 AATCCATAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.23
Consensus pattern (20 bp):
AAACAATAATATTAAGTCTA
Found at i:81666 original size:20 final size:20
Alignment explanation
Indices: 81603--81671 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
81593 ATTAAGTCTA
81603 AAACAATAAAATCCATAAAC
1 AAACAATAAAATCCATAAAC
* * ** **
81623 AAACCATAATATTAAGTCTA-
1 AAACAATAAAATCCA-TAAAC
81643 AAACAATAAAATCCATAAAC
1 AAACAATAAAATCCATAAAC
*
81663 AAACCATAA
1 AAACAATAA
81672 TTTTAAAGTT
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.61, C:0.19, G:0.01, T:0.19
Consensus pattern (20 bp):
AAACAATAAAATCCATAAAC
Done.