Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:3225 original size:2 final size:2
Alignment explanation
Indices: 3218--3253 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3208 ACTTCAATAC
3218 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
3254 TTCAAAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3789 original size:50 final size:50
Alignment explanation
Indices: 3714--3862 Score: 208
Period size: 50 Copynumber: 3.0 Consensus size: 50
3704 AAGTGATTTG
*
3714 ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGGCCGTAATTGTTA
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTA
* * *
3764 ACTATTCTTCATCAACCTTTGACAATCGAGAGAGGTAGCCGTAATTATTA
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTA
* * * * * *
3814 ACTATTCTTTACCAACTTTTGACAATAGAAAAAGGTGACCGTAATTGTT
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTT
3863 GACTCTAAGC
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (50 bp):
ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTA
Found at i:8156 original size:50 final size:50
Alignment explanation
Indices: 8090--8394 Score: 423
Period size: 50 Copynumber: 6.1 Consensus size: 50
8080 AAGTGATTTA
* *
8090 ACTATTTTTCACCAACCTTTGACAATCGAAAGAGGTGGCCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
* * * * *
8140 ATTATTCTTCACCAACCTTTGATAATCGAGAGAAGTGACCGTAATTGTTC
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
* * *
8190 ATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
* * *
8240 ACTATTGTTCACCAACCTTTGACAATCGAGAGAGGTGACCATAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
* * * *
8290 ACTATTCTTCACCAACATTTGACAATCAAAAGAGGT-AGCCATAATTATTG
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGA-CCGTAATTGTTG
* *
8340 ACTATTCTTCACCAACCTTTGACAATAGAAAAAGGTGACCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
8390 ACTAT
1 ACTAT
8395 AAGCATCTCA
Statistics
Matches: 227, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.00
50 225 0.99
51 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
ACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTAATTGTTG
Found at i:8847 original size:5 final size:5
Alignment explanation
Indices: 8837--8932 Score: 85
Period size: 5 Copynumber: 19.8 Consensus size: 5
8827 ACATAAATTT
* * * *
8837 TTTTC TTTTC TTTGT- TTCTTC TTTTC TTTCC CTTCC TTTCC TTTTC TTTTC
1 TTTTC TTTTC TTT-TC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* *
8888 TTTT- TTTT- TTTTC -TTT- TTTTC TTTTC TTTTC ATTTC TTTCC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
8933 TCTATTTATT
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
4 14 0.18
5 59 0.77
6 4 0.05
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:8917 original size:36 final size:40
Alignment explanation
Indices: 8837--8926 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 40
8827 ACATAAATTT
8837 TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCCTTCCTTTCC
1 TTTTCTTTTCTTTGTTTCTTCTTTTCTTT-CCTTCCTTTCC
* * *
8878 TTTTCTTTTCTTT-TTT-TT-TTTTCTTT-TTTTCTTTTC
1 TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCTTCCTTTCC
*
8914 TTTTCATTTCTTT
1 TTTTCTTTTCTTT
8927 CCTTTTTCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
36 19 0.42
38 8 0.18
39 2 0.04
40 3 0.07
41 13 0.29
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (40 bp):
TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCTTCCTTTCC
Found at i:8932 original size:46 final size:46
Alignment explanation
Indices: 8837--8932 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
8827 ACATAAATTT
* *
8837 TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCCTTCCTTTCCTTTTC
1 TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCCTTCATTTCCTTTCC
* * * **
8883 TTTTCTTTTTTTTTTTTCTTTTTTTCTTTTCTTTTCATTT-CTTTCC
1 TTTTCTTTTCTTTGTTTCTTCTTTTC-TTTCCCTTCATTTCCTTTCC
8929 TTTT
1 TTTT
8933 TCTATTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 32 0.76
47 10 0.24
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (46 bp):
TTTTCTTTTCTTTGTTTCTTCTTTTCTTTCCCTTCATTTCCTTTCC
Found at i:15132 original size:18 final size:19
Alignment explanation
Indices: 15102--15150 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
15092 AACATTATAA
*
15102 TAATATTAAATTAAGAATG
1 TAATAATAAATTAAGAATG
*
15121 TAATAA-AAATTAATAATG
1 TAATAATAAATTAAGAATG
*
15139 TTATAATAAATT
1 TAATAATAAATT
15151 TAATAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
TAATAATAAATTAAGAATG
Found at i:16946 original size:24 final size:24
Alignment explanation
Indices: 16919--16967 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16909 AATTTTAGTA
16919 TTAATTTATTGGGCAGATTTCTAT
1 TTAATTTATTGGGCAGATTTCTAT
16943 TTAATTTATTGGGCAGATTTCTAT
1 TTAATTTATTGGGCAGATTTCTAT
16967 T
1 T
16968 AGTTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (24 bp):
TTAATTTATTGGGCAGATTTCTAT
Found at i:18530 original size:40 final size:39
Alignment explanation
Indices: 18476--18554 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
18466 AAAAGGCAAC
* *
18476 AGAGAAACAAACATGTTTGCTTTATGTTGTGTTTAGGAT
1 AGAGAAAAAAACATGTTTGCTTCATGTTGTGTTTAGGAT
18515 AGAGAAAAAAAACATGTTTGCTTCATGTTGTGTTTAGGAT
1 AGAG-AAAAAAACATGTTTGCTTCATGTTGTGTTTAGGAT
18555 GTTAGCCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (39 bp):
AGAGAAAAAAACATGTTTGCTTCATGTTGTGTTTAGGAT
Found at i:21421 original size:26 final size:25
Alignment explanation
Indices: 21374--21435 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
21364 CACGAACAGA
* *
21374 ATAAAAAAATATAATTAAAATACGAT
1 ATAAAAAATTATAATTAAAATA-AAT
*
21400 ATAAAAAATTATGAA-TATAATAAAT
1 ATAAAAAATTAT-AATTAAAATAAAT
21425 AGTAAAAAATT
1 A-TAAAAAATT
21436 TTAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 26 0.84
27 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAAAAAATTATAATTAAAATAAAT
Found at i:24178 original size:50 final size:50
Alignment explanation
Indices: 24081--24336 Score: 361
Period size: 50 Copynumber: 5.1 Consensus size: 50
24071 ATTTTCATTT
* * * * *
24081 TTGACTATCCTTCATCAACCTTTAGACAATAAAAGGAGGTGATCATAATTG
1 TTGACGATTCTTCACCAACCTTT-GACAATAGAAGGAGGTGACCATAATTG
* *
24132 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTA
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATAATTG
* * * *
24182 TTAACGATTTTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATAATTG
* *
24232 TTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGATGACCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATAATTG
*
24282 TTGACGATTCTTCACCGACCTTTGACAATAG-AGAGAGGTGACCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGACCATAATTG
24332 TTGAC
1 TTGAC
24337 TCTATATCAA
Statistics
Matches: 186, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
49 1 0.01
50 165 0.89
51 20 0.11
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (50 bp):
TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATAATTG
Found at i:28799 original size:50 final size:50
Alignment explanation
Indices: 28711--28867 Score: 237
Period size: 50 Copynumber: 3.2 Consensus size: 50
28701 GTTGCCATTG
* * *
28711 TTGACTATCCTTCACCAACCTTTGACAATAG-AGAGAGGTGACCATAATTA
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGGCCATAATTA
* *
28761 TTAACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTA
*
28811 TTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAA-TA
1 TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTA
28860 TTGACGAT
1 TTGACGAT
28868 CTCCACTTGA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 9 0.09
50 87 0.89
51 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
TTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATAATTA
Found at i:28952 original size:50 final size:50
Alignment explanation
Indices: 28893--28997 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 50
28883 GAGGTGCATA
*
28893 TTGACGATTCTTCACCAACTTTTGACAATAGA-AGGAGGTGGCCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATAATTG
28943 TTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTG
1 TTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTG
28993 TTGAC
1 TTGAC
28998 TCTAAGTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
50 52 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (50 bp):
TTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTG
Found at i:36884 original size:17 final size:17
Alignment explanation
Indices: 36858--36944 Score: 59
Period size: 17 Copynumber: 5.0 Consensus size: 17
36848 AAAATCGATT
*
36858 AAAATAAATTTAATTAA
1 AAAATTAATTTAATTAA
*
36875 AAAATTAATTAAATTTAA
1 AAAATTAATTTAA-TTAA
**
36893 TTTAATTAATTTAAGTT-A
1 -AAAATTAATTTAA-TTAA
** * *
36911 AATTTTAATTGATTTAA
1 AAAATTAATTTAATTAA
*
36928 AATATTAATTTAATTAA
1 AAAATTAATTTAATTAA
36945 TTAATTTGAT
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
16 2 0.04
17 33 0.63
18 5 0.10
19 12 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:36901 original size:9 final size:9
Alignment explanation
Indices: 36864--36960 Score: 67
Period size: 9 Copynumber: 10.6 Consensus size: 9
36854 GATTAAAATA
36864 AATTTAATT
1 AATTTAATT
**
36873 AA-AAAATT
1 AATTTAATT
*
36881 AATTAAATTT
1 AATTTAA-TT
36891 AATTTAATT
1 AATTTAATT
36900 AATTTAAGTT
1 AATTTAA-TT
36910 AAATTTTAATT
1 -AA-TTTAATT
*
36921 GATTTAA--
1 AATTTAATT
36928 AATATTAATTT
1 AAT-TTAA-TT
36939 AA-TTAATT
1 AATTTAATT
*
36947 AATTTGATT
1 AATTTAATT
36956 AATTT
1 AATTT
36961 TTAATTATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
7 2 0.03
8 14 0.20
9 33 0.46
10 11 0.15
11 6 0.08
12 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTTAATT
Found at i:36914 original size:15 final size:15
Alignment explanation
Indices: 36855--36906 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
36845 GCAAAAATCG
*
36855 ATTAAAATAAATTTA
1 ATTAAATTAAATTTA
36870 ATTAAA--AAA-TTA
1 ATTAAATTAAATTTA
*
36882 ATTAAATTTAATTTA
1 ATTAAATTAAATTTA
*
36897 ATTAATTTAA
1 ATTAAATTAA
36907 GTTAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 9 0.29
13 3 0.10
14 2 0.06
15 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATTAAATTTA
Found at i:39280 original size:2 final size:2
Alignment explanation
Indices: 39273--39299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39263 CGAATTATAT
39273 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
39300 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39304 original size:2 final size:2
Alignment explanation
Indices: 39299--39328 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39289 TCTCTCTCTC
*
39299 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39329 GATGAATTTG
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:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40134 original size:19 final size:21
Alignment explanation
Indices: 40112--40151 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40102 AAAATTAAGA
40112 TTAAACTT-AT-TTTTTATTT
1 TTAAACTTAATATTTTTATTT
*
40131 TTAAATTTAATATTTTTATTT
1 TTAAACTTAATATTTTTATTT
40152 AAATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTAAACTTAATATTTTTATTT
Found at i:41263 original size:16 final size:18
Alignment explanation
Indices: 41223--41263 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
41213 ATCTATTAAT
* *
41223 ATATATATATATATATAA
1 ATATAAATATATATAAAA
41241 ATATAAATATAT-TAAAA
1 ATATAAATATATATAAAA
41258 AT-TAAA
1 ATATAAA
41264 AATTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATATATAAAA
Found at i:43231 original size:24 final size:26
Alignment explanation
Indices: 43204--43254 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
43194 GCTTCCTCAC
*
43204 ACAC-ATCT-ATCCCTGAAAATGATG
1 ACACGATCTCATCCCTAAAAATGATG
*
43228 ACACTGATCTCTTCCCTAAAAATGATG
1 ACAC-GATCTCATCCCTAAAAATGATG
43255 CAACACCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
26 4 0.18
27 14 0.64
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (26 bp):
ACACGATCTCATCCCTAAAAATGATG
Found at i:45118 original size:27 final size:27
Alignment explanation
Indices: 45088--45141 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
45078 TTAAAAAGAA
45088 AAAAAAAAAACTTTCCCATAAATCCAT
1 AAAAAAAAAACTTTCCCATAAATCCAT
*
45115 AAAAAGAAAACTTTCCCATAAATCCAT
1 AAAAAAAAAACTTTCCCATAAATCCAT
45142 GCTAAAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.22
Consensus pattern (27 bp):
AAAAAAAAAACTTTCCCATAAATCCAT
Found at i:46841 original size:2 final size:2
Alignment explanation
Indices: 46834--46862 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46824 TCACTTGGAT
46834 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 T
46863 GGGTAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48076 original size:24 final size:24
Alignment explanation
Indices: 48039--48085 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
48029 CAGATCAACC
48039 TTTTTACCATTTTTATAAAATTTG
1 TTTTTACCATTTTTATAAAATTTG
*
48063 TTTTT-CCATATTTTATCAAATTT
1 TTTTTACCAT-TTTTATAAAATTT
48086 TAGTGCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTACCATTTTTATAAAATTTG
Found at i:49542 original size:13 final size:13
Alignment explanation
Indices: 49524--49550 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49514 ACTTATGTAA
49524 ACTTTATTTAATG
1 ACTTTATTTAATG
49537 ACTTTATTTAATG
1 ACTTTATTTAATG
49550 A
1 A
49551 TTATTGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
ACTTTATTTAATG
Found at i:51850 original size:3 final size:3
Alignment explanation
Indices: 51842--51867 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51832 TGACTAAACT
51842 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
51868 TGTTGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53575 original size:15 final size:15
Alignment explanation
Indices: 53552--53587 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53542 ATGTTATTAT
* *
53552 AAAGGGAAGAGAAGA
1 AAAGAGAAGAAAAGA
53567 AAAGAGAAGAAAAGA
1 AAAGAGAAGAAAAGA
53582 AAAGAG
1 AAAGAG
53588 GGATGGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAAGA
Found at i:53807 original size:2 final size:2
Alignment explanation
Indices: 53800--53831 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
53790 CCGACTGAAT
53800 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53832 GTTTATCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:54993 original size:19 final size:20
Alignment explanation
Indices: 54956--54998 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
54946 AAATGGTTTA
* * *
54956 GAAATTTTTTTTGATAATT-
1 GAAATTTTATTTCAAAATTC
54975 GAAATTTTATTTCAAAATTC
1 GAAATTTTATTTCAAAATTC
54995 GAAA
1 GAAA
54999 GAAGCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
GAAATTTTATTTCAAAATTC
Found at i:57878 original size:109 final size:111
Alignment explanation
Indices: 57684--57910 Score: 343
Period size: 109 Copynumber: 2.1 Consensus size: 111
57674 ATGTCAACTA
** *
57684 TTTAACCTTTTTATTGAAAAAAAAATCCAACCCAATTCCCTTTTTTTTGTGTTGATTTCACAAGT
1 TTTAACCTTTTTATTGAAAAAAAAATCCAA-CCAATTCCCTTTGCTTTGGGTTGATTTCACAAGT
* * * * *
57749 GTATATAAGCACCAGTTAAATATTATCTAATTACTCTTTT-AGTTTT
65 ATATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
57795 TTTAACCTTTTTATTGAAAAAAAAAATCCAA-CAATTCCC-TTGCTTTGGGTTGATTTCACAAGT
1 TTTAACCTTTTTATTG-AAAAAAAAATCCAACCAATTCCCTTTGCTTTGGGTTGATTTCACAAGT
57858 ATATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
65 ATATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
57905 TTTAAC
1 TTTAAC
57911 ATAAATATTT
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
109 57 0.54
110 19 0.18
111 16 0.15
112 14 0.13
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (111 bp):
TTTAACCTTTTTATTGAAAAAAAAATCCAACCAATTCCCTTTGCTTTGGGTTGATTTCACAAGTA
TATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
Found at i:58141 original size:2 final size:2
Alignment explanation
Indices: 58129--58170 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
58119 ATGAAGGAGC
*
58129 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58170 T
1 T
58171 CTCTGACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58310 original size:2 final size:2
Alignment explanation
Indices: 58305--58335 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58295 AATATCCTTT
*
58305 TA TA TA TA TA TA CA 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
58336 CCTTTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:58321 original size:28 final size:28
Alignment explanation
Indices: 58273--58327 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
58263 TGGACTAAAA
*
58273 CTTTTAGATAATGATATATATAAATATC
1 CTTTTAGATAATGATACATATAAATATC
* *
58301 CTTTTATATATAT-ATACATATATATAT
1 CTTTTAGATA-ATGATACATATAAATAT
58328 ATATATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (28 bp):
CTTTTAGATAATGATACATATAAATATC
Found at i:59833 original size:2 final size:2
Alignment explanation
Indices: 59826--59862 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
59816 TGTTATCTTC
*
59826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59863 CATACGCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:60923 original size:2 final size:2
Alignment explanation
Indices: 60916--60948 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60906 CTTTACAACG
60916 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
60949 GTGAACGTGA
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:64435 original size:92 final size:92
Alignment explanation
Indices: 64277--64449 Score: 249
Period size: 92 Copynumber: 1.9 Consensus size: 92
64267 TTTTGGAAAG
* * * *
64277 CTATGGAGAAAGACTATGAAGTTCTTCCATTACCTCCAAATCCAACTATGGCGCAGATCAAGAAT
1 CTATGGAGAAAGACTATGAAGTTCCTCCATTACCTCCAAATCCAACTACGGCGCAAATCAAAAAT
*
64342 CACAAAGAGAAAAAATTAAGTGGGCAA
66 CACAAAAAGAAAAAATTAAGTGGGCAA
* * * *
64369 CTATGGAGGAGGACTACT-AAGTTCCTCCATTCCCTCCAAATCTAACTACGGCGCAAATCAAAAA
1 CTATGGAGAAAGACTA-TGAAGTTCCTCCATTACCTCCAAATCCAACTACGGCGCAAATCAAAAA
64433 TCACAAAAAGAAAAAAT
65 TCACAAAAAGAAAAAAT
64450 CAAGAAAGTC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 70 0.99
93 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (92 bp):
CTATGGAGAAAGACTATGAAGTTCCTCCATTACCTCCAAATCCAACTACGGCGCAAATCAAAAAT
CACAAAAAGAAAAAATTAAGTGGGCAA
Found at i:69884 original size:3 final size:3
Alignment explanation
Indices: 69876--69908 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
69866 TAAAATGGAA
*
69876 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69909 CCATGCTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:70982 original size:2 final size:2
Alignment explanation
Indices: 70975--71011 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
70965 ATCAGTTGCC
70975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71012 CAAGCTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71138 original size:3 final size:3
Alignment explanation
Indices: 71125--71162 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
71115 AGATCAAGCC
*
71125 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
71163 GTACTTACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:72017 original size:31 final size:29
Alignment explanation
Indices: 71946--72019 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
71936 ATTTATTTGT
*
71946 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
71976 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
72009 TT-TATTTTATT
1 TTATATTTTATT
72020 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:73553 original size:17 final size:17
Alignment explanation
Indices: 73527--73566 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
73517 AATTATAATT
73527 ATATTT-AAATATTATA
1 ATATTTAAAATATTATA
*
73543 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
73560 ATATTTA
1 ATATTTA
73567 TATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:73599 original size:20 final size:20
Alignment explanation
Indices: 73551--73602 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
73541 TAATATTTAA
73551 AATATTATTATATTTATATAT
1 AATATTA-TATATTTATATAT
* *
73572 ATTTTTATATATTTATA-ATT
1 AATATTATATATTTATATA-T
73592 AATATTATATA
1 AATATTATATA
73603 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATATATTTATATAT
Found at i:73635 original size:60 final size:59
Alignment explanation
Indices: 73518--73652 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 59
73508 TATTTATCAA
* * * *
73518 ATTATAATTATATTTAAATATTATAATATTTAAAATATTATTATATTTATATATATTTTT
1 ATTATATTTATAATT-AATATTATAAAATTTAAAATATTATAATATTTATATATATTTTT
* * *
73578 A-TATATTTATAATTAATATTATATAAATTTTAAAGTATT-TAATATTATATTTTTATTTTT
1 ATTATATTTATAATTAATATTATA-AAA-TTTAAAATATTATAATATT-TATATATATTTTT
73638 ATTATATTT-TAATTA
1 ATTATATTTATAATTA
73653 TTTTTTATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 9 0.14
59 19 0.30
60 29 0.45
61 7 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (59 bp):
ATTATATTTATAATTAATATTATAAAATTTAAAATATTATAATATTTATATATATTTTT
Found at i:73645 original size:11 final size:11
Alignment explanation
Indices: 73631--73664 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
73621 ATTATATTTT
73631 TATTTTTATTA
1 TATTTTTATTA
*
73642 TATTTTAATTA
1 TATTTTTATTA
73653 T-TTTTTATTA
1 TATTTTTATTA
73663 TA
1 TA
73665 ATGATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:73653 original size:20 final size:20
Alignment explanation
Indices: 73555--73664 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 20
73545 ATTTAAAATA
73555 TTATTATA-TTTATATATATTT
1 TTATTATATTTTA-AT-TATTT
* *
73576 TTA-TATATTTATAATTAATA
1 TTATTATATTT-TAATTATTT
* *
73596 TTATATAAATTTTAAAGTATTT
1 TTAT-TATATTTT-AATTATTT
*
73618 AATATTATA-TTT--TTATTT
1 -TTATTATATTTTAATTATTT
73636 TTATTATATTTTAATTATTTT
1 TTATTATATTTTAATTA-TTT
73657 TTATTATA
1 TTATTATA
73665 ATGATAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.10
18 8 0.12
20 13 0.19
21 22 0.32
22 16 0.23
23 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTATATTTTAATTATTT
Found at i:73769 original size:4 final size:4
Alignment explanation
Indices: 73762--73796 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
73752 TATGTAGTGG
*
73762 GAAA GAAA GAAA GAAA AAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
73797 AAAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:73784 original size:16 final size:17
Alignment explanation
Indices: 73763--73798 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
73753 ATGTAGTGGG
73763 AAAGAAAGAAAGAA-AA
1 AAAGAAAGAAAGAAGAA
73779 AAAGAAAGAAAGAAGAA
1 AAAGAAAGAAAGAAGAA
73796 AAA
1 AAA
73799 AAAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAGAA
Found at i:74007 original size:17 final size:17
Alignment explanation
Indices: 73972--74009 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
73962 TATTATTTAA
73972 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
73990 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
74007 AAT
1 AAT
74010 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:75158 original size:74 final size:74
Alignment explanation
Indices: 75037--75184 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
75027 CTTAACAAGA
75037 ATATGAGATATTAAGTTCTAGGAATTTAAAAGTGTTTTTCATTGCATCTCGAATATTATATCTTC
1 ATATGAGATATTAAGTTCTAGGAATTTAAAAGTGTTTTTCATTGCATCTCGAATATTATATCTTC
75102 AATTTATTG
66 AATTTATTG
75111 ATATGAGATATTAAGTTCTAGGAATTTAAAAGTGTTTTTCATTGCATCTCGAATATTATATCTTC
1 ATATGAGATATTAAGTTCTAGGAATTTAAAAGTGTTTTTCATTGCATCTCGAATATTATATCTTC
75176 AATTTATTG
66 AATTTATTG
75185 TTTAGAAAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (74 bp):
ATATGAGATATTAAGTTCTAGGAATTTAAAAGTGTTTTTCATTGCATCTCGAATATTATATCTTC
AATTTATTG
Found at i:81850 original size:2 final size:2
Alignment explanation
Indices: 81845--81869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81835 ATTAAAAAAG
81845 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 T
81870 CATCCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84247 original size:16 final size:16
Alignment explanation
Indices: 84226--84260 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
84216 AATTCACACA
* *
84226 TATATATATATATGTG
1 TATATAAATATACGTG
84242 TATATAAATATACGTG
1 TATATAAATATACGTG
84258 TAT
1 TAT
84261 CAATCTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (16 bp):
TATATAAATATACGTG
Found at i:84837 original size:36 final size:36
Alignment explanation
Indices: 84791--84863 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
84781 TCTCAAAATC
84791 TTTTTTTTAAAAAGAAAAAGACGAACACAAAACAAA
1 TTTTTTTTAAAAAGAAAAAGACGAACACAAAACAAA
84827 TTTTTTTTAAAAAGAAAAAGACGAACACAAAACAAA
1 TTTTTTTTAAAAAGAAAAAGACGAACACAAAACAAA
84863 T
1 T
84864 AAACGAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.23
Consensus pattern (36 bp):
TTTTTTTTAAAAAGAAAAAGACGAACACAAAACAAA
Found at i:85108 original size:21 final size:20
Alignment explanation
Indices: 85071--85114 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
85061 TACACATAAT
* *
85071 ATAAAAATATAATATATTTA
1 ATAAAAATATAAAATATATA
85091 ATAAAAATATTAAAATATATA
1 ATAAAAATA-TAAAATATATA
85112 ATA
1 ATA
85115 TGATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAAATATAAAATATATA
Found at i:85135 original size:25 final size:25
Alignment explanation
Indices: 85100--85191 Score: 84
Period size: 25 Copynumber: 3.7 Consensus size: 25
85090 AATAAAAATA
85100 TTAAA-AT-ATATAATATGATATAT
1 TTAAATATAATATAATATGATATAT
* *
85123 TTATAATA-AATATAATATAAAATAT
1 TTA-AATATAATATAATATGATATAT
*
85148 TTAAATATAAT-TAATATGATACAT
1 TTAAATATAATATAATATGATATAT
* *
85172 ATAATATATATATATTATAT
1 TTAA-ATATA-ATATAATAT
85192 TAATATCAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
23 3 0.05
24 19 0.35
25 26 0.47
26 2 0.04
27 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAAATATAATATAATATGATATAT
Found at i:85138 original size:9 final size:9
Alignment explanation
Indices: 85068--85183 Score: 58
Period size: 9 Copynumber: 12.7 Consensus size: 9
85058 TTTTACACAT
85068 AATATAA-A
1 AATATAATA
85076 AATATAATA
1 AATATAATA
* *
85085 TATTTAATA
1 AATATAATA
* *
85094 AAAATATTA
1 AATATAATA
85103 AA-AT-ATA
1 AATATAATA
85110 TAATATGATATA
1 -AATAT-A-ATA
**
85122 TTTATAATA
1 AATATAATA
85131 AATATAATA
1 AATATAATA
* *
85140 TAAAATATTTA
1 -AATATA-ATA
*
85151 AATATAATT
1 AATATAATA
*
85160 AATATGATA
1 AATATAATA
*
85169 CATATAATA
1 AATATAATA
*
85178 TATATA
1 AATATA
85184 TATTATATTA
Statistics
Matches: 79, Mismatches: 21, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
7 2 0.03
8 11 0.14
9 47 0.59
10 11 0.14
11 5 0.06
12 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (9 bp):
AATATAATA
Found at i:85175 original size:47 final size:44
Alignment explanation
Indices: 85077--85183 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 44
85067 TAATATAAAA
* *
85077 ATATAATATATTTAATAAAAATATTAAAATATATAATATGATAT
1 ATATAATATATATAATAAAAATATTAAAATATATAATATGATAC
* *
85121 ATTTATAATAAATATAATATAAAATATTTAAATATAATTAATATGATAC
1 A--TATAATATATATAATA-AAAATATTAAAATAT-A-TAATATGATAC
85170 ATATAATATATATA
1 ATATAATATATATA
85184 TATTATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
46 14 0.26
47 26 0.49
48 1 0.02
49 11 0.21
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (44 bp):
ATATAATATATATAATAAAAATATTAAAATATATAATATGATAC
Found at i:86791 original size:60 final size:60
Alignment explanation
Indices: 86723--86971 Score: 354
Period size: 60 Copynumber: 4.2 Consensus size: 60
86713 ATAACCAATC
* * *
86723 AGATGATGACAGCCTGACGGATTCTGTGGAGGACTCACCAGAGGAACGGTCCGAGGAAGA
1 AGATGATGACAGCCTGTCGGATTCAGTGGAGGACTCACCAAAGGAACGGTCCGAGGAAGA
** *
86783 AGATGATGACAGCCTGTCGGATTCAGCAGAGGACTCACCAGAGGAACGGTCCGAGGAAGA
1 AGATGATGACAGCCTGTCGGATTCAGTGGAGGACTCACCAAAGGAACGGTCCGAGGAAGA
** * * *
86843 AGATGACAACAGCCTGTCAGATTCAATGGAGGACTCACCAAAGGAACGATCCGAGGAAGA
1 AGATGATGACAGCCTGTCGGATTCAGTGGAGGACTCACCAAAGGAACGGTCCGAGGAAGA
* * * * *
86903 AGATGATGACAGCCTGTCGGACTCTGGGGTGGACTCACCAAAGGAACGGTCTGAGGAAGA
1 AGATGATGACAGCCTGTCGGATTCAGTGGAGGACTCACCAAAGGAACGGTCCGAGGAAGA
86963 AGATGATGA
1 AGATGATGA
86972 TGATAACGGG
Statistics
Matches: 167, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 167 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (60 bp):
AGATGATGACAGCCTGTCGGATTCAGTGGAGGACTCACCAAAGGAACGGTCCGAGGAAGA
Found at i:89939 original size:2 final size:2
Alignment explanation
Indices: 89927--89982 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
89917 ATGATTAGAA
* *
89927 AG AG AG GG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
89969 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
89983 GGAAGAAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:100146 original size:3 final size:3
Alignment explanation
Indices: 100131--100177 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
100121 AGTTTCTCCA
*
100131 TCT TCT GCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
100178 CTAAATAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:101618 original size:10 final size:10
Alignment explanation
Indices: 101598--101644 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
101588 AACGATGGTA
*
101598 ATATGTACAT
1 ATATATACAT
*
101608 ATACATACAT
1 ATATATACAT
*
101618 ATATATATAT
1 ATATATACAT
*
101628 ATATATATAT
1 ATATATACAT
101638 ATATATA
1 ATATATA
101645 AATGTGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATACAT
Found at i:101623 original size:2 final size:2
Alignment explanation
Indices: 101606--101644 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
101596 TAATATGTAC
* *
101606 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
101645 AATGTGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:108627 original size:2 final size:2
Alignment explanation
Indices: 108614--108661 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
108604 TTTCCCTCTT
*
108614 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108656 TA TA TA
1 TA TA TA
108662 AGATTAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109942 original size:2 final size:2
Alignment explanation
Indices: 109935--109968 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
109925 CGTTTTTACA
109935 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
109969 GAAAATGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110464 original size:50 final size:50
Alignment explanation
Indices: 110405--110508 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
110395 GGGGCCAAAT
110405 GGGTAAAAACACAAAACGTTGATACCGAGAAAACTCAAGATGTTCTTCCA
1 GGGTAAAAACACAAAACGTTGATACCGAGAAAACTCAAGATGTTCTTCCA
* * *
110455 GGGTGAAAACTCAAAACGTTGATACCGAGAAAACTCAATATGTTCTTCCA
1 GGGTAAAAACACAAAACGTTGATACCGAGAAAACTCAAGATGTTCTTCCA
110505 GGGT
1 GGGT
110509 CTTCCCCCTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (50 bp):
GGGTAAAAACACAAAACGTTGATACCGAGAAAACTCAAGATGTTCTTCCA
Found at i:110491 original size:24 final size:24
Alignment explanation
Indices: 110410--110492 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
110400 CAAATGGGTA
*
110410 AAAACACAAAACGTTGATACCGAG
1 AAAACTCAAAACGTTGATACCGAG
* * * * *
110434 AAAACTCAAGATGTT-CTTCCAGGGTG
1 AAAACTCAAAACGTTGATACC---GAG
110460 AAAACTCAAAACGTTGATACCGAG
1 AAAACTCAAAACGTTGATACCGAG
110484 AAAACTCAA
1 AAAACTCAA
110493 TATGTTCTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 3 0.07
24 23 0.52
26 15 0.34
27 3 0.07
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (24 bp):
AAAACTCAAAACGTTGATACCGAG
Found at i:112047 original size:5 final size:5
Alignment explanation
Indices: 112028--112080 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
112018 TATTATATAT
* *
112028 ATTT- ATTTAA ATTTA ATTTA ATTTA ATTTA TTTTTA ATTTT ATTTA TATTTA
1 ATTTA ATTT-A ATTTA ATTTA ATTTA ATTTA -ATTTA ATTTA ATTTA -ATTTA
112080 A
1 A
112081 AAATTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.10
5 24 0.59
6 13 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATTTA
Found at i:112053 original size:16 final size:16
Alignment explanation
Indices: 112025--112080 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
112015 TAATATTATA
112025 TATATTT-ATTTAAATT
1 TATATTTAATTT-AATT
112041 TA-ATTTAATTTAATT
1 TATATTTAATTTAATT
* *
112056 TATTTTTAATTTTATT
1 TATATTTAATTTAATT
112072 TATATTTAA
1 TATATTTAA
112081 AAATTTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTAATTTAATT
Found at i:112149 original size:37 final size:37
Alignment explanation
Indices: 112108--112189 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
112098 CCTATTTAGT
* * *
112108 TTATATTATTTTATTTTCTAAAATA-TTTTAATATATA
1 TTATATTATATTATATTATAAAATATTTTTAATA-ATA
***
112145 TTATATTATATTATATTATATTTTATTTTTAATAATA
1 TTATATTATATTATATTATAAAATATTTTTAATAATA
112182 TTATATTA
1 TTATATTA
112190 CCTATTAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 30 0.79
38 8 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (37 bp):
TTATATTATATTATATTATAAAATATTTTTAATAATA
Found at i:112151 original size:5 final size:5
Alignment explanation
Indices: 112141--112189 Score: 59
Period size: 5 Copynumber: 10.4 Consensus size: 5
112131 TATTTTAATA
* *
112141 TATAT TATAT TATAT TATAT TATAT TTTAT T-T-T TA-AT AATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
112188 TA
1 TA
112190 CCTATTAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
3 2 0.05
4 3 0.08
5 33 0.87
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:112155 original size:22 final size:22
Alignment explanation
Indices: 112130--112189 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
112120 ATTTTCTAAA
112130 ATATTTTAATATATATTATATT
1 ATATTTTAATATATATTATATT
*
112152 ATA--TT-ATAT-TA-TATTTT
1 ATATTTTAATATATATTATATT
112169 AT-TTTTAATA-ATATTATATT
1 ATATTTTAATATATATTATATT
112189 A
1 A
112190 CCTATTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
17 7 0.23
18 4 0.13
19 9 0.29
20 8 0.26
22 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTAATATATATTATATT
Found at i:120410 original size:7 final size:7
Alignment explanation
Indices: 120398--120423 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
120388 TCATTTAAAC
120398 CAAAGGG
1 CAAAGGG
120405 CAAAGGG
1 CAAAGGG
120412 CAAAGGG
1 CAAAGGG
120419 CAAAG
1 CAAAG
120424 AGCAGAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.38, T:0.00
Consensus pattern (7 bp):
CAAAGGG
Found at i:120432 original size:14 final size:14
Alignment explanation
Indices: 120398--120432 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
120388 TCATTTAAAC
*
120398 CAAAGGGCAAAGGG
1 CAAAGGGCAAAGAG
120412 CAAAGGGCAAAGAG
1 CAAAGGGCAAAGAG
*
120426 CAGAGGG
1 CAAAGGG
120433 GACCATTTGG
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:0.43, C:0.14, G:0.43, T:0.00
Consensus pattern (14 bp):
CAAAGGGCAAAGAG
Found at i:129203 original size:2 final size:2
Alignment explanation
Indices: 129198--129228 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
129188 ACACACACAC
129198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129229 GCTTCAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129466 original size:2 final size:2
Alignment explanation
Indices: 129459--129490 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
129449 TAACCTTTGC
129459 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
129491 TCTTTCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130523 original size:32 final size:32
Alignment explanation
Indices: 130487--130550 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
130477 ATCTTATTAA
*
130487 ACCCTCTATCTTTAAAAATATTTTAATAATAT
1 ACCCTCGATCTTTAAAAATATTTTAATAATAT
* *
130519 ACCCTCGATTTTTAAAAATATTTTAGTAATAT
1 ACCCTCGATCTTTAAAAATATTTTAATAATAT
130551 GCATGTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (32 bp):
ACCCTCGATCTTTAAAAATATTTTAATAATAT
Found at i:131702 original size:33 final size:33
Alignment explanation
Indices: 131665--131731 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
131655 TTCAACGATT
131665 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
131698 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
131731 T
1 T
131732 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:131703 original size:13 final size:13
Alignment explanation
Indices: 131685--131709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131675 CATAAAATGT
131685 TGTATCGATACAA
1 TGTATCGATACAA
131698 TGTATCGATACA
1 TGTATCGATACA
131710 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:131793 original size:13 final size:13
Alignment explanation
Indices: 131775--131799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131765 ATTACTCACA
131775 TGTATCGATACAT
1 TGTATCGATACAT
131788 TGTATCGATACA
1 TGTATCGATACA
131800 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:135687 original size:22 final size:24
Alignment explanation
Indices: 135660--135707 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
135650 ACAATATATC
135660 TAAAATA-TA-TTAAATATAAATA
1 TAAAATATTATTTAAATATAAATA
* *
135682 TAAAATATTATTTTAATATATATA
1 TAAAATATTATTTAAATATAAATA
135706 TA
1 TA
135708 TATATAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATATTATTTAAATATAAATA
Found at i:136387 original size:13 final size:13
Alignment explanation
Indices: 136369--136394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
136359 TCAGTTGGAG
136369 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
136382 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
136395 GTCTTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:145287 original size:33 final size:33
Alignment explanation
Indices: 145210--145299 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 33
145200 TATTTATAAA
* *
145210 AAAATAATATTATATTATATTAATATACTAATT
1 AAAATATTATTATATTATATTAATATACTAATG
* * *
145243 AATAATTTTATT-TATTATTTTAATATATTACATG
1 AA-AATATTATTATATTATATTAATATACTA-ATG
*
145277 AAAATATTATTATA-TATAATAAT
1 AAAATATTATTATATTATATTAAT
145300 TTAAAATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (33 bp):
AAAATATTATTATATTATATTAATATACTAATG
Found at i:145865 original size:12 final size:11
Alignment explanation
Indices: 145847--145873 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
145837 TAATTATCTC
145847 GAAAAAAAAAA
1 GAAAAAAAAAA
145858 GAAAAAAAAAA
1 GAAAAAAAAAA
145869 GAAAA
1 GAAAA
145874 TGAAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:149282 original size:27 final size:27
Alignment explanation
Indices: 149217--149284 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
149207 TAAAATCTAT
149217 ATTTTATATATATTTAAATATAAATAAAA
1 ATTTTATATAT-TTTAAATAT-AATAAAA
* **
149246 AATACA-ATATTTTAAATAT-ATAAAA
1 ATTTTATATATTTTAAATATAATAAAA
149271 ATTTTTATATATTT
1 A-TTTTATATATTT
149285 ATATTAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
25 7 0.23
26 2 0.06
27 15 0.48
28 4 0.13
29 3 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTTATATATTTTAAATATAATAAAA
Found at i:151025 original size:2 final size:2
Alignment explanation
Indices: 151014--151049 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
151004 ATTAATTAAT
151014 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
151050 CTTGGTGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155234 original size:20 final size:21
Alignment explanation
Indices: 155202--155245 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
155192 TACGGCTCAT
*
155202 TTTTAATTATATAATATGTTA
1 TTTTAATTATATAATATGTAA
*
155223 TTTTAA-TATATATTATGTAA
1 TTTTAATTATATAATATGTAA
155243 TTT
1 TTT
155246 ATATCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTAATTATATAATATGTAA
Found at i:155298 original size:29 final size:28
Alignment explanation
Indices: 155240--155297 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
155230 ATATATTATG
*
155240 TAATTTATATCATATAAAGATTAAATATA
1 TAATTTATA-CATATAAACATTAAATATA
*
155269 TAATTTATA-ATATAAACATTAAAAATA
1 TAATTTATACATATAAACATTAAATATA
155296 TA
1 TA
155298 TTAAATTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 18 0.67
29 9 0.33
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATTTATACATATAAACATTAAATATA
Found at i:155347 original size:17 final size:16
Alignment explanation
Indices: 155325--155356 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
155315 AATAACTTAA
155325 TAAAAATATAAAATTAC
1 TAAAAAT-TAAAATTAC
155342 TAAAAATTAAAATTA
1 TAAAAATTAAAATTA
155357 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATTAAAATTAC
Found at i:155448 original size:12 final size:12
Alignment explanation
Indices: 155431--155473 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
155421 ATAAATATAA
155431 AAAATTTTAAAT
1 AAAATTTTAAAT
*
155443 AAAATTTATAATT
1 AAAATTT-TAAAT
*
155456 AATATTTTAAAT
1 AAAATTTTAAAT
*
155468 CAAATT
1 AAAATT
155474 AAAAATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATTTTAAAT
Found at i:155484 original size:25 final size:25
Alignment explanation
Indices: 155434--155484 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
155424 AATATAAAAA
* * *
155434 ATTTTAAATAAAATTTATAATTAAT
1 ATTTTAAATAAAATTAAAAATAAAT
*
155459 ATTTTAAATCAAATTAAAAATAAAT
1 ATTTTAAATAAAATTAAAAATAAAT
155484 A
1 A
155485 AATATATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTTTAAATAAAATTAAAAATAAAT
Found at i:155813 original size:2 final size:2
Alignment explanation
Indices: 155806--155838 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
155796 AATAATTTTG
155806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
155839 CGTATGTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:156222 original size:16 final size:16
Alignment explanation
Indices: 156191--156223 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
156181 TTATTTTTAT
156191 ATTAATAAAAATATAA
1 ATTAATAAAAATATAA
156207 ATTAA-AAAAATAATAA
1 ATTAATAAAAAT-ATAA
156223 A
1 A
156224 AATTATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATTAATAAAAATATAA
Found at i:156898 original size:2 final size:2
Alignment explanation
Indices: 156891--156917 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
156881 TTATATCATC
156891 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 T
156918 TGTTAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:160918 original size:19 final size:19
Alignment explanation
Indices: 160886--160928 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
160876 AGTTTAAAAT
160886 TTTTTATTTATATTAATTAA
1 TTTTTATTTATATT-ATTAA
* *
160906 TTTTTA-TTGTATTCTTAA
1 TTTTTATTTATATTATTAA
160924 TTTTT
1 TTTTT
160929 TATATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTATTTATATTATTAA
Found at i:160929 original size:19 final size:20
Alignment explanation
Indices: 160883--160931 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
160873 AAAAGTTTAA
160883 AATTTTTTATTTATATTAATT
1 AATTTTTTA-TTATATTAATT
* *
160904 AA-TTTTTATTGTATT-CTT
1 AATTTTTTATTATATTAATT
160922 AATTTTTTAT
1 AATTTTTTAT
160932 ATTTTAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 6 0.24
21 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
AATTTTTTATTATATTAATT
Found at i:164291 original size:17 final size:18
Alignment explanation
Indices: 164247--164292 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
164237 CTTTTTATTT
164247 TTATGAATAA-AAATTTAA
1 TTAT-AATAATAAATTTAA
*
164265 TTATAA-AATAAATTTGA
1 TTATAATAATAAATTTAA
164282 TTA-AATAATAA
1 TTATAATAATAA
164293 TTATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
TTATAATAATAAATTTAA
Found at i:165438 original size:15 final size:15
Alignment explanation
Indices: 165418--165463 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
165408 TTTTTAAATA
165418 AATTTTATTAATTAT
1 AATTTTATTAATTAT
*
165433 AATTTTATTTAATTAAA
1 AATTTTA-TTAATT-AT
165450 AATTTTA-TAATTAT
1 AATTTTATTAATTAT
165464 TAAAACCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 12 0.44
16 6 0.22
17 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTATTAATTAT
Found at i:165444 original size:16 final size:17
Alignment explanation
Indices: 165417--165457 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
165407 ATTTTTAAAT
165417 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
165432 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
165449 AAATTTTAT
1 AAATTTTAT
165458 AATTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:165765 original size:18 final size:19
Alignment explanation
Indices: 165732--165792 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 19
165722 TATAAAAAAA
165732 TATATAAAATAATAATTAT
1 TATATAAAATAATAATTAT
165751 TATATAAAA-AATAATTA-
1 TATATAAAATAATAATTAT
165768 TA-A-AAACATAA-AATT-T
1 TATATAAA-ATAATAATTAT
165784 TATATAAAA
1 TATATAAAA
165793 AACAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.08
16 8 0.22
17 6 0.16
18 11 0.30
19 9 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATAAAATAATAATTAT
Found at i:165787 original size:33 final size:32
Alignment explanation
Indices: 165718--165794 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 32
165708 TAAATATACG
*
165718 TATATATAAAAAAATATATAAAATAATAATTAT
1 TATATA-AAAAAAATATAAAAAATAATAATTAT
165751 TATATAAAAAATAATTATAAAAACATAA-AATT-T
1 TATATAAAAAA-AA-TATAAAAA-ATAATAATTAT
165784 TATATAAAAAA
1 TATATAAAAAA
165795 CAAAAATATG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 5 0.12
33 20 0.50
34 11 0.28
35 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (32 bp):
TATATAAAAAAAATATAAAAAATAATAATTAT
Found at i:166070 original size:20 final size:21
Alignment explanation
Indices: 166023--166070 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
166013 ATACGATGTG
166023 AATATAACATAAATAAAAAATA
1 AATA-AACATAAATAAAAAATA
*
166045 ATTAAACAT-AAT-AAAAATA
1 AATAAACATAAATAAAAAATA
166064 ACATAAA
1 A-ATAAA
166071 TATGATACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 5 0.22
22 3 0.13
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AATAAACATAAATAAAAAATA
Found at i:166425 original size:35 final size:33
Alignment explanation
Indices: 166348--166447 Score: 87
Period size: 35 Copynumber: 2.9 Consensus size: 33
166338 TAAAAAATAC
*
166348 ATAAAAATATATATAATAAA-ATAAATTATTAAT
1 ATAAAAAAATATATAA-AAATATAAATTATTAAT
*
166381 ATATCAAAAATATATAAAAATATAATATT-TTAAAT
1 ATA-AAAAAATATATAAAAATATAA-ATTATT-AAT
* * **
166416 ATTAAAAAAATAAATATAAATATTTATTATTA
1 A-TAAAAAAATATATAAAAATATAAATTATTA
166448 TTTTTTTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
33 6 0.11
34 21 0.39
35 25 0.46
36 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAAAAAATATATAAAAATATAAATTATTAAT
Found at i:166468 original size:2 final size:2
Alignment explanation
Indices: 166463--166503 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
166453 TTTCATCCTT
*
166463 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
166504 TGAAAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:168175 original size:2 final size:2
Alignment explanation
Indices: 168168--168200 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
168158 GCTTTATATT
168168 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
168201 GGTGGGAGGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:173460 original size:15 final size:15
Alignment explanation
Indices: 173442--173488 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
173432 AATTAATATA
*
173442 ATATTTATTATATTT
1 ATATTTAATATATTT
173457 ATATTTAATAT-TTT
1 ATATTTAATATATTT
173471 AATAATTTAATA-ATTT
1 -AT-ATTTAATATATTT
173487 AT
1 AT
173489 GTTATATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.11
15 14 0.50
16 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTAATATATTT
Found at i:175835 original size:14 final size:15
Alignment explanation
Indices: 175807--175845 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
175797 TAAGAGTGAC
*
175807 ATTAAAAAATTTTAT
1 ATTAAAAAATATTAT
175822 ATTAAAAAA-ATTAT
1 ATTAAAAAATATTAT
*
175836 AATAAAAAAT
1 ATTAAAAAAT
175846 GTAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTAAAAAATATTAT
Found at i:178528 original size:20 final size:20
Alignment explanation
Indices: 178490--178528 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
178480 TATTTTTATG
*
178490 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
178510 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
178529 CTTTGATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:179084 original size:30 final size:28
Alignment explanation
Indices: 179049--179154 Score: 97
Period size: 30 Copynumber: 3.6 Consensus size: 28
179039 ATGTTAAGAG
179049 TTTATTTAAATATAAATTAAAGATTACAAA
1 TTTATTTAAATATAAATTAAA-ATTA-AAA
* * **
179079 TTTATTTGAGT-TAAAATTAAAAATTAATG
1 TTTATTTAAATAT-AAATT-AAAATTAAAA
*
179108 CTTATTTAAATATAAATTAAAAGTTAAAAA
1 TTTATTTAAATATAAATTAAAA-TT-AAAA
179138 TTTATTTAAATAATAAA
1 TTTATTTAAAT-ATAAA
179155 AAAAAAGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.07
29 17 0.28
30 31 0.52
31 8 0.13
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (28 bp):
TTTATTTAAATATAAATTAAAATTAAAA
Found at i:184182 original size:2 final size:2
Alignment explanation
Indices: 184175--184204 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
184165 TGTGCCTCAA
184175 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
184205 TCTTAGTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184343 original size:2 final size:2
Alignment explanation
Indices: 184336--184361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
184326 ACATGAATTT
184336 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
184362 CACCCTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:185336 original size:17 final size:17
Alignment explanation
Indices: 185316--185360 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
185306 ATTATGATTG
185316 ATAATATTATAATAAAT
1 ATAATATTATAATAAAT
*
185333 ATAATATAATTAA-AAAT
1 ATAATATTA-TAATAAAT
185350 AT-AT-TTATAAT
1 ATAATATTATAAT
185361 TATAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 2 0.08
17 14 0.58
18 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATTATAATAAAT
Found at i:185350 original size:29 final size:31
Alignment explanation
Indices: 185286--185366 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 31
185276 ATTTATTTTT
* * * *
185286 AATATTTATTAATAATATATATTATGATTGAT
1 AATA-TTATTAATAATATATAATATAATTAAA
185318 AATATTA-TAATAA-ATATAATATAATTAAA
1 AATATTATTAATAATATATAATATAATTAAA
*
185347 AATA-TATTTATAAT-TATAAT
1 AATATTATTAATAATATATAAT
185367 TTAAATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 2 0.05
29 27 0.64
30 6 0.14
31 3 0.07
32 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (31 bp):
AATATTATTAATAATATATAATATAATTAAA
Found at i:186550 original size:13 final size:13
Alignment explanation
Indices: 186532--186588 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
186522 TCTCAATTGA
*
186532 ATTTATGATAAAT
1 ATTTATAATAAAT
*
186545 ATTTATAATTAAT
1 ATTTATAATAAAT
* *
186558 ATTTATTATAATT
1 ATTTATAATAAAT
186571 ATTTATAAT-AAT
1 ATTTATAATAAAT
186583 ATTTAT
1 ATTTAT
186589 TATACCTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
12 8 0.22
13 29 0.78
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
ATTTATAATAAAT
Found at i:186588 original size:25 final size:26
Alignment explanation
Indices: 186532--186592 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
186522 TCTCAATTGA
*
186532 ATTTATGATAAATATTTATAATTAAT
1 ATTTATTATAAATATTTATAATTAAT
*
186558 ATTTATTATAATTATTTATAA-TAAT
1 ATTTATTATAAATATTTATAATTAAT
186583 ATTTATTATA
1 ATTTATTATA
186593 CCTATTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 14 0.42
26 19 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTATTATAAATATTTATAATTAAT
Found at i:187205 original size:16 final size:17
Alignment explanation
Indices: 187166--187199 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
187156 ATTGACATTA
187166 AATAACAATAATAATAAT
1 AATAA-AATAATAATAAT
187184 AATAAAATAAT-ATAAT
1 AATAAAATAATAATAAT
187200 TTTAAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:190085 original size:120 final size:122
Alignment explanation
Indices: 189843--190075 Score: 310
Period size: 123 Copynumber: 1.9 Consensus size: 122
189833 TGTTAAAAAG
* *
189843 AAATATAAAAAATAAATCAATGACAACAAATATGAAAAAAAATGAGAGAAAAAAATAAATTTAAA
1 AAATATAAAAAATAAATCAATGACAACAAAAAT-AAAAAAAATAAGAGAAAAAAATAAATTTAAA
* * *
189908 TTAGATAATAGTCACTATAAATTTAAACTATTTTATGAATGTGAAATTTCACTATTAT
65 TTAGAAAATAGTCACTAAAAATTTAAACTATTTTATGAATGTAAAATTTCACTATTAT
* * * ** * *
189966 AAATATAAAAAATAAATCAGTGACAACAAAAAT-AAAAATATAAGATAAAAACTTTAGTTTAAAT
1 AAATATAAAAAATAAATCAATGACAACAAAAATAAAAAAAATAAGAGAAAAAAATAAATTTAAAT
*
190030 TATTAAAATAGTCACTAAAAATTTAAA-TA-TTTATGAATGTAAAATT
66 TA-GAAAATAGTCACTAAAAATTTAAACTATTTTATGAATGTAAAATT
190076 ATGCTATTAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
120 16 0.17
121 28 0.29
122 21 0.22
123 31 0.32
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.30
Consensus pattern (122 bp):
AAATATAAAAAATAAATCAATGACAACAAAAATAAAAAAAATAAGAGAAAAAAATAAATTTAAAT
TAGAAAATAGTCACTAAAAATTTAAACTATTTTATGAATGTAAAATTTCACTATTAT
Found at i:190369 original size:15 final size:16
Alignment explanation
Indices: 190349--190383 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
190339 TATATTTACG
190349 TTAAAA-TTTAAATTT
1 TTAAAATTTTAAATTT
*
190364 TTAAAATTTTATATTT
1 TTAAAATTTTAAATTT
190380 TTAA
1 TTAA
190384 TTGGCTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAAATTTTAAATTT
Found at i:196683 original size:2 final size:2
Alignment explanation
Indices: 196676--196708 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
196666 GGGATACAAA
196676 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
196709 AAACATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:197917 original size:20 final size:20
Alignment explanation
Indices: 197892--197947 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
197882 AAAAAATATC
197892 ATTTAAAATAATAATTTTTT
1 ATTTAAAATAATAATTTTTT
** *
197912 ATTTAAAATTGTAAATTTTT
1 ATTTAAAATAATAATTTTTT
**
197932 AAATAAAATAA-AATTT
1 ATTTAAAATAATAATTT
197948 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTAAAATAATAATTTTTT
Found at i:198495 original size:10 final size:8
Alignment explanation
Indices: 198459--198493 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
198449 AAGTAACTCC
198459 ATACATAT
1 ATACATAT
198467 ATACATAT
1 ATACATAT
198475 ATACATAT
1 ATACATAT
198483 ATACATAT
1 ATACATAT
198491 ATA
1 ATA
198494 TAAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:198500 original size:16 final size:16
Alignment explanation
Indices: 198459--198501 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
198449 AAGTAACTCC
*
198459 ATACATATATACATAT
1 ATACAAATATACATAT
*
198475 ATACATATATACATAT
1 ATACAAATATACATAT
*
198491 ATATAAATATA
1 ATACAAATATA
198502 AAATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
ATACAAATATACATAT
Done.