Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004892.1 Hibiscus syriacus cultivar Beakdansim tig00011011_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: 84477
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1487 original size:18 final size:18
Alignment explanation
Indices: 1464--1500 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1454 ATGAGGAGTT
*
1464 TGGTAAAATGAAATTAAA
1 TGGTAAAAAGAAATTAAA
*
1482 TGGTAAAAAGAGATTAAA
1 TGGTAAAAAGAAATTAAA
1500 T
1 T
1501 AAATAAAGAT
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:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (18 bp):
TGGTAAAAAGAAATTAAA
Found at i:2105 original size:25 final size:26
Alignment explanation
Indices: 2076--2124 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2066 TTAGCATATT
*
2076 AAAAACAAAGCTTGAAAA-TAAAAGA
1 AAAAACAAAACTTGAAAAGTAAAAGA
*
2101 AAAAATAAAACTTGAAAAGTAAAA
1 AAAAACAAAACTTGAAAAGTAAAA
2125 AAGAGAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAACAAAACTTGAAAAGTAAAAGA
Found at i:4855 original size:14 final size:13
Alignment explanation
Indices: 4833--4864 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
4823 CAATTGAAAT
4833 AAAAATAAAAGTA
1 AAAAATAAAAGTA
4846 AAAAAGTAAAAGTA
1 AAAAA-TAAAAGTA
4860 AAAAA
1 AAAAA
4865 ATGTAACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAGTA
Found at i:4870 original size:16 final size:15
Alignment explanation
Indices: 4833--4879 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4823 CAATTGAAAT
4833 AAAAA-TAAAAGT-A
1 AAAAAGTAAAAGTAA
4846 AAAAAGTAAAAGTAA
1 AAAAAGTAAAAGTAA
*
4861 AAAAATGTAACAG-AA
1 AAAAA-GTAAAAGTAA
4876 AAAA
1 AAAA
4880 CAATGGGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 12 0.40
16 6 0.20
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (15 bp):
AAAAAGTAAAAGTAA
Found at i:8639 original size:26 final size:26
Alignment explanation
Indices: 8603--8691 Score: 151
Period size: 26 Copynumber: 3.4 Consensus size: 26
8593 CTGAGGGGGT
8603 CTTCTAGAAACCGCCGTTGACTGGAC
1 CTTCTAGAAACCGCCGTTGACTGGAC
* **
8629 CTTCTAGAAACCGTCACTGACTGGAC
1 CTTCTAGAAACCGCCGTTGACTGGAC
8655 CTTCTAGAAACCGCCGTTGACTGGAC
1 CTTCTAGAAACCGCCGTTGACTGGAC
8681 CTTCTAGAAAC
1 CTTCTAGAAAC
8692 TGTCACGTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (26 bp):
CTTCTAGAAACCGCCGTTGACTGGAC
Found at i:9416 original size:16 final size:16
Alignment explanation
Indices: 9386--9444 Score: 72
Period size: 15 Copynumber: 3.8 Consensus size: 16
9376 GACATATCTC
9386 TATA-AATATTATTATGA
1 TATATAATA-TATTAT-A
9403 TAT-TAATATATTATA
1 TATATAATATATTATA
9418 TATATAATATA-TATA
1 TATATAATATATTATA
9433 TATAT-ATATATT
1 TATATAATATATT
9445 GTCACTACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.13
15 14 0.36
16 13 0.33
17 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATAATATATTATA
Found at i:9419 original size:2 final size:2
Alignment explanation
Indices: 9408--9443 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9398 TATGATATTA
9408 AT AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9444 TGTCACTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9440 original size:17 final size:17
Alignment explanation
Indices: 9386--9440 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
9376 GACATATCTC
9386 TATA-AATAT-TAT-TA
1 TATATAATATATATATA
9400 TGATATTAATATAT-TATA
1 T-ATA-TAATATATATATA
9418 TATATAATATATATATA
1 TATATAATATATATATA
9435 TATATA
1 TATATA
9441 TATTGTCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 8 0.23
17 19 0.54
18 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATAATATATATATA
Found at i:14214 original size:20 final size:22
Alignment explanation
Indices: 14189--14243 Score: 87
Period size: 20 Copynumber: 2.6 Consensus size: 22
14179 ATTTTGTGCA
14189 CTTAGTATCGATATTGTTCAT-
1 CTTAGTATCGATATTGTTCATG
*
14210 C-TAGTATCGATATTGTTCTTG
1 CTTAGTATCGATATTGTTCATG
14231 CTTAGTATCGATA
1 CTTAGTATCGATA
14244 CTATTCATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 18 0.58
21 2 0.06
22 11 0.35
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (22 bp):
CTTAGTATCGATATTGTTCATG
Found at i:14239 original size:22 final size:21
Alignment explanation
Indices: 14189--14252 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 21
14179 ATTTTGTGCA
14189 CTTAGTATCGATATTGTTCAT
1 CTTAGTATCGATATTGTTCAT
*
14210 C-TAGTATCGATATTGTTCTT
1 CTTAGTATCGATATTGTTCAT
* *
14230 GCTTAGTATCGATACTATTCAT
1 -CTTAGTATCGATATTGTTCAT
14252 C
1 C
14253 ATTTTCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 16 0.43
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (21 bp):
CTTAGTATCGATATTGTTCAT
Found at i:15153 original size:95 final size:95
Alignment explanation
Indices: 14988--15164 Score: 273
Period size: 95 Copynumber: 1.9 Consensus size: 95
14978 AAAATTGTAC
* * *
14988 CGATACTATCAAAACATAATGCTATAATGGTACTGATACCATATATGATATCGATACTACACAGA
1 CGATACTATCAAAACAGAATGCTAGAATGGTACCGATACCATATATGATATCGATACTACACAGA
15053 GTAGTAGTACCGATACTGCTGAGGCAGTAA
66 GTAGTAGTACCGATACTGCTGAGGCAGTAA
* * **
15083 CGATACTTTCAAAACAGAATTCTAGAATGGTACCGATACCATATATGATATCGATACTACTTAGA
1 CGATACTATCAAAACAGAATGCTAGAATGGTACCGATACCATATATGATATCGATACTACACAGA
* *
15148 TTAGTAGTATCGATACT
66 GTAGTAGTACCGATACT
15165 TTGAGTAATG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (95 bp):
CGATACTATCAAAACAGAATGCTAGAATGGTACCGATACCATATATGATATCGATACTACACAGA
GTAGTAGTACCGATACTGCTGAGGCAGTAA
Found at i:16271 original size:35 final size:36
Alignment explanation
Indices: 16225--16298 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
16215 AACTAAAAAT
*
16225 TAAGTCCATTCACTAAGTGACATGACTTATTATA-A
1 TAAGTCCATTCACCAAGTGACATGACTTATTATAGA
*
16260 TAAGTCTATTCACCAAGTGACATGACTTATTATAGA
1 TAAGTCCATTCACCAAGTGACATGACTTATTATAGA
16296 TAA
1 TAA
16299 CATCAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (36 bp):
TAAGTCCATTCACCAAGTGACATGACTTATTATAGA
Found at i:21795 original size:31 final size:31
Alignment explanation
Indices: 21752--21822 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
21742 TATTAAAATG
21752 AATTTAAGGTTAGATTTCACGCTAGTCCTTTT
1 AATTT-AGGTTAGATTTCACGCTAGTCCTTTT
21784 AATTTAGGTTAGATTTCACGCTAGTCCTTTT
1 AATTTAGGTTAGATTTCACGCTAGTCCTTTT
21815 AATTTAGG
1 AATTTAGG
21823 GGATAATTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (31 bp):
AATTTAGGTTAGATTTCACGCTAGTCCTTTT
Found at i:24048 original size:3 final size:3
Alignment explanation
Indices: 24040--24092 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
24030 CTGATTGCAA
24040 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24088 AAT AA
1 AAT AA
24093 ATAAGGTCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:24951 original size:15 final size:16
Alignment explanation
Indices: 24919--24953 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
24909 ATTGAACTGG
24919 ATTTTAAAAATATTTT
1 ATTTTAAAAATATTTT
*
24935 ATTTTCAAAAT-TTTT
1 ATTTTAAAAATATTTT
24950 ATTT
1 ATTT
24954 AATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAAAAATATTTT
Found at i:25008 original size:16 final size:17
Alignment explanation
Indices: 24987--25020 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24977 ATAGTTTAAA
*
24987 TTAAATTTTTAA-ATTT
1 TTAAATATTTAATATTT
25003 TTAAATATTTAATATTT
1 TTAAATATTTAATATTT
25020 T
1 T
25021 ATTTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAATATTTAATATTT
Found at i:25134 original size:17 final size:16
Alignment explanation
Indices: 25112--25158 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
25102 AATTAAATCT
25112 TATATTAATTTATT-TAA
1 TATATTAATTT-TTCT-A
25129 TATATT-ATTTTTCTA
1 TATATTAATTTTTCTA
25144 TATATTAATATTTTC
1 TATATTAAT-TTTTC
25159 CAATTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.33
16 7 0.26
17 11 0.41
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTAATTTTTCTA
Found at i:25194 original size:41 final size:37
Alignment explanation
Indices: 25156--25230 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 37
25146 TATTAATATT
*
25156 TTCCA-ATTAAAATTTTATTTCGTATATAAGAATTTAATA
1 TTCCAGATAAAAATTTTATTT--TATATAA-AATTTAATA
*
25195 TTCCAGGTAAAAATTTTATTTTATATAAAATTTAAT
1 TTCCAGATAAAAATTTTATTTTATATAAAATTTAAT
25231 CTTAGTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 5 0.15
40 13 0.39
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (37 bp):
TTCCAGATAAAAATTTTATTTTATATAAAATTTAATA
Found at i:25244 original size:21 final size:21
Alignment explanation
Indices: 25218--25271 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
25208 TTTTATTTTA
25218 TATAAAATTTAATCTTAGTT-T
1 TATAAAATTTAAT-TTAGTTAT
* *
25239 TATAAAATAATAATTTATTTAT
1 TATAAAAT-TTAATTTAGTTAT
25261 TATAAAATTTA
1 TATAAAATTTA
25272 TTTCGTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATAAAATTTAATTTAGTTAT
Found at i:25263 original size:22 final size:20
Alignment explanation
Indices: 25209--25268 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 20
25199 AGGTAAAAAT
*
25209 TTTATTTTATATAAAATTTAA
1 TTTATTTT-TATAAAATATAA
*
25230 TCTTAGTTTTATAAAATAATAA
1 T-TTATTTTTATAAAAT-ATAA
25252 TTTATTTATTATAAAAT
1 TTTATTT-TTATAAAAT
25269 TTATTTCGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTATTTTTATAAAATATAA
Found at i:25573 original size:20 final size:20
Alignment explanation
Indices: 25509--25574 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
25499 GAGAATTTAA
25509 TTTATTTATTAT-TATTATTATT
1 TTTATTT-TTATATA-TATT-TT
**
25531 TTTATTTTTATATATATAAT
1 TTTATTTTTATATATATTTT
*
25551 TTTATTTTTCTATATATTTT
1 TTTATTTTTATATATATTTT
25571 TTTA
1 TTTA
25575 ATTATTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 22 0.58
21 7 0.18
22 9 0.24
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTTTATATATATTTT
Found at i:28023 original size:2 final size:2
Alignment explanation
Indices: 28018--28047 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28008 TTACTTTATG
*
28018 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28048 AACCAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29538 original size:16 final size:16
Alignment explanation
Indices: 29490--29537 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
29480 GATCAGGATA
29490 TTTT-GATATCCG-A-
1 TTTTGGATATCCGAAT
*
29503 TTTCGGATATCCGAAT
1 TTTTGGATATCCGAAT
29519 TTTTGGATATCC-AAT
1 TTTTGGATATCCGAAT
29534 TTTT
1 TTTT
29538 TCAGATCGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 3 0.10
14 8 0.27
15 8 0.27
16 11 0.37
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (16 bp):
TTTTGGATATCCGAAT
Found at i:32078 original size:21 final size:20
Alignment explanation
Indices: 32054--32099 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
32044 TTCATCTTAA
* *
32054 TATTTAATTTATTTTTAAAAT
1 TATTTAATTTAATCTT-AAAT
*
32075 TATTTATTTTAATCTTAAAT
1 TATTTAATTTAATCTTAAAT
32095 TATTT
1 TATTT
32100 TAAAATTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTAATTTAATCTTAAAT
Found at i:32533 original size:2 final size:2
Alignment explanation
Indices: 32526--32575 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
32516 ATTTATTTTC
32526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32568 AT AT AT AT
1 AT AT AT AT
32576 GTACATAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33917 original size:32 final size:31
Alignment explanation
Indices: 33872--33960 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
33862 GACCTAAACC
*
33872 AAAAATCAGCCGATCAGATATTGACCCGACC-
1 AAAAATCAACCGATC-GATATTGACCCGACCT
** * *
33903 CGAAATCTAACCGATCCGGTATTAACCCGACCT
1 AAAAATC-AACCGAT-CGATATTGACCCGACCT
33936 AAAAATCAACCGATTCGATATTGAC
1 AAAAATCAACCGA-TCGATATTGAC
33961 AGACCATATA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
31 5 0.11
32 33 0.73
33 7 0.16
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (31 bp):
AAAAATCAACCGATCGATATTGACCCGACCT
Found at i:34838 original size:20 final size:21
Alignment explanation
Indices: 34805--34848 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
34795 ATTTGTATTT
34805 TATTTTTCACTTTTAGATAAA
1 TATTTTTCACTTTTAGATAAA
* *
34826 TATTTTTTA-TTTTTGATAAA
1 TATTTTTCACTTTTAGATAAA
34846 TAT
1 TAT
34849 AATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTTTCACTTTTAGATAAA
Found at i:40926 original size:9 final size:9
Alignment explanation
Indices: 40868--40929 Score: 90
Period size: 9 Copynumber: 6.9 Consensus size: 9
40858 TAAAAATATA
40868 ATAATAA-T
1 ATAATAATT
40876 AGTAATAATT
1 A-TAATAATT
*
40886 ATAACAATT
1 ATAATAATT
40895 ATAATAATT
1 ATAATAATT
*
40904 ATAACAATT
1 ATAATAATT
40913 ATAATAATT
1 ATAATAATT
40922 ATAATAAT
1 ATAATAAT
40930 AAAATAGGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
8 1 0.02
9 45 0.94
10 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATAATT
Found at i:41578 original size:124 final size:116
Alignment explanation
Indices: 41217--42023 Score: 812
Period size: 113 Copynumber: 6.9 Consensus size: 116
41207 CAACTTTATA
* * *
41217 TGTGATAAATT-AAGGC--AAGGTTGAACAAATTATTCTCATTATGAATTTCTTC-TCCTTCTTC
1 TGTGATAAATTCAA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * * *
41278 AGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGTTC-AACTTTATA
65 AGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCTATCTCT-TC
* * *
41330 TGTGATAAATT-AAGGC--AAGGTTGAACAAATTCTTCTCATTATGAATTTC-TCCTCCTTCTTC
1 TGTGATAAATTCAA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
41391 AGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTTTCTCCTTC
65 AGATGAGTTCTTCTCATTATGAACTCTTCTGG-AA-----ATGTTGATCTATCT-CTTC
* *
41450 TGTGATAAATTCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 TGTGATAAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
41515 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTC
66 GATGAGTTCTTCTCATTATGAACTCT-TCTGG--AAA-TG-T--TGATCTATCT-CTTC
* * * * *
41574 TGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTTCATTCTTCA
1 TGTGATAAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
41636 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTC
66 GATGAGTTCTTCTCATTATGAACTCT-TCTGG--AAA-TG-T--TGATCTATCT-CTTC
* * *
41695 TGTGATAGAA-TCATGAAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
1 TGTGATA-AATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * *
41759 AGATGAGTTCTTCTCATTATGAACTCTACATGGCAATGTTGATCCA--TC--G
65 AGATGAGTTCTTCTCATTATGAACTCTTC-TGGAAATGTTGATCTATCTCTTC
* * *
41808 TGTGGTGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 TGTGATAAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
41873 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCA--TC--G
66 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCTATCTCTTC
** * * * * *
41920 AATGATGAATTGAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTTTTCCTTCTTCA
1 TGTGATAAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
41985 TG-TGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTT
66 -GATGAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTT
42024 TTATGAAAAA
Statistics
Matches: 623, Mismatches: 44, Indels: 54
0.86 0.06 0.07
Matches are distributed among these distances:
112 103 0.17
113 186 0.30
114 2 0.00
115 1 0.00
116 1 0.00
118 6 0.01
119 8 0.01
120 17 0.03
121 121 0.19
122 34 0.05
123 37 0.06
124 104 0.17
125 3 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (116 bp):
TGTGATAAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCTATCTCTTC
Found at i:41991 original size:112 final size:113
Alignment explanation
Indices: 41710--42023 Score: 508
Period size: 112 Copynumber: 2.8 Consensus size: 113
41700 TAGAATCATG
41710 AAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
41775 TTATGAACTCTACATGGCAATGTTGATCCATCGTGTGGTGAATTCAAGC
66 TTATGAACTCTAC-TGGAAATGTTGATCCATCGAATGATGAATTCAAGC
41824 -AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
41888 TTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTGAAGC
66 TTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAATTCAAGC
* *
41936 AAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTATTTTTCCTTCTTCATG-TGAGTTCTTCTC
1 AAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTC
41999 ATTATGAACTCTACCTGGAAATGTT
65 ATTATGAACTCTA-CTGGAAATGTT
42024 TTATGAAAAA
Statistics
Matches: 188, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
112 95 0.51
113 93 0.49
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
AAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAATTCAAGC
Found at i:42159 original size:76 final size:76
Alignment explanation
Indices: 42033--42290 Score: 446
Period size: 76 Copynumber: 3.4 Consensus size: 76
42023 TTTATGAAAA
* * * *
42033 AAACATTC-TGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
42097 AAGGCTTTTTGG
65 AAGGCTTTTTGG
42109 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
42174 AGGCTTTTTGG
66 AGGCTTTTTGG
*
42185 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
42250 AGGCTTTTTGG
66 AGGCTTTTTGG
*
42261 AAACATCATGCATTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
42291 TGAGAAATAG
Statistics
Matches: 176, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 2 0.01
76 174 0.99
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:42987 original size:22 final size:22
Alignment explanation
Indices: 42962--43038 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
42952 AATAAAGCTT
*
42962 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
42984 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
43006 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
43028 TCATCTTTGAA
1 TCATCTTTGAA
43039 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:47147 original size:32 final size:32
Alignment explanation
Indices: 47106--47168 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
47096 TGAAGAAATG
*
47106 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCTCATCTGGTAGAGATACTTCTC
47138 ATTGTTATGCTCATCTGGTAGAGATACTTCT
1 ATTGTTATGCTCATCTGGTAGAGATACTTCT
47169 TGTGTCTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (32 bp):
ATTGTTATGCTCATCTGGTAGAGATACTTCTC
Found at i:47785 original size:1 final size:1
Alignment explanation
Indices: 47779--47848 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
47769 TCAATTTTCC
* * * * * * * * * *
47779 TTTTTTTCTTTCTTTTTTTTTCTTTTTCTTTTTCTTTTTCTTTTGTTTTTTCTTTTTCTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47844 TTTTT
1 TTTTT
47849 CCTTCTTCTT
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.13, G:0.01, T:0.86
Consensus pattern (1 bp):
T
Found at i:47806 original size:6 final size:6
Alignment explanation
Indices: 47773--47847 Score: 95
Period size: 6 Copynumber: 12.8 Consensus size: 6
47763 CTTGATTCAA
*
47773 TTTTCC TTTTT- TTCTTTC -TTTT- TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
47819 TTTTGT- TTTTTC TTTTTC TTTTTC TTTTT
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTT
47848 TCCTTCTTCT
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
5 10 0.16
6 51 0.82
7 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:47860 original size:18 final size:17
Alignment explanation
Indices: 47784--47863 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 17
47774 TTTCCTTTTT
*
47784 TTCTTTCTTTTTTTTTC
1 TTCTTTCTTTTTTCTTC
*
47801 TT-TTTC-TTTTTCTTT
1 TTCTTTCTTTTTTCTTC
* *
47816 TTCTTTTGTTTTTTCTTT
1 TTC-TTTCTTTTTTCTTC
47834 TTCTTTTTCTTTTTTCCTTC
1 TTC--TTTCTTTTTT-CTTC
47854 TTCTTTCTTT
1 TTCTTTCTTT
47864 GCTGGATAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
15 9 0.17
16 4 0.08
17 5 0.09
18 19 0.36
19 10 0.19
20 6 0.11
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (17 bp):
TTCTTTCTTTTTTCTTC
Found at i:47861 original size:30 final size:30
Alignment explanation
Indices: 47791--47863 Score: 50
Period size: 30 Copynumber: 2.5 Consensus size: 30
47781 TTTTTCTTTC
*
47791 TTTT-TTTTTCTTTTTCTTTTTCTT-TTTCT
1 TTTTCTTTTTCTTTTTC-TCTTCTTCTTTCT
47820 TTTGT-TTTTTCTTTTTCT-TT-TTCTTT-T
1 TTT-TCTTTTTCTTTTTCTCTTCTTCTTTCT
47847 TTCCTTCTTCTTTCTTT
1 TT--TTCTT-TTTCTTT
47864 GCTGGATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
27 5 0.13
28 6 0.16
29 7 0.18
30 20 0.53
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (30 bp):
TTTTCTTTTTCTTTTTCTCTTCTTCTTTCT
Found at i:48163 original size:2 final size:2
Alignment explanation
Indices: 48158--48185 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48148 ACAAAAAAGG
48158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48186 TTAAAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49848 original size:21 final size:21
Alignment explanation
Indices: 49822--49864 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49812 TGTAAAAATG
*
49822 AAAATGTAAATACAAACGTAA
1 AAAATGCAAATACAAACGTAA
* *
49843 AAAATGCAAATGCAAATGTAA
1 AAAATGCAAATACAAACGTAA
49864 A
1 A
49865 TGCAAACGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (21 bp):
AAAATGCAAATACAAACGTAA
Found at i:53840 original size:3 final size:3
Alignment explanation
Indices: 53832--53905 Score: 64
Period size: 3 Copynumber: 25.7 Consensus size: 3
53822 CTGTAATATG
* * * *
53832 TAA TAA TAA TAT TAT TAA TAA -AA T-A TAA TAA TAG TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
53878 CAA TTA TAA TAA TTA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53906 GGCAAAAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 6 0.11
3 50 0.89
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:55174 original size:35 final size:38
Alignment explanation
Indices: 55102--55175 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 38
55092 GTTGAAAAAT
* *
55102 ATTTATATATATTTTCTTTACAAATTTAAATTCATAAA
1 ATTTATATATATTTTCTTTACAAATTGAAAATCATAAA
55140 ATTTATATA-A-TTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATATTTTCTTTAC-AAATTGAAAATCATAAA
55175 A
1 A
55176 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 11 0.33
36 12 0.36
37 1 0.03
38 9 0.27
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (38 bp):
ATTTATATATATTTTCTTTACAAATTGAAAATCATAAA
Found at i:56707 original size:179 final size:177
Alignment explanation
Indices: 56142--56818 Score: 682
Period size: 179 Copynumber: 3.7 Consensus size: 177
56132 ATCAGAGTAC
* * * * * *
56142 GTTATGAACATATATAAGAAATACGATTGCTCCCAATAATATCATGATTTAATAATAGAAAAGGT
1 GTTATGAATATATATAAGAAATACGGTTGC-CCCAATAATTTCATGGTTCAATAATA-AAAAGAT
* * * *
56207 TGTAATCTGGAATTTTAATACTTTTAAATAAT-AAACAGGTTGCGTCGAAAATATTATCAGAGTT
64 TGTAATATGGAATGTTAATACTTTT-AATAATAAAACAGGTTGCGCCGAAAATGTTATCAGAG-T
*
56271 TAAGATAATGGAGTCTTGGATTATCCTAGTATAA-AAAATTAAGTTTAAATA-TGAAAAAT
127 T----TAA---AGTCTTGGATTATCCCAGTATAAGAAAA-TAAGTTTAAA-ACTG-AAAAT
* * *
56330 GTTATGAACATATATATAAGAAATACAGTTGTACCCAATAATTTCATGGTTCAATACTAAAAAAG
1 GTTATG-A-ATATATATAAGAAATACGGTTG-CCCCAATAATTTCATGGTTCAATAAT-AAAAAG
* * ** * * * * *
56395 ATTGTAATATGGAATGCTAATATTTTTAATAATAAAGTAGCTTGTGCCGAAAATTTTATTATA-T
62 ATTGTAATATGGAATGTTAATACTTTTAATAATAAAACAGGTTGCGCCGAAAATGTTATCAGAGT
* * * *
56459 TT--TGCCTTGGATTATCACAGTATAAGAAAATAAGTTTAAAACTTAAAAT
127 TTAAAGTCTTGGATTATCCCAGTATAAGAAAATAAGTTTAAAACTGAAAAT
* * *
56508 GTAATAAATATATATAAGAAATACGGTTGCCCCTAATAATTTCATGGTTCAATAATAAAATAGGT
1 GTTATGAATATATATAAGAAATACGGTTGCCCC-AATAATTTCATGGTTCAATAATAAAA-AGAT
* * * * *
56573 GGTAATATAGAATGTTAATACTTTTAATAATAAAACAGATTGCACCGAAAATGTTGTCAGAGTTT
64 TGTAATATGGAATGTTAATACTTTTAATAATAAAACAGGTTGCGCCGAAAATGTTATCAGAGTTT
* *
56638 AAAGTCTTGGATTATCCCAATATAAGAAAATAAATTTAAAACTGAAAAT
129 AAAGTCTTGGATTATCCCAGTATAAGAAAATAAGTTTAAAACTGAAAAT
* ** * * *
56687 GTTTTGAATATATATAAGAAATACGGTTGTGTCTAATAATTTCATAGTTCAATAATGAAAAAAAT
1 GTTATGAATATATATAAGAAATACGGTTG-CCCCAATAATTTCATGGTTCAATAAT-AAAAAGAT
* ** * *
56752 TGTAATATGGAATGTTAATATTTTTAATAATAAAGTAGGTTACGCCGAAAATGTTATCAAAGTTT
64 TGTAATATGGAATGTTAATACTTTTAATAATAAAACAGGTTGCGCCGAAAATGTTATCAGAGTTT
56817 AA
129 AA
56819 GCGGATAAGA
Statistics
Matches: 405, Mismatches: 70, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
175 7 0.02
176 93 0.23
177 4 0.01
178 10 0.02
179 177 0.44
180 9 0.02
184 1 0.00
188 8 0.02
189 7 0.02
190 88 0.22
191 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (177 bp):
GTTATGAATATATATAAGAAATACGGTTGCCCCAATAATTTCATGGTTCAATAATAAAAAGATTG
TAATATGGAATGTTAATACTTTTAATAATAAAACAGGTTGCGCCGAAAATGTTATCAGAGTTTAA
AGTCTTGGATTATCCCAGTATAAGAAAATAAGTTTAAAACTGAAAAT
Found at i:56920 original size:366 final size:360
Alignment explanation
Indices: 56142--56920 Score: 853
Period size: 366 Copynumber: 2.1 Consensus size: 360
56132 ATCAGAGTAC
* * * *
56142 GTTATGAACATATATAAGAAATACGATTGCTCCCAATAATATCATGATTTAATAATAGAAAAGGT
1 GTTATGAACATATATAAGAAATACGGTTGC-CCCAATAATTTCATGGTTCAATAATAGAAAAGGT
* * * * * **
56207 TGTAATCTGGAATTTTAATACTTTTAAATAATAAACAGGTTGCGTCGAAAATATTATCAGAGTTT
65 GGTAATATAGAATGTTAATACTTTTAAATAATAAACAGATTGCACCGAAAATATTATCAGAGTTT
* * *
56272 AAGATAATGGAGTCTTGGATTATCCTAGTATAAAAAATTAAGTTTAAATATGAAAAATGTTATGA
130 ---ATAA--GAGTCTTGGATTATCCCAATATAAAAAATTAAATTTAAATATGAAAAATGTTATGA
* *
56337 ACATATATATAAGAAATACAGTTGTACCCAATAATTTCATGGTTCAATACTAAAAAAGATTGTAA
190 ACATATATATAAGAAATACAGTTGTACCCAATAATTTCATAGTTCAATAATAAAAAAGATTGTAA
** * * *
56402 TATGGAATGCTAATATTTTTAATAATAAAGTAGCTTGTGCCGAAAATTTTATTATATTTTGCCTT
255 TATGGAATGCTAATATTTTTAATAATAAAGTAGCTTACGCCGAAAATGTTATCAAATTTTGCCTT
* *
56467 GGATTATCACAGTATAAGAAAATAAGTTTAAAACTTAAAAT
320 GGATTATCACAATATAAGAAAATAAGTTTAAAACTAAAAAT
* * *
56508 GTAATAAATATATATAAGAAATACGGTTGCCCCTAATAATTTCATGGTTCAATAATA-AAATAGG
1 GTTATGAACATATATAAGAAATACGGTTGCCCC-AATAATTTCATGGTTCAATAATAGAAA-AGG
* *
56572 TGGTAATATAGAATGTTAATACTTTT-AATAATAAAACAGATTGCACCGAAAATGTTGTCAGAG-
64 TGGTAATATAGAATGTTAATACTTTTAAATAAT-AAACAGATTGCACCGAAAATATTATCAGAGT
*
56635 TT-TAA-AGTCTTGGATTATCCCAATATAAGAAAA-TAAATTTAAA-ACTG-AAAATGTTTTG-A
128 TTATAAGAGTCTTGGATTATCCCAATATAA-AAAATTAAATTTAAATA-TGAAAAATGTTATGAA
* ** *
56694 -ATATATATAAGAAATACGGTTGTGTCTAATAATTTCATAGTTCAATAATGAAAAAA-ATTGTAA
191 CATATATATAAGAAATACAGTTGTACCCAATAATTTCATAGTTCAATAAT-AAAAAAGATTGTAA
* *
56757 TATGGAATGTTAATATTTTTAATAATAAAGTAGGTTACGCCGAAAATGTTATCAAAGTTTAAGCG
255 TATGGAATGCTAATATTTTTAATAATAAAGTAGCTTACGCCGAAAATGTTATCAAA-TTT-----
* **
56822 GATAAGACCTTGGATTTTC-CGAATATTGGAAAATAAGTTTAAAACTAAAAAT
314 --T--G-CCTTGGATTATCAC-AATATAAGAAAATAAGTTTAAAACTAAAAAT
* * ** * *
56874 TTTATGAACATATATAAAAAATGTGGTTGCGCACATTAATTTCATGG
1 GTTATGAACATATATAAGAAATACGGTTGC-CCCAATAATTTCATGG
56921 GTCACTAAGA
Statistics
Matches: 347, Mismatches: 47, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
355 99 0.29
356 10 0.03
357 11 0.03
358 32 0.09
359 4 0.01
361 3 0.01
363 1 0.00
365 16 0.05
366 169 0.49
367 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (360 bp):
GTTATGAACATATATAAGAAATACGGTTGCCCCAATAATTTCATGGTTCAATAATAGAAAAGGTG
GTAATATAGAATGTTAATACTTTTAAATAATAAACAGATTGCACCGAAAATATTATCAGAGTTTA
TAAGAGTCTTGGATTATCCCAATATAAAAAATTAAATTTAAATATGAAAAATGTTATGAACATAT
ATATAAGAAATACAGTTGTACCCAATAATTTCATAGTTCAATAATAAAAAAGATTGTAATATGGA
ATGCTAATATTTTTAATAATAAAGTAGCTTACGCCGAAAATGTTATCAAATTTTGCCTTGGATTA
TCACAATATAAGAAAATAAGTTTAAAACTAAAAAT
Found at i:56967 original size:37 final size:37
Alignment explanation
Indices: 56899--56969 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
56889 AAAAAATGTG
* * * *
56899 GTTGCGCACATTAATTTCATGGGTCACTAAGAAAAAA
1 GTTGCGCACAATAATATCATGGCTAACTAAGAAAAAA
* *
56936 GTTGCGCCCAATAATATCATGGCTAAGTAAGAAA
1 GTTGCGCACAATAATATCATGGCTAACTAAGAAA
56970 GCAGGTTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (37 bp):
GTTGCGCACAATAATATCATGGCTAACTAAGAAAAAA
Found at i:57931 original size:54 final size:54
Alignment explanation
Indices: 57873--58032 Score: 124
Period size: 54 Copynumber: 3.1 Consensus size: 54
57863 AATATAAAAG
57873 GTTATAAACATATAACGTAAAAGGTTGAAAATTAAAAAAGGTACTACCTATAAT
1 GTTATAAACATATAACGTAAAAGGTTGAAAATTAAAAAAGGTACTACCTATAAT
** **** * ** * * *
57927 GTTATACTCATA-AATC-TATTTTGTAT-TACTTTTAATAA--TA-TA---A-AAG
1 GTTATAAACATATAA-CGTAAAAGGT-TGAAAATTAAAAAAGGTACTACCTATAAT
57973 GTTATAAACATATAACGTAAAAGGTTGAAAATTAAAAAAGGTACTACCTATAAT
1 GTTATAAACATATAACGTAAAAGGTTGAAAATTAAAAAAGGTACTACCTATAAT
58027 GTTATA
1 GTTATA
58033 CTTGTAGACC
Statistics
Matches: 70, Mismatches: 24, Indels: 24
0.59 0.20 0.20
Matches are distributed among these distances:
46 14 0.20
47 14 0.20
49 2 0.03
50 4 0.06
51 2 0.03
53 14 0.20
54 20 0.29
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (54 bp):
GTTATAAACATATAACGTAAAAGGTTGAAAATTAAAAAAGGTACTACCTATAAT
Found at i:58047 original size:100 final size:100
Alignment explanation
Indices: 57821--58034 Score: 428
Period size: 100 Copynumber: 2.1 Consensus size: 100
57811 ATGTGTATTT
57821 TATAATGTTATACTCATAAATCTATTTTGTATTACTTTTAATAATATAAAAGGTTATAAACATAT
1 TATAATGTTATACTCATAAATCTATTTTGTATTACTTTTAATAATATAAAAGGTTATAAACATAT
57886 AACGTAAAAGGTTGAAAATTAAAAAAGGTACTACC
66 AACGTAAAAGGTTGAAAATTAAAAAAGGTACTACC
57921 TATAATGTTATACTCATAAATCTATTTTGTATTACTTTTAATAATATAAAAGGTTATAAACATAT
1 TATAATGTTATACTCATAAATCTATTTTGTATTACTTTTAATAATATAAAAGGTTATAAACATAT
57986 AACGTAAAAGGTTGAAAATTAAAAAAGGTACTACC
66 AACGTAAAAGGTTGAAAATTAAAAAAGGTACTACC
58021 TATAATGTTATACT
1 TATAATGTTATACT
58035 TGTAGACCTA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 114 1.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (100 bp):
TATAATGTTATACTCATAAATCTATTTTGTATTACTTTTAATAATATAAAAGGTTATAAACATAT
AACGTAAAAGGTTGAAAATTAAAAAAGGTACTACC
Found at i:67960 original size:6 final size:6
Alignment explanation
Indices: 67951--67975 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
67941 GTGTTTGTGT
67951 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
67976 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:68478 original size:20 final size:19
Alignment explanation
Indices: 68440--68482 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
68430 AGAGTTATAT
*
68440 TCAACTTCTCAACTCACTC
1 TCAACTTCACAACTCACTC
*
68459 TCAACATTCACAATTCACTC
1 TCAAC-TTCACAACTCACTC
68479 TCAA
1 TCAA
68483 AGTGTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (19 bp):
TCAACTTCACAACTCACTC
Found at i:69971 original size:101 final size:100
Alignment explanation
Indices: 69740--69983 Score: 246
Period size: 101 Copynumber: 2.4 Consensus size: 100
69730 AACTACCTGC
**
69740 ATTGTTATAAATATAACCTTTTTTGTCTTACATAATCATAATGAAAAAGGTTTCACACATATAAC
1 ATTGTTATAAATATAACCTTTTTTGTCTTACATAATCATAATGAAAAAGAATTCACACATATAAC
* * * *
69805 TGAAACGATTAACAGTATAAGAAGGCACTACATGT
66 TGAAACGATTAACAATAAAAAAAGGCACTACATAT
* * * *
69840 ATTGTTATAAATTTAAACATGGTTTT-TCTTACATAGT-ATTAAT-AAAAA-AATTCGA-ACATA
1 ATTGTTATAAATAT-AACCT-TTTTTGTCTTACATAATCA-TAATGAAAAAGAATTC-ACACATA
* * * * * *
69900 TCACTTAAATGGTTGACACAATAAAAAAAGGCGCTACCTAT
62 TAACTGAAACGATT-A-ACAATAAAAAAAGGCACTACATAT
69941 ATTGTTATAAATATAACCCTTTTTTGTCTTACATAATCATAAT
1 ATTGTTATAAATATAA-CCTTTTTTGTCTTACATAATCATAAT
69984 TGTATCAGTT
Statistics
Matches: 115, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
99 18 0.16
100 27 0.23
101 65 0.57
102 5 0.04
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (100 bp):
ATTGTTATAAATATAACCTTTTTTGTCTTACATAATCATAATGAAAAAGAATTCACACATATAAC
TGAAACGATTAACAATAAAAAAAGGCACTACATAT
Found at i:70152 original size:177 final size:178
Alignment explanation
Indices: 69820--70160 Score: 492
Period size: 177 Copynumber: 1.9 Consensus size: 178
69810 CGATTAACAG
* *
69820 TATAAGAAGGCACTACATGTATTGTTATAAATTTAAACATGGTTTTTCTTACATAGTATTAATAA
1 TATAAGAAGACACTACATGTATTGTTATAAATTTAAACATGATTTTTCTTACATAGTATTAATAA
* * * *
69885 AAAAATTCGAACATATCACTTAAATGGTTGACACAATAAAAAAAGGCGCTACCTATATTGTTATA
66 AAAAATTCGAACATATCACGTAAACGGTTGACAC-ATAAAAAAAGACGCTACCTATATTATTATA
* *
69950 AATATAACCCTTTTTTGTCTTACATAATCATAATTGTATCAGTTGACAA
130 AATATAACCCTGTTTTGTCTTACATAACCATAATTGTATCAGTTGACAA
*
69999 TATAAGAAGACACTACCTGTATTGTTATAAATTT-AACAT-ATTTTTCTTACAGT-GTATTAATA
1 TATAAGAAGACACTACATGTATTGTTATAAATTTAAACATGATTTTTCTTACA-TAGTATTAATA
* * * *
70061 AAAAAGGTTTTGAACATATCACGTAAACGGTTGACAC-TATAAAAAGACGCTACCTGTATTATTA
65 AAAAA--ATTCGAACATATCACGTAAACGGTTGACACATAAAAAAAGACGCTACCTATATTATTA
*
70125 TAAATATAACCCTGTTTTGTTTTACATAACCATAAT
128 TAAATATAACCCTGTTTTGTCTTACATAACCATAAT
70161 GAATTGGGTT
Statistics
Matches: 145, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
177 81 0.56
178 6 0.04
179 58 0.40
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (178 bp):
TATAAGAAGACACTACATGTATTGTTATAAATTTAAACATGATTTTTCTTACATAGTATTAATAA
AAAAATTCGAACATATCACGTAAACGGTTGACACATAAAAAAAGACGCTACCTATATTATTATAA
ATATAACCCTGTTTTGTCTTACATAACCATAATTGTATCAGTTGACAA
Found at i:70378 original size:203 final size:200
Alignment explanation
Indices: 70023--70416 Score: 472
Period size: 203 Copynumber: 2.0 Consensus size: 200
70013 ACCTGTATTG
** *
70023 TTATAAATTTAACATATTTTTCTTACAGTGTATTAATAAAAAAGGTTTTGAACATATCACGTAAA
1 TTATAAATTTAACATATTTTTCTTACAGTGTATTAATAAAAAAGGTTTCAAACATATCAAGTAAA
* * * * *
70088 CGGTTGACACTATAAAAAGACGCTACCTGTATTATTATAAATATAACCCTGTTTTGTTTTACATA
66 CAGTTGACACTATAAAAAGACGATACATGTATTATTATAAATATAACCCTGTTTTATCTTACATA
* *** *
70153 ACCATAATGAATTGGGTTTCGCACATATAACTTA-A-ACTTTTGACAACATAAAAAGGCACTAAC
131 ACCATAATAAAACAGGTTTCGCACATATAACTTACAGA-GTTT-ACAACATAAAAAGGCACTAAC
70216 TATAATA
194 TATAATA
* * * *
70223 TTATAAATTTAAACCA-ATTTTCTGTTATAGTTTATTAATAATAAAGGTTTCAAACATATCAAGT
1 TTATAAATTT-AA-CATATTTT-TCTTACAGTGTATTAATAAAAAAGGTTTCAAACATATCAAGT
* * *
70287 AAACAGTTGATACTATAAAAAAGATGATACATGTATTGTTATAAATATAACCCTGTTTTATCTTA
63 AAACAGTTGACACTAT-AAAAAGACGATACATGTATTATTATAAATATAACCCTGTTTTATCTTA
* ** * *
70352 TAT-GTCATTAATAAAACATGTTTCGCACATATAACTTACAGAGTTTACAATATAAAAAGGCACT
127 CATAACCA-TAATAAAACAGGTTTCGCACATATAACTTACAGAGTTTACAACATAAAAAGGCACT
70416 A
191 A
70417 CATGGTTTGT
Statistics
Matches: 162, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
200 10 0.06
201 7 0.04
202 53 0.33
203 87 0.54
204 4 0.02
205 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (200 bp):
TTATAAATTTAACATATTTTTCTTACAGTGTATTAATAAAAAAGGTTTCAAACATATCAAGTAAA
CAGTTGACACTATAAAAAGACGATACATGTATTATTATAAATATAACCCTGTTTTATCTTACATA
ACCATAATAAAACAGGTTTCGCACATATAACTTACAGAGTTTACAACATAAAAAGGCACTAACTA
TAATA
Found at i:76716 original size:15 final size:15
Alignment explanation
Indices: 76696--76730 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
76686 CACGTGAGGA
76696 TTATTT-TCTTCTTAT
1 TTATTTATCTT-TTAT
76711 TTATTTATCTTTTAT
1 TTATTTATCTTTTAT
76726 TTATT
1 TTATT
76731 GTTTTACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATCTTTTAT
Found at i:83018 original size:20 final size:20
Alignment explanation
Indices: 82976--83023 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
82966 TAACTTTTTC
82976 TTTTATCTTTCATTTTTAAT
1 TTTTATCTTTCATTTTTAAT
* *
82996 TTTTCTCTTTCA-TTTTAAC
1 TTTTATCTTTCATTTTTAAT
83015 TTTTA-CTTT
1 TTTTATCTTT
83024 TCTTTCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 11 0.44
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATCTTTCATTTTTAAT
Found at i:83018 original size:27 final size:26
Alignment explanation
Indices: 82960--83036 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
82950 TTCCCTCCCA
82960 AATTTTTAACTTTTTCT-TTT-ATCTTT
1 AATTTTTAA-TTTTTCTCTTTCAT-TTT
*
82986 CATTTTTAATTTTTCTCTTTCATTTT
1 AATTTTTAATTTTTCTCTTTCATTTT
* * *
83012 AACTTTTACTTTTCTTTCTTTCATT
1 AATTTTTAATTTT-TCTCTTTCATT
83037 CATCTTCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.16
26 24 0.56
27 12 0.28
ACGTcount: A:0.17, C:0.16, G:0.00, T:0.68
Consensus pattern (26 bp):
AATTTTTAATTTTTCTCTTTCATTTT
Done.